]> Darrell R. Abernethy CTCAE-OAEview is an OAE view that contains all CTCAE-related OAE terms and additional OAE terms associated with these CTCAE-related terms. Edison Ong Rebecca Racz Meiu Wong Yongqun "Oliver" He (YH) An ontology for the annotation of the CTCAE adverse event domain. OWL-DL BFO OWL specification label BFO OWL specification label Really of interest to developers only Relates an entity in the ontology to the name of the variable that is used to represent it in the code that generates the BFO OWL file from the lispy specification. BFO CLIF specification label BFO CLIF specification label Person:Alan Ruttenberg Really of interest to developers only Relates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2 editor preferred term editor preferred term~editor preferred label editor preferred label editor preferred term editor preferred term~editor preferred label GROUP:OBI:<http://purl.obolibrary.org/obo/obi> PERSON:Daniel Schober The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English) editor preferred term example of usage example of usage A phrase describing how a class name should be used. May also include other kinds of examples that facilitate immediate understanding of a class semantics, such as widely known prototypical subclasses or instances of the class. Although essential for high level terms, examples for low level terms (e.g., Affymetrix HU133 array) are not GROUP:OBI:<http://purl.obolibrary.org/obo/obi> PERSON:Daniel Schober example of usage has curation status has curation status OBI_0000281 PERSON:Alan Ruttenberg PERSON:Bill Bug PERSON:Melanie Courtot has curation status definition textual definition definition definition definition GROUP:OBI:<http://purl.obolibrary.org/obo/obi> PERSON:Daniel Schober The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. definition editor note editor note editor note 1 IAO:0000116 editor_note editor_note uberon An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology. GROUP:OBI:<http://purl.obfoundry.org/obo/obi> PERSON:Daniel Schober editor note term editor definition editor term editor 20110707, MC: label update to term editor and definition modified accordingly. See http://code.google.com/p/information-artifact-ontology/issues/detail?id=115. GROUP:OBI:<http://purl.obolibrary.org/obo/obi> Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people PERSON:Daniel Schober term editor alternative term alternative term An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent) GROUP:OBI:<http://purl.obolibrary.org/obo/obi> PERSON:Daniel Schober alternative term definition source definition source Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w GROUP:OBI:<http://purl.obolibrary.org/obo/obi> PERSON:Daniel Schober definition source formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007 curator notes curator note curator note 1 IAO:0000232 curator_notes curator_notes uberon An administrative note of use for a curator but of no use for a user PERSON:Alan Ruttenberg curator note imported from imported from For external terms/classes, the ontology from which the term was imported GROUP:OBI:<http://purl.obolibrary.org/obo/obi> PERSON:Alan Ruttenberg PERSON:Melanie Courtot imported from expand expression to expand assertion to elucidation elucidation has associated axiom(nl) has associated axiom(nl) has associated axiom(fol) has associated axiom(fol) Chinese translation YH, JX a chinese translation represents a chinese translation of the existing term. adverse event outcome The AE 'cough AE' has the 'label of AE outcome' of 'cough'; 'infection AE' has the 'label of AE outcom' of 'infection'. an annotation property that represents the label of an adverse event label of adverse event outcome Yongqun Oliver He, Jiangan Hardy Xie has_meddra_id temporal interpretation https://github.com/oborel/obo-relations/wiki/ROAndTime An assertion that holds between an OWL Object Property and a temporal interpretation that elucidates how OWL Class Axioms that use this property are to be interpreted in a temporal context. never in taxon x never in taxon T if and only if T is a class, and x does not instantiate the class expression "in taxon some T". Note that this is a shortcut relation, and should be used as a hasValue restriction in OWL. ?X DisjointWith RO_0002162 some ?Y Chris Mungall tooth SubClassOf 'never in taxon' value 'Aves' taxonomic class assertion An assertion that holds between an ontology class and an organism taxon class, which is intepreted to yield some relationship between instances of the ontology class and the taxon. dubious_for_taxon 1 1 RO:0002174 S dubious_for_taxon T if it is probably the case that no instances of S can be found in any instance of T. dubious_for_taxon dubious_for_taxon this relation lacks a strong logical interpretation, but can be used in place of never_in_taxon where it is desirable to state that the definition of the class is too strict for the taxon under consideration, but placing a never_in_taxon link would result in a chain of inconsistencies that will take time to resolve. Example: metencephalon in teleost uberon present_in_taxon 1 1 RO:0002175 S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S applicable for taxon present_in_taxon present_in_taxon uberon logical macro assertion https://github.com/oborel/obo-relations/wiki/ShortcutRelations An assertion that involves at least one OWL object that is intended to be expanded into one or more logical axioms. The logical expansion can yield axioms expressed using any formal logical system, including, but not limited to OWL2-DL. logical macro assertion on a class A logical macro assertion whose domain is an IRI for a class The domain for this class can be considered to be owl:Class, but we cannot assert this in OWL2-DL logical macro assertion on a property A logical macro assertion whose domain is an IRI for a property logical macro assertion on an object property logical macro assertion on an annotation property is direct form of Chris Mungall relation p is the direct form of relation q iff p is a subPropertyOf q, p does not have the Transitive characteristic, q does have the Transitive characteristic, and for all x, y: x q y -> exists z1, z2, ..., zn such that x p z1 ... z2n y If we have the annotation P is-direct-form-of Q, and we have inverses P' and Q', then it follows that P' is-direct-form-of Q' external_definition 1 An alternate textual definition for a class taken unmodified from an external source. This definition may have been used to derive a generalized definition for the new class. This annotation property may be replaced with an annotation property from an external ontology such as IAO UBPROP:0000001 external_definition external_definition uberon axiom_lost_from_external_ontology 1 A textual description of an axiom loss in this ontology compared to an external ontology. This annotation property may be replaced with an annotation property from an external ontology such as IAO UBPROP:0000002 axiom_lost_from_external_ontology axiom_lost_from_external_ontology uberon homology_notes 1 Notes on the homology status of this class. This annotation property may be replaced with an annotation property from an external ontology such as IAO UBPROP:0000003 homology_notes homology_notes uberon external_comment 1 An alternate comment for a class taken unmodified from an external source. Note that obo format only allows a single comment for a class, and does not provide a structured means of adding provenance info. This annotation property may be replaced with an annotation property from an external ontology such as IAO UBPROP:0000005 external_comment external_comment uberon implements_design_pattern 1 UBPROP:0000006 implements_design_pattern implements_design_pattern uberon has_relational_adjective 1 UBPROP:0000007 Used to connect a class to an adjectival form of its label. For example, a class with label 'intestine' may have a relational adjective 'intestinal'. has_relational_adjective has_relational_adjective uberon taxon_notes 1 Notes on the how instances of this class vary across species. UBPROP:0000008 taxon_notes taxon_notes uberon function_notes 1 Notes on the evolved function of instances of this class. This annotation property may be replaced with an annotation property from an external ontology such as IAO UBPROP:0000009 function_notes function_notes uberon structure_notes 1 Notes on the structure, composition or histology of instances of this class. This annotation property may be replaced with an annotation property from an external ontology such as IAO UBPROP:0000010 structure_notes structure_notes uberon development_notes 1 Notes on the ontogenic development of instances of this class. This annotation property may be replaced with an annotation property from an external ontology such as IAO UBPROP:0000011 development_notes development_notes uberon external_ontology_notes 1 Notes on how similar or equivalent classes are represented in other ontologies. This annotation property may be replaced with an annotation property from an external ontology such as IAO UBPROP:0000012 external_ontology_notes external_ontology_notes uberon terminology_notes 1 Notes on how lexical conventions regarding this class, in particular any issues that may arise due to homonyny or synonymy. This annotation property may be replaced with an annotation property from an external ontology such as IAO UBPROP:0000013 terminology_notes terminology_notes uberon is count of 1 UBPROP:0000100 is_count_of is_count_of uberon preceding element is 1 A property used in conjunction with repeated_element_number to indicate an axis and directionality along that axis. If P preceding_element_is R, and P is_count_of S, and X P N, and X' P N+1, then it follows that every X R some X', and the class expression [S and R some X' and inv(R) some X] is empty (i.e. X is followed by X', with no intermediates) UBPROP:0000101 preceding_element_is preceding_element_is uberon pharyngeal arch number 1 UBPROP:0000103 gill arch N = PA N-2. the term branchial_arch is ambiguous. pharyngeal_arch_number pharyngeal_arch_number uberon x pharyngeal_arch_number N if and only if (i) x is a pharyngeal arch, and (ii) x is ancestrally pharyngeal arch number N in a series of pharyngeal arches repeated along a antero-posterior axis, with arch_number 1 being the mandibular arch. phalanx number 1 Most land mammals including humans have a 2-3-3-3-3 formula in both the hands (or paws) and feet. Primitive reptiles typically had the formula 2-3-4-4-5, and this pattern, with some modification, remained in many later reptiles and in the mammal-like reptiles. The phalangeal formula in the flippers of cetaceans (marine mammals) is 2-12-8-1 UBPROP:0000105 phalanx_number phalanx_number uberon x phalanx_number N if and only if (i) x is a phalanx, and (ii) x is phalanx number N in a series of phalanges repeated along an prixomo-distal axis, with phalanx_number 1 being the proximalmost phalanx. Note that in humans, the distalmost phalanx has phlanax_number 3, except in ray_number 1, where the distalmost has phalanx_number 2 fma_set_term 1 FMA has terms like 'set of X'. In general we do not include set-of terms in uberon, but provide a mapping between the singular form and the FMA set term UBPROP:0000202 fma_set_term fma_set_term uberon eco subset CUMBO developmental_classification A class that represents an early developmental structure, like a blastocyst. This part of the ontology is undergoing review to remove inappropriate grouping classes. EFO slim derived from the union of EHDAA2 and EMAPA - still to be checked functional_classification Subset consisting of classes creating for grouping purposes A grouping class that depends on an assumption of homology between subclasses classes that have some inconsistency with FMA somewhat fuzzy grouping for analysis purposes, currently composed of something like: liver, heart, skeletal, kidney, bladder, brain, skin, mouth, esophagus, stomach, small intestine, large intestines, trachea nose, lungs, brain, spinal cord, peripheral nerves, kidneys, ureters, bladder, urethra, gonads abstract class brought in to group ontology classes but not informative organs, excluding individual muscles and skeletal elements Phenotype slim Uberon slim - subset that excludes obscure terms and deep compositional terms abstract upper-level terms not directly useful for analysis core classes typically found across vertebrates. one purpose is to create a rough set of terms that could be used to start a new vertebrate AO contributor 1 dc-contributor dc-contributor uberon Source Source subset_property has_alternative_id has_alternative_id has_broad_synonym database_cross_reference database_cross_reference has_exact_synonym has_exact_synonym has_narrow_synonym has_narrow_synonym has_obo_namespace has_related_synonym has_related_synonym in_subset in_subset shorthand label depicted_by 1 foaf-depicted_by foaf-depicted_by uberon part of part of BFO:0000050 part_of part_of uberon Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other. Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime a core relation that holds between a part and its whole http://www.obofoundry.org/ro/#OBO_REL:part_of is part of my brain is part of my body (continuant parthood, two material entities) my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity) part_of this day is part of this year (occurrent parthood) has part has part BFO:0000051 has_part has_part uberon Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime a core relation that holds between a whole and its part has part has_part my body has part my brain (continuant parthood, two material entities) my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) this year has part this day (occurrent parthood) preceded_by preceded by BFO:0000062 X preceded_by Y iff: end(Y) before_or_simultaneous_with start(X) is preceded by preceded_by preceded_by takes place after uberon An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. http://www.obofoundry.org/ro/#OBO_REL:preceded_by is preceded by preceded by preceded_by x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. precedes precedes BFO:0000063 precedes precedes uberon precedes x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. occurs in Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t occurs in occurs_in unfolds in unfolds_in contains process Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant [copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t site of anterior_to 2009-07-31T02:15:46Z BSPO:0000096 anterior_to anterior_to cjm uberon x anterior_to y iff x is further along the antero-posterior axis than y, towards the head. An antero-posterior axis is an axis that bisects an organism from head end to opposite end of body or tail: bearer distal_to BSPO:0000097 distal_to distal_to uberon x distal_to y iff x is further along the proximo-distal axis than y, towards the appendage tip. A proximo-distal axis extends from tip of an appendage (distal) to where it joins the body (proximal). dorsal_to BSPO:0000098 dorsal_to dorsal_to uberon x dorsal_to y iff x is further along the dorso-ventral axis than y, towards the back. A dorso-ventral axis is an axis that bisects an organism from back (e.g. spinal column) to front (e.g. belly). posterior_to BSPO:0000099 caudal_to posterior_to posterior_to uberon x posterior_to y iff x is further along the antero-posterior axis than y, towards the body/tail. An antero-posterior axis is an axis that bisects an organism from head end to opposite end of body or tail. proximal_to BSPO:0000100 proximal_to proximal_to uberon x proximal_to y iff x is closer to the point of attachment with the body than y. ventral_to BSPO:0000102 uberon ventral_to ventral_to x ventral_to y iff x is further along the dorso-ventral axis than y, towards the front. A dorso-ventral axis is an axis that bisects an organism from back (e.g. spinal column) to front (e.g. belly). deep_to BSPO:0000107 Further away from the surface of the organism. Thus, the muscular layer is deep to the skin, but superficial to the intestines. deep_to deep_to uberon superficial_to BSPO:0000108 Near the outer surface of the organism. Thus, skin is superficial to the muscle layer. superficial_to superficial_to uberon in_left_side_of BSPO:0000120 X in_left_side_of Y <=> if Y is subdivided into left and right portions, X is part_of the left portion. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern in_left_side_of in_left_side_of uberon in_right_side_of BSPO:0000121 X in_right_side_of Y <=> if Y is subdivided into left and right portions, X is part_of the right portion. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern in_right_side_of in_right_side_of uberon in_posterior_side_of BSPO:0000122 X posterior_side_of Y <=> if Y is subdivided into two anterior and posterior portions, X is part_of the posterior portion. in_posterior_side_of in_posterior_side_of uberon in_anterior_side_of BSPO:0000123 X anterior_side_of Y <=> if Y is subdivided into two anterior and posterior portions, X is part_of the anterior portion. in_anterior_side_of in_anterior_side_of uberon in_proximal_side_of BSPO:0000124 X proximal_side_of Y <=> if Y is subdivided into distal and proximal portions, X is part_of the proximal portion. in_proximal_side_of in_proximal_side_of uberon in_distal_side_of BSPO:0000125 X distal_side_of Y <=> if Y is subdivided into distal and proximal portions, X is part_of the distal portion. in_distal_side_of in_distal_side_of uberon in_lateral_side_of BSPO:0000126 X in_lateral_side_of Y <=> if X is in_left_side_of Y or X is in_right_side_of Y. X is often, but not always a paired structure https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern in_lateral_side_of in_lateral_side_of uberon proximalmost_part_of BSPO:0001106 X proximalmost_part_of Y <=> X is part_of Y and X is adjacent_to the proximal boundary of Y proximalmost_part_of proximalmost_part_of uberon distalmost_part_of BSPO:0001108 X distalmost_part_of Y <=> X is part_of Y and X is adjacent_to the distal boundary of Y distalmost_part_of distalmost_part_of uberon is evidence of This represents a relation between two adverse events AE1 and AE2. However, AE1 may be an evidence of another adverse event AE3, and a dfferent adverse event AE4 may also be an evidence of the same AE2. AE1 is_evidence_of AE2 if and only if: given an adverse event instance ae1 that instantiates class AE1 (e.g., electrocardiogram qt prolonged AE) and another adverse event instance ae2 that instantiates class AE2 (e.g., arrhythmia AE), both ae1 and ae2 are adverse events that are clinically observed after a medical intervention (at time t0) on the same patient. The presence of ae1 is supported by priori knowledge of medicine to imply the presence of ae2 with some probability P (P is NOT always 1, thus transitivity does not apply to is_evidence_of relation. AE1 is_evidence_of AE2 and AE2 is_evidence_of AE3 DOES NOT imply AE1 is_evidence_of AE3). The instance ae1 and ae2 are observed or detected at time t1 and t2, respectively. The biological onset time for ae1 or ae2 may occur before t1 or t2. The t1 and t2 can be the same time point or different time points. SS, YH, YL An electrocardiogram qt prolonged AE is_evidence_of arrhythmia AE; arrhythmia AE is_evidence_of cardiomyopathy AE; fever AE is_evidence_of inflammation AE; fever AE is_evidence_of viral infection AE; plural effusion AE is_evidence_of cardiac disorder AE. has participant quality an object property that represents a relation between a process and a quality, in which the process has a participant that has the quality. An adverse event has a participant quality, such as a hyperkalemia AE has a participatn quality blood potassium increased. Yongqun He This is a shortcut relation of the following full version: 'has participant' some (participant 'has quality' ) in: process 'has participant' some (participant 'has quality' some quality) adverse event occurs in a 'occurs in' relation that is applied at the adverse event setting and indicates where an adverse event occurs in. Yongqun He has participant undergoing Yongqun He A shortcut relation that represents the full path of ‘has participant’ some participant that ‘participates in’ some process. adverse event preceded by a specific 'preceded by' object property that has a domain of an adverse event. Yongqun He location_of RO:0001015 location_of location_of uberon located_in RO:0001025 located_in located_in uberon has boundary RO:0002002 has_boundary has_boundary uberon innervated_by FMA:85999 RO:0002005 dbprop:nerve http://code.google.com/p/obo-relations/issues/detail?id=6 innervated_by innervated_by nerve supply uberon bounding layer of A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane. RO:0002007 bounding_layer_of bounding_layer_of uberon before or simultaneous with <= David Osumi-Sutherland Primitive instance level timing relation between events simultaneous_with simultaneous with RO:0002082 Relation between occurrents, shares start and end boundaries. coincides_with is_equal_to simultaneous_with simultaneous_with uberon David Osumi-Sutherland t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2) ends after David Osumi-Sutherland X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) immediately_preceded_by immediately preceded by A non-transitive temporal relation in which one process immediately precedes another process, such that there is no interval of time between the two processes[SIO:000251]. RO:0002087 X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) directly preceded by immediately_preceded_by immediately_preceded_by is directly preceded by is immediately preceded by starts_at_end_of uberon starts_at_end_of David Osumi-Sutherland X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) immediately precedes X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) ends_at_start_of meets David Osumi-Sutherland starts during David Osumi-Sutherland X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y)) io happens during X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y)) d during David Osumi-Sutherland ends during David Osumi-Sutherland o overlaps X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y). overlaps http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y) x overlaps y if and only if there exists some z such that x has part z and z part of y innervates RO:0002134 http://code.google.com/p/obo-relations/issues/detail?id=6 innervates innervates uberon continuous_with RO:0002150 continuous_with continuous_with uberon homologous_to RO:0002158 homologous_to homologous_to uberon connected to Binary relationship: x connected_to y if and only if there exists some z such that z connects x and y in a ternary connected_to(x,y,z) relationship. Connection does not imply overlaps. RO:0002170 connected_to connected_to uberon connects Binary relationship: z connects x if and only if there exists some y such that z connects x and y in a ternary connected_to(x,y,z) relationship. RO:0002176 connects connects this is currently used for both structural relationships (such as between a valve and the chamber it connects) and abstract relationships (anatomical lines and the entities they connect) uberon attaches_to_part_of RO:0002177 attaches_to_part_of attaches_to_part_of uberon supplies FMA:86003 RO:0002178 arterial supply of relation between an artery and the structure is supplies with blood. source: FMA supplies supplies uberon develops_from RO:0002202 develops_from develops_from uberon develops_into RO:0002203 develops_into develops_into uberon surrounded_by RO:0002219 surrounded_by surrounded_by uberon x surrounded_by y iff: x is adjacent to y and for every region r adjacent to x, r overlaps y adjacent_to RO:0002220 adjacent_to adjacent_to uberon x adjacent_to y iff: x and y share a boundary surrounds RO:0002221 inverse of surrounded_by surrounds surrounds uberon temporally related to https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 Chris Mungall Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends. A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. starts RO:0002223 Relation between occurrents, shares a start boundary with. starts starts uberon starts with starts with RO:0002224 starts_with starts_with uberon started by x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor Chris Mungall ends RO:0002229 Relation between occurrents, shares an end boundary with. ends ends finishes uberon ends with ends with RO:0002230 ends_with ends_with uberon Chris Mungall finished by x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. has developmental contribution from RO:0002254 has_developmental_contribution_from has_developmental_contribution_from uberon developmentally_induced_by RO:0002256 developmentally_induced_by developmentally_induced_by sources for developmentally_induced_by relationships in Uberon: Developmental Biology, Gilbert, 8th edition, figure 6.5(F) t1 developmentally_induced_by t2 if there is a process of organ induction (GO:0001759) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor tissue type T to T', where T' develops_from T. uberon developmentally preceded by RO:0002258 developmentally_preceded_by developmentally_preceded_by uberon developmentally_replaces RO:0002285 developmentally_replaces developmentally_replaces uberon results in formation of example of usage: every "endocardial cushion formation" (GO:0003272) results_in_formation_of some "endocardial cushion" (UBERON:0002062); an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists. Chris Mungall mereotopologically related to A mereological relationship or a topological relationship Chris Mungall Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships has member RO:0002351 has_member has_member uberon attaches_to FMA:85990 RO:0002371 attaches_to attaches_to uberon branching_part_of FMA:85994 RO:0002380 branching_part_of branching_part_of uberon we need to check if FMA branch_of implies part_of. the relation we intend to use here should - for example, see vestibulocochlear nerve has potential to developmentally contribute to RO:0002385 has_potential_to_developmentally_contribute_to has_potential_to_developmentally_contribute_to uberon x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y has potential to develop into RO:0002387 has_potential_to_develop_into has_potential_to_develop_into uberon x has the potential to develop into y iff x develops into y or if x is capable of developing into y contributes to morphology of RO:0002433 contributes_to_morphology_of contributes_to_morphology_of uberon composed primarily of RO:0002473 UBREL:0000002 composed_primarily_of composed_primarily_of uberon x composed_primarily_of y iff: more than half of the mass of x is made from parts of y existence starts during BFO:0000068 RO:0002488 Relation between continuant c and occurrent s, such that every instance of c comes into existing during some s. begins_to_exist_during existence_starts_during existence_starts_during uberon existence starts with RO:0002489 Relation between continuant and occurrent, such that c comes into existence at the start of p. existence_starts_with existence_starts_with uberon existence ends during BFO:0000069 RO:0002492 Relation between continuant c and occurrent s, such that every instance of c ceases to exist during some s, if it does not die prematurely. ceases_to_exist_during existence_ends_during existence_ends_during uberon existence ends with RO:0002493 Relation between continuant and occurrent, such that c ceases to exist at the end of p. existence_ends_with existence_ends_with uberon transformation of RO:0002494 transformation_of transformation_of transforms from uberon immediate transformation of RO:0002495 direct_transformation_of immediate_transformation_of immediate_transformation_of immediately transforms from uberon existence starts during or after RO:0002496 existence_starts_during_or_after existence_starts_during_or_after uberon existence ends during or before RO:0002497 existence_ends_during_or_before existence_ends_during_or_before uberon has material contribution from RO:0002507 has_material_contribution_from has_material_contribution_from uberon has skeleton A relation between a subdivision of an organism and the single subdivision of skeleton that provides structural support for that subdivision. RO:0002551 has sekeletal support has supporting framework has_skeleton has_skeleton uberon has_branching_part RO:0002569 has_branching_part has_branching_part uberon luminal space of RO:0002572 luminal_space_of luminal_space_of uberon skeleton of RO:0002576 skeleton_of skeleton_of uberon produces RO:0003000 produces produces uberon produced_by RO:0003001 produced_by produced_by uberon anteriorly connected to anteriorly_connected_to uberon x anteriorly_connected_to y iff the anterior part of x is connected to y. i.e. x connected_to y and x posterior_to y. channel for carries channel_for uberon channels_from channels_from uberon channels_into channels_into uberon conduit for conduit_for uberon x is a conduit for y iff y passes through the lumen of x. distally connected to distally_connected_to uberon x distally_connected_to y iff the distal part of x is connected to y. i.e. x connected_to y and x proximal_to y. evolved_from Status: experimental evolved_from uberon existence starts and ends during existence_starts_and_ends_during uberon extends_fibers_into extends_fibers_into uberon in_central_side_of X in_central_side Y <=> if Y is subdivided into left and right portions around some median divisor, all parts of X are closer to the median divisor than the outermost lateral sides. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern in_central_side_of uberon posteriorly connected to posteriorly_connected_to uberon x posteriorly_connected_to y iff the posterior part of x is connected to y. i.e. x connected_to y and x anterior_to y. protects protects uberon proximally connected to proximally_connected_to uberon x proximally_connected_to y iff the proximal part of x is connected to y. i.e. x connected_to y and x distal_to y. subdivision of placeholder relation. X = 'subdivision of A' and subdivision_of some B means that X is the mereological sum of A and B subdivision_of uberon transitively anteriorly connected to . transitively_anteriorly_connected_to uberon transitively_connected to transitively_connected_to uberon transitively distally connected to . transitively_distally_connected_to uberon transitively proximally connected to . transitively_proximally_connected_to uberon has size Yongqun He A data property that indicates that a material entity has a particular size. has diameter in cm A 'has size' object property that indicates a material entity of round shape has a diameter of a particular length with the cm (centimeter) unit. A ulcer has a diameter in cm some specific decimal length Yongqun He entity entity BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81 Entity An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf Julius Caesar Verdi’s Requiem the Second World War your body mass index continuant continuant Continuant (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240 Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) occurrent (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] An entity that has temporal parts and that happens, unfolds or develops through time. BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players. Occurrent occurrent Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) independent continuant IndependentContinuant (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) a heart ic a chair a leg a molecule a spatial region an atom an orchestra. an organism b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) the bottom right portion of a human torso the interior of your mouth process Process (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war) a process of cell-division, \ a beating of the heart a process of meiosis a process of sleeping p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) process the course of a disease the flight of a bird the life of an organism your process of aging. quality (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] quality Quality (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) the ambient temperature of this portion of air the color of a tomato the length of the circumference of your waist the mass of this piece of gold. the shape of your nose the shape of your nostril specifically dependent continuant (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] SpecificallyDependentContinuant A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) of one-sided specifically dependent continuants: the mass of this tomato of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates. sdc the disposition of this fish to decay the function of this heart: to pump blood the mutual dependence of proton donors and acceptors in chemical reactions [79 the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction the pink color of a medium rare piece of grilled filet mignon at its center the role of being a doctor the shape of this hole. the smell of this portion of mozzarella site (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] Manhattan Canyon) site Site a hole in the interior of a portion of cheese a rabbit hole an air traffic control region defined in the airspace above an airport b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002]) the Grand Canyon the Piazza San Marco the cockpit of an aircraft the hold of a ship the interior of a kangaroo pouch the interior of the trunk of your car the interior of your bedroom the interior of your office the interior of your refrigerator the lumen of your gut your left nostril (a fiat part – the opening – of your left nasal cavity) material entity material (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60 BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity. BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here. Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) MaterialEntity a flame a forest fire a human being a hurricane a photon a puff of smoke a sea wave a tornado an aggregate of human beings. an energy wave an epidemic every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) the undetached arm of a human being immaterial entity immaterial BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10 ImmaterialEntity biological_process Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end. GO:0000004 GO:0007582 GO:0008150 Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. Note that when this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code ND, no data, is used to indicate this. Wikipedia:Biological_process biological process biological_process physiological process cell death Any biological process that results in permanent cessation of all vital functions of a cell. A cell should be considered dead when any one of the following molecular or morphological criteria is met: (1) the cell has lost the integrity of its plasma membrane; (2) the cell, including its nucleus, has undergone complete fragmentation into discrete bodies (frequently referred to as "apoptotic bodies"); and/or (3) its corpse (or its fragments) have been engulfed by an adjacent cell in vivo. GO:0008219 This term should not be used for direct annotation. The only exception should be when experimental data (e.g., staining with trypan blue or propidium iodide) show that cell death has occurred, but fail to provide details on death modality (accidental versus programmed). When information is provided on the cell death mechanism, annotations should be made to the appropriate descendant of 'cell death' (such as, but not limited to, GO:0097300 'programmed necrotic cell death' or GO:0006915 'apoptotic process'). Also, if experimental data suggest that a gene product influences cell death indirectly, rather than being involved in the death process directly, consider annotating to a 'regulation' term. accidental cell death biological_process necrosis cellular process Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. GO:0008151 GO:0009987 GO:0050875 biological_process cell growth and/or maintenance cell physiology cellular physiological process death A permanent cessation of all vital functions: the end of life; can be applied to a whole organism or to a part of an organism. GO:0016265 See also the biological process term 'apoptosis ; GO:0006915'. Wikipedia:Death biological_process single-organism process 2012-09-19T15:05:24Z A biological process that involves only one organism. GO:0044699 biological_process janelomax single organism process single-organism cellular process 2012-12-11T16:56:55Z Any process that is carried out at the cellular level, occurring within a single organism. GO:0044763 biological_process janelomax necrotic cell death A type of cell death that is morphologically characterized by an increasingly translucent cytoplasm, swelling of organelles, minor ultrastructural modifications of the nucleus (specifically, dilatation of the nuclear membrane and condensation of chromatin into small, irregular, circumscribed patches) and increased cell volume (oncosis), culminating in the disruption of the plasma membrane and subsequent loss of intracellular contents. Necrotic cells do not fragment into discrete corpses as their apoptotic counterparts do. Moreover, their nuclei remain intact and can aggregate and accumulate in necrotic tissues. GO:0070265 Note that the word necrosis has been widely used in earlier literature to describe forms of cell death which are now known by more precise terms, such as apoptosis. Necrosis can occur in a regulated fashion, involving a precise sequence of signals; in this case, consider annotating to GO:0097300 'programmed necrotic cell death' or to its more specific child GO:0070266 'necroptotic process'. biological_process cellular necrosis necrosis adverse event Melanie Courtot and YH: More work is needed on how to restrict the scope of a term to be an 'adverse event', notably regarding temporal association. When is an appropirate time interval between a medical intervention and an adverse event observed? One week, one month, one year, or a lifetime? For some well-studied medical interventions (e.g., administration of many vaccines or drugs), we probably have a general idea. For many new interventions, we don't know much. In OAE, this issue is associated with defining the 'adverse event incubation time'. YH: The current term 'adverse event' is different from the term definition shown in our paper: He Y, Xiang Z, Sarntivijai S, Toldo L, Ceusters W. OAE: a realism-based biomedical ontology for the representation of adverse events. Adverse Event Representation Workshop, International Conference on Biomedical Ontologies (ICBO), University at Buffalo, NY, July 26-30, 2011. Full lenghth conference proceeding paper. We made the name changing in order to make OAE cover the broader sense of the 'adverse event' which does not assume definite causal effect between an adverse event and a medical intervention. In current definition, the adverse event emphasizes the time association and assumes a likelihood of such a causal association. This term 'adverse event' is stil under the OGMS:pathological bodily process. The 'adverse event' defined in the above paper has now been changed to a new term: 'causal adverse event'. See more information in the new publication: Yongqun He Y, Sirarat Sarntivijai, Yu Lin, Zuoshuang Xiang, Abra Guo, Shelley Zhang, Desikan Jagannathan, Luca Toldo, Cui Tao and Barry Smith. OAE: The Ontology of Adverse Events. Journal of Biomedical Semantics. 2014, 5:29 doi:10.1186/2041-1480-5-29. PMID: 25093068.PMCID: PMC4120740. YH: In development of OAE, we initially use vaccine adverse event as our use case. A vaccine adverse event is associated with a vaccination (i.e. a medical intervention), regardless of whether it is considered vaccine-related, and includes any side effect, injury, toxicity, or sensitivity reaction or significant failure of immunization (i.e., a pharmacologic action). Ref: Baylor NW and Midthum K. Regulation and testing of vaccines. In: Vaccines (Editors: Plotkin S, Orenstein W, and Offit P). 2008. p1623. AE YH: There has been discussion regarding whether the term 'side effect' is an alternative term for 'adverse event'. In AERO, the term 'AERO:adverse event' represents a subset of those adverse events for which causality has been established. In OAE, an adverse event for which causality has been established is called 'causal adverse event'. a pathological bodily process that occurs after a medical intervention. An adverse event is likely caused by the medical intervention; however, such a causal association is not required to be an adverse event. YH: The main scope of OAE includes: (1) represent terms and relations in the area of adverse events, (2) assess possible associations between an adverse event and a medical intervention, particularly, identify any causal effect of a medical intervention to an adverse event; and (2) understand the mechanism (including molecular mechanisms) of causal adverse events. WEB: http://www.ncbi.nlm.nih.gov/pubmed/25093068 The OAE official website is: http://www.oae-ontology.org/. WEB: http://www.fda.gov/Safety/MedWatch/HowToReport/ucm053087.htm adverse reaction YH: An adverse event is a process that has specified output of some adverse medical outcome (e.g., symptom, sign or accident) after a medical intervention (or process) (e.g., administration of drug or vaccine). The medical intervention can be an administration of a drug, a vaccine (i.e., vaccination), or a special nutritional product (for example, dietary supplement, infant formula, medical food), surgery, or usage of a medical device. WEB: http://en.wikipedia.org/wiki/Adverse_event YH: An adverse event is possibly induced by the medical intervention. It can be caused by the medical intervention, or may not be caused by the medical intervention. One ultimate goal (or the goal in clinics) of study adverse events is to assess if the adverse event outcome is due to the medical intervention. Yongqun He medical intervention medical intervention is a planned process that has the goal of diagnosing, preventing or relieving illness or injury. The act of intervening, interfering or interceding with the intent of modifying the outcome. In medicine, an intervention is usually undertaken to help treat or cure a condition. For example, "Acupuncture as a therapeutic intervention is widely practiced in the United States," Reference: http://www.medterms.com/script/main/art.asp?articlekey=34214 . Some interventions can be used for diagnosis. YH WEB: http://wiki.answers.com/Q/What_is_medical_intervention flushing AE 10016825 a skin discoloration AE which has an outcome of flushing, a sudden reddening of the face, neck, or upper chest SS, YH HPO: HP_0001033 SIDER: C0016382 脸红 CTCAE:E13771 NCIt:C26775 WEB: http://www.nlm.nih.gov/medlineplus/ency/article/003241.htm pain in extremity AE 10033425 CTCAE: E12512 SIDER: C0030196 NCIt: C78515 a pain AE where the pain reachs an extreme level. SS, YH, MW HPO: HP_0009763 postnasal drip AE 10036402 CTCAE: E13514 PDN NCIt: C78566 WEB: http://en.wikipedia.org/wiki/Post-nasal_drip Upper Airway Cough Syndrome SS, YH UACS a respiratory system AE which has an outcome of postnasal drip, which occurs when excessive mucus is produced by the nasal Mucosa. The excess mucus accumulates in the throat or back of the nose. musculoskeletal or connective tissue AE 10028395 an adverse event that has an outcome of abnormal sign in a musculoskeletal or connective tissue. YH, RR, JX WEB: http://www.cdc.gov/niosh/programs/msd/ musculoskeletal and connective tissue disorder AE A musculoskeletal disorder is an injury or disorder of the muscles, nerves, tendons, joints, cartilage, or supporting structures of the upper or lower limbs, neck, or lower back that are caused, precipitated, or exacerbated by sudden exertion or prolonged exposure to physical factors such as repetition, force, vibration, or awkward posture CTCAE: E13872 fatigue AE 10016256 10024264 SS, YH, MW NCIt: C3036; NCIt: C78416 CTCAE: E11098 (fatigue); CTCAE: E12709 (lethargy) lethargy AE HPO: HP_0003388 WEB: http://en.wikipedia.org/wiki/Fatigue_%28medical%29 lethargy is sometimes reported as an extreme fatigue: http://the-difference-between.com/lethargy/fatigue they are sometimes regarded as synonyms: https://www.nlm.nih.gov/medlineplus/ency/article/003088.htm SIDER: C0015672 a behavior and neurological AE that has an outcome of fatigue, which is a state of awareness describing a range of afflictions, usually associated with physical and/or mental weakness, though varying from a general state of lethargy to a specific work-induced burning sensation within one's muscles. Physical fatigue is the inability to continue functioning at the level of one's normal abilities. myocardial infarction AE 10028596 a cardiac disorder AE that is characterized by a necrosis of the myocardium caused by an obstruction of the blood supply to the heart SIDER: C0027051 HPO: HP_0001658 SS 心肌梗塞 NCIt: C27996 WEB: http://www.ncbi.nlm.nih.gov/mesh/68009203 CTCAE: E10152 procedural complication AE SS, YH post-procedural AE an adverse event that shows a complication that occurs after a medical procedure and is directly related to the precedure itself. procedural disorder AE procedure AE injury AE 10022116 SS, YH an injury and procedural complication AE which has an outcome of injury nystagmus AE 10029864 眼球震颤 CTCAE:E12748 WEB: http://en.wikipedia.org/wiki/Nystagmus JX, LW, YH NCIt:C3282 Nystagmus AE is an eye AE that is a condition of involuntary eye movement, acquired in infancy or later in life, that may result in reduced or limited vision. Due to the involuntary movement of the eye, it is often called "dancing eyes". hot flushes AE 10020407 HPO: HP_0008209 hot flashes AE hot flash AE hot flush AE SS, YH, MW SIDER: C0600142 a skin adverse event that is characterized by an uncomfortable and temporary sensation of intense body warmth, flushing, sometimes accompanied by sweating upon cooling. NCIt: C3109 CTCAE: E13781 tumor AE 10026865 YH, RR an adverse event that results in the outcome of a tumor. nodule AE tumour AE mass AE wheezing AE 10047924 NCIt:C78718 SS, YH, MW CTCAE:E13605 a respiratory system AE which has an outcome of wheezing, a high-pitched whistling sound made while breathing. WEB: http://www.mayoclinic.org/symptoms/wheezing/basics/definition/sym-20050764 systematic AE an adverse event that occurs systematically throughout the systemic circulation. This is different from local adverse event that is limited or a certain location. systematic adverse event URL: https://en.wikipedia.org/wiki/Adverse_drug_reaction YH, JX pregnancy AE prenatal AE WEB: https://en.wikipedia.org/wiki/Prenatal_diagnosis YH, JX WEB: https://en.wikipedia.org/wiki/Complications_of_pregnancy A pregnancy, neonatal and perinatal AE that displays a disorder associated with pregnancy. surgery AE a procedure complication AE that occurs after a surgery. surgery adverse event The key difference between a surgery and a procedure is the need for an incision. Making an incision, or cutting into the skin to gain access to the body’s deeper tissues or organs, is a defining characteristic of surgery. Technically speaking, a surgery is a specific type of procedure. A procedure is a broad general term that refers to any series of pre-defined steps that should be followed to achieve a desired result. Therefore, a “surgical procedure” is synonymous with a “surgery.” See more: http://www.wisegeekhealth.com/what-is-the-difference-between-a-surgery-and-a-procedure.htm. YH surgical procedure AE surgery 10042609 Surgery is a medical procedure that uses operative manual and instrumental techniques on a patient to investigate and/or treat a pathological condition such as disease or injury, to help improve bodily function or appearance. The key difference between a surgery and a general procedure is the need for an incision. Making an incision, or cutting into the skin to gain access to the body’s deeper tissues or organs, is a defining characteristic of surgery. WEB: http://www.wisegeekhealth.com/what-is-the-difference-between-a-surgery-and-a-procedure.htm YH, SS surgical procedure WEB: http://en.wikipedia.org/wiki/Surgery metabolism, endocrine or exocrine system AE 10027433 SS, YH, JX metabolism, endocrine, and exocrine system AE MP: 0005266 an adverse event which occurs in a metabolism process (including anabolism and catabolism), endocrine system, or exocrine system. female reproductive system AE 10038604 YH a reproductive system AE that occurs on the female side. male reproductive system AE a reproductive system AE that occurs on the male side. YH cardiac disorder AE 10007541 10061024 HPO: HP_0001627 SIDER: C0018799 a cardiovascular disorder AE that has a cardiac disorder outcome. SS, YH WEB: Primary Source: http://medical-dictionary.thefreedictionary.com/heart+disease Secondary Source: http://www.ncbi.nlm.nih.gov/pubmed/23091623 vascular disorder AE 10047065 a cardiovascular disorder AE that has a vascular disorder outcome sensory neuropathy AE a peripheral neuropathy AE which has an outcome of sensory neuropathy that involves damage to nerves of the peripheral nervous system. sensory neuropathy AE YH, AG tremor AE 10044565 SS, YH SIDER: C0040822 WEB: http://www.nlm.nih.gov/medlineplus/tremor.html NCIt: C38038 HPO: HP_0001337 CTCAE: E12837 Tremor AE is a behavior and neurological AE that has an outcome of an involuntary trembling or quivering, and muscle contraction and relaxation. motor neuropathy AE a peripheral neuropathy AE which is caused by a damage to motor neurons AG, YH distal neuropathy AE AG, YH a peripheral neuropathy AE which affects extremities, such as, toes, fingers, hand and feet. axonal neuropathy AE WEB: http://www.livestrong.com/article/184686-distal-neuropathy-symptoms/ dementia AE 10012272 HPO: HP_0000726 WEB: https://en.wikipedia.org/wiki/Dementia a psychiatric disorder AE that has an outcome of a loss of brain function and causes a long term and often gradual decrease in the ability to think and remember such that a person's daily functioning is affected. 痴呆 YH, MW Dementia is a loss of brain function that occurs with certain diseases or pathological processes. SIDER: C0497327 thrombosis AE 10043607 SS, YH, MW SIDER: C0040053 HPO: HP_0004419 血栓症; 血栓生成 A vascular disorder AE that results in the presence of blood clot along the wall of a blood vessel, frequently causing vascular obstruction. Some authorities differentiate thrombus formation from simple coagulation or clot formation. cell death AE 10057248 HPO: HP_0010885 SIDER: C0007587 SS, YH a metabolic disorder AE that has an outcome of cell death. phlebitis AE 10034879 an inflammation AE that shows the result of an inflammation located in a vein, usually in the legs. CTCAE:E13815 SIDER: C0031542 NCIt:C38003 HPO: HP_0004419 YH, MW pancreatitis AE 10033645 10033646 HPO: HP_0001733 YH, MW SIDER: C0030305 NCIt: C3306 CTCAE: E10930 a liver, biliary, and pancreatic AE that has an outcome of pancreatitis. necrosis AE SS, YH SIDER: C0027540 HPO: HP_0003713 a cell death AE that has an outcome of necrosis ischemia AE 10061255 HPO: HP_0002597 ischaemia AE SIDER: C0022116 SS, YH A cardiovascular disorder AE that results in Insufficient blood supply for the need of a part of the body, usually as a result of a disease of the blood vessels supplying that part. Note: also spelt ischemia. hair, skin or nail AE YH, SS, JX an adverse event that occurs in hair, skin, or nail. hair, skin, and nail AE hair AE YH, SS a hair, skin, and nail AE that occurs in hair. nail AE a hair, skin, and nail AE that occurs in nail. YH, SS endocrine system AE 10014698 a metabolism, endocrine, and exocrine system AE that occurs in endocrine system. YH, SS paresis AE 10033800 WEB: https://en.wikipedia.org/wiki/Paresis SIDER: C0030552 HPO: HP_0008153 局部麻痹 Neurologists use the term paresis to describe weakness, and plegia to describe paralysis in which all voluntary movement is lost. (Reference: https://en.wikipedia.org/wiki/Paresis) a muscular weakness AE that shows weakness or inability to move a body part, often used to describe a neurologic condition. hepatitis AE HPO: HP_0006562 a liver, biliary, and pancreatic AE that has an outcome of hepatitis. YH SIDER: C0019158 ulcer AE an adverse event that displays an outcome of ulcer. SIDER: C0041582 HPO: HP_0005229 YH, SS fistula AE 10067143 SIDER: C0016169 YH, SS a musculoskeletal and connective tissue AE that displays an outcome of fistula, a permanent abnormal passageway between two organs in the body or between an organ and the exterior of the body. WEB: http://medical-dictionary.thefreedictionary.com/fistula HPO: HP_0010294 bradycardia AE 10006093 WEB: http://en.wikipedia.org/wiki/Bradycardia HPO: HP_0001662 WEB: http://medical-dictionary.thefreedictionary.com/bradycardia SIDER: C0428977 a decreased heart rate AE that results in a resting heart rate of under 60 beats per minutes (BPM). prenatal, perinatal or neonatal disorder AE 10036585 pregnancy, neonatal and perinatal disorder AE an adverse event that displays a disorder associated with child birth, newborn infant, or an infant. YH, JX medical intervention site AE 10003055 application site reaction an adverse event that occurs in the site of a medical intervention (e.g., vaccination injection site). YH medical intervention site a site that is used for a medical intervention YH perinatal AE A pregnancy, neonatal and perinatal AE that displays a disorder associated with childbirth YH arterial disorder AE arterial disease AE SS SIDER: C0852949 a vascular disorder AE that affects the artery HPO: HP_0002620 abdominal distension AE 10000060 NCIt: C78161 a sensory capability AE that results in a sensation of elevated abdominal pressure and volume DJ, SS, YH HPO: HP_0003270 WEB: http://www.ncbi.nlm.nih.gov/pubmedhealth/PMH0003609/ SIDER: C0000731 CTCAE: E10456 activated partial thromboplastin time prolonged AE 10000636 DJ, SS, YH SIDER: C0853223 WEB: http://www.nlm.nih.gov/medlineplus/ency/article/003653.htm HPO: HP_0003645 CTCAE: E12073 NCIt: C27028 a hematopoietic system AE that has an outcome of a prolonged time taken for blood to clot. The partial thromboplastin time (PTT) is a blood test that looks at how long it takes for blood to clot. PTT measures the efficacy of the comon coagulation pathways and helps tell if bleeding or clotting problems exist. alanine aminotransferase level abnormal AE 10001547 WEB: http://www.ncbi.nlm.nih.gov/pubmed/23139615 DJ, SS, YH a liver related investigation result abnormal AE that has an outcome of an abnormal blood level of alanine aminotransferase alanine aminotransferase level increased AE 10001551 DJ, SS, YH, EB WEB: http://www.ncbi.nlm.nih.gov/pubmed/23139615 NCIt: C26948 CTCAE: E12077 an alanine aminotransferase level abnormal AE that has an outcome of elevated levels of alanine transaminase, an enzyme most commonly found in the liver anal ulcer AE 10002180 CTCAE: E10496 WEB: http://www.ncbi.nlm.nih.gov/pubmed/17073250 DJ, SS, YH an ulcer AE that has an outcome of an ulcer in the anal cavity NCIt: C79536 anxiety AE 10002855 a psychiatric disorder AE that has an outcome of a psychological and physiological state characterized by cognitive, somatic, emotional, and behavioral components. These components combine to create an unpleasant feeling that is typically associated with uneasiness, fear, or worry. CTCAE: E12883 SIDER: C0003467 NCIt: C26696 HPO: HP_0000739 SS, YH WEB: http://en.wikipedia.org/wiki/Anxiety atrial flutter AE 10003662 HPO: HP_0004749 SS NCIt: C51224 CTCAE: E10087 auricular flutter SIDER: C0004239 WEB: http://medical-dictionary.thefreedictionary.com/atrial+flutter AF an arrhythmia AE that is characterized by rapid regular atrial contractions occurring usually at rates between 250 and 400 per minute and often producing saw-tooth waves in an electrocardiogram. dysgeusia AE 10013911 WEB: http://en.wikipedia.org/wiki/Dysgeusia NCIt:C28145 SIDER: C0013378 HPO: HP_0000223 a behavior and neurological AE that has an outcome of distortion of the sense of taste SS, YH, MW CTCAE:E12643 dyspnea AE 10013963 10013968 SS, YH WEB: http://en.wikipedia.org/wiki/Dyspnoea HPO: HP_0002094 UMLS CUI: C0013404 MedDRA: 10013968 is for "dyspnoea"; MedDRA: 10013963 is for "dyspnea". NCIt: C2998 SIDER: C0013404 呼吸困难 CTCAE: E13368 dyspnoea AE is an abnormal respiration AE debilitating symptom that is the experience of unpleasant or uncomfortable respiratory sensations, shortness of breath, air hunger dyspnoea AE conduction system disorder AE 10000032 10010276 a cardiac disorder AE of the electrical conduction system that controls the heart rate, generates and conducts electrical impulses throughout the muscle of the heart, stimulating the heart to contract and pump blood. conduction disorder AE NCIt: C78245 CTCAE: E10114 WEB: http://www.medterms.com/script/main/art.asp?articlekey=8407 SS cardiac conduction disorder AE arteriosclerosis coronary artery AE 10003211 SIDER: C0010054 WEB: http://medical-dictionary.thefreedictionary.com/Coronary+Arteriosclerosis a coronary artery disease AE with the outcome hardening of the coronary artery due to a build up of waxy plaque on the inside of blood vessels HPO: HP_0004929 DJ, SS, YH kidney AE 10038428 abnormal renal function AE SS, YH an adverse event that occurs in kidney. mobility decreased AE 10048334 SS, YH SIDER: C0700572 mobility decreased AE is a nervous system AE that results in difficulty in movement leading to less ability to move part(s) of body HPO: HP_0006217 muscular weakness AE 10028372 HPO: HP_0001324 a muscle AE that has an outcome of muscular weakness AE (i.e., lack of muscle strength). SS, YH SIDER: C0151786 WEB: http://en.wikipedia.org/wiki/Muscular_weakness nasal congestion AE 10028735 WEB: http://en.wikipedia.org/wiki/Nasal_congestion SS, YH HPO: HP_0001742 nasal congestion AE is a respiratory system AE that results in a blockage of the nasal passages usually due to membranes lining the nose becoming swollen from inflamed blood vessels SIDER: C0027424 NCIt: C78500 CTCAE: E13450 peripheral neuropathy AE 10029331 an neuropathy AE that results in a damage to the peripheral nervous system (PNS, outside the brain and spinal cord), the vast communication network that transmits information from the brain and the spinal cord (the central nervous system) to every other part of the body. neuropathy peripheral AE WEB: http://www.ninds.nih.gov/disorders/peripheralneuropathy/detail_peripheralneuropathy.htm SS, YH WEB: http://en.wikipedia.org/wiki/Peripheral_neuropathy otitis media AE 10033078 CTCAE: E11477 WEB: http://en.wikipedia.org/wiki/Otitis_media HPO: HP_0008623 NCIt: C34885 SIDER: C0029882 SS, YH an ear disorder AE which has an outcome of otitis media that results in inflammation of the middle ear, or middle ear infection pericarditis AE 10034484 HPO: HP_0001701 SS, YH an inflammation AE that has an outcome of pericaditis, which is a cardiovascular disorder that results in a condition in which the sac-like covering around the heart (pericardium) becomes inflamed NCIt: C34915 WEB: http://www.nlm.nih.gov/medlineplus/ency/article/000182.htm CTCAE: E10180 SIDER: C0031046 pharyngitis AE 10034835 WEB: http://en.wikipedia.org/wiki/Pharyngitis SS, YH SIDER: C0031350 NCIt: C26851 HPO: HP_0100776 pharyngitis AE is a digestive system AE that results in an inflammation of the throat or pharynx CTCAE: E11525 pharyngolaryngeal pain AE 10034844 WEB: http://www.wordinfo.info/words/index/info/view_unit/1631/ HPO: HP_0010833 CTCAE: E13482 a pain AE that shows a pain in sinus and throat NCIt: C78556 SS, YH, MW SIDER: C0858635 rhinitis AE 10028116 runny nose WEB: http://en.wikipedia.org/wiki/Rhinitis SIDER: C0035455 WEB: http://medical-dictionary.thefreedictionary.com/rhinitis HPO: HP_0002257 SS, YH rhinitis AE is a respiratory system inflammation characterized by runny nose,irritation and inflammation of some internal areas of the nose sneezing AE 10041232 sneezing AE is a respiratory system adverse event that results in sternutation, a semi-autonomous, convulsive expulsion of air from the lungs through the nose and mouth, usually caused by foreign particles irritating the nasal mucosa CTCAE:E13572 WEB: http://en.wikipedia.org/wiki/Sneezing sternutation SS, YH, MW NCIt:C50746 tachycardia AE 10043071 SIDER: C0039231 WEB: http://en.wikipedia.org/wiki/Tachycardia an increased heart rate AE where the heart rate exceeds the normal range for a resting heartrate (heartrate in an inactive or sleeping individual) SS, YH HPO: HP_0001649 upper respiratory tract infection AE 10046300 SS, YH CTCAE: E11604 NCIt: C35650 an infection AE is a respiratory system AE that results in illnesses caused by an acute infection which involves the upper respiratory tract: nose, sinuses, pharynx or larynx SIDER: C0041912 URI, URTI HPO: HP_0002788 WEB: http://en.wikipedia.org/wiki/Upper_respiratory_tract_infection fever AE 10005911 10016558 10037660 Axelrod YK1, Diringer MN. Temperature management in acute neurologic disorders. Neurol Clin. 2008 May;26(2):585-603, xi. doi: 10.1016/j.ncl.2008.02.005. PMID: 18514828. YH, SS, MW WEB: http://en.wikipedia.org/wiki/Pyrexia febrile response an abnormal body temperature AE which has an outcome of fever CTCAE: E11102 body temperature increased AE pyrexia AE NCIt: C3038 Fever is a frequent medical sign that describes an increase in internal body temperature to levels above normal. Fever is characterized as a temporary elevation in the body's thermoregulatory set-point, usually by about 1-2 °F). rash AE 10037844 YH SIDER: C0015230 URL: http://en.wikipedia.org/wiki/Rash Drug-induced rash is the most commonly reported drug reaction. URL: http://www.webmd.com/skin-problems-and-treatments/guide/common-rashes Wick JY. Drug-induced rash: nuisance or threat? Consult Pharm. 2013 Mar;28(3):160-6. PMID: 23462025. a skin AE that shows the symptom of rash, i.e., an abnormal change in skin color, appearance, or texture. A rash may cause the skin to change color, itch, become warm, bumpy, dry, cracked or blistered, swell and may be painful. HPO: HP_0000988 infection AE 10021789 YH, JX change of name from 'infection adverse event' to 'infectious adverse event' on 09/23/13 for a better clinical relevance, move 'infection adverse event' as an alternative term - SS an adverse event that has an outcome of a pathogen infection, i.e., an infection caused by a pathogen such as a virus, bacterium, or parasite. infection infectious adverse event WEB: http://medical-dictionary.thefreedictionary.com/infection syndrome AE An AE that has an outcome of syndrome. Syndrome is the association of several clinically recognizable features, signs (observed by a physician), symptoms (reported by the patient), phenomena or characteristics that often occur together, so that the presence of one feature alerts the physician to the presence of the others. YH agitation AE 10001497 HPO: HP_0000711 a psychiatric disorder AE that has an outcome of emotional state of excitement or restlessness CTCAE:E12874 YH, MW SIDER: C0085631 NCIt:C79530 injection-site AE 10022095 injection site AE YH, JX, SS injection-site AE is an AE that occurs in an injection site (e.g., during vaccination). CTCAE: E11138 NCIt: C3508 injection-site adverse event injection-site reaction local reaction AE pruritus AE 10037087 NCIt:C3344 SIDER: C0033774 WEB: http://www.ncbi.nlm.nih.gov/sites/entrez?db=mesh&cmd=DetailsSearch&term=pruritus+generalised&log$=activity CTCAE:E13686 itching YH, SS, MW pruritus generalised AE itch Pruritus is an itch (Latin: pruritus), i.e., an unpleasant sensation that evokes the desire or reflex to scratch. HPO: HP_0000989 a skin adverse event that has an outcome of pruritus pain AE 10033371 CTCAE: E11167 SIDER: C0030193 HPO: HP_0010833 NCIt: C3303 YH, MW a sensory capability AE that has an outcome of pain in a patient myalgia AE 10028411 SIDER: C0231528 NCIt:C27009 YH, MW HPO: HP_0003326 muscle pain AE CTCAE:E12485 a pain AE that has outcome of myalgia. Myalgia means "muscle pain" and is a symptom of many diseases and disorders. urticaria AE 10046735 SIDER: C0042109 Urticaria AE is a rash AE notable for dark red, raised, itchy bumps. YH, MW hives CTCAE:E13746 HPO: HP_0001025 NCIt:C3432 headache AE 10019211 CTCAE: E12678 SIDER: C0018681 a pain AE that has an outcome of headache HPO: HP_0002315 NCIt: C34661 YH, MW respiratory system AE I created this term and make it to be an umbrella term for different disorder terms related to respiratory system. --Oliver He YH an AE that occurs in respiratory system. leukocyte cell number increased AE 10024378 10047943 CTCAE: E10048 WEB: http://en.wikipedia.org/wiki/Leukocytosis According to the Vaccine Adverse Event Reporting System (VAERS), 'leukocytosis' is an adverse event that was mentioned in 1,021 VAERS reports (0.8%) during1991-2001 (Reference: PMID: 12825543). white blood cell count increased AE NCIt: C35524 leukocytosis AE increased leukocyte cell number AE MP: MP_0000218 SS, YH, EB a leukocyte cell number abnormal AE that has an outcome of greater than normal number of leukocytes, or nucleated cells of the myeloid or lymphoid lineages, found in blood or other tissue leukocyte cell number decreased AE 10047942 CTCAE: E12232 white blood cell count decreased AE NCIt: C26816 a leukocyte cell number abnormal AE that has an outcome of reduction in the number of leukocytes, or of nucleated cells of the myeloid or lymphoid lineages, found in blood or other tissue decreased leukocyte cell number AE According to the Vaccine Adverse Event Reporting System (VAERS), 'leukopenia' is an adverse event that was mentioned in 417 VAERS reports (0.3%) during1991-2001 (Reference: PMID: 12825543). MP: MP_0000221 abnormal blood pressure AE MP: MP_0000230 a cardiovascular disorder AE that has an outcome of abnormal blood pressure, representing altered tension of the blood within the systemic arteries maculo-papular rash AE 10037868 YH, MW maculopapular rash AE WEB: http://en.wikipedia.org/wiki/Maculopapular_rash The term "maculopapular" is a compound: macules are small, flat discolored spots on the surface of the skin; and papules are small, raised bumps. CTCAE:E13700 rash maculopapular AE rash maculo-papular AE A rash AE that shows a flat, red area on the skin overed with small confluent bumps. NCIt:C75579 arthralgia AE 10003239 An joint disorder AE that has an outcome of arthralgia. Arthralgia means joint pain. It is a symptom of injury, infection, illnesses (in particular arthritis) or an allergic reaction to medication. According to MeSH, the term "arthralgia" should only be used when the condition is non-inflammatory, and the term "arthritis" should be used when the condition is inflammatory. CTCAE:E12374 NCIt:C50464 SIDER: C0003862 HPO: HP_0002829 YH, MW dizziness AE 10013573 HPO: HP_0002321 YH, SS, MW a sensory capability AE that has an outcome of dizziness Dizziness describes a number of subjective symptoms, which the patient may describe as feelings of lightheadedness, floating, wooziness, giddiness, confusion, disorientation or loss of balance. Medical terms include vertigo, disequilibrium, pre-syncope or syncoptic episode. Causes may stem from a variety of failures of equilibrioception, hypotension, cerebral hypoxia or a reaction to environmental chemicals or drugs. CTCAE:E12631 NCIt:C37943 SIDER: C0012833 edema limbs AE 10030124 10050068 CTCAE: E11086 NCIt: C78262 YH, SS oedema peripheral AE peripheral edema AE edema peripheral AE peripheral edema AE is an edema AE that results in swelling of tissues, usually in the lower limbs, due to the accumulation of fluids WEB: http://en.wikipedia.org/wiki/Peripheral_edema malaise AE 10025482 YH HPO: HP_0002321 CTCAE: E11152 Malaise is a feeling of general discomfort or uneasiness, an "out of sorts" feeling. Malaise is often the first indication of an infection or other disease. Vaccination may induce malaise. a sensory capability AE that has an outcome of malaise NCIt: C3832 SIDER: C0231218 somnolence AE 10041349 CTCAE:E12814 HPO: HP_0001262 drowsiness a behavior and neurological AE that has an outcome of somnolence Somnolence (or "drowsiness") is a state of near-sleep, a strong desire for sleep, or sleeping for unusually long periods (c.f. hypersomnia). SIDER: C2830004 YH, SS, MW NCIt:C26754 paresthesia AE 10033775 10033987 a sensory neuropathy AE that shows a sensation of tingling, pricking, or numbness of a person's skin with no apparent long-term physical effect. CTCAE: E12758 Paresthesia is more generally known as the feeling of "pins and needles" or of a limb being "asleep" (although this is not directly related to the phenomenon of sleep). The manifestation of paresthesia may be transient or chronic. YH, MW paraesthesia AE WEB: http://en.wikipedia.org/wiki/Paraesthesia NCIt: C28177 chills AE 10008531 feeling cold AE YH CTCAE: E11074 SIDER: C0085593 Chills refers to feeling cold after an exposure to a cold environment. The word can also refer to an episode of shivering, accompanied by paleness and feeling cold. HPO: HP_0001945 a sensory capability AE that has an outcome of chills NCIt: C35143 anorexia AE 10002646 10002649 10061428 decreased appetite AE YH, MW NCIt: C2875 HPO: HP_0002039 a gustatory system AE which demonstrates a decreased sensation of appetite. WEB: http://www.mayoclinic.org/diseases-conditions/anorexia/basics/definition/con-20033002 anorexia nervosa AE CTCAE: E12252 SIDER: C0003123 厌食症 face edema AE 10014222 10016029 10042682 NCIt: C78289 swelling face face oedema AE WEB:http://www.nlm.nih.gov/medlineplus/ency/article/003105.htm CTCAE: E11082 oedema face AE emema face AE face edema AE is an edema AE that results in facial swelling, the build-up of fluid in the tissues of the face. Swelling may also affect the neck and upper arms YH, SS, MW cough AE 10011224 WEB: http://medical-dictionary.thefreedictionary.com/cough YH, SS, MW coughing AE cough WEB: http://www.nlm.nih.gov/medlineplus/cough.html an abnormal respiration AE that shows a sudden and often repetitively occurring reflex to keep the throat and airways clear CTCAE:E13364 NCIt:C37935 flu syndrome AE YH NCIt: C78302 CTCAE: E11108 flu-like symptom AE a syndrome AE that has an outcome of a flu syndrome AE and occurs after a medical intervention. syncope AE 10024855 10042772 SIDER: C0039070 a sensory capability AE that has an outcome of loss of consciousness, fainting WEB: http://en.wikipedia.org/wiki/Unconsciousness fainting Syncope is the medical term for fainting, a sudden, usually temporary, loss of consciousness. CTCAE: E12832 NCIt: C35053 YH, SS, MW HPO: HP_0001279 WEB: http://en.wikipedia.org/wiki/Syncope_%28medicine%29 sweating AE YH a skin adverse event that has an outcome of sweating SIDER: C0038990 According to the Vaccine Adverse Event Reporting System (VAERS), 'sweating' is an adverse event that was mentioned in 2,301 VAERS reports (1.8%) during1991-2001 (Reference: PMID: 12825543). HPO: HP_0000975 abdominal pain AE 10000081 WEB: http://en.wikipedia.org/wiki/Abdominal_pain HPO: HP_0002027 SIDER: C0000737 YH, SS According to the Vaccine Adverse Event Reporting System (VAERS), 'abdominal pain' is an adverse event that was mentioned in 2,254 VAERS reports (1.8%) during1991-2001 (Reference: PMID: 12825543). a pain AE that is observed in abdominal cavity hypertension AE 10005750 10020772 CTCAE: E13785 NCIt: C3117 HPO: HP_0000822 blood pressure increased SIDER: C0020538 WEB: http://www.ncbi.nlm.nih.gov/pubmed/21722707 YH, SS, MW an abnormal blood pressure AE that has an outcome of sustained high blood pressure at a level that is likely to result in cardiovascular disease and/or other pathological states MP: MP_0000231 chest pain AE 10008479 SIDER: C0008031 YH HPO: HP_0001681 According to the Vaccine Adverse Event Reporting System (VAERS), 'chest pain' was mentioned in 1,752 VAERS reports (1.4%) during1991-2001 (Reference: PMID: 12825543). a pain AE that occurs at the chest neck pain AE 10028836 SIDER: C0007859 CTCAE: E12493 NCIt: C50663 YH, MW According to the Vaccine Adverse Event Reporting System (VAERS), 'neck pain' was mentioned in 1,323 VAERS reports (1.0%) during1991-2001 (Reference: PMID: 12825543). HPO: HP_0003418 a pain AE that has an outcome of neck pain back pain AE 10003988 According to the Vaccine Adverse Event Reporting System (VAERS), 'back pain' was mentioned in 1,277 VAERS reports (1.0%) during1991-2001 (Reference: PMID: 12825543). YH, MW HPO: HP_0003418 NCIt:C41830 CTCAE:E12388 a pain AE that has an outcome of back pain SIDER: C0004604 alopecia AE 10001760 SIDER: C0002170 VAE, MW NCIt:C50575 alopecia means the absence of hair or loss of hair. It is not usually in reference to primary genetic hairlessness but may be due to dietary, stress, secondary to immune condition. HPO: HP_0001596 CTCAE:E13611 MP: MP_0000414 a hair AE that has an outcome of alopecia and occurs after a medical intervention. gastrointestinal hemorrhage AE 10017955 MP: MP_0000465 a hemorrhage AE that has an outcome of gastrointestinal hemorrhage gastrointestinal haemorrhage AE WEB: http://medical-dictionary.thefreedictionary.com/gastrointestinal+hemorrhage bleeding in the stomach and/or the intestines neuropathy AE WEB: http://www.neuropathy.org/ SIDER: C0442874 a nervous system AE that shows a damage to or disease affecting the nerves. 神经病变 WEB: http://www.medicalnewstoday.com/articles/147963.php YH, RR WEB: http://www.emedicinehealth.com/neuropathy/article_em.htm#types_of_neuropathy WEB: http://www.emedicinehealth.com/neuropathy/article_em.htm Neuropathy is often classified according to the types or location of nerves that are affected. Neuropathy can also be classified according to the disease causing it. (For example, neuropathy from the effects of diabetes is called diabetic neuropathy. Ref: http://www.emedicinehealth.com/neuropathy/article_em.htm#types_of_neuropathy. HPO: HP_0007141 skin discoloration AE 10040829 skin discoloration AE is a skin adverse event that results in change in color of skin or mucus membranes skin discolouration AE YH, SS According to the Vaccine Adverse Event Reporting System (VAERS), 'skin discoloration' is an adverse event that was mentioned in 909 VAERS reports (0.7%) during1991-2001 (Reference: PMID: 12825543). speech disorder AE 10041466 YH a behavior and neurological AE that has an outcome of disorder in speech SIDER: C0037822 HPO: HP_0006977 hemorrhage AE 10055798 WEB: http://medical-dictionary.thefreedictionary.com/hemorrhage haemorrhage AE bleeding AE MP: MP_0001914 a cardiovascular disorder AE that has an outcome of hemorrhage loss of blood from the vascular compartment to the exterior or into nonvascular body space as a result of rupture or severance of the blood vessels lung AE 10025082 YH SIDER: C0024115 lung disorder AE a respiratory system AE which has an outcome of lung disorder HPO: HP_0006552 muscle AE a musculoskeletal system AE that occurs in muscle. YH hepatobiliary or pancreatic AE YH, JX an adverse event that occurs in liver, biliary, and pancreatic areas. URL: http://www.ijhpd.com/ WEB: http://www.uchospitals.edu/online-library/content=P00670 liver, biliary, and pancreatic disorder AE meningitis AE 10027199 WEB: http://www.cdc.gov/meningitis/index.html SIDER: C0025289 脑膜炎 a brain inflammation AE which results in an inflammation of the protective membranes covering the brain and spinal cord, known collectively as the meninges. The inflammation is caused by infection with viruses, bacteria, or other microorganisms, and less commonly by certain drugs or diseases. YH, JX HPO: HP_0001287 CTCAE: E11458 NCIt: C26828 digestive system AE YH an AE that occurs in digestive system. confusion AE 10010300 10010305 YH, KM WEB: http://medical-dictionary.thefreedictionary.com/mental+confusion NCIt: C37928 a psychiatric disorder AE that has an outcome of confusion, which is a mild form of delirium. mental confusion AE CTCAE: E12889 confused state AE joint disorder AE a musculoskeletal system AE which has an outcome of joint disorder YH eye AE 10015916 YH an AE that occurs in eye. eye disorder AE HPO: HP_0000496 SIDER: C0015397 erythema multiforme AE 10015218 a rash AE which shows red, target-shaped or "bulls-eye" patches or sores on the skin. WEB: https://en.wikipedia.org/wiki/Erythema_multiforme The erythema multiforme rash usually begins on the arms, hands, legs, and feet, but you might also find it on the face, neck, and body. It also can affect the lips and inside the mouth. It usuallys follows an infection or drug exposure. HPO: HP_0010783 WEB: http://kidshealth.org/parent/infections/skin/erythema_multiforme.html SIDER: C0014742 YH, MW CTCAE:E13627 NCIt:C3024 dyspepsia AE 10013946 CTCAE: E10617 NCIt: C26756 HPO: HP_0002577 According to the Vaccine Adverse Event Reporting System (VAERS), 'dyspepsia' is an adverse event that was mentioned in 454 VAERS reports (0.4%) during1991-2001 (Reference: PMID: 12825543). an abnormal digestion AE which has an outcome of dyspepsia SIDER: C0013395 Dyspepsia is popularly known as indigestion, meaning hard or difficult digestion. It is a medical condition characterized by chronic or recurrent pain in the upper abdomen, upper abdominal fullness and feeling full earlier than expected when eating. YH gastrointestinal disorder AE SIDER: C0017178 According to the Vaccine Adverse Event Reporting System (VAERS), 'gastrointestinal disorder' is an adverse event that was mentioned in 449 VAERS reports (0.3%) during1991-2001 (Reference: PMID: 12825543). a digestive system AE which has an outcome of a gastrointestinal disorder YH HPO: HP_0011024 ascites AE 10003445 DJ, SS, YH HPO: HP_0001541 SIDER: C0003962 WEB: http://www.ncbi.nlm.nih.gov/pubmed/23296107 an edema AE that has an outcome of accumulation of fluid in the peritoneal cavity CTCAE: E10502 NCIt: C2885 serum sickness AE 10040400 a hypersensitivity AE which has an outcome of serum sickness Serum sickness is a reaction to proteins in antiserum derived from an animal source. It is a type of hypersensitivity, specifically immune complex hypersensitivity (type III). According to the Vaccine Adverse Event Reporting System (VAERS), 'serum sickness' is an adverse event that was mentioned in 428 VAERS reports (0.3%) during1991-2001 (Reference: PMID: 12825543). YH, MW NCIt: C79718 CTCAE: E11276 vertigo AE 10047340 According to the Vaccine Adverse Event Reporting System (VAERS), 'vertigo' was mentioned in 412 VAERS reports (0.3%) during1991-2001 (Reference: PMID: 12825543). NCIt: C38057 Vertigo is a specific type of dizziness, a major symptom of a balance disorder. It is the sensation of spinning or swaying while the body is actually stationary with respect to the surroundings. The effects of vertigo may be slight. It can cause nausea and vomiting and, in severe cases, it may give rise to difficulties with standing and walking. HPO: HP_0002321 SIDER: C0042571 CTCAE: E10291 YH a dizziness AE that has an outcome of vertigo cardiac arrest 10007515 10007617 10028596 WEB: http://medical-dictionary.thefreedictionary.com/cardiac+arrest a cardiac disorder AE that has an outcome of heartarrest, the abrupt cessation of normal circulation of the blood due to failure of the heart to contract effectively during systole. cardiopulmonary arrest YH circulatory arrest NCIT: C50479 WEB: http://en.wikipedia.org/wiki/Myocardial_infarction CTCAE: E10101 heart arrest AE ear AE an AE that occurs in ear. SIDER: C0013447 ear disorder AE YH HPO: HP_0000598 eye pain AE 10015958 SIDER: C0151827 According to the Vaccine Adverse Event Reporting System (VAERS), 'eye pain' is an adverse event that was mentioned in 316 VAERS reports (0.2%) during1991-2001 (Reference: PMID: 12825543). a pain AE that has an outcome of eye pain CTCAE: E10376 NCIt: C78287 HPO: HP_0200025 YH ear pain AE 10014020 NCIt: C37944 HPO: HP_0010833 YH CTCAE: E10262 SIDER: C0013456 a pain AE that has an outcome of ear pain According to the Vaccine Adverse Event Reporting System (VAERS), 'ear pain' was mentioned in 302 VAERS reports (0.2%) during1991-2001 (Reference: PMID: 12825543). immune system AE According to the Vaccine Adverse Event Reporting System (VAERS), 'immune system disorder' was mentioned in 292 VAERS reports (0.2%) during1991-2001 (Reference: PMID: 12825543). HPO: HP_0002715 YH SIDER: C0021053 immune system disorder AE an AE that occurs in immune system. myelitis AE 10028524 a nervous system AE which involves inflammation of the spinal cord, which disrupts central nervous system functions linking the brain and limbs. CTCAE: E12732 YH, MW NCIt: C26832 thrombocytopenic purpura AE 10043561 According to the Vaccine Adverse Event Reporting System (VAERS), 'thrombocytopenic purpura'; is an adverse event that was mentioned in 267 VAERS reports (0.2%) during1991-2001 (Reference: PMID: 12825543). HPO: HP_0004829 Thrombocytopenic purpura AE are purpura AE associated with a reduction in circulating blood platelets which can result from a variety of causes. YH SIDER: C0857305 amnesia AE 10001949 NCIt:C2867 YH, MW a behavior and neurological AE that has an outcome of amnesia in a patient HPO: HP_0002354 CTCAE:E12585 SIDER: C0002622 Amnesia is a short term memory condition in which memory is disturbed. In simple terms it is the loss of memory. voice alteration AE 10047681 YH, MW a speech disorder that has an outcome of voice alteration CTCAE: E13601 NCIt: C61043 purpura AE 10037549 HPO: HP_0000979 Purpura is the appearance of red or purple discolorations on the skin that do not blanch on applying pressure. They are caused by bleeding underneath the skin. This is common with typhus and can be present with meningitis caused by meningococcal meningitis or septicaemia. Reference: http://en.wikipedia.org/wiki/Purpura. NCIt:C78787 YH, MW CTCAE:E13690 紫癜 SIDER: C0034150 According to the Vaccine Adverse Event Reporting System (VAERS), 'purpura'; is an adverse event that was mentioned in 251 VAERS reports (0.2%) during1991-2001 (Reference: PMID: 12825543). a skin discoloration AE which has an outcome of purpura acute brain syndrome AE a syndrome AE that has an outcome of an acute brain syndrome AE and occurs after a medical intervention. YH cardiovascular AE 10007649 HPO: HP_0001626 SIDER: C0007222 YH an AE that occurs in cardiovascular system. cardiovascular disorder AE encephalopathy AE 10014625 SIDER: C0085584 CTCAE:E12652 NCIt:C26920 a nervous system AE which has an outcome of encephalopathy, which is disorder or disease of the brain. YH, MW HPO: HP_0007239 urine abnormality AE SIDER: C0235639 a urinary system AE that has an outcome of urine abnormality AE HPO: HP_0011036 YH urinary tract infection AE 10046571 SIDER: C0042029 HPO: HP_0000094 YH CTCAE: E11614 NCIt: C50791 a urinary system AE that has an outcome of urnary tract infection AE depression AE 10012378 CTCAE:E12909 NCIt:C2982 SIDER: C0011570 YH, MW WEB: http://www.mayoclinic.org/diseases-conditions/depression/basics/definition/con-20032977 HPO: HP_0000716 a psychiatric disorder AE that has an outcome of depression. Depression causes a persistent feeling of sadness and loss of interest. laryngitis AE 10023874 CTCAE: E11435 YH SIDER: C0023067 Laryngitis is an inflammation of the larynx. It causes hoarse voice or the complete loss of the voice because of irritation to the vocal folds (vocal cords). NCIt: C26811 HPO: HP_0001600 a respiratory system inflammation AE which has an outcome of laryngitis According to the Vaccine Adverse Event Reporting System (VAERS), 'laryngitis'; is an adverse event that was mentioned in 190 VAERS reports (0.1%) during1991-2001 (Reference: PMID: 12825543). dry mouth AE 10013781 xerostomia NCIt: C26917 HPO: HP_0000217 a digestive system AE which has an outcome of dry mouth, which is dryness of the mouth resulting from reduced salivary secretion YH According to the Vaccine Adverse Event Reporting System (VAERS), 'dry mouth'; is an adverse event that was mentioned in 171 VAERS reports (0.1%) during1991-2001 (Reference: PMID: 12825543). CTCAE: E10578 SIDER: C0043352 epistaxis AE 10015090 YH, MW NCIt:C26766 nosebleed Epistaxis is the relatively common occurrence of hemorrhage from the nose, usually noticed when the blood drains out through the nostrils. SIDER: C0014591 HPO: HP_0000421 a hemorrhage AE that has an outcome of epistaxis CTCAE:E13374 photophobia AE 10034960 Photophobia is a symptom of excessive sensitivity to light and the aversion to sunlight or well-lit places. In medical terms it is not fear, but an experience of discomfort or pain to the eyes due to light exposure. NCIt: C28210 HPO: HP_0000613 CTCAE: E10416 an eye disorder AE which has an outcome of photophobia SIDER: C0085636 YH hallucination AE 10019063 10019077 NCIt: C37961 HPO: HP_0000738 A hallucination, in the broadest sense, is a perception in the absence of a stimulus. In a stricter sense, hallucinations are defined as perceptions in a conscious and awake state in the absence of external stimuli which have qualities of real perception, in that they are vivid, substantial, and located in external objective space. YH, MW hallucinations AE SIDER: C0018524 a psychiatric disorder AE that has an outcome of hallucination CTCAE: E12919 neuralgia AE 10029223 CTCAE:E12744 a pain AE that has an outcome of neuralgia Neuralgia or neuropathic pain can be defined most simply as non-nociceptive pain. Neuralgia is pain produced by a change in neurological structure or function. Unlike nociceptive pain, Neuralgia exists with no continuous nociceptive input. Neuralgia falls into two categories: central Neuralgia and peripheral Neuralgia. According to the Vaccine Adverse Event Reporting System (VAERS), 'neuralgia'; is an adverse event that was mentioned in 155 VAERS reports (0.1%) during1991-2001 (Reference: PMID: 12825543). NCIt:C79695 HPO: HP_0003489 SIDER: C0027796 YH, MW bone AE 10005956 HPO: HP_0000924 SIDER: C0005940 YH a musculoskeletal system AE that occurs in the bone bone disorder fetal disorder AE a perinatal AE that displays fetal disorder. YH muscle spasm AE 10028334 MP: MP_0000743 SS, YH WEB: http://en.wikipedia.org/wiki/Spasm a muscle adverse event which has an outcome of muscle spasm, which is an involuntary and often painful muscle contraction or cramps having a number of causes ranging from nutritional deficiency to serious nervous system conditions pustular rash AE 10037888 According to the Vaccine Adverse Event Reporting System (VAERS), 'pustular rash'; is an adverse event that was mentioned in 128 VAERS reports (<0.1%) during1991-2001 (Reference: PMID: 12825543). CTCAE: E11545 a rash AE that is characterized by a circumscribed and elevated skin lesion filled with pus. rash pustular AE NCIt: C80119 YH bone pain AE 10006002 NCIt:C38644 YH, MW SIDER: C0151825 a pain AE that has an outcome of bone pain CTCAE:E12392 HPO: HP_0002653 According to the Vaccine Adverse Event Reporting System (VAERS), 'bone pain' was mentioned in 109 VAERS reports (<0.1%) during1991-2001 (Reference: PMID: 12825543). flatulence AE 10016766 YH a movement disorder AE that has an outcome of flatulence CTCAE: E10697 SIDER: C0016204 NCIt: C37954 Flatulence is the production of a mixture of gases in the digestive tract of mammals or other animals that are byproducts of the digestion process. Such a mixture of gases is known as flatus, and is expelled from the rectum in a process colloquially referred to as "passing gas" or "farting". HPO: HP_0011024 According to the Vaccine Adverse Event Reporting System (VAERS), 'flatulence' was mentioned in 102 VAERS reports (<0.1%) during1991-2001 (Reference: PMID: 12825543). sore throat AE 10041367 CTCAE: E13575 NCIt: C50747 a respiratory system AE which has an outcome of sore throat YH, MW paralysis AE 10033799 a movement disorder AE that results in the loss of power of voluntary movement in a muscle through injury or disease of its nerve supply HPO: HP_0010549 SIDER: C0522224 MP: MP_0000753 瘫痪 WEB: https://www.nlm.nih.gov/medlineplus/paralysis.html SS, YH According to the Vaccine Adverse Event Reporting System (VAERS), 'paralysis' is an adverse event that was mentioned in 574 VAERS reports (0.4%) during1991-2001 (Reference: PMID: 12825543). weight loss AE 10047895 10047900 MP: MP_0001263 CTCAE: E12228 a physical examination result abnormal AE that has an outcome of weight loss, which is the progressive reduction of body weight below normal average for age NCIt: C3445 MW, YH weight decreased AE ataxia AE 10003591 CTCAE:E12597 SIDER: C0004134 HPO: HP_0001251 a movement disorder AE that has an outcome of ataxia, inability to coordinate voluntary muscular movements According to the Vaccine Adverse Event Reporting System (VAERS), 'ataxia' is an adverse event that was mentioned in 555 VAERS reports (0.4%) during1991-2001 (Reference: PMID: 12825543). YH, MW NCIt:C26702 MP: MP_0001393 skin AE 10040831 WEB: http://www.thefreedictionary.com/skin+disorder a hair, skin, and nail AE that occurs in skin. YH abnormal gait AE 10017577 gait disturbance AE NCIt: C78303 WEB: http://www.ncbi.nlm.nih.gov/pubmed/21224774 According to the Vaccine Adverse Event Reporting System (VAERS), 'abnormal gait' is an adverse event that was mentioned in 998 VAERS reports (0.8%) during1991-2001 (Reference: PMID: 12825543). a movement disorder AE that has an outcome of unusual or distinctive way of walking SS, YH CTCAE: E11112 MP: MP_0001406 dehydration AE 10012174 hypohydration an abnormal fluid regulation AE which has an outcome of dehydration, which is an excessive water loss from the body or from an organ or bodily part CTCAE:E12258 YH, SS, MW MP: MP_0001429 NCIt:C26740 SIDER: C0011175 HPO: HP_0001944 abnormal fluid regulation AE MP: MP_0001784 a homeostasis AE which has an outcome of abnormal fluid regulation, which is any anomaly in the control of intracellular and/or extracellular fluid hyperglycemia AE 10020635 10020639 MP: MP_0001559 WEB: http://medical-dictionary.thefreedictionary.com/hyperglycemia a glucose homeostasis AE which has an outcome of hyperglycemia, which is an abnormally high concentration of glucose in the blood; generally refers to a pathological state CTCAE: E12276 YH, MW NCIt: C26797 anemia AE 10002034 10002272 WEB: http://www.ncbi.nlm.nih.gov/pubmedhealth/PMH0001586/ a hematopoietic system AE which has an outcome of anemia, which is less than normal levels of red blood cells and/or hemoglobin within red blood cells, or volume of packed red blood cells in the bloodstream, resulting in insufficient oxygenation of tissues and organs anaemia AE NCIt: C2869 MP: MP_0001577 CTCAE: E10010 hypotension AE 10005734 10021097 HPO: HP_0002615 NCIt: C3128 YH, MW CTCAE: E13791 blood pressure decreased, low blood pressure MP: MP_0001596 an abnormal blood pressure AE that has an outcome of sustained low blood pressure at a level that is likely to result in cardiovascular disease and/or other pathological states SIDER: C0020649 electrolyte blood test abnormal AE an electrolyte lab test abnormal AE that shows an abnormal level of an electrolyte in the blood YH, MW abnormal digestion AE MP: MP_0001664 a digestive system AE which has an outcome of abnormal digestion, which is an altered ability of the mechanical, chemical, and enzymatic processes of the body to convert ingested food into material suitable for assimilation for synthesis of tissues or liberation of energy homeostasis AE an AE that occurs in the homeostasis system. anomaly in the processes involved in the maintenance of an internal equilibrium of various functions and chemical or protein composition of the fluids and tissues MP: MP_0001764 edema AE 10016807 10030095 10042674 MP: MP_0001785 WEB: http://en.wikipedia.org/wiki/Oedema an abnormal fluid regulation AE which has an outcome of edema, which is an accumulation of an excessive amount of watery fluid in cells or intercellular tissues oedema, swelling, dropsy WEB: http://en.wikipedia.org/wiki/Swelling_(medical) inflammation AE 10061218 SIDER: C0021368 SS, YH HPO: HP_0007891 WEB: http://en.wikipedia.org/wiki/Inflammation MP: MP_0001846 an immune system disorder AE that results in complex biological response of vascular tissues to harmful stimuli, such as pathogens, damaged cells, or irritants. Inflammation is a protective attempt by the organism to remove the injurious stimuli as well as initiate the healing process for the tissue greater than expected response to injury, infection, or insult. brain inflammation AE According to the Vaccine Adverse Event Reporting System (VAERS), 'encephalitis' is an adverse event that was mentioned in 480 VAERS reports (0.4%) during1991-2001 (Reference: PMID: 12825543). MP: MP_0001847 an inflammation AE which has an outcome of brain inflammation, which is local accumulation of fluid, plasma proteins, and leukocytes in the brain eye inflammation AE 10015943 MP: MP_0001851 HPO: HP_0100533 an eye disorder AE which has an outcome of eye inflammation, which is local accumulation of fluid, plasma proteins, and leukocytes in the eye SIDER: C0239429 conjunctivitis AE 10010741 an eye inflammation AE which has an outcome of conjunctivitis, which is inflammation of the mucous membrane that lines the inner surface of the eyelids and the front of the eyeball SIDER: C0009763 NCIt: C34504 MP: MP_0001852 HPO: HP_0000509 CTCAE: E10355 liver inflammation AE YH, JX MP: MP_0001860 According to the Vaccine Adverse Event Reporting System (VAERS), 'hepatitis' was mentioned in 387 VAERS reports (0.3%) during1991-2001 (Reference: PMID: 12825543). an inflammation AE that shows a local accumulation of fluid, plasma proteins, and leukocytes in the liver lung inflammation AE According to the Vaccine Adverse Event Reporting System (VAERS), 'pneumonia' was mentioned in 879 VAERS reports (0.7%) during1991-2001 (Reference: PMID: 12825543). MP: MP_0001861 aa inflammation AE which has an outcome of lung inflammation, a local accumulation of fluid, plasma proteins, and leukocytes in the lung respiratory system inflammation AE MP: MP_0002405 an inflammation AE which occurs in the respiratory system, which is reflected with the local accumulation of fluid, plasma proteins, and leukocytes in the respiratory system vasculitis AE 10047115 NCIt:C26912 MP: MP_0001864 CTCAE:E13837 YH, MW HPO: HP_0002633 an inflammation AE that has an outcome of vasculitis, which is an inflammation of a blood or lymph vessel SIDER: C0042384 It's an inflammation. sinusitis AE 10040753 SS, YH, RR CTCAE: E11563 According to the Vaccine Adverse Event Reporting System (VAERS), 'sinusitis'; is an adverse event that was mentioned in 298 VAERS reports (0.2%) during1991-2001 (Reference: PMID: 12825543). MP: MP_0001872 WEB: http://en.wikipedia.org/wiki/Sinusitis sinus inflammation AE HPO: HP_0000246 SIDER: C0037199 NCIt: C35024 a respiratory system inflammation AE which has an outcome of sinus inflammation, an inflammation of paranasal sinuses, which may be due to infection, allergy, or autoimmune issues. allergy AE 10001718 10001738 anaphylactic reaction AE allergic reaction AE CTCAE: E11248 MP: MP_0001878 过敏反应 NCIt: C3114 WEB: http://en.wikipedia.org/wiki/Allergy allergic response AE JX, LW, YH a hypersensitivity AE which results in an allergic response showing a marked increase in reactivity to an antigen upon subsequent exposure. 变态反应 nervous system AE 10029202 KY, YH an AE that occurs in nervous system. MP: MP_0003633 nervous system disorder AE URL: http://www.hopkinsmedicine.org/healthlibrary/conditions/nervous_system_disorders/overview_of_nervous_system_disorders_85,P00799/ abnormal respiration AE Not sure if it is same as respiratory system disorder or abnormal respiration. --Oliver He MP: MP_0001943 According to the Vaccine Adverse Event Reporting System (VAERS), 'respiratory disorder' is an adverse event that was mentioned in 556 VAERS reports (0.4%) during1991-2001 (Reference: PMID: 12825543). a respiratory system AE which has an outcome of abnormal respiration, an anomaly in the movement of gases into and out of the lung apnea AE respiratory arrest AE JX, YH, MW NCIt: C26698 MedDRA: 10002974 is for "apnoea"; MedDRA: 10002972 is for "apnea". According to the Vaccine Adverse Event Reporting System (VAERS), 'apnea' is an adverse event that was mentioned in 1,618 VAERS reports (1.3%) during1991-2001 (Reference: PMID: 12825543). CTCAE: E13306 apnoea AE UMLS CUI: C0003578 WEB: http://medical-dictionary.thefreedictionary.com/apnea MP: MP_0001957 an abnormal respiration AE which has an outcome of apnea, temporary cessation of breathing; sometimes episodic gustatory system AE MP: MP_0001985 YH, JX an adverse event that occurs in a gustatory system abnormal vision AE MP: MP_0002090 an eye disorder AE which has an outcome of abnormal vision, which is an inability or decreased ability to see seizure AE 10039906 10039910 CTCAE: E12804 WEB: http://www.healthline.com/symptom/seizures 突然发作 YH, JX, YH MP: MP_0002064 NCIt: C2962 a behavior and neurological AE that shows a sudden surge of electrical activity in the brain. behavioral and neurological AE WEB: http://www.psychguides.com/guides/behavioral-disorder-symptoms-causes-and-effects/ YH, JX any anomaly in the actions, reactions, or performance of an organism in response to external or internal stimuli compared to controls behavior AE disruptive behavioral disorder AE MP: MP_0004924 an adverse event that has an outcome of an abnormal behavior and neurological phenotype. behavioral AE behavioral disorder AE movement disorder AE 10028035 HPO: HP_0100022 SIDER: C0026650 MP: MP_0002066 a behavior and neurological AE that has an outcome of altered ability to coordinate voluntary movement or repetitive, compulsive movements sensory capability AE MP: MP_0002067 a behavior and neurological AE that has an outcome of inability or altered ability to respond to a sensory stimulus glucose homeostasis AE MP: MP_0002078 a homeostasis AE which has an outcome of glucose homeostasis, which is an anomaly in the processes involved in the maintenance of an internal equilibrium of glucose in the fluids and tissues hypersensitivity AE 10020751 Hypersensitivity AE is a immune system AE that is a set of undesirable reactions produced by the normal immune system, including allergies and autoimmunity. These reactions may be damaging, uncomfortable, or occasionally fatal. JX, LW, YH MP: MP_0002148 HPO: HP_0100326 WEB: http://en.wikipedia.org/wiki/Hypersensitivity hypersensitivity reaction AE 超敏反应 SIDER: C0020517 hematopoietic system AE MP: MP_0002396 an adverse event which occurs in a hematopoietic system, which is any structural or developmental anomaly of the blood cells or the organs associated with the development and formation of blood cells increased heart rate AE 10019303 WEB: http://en.wikipedia.org/wiki/Tachycardia tachycardia MP: MP_0002626 an arrhythmia AE that has an outcome of greater than average resting heart beats per minute, usually measured by the number of times the heart ventricles contract per unit of time, usually per minute joint inflammation AE An joint disorder AE that has an outcome of joint inflammation, which is local accumulation of fluid, plasma proteins, and leukocytes in the joints MP: MP_0002933 YH arthritis AE 10003246 A joint inflammation AE that has an outcome of arthritis, marked by changes in the synovial membranes and thickening of articular structures, widespread degeneration of the collagen fibers in connective tissues, and by atrophy and rarefaction of bony structures SIDER: C0003864 CTCAE:E12378 HPO: HP_0001369 MP: MP_0002993 NCIt:C2883 YH, MW 关节炎 dysphagia AE 10013950 CTCAE: E10621 HPO: HP_0002015 SIDER: C0011168 NCIt: C2980 MP: MP_0003158 a digestive system AE which has an outcome of dysphagia, which is a behavior and neurological AE that has an outcome of difficulty in swallowing food or liquid platelet count decreased AE 10035528 HPO: HP_0001873 MP: MP_0003179 NCIt: C3408 CTCAE: E12207 SS, YH SIDER: C0392386 a hematopoietic system AE which has an outcome of decreased platelet count, which is fewer than the normal numbers of the non-nucleated cells found in the blood and involved in blood coagulation decreased platelet cell number AE nausea AE 10028813 CTCAE: E10878 NCIt: C3258 MP: MP_0003259; MDR: 10028813 HPO: HP_0002018 SIDER: C0027497 an abnormal digestion AE which has an outcome of nausea, a gastric discomfort associated with the inclination to vomit vomiting AE 10047700 NCIt: C3442 regurgitation AE SIDER: C0042963 MP: MP_0003260; MDR: 10047700 CTCAE: E11068 HPO: HP_0002013 an abnormal digestion AE which has an outcome of vomiting, the retrograde expulsion of gastric contents through the oral cavity constipation AE 10010774 CTCAE: E10562 MP: MP_0003267 an abnormal defecation AE that has an outcome of constipation, which is incomplete, infrequent or difficult evacuation of fecal matter infrequent bowel movements AE SIDER: C0009806 NCIt: C37930 HPO: HP_0002019 According to the Vaccine Adverse Event Reporting System (VAERS), 'constipation'; is an adverse event that was mentioned in 242 VAERS reports (0.2%) during1991-2001 (Reference: PMID: 12825543). abnormal defecation AE MP: MP_0003866 a digestive system AE that has an outcome of abnormal defecation, an anomaly in the production and excretion of feces urinary incontinence AE MP: MP_0003280 HPO: HP_0000020 SIDER: C0042024 YH, MW MedDRA: 10046543 CTCAE: E13042 NCIt: C78497 WEB: http://www.nlm.nih.gov/medlineplus/urinaryincontinence.html a urinary system AE that has an outcome of the symptom of urinary incontinence, which is the inability to control the urinary excretory functions. tinnitus AE 10043882 HPO: HP_0000360 MP: MP_0003741 CTCAE: E10287 NCIt: C50772 SIDER: C0040264 an hearing disorder AE that shows a persistent sensation of buzzing, ringing, clicking, or other noises in the ear myositis AE 10028653 YH, MW SIDER: C0027121 MP: MP_0004510 NCIt:C27578 CTCAE:E12489 HPO: HP_0009071 a muscle inflammation AE which has an outcome of myositis, which is an inflammation of skeletal muscle; local accumulation of fluid, plasma proteins, and leukocytes in the striated muscle muscle inflammation AE YH MP: MP_0004511 a muscle adverse event which has an outcome of muscle inflammation, which is a local accumulation of fluid, plasma proteins, and leukocytes in muscle lymphocyte count increased AE 10025258 MP: MP_0005013 increased lymphocyte cell number AE NCIt: C34791 EB According to the Vaccine Adverse Event Reporting System (VAERS), 'lymphocytosis'; is an adverse event that was mentioned in 129 VAERS reports (0.1%) during1991-2001 (Reference: PMID: 12825543). a lymphocyte count abnormal AE that has an outcome of greater than normal number of the cells involved in adaptive immune reactions of the body in most inflammatory and autoimmune diseases, including B cells, T cells and natural killer cells lymphocyte cell number increased AE CTCAE: E12195 diarrhea AE 10012735 NCIt: C2987 diarrhoea AE MP: MP_0005036 WEB: http://medical-dictionary.thefreedictionary.com/diarrhea CTCAE: E10572 an abnormal defecation AE that has an outcome of diarrhea, which is abnormally frequent discharge of semi-solid or fluid fecal matter from the bowel hypoxia AE 10021143 YH, MW MP: MP_0005039 WEB: http://medical-dictionary.thefreedictionary.com/hypoxia SIDER: C0242184 CTCAE:E13388 NCIt:C3890 HPO: HP_0002795 a homeostasis AE which has an outcome of hypoxia, which is a reduced concentration of O2 in the blood, alveoli or other tissues resulting in the decreased pressure of this component of body gases sepsis AE 10040047 HPO: HP_0002718 CTCAE: E11560 SIDER: C0243026 According to the Vaccine Adverse Event Reporting System (VAERS), 'sepsis' was mentioned in 416 VAERS reports (0.3%) during1991-2001 (Reference: PMID: 12825543). MP: MP_0005044 SS NCIt: C3364 an infectious adverse event which has an outcome of the presence of various pathogenic organisms, or their toxins, in the blood or tissues that results in the infections in blood stream. hematuria AE 10018867 10018870 10019450 MP: MP_0005161 YH, SJ, MW WEB: http://kidney.niddk.nih.gov/kudiseases/pubs/hematuria/ NCIt: C3090 a urinary system AE that results in the presence of blood in the urine blood urine blood urine presence haematuria AE UMLS CUI: C0018965 (hematuria AND haematuria); UMLS CUI: C0947999 (blood urine presence) CTCAE: E13000 Hematuria AE can be caused by menstruation, vigorous exercise, sexual activity, viral illness, trauma, or infection, such as a urinary tract infection (UTI), along with more serious disorders such as cancer, disease, and clotting. decreased heart rate AE 10019301 an arrhythmia AE that has an outcome of fewer than average resting heart beats per minute, usually measured by the number of times the heart ventricles contract per unit of time, usually per minute YH, JX heart rate decreased AE MP: MP_0005333 urinary system AE MP: MP_0005502 YH an adverse event that has an outcome of urinary system AE is a functional anomaly of any of the organs involved in the production or excretion of urine hypothermia AE 10021113 MP: MP_0005534 NCIt: C78351 YH, SJ decreased body temperature AE CTCAE: E11122 Hypothermia AE is a medical emergency that occurs when your body loses heat faster than it can produce heat, causing a dangerously low body temperature. an abnormal body temperature AE which has an outcome of decreased body temperature, which is less than the level of heat natural to a living being abnormal body temperature AE MP: MP_0005535 a homeostasis AE whic has an outcome of abnomal body temperature, which is a deviation in the level of heat natural to a living being investigation result abnormal AE 10061253 EB, SS, YH This term is used to replace 'lab test abnormal AE'. The reason for this is that some test, like X-ray test, is not considered by many physicians as a lab test. Therefore, we have used this new term to cover a broader scope. All terms asserted under this term represent the investigation results without defined conclusion of disease. laboratory test abnormal an adverse event that is indicated by an abnormal result of an investigation that uses some laboratory equipment, device, or medical technology. serious adverse event serious adverse event WEB: http://www.google.ca/url?sa=t&source=web&ct=res&cd=1&ved=0CA4QFjAA&url=http%3A%2F%2Fwww.irrd.ca%2Fethics%2Fimages%2FAdverse-event-definition.doc&ei=eqFMS-yFNZSoswOt6siKAQ&usg=AFQjCNGnQcwI8OXH7dqxwo4RgZEEn8X6lg&sig2=UNngkCdO5ZTFvbIB1pKuaA WEB: http://www.fda.gov/Safety/MedWatch/HowToReport/ucm053087.htm WEB: http://en.wikipedia.org/wiki/Serious_adverse_event YH, MC severe adverse event serious adverse event is an adverse event that requires in-patient hospitalization, or prolongation of existing hospitalization, or that causes congenital malformation, or that results in persistent or significant disability or incapacity, or that is life threatening or results in death. death AE 10011906 10011914 a serious adverse event that has an outcome of death. HPO: HP_0001645 NCIt: C28554 SIDER: C1306577 YH WEB: http://www.fda.gov/Safety/MedWatch/HowToReport/ucm053087.htm CTCAE: E11080 hematoma AE 10006504 10018852 10019428 SS, YH bruising AE an cardiovascular adverse event that is a collection of blood outside the blood vessels, generally the result of hemorrhage, or more specifically, internal bleeding. It is commonly called a bruise. SIDER: C0018944 YH: MedDRA ID: 10018852 is for "haematoma"; MedDRA ID: 10019428 is for "hematoma". WEB: http://en.wikipedia.org/wiki/Hematoma HPO: HP_0001892 CTCAE: E13775 (hematoma); CTCAE: E11666 (brruising) ecchymoses AE NCIt: C37921 (Bruising); NCIt: C50579 (Hematoma) bruise AE haematoma AE reproductive system AE YH, SS reproductive system AE is an AE that occurs in the reproductive system. aspartate aminotransferase level increased AE 10003481 DJ, SS, YH, EB CTCAE: E12087 WEB: http://medical-dictionary.thefreedictionary.com/aspartate+aminotransferase an aspartate aminotransferase level abnormal AE that has an outcome of an increased amount of AST, an enzyme normally present in body tissues especially of the heart and liver NCIt: C26947 atrial fibrillation AE 10003658 WEB: http://medical-dictionary.thefreedictionary.com/atrial+fibrillation NCIt: C50466 AF SS, YH Atrial fibrillation (AF or A-fib) is the most common cardiac arrhythmia (abnormal heart rhythm), and involves the two upper chambers (atria) of the heart. Its name comes from the fibrillating (i.e., quivering) of the heart muscles of the atria, instead of a coordinated contraction. WEB: http://en.wikipedia.org/wiki/Atrial_fibrillation HPO: HP_0005110 SIDER: C0004238 CTCAE: E10081 an arrhythmia AE that involves the two upper chambers (atria) of the heart arrhythmia AE 10003119 abnormal heartbeat AE HPO: HP_0011675 SS, YH WEB: http://www.nhlbi.nih.gov/health/health-topics/topics/arr/ SIDER: C0003811 cardiac arrhythmia AE a cardiac disorder AE which has an outcome of abnormal heart rhythm MP: MP_0004085 aspiration AE 10003504 DJ, SS, YH, MW CTCAE:E13310 a respiratory system AE that has an outcome of the drawing of a foreign substance into the respiratory tract during inhalation WEB: http://medical-dictionary.thefreedictionary.com/aspiration HPO: HP_0002835 NCIt:C15631 SIDER: C0700198 facial pain AE 10016059 a pain AE that has an outcome of facial pain facial pain is a pain in facial area (eyes, eyebrows, forehead, nose, cheeks, mouth, teeth and chin). Facial pain may include injuries to the nerves or bones that coordinate many of your face’s actions. SS, YH WEB: http://www.bettermedicine.com/article/facial-pain CTCAE: E11094 HPO: HP_0100661 SIDER: C0015468 NCIt: C79594 atelectasis AE 10003598 HPO: HP_0001642 WEB: http://www.ncbi.nlm.nih.gov/pubmedhealth/PMH0001130/ CTCAE:E13316 DJ, SS, YH, MW SIDER: C0004144 NCIt:C2888 a lung disorder AE that has an outcome of collapse in part of or all of a lung joint range of motion decreased AE 10048706 NCIt: C78403 CTCAE: E12435 joint range of motion decreased AE is a mobility decreased AE that results in limited or decreased range of joint motion SS, YH, MW laryngospasm AE 10023891 a muscle spasm AE which has an outcome of laryngospasm, which is an uncontrolled/involuntary muscular contraction (spasm) of the laryngeal cords. The condition typically lasts less than 60 seconds, and causes a partial blocking of breathing in, while breathing out remains easier. It may be triggered when the vocal cords or the area of the trachea below the cords detects the entry of water, mucus, blood, or other substance. It is characterized by stridor and or retractions. SS, YH, MW NCIt:C79609 HPO: HP_0006511 WEB: http://en.wikipedia.org/wiki/Laryngospasm CTCAE:E13439 SIDER: C0023066 periorbital edema AE periorbial edema AE is an edema AE that has an outcome of swelling around the eye. NCIt: C78530 Periorbital puffiness, also known as "puffy eyes" or swelling around the eyes, refers to the appearance of swelling in the tissues around the eyes, called the orbits. WEB: http://en.wikipedia.org/wiki/Periorbital_puffiness CTCAE: E13676 UMLS CUI: C0151205 periorbital oedema AE SS, YH MedDRA: 10034545 is for "periorbital edema"; MedDRA: 10054541 is for "periorbital oedema" periorbital puffiness hypermagnesemia AE 10020670 a blood magnesium abnormal AE that has an outcome of an abnormally high concentration of magnesium in the blood plasma, and may cause nausea, weakness and tremors. NCIt: C37969 UMLS CUI: C0151714 YH, MW WEB: http://emedicine.medscape.com/article/246489-overview CTCAE: E12288 stridor AE 10042241 a wheezing AE which has an outcome of stridor, a high pitched wheezing sound resulting from turbulent air flow in the upper airway. It is primarily inspiratory. It can be indicative of serious airway obstruction from severe conditions such as epiglottitis, a foreign body lodged in the airway, or a laryngeal tumor. SS, YH, MW SIDER: C0038450 WEB: http://en.wikipedia.org/wiki/Stridor NCIt:C78632 CTCAE:E13579 HPO: HP_0010307 skin ulceration AE 10040943 10040947 SIDER: C0037299 skin ulcer AE WEB: http://en.wikipedia.org/wiki/Ulcer_%28dermatology%29 HPO: HP_0200042 NCIt: C54247 CTCAE: E13730 a skin AE that shows a result of skin ulcer, i.e., a sore on the skin or a mucous membrane, accompanied by the disintegration of tissue. Ulcers can result in complete loss of the epidermis and often portions of the dermis and even subcutaneous fat. SS, YH, MW vaginal hemorrhage AE NCIt: C26945 CTCAE: E13264 MedDRA: 10046910 is for "vaginal haemorrhage"; MedDRA: 10046912 is for "vaginal hemorrhage" vaginal hemorrhage is irregular/heavy bleeding from the vagina. Vaginal hemorrhage is more often associated with pregnancy complications such as miscarriage or placental abruption, but certainly can occur in the absence of pregnancy. a hemorrhage AE that has an outcome of vaginal hemorrhage SS, YH, MW WEB: http://www.brooksidepress.org/Products/Military_OBGYN/Textbook/AbnormalBleeding/Bleeding.htm vaginal haemorrhage AE vasodilatation AE a cardiovascular disorder AE which has an outcome of vasodilatation, which refers to the widening of blood vessels resulting from relaxation of smooth muscle cells within the vessel walls, particularly in the large arteries, smaller arterioles and large veins. WEB: http://en.wikipedia.org/wiki/Vasodilation SS, YH HPO: HP_0004927 SIDER: C0595862 blood alkaline phosphatase level abnormal AE 10059571 DJ, SS, YH, EB a liver related investigation result abnormal AE that has an outcome of an abnormal level of alkaline phosphatase in the blood blood alkaline phosphatase increased AE 10001675 10059570 CTCAE: E12082 HPO: HP_0003155 SIDER: C0852911 a blood alkaline phosphatase abnormal AE that has an outcome of elevated levels of alkaline phosphatase, an enzyme responsible for removing phosphate groups. a liver/biliary system AE that has an outcome of an increased amount of ALP, an isoenzyme that removes phosphate groups commonly found in the bile ducts but also found in the bone DJ, SS, YH NCIt: C35607 WEB: http://medical-dictionary.thefreedictionary.com/alkaline+phosphatase blood amylase level increased AE 10005328 10040139 DJ, SS, YH, EB CTCAE: E12212 serum amylase increased AE NCIt: C78608 a blood amylase level abnormal AE that has an outcome of an increased amount of amylase, an enzyme that helps digest carbohydrates; may indicate disease or inflammation of the pancreas WEB: http://www.nlm.nih.gov/medlineplus/ency/article/003464.htm blood bilirubin level abnormal AE 10058477 a liver related investigation result abnormal AE that has an outcome of an abnormal amount of bilirubin in the blood DJ, SS, YH, EB WEB: http://medical-dictionary.thefreedictionary.com/bilirubin blood bilirubin level increased AE 10005364 WEB: http://medical-dictionary.thefreedictionary.com/bilirubin a blood bilirubin level abnormal AE with an outcome of a increased amount of bilirubin, or a yellow breakdown product (broken down hemoglobin) of normal heme catabolism, in the blood DJ, SS, YH, EB CTCAE: E12096 NCIt: C27088 blood calcium decreased 10005395 a physical quality that has a decreased amount of calcium in the bloodstream DJ, SS, YH blood cholesterol increased AE 10005425 HPO: HP_0003124 NCIt: C37967 CTCAE: E12127 DJ, SS, YH, EB SIDER: C0595930 a blood cholesterol abnormal AE with the result of an increase in cholesterol level in the blood blood creatinine level increased AE 10005483 10011368 creatinine increased AE a blood creatinine level abnormal AE that has an outcome of an increased level of creatinine in the blood (due to lack of kidney activity) WEB: http://medical-dictionary.thefreedictionary.com/creatinine NCIt: C78249 serum creatinine increased CTCAE: E12137 DJ, SS, YH, EB blood magnesium decreased 10005654 HPO: HP_0002917 WEB: http://www.medterms.com/script/main/art.asp?articlekey=4243 A physical quality that has an decreased level of magnesium, a mineral involved in nerve signaling and bone health. Deficiency can cause spasms, and muscular cramps. SIDER: C0853750 DJ, SS, YH blood potassium decreased 10005724 HPO: HP_0002900 DJ, SS, YH, LW, MW 血钾下降 a physical quality where the blood potassium level is decreased. blood sodium decreased 10005802 A physical quality that has an decreased level of sodium concentration in the blood DJ, SS, YH, MW bone marrow depression AE 10005986 10048580 DJ, SS, YH, MW hypocellular bone marrow UMLS: C0151773 SIDER: C0151773 Bone marrow produces three types of blood cells; red blood cells, white blood cells and platelets. Bone marrow depression is characterized by an inability or reduced ability of the bone marrow to produce these cells. A low blood count can involve just one or all three types of blood cells. HPO: HP_0012145 NCIt: C35167 bone marrrow hypocellular WEB: http://www.drugs.com/condition/bone-marrow-depression-low-blood-counts.html CTCAE: E10022 a bone marrow disorder AE that has an outcome of an abnormal condition in which the bone marrow is unable to produce normal amounts of red blood cells, white blood cells and platelets WEB: http://en.diagnosispro.com/differential_diagnosis-for/bx-bone-marrow-biopsy-hypocellular/29777-154.html bone marrow disorder AE 10061729 a hematopoietic system AE that has an outcome of disease in the bone marrow, the spongy tissue inside of some bones that contain stem cells that can develop into red blood cells, white blood cells or platelets WEB: http://www.nlm.nih.gov/medlineplus/bonemarrowdiseases.html DJ, SS, YH brain edema AE 10048962 DJ, SS, YH HPO: HP_0002181 an edema AE that has an outcome of edema or swelling of the extravascular compartment from uptake of water in the gray and white matter brain oedema AE WEB: http://medical-dictionary.thefreedictionary.com/cerebral+edema SIDER: C1527311 breast infection AE 10006259 SIDER: C0392317 HPO: HP_0002726 an infection AE that results in the breast becoming infected CTCAE: E11318 DJ, SS, YH NCIt: C53662 breast pain AE 10006298 a pain AE that results in pain in the breast HPO: HP_0000769 NCIt:C78223 CTCAE:E13073 SIDER: C0024902 DJ, SS, YH, MW bronchospasm AE 10006482 HPO: HP_0002099 SIDER: C0006266 CTCAE:E13352 DJ, SS, YH, MW a lung disorder AE that has an outcome of a sudden constriction of the muscles in the walls of the bronchioles WEB: http://medical-dictionary.thefreedictionary.com/bronchospasm NCIt:C34439 cecitis AE 10006919 10045271 NCIt: C38043 a digestive system AE that has an outcome of inflammation of the caecum, part of the large intestine typhlitis AE caecitis AE WEB: http://medical-dictionary.thefreedictionary.com/caecitis DJ, SS, YH CTCAE: E11058 capillary leak syndrome AE 10007196 NCIt:C62578 CTCAE:E13766 DJ, SS, YH, MW a cardiovascular disorder AE that has an outcome of self-reversing episodes during which the endothelial cells which line the capillaries are thought to separate for a few days, allowing for a leakage of fluid from the circulatory system to the interstitial space, resulting in hypotension, hemoconcentration, and hypoalbuminemia Clarkson's Disease AE WEB: http://www.ncbi.nlm.nih.gov/pubmed/22873043 cardiac failure AE 10007554 10019279 DJ, SS, YH heart failure NCIt: C50577 a cardiovascular disorder AE that results in the inability of the heart to provide sufficient pump action to distribute blood flow to meet the needs of the body WEB: http://medical-dictionary.thefreedictionary.com/cardiac+failure SIDER: C0018801 HPO: HP_0001635 CTCAE: E10124 cardiac ventricular disorder AE 10057455 DJ, SS, YH a cardiac disorder AE that has an outcome of a disorder involving the ventricle(s) in the heart WEB: Primary Source: http://medical-dictionary.thefreedictionary.com/ventricular Secondary Source: http://www.ncbi.nlm.nih.gov/pubmed/15473469 cardiomyopathy AE 10007636 WEB: https://en.wikipedia.org/wiki/Cardiomyopathy DJ, SS, YH a cardiovascular disorder AE that has an outcome of deterioration of the function of the myocardium, usually leads to heart failure SIDER: C0878544 HPO: HP_0001638 WEB: http://medical-dictionary.thefreedictionary.com/cardiomyopathy cataract AE 10007739 SIDER: C0086543 HPO: HP_0000518 WEB: http://medical-dictionary.thefreedictionary.com/cataract DJ, SS, YH NCIt: C26713 CTCAE: E10350 a eye disorder AE that results in cloudiness that develops in the eye catheter related infection AE 10007810 10056520 CTCAE: E11328 DJ, SS, YH NCIt: C78232 HPO: HP_0002719 an infection AE that has an outcome of an infection (e.g., bacterial colonisation) at the catheter site SIDER: C0860239 WEB: http://www.ncbi.nlm.nih.gov/pubmed/8825104 cheilitis AE 10008417 WEB: http://medical-dictionary.thefreedictionary.com/cheilitis an inflammation AE that occurs in the lip SIDER: C0007971 CTCAE: E10517 DJ, SS, YH HPO: HP_0100825 NCIt: C79545 chylothorax AE 10051228 a lung disorder AE that has an outcome of lymphatic fluid accumulating in the pleural cavity, the space between two pleura of the lungs CTCAE:E13358 DJ, SS, YH, MW NCIt:C79546 WEB: http://medical-dictionary.thefreedictionary.com/chylothorax colitis AE 10009887 DJ, SS, YH WEB: http://www.ncbi.nlm.nih.gov/pubmedhealth/PMH0002112/ SIDER: C0009319 an inflammation AE that occurs at the large intestine NCIt: C26723 HPO: HP_0002583 CTCAE: E10521 connective tissue disorder AE 10061087 DJ, SS, YH HPO: HP_0003549 an adverse event that has an outcome of disease in the biological tissue that supports, binds together and protects organs SIDER: C0009782 WEB: http://medical-dictionary.thefreedictionary.com/connective+tissue+disease viral cardiomyopathy AE cytokine release syndrome AE 10052015 WEB: http://encyclopedia.thefreedictionary.com/cytokine+release+syndrome DJ, SS, YH NCIt: C78251 an inflammation AE that has an outcome of release of cytokines by T cells that causes inflammation CTCAE: E11264 delirium AE 10012218 NCIt:C2981 a psychiatric disorder AE that results in a decline in level of cognitive function CTCAE:E12898 DJ, SS, YH, MW WEB: http://medical-dictionary.thefreedictionary.com/delirium dental caries AE 10012318 a tooth disorder AE that has an outcome of bacterial infection that causes demineralization and destruction of the hard tissues, resulting in dental cavities WEB: http://medical-dictionary.thefreedictionary.com/dental+caries SIDER: C0011334 NCIt: C52593 DJ, SS, YH CTCAE: E10568 HPO: HP_0000670 depressed level of consciousness AE 10012373 WEB: http://www.ncbi.nlm.nih.gov/pubmed/23167919 SIDER: C0549249 DJ, SS, YH, MW a sensory capability AE that results in a lower level of arousal than normal NCIt:C78253 CTCAE:E12625 HPO: HP_0004372 device related infection AE 10064687 NCIt: C79705 SIDER: C1619702 CTCAE: E11356 HPO: HP_0002719 an injury and procedural complication AE that results in an infection related to medical device DJ, SS, YH disseminated intravascular coagulation AE 10013442 CTCAE: E10028 SIDER: C0012739 DJ, SS, YH NCIt: C2992 HPO: HP_0005521 a hematopoietic system AE with an outcome of a serious disorder in which proteins that control blood clotting become abnormally active WEB: http://www.nlm.nih.gov/medlineplus/ency/article/000573.htm dry skin AE 10013786 DJ, SS, YH, MW NCIt:C74592 a skin AE that is characterized by epidermis that lacks moisture, has an outcome of fine lines, scaling and itching CTCAE:E13623 HPO: HP_0000958 SIDER: C0151908 WEB: http://medical-dictionary.thefreedictionary.com/dry+skin duodenal ulcer AE 10013836 HPO: HP_0002588 a duodenum AE that has an outcome of a peptic ulcer, or a defect in the lining of the stomach or the first part of the small intestine, located in the duodenum SIDER: C0013295 CTCAE: E10611 DJ, SS, YH NCIt: C26755 peptic ulcer AE WEB: http://www.ncbi.nlm.nih.gov/pubmedhealth/PMH0001255/ dysarthria AE 10013887 DJ, SS, YH, MW CTCAE:E12635 WEB: http://medical-dictionary.thefreedictionary.com/dysarthria HPO: HP_0001260 SIDER: C0013362 a speech disorder that results in a motor speech disorder NCIt:C79549 ejection fraction decreased AE 10050528 a left ventricular dysfunction AE that has an outcome of decreased percentage of blood leaving the heart each time it contracts DJ, SS, YH NCIt: C83492 CTCAE: E12142 WEB: http://www.mayoclinic.com/health/ejection-fraction/AN00360 electrocardiogram result abnormal AE 10014363 a cardiac function test abnormal AE that has an outcome of abnormal electrical activity in the heart WEB: http://www.nlm.nih.gov/medlineplus/ency/article/003868.htm DJ, SS, YH, EB electrocardiogram qt prolonged AE 10014387 WEB: http://www.ncbi.nlm.nih.gov/pubmed/23275261 SIDER: C0151878 an electrocardiogram result abnormal AE that has an outcome of a prolonged time between the start of the Q wave and the end of the T wave in the heart's electrical cycle; a biomarker for ventricular tachyarrhythmias HPO: HP_0001657 DJ, SS, YH, EB enterocolitis AE 10014893 HPO: HP_0004387 CTCAE: E10627 SIDER: C0014356 WEB: http://medical-dictionary.thefreedictionary.com/enterocolitis DJ, SS, YH NCIt: C79573 a digestive system AE that has an outcome of disease in the digestive tract caused by infection erectile dysfunction AE 10061461 astyphia AE WEB: http://en.wikipedia.org/wiki/Erectile_dysfunction SIDER: C0242350 CTCAE:E13088 DJ, SS, JX, LW, YH, MW HPO: HP_0008652 a male reproductive system AE that results in the inability to develop/maintain an erection of penis impotence AE 阳痿/勃起功能障碍 NCIt:C3133 extraocular muscle paresis AE 10015829 a paresis AE that results in a partial loss of voluntary movement in their extraocular muscles DJ, SS, YH NCIt: C78286 CTCAE: E10367 WEB: http://www.ncbi.nlm.nih.gov/pubmed/22824489 fall AE 10016173 CTCAE: E11687 NCIt: C50558 HPO: HP_0002359 a behavior and neurological AE that has an outcome of patient falling DJ, SS, YH SIDER: C0085639 febrile neutropenia AE 10016288 CTCAE: E10033 a neutropenia AE, generally a complication of chemotherapy, that has an outcome of an abnormally low neutrophil granulocyte count, accompanied by fever NCIt: C35665 WEB: http://www.ncbi.nlm.nih.gov/pubmed/23303687 neutropenic sepsis AE SIDER: C0746883 DJ, SS, YH HPO: HP_0001875 forced expiratory volume decreased AE 10016987 CTCAE: E12156 DJ, SS, YH WEB: http://medical-dictionary.thefreedictionary.com/forced+expiratory+volume NCIt: C50524 a respiratory system AE that has an outcome of a decreased volume of air expired from the lungs fracture AE 10017076 DJ, SS, YH a bone disorder AE that has an outcome of complete or incomplete break in a bone resulting from the application of excessive force NCIt: C3046 WEB: http://medical-dictionary.thefreedictionary.com/Fractures CTCAE: E11703 gallbladder enlargement AE 10062693 a digestive system AE that has an outcome of an abnormal enlargement in the size of the gallbladder DJ, SS, YH gallbladder perforation AE 10017639 DJ, SS, YH WEB: http://medical-dictionary.thefreedictionary.com/gallbladder+perforation NCIt: C78309 a digestive system AE that has an outcome of an abnormal hole in the patient's gallbladder CTCAE: E11208 gamma-glutamyltransferase level abnormal AE 10017688 a liver related investigation result abnormal AE that has an outcome of an abnormal level of gamma-glutamyltransferase (GGT); GGT is involved in the transfer of amino acids across the cellular membrane DJ, SS, YH, EB WEB: http://www.nlm.nih.gov/medlineplus/ency/article/003458.htm gamma-glutamyltransferase level increased AE 10017693 10056910 CTCAE: E12161 WEB: http://www.ncbi.nlm.nih.gov/pubmed/23258530 DJ, SS, YH, EB a gamma-glutamyltransferase level abnormal AE that has an outcome of an increase in gamma-glutamyltransferase enzyme presence in the liver GGT increased NCIt: C26943 gastric ulcer AE 10017822 DJ, SS, YH CTCAE: E10727 HPO: HP_0002592 a gastric disorder AE that has an outcome of a defect in the lining of the stomach 胃溃疡 WEB: http://www.ncbi.nlm.nih.gov/pubmedhealth/PMH0001255/ SIDER: C0038358 NCIt: C3388 gastritis AE 10017853 SIDER: C0017152 NCIt: C26780 a gastric disorder AE that has an outcome of inflammation in the lining of the stomach WEB: http://www.ncbi.nlm.nih.gov/pubmedhealth/PMH0002135/ CTCAE: E10733 DJ, SS, YH HPO: HP_0005263 gastroesophageal reflux disease AE 10017885 10066874 NCIt: C26781 esophageal reflux AE WEB: http://www.ncbi.nlm.nih.gov/pubmed/23301861 GERD AE CTCAE: E10739 a digestive system AE that results in mucosal damage caused by acid from stomach coming up to the esophagus gastrooesophageal reflux disease AE DJ, SS, YH gastrointestinal perforation AE 10018001 HPO: HP_0011024 SIDER: C0151664 a gastrointestinal disorder AE that results in a hole in the wall of the esophagus, stomch, small intestine, large bowel, rectum or gallbladder DJ, SS, YH WEB: http://www.ncbi.nlm.nih.gov/pubmedhealth/PMH0001282/ hemoglobin level abnormal AE 10018879 WEB: http://medical-dictionary.thefreedictionary.com/hemoglobin a red blood cell profile abnormal AE that has an outcome of an abnormal count of hemoglobin, or iron-containing oxygen-transport metalloprotein in red blood cells haemoglobin abnormal AE DJ, SS, YH, EB hemolytic uremic syndrome AE 10018932 10019515 DJ, SS, YH HPO: HP_0005575 SIDER: C0019061 a hematopoietic system AE that has an outcome of hemolytic anemia, acute kidney failure and a low platelet count haemolytic uraemic syndrome AE CTCAE: E10043 NCIt: C75545 WEB: http://www.ncbi.nlm.nih.gov/pubmed/23307876 hemorrhoidal hemorrhage AE 10054787 10060640 haemorrhoidal haemorrhage AE CTCAE: E10767 WEB: http://medical-dictionary.thefreedictionary.com/hemorrhoid DJ, SS, YH NCIt: C78337 a digestive system AE that has an outcome of bleeding in hemorrhoids, vascular structures in the anal canal which help with stool control hemorrhoids AE 10019022 10019611 CTCAE: E10773 haemorrhoids AE HPO: HP_0004296 a digestive system AE that has an outcome of painful, swollen veins in the lower portion of the rectum or anus DJ, SS, YH WEB: http://www.ncbi.nlm.nih.gov/pubmedhealth/PMH0001337/ NCIt: C26792 hair growth abnormal AE 10019044 WEB: http://medical-dictionary.thefreedictionary.com/Hair+growth a hair AE that has an outcome of abnormal growth of facial or body hair HPO: HP_0010720 SIDER: C0232409 DJ, SS, YH hepatic failure AE 10019663 a liver/biliary system AE that has an outcome of the inability of the liver to perform its normal synthetic and metabolic function WEB: http://medical-dictionary.thefreedictionary.com/liver+failure HPO: HP_0001399 NCIt: C26922 DJ, SS, YH CTCAE: E11211 SIDER: C0085605 hepatic necrosis AE 10019692 WEB: http://medical-dictionary.thefreedictionary.com/hepatic+necrosis CTCAE: E11221 DJ, SS, YH NCIt: C78340 SIDER: C0151798 a liver/biliary system AE that has an outcome of death of hepatic parenchyma which may be single cell, or multicell in piecemeal, focal, periacinar, midzonal, periportal or paracentral locations HPO: HP_0002605 hepatitis viral AE 10019799 DJ, SS, YH SIDER: C0042721 HPO: HP_0006562 WEB: http://medical-dictionary.thefreedictionary.com/viral+hepatitis CTCAE: E11410 NCIt: C35124 a hepatitis AE that has an outcome of liver inflammation due to a hepatitis viral infection hypercalcemia AE 10020583 10020587 HPO: HP_0003072 SIDER: C0020437 CTCAE: E12270 NCIt: C3112 YH, MW hypercalcaemia AE WEB: http://medical-dictionary.thefreedictionary.com/hypercalcemia a blood calcium abnormal AE that has an outcome of an elevated calcium level in the blood, above normal range of 9-10.5 mg/dL hyperhidrosis AE 10020642 CTCAE:E13645 DJ, SS, YH, MW WEB: http://medical-dictionary.thefreedictionary.com/hyperhidrosis a skin AE that results in excess perspiration HPO: HP_0000975 SIDER: C0020458 NCIt:C78345 hyperkalemia AE 10020646 10020647 CTCAE: E12282 a blood potassium abnormal AE that has a lab test outcome of an abnormally increased concentration of potassium in blood HPO: HP_0002153 SIDER: C0020461 hyperkalaemia AE WEB: http://medical-dictionary.thefreedictionary.com/hyperkalemia NCIt: C37968 YH, MW toxin-induced cardiomyopathy AE hypertriglyceridemia AE 10020869 10020870 SIDER: C0020557 HPO: HP_0002155 DJ, SS, YH, MW CTCAE: E12299 a hematopoietic system AE that has an outcome of high blood levels of triglycerides, abundant fatty molecules WEB: http://medical-dictionary.thefreedictionary.com/hypertriglyceridemia NCIt: C37971 hypertriglyceridaemia AE hyperuricemia AE 10020903 10020907 NCIt: C3961 HPO: HP_0002149 gout AE CTCAE: E12305 DJ, SS, YH, MW an arthritis AE that has an outcome of uric acid building up in blood and causes joint inflammation SIDER: C0740394 hyperuricaemia AE WEB: http://www.ncbi.nlm.nih.gov/pubmedhealth/PMH0001459/ hypoalbuminemia AE 10020942 10020943 CTCAE: E12310 SIDER: C0239981 NCIt: C37972 hypoalbuminaemia AE a blood albumin abnormal AE that shows an abnormally low level of albumin protein in the blood. WEB: http://medical-dictionary.thefreedictionary.com/hypoalbuminemia HPO: HP_0003073 DJ, SS, YH hypocalcemia AE 10020947 10020949 NCIt: C37973 WEB: http://medical-dictionary.thefreedictionary.com/hypocalcemia hypocalcaemia AE 低血钙 a blood calcium abnormal AE that has an outcome of abnormally low calcium levels, can present with convulsions, arrythmias, tetany and numbness YH, MW HPO: HP_0002901 SIDER: C0020598 CTCAE: E12316 hypoglycemia AE 10020993 10021005 SIDER: C0020615 hypoglycaemia AE WEB: http://medical-dictionary.thefreedictionary.com/hypoglycemia CTCAE: E12322 a glucose homeostasis AE that results in a abnormally diminished content of glucose in the blood DJ, SS, YH, MW HPO: HP_0005969 NCIt: C3126 hypomagnesemia AE 10021027 10021028 HPO: HP_0002917 YH, MW UMLS CUI: C0151723 WEB: http://medical-dictionary.thefreedictionary.com/Hypomagnesaemia NCIt: C37975 SIDER: C0151723 hypomagnesaemia AE a blood magnesium abnormal AE that has an outcome of an abnormal concentration of magnesium in the blood plasma, and may cause nausea, weakness and tremors. CTCAE: E12333 hypophosphatemia AE 10021058 10021059 NCIt: C37977 DJ, SS, YH, MW a hematopoietic system AE that has an outcome of abnormally low phosphate levels, can present with muscle dysfunction, white cell dysfunction, pulp chambers and mental status changes hypophosphataemia AE HPO: HP_0008285 UMLS CUI: C0085682 CTCAE: E12344 SIDER: C0085682 WEB: http://medical-dictionary.thefreedictionary.com/hypophosphatemia hypothyroidism AE 10021114 HPO: HP_0008245 SIDER: C0020676 an endocrine system AE with the outcome of the thyroid gland does not make enough thyroid hormone DJ, SS, YH WEB: http://www.ncbi.nlm.nih.gov/pubmedhealth/PMH0001393/ NCIt: C26800 CTCAE: E10334 ileal perforation AE 10021305 DJ, SS, YH a digestive system AE that has an outcome of holes in the ileum of the small intestine WEB: http://medical-dictionary.thefreedictionary.com/ileum NCIt: C78355 CTCAE: E10795 ileus AE 10021328 HPO: HP_0002595 WEB: http://www.ncbi.nlm.nih.gov/pubmedhealth/PMH0001306/ DJ, SS, YH intestinal obstruction AE a digestive system AE that has an outcome of a partially or completely blocked bowel SIDER: C1258215 CTCAE: E10812 NCIt: C37979 infusion related reaction AE 10051792 10053483 WEB: http://www.ons.org/Publications/VJC/media/ons/docs/publications/VJC/vjc-apr10cjon.pdf a immune system AE that results in an allergic reaction to foreign protein, but can also be caused by cytokine release. SZ, DJ, SS, YH NCIt: C78361 CTCAE: E11127 infusion site extravasation AE 10064774 CTCAE: E11133 NCIt: C78362 an extravasation AE that has an outcome of leaking of pharmacologic or biological substance from infusion site into surrounding tissue. Symptoms include induration, erythema, swelling, burning sensation and pain WEB: http://medical-dictionary.thefreedictionary.com/extravasation SZ, DJ, SS, YH irritability AE 10022998 SZ, DJ, SS, YH HPO: HP_0000737 Behavior and Neurological AE that results in the patient being easily annoyed/irritated feverish (subjective) AE SIDER: C0022107 NCIt: C50623 CTCAE: E11144 left ventricular dysfunction AE 10049694 WEB: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1766527/ SZ, DJ, SS, YH CTCAE: E10130 a cardiac ventricular disorder AE that has an outcome of inability of the left ventricle to pump blood, may lead to heart failure NCIt: C64251 leukoencephalopathy AE 10024382 SZ, DJ, SS, YH, MW SIDER: C0270612 WEB: http://medical-dictionary.thefreedictionary.com/leukoencephalopathy CTCAE:E12712 HPO: HP_0002352 NCIt:C27059 an encephalopathy AE that has an outcome of brain white matter disease leukopenia AE 10024384 SIDER: C0023530 WEB: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2154209/ HPO: HP_0001882 a hematopoietic system AE that has an outcome of a lower than normal number of leukocytes, or nucleated cells of the myeloid or lymphoid lineages, found in blood or other tissue SZ, DJ, SS, YH libido disorder AE 10061221 WEB: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2695750/ SZ, DJ, SS, YH a psychiatric disorder AE that results in a disorder in the patient's desire for sexual interaction lipase increased AE 10024574 CTCAE: E12185 WEB: http://www.ncbi.nlm.nih.gov/pubmed/15653991 a digestive system AE that has an outcome of an excess of lipase, a pancreatic enzyme, may indicate a problem related to pancreas hyperlipasemia AE NCIt: C78435 SZ, DJ, SS, YH liver AE 10024670 WEB: http://www.nlm.nih.gov/medlineplus/liverdiseases.html Liver/biliary system AE that results in the disease of the liver SIDER: C0023895 SZ, DJ, SS, YH HPO: HP_0006706 liver disorder localized edema AE 10048961 10062466 SIDER: C0013609 CTCAE: E11148 NCIt: C78437 HPO: HP_0000969 SZ, DJ, SS, YH localised oedema AE WEB: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1115975/ an edema AE occuring in a specific region localised edema AE lung infection AE 10061229 WEB: http://www.livestrong.com/lung-infection/ HPO: HP_0002783 an infection AE that has an outcome of infection in the lungs SIDER: C0876973 CTCAE: E11444 SZ, DJ, SS, YH NCIt: C26873 lymphocyte count decreased AE 10025256 WEB: http://www.nlm.nih.gov/medlineplus/ency/article/003657.htm SZ, SS, YH a lymphocyte count abnormal AE that has an outcome of a decreased amount of lymphocytes in the blood, a type of white blood cell in the immune system CTCAE: E12190 NCIt: C26823 coronary artery disorder AE 10011078 10011082 YH, SS an arterial disorder AE that resuts in arteries that supply blood to heart muscle become hardened and narrowed. WEB: http://www.nlm.nih.gov/medlineplus/coronaryarterydisease.html coronary artery disese AE memory impairment AE 10027175 SIDER: C0233794 SZ, SS, YH, MW Behavior and Neurological AE that results in the loss of memory WEB: http://medical-dictionary.thefreedictionary.com/impaired+memory NCIt:C78444 CTCAE:E12718 HPO: HP_0002354 menorrhagia AE 10027313 CTCAE:E13132 SIDER: C0025323 NCIt:C26829 HPO: HP_0000132 WEB: http://www.ncbi.nlm.nih.gov/pubmedhealth/PMH0014910/ Female Reproductive System AE that results in abnormally heavy and prolonged menstrual period SZ, SS, YH, MW metabolic disorder AE 10058097 SZ, SS, YH WEB: http://www.nlm.nih.gov/medlineplus/metabolicdisorders.html a metabolism, endocrine, and exocrine system AE that has an outcome of abnormal chemical reactions in the body that disrupts a metabolic process muscle enzyme level increased AE 10057945 a muscle enzyme level abnormal AE that results in an increased level of muscle enzyme SZ, SS, YH myelodysplastic syndrome AE 10028533 CTCAE:E12552 HPO: HP_0006730 SIDER: C0026986 WEB: http://www.nlm.nih.gov/medlineplus/myelodysplasticsyndromes.html SZ, SS, YH, MW NCIt:C3247 a hematopoietic system AE that has an outcome of ineffective production of the myeloid class of blood cells myocarditis AE 10028606 WEB: http://www.ncbi.nlm.nih.gov/pubmedhealth/PMH0001204/ SZ, SS, YH NCIt: C34831 an inflammation AE that has an outcome of inflammation of the heart muscle CTCAE: E10157 nail infection AE 10061304 SIDER: C0343026 SZ, SS, YH WEB: http://www.emedicinehealth.com/paronychia_nail_infection/article_em.htm a nail AE around the nail area, tends to be fungal HPO: HP_0008396 neutropenia AE 10029354 HPO: HP_0001875 a neutropenia AE that compromises the immune system where the number of neutrophil granulocytes, a type of white blood cell, is abnormally low. A neutropenia makes body vulnerable to bacterial and fungal infections. SZ, SS, YH WEB: http://medical-dictionary.thefreedictionary.com/neutropenia SIDER: C0027947 neutrophil count abnormal AE 10061313 SZ, SS, YH, EB WEB: http://www.medterms.com/script/main/art.asp?articlekey=20030 a white blood cell profile abnormal AE that results in an abnormal number of neutrophil granulocytes, a type of white blood cell (outside the normal range of ~1700 per microliter) neutrophil count decreased AE 10029366 SZ, SS, YH, EB WEB: http://www.mayoclinic.com/health/neutropenia/MY00110 CTCAE: E12198 neutropenia AE a neutrophil count abnormal AE that has an outcome of decreased neutrophil count SIDER: NA NCIt: C80520 HPO: HP_0011991 esophageal pain AE 10015388 10030180 SZ, SS, YH CTCAE: E10661 HPO: HP_0010833 SIDER: C0221727 WEB: http://medical-dictionary.thefreedictionary.com/oesophageal oesophageal pain AE a pain AE located in the esophagus NCIt: C78280 esophageal stenosis AE 10015448 10030194 an esophagus AE that results in a narrowing in the esophagus caused by buildup of scar tissue or by a congenital defect WEB: http://esophagealstenosis.org/ SZ, SS, YH oesophageal stenosis AE CTCAE: E10670 SIDER: C0014866 NCIt: C34595 HPO: HP_0010450 esophagitis AE 10015461 10030216 oesophagitis AE NCIt: C9224 HPO: HP_0100633 WEB: http://www.ncbi.nlm.nih.gov/pubmedhealth/PMH0002138/ CTCAE: E10687 SIDER: C0014868 SZ, SS, YH an esophagus AE located in the esophagus, can present with heartburn, and nausea oral cavity fistula AE 10065720 NCIt: C78506 a digestive system AE that has an outcome of fistula, or an abnormal connection between two epithelium-lined organs or vessels, located in the oral cavity CTCAE: E10888 WEB: http://medical-dictionary.thefreedictionary.com/fistula SZ, SS, YH oral pain AE 10031009 SZ, SS, YH NCIt: C78509 WEB: http://medical-dictionary.thefreedictionary.com/oral HPO: HP_0010833 a pain AE located in the oral cavity, pertaining to the mouth SIDER: C0221776 CTCAE: E10904 pain of skin AE 10033474 a pain AE located in the skin CTCAE:E13668 HPO: HP_0010833 SIDER: C0241136 SZ, SS, YH, MW NCIt:C78516 palmar-plantar erythrodysesthesia syndrome AE CTCAE: E13672 YH: MedDRA: 10033553 is for "palmar-plantar erythrodysaesthesia syndrome"; MedDRA: 10054524 is for "palmar-plantar erythrodysesthesia syndrome". Hand Food Syndrome AE WEB: http://news.cancerconnect.com/hand-foot-syndrome-palmar-plantar-erythrodysesthesia/ NCIt: C27177 SZ, SS, YH, MW palmar-plantar erythrodysaesthesia syndrome AE a skin AE generally caused by chemotherapy that is characterized by the palms and soles becoming red, swollen, numb and the skin peeling. UMLS CUI: C0549410 papilloedema AE 10033703 10033712 SZ, SS, YH an edema AE that has an outcome of optic disc swelling that is caused by increased intracranial pressure HPO: HP_0001085 CTCAE: E10411 papilledema AE WEB: http://medical-dictionary.thefreedictionary.com/Papilloedema SIDER: C0030353 NCIt: C3307 paronychia AE 10034016 SZ, SS, YH, MW a skin infection AE thar occurs around the fingernails and toenailsnail. Bacteria or a type of yeast called Candida cause this infection. Bacteria and yeast can even combine into one infection. nail infection AE WEB: http://www.healthline.com/health/paronychia HPO: HP_0001818 SIDER: C0030578 WEB: https://en.wikipedia.org/wiki/Paronychia pericardial effusion AE 10034474 CTCAE: E10172 HPO: HP_0001698 WEB: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3110902/ NCIt: C3319 SIDER: C0031039 a cardiac disorder AE that has an outcome of abnormal accumulation of fluid in the pericardial cavity SZ, SS, YH perineal pain AE 10061339 CTCAE:E13175 a pain AE that results in soreness around the vaginal opening after giving birth SZ, SS, YH, MW WEB: http://www.ncbi.nlm.nih.gov/pubmed/20002420 NCIt:C78529 periodontal disease AE 10034536 CTCAE: E10935 牙龈炎 SIDER: C0031090 SZ, SS, YH NCIt: C63743 a digestive system AE that has an outcome of inflammation and infection that destroys the tissues that support the teeth, including the gums, the periodontal ligaments and the tooth sockets HPO: HP_0000704 WEB: http://www.ncbi.nlm.nih.gov/pubmedhealth/PMH0002051/ gingivitis AE peripheral ischemia AE 10034576 10034578 HPO: HP_0002597 CTCAE:E13810 peripheral ischaemia AE SIDER: C0235490 WEB: Primary Source: http://www.medterms.com/script/main/art.asp?articlekey=4052 Secondary Source: http://www.ncbi.nlm.nih.gov/pubmed/6430442 an ischaemia AE that has an outcome of restriction in blood supply to tissues, causing a shortage of oxygen and glucose needed for cellular metabolism NCIt: C78535 外周缺血 YH: MedDRA: 10034576 is for "peripheral ischaemia"; MedDRA: 10034578 is for "peripheral ischemia". SZ, SS, YH peripheral motor neuropathy AE 10034580 SZ, SS, YH, MW NCIt:C3500 SIDER: C0235025 CTCAE:E12762 HPO: HP_0007178 a motor neuropathy AE that results in damage to the nerves outside of the brain and spinal cord WEB: http://www.ncbi.nlm.nih.gov/pubmedhealth/PMH0001619/ peripheral sensory neuropathy AE 10034620 WEB: http://medical-dictionary.thefreedictionary.com/Peripheral+sensory+neuropathy SIDER: C0151313 a sensory neuropathy AE that has an outcome of damaged nerves outside the brain and spinal cord HPO: HP_0000763 SZ, SS, YH, MW NCIt:C3501 CTCAE:E12768 photosensitivity reaction AE 10034966 10034972 a skin AE that shows a cutaneous disease as a result of sun allergy and may be induced by different triggers such as a chemical. WEB: http://emedicine.medscape.com/article/1049648-overview NCIt: C38004 photosensitivity AE SIDER: C0162830 SZ, SS, YH, MW CTCAE: E13680 MedDRA: 10034972 and UMLS CUI: C0162830 are for "photosensitivity reaction"; MedDRA: 10034966 and UMLS CUI: C0349506 are for "photosensitivity". UMLS CUI: C0349506; UMLS CUI: C0162830 HPO: HP_0000992 WEB: http://www.merckmanuals.com/home/skin-disorders/sunlight-and-skin-damage/photosensitivity-reactions atrioventricular block AE 10003671 SIDER: C0004245 HPO: HP_0001678 WEB: http://www.medilexicon.com/medicaldictionary.php?t=10751 heart block SS AV block a conduction system disorder AE that refers to partial or complete block of electrical impulses originating in the atrium or sinus node, preventing them from reaching the AV node and ventricles pleural effusion AE 10035598 a respiratory system AE that has an outcome of fluid buildup between the layers of tissue that line the lungs and chest cavity SIDER: C0032227 SZ, SS, YH, MW HPO: HP_0002202 WEB: http://www.ncbi.nlm.nih.gov/pubmedhealth/PMH0001150/ NCIt:C3331 CTCAE:E13486 pleural hemorrhage AE 10035601 10055319 MedDRA: 10035601 is for "pleural haemorrhage"; MedDRA: 10055319 is for "pleural hemorrhage". UMLS CUI: C0019123 SZ, SS, YH a hemorrhage AE that has an outcome of bleeding in the pleural cavity, the potential space between the two pleura of the lungs CTCAE: E13492 WEB: http://medical-dictionary.thefreedictionary.com/hemothorax NCIt: C50582 pleural haemorrhage AE pleuritic pain AE 10035623 SZ, SS, YH, MW a pain AE induced by inflammation in the lungs that is characterized by sharp or stabbing pain in the chest WEB: http://pleuriticchestpain.net/, http://medical-dictionary.thefreedictionary.com/Pleuritic+chest+pain CTCAE:E13498 NCIt:C78564 pneumonitis AE 10035742 CTCAE:E13502 NCIt:C3333 pulmonitis AE WEB: http://medical-dictionary.thefreedictionary.com/pneumonitis SZ, SS, YH, MW a lung inflammation AE located in the lung tissue pneumothorax AE 10035759 CTCAE:E13508 SZ, SS, YH, MW NCIt:C38006 WEB: http://www.ncbi.nlm.nih.gov/pubmedhealth/PMH0001151/ HPO: HP_0006522 SIDER: C0032326 a lung disorder AE that has an outcome of a collapsed lung due to collection of air in the space around the lungs. portal hypertension AE 10036200 http://www.merriam-webster.com/medlineplus/portal%20hypertension SZ, SS, YH CTCAE: E11238 SIDER: C0020541 WEB: http://www.ncbi.nlm.nih.gov/pubmed/21129318 a hypertension AE located in the heptatic portal system caused by obstruction or occlusion that produces splenomegaly and ascites in its later stages NCIt: C3119 HPO: HP_0001409 portal vein thrombosis AE 10036206 a thrombosis AE that has an outcome of formation of a blood clot affecting the hepatic portal vein, can lead to hypertension or reduction of blood supply to the liver SZ, SS, YH WEB: http://medical-dictionary.thefreedictionary.com/portal+vein+thrombosis PVT CTCAE: E11243 NCIt: C78565 presyncope AE 10036653 SZ, SS, YH, MW WEB: http://medical-dictionary.thefreedictionary.com/presyncope SIDER: C0700200 CTCAE:E12778 HPO: HP_0002321 NCIt:C80100 a sensory capability AE that has an outcome of a near-fainting episode which may include lightheadedness, dizziness, severe weakness, blurred vision, which may precede syncopal episode prinzmetal angina AE 10036759 coronary vessel spasm AE WEB: http://medical-dictionary.thefreedictionary.com/prinzmetal+angina Prinzmetal's angina AE SIDER: C0002963 HPO: HP_0001681 SZ, SS, YH a coronary artery disorder AE that results in cardiac pain at rest that occurs in cycles productive cough AE 10036790 SZ, SS, YH, MW CTCAE:E13517 WEB: http://coldflu.about.com/od/glossary/g/productivecough.htm NCIt:C78569 a cough AE that has an outcome of secretions that could be mucous or blood pulmonary fibrosis AE 10037383 NCIt:C26869 WEB: http://www.mayoclinic.com/health/pulmonary-fibrosis/DS00927 SZ, SS, YH, MW SIDER: C0034069 HPO: HP_0002206 CTCAE:E13527 a lung disorder AE wih the outcome of damaged or scarred lung tissue. Thickened tissue impairs lung function pulmonary hypertension AE 10037400 NCIt:C3120 WEB: http://www.ncbi.nlm.nih.gov/pubmedhealth/PMH0001171/ CTCAE:E13539 HPO: HP_0002092 SIDER: C0020542 a lung disorder AE that has an outcome of abnormally high blood pressure in the arteris of the lungs SZ, SS, YH, MW pulmonary edema AE a lung disorder AE that has an outcome of edema or abnormal buildup of fluid in the air sacs of the lungs, leads to shortness of breath HPO: HP_0100598 SIDER: C0034063 UMLS CUI: C0034063 SZ, SS, YH, MW WEB: http://www.ncbi.nlm.nih.gov/pubmedhealth/PMH0001195/ NCIt: C26868 MedDRA: 10037423 is for "pulmonary oedema"; MedDRA: 10037375 is for "pulmonary edema" pulmonary oedema AE CTCAE: E13521 radiation skin injury AE 10063562 NCIt: C3349 SZ, SS, YH a skin AE that has an outcome of injury to the skin and underlying tissues from exposure to a large external dose of radiation WEB: http://www.bt.cdc.gov/radiation/criphysicianfactsheet.asp recall phenomenon AE 10060856 WEB: http://www.ncbi.nlm.nih.gov/pubmed/7577597 SZ, SS, YH an inflammation AE that has an outcome of an inflammatory reaction limited to a previously X-irradiated field when the patient is treated months/years later with certain drugs rectal hemorrhage AE 10038063 10038064 NCIt: C27054 HPO: HP_0002573 rectal haemorrhage AE SIDER: C0267596 SZ, SS, YH CTCAE: E10955 Digestive System AE that results in bleeding in the rectal area renal failure AE 10038435 renal insufficiency AE WEB: http://medical-dictionary.thefreedictionary.com/renal+failure SIDER: C0035078 kidney failure AE HPO: HP_0000083 a kidney disorder AE that results in kidneys failing to adequately filter toxins and waste from the blood SZ, SS, YH acute kidney injury AE 10038436 10069339 NCIt:C26808 As shown on the renal.org website (http://www.renal.org/guidelines/modules/acute-kidney-injury), Acute kidney injury (AKI) has now replaced the term acute renal failure. renal failure acute AE CTCAE:E12973 SZ, SS, YH, Izabela Birsanescu, MW SIDER: C0022660 AKI Acute kidney failure occurs when kidneys become unable to filter waste products from blood. HPO: HP_0001919 WEB: http://www.mayoclinic.org/diseases-conditions/kidney-failure/basics/definition/con-20024029 WEB: http://medical-dictionary.thefreedictionary.com/acute+renal+failure a kidney disorder AE that results in the rapid loss or decline of kidney function respiratory acidosis AE 10038695 NCIt:C26872 respiratory failure AE a respiratory system AE that has an outcome of a condition where lungs cannot remove all the carbon dioxide the body produces, makes body fluid too acidic SIDER: C1145670 WEB: http://www.ncbi.nlm.nih.gov/pubmedhealth/PMH0001154/ SZ, SS, YH CTCAE:E13545 HPO: HP_0004877 reversible posterior leukoencephalopathy syndrome AE 10063761 SZ, SS, YH, MW an encephalopathy AE that is characterized by headache, confusion, seizures and visual loss, tends to resolve over time NCIt:C78598 CTCAE:E12798 sinus disorder AE 10062244 CTCAE:E13560 SZ, SS, YH, MW NCIt:C26843 WEB: http://medical-dictionary.thefreedictionary.com/paranasal+sinuses a respiratory system AE that has an outcome of disease in the air-filled spaces that surround the nasal cavity, above the eyes and behind the ethmoids sinus tachycardia AE 10040752 a tachycardia AE that has an outcome of elevated impulses originating from the sinoatrial node, greater than 100 bpm NCIt: C26889 CTCAE: E10214 SZ, SS, YH WEB: http://medical-dictionary.thefreedictionary.com/sinus+tachycardia SIDER: C0039239 HPO: HP_0001649 skin hyperpigmentation AE 10040865 a skin AE that has an outcome of darkening in an area of skin or nails caused by increased melanin WEB: http://medical-dictionary.thefreedictionary.com/hyperpigmentation HPO: HP_0010284 SIDER: C0162834 CTCAE:E13718 SZ, SS, YH, MW NCIt:C79731 skin infection AE 10040872 WEB: http://medical-dictionary.thefreedictionary.com/skin+infection HPO: HP_0001581 NCIt: C35025 CTCAE: E11568 a skin AE that has an outcome of infection. Can be bacterial, fungal, parasitic or viral SZ, SS, YH SIDER: C0037278 sleep disorder AE 10040984 SIDER: C0851578 a behavior and neurological AE that results in irregular sleep patterns SZ, SS, YH WEB: http://medical-dictionary.thefreedictionary.com/sleep+disorder HPO: HP_0002360 small intestinal obstruction AE 10041101 WEB: http://www.mayoclinic.com/health/intestinal-obstruction/DS00823 HPO: HP_0005214 a gastrointestinal disorder AE that has an outcome of a blockage that keeps substance from passing through the small intestine, may be caused by fibrous bands of tissue in the abdomen, inflamed/infected pouches in the intestine, or hernias and tumors CTCAE: E11021 NCIt: C78615 SZ, SS, YH SIDER: C0235329 small intestinal stenosis AE 10062263 WEB: http://medical-dictionary.thefreedictionary.com/stenosis SZ, SS, YH a gastrointestinal disorder AE in which the blood vessels in the small intestine narrow NCIt: C78617 CTCAE: E11032 small intestine ulcer AE 10041133 SZ, SS, YH a gastrointestinal disorder AE that results in an ulcer in the patient's small intestine CTCAE: E11038 NCIt: C78619 soft tissue infection AE 10062255 NCIt: C79745 SIDER: C0149778 HPO: HP_0002719 WEB: http://www.reference.md/files/D018/mD018461.html SZ, SS, YH CTCAE: E11579 a connective tissue disorder AE that occurs in the non-skeletal tissue, usually subcutaneous and muscle tissue stevens-johnson syndrome AE 10042033 WEB: http://www.ncbi.nlm.nih.gov/pubmedhealth/PMH0001854/ SIDER: C0038325 HPO: HP_0000951 SZ, SS, YH, MW a skin adverse event that is characterized by cell death causing the epidermis to separate from the dermis CTCAE:E13736 NCIt:C79484 gastric hemorrhage AE 10017788 10017789 gastric haemorrhage AE YH, SS NCIt: C54582 A gastrointestinal hemorrhage AE that has an outcome of the bleeding in the stomach CTCAE: E10706 sudden death AE 10042434 10042435 SZ, SS, YH WEB: http://medical-dictionary.thefreedictionary.com/sudden+death HPO: HP_0001645 SIDER: C0011071 CTCAE: E11171 a death AE that has an outcome of unexpected death, 1 to 24 hours after the onset of symptoms NCIt: C50911 suicidal ideation AE 10042458 WEB: Primary Source: http://medical-dictionary.thefreedictionary.com/Suicidal+ideation Secondary Source: http://www.ncbi.nlm.nih.gov/pubmed/10193592 SZ, SS, YH, MW a psychiatric disorder AE that results in thoughts about suicide CTCAE:E12964 NCIt:C80102 suicide attempt AE 10042464 HPO: HP_0000708 a psychiatric disorder AE that results in attempted suicide NCIt:C80111 CTCAE:E12969 SZ, SS, YH, MW SIDER: C0038663 supraventricular tachycardia AE 10042604 SIDER: C0039240 NCIt: C35061 a tachycardia AE that has an outcome of rapid heart rhythm originating at or above the atrioventricular node HPO: HP_0004765 CTCAE: E10218 WEB: Primary Source: http://www.ncbi.nlm.nih.gov/pubmedhealth/PMH0001235/ Secondary Source: http://www.ncbi.nlm.nih.gov/pubmed/23233691 SZ, SS, YH thrombophlebitis AE 10043570 WEB: http://www.nlm.nih.gov/medlineplus/ency/article/001108.htm SIDER: C0040046 SZ, SS, YH HPO: HP_0004418 WEB: http://www.ncbi.nlm.nih.gov/pubmedhealth/PMH0002098/ a phlebitis AE located in the vein, caused by a blood clot tooth disorder AE 10044034 SIDER: C0040435 a bone disorder AE that has an outcome of disease in the teeth SZ, SS, YH WEB: http://www.nlm.nih.gov/medlineplus/toothdisorders.html HPO: HP_0000164 toothache AE 10044055 odontalgia AE HPO: HP_0000164 a bone disorder AE that has an outcome of an aching pain in or around a tooth CTCAE: E11054 SZ, SS, YH WEB: Primary Source: http://medical-dictionary.thefreedictionary.com/toothache Seconday Source: http://www.ncbi.nlm.nih.gov/pubmed/22157099 NCIt: C78640 SIDER: C0040460 tracheitis AE 10044302 10066798 SZ, SS, YH NCIt: C78647 WEB: http://www.ncbi.nlm.nih.gov/pubmedhealth/PMH0001983/ a respiratory system AE that results in the trachea being infected by a bacteria CTCAE: E11599 troponin level increased AE 10058267 WEB: http://www.nlm.nih.gov/medlineplus/ency/article/007452.htm a troponin level abnormal AE that has an outcome of an increased amount of troponin, a protein released when the heart muscle is damaged SZ, SS, YH, EB tumor lysis syndrome AE 10045152 10045170 NCIt: C3425 CTCAE: E12365 a syndrome AE that has an outcome of a group of metabolic complications that can occur after treatment of cancer SZ, SS, YH WEB: http://www.ncbi.nlm.nih.gov/pubmed/15384972 tumour lysis syndrome AE ulcerative keratitis AE 10064996 WEB: http://medical-dictionary.thefreedictionary.com/Ulcerative+keratitis a keratitis AE that has an outcome of disrupted epithelial layer and stroma of the cornea, may become blind SZ, SS, YH HPO: HP_0007812 corneal ulcer AE SIDER: C0010043 upper gastrointestinal hemorrhage AE 10046274 10055356 SIDER: C0041909 HPO: HP_0002239 SZ, SS, YH upper gastrointestinal haemorrhage AE NCIt: C78660 WEB: Primary Source: http://medical-dictionary.thefreedictionary.com/gastrointestinal+bleeding Secondary Source: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1237869/ CTCAE: E11062 a gastrointestinal hemorrhage AE that has an outcome of bleeding in the upper gastrointestinal tract urinary retention AE 10046555 HPO: HP_0000016 Urinary system AE that results in an inability to urinate SZ, SS, YH, MW WEB: Primary Source: http://medical-dictionary.thefreedictionary.com/urinary+retention Secondary Source: http://www.medtronic.com/patients/urinary-retention/index.htm NCIt:C50790 CTCAE:E13046 SIDER: C0080274 urine output decreased AE 10059895 WEB: http://www.nlm.nih.gov/medlineplus/ency/article/003147.htm NCIt: C80522 a urine abnormality AE that has an outcome of decreased urine output, less than 500 milliliters of urine in 24 hours CTCAE: E12217 SZ, SS, YH uterine hemorrhage AE 10046788 10046789 NCIt: C78686 CTCAE: E13237 SZ, SS, YH, MW uterine haemorrhage AE HPO: HP_0000130 a uterine AE that has an outcome of bleeding from the uterus MedDRA: 10046788 is for "uterine haemorrhage"; MedDRA: 10046789 is for "uterine hemorrhage" SIDER: C0042134 vaginal infection AE 10046914 CTCAE: E11624 NCIt: C26911 SIDER: C0404521 HPO: HP_0000142 SZ, SS, YH an infection AE that results in infection of the vagina vein discoloration AE 10047183 a vascular disorder AE that results in the veins becoming discoloured vein discolouration AE SZ, SS, YH venous injury AE 10047228 NCIt: C78711 SZ, SS, YH CTCAE: E12051 a vascular disorder AE that results in an injury to the vein(s) vision blurred AE 10005886 10047513 an abnormal vision AE that results in unclear vision blurred vision AE NCIt: C27123 WEB: Primary Source: http://www.nlm.nih.gov/medlineplus/ency/article/003029.htm Secondary Source: http://www.ncbi.nlm.nih.gov/pubmed/23111613 HPO: HP_0000622 SIDER: C0344232 CTCAE: E10346 SZ, SS, YH weight increased AE 10047896 10047899 CTCAE: E12224 SZ, SS, YH NCIt: C62754 a physical examination result abnormal AE that shows an increase (gain) in weight of a patient SIDER: C0043094 weight gain AE HPO: HP_0004324 wolff-parkinson-white syndrome AE 10048015 CTCAE: E10244 NCIt: C35132 SZ, SS, YH a conduction system disorder AE that results in an abnormal accessory electrical conduction pathway between the atria and ventricles WEB: http://www.ncbi.nlm.nih.gov/pubmedhealth/PMH0001206/ wound complication AE 10053692 SZ, SS, YH WEB: https://en.wikipedia.org/wiki/Wound CTCAE: E12057 a wound AE that has an outcome of complication to the wound NCIt: C78719 wound dehiscence AE 10048031 NCIt: C50863 WEB: http://medical-dictionary.thefreedictionary.com/wound+dehiscence a wound AE that has an outcome of a wound breaking open along the surgical sutures SZ, SS, YH CTCAE: E12063 mucosal inflammation AE 10028116 10028130 NCIt: C26887 An inflammation AE that has an outcome of tissue swelling and other inflammatory response in the mouth oral mucositis CTCAE: E10872 YH, SS multi-organ failure AE 10028154 YH, SS A systematic adverse event that has an outcome of failure in mulitple organs CTCAE: E11155 NCIt: C75568 osteoporosis AE 10031282 WEB: http://www.mayoclinic.com/health/osteoporosis/DS00128 NCIt:C3298 A bone disorder AE that has an outcome of the weakening or brittle bone CTCAE:E12508 SIDER: C0029456 HPO: HP_0000939 YH, SS, MW restrictive cardiomyopathy AE 10038748 CTCAE: E10192 NCIt: C62798 WEB: http://www.nlm.nih.gov/medlineplus/ency/article/000189.htm YH, SS infiltrative cardiomyopathy A cardiomyopathy AE that has an outcome of a condition that the heart cannot relax normally during the time between heartbeats when the blood returns from the body (diastole). ventricular fibrillation AE 10047290 SIDER: C0042510 NCIt: C50799 YH, SS CTCAE: E10236 VF HPO: HP_0001663 WEB: http://www.ncbi.nlm.nih.gov/pubmedhealth/PMH0004467/ An arrythmia AE that has an outcome of a severely abnormal heart rhythm (arrhythmia) that can be life-threatening. first degree atrioventricular block AE 10003674 NCIt: C62015 atrioventricular block first degree CTCAE: E10098 SS first degree heart block an atrioventricular block AE that there is some prolongation of AV conduction time (PR interval). The heart's electrical signals are slowed as they move from the atria to the ventricles (the heart's upper and lower chambers, respectively). This results in a longer, flatter line between the P and the R waves on the EKG (electrocardiogram). WEB: http://www.medilexicon.com/medicaldictionary.php?t=10751 WEB: http://www.nhlbi.nih.gov/health//dci/Diseases/hb/hb_types.html brain AE YH an adverse event that occurs in brain. brain disorder AE restlessness AE 10038743 a psychiatric disorder AE that shows restlessness NCIt:C74533 UMLS_CUI: C0085631 YH, MW CTCAE:E12960 WEB: http://dictionary.reference.com/browse/restlessness cardiovascular investigation result abnormal AE 10007512 an investigation result abnormal AE that involves an abnormal result of an investigation involving the cardiovascular system EB, YH second degree atrioventricular block AE 10003677 an atrioventricular block AE that some but not all atrial impulses fail to reach the ventricles, thus some ventricular beats are dropped. Electrical signals between the atria and ventricles are slowed to a large degree. Some signals don't reach the ventricles. On an EKG, the pattern of QRS waves doesn't follow each P wave as it normally would. SS second degree heart block atrioventricular block second degree WEB: http://www.medilexicon.com/medicaldictionary.php?t=10751 WEB: http://www.nhlbi.nih.gov/health//dci/Diseases/hb/hb_types.html electrolyte lab test abnormal AE 10047843 EB an investigation result abnormal AE that involves an abnormal electrolyte value blood phosphorus abnormal AE 10054823 EB an electrolyte lab test abnormal AE that shows an abnormal blood phosphorus level complete atrioventricular block AE 10003673 third degree heart block SS an atrioventricular block AE that complete atrioventricular dissociation occurs; atria and ventricles beat independently. None of the electrical signals reach the ventricles. This type also is called complete heart block or complete AV block. When complete heart block occurs, special areas in the ventricles may create electrical signals to cause the ventricles to contract. This natural backup system is slower than the normal heart rate and isn't coordinated with the contraction of the atria. On an EKG, the normal pattern is disrupted. The P waves occur at a faster rate that isn't coordinated with the QRS waves. third degree atrioventricular block CTCAE: E10093 WEB: http://www.medilexicon.com/medicaldictionary.php?t=10751 WEB: http://www.nhlbi.nih.gov/health//dci/Diseases/hb/hb_types.html NCIt: C50501 complete heart block atrioventricular block complete blood potassium abnormal AE 10005722 HPO: HP_0011042 SIDER: C0853759 an electrolyte lab test abnormal AE that results in an abnormal level of potassium in the blood EB blood potassium increased 10005725 HPO: HP_0002513 SIDER: C0853760 hyperkalemia AE a physical quality where the blood potassium level is increased. EB, YH, MW blood sodium abnormal AE 10005800 an electrolyte lab test abnormal AE that results in an abnormal level of sodium in the blood EB blood sodium increased 10005803 HPO: HP_0003228 SIDER: C0595878 A physical quality that has an increased level of sodium in the blood EB, YH, MW blood magnesium abnormal AE 10005652 EB an electrolyte lab test abnormal AE that results in an abnormal level of magnesium in the blood blood calcium abnormal AE 10005393 EB an electrolyte lab test abnormal AE that results in an abnormal level of calcium in the blood blood calcium increased 10005396 EB, YH, MW A physical quality that has an increased level of calcium in the blood urinary system investigation result abnormal AE 10038362 renal and urinary tract investigation and urinalysis result abnormal AE an investigation result abnormal AE that involves the renal and urinary tract and urinalyses EB, YH renal system investigation result abnormal AE blood creatinine level abnormal AE 10005481 a urinary system investigation result abnormal AE that is characterized by an abnormal level of creatinine in the blood EB lipid analysis result abnormal AE 10024580 EB an investigation result abnormal AE that involves an abnormal result of a lipid analyses blood cholesterol abnormal AE 10005423 EB a lipid analysis result abnormal AE that results in an abnormal blood cholesterol level immunology and allergy investigation result abnormal AE 10021505 EB an investigation result abnormal AE that involves an abnormal result for an immunology and allergy investigation Mobitz type I block AE 10027787 10047908 10047909 10050797 Wenckebach's block Mobitz type 1 block type 1 second degree atrioventricular block NCIt: C62017 a second degree atrioventricular block AE that the electrical signals are delayed more and more with each heartbeat, until the heart skips a beat. On the EKG, the delay is shown as a line (called the PR interval) between the P and QRS waves. The line gets longer and longer until the QRS waves don't follow the next P wave. WEB: https://www.nhlbi.nih.gov/health/health-topics/topics/hb/types CTCAE: E10146 Wenckebach Phenomenon SS, MW, YH type I second degree atrioventricular block MedDRA: 10050797 is a LLT for type I second degree atrioventricular block MedDRA (LLT): 10047909 exists for Wenckebach phenomeono MedDRA (LLT): 10047908 exists for Wenchebach MedDRA (LLT): 10027787 for Mobit type I Mobitz type II block AE 10027786 10050798 type 2 second degree atrioventricular block WEB: http://www.nhlbi.nih.gov/health//dci/Diseases/hb/hb_types.html Mobitz (type) II atrioventricular block AE type II second degree atrioventricular block SS, YH, MW CTCAE: E10140 a second degree atrioventricular block AE that some of the electrical signals don't reach the ventricles. However, the pattern is less regular than it is in Mobitz type I. Some signals move between the atria and ventricles normally, while others are blocked. On an EKG, the QRS wave follows the P wave at a normal speed. Sometimes, though, the QRS wave is missing (when a signal is blocked). Mobitz type 2 block NCIt: C62018 physical examination result abnormal AE 10062078 10071940 EB an investigation result abnormal AE resulting from an abnormal physical examination finding respiratory and pulmonary investigation result abnormal AE 10038668 an investigation result abnormal AE that involves an abnormal respiratory and pulmonary investigation EB endocrine investigation result abnormal AE 10014706 EB an investigation result abnormal AE that involves an abnormal result of an endocrine investigation enzyme investigation result abnormal AE 10014938 an investigation result abnormal AE that is characterized by an abnormal result of an enzyme investigation EB hematology investigation result abnormal AE 10018851 haematology investigation abnormal AE an investigation result abnormal AE that is characterized by an abnormal result of a hematology investigation MedDRA: 10057755 EB red blood cell profile abnormal AE 20000029 EB a hematology investigation result abnormal AE that results in an abnormal red blood cell profile white blood cell profile abnormal AE 20000030 a hematology investigation result abnormal AE that is characterized by an abnormal white blood cell profile EB leukocyte cell number abnormal AE a white blood cell profile abnormal AE that is characterized by an abnormal leukocyte cell number EB lymphocyte count abnormal AE 10025252 EB a white blood cell profile abnormal AE that is characterized by an abnormal lymphocyte cell number troponin level abnormal AE an enzyme investigation result abnormal AE that is characterized by an abnormal troponin level EB muscle enzyme level abnormal AE EB an enzyme investigation result abnormal AE that is characterized by an abnormal muscle enzyme level gastrointestinal investigation result abnormal AE 10017971 EB an investigation result abnormal AE that is characterized by an abnormal result of a gastrointestinal investigation blood amylase level abnormal AE 10054822 EB a gastrointestinal investigation result abnormal AE that is characterized by an abnormal blood amylase level liver related investigation result abnormal AE 20000008 EB an investigation result abnormal AE that is characterized by an abnormal liver related investigation result aspartate aminotransferase level abnormal AE 10003477 EB a liver related investigation result abnormal AE that is characterized by an abnormal aspartate aminotransferase level hemoglobin level increased AE 10055599 CTCAE: E12171 a hemoglobin level abnormal AE that is characterized by an increased hemoglobin level NCIt: C78333 EB platelet count abnormal AE 10035526 a hematology investigation result abnormal AE that is characterized by an abnormal platelet count EB HPO: HP_0011873 SIDER: C0580317 right ventricular dysfunction AE 10058597 NCIt: C50733 a cardiac ventricular disorder AE that is a condition in nwhich the right ventricle of the heart was functionally impaired. This condition usually leads to heart failure or myocardial infarction, and other cardiovascular complicationns. WEB: http://www.ncbi.nlm.nih.gov/mesh/?term=right%20ventricular%20dysfunction SS CTCAE: E10196 cardiac embolism AE SS heart embolism AE an embolism disorder AE that is a result of an obstruction in a cardiac vessel due to a blood clot or other foreign matters WEB: http://medical-dictionary.thefreedictionary.com/Heart+embolism embolism AE 10014523 SIDER: C0013922 HPO: HP_0001907 SS WEB: http://medical-dictionary.thefreedictionary.com/embolism a vascular disorder AE that is characterized by an obstruction in a blood vessel due to a blood clot or other foreign matter that gets stuck while traveling through the bloodstream. 栓塞 severity of adverse event AE severity YH, SS a process quality that represents the level of severity of an adverse event. eye inflammation AE an inflammation AE that occurs in eye. YH, JX superficial thrombophlebitis AE WEB: http://www.nlm.nih.gov/medlineplus/ency/article/000199.htm NCIt: C78634 CTCAE: E13817 YH: MedDRA: 10043595 is for "thrombophlebitis superficial"; MedDRA: 10042554 is for "superficial thrombophlebitis" SS, YH, MW a thrombophlebitis AE that is characterized by an inflammation of a vein due to a blood clot in a vein located just below the skin's surface. 表在性血栓性静脈炎 UMLS CUI: C1510431 thrombophlebitis superficial AE sleep apnea AE 10040975 CTCAE: E13566 MW, YH NCIt: C26884 WEB: http://www.mayoclinic.org/diseases-conditions/sleep-apnea/basics/definition/con-20020286 a sleep apnea AE is a sleep disorder AE in which breathing repeatedly stops and starts. Basically, it is a crossproduct of sleep disorder AE and apnea AE. stroke AE 10042244 WEB: http://www.nhlbi.nih.gov/health/health-topics/topics/stroke/ cardiovascular accident AE CTCAE: E12826 WEB: http://en.wikipedia.org/wiki/Stroke JX, LW, YH 中风 a brain AE that occurs when flow of oxygen-rich blood to a portion of the brain is blocked NCIt: C3390 psychiatric disorder AE 10037175 WEB: http://en.wikipedia.org/wiki/Mental_disorder a behavior and neurological AE that has an outcome of a mental illness or psychiatiric disorder. The mental illness is a mental or behavioral pattern or anomaly that causes either suffering or an impaired ability to function in ordinary life (disability), and which is not developmentally or socially normative. YH, Izabela Birsanescu mental disorder AE Intraoperative hemorrhage AE 10055298 CTCAE: E11810 a hemorrhage AE that has an outcome of massive amounts of blood loss. A typical Intraoperative hemorrhage has a blood loss exceeding 1000 mL or requires a blood transfusion NCIt: C35135 WEB: http://www.uptodate.com/contents/management-of-hemorrhage-in-gynecologic-surgery Yongqun He, Izabela Birsanescu AE severity G1 AE severity Grade 1 CTCAE4: E10005 (Grade 1 Adverse Event) YH, SS a severity of AE that shows asymptomatic, or involves mild or minor symptoms, or is of marginal clinical relevance, or consists of clinical or diagnostic observations alone, or where intervention is not indicated, or where only non-prescription intervention is indicated. Note the AE severity Grade 1 equals to CTCAE G1 AE severity. Web: http://ncicb.nci.nih.gov/xml/owl/EVS/ctcae.owl#Grade_1_Adverse_Event AE severity G2 a severity of AE for which only minimal, local, or noninvasive intervention (e.g. packing, cautery) is indicated, or that limits instrumental activities of daily living (ADLs, e.g., shopping, laundry, transportation, or ability to conduct finances). Note the AE severity Grade 2 equals to CTCAE G2 AE severity. Web: http://ncicb.nci.nih.gov/xml/owl/EVS/ctcae.owl#Grade_2_Adverse_Event YH, SS CTCAE4: E10006 (Grade 2 Adverse Event) AE severity Grade 2 AE severity G3 Web: http://ncicb.nci.nih.gov/xml/owl/EVS/ctcae.owl#Grade_3_Adverse_Event AE severity Grade 3 YH, SS CTCAE4: E10007 (Grade 3 Adverse Event) Note the AE severity Grade 3 equals to CTCAE G3 AE severity. a severity of AE that shows an outcome which is medically significant but not life-threatening; or for which inpatient care or prolongation of hospitalization are indicated; or that is an important medical event that does not result in hospitalization, but may jeopardize the patient or may require intervention either to prevent hospitalization, to prevent the AE from becoming life-threatening or causing death; or that is disabling; or that results in persistent or significant disability, incapacity, or limitation of self care activities of daily living (ADLs, getting in and out of bed, dressing, eating, getting around inside, bathing, or using the toilet). AE severity G4 AE severity Grade 4 Web: http://ncicb.nci.nih.gov/xml/owl/EVS/ctcae.owl#Grade_4_Adverse_Event a severity of AE that has life-threatening consequences, for which urgent intervention is indicated, that puts the patient is at risk of death at the time of the event if immediate intervention is not undertaken, or that causes blindness or deafness (need to decide if unilateral or bilateral). Note the AE severity Grade 4 equals to CTCAE G4 AE severity. CTCAE4: E10008 (Grade 4 Adverse Event) YH, SS AE severity G5 Note the AE severity Grade 5 equals to CTCAE G5 AE severity. YH, SS AE severity Grade 5 Web: http://ncicb.nci.nih.gov/xml/owl/EVS/ctcae.owl#Grade_5_Adverse_Event CTCAE4: E10009 (Grade 5 Adverse Event) a severity of AE that results in death. joint effusion AE 10023215 CTCAE:E12431 RR, YH, MW A joint disorder AE that has the presence of increased intra-articular fluid. It can be caused by trauma, arthritis, or gout and often affects the knee. PMID: 19915432 NCIt:C49052 WEB: http://en.wikipedia.org/wiki/Joint_effusion gastric disorder AE 10056819 stomach disorder AE a gastrointestinal disorder AE that shows a problem with the stomach, ranging from indigestion and heartburn to peptic ulcers and GERD. RR, YH WEB: http://www.nlm.nih.gov/medlineplus/stomachdisorders.html urgent urination AE 10046593 urinary urgency UMLS CUI: C0439609 NCIt: C50792 CTCAE: E13062 Urgent urination AE is a urinary system AE that has an outcome of a sudden, compelling urge to urinate, along with discomfort in the bladder. WEB: http://sideeffects.embl.de/se/C0085606/ WEB: http://www.nlm.nih.gov/medlineplus/ency/article/003140.htm JX, LW, YH 尿急 micturition urgency pelvic pain AE 10034263 骨盆痛 Pelvic pain AE is a pain AE that occurs in the lower abdomen area. The pain might be steady, or it might come and go. If the pain is severe, it might get in the way of people's daily activities. JX, LW, YH, MW CTCAE:E13167 NCIt:C40122 WEB: http://www.nlm.nih.gov/medlineplus/pelvicpain.html uveitis AE 10046851 色素层炎 JX, LW, YH CTCAE: E10442 Uveitis AE is an inflammation AE that is inflammation of the uvea, which lines the inside of the eye behind the cornea. NCIt: C26909 WEB: http://en.wikipedia.org/wiki/Uveitis allergic rhinitis AE 10001723 Allergic rhinitis AE is a rhinitis AE that is an allergic inflammation of the nasal airways. It occurs when an allergen, such as pollen, dust, or animal dander (particles of shed skin and hair) is inhaled by an individual with a sensitized immune system. 过敏性鼻炎 WEB: http://en.wikipedia.org/wiki/Allergic_rhinitis NCIt:C79532 CTCAE:E13303 JX, LW, YH, MW cystitis AE 10011781 膀胱炎 JX, LW, YH Cystitis AE is an inflammation AE that is the medical term for inflammation of the bladder. Most of the time, the inflammation is caused by a bacterial infection, and it's called a urinary tract infection. WEB: http://www.mayoclinic.org/diseases-conditions/cystitis/basics/definition/con-20024076 stomach ache AE 10042126 NCIt: C26682 胃痛 abdominal pain AE stomach pain AE stomachache AE CTCAE: E10460 JX, LW, YH WEB: http://en.wikipedia.org/wiki/Abdominal_pain http://www.nhs.uk/conditions/stomach-ache-abdominal-pain/Pages/Introduction.aspx Stomachache AE is a pain AE that the pain in or near your stomach. It is a common symptom associated with transient disorders or serious disease. hoarseness AE 10020201 CTCAE:E13384 NCIt:C47813 WEB: http://www.nlm.nih.gov/medlineplus/ency/article/003054.htm Hoarseness AE is a hoarseness AE that refers to a difficulty making sounds when trying to speak. Vocal sounds may be weak, breathy, scratchy, or husky, and the pitch or quality of the voice may change. 声音嘶哑 JX, LW, YH, MW renal calculus AE 10038385 10038386 renal calculi AE NCIt: C26807 Renal calculus AE is a kidney AE that is a solid concretion or crystal aggregation formed in the kidneys from minerals in the urine. Kidney stones typically leave the body by passage in the urine stream, and many stones are formed and passed without causing symptoms. If stones grow to sufficient size (usually at least 3 millimeters (0.12 in)) they can cause blockage of the ureter. This leads to pain, most commonly beginning in the flank or lower back and often radiating to the groin or genitals. 肾结石 kidney stone AE CTCAE: E13018 WEB: http://en.wikipedia.org/wiki/Kidney_stone nephrolithiasis AE JX, LW, YH ventricular tachycardia AE 10047302 WEB: http://en.wikipedia.org/wiki/Ventricular_tachycardia NCIt: C50802 CTCAE: E10239 Ventricular tachycardia AE is a tachycardia AE that is a type of tachycardia, or a rapid heart beat that arises from improper electrical activity of the heart presenting as a rapid heart rhythm, that starts in the bottom chambers of the heart, called the ventricles. JX, LW, YH 心室性心搏过速 genital edema AE 10018146 生殖器水肿 CTCAE:E13111 JX, LW, YH, MW WEB: http://www.lymphoedemanz.org.nz/About+Lymphoedema/Genital+Oedema.html NCIt:C78324 Genital edema AE is an edema AE that can be the result of interruption to the lymphatic drainage of this area caused by tumor, surgical removal of lymph nodes, radiotherapy or infection. Congenital disorders causing inadequate lymphatics can sometimes lead to the development of this condition. sinus bradycardia AE 10040741 WEB: http://en.wikipedia.org/wiki/Sinus_bradycardia CTCAE: E10208 Sinus bradycardia AE is a bradycardia AE that is a heart rhythm that originates from the sinus node and has a rate that is lower than normal. In humans, bradycardia is generally defined to be a rate of under 60 beats per minute. JX, LW, YH NCIt: C26923 窦性心动过缓 hyperthyroidism AE 10020850 CTCAE: E10322 JX, LW, YH WEB: http://en.wikipedia.org/wiki/Hyperthyroidism 甲状腺机能亢进 NCIt: C3123 Hyperthyroidism AE is an endocrine system AE that is a condition in which the thyroid gland produces and secretes excessive amounts of the free (not protein bound circulating in the blood) thyroid hormones -triiodothyronine (T3) and/or thyroxine (T4). akathisia AE 10001540 WEB: http://en.wikipedia.org/wiki/Akathisia acathisia AE CTCAE:E12581 静坐困难 NCIt:C78163 JX, LW, YH, MW Akathisia AE is a behavior and neurological AE that is a movement disorder characterized by a feeling of inner restlessness and a compelling need to be in constant motion, as well as by actions such as rocking while standing or sitting, lifting the feet as if marching on the spot, and crossing and uncrossing the legs while sitting. People with akathisia are unable to sit or keep still, complain of restlessness, fidget, rock from foot to foot, and pace. retinopathy AE 10038923 JX, LW, YH CTCAE: E10432 WEB: http://en.wikipedia.org/wiki/Retinopathy NCIt: C62601 Retinopathy AE is an eye AE that is due to persistent or acute damage to the retina of the eye. Ongoing inflammation and vascular remodeling may occur over periods of time where the patient is not fully aware of the extent of the disease. Frequently, retinopathy is an ocular manifestation of systemic disease as seen in diabetes or hypertension. 视网膜病变 hearing loss AE 10019245 10019246 hearing impairment AE a hearing disorder AE that is a partial or total inability to hear. In children it may affect the development of language and can cause work related difficulties for adults. CTCAE: E10276 WEB: http://en.wikipedia.org/wiki/Hearing_loss JX, LW, YH hearing impaired AE anacusis AE NCIt: C50576 听力下降 deafness AE hard of hearing AE toxic epidermal necrolysis AE 10044223 中毒性表皮坏死溶解症 JX, LW, YH, MW CTCAE:E13743 WEB: http://en.wikipedia.org/wiki/Toxic_epidermal_necrolysis Toxic epidermal necrolysis AE is a skin AE that is a rare, life-threatening skin condition which is usually caused by a reaction to drugs. Lyell's syndrome AE NCIt:C79777 induration AE 10060708 RR WEB: http://www.merriam-webster.com/medical/induration a skin AE with the outcome of induration, which is an increase in the fibrous elements in tissue commonly associated with inflammation and marked by loss of elasticity and pliability or a hardened mass or formation lymph node pain AE 10025182 a pain AE that has an outcome of lymph node pain NCIt: C78440 RR CTCAE: E10052 aphonia AE 10002953 a speech disorder AE with an outcome of aphonia, or loss of voice and of all but whispered speech WEB: http://www.merriam-webster.com/dictionary/aphonia NCIt:C79539 CTCAE:E12589 RR, MW international normalized ratio increased AE 10022402 10022595 a lab test abnormal AE that has an outcome of an increased international normalized ratio, indicating an individual is more prone to bleeding INR increased AE CTCAE: E12175 WEB: http://circ.ahajournals.org/content/126/5/e52.full RR, MW, YH NCIt: C78366 fecal incontinence AE 10016092 10016296 RR, MW, YH faecal incontinence AE CTCAE: E10693 NCIt: C78498 WEB: http://digestive.niddk.nih.gov/ddiseases/pubs/fecalincontinence/#what an abnormal defecation AE that has an outcome of fecal incontinence, the accidental passing of solid or liquid stool or mucus from the rectum gingival pain AE 10018286 RR CTCAE: E10763 NCIt: C78325 a pain AE that has an outcome of pain in gums WEB: http://www.merriam-webster.com/dictionary/gingival thrombotic thrombocytopenic purpura AE 10043648 WEB: http://en.wikipedia.org/wiki/Thrombotic_thrombocytopenic_purpura 血栓性血小板减少性紫癜 moschcowitz syndrome AE NCIt: C78797 CTCAE: E10061 Thrombotic thrombocytopenic purpura AE is a thrombocytopenic purpura AE that is a rare disorder of the blood-coagulation system, causing extensive microscopic clots to form in the small blood vessels throughout the body. JX, LW, YH glaucoma AE 10018304 Glaucoma AE is an eye AE that is a term describing a group of ocular (eye) disorders resulting in optic nerve damage or loss to the field of vision, in many patients caused by a clinically characterized pressure buildup in regards to the fluid of the eye (intraocular pressure-associated optic neuropathy). JX, LW, YH NCIt: C26782 青光眼 CTCAE: E10392 WEB: http://en.wikipedia.org/wiki/Glaucoma anaphylaxis AE 10002218 an allergy AE that shows a serious allergic reaction that is rapid in onset and may cause death. It typically causes a number of symptoms including an itchy rash, throat swelling, and low blood pressure. Common causes include insect bites and stings, foods, and medications. CTCAE: E11254 JX, LW, YH NCIt: C50460 过敏症 WEB: http://en.wikipedia.org/wiki/Anaphylaxis hyponatremia AE 10021036 10021038 a blood sodium abnormal AE with an abnormally decreased sodium concentration in the blood hyponatraemia AE YH, MW CTCAE: E12339 WEB: http://www.mayoclinic.org/diseases-conditions/hyponatremia/basics/definition/con-20031445 NCIt: C37976 angina AE 10002383 10008481 NCIt: C51221 DJ, SS, YH a chest pain that is caused when your heart muscle doesn't get enough oxygen-rich blood. chest pain - cardiac AE SIDER: C0002962 WEB: http://www.ncbi.nlm.nih.gov/pubmed/23016723 CTCAE: E10110 HPO: HP_0001681 tight chest AE hearing disorder AE 10019243 JX, LW, YH Hearing disorder AE is an ear disorder that shows impairment of the sense of hearing. 听觉障碍 coronary heart disease AE 10068617 Coronary heart disease AE is a cardiovascular disorder AE that is a disease in which a waxy substance called plaque (plak) builds up inside the coronary arteries. These arteries supply oxygen-rich blood to your heart muscle. JX, LW, YH WEB: http://www.nhlbi.nih.gov/health/health-topics/topics/cad/ 冠心病 insomnia AE 10022437 a sleep disorder AE in which there is an inability to fall asleep or to stay asleep as long as desired. SIDER: C0917801 YH, MW HPO: HP_0002360 WEB: https://en.wikipedia.org/wiki/Insomnia CTCAE: E12925 Insomnia is a symptom of a sleeping disorder characterized by persistent difficulty falling asleep or staying asleep despite the opportunity. Insomnia is a symptom, not a stand-alone diagnosis or a disease. retinal detachment AE 10038848 CTCAE: E10420 JX, LW, YH NCIt: C26874 WEB: http://www.medicinenet.com/retinal_detachment/article.htm 视网膜脱离 NCIT: C26874 Retinal detachment AE is an eye AE that is a separation of the retina from its attachments to the underlying tissue within the eye. laryngeal edema AE 10023838 laryngeal oedema AE NCIt:C79607 Laryngeal edema AE is an edema AE that shows abnormal accumulation of fluid in tissues of any part of the larynx, commonly associated with laryngeal injuries and allergic reactions. JX, LW, YH, MW CTCAE:E13393 喉肿胀 hemolysis AE 10019491 NCIt: C37965 JX, LW, YH 溶血 CTCAE: E10037 Hemolysis AE is a hematopoietic system AE that is the rupturing of erythrocytes (red blood cells) and the release of their contents (cytoplasm) into surrounding fluid. WEB: http://en.wikipedia.org/wiki/Hemolysis acidosis AE 10000486 10005706 CTCAE:E12237 a metabolism, endocrine, and exocrine system AE that has an outcome of acidosis, i.e., too much acid in the body fluids. URL: http://www.nlm.nih.gov/medlineplus/ency/article/001181.htm Blood pH Decreased YH, SJ, MW NCIt:C28228 anal fistula AE 10002156 CTCAE: E10464 an anus AE that results in the development of a small channel between the end of the bowel and the skin near the anus WEB: http://www.webmd.boots.com/digestive-disorders/anal-fistula NCIt: C60785 SJ, YH arachnoiditis AE 10003074 CTCAE:E12591 SJ, YH, MW NCIt:C37913 WEB: http://en.wikipedia.org/wiki/Arachnoiditis a brain disorder AE that causes inflammation of the arachnoid, one of the membranes known as meninges that surround and protect the nerves of the central nervous system, including the brain and spinal cord. atrial tachycardia AE 10003668 10034040 CTCAE: E10166 paroxysmal atrial tachycardia paroxysmal supraventricular tachycardia WEB: http://www.heart.org/HEARTORG/Conditions/Arrhythmia/AboutArrhythmia/Tachycardia-Fast-Heart-Rate_UCM_302018_Article.jsp# SJ, YH supraventricular tachycardia atrial tachycardia AE is a tachycardia AE that results in a fast heart rate beginning in the upper chambers of the heart NCIt: C34900 eyelid disorder AE 10061130 WEB: http://www.healthline.com/health/eyelid-disorders#Overview1 Eyelid disorder AE is a eye AE that is a condition specifically affects the eyelid. It can include drooping, twitching, inflammation, paralysis, and growths. Occasional fluttering of one eyelid is normal. JX, LW cholecystitis AE 10008612 CTCAE: E11184 NCIT: C34465 KM, YH WEB: http://en.wikipedia.org/wiki/Cholecystitis, http://www.mayoclinic.org/diseases-conditions/cholecystitis/basics/definition/con-20034277 NCIt: C34465 cholecystitis AE is an gallbladder enlargement AE that has an outcome of cholecystitis, which is an acute or chronic inflammation involving the gallbladder wall. It may be associated with the presence of gallstones. menstrual disorder AE 10027327 Menstrual disorder AE is an abnormal condition in a woman's menstrual cycle. WEB: http://en.wikipedia.org/wiki/Menstrual_disorder JX, YH cognitive disorder AE 10057668 a psychiatric disorder AE that is a category of mental health disorders that primarily affect learning, memory, perception, and problem solving, and include amnesia, dementia, and delirium. JX, YH WEB: http://en.wikipedia.org/wiki/Cognitive_disorder autoimmune disorder AE 10061664 NCIt: C2889 JX, YH CTCAE: E11258 WEB: http://en.wikipedia.org/wiki/Autoimmune_disease Autoimmune disorder AE is an immune system AE that arises from an abnormal immune response of the body against substances and tissues normally present in the body (autoimmunity). menstruation irregular AE 10022992 10027339 Menstruation irregular AE is a endocrine system AE that is an abnormal variation in length of menstrual cycles in a female. NCIt: C35219 irregular menstruation AE JX, YH, MW WEB: http://en.wikipedia.org/wiki/Irregular_menstruation CTCAE: E13125 buttock pain AE 10048677 CTCAE:E12396 Buttock pain AE is a pain AE that is a common problem in the butt, it can be due to bursitis, bruising, piriformis syndrome, and shingles,or due to more serious diseases with long-term consequences, such as cancer, arthritis of the sacroiliac joints, and herniated disc with sciatica. WEB:http://www.medicinenet.com/buttock_pain/symptoms.htm NCIt:C78228 SJ, YH, MW Butt Pain cerebrospinal fluid leak AE 10008164 NCIt: C50487 a nervous system AE that occurs when the cerebrospinal fluid leaks through a defect in the dura or the skull and out through the nose or ear resulting from a tear in the dura. CTCAE: E12611 WEB: http://www.hopkinsmedicine.org/neurology_neurosurgery/centers_clinics/brain_tumor/center/skull-base/types/csf-leak.html cerebrospinal fluid leakage AE SJ, YH, MW muscle spasticity AE 10028335 10041416 WEB: http://www.webmd.com/pain-management/pain-management-spasticity KM, YH, MW, MW spasticity AE NCIt: C79750 CTCAE: E12820 A muscle spasm AE that has an outcome of tight or stiff muscles and an inability to control those muscles. palpitations AE 10033557 KM, YH WEB: http://en.wikipedia.org/wiki/Palpitations An arrhythmia AE that has an outcome of palpitations, an abnormality of heartbeat characterized by simultaneous awareness of one’s pulse and discomfort. CTCAE: E10163 NCIt: C37999 prostatic disorder AE 10036956 A male reproductive system AE that affects prostatic gland in the male reproductive system. WEB: http://www.britannica.com/EBchecked/topic/479519/prostatic-disorder KM, YH hypernatremia AE 10020679 10020680 hypernaetremia CTCAE: E12293 SIDER: C0595878 a blood sodium abnormal AE that is characterized by an abnormally high level of sodium in the blood HPO: HP_0003228 NCIt: C37970 YH, MW WEB: http://emedicine.medscape.com/article/241094-overview skin atrophy AE 10040799 KM, YH, MW WEB: http://www.wisegeek.com/what-is-skin-atrophy.htm NCIT: C35163 NCIt:C35163 CTCAE:E13714 atrophy of the skin A skin AE that results in the degeneration and thinning of the epidermis and dermis. skin hypopigmentation AE 10040868 CTCAE:E13721 NCIt:C78610 http://en.wikipedia.org/wiki/Hypopigmentation Vitiligo, albinism, and leukoderma are among the disorders that are associated with skin hypopigmentation. A skin discoloration AE that shows abnormal lightening of skin due to decreased melanin production or deposition. KM, YH, MW WEB: http://en.wikipedia.org/wiki/Hypopigmentation Hypopigmentation, Pigment Dilution spleen disorder AE 10041633 NCIt: C35823 splenic diseases KM, YH CTCAE: E10056 WEB: http://www.livescience.com/44725-spleen.html An immune system disorder AE that has an disorder in spleen, the largest organ in the lymphatic system. WEB: http://en.wikipedia.org/wiki/Splenic_disease telangiectasia AE 10043189 NCIT: C28194 http://en.wikipedia.org/wiki/Telangiectasia KM, YH, MW CTCAE:E13740 A vein discoloration AE that has an outcome of local dilatation of small vessels resulting in red discoloration of the skin or mucous membranes. NCIt:C28194 trismus AE 10044684 A muscle spasm AE that results in the lack of ability to open the mouth fully due to decreased range of motion of the muscles of mastication. Trismus is a symptom of tetanus. KM, YH, MW WEB: http://www.medicinenet.com/script/main/art.asp?articlekey=40739 NCIt: C78651 CTCAE:E12541 burn AE 10006634 NCIt: C34441 an injury AE that displays a type of injury to flesh or skin caused by heat, electricity, chemicals, friction, or radiation. YH WEB: http://en.wikipedia.org/wiki/Burn CTCAE: E11669 wound AE 10052428 an injury AE that breaks the skin or other body tissues. WEB: http://www.nlm.nih.gov/medlineplus/woundsandinjuries.html KM, YH ventricular arrhythmia AE 10047281 an arrhythmia AE that shows abnormal heart rhythms that originate in the bottom chambers of the heart called the ventricles. 室性心律失常 WEB: http://my.clevelandclinic.org/services/heart/departments-centers/ventricular-arrhythmia-center NCIt: C26924 CTCAE: E10230 LW, YH hypokalaemia AE 10021015 10021018 CTCAE: E12327 NCIt: C37974 hypopotassemia AE a blood potassium abnormal AE that has a lab test outcome of abnormally lower than normal amount of potassium in the blood hypopotassaemia AE hypokalemia AE WEB: http://en.wikipedia.org/wiki/Hypokalemia WEB: http://www.emedicinehealth.com/low_potassium/article_em.htm YH, MW potassium depletion AE 血钾过少 WEB: http://medical-dictionary.thefreedictionary.com/hyperkalemia blood phosphate abnormal AE 10054823 a blood phosphorus abnormal AE that shows an abnormal blood phosphate level EB blood albumin abnormal AE 10005800 a hematology investigation result abnormal AE that results in an abnormal level of albumin in the blood EB blood glucose decreased 10005555 UMLS CUI: C0595883 EB, YH, MW A physical quality that has an decreased level of glucose in the blood blood glucose increased 10005557 EB, YH, MW UMLS CUI: C0595877 A physical quality that has an increased level of glucose in the blood acneiform rash AE 10037847 rash acneiform AE WEB: http://en.wikipedia.org/wiki/Acne_vulgaris The term "acneiform", literally, refers to an appearance similar to acne. Acne vulgaris (or simply acne) is a long-term skin condition characterized by areas of blackheads, whiteheads, pimples, greasy skin, and possibly scarring. acneiform eruption AE CTCAE: E13694 YH, MW NCIt: C35277 WEB: http://en.wikipedia.org/wiki/Acneiform_eruption a rash AE that shows follicular eruptions characterized by papules and pustules resembling acne. papulopustular rash AE 10069138 A rash AE that is characterized by an eruption consisting of papules (a small, raised pimple) and pustules (a small pus filled blister), typically appearing in face, scalp, and upper chest and back. NCIt: C80119 YH CTCAE: E11491 Unlike acne, papulopustular rash does not present with whiteheads or blackheads, and can be symptomatic, with itchy or tender lesions. WEB: http://www.medaphile.com/medical-dictionary/papulopustular-rash cranial neuropathy AE 10061096 an neuropathy AE that occurs when any of the twelve cranial nerves (nerves that exit from the brain directly) are damaged. WEB: http://www.emedicinehealth.com/neuropathy/article_em.htm#types_of_neuropathy MW, YH cognitive disturbance AE 10009845 CTCAE: E12617 MW, YH NCIt: C27101 a cognitive disorder AE that shows conspicuous changes in cognitive functions. thromboembolism AE 10043565 WEB: http://www.medicinenet.com/script/main/art.asp?articlekey=25032 MW, YH CTCAE: E13825 thromboembolic event AE a vascular disorder AE that form in a blood vessel a clot (thrombus) that breaks loose and is carried by the blood stream to plug another vessel. cardiovascular injury AE 10007654 UMLS CUI: C0560570 YH an injury AE that occurs in the cardiovascular system cardiac function test abnormal AE 10058479 UMLS CUI: C0438177 a cardiovascular investigation result abnormal AE that results in an abnormal result on a test used to evaluate heart function YH WEB: http://www.drsinatra.com/heart-function-tests-to-assess-heart-disease-risk/ WEB: https://en.wikipedia.org/wiki/Cardiology_diagnostic_tests_and_procedures device AE YH a procedural complication AE that occurs after the usage of a device. Grade 1 skin ulceration AE MW, YH WEB: http://www.nhs.uk/Conditions/Pressure-ulcers/Pages/Symptoms.aspx CTCAE: E13731 a skin ulceration AE that has a combined area of ulcers <1 cm and nonblanchable erythema of intact skin with associated warmth or edema Grade 2 skin ulceration AE 1 0 WEB: http://www.nhs.uk/Conditions/Pressure-ulcers/Pages/Symptoms.aspx a skin ulceration AE that has a combined area of ulcers 1 - 2 cm and partial thickness skin loss involving skin or subcutaneous fat MW, YH CTCAE: E13732 Grade 3 skin ulceration AE CTCAE: E13733 MW, YH WEB: http://www.nhs.uk/Conditions/Pressure-ulcers/Pages/Symptoms.aspx a skin ulceration AE that has a combined area of ulcers >2 cm and full-thickness skin loss involving damage to or necrosis of subcutaneous tissue that may extend down to fascia Grade 4 skin ulceration AE a skin ulceration AE that has any size ulcer with extensive destruction, tissue necrosis, or damage to muscle, bone, or supporting structures with or without full thickness skin loss WEB: http://www.nhs.uk/Conditions/Pressure-ulcers/Pages/Symptoms.aspx MW, YH CTCAE: E13734 Laryngopharyngeal dysesthesia AE 10062667 NCIt: C78414 MW, YH A dysesthesia AE that shows an uncomfortable persistent sensation in the area of the laryngopharynx. CTCAE: E13433 local AE an adverse event that occurs locally in a certain location. This is different from the systematci adverse event that occurs throughout the systemtic circulation. YH, JX URL: https://en.wikipedia.org/wiki/Adverse_drug_reaction injury or procedural complication AE injury and procedural complication AE an adverse event that shows a result of injury or procedural complication. JX, YH meninges inflammation AE an inflammation AE which has an outcome of brain inflammation, which is local accumulation of fluid, plasma proteins, and leukocytes in the brain According to the Vaccine Adverse Event Reporting System (VAERS), 'encephalitis' is an adverse event that was mentioned in 480 VAERS reports (0.4%) during1991-2001 (Reference: PMID: 12825543). MP: MP_0001847 delusions AE 10012260 a mental disorder that has false personal beliefs held contrary to reality, despite contradictory evidence and common sense. NCIt: C26741 CTCAE: E12904 MW, YH laryngeal inflammation AE 10065735 an inflammation AE that has an inflammation involving the larynx. MW, YH NCIt: C26811 CTCAE: E13411 testicular disorder AE 10043306 a male reproductive system AE that has involvement of the testis. CTCAE: E13215 NCIt: C26890 MW, YH urinary frequency AE 10046539 MW, YH NCIt: C26906 CTCAE: E13039 an urinary system AE that has urination at short intervals. vaginal inflammation AE 10046916 a reproduction system inflammation AE that has inflammation involving the vagina. Symptoms may include redness, edema, marked discomfort and an increase in vaginal discharge. NCIt: C26911 MW, YH CTCAE: E13270 trigeminal nerve disorder AE 10060890 MW, YH a cranial neuropathy AE that has involvement of the trigeminal nerve (fifth cranial nerve). CTCAE: E12841 NCIt: C26952 accessory nerve disorder AE 10060929 NCIt: C26953 MW, YH cranial neuropathy AE that has involvement of the accessory nerve (eleventh cranial nerve). CTCAE: E12573 hypoglossal nerve disorder AE 10061212 a cranial neuropathy AE that has involvement of the hypoglossal nerve (twelfth cranial nerve). NCIt: C26954 CTCAE: E12692 MW, YH pharyngeal hemorrhage AE 10055315 MW, YH CTCAE: E13460 NCIt: C26986 a hemorrhage AE that has bleeding from the pharynx. brachial plexopathy AE 10065417 NCIt: C27194 a distal neuropathy AE that has regional paresthesia of the brachial plexus, marked discomfort and muscle weakness, and limited movement in the arm or hand. CTCAE: E12601 MW, YH acoustic nerve disorder NOS AE 10000521 MW, YH a cranial neuropathy AE that has involvement of the acoustic nerve (eighth cranial nerve) NCIt: C27207 CTCAE: E12577 olfactory nerve disorder AE 10056388 a cranial neuropathy AE that has involvement of the olfactory nerve (first cranial nerve). CTCAE: E12755 MW, YH NCIt: C27210 glossopharyngeal nerve disorder AE 10061185 NCIt: C27211 a cranial neuropathy AE that has involvement of the glossopharyngeal nerve (ninth cranial nerve). MW, YH CTCAE: E12672 vagus nerve disorder AE 10061403 NCIt: C27591 MW, YH a cranial neuropathy AE that has involvement of the vagus nerve (tenth cranial nerve). CTCAE: E12845 abducens nerve disorder AE 10053662 MW, YH NCIt: C27593 a cranial neuropathy AE that has involvement of the abducens nerve (sixth cranial nerve). CTCAE: E12569 facial nerve disorder AE 10061457 a cranial neuropathy AE that has involvement of the facial nerve (seventh cranial nerve). NCIt: C27594 MW, YH CTCAE: E12668 oculomotor nerve disorder AE 10053661 CTCAE: E12751 MW, YH a cranial neuropathy AE that has involvement of the oculomotor nerve (third cranial nerve). NCIt: C27598 dysesthesia AE 10062872 CTCAE: E12639 a sensory neuropathy AE that has distortion of sensory perception, resulting in an abnormal and unpleasant sensation. NCIt: C28246 MW, YH dyspareunia AE 10013941 NCIt: C2997 CTCAE: E13081 a pain AE that has painful or difficult coitus. MW, YH exostosis AE 10015688 CTCAE: E12404 MW, YH NCIt: C3029 a bone disorder AE that has non-neoplastic overgrowth of bone. gynecomastia AE 10018801 CTCAE: E13115 NCIt: C3073 MW, YH an endocrine system AE that has excessive development of the breasts in males. hydrocephalus AE 10020508 NCIt: C3111 MW, YH a brain edema AE that has an abnormal increase of cerebrospinal fluid in the ventricles of the brain. CTCAE: E12682 lymphedema AE 10025233 NCIt: C3207 CTCAE: E13802 an edema AE that has excessive fluid collection in tissues that causes swelling. MW, YH menopause AE 10027308 NCIt: C3231 a menstrual disorder AE that has the permanent cessation of menses, usually defined by 12 consecutive months of amenorrhea in a woman over 45 years of age. MW, YH CTCAE: E13750 obesity AE 10029883 CTCAE: E12361 a physical examination result abnormal AE that is having a high amount of body fat. NCIt: C3283 MW, YH adult respiratory distress syndrome AE 10001409 MW, YH a lung inflammation AE that has progressive and life-threatening pulmonary distress in the absence of an underlying pulmonary condition, usually following major trauma or surgery. CTCAE: E13299 NCIt: C3353 Superior vena cava syndrome AE CTCAE: E13819 NCIt: C3396 MW, YH a cardiovascular AE that has obstruction of the blood flow in the superior vena cava. Signs and symptoms include swelling and cyanosis of the face, neck, and upper arms, cough, orthopnea and headache. dysmenorrhea AE 10013934 a menstrual disorder AE that has abnormally painful abdominal cramps during menses. MW, YH NCIt: C34559 CTCAE: E13077 euphoria AE 10015533 a behavior and neurological AE that has an exaggerated feeling of well-being which is disproportionate to events and stimuli. CTCAE: E12915 MW, YH NCIt: C34598 flank pain AE 10016750 CTCAE: E12414 a pain AE that has marked discomfort sensation on the lateral side of the body in the region below the ribs and above the hip. MW, YH NCIt: C34615 glucose intolerance AE 10052426 CTCAE: E12264 a metabolic disorder AE that has an inability to properly metabolize glucose. MW, YH NCIt: C34646 hemoglobinuria AE 10019489 MW, YH CTCAE: E13006 NCIt: C34677 an urine abnormality AE that has laboratory test results that indicate the presence of free hemoglobin in the urine. hypohidrosis AE 10021013 a sweating AE that has reduced sweating. MW, YH NCIt: C34718 CTCAE: E13652 kyphosis AE 10023509 NCIt: C34754 a bone disorder AE that has an abnormal increase in the curvature of the thoracic portion of the spine. CTCAE: E12447 MW, YH lordosis AE 10024842 MW, YH CTCAE: E12451 a bone disorder AE that has an abnormal increase in the curvature of the lumbar portion of the spine. NCIt: C34787 oligospermia AE 10030300 a male reproductive system AE that has a decrease in the number of spermatozoa in the semen. CTCAE: E13141 NCIt: C34860 MW, YH avascular necrosis AE 10066480 MW, YH a necrosis AE that has necrotic changes in the bone tissue due to interruption of blood supply. Most often affecting the epiphysis of the long bones, the necrotic changes result in the collapse and the destruction of the bone structure. CTCAE: E12382 NCIt: C34880 bullous dermatitis AE 10006556 CTCAE: E13617 NCIt: C35149 an inflammation AE that has inflammation of the skin characterized by the presence of bullae which are filled with fluid. MW, YH dysphasia AE 10013951 CTCAE: E12646 MW, YH NCIt: C35546 a speech disorder AE that has impairment of verbal communication skills, often resulting from brain damage. vaginal stricture AE 10053496 NCIt: C36064 MW, YH CTCAE: E13290 a female reproductive system AE that has a narrowing of the vaginal canal. alkalosis AE 10001680 CTCAE: E12247 MW, YH a metabolism, endocrine, and exocrine system AE that has abnormally high alkalinity (low hydrogen-ion concentration) of the blood and other body tissues. NCIt: C37909 Hiccups AE 10020039 CTCAE: E13380 a gastrointestinal disorder AE that has repeated gulp sounds that result from an involuntary opening and closing of the glottis. This is attributed to a spasm of the diaphragm. MW, YH NCIt: C37966 proteinuria AE 10037032 MW, YH CTCAE: E13008 an urine abnormality AE that has laboratory test results that indicate the presence of excessive protein in the urine. It is predominantly albumin, but also globulin. NCIt: C38012 erythroderma AE 10015277 MW, YH NCIt: C39646 an inflammation AE that has generalized inflammatory erythema and exfoliation. The inflammatory process involves > 90% of the body surface area. CTCAE: E13633 pyramidal tract syndrome AE 10063636 CTCAE: E12780 a syndrome AE that has dysfunction of the corticospinal (pyramidal) tracts of the spinal cord. Symptoms include an increase in the muscle tone in the lower extremities, hyperreflexia, positive Babinski and a decrease in fine motor coordination. MW, YH NCIt: C43245 edema cerebral AE 10014217 MW, YH NCIt: C4909 CTCAE: E12650 a brain edema AE that has swelling due to an excessive accumulation of fluid in the brain. treatment related secondary malignancy AE 10049737 a tumor AE that has development of a malignancy most probably as a result of treatment for a previously existing malignancy. CTCAE: E12561 MW, YH NCIt: C4969 intracranial hemorrhage AE 10022763 a hemorrhage AE that has bleeding from the cranium. MW, YH NCIt: C50438 CTCAE: E12696 fetal death AE 10016479 NCIt: C50620 a death AE that has death in utero; failure of the product of conception to show evidence of respiration, heartbeat, or definite movement of a voluntary muscle after expulsion from the uterus, without possibility of resuscitation. CTCAE: E12855 MW, YH transient ischemic attacks AE 10044391 MW, YH a ischemia AEE that has a brief attack (less than 24 hours) of cerebral dysfunction of vascular origin, with no persistent neurological deficit. CTCAE: E12834 NCIt: C50781 vaginal discharge AE 10046901 CTCAE: E13251 NCIt: C50795 afemale reproductive system AE that has vaginal secretions. Mucus produced by the cervical glands is discharged from the vagina naturally, especially during the childbearing years. MW, YH vasovagal reaction AE 10047166 CTCAE: E12851 MW, YH NCIt: C50798 a sensory capability AE that has a sudden drop of the blood pressure, bradycardia, and peripheral vasodilation that may lead to loss of consciousness. It results from an increase in the stimulation of the vagus nerve. premature delivery AE 10036595 apregnancy AE that has delivery of a viable infant before the normal end of gestation. Typically, viability is achievable between the twentieth and thirty-seventh week of gestation. MW, YH NCIt: C50917 早产 CTCAE: E12867 mania AE 10026749 MW, YH CTCAE: E12936 NCIt: C61374 a psychiatric disorder AE that has excitement of psychotic proportions manifested by mental and physical hyperactivity, disorganization of behavior and elevation of mood. hirsutism AE 10020112 MW, YH NCIt: C61444 a hair growth abnormal AE that has the presence of excess hair growth in women in anatomic sites where growth is considered to be a secondary male characteristic and under androgen control (beard, moustache, chest, abdomen) CTCAE: E13642 osteonecrosis of jaw AE 10064658 NCIt: C63924 CTCAE: E12502 a necrosis AE that has a necrotic process occurring in the bone of the mandible. MW, YH abdominal soft tissue necrosis AE 10065775 MW, YH CTCAE: E12369 a necrosis AE that has a necrotic process occurring in the soft tissues of the abdominal wall. NCIt: C78165 alcohol intolerance AE 10001598 CTCAE: E12242 a metabolic disorder AE that has an increase in sensitivity to the adverse effects of alcohol, which can include nasal congestion, skin flushes, heart dysrhythmias, nausea, vomiting, indigestion and headaches. MW, YH NCIt: C78167 anorgasmia AE 10002652 NCIt: C78177 MW, YH a psychiatric disorder AE that has an inability to achieve orgasm. CTCAE: E12880 bladder perforation AE 10063575 CTCAE: E12979 NCIt: C78208 an urinary system AE that has a rupture in the bladder wall. MW, YH bladder spasm AE 10048994 CTCAE: E12984 MW, YH NCIt: C78210 an urinary system AE that has a sudden and involuntary contraction of the bladder wall. bronchopulmonary hemorrhage AE 10065746 a hemorrhage AE that is bleeding from the bronchial wall and/or lung parenchyma. CTCAE: E13346 MW, YH NCIt: C78224 bronchial obstruction AE 10006440 MW, YH NCIt: C78225 a respiratory system AE that has blockage of a bronchus passage, most often by bronchial secretions and exudates. CTCAE: E13328 bronchial stricture AE 10063524 a respiratory system AE that has a narrowing of the bronchial tube. NCIt: C78226 CTCAE: E13334 MW, YH central nervous system necrosis AE 10065784 a necrosis AE that has a necrotic process occurring in the brain and/or spinal cord. MW, YH CTCAE: E12605 NCIt: C78236 chest wall pain AE 10008496 NCIt: C78238 MW, YH CTCAE: E12400 a pain AE that has marked discomfort sensation in the chest wall region. cystitis noninfective AE 10063057 NCIt: C78250 CTCAE: E12994 MW, YH a cystitis AE that has inflammation of the bladder which is not caused by an infection of the urinary tract. delayed orgasm AE 10057066 MW, YH a psychiatric disorder AE that has sexual dysfunction characterized by a delay in climax. NCIt: C78252 CTCAE: E12895 ejaculation disorder AE 10014326 CTCAE: E13085 NCIt: C78264 MW, YH a male reproductive system AE that has problems related to ejaculation. This category includes premature, delayed, retrograde and painful ejaculation. facial muscle weakness AE 10051272 CTCAE: E12664 MW, YH NCIt: C78290 a muscular weakness AE that has a reduction in the strength of the facial muscles. fallopian tube obstruction AE 10065789 NCIt: C78293 CTCAE: E13092 MW, YH a female reproductive system AE that has blockage of the normal flow of the contents in the fallopian tube. fallopian tube stenosis AE 10065791 a female reproductive system AE that has a narrowing of the fallopian tube lumen. MW, YH NCIt: C78295 CTCAE: E13096 fat atrophy AE 10016241 CTCAE: E13638 a connective tissue disorder AE that has shrinking of adipose tissue. MW, YH NCIt: C78297 female genital tract fistula AE 10061149 NCIt: C78298 CTCAE: E13102 a fistula AE that has an abnormal communication between a female reproductive system organ and another organ or anatomic site. MW, YH feminization acquired AE 10054382 CTCAE: E13108 MW, YH NCIt: C78299 an endocrine system AE that has the development of secondary female sex characteristics in males due to extrinsic factors. fibrosis deep connective tissue AE 10065799 MW, YH CTCAE: E12408 NCIt: C78301 a connective tissue disorder AE that has fibrotic degeneration of the deep connective tissues. generalized muscle weakness AE 10062572 MW, YH CTCAE: E12418 NCIt: C78323 a muscular weakness AE that has a reduction in the strength of muscles in multiple anatomic sites. growth suppression AE 10018761 a musculoskeletal and connective tissue AE that has stature that is smaller than normal as expected for age. NCIt: C78328 CTCAE: E12422 MW, YH head soft tissue necrosis AE 10065779 CTCAE: E12426 MW, YH NCIt: C78331 a necrosis AE that has a necrotic process occurring in the soft tissues of the head. hematosalpinx AE 10060602 a female reproductive system AE that has the presence of blood in a fallopian tube. NCIt: C78332 MW, YH CTCAE: E13119 hypersomnia AE 10020765 a sleep disorder AE that has characterized by excessive sleepiness during the daytime. NCIt: C78346 CTCAE: E12688 MW, YH iron overload AE 10065973 NCIt: C78393 CTCAE: E12350 a homeostasis AE that has accumulation of iron in the tissues. MW, YH ischemia cerebrovascular AE 10023030 an ischemia AE that has a decrease or absence of blood supply to the brain caused by obstruction (thrombosis or embolism) of an artery resulting in neurological damage. MW, YH NCIt: C78394 CTCAE: E12702 IVth nerve disorder AE 10065836 CTCAE: E12705 a cranial neuropathy AE that has involvement of the trochlear nerve (fourth cranial nerve). MW, YH NCIt: C78395 joint range of motion decreased cervical spine AE 10065796 NCIt: C78404 a joint disorder AE that has a decrease in flexibility of a cervical spine joint. MW, YH CTCAE: E12439 joint range of motion decreased lumbar spine AE 10065800 NCIt: C78405 MW, YH CTCAE: E12443 a joint disorder AE that has a decrease in flexibility of a lumbar spine joint. laryngeal fistula AE 10065786 CTCAE: E13399 a fistula AE that has an abnormal communication between the larynx and another organ or anatomic site. MW, YH NCIt: C78410 laryngeal hemorrhage AE 10065759 MW, YH CTCAE: E13405 NCIt: C78411 a hemorrhage AE that has bleeding from the larynx. laryngeal mucositis AE 10065880 an inflammation AE that has an inflammation involving the mucous membrane of the larynx. NCIt: C78412 CTCAE: E13415 MW, YH laryngeal obstruction AE 10059639 NCIt: C78413 a respiratory system AE that has blockage of the laryngeal airway. MW, YH CTCAE: E13421 libido decreased AE 10024419 CTCAE: E12929 a libido disorder AE that has a decrease in sexual desire. MW, YH NCIt: C78432 libido increased AE 10024421 CTCAE: E12932 a libido disorder AE that has an increase in sexual desire. MW, YH NCIt: C78433 lipohypertrophy AE 10062315 a skin AE that has hypertrophy of the subcutaneous adipose tissue at the site of multiple subcutaneous injections of insulin. NCIt: C78436 CTCAE: E13657 MW, YH lymph leakage AE 10065773 CTCAE: E13797 MW, YH an immune system AE that has the loss of lymph fluid into the surrounding tissue or body cavity. NCIt: C78439 lymphocele AE 10048642 CTCAE: E13806 an immune system AE that has a cystic lesion containing lymph. MW, YH NCIt: C78442 mediastinal hemorrhage AE 10056356 CTCAE: E13444 NCIt: C78443 MW, YH a hemorrhage AE that has bleeding from the mediastinum. movements involuntary AE 10028041 MW, YH CTCAE: E12728 a movement disorder AE that has uncontrolled and purposeless movements. NCIt: C78453 muscle weakness left-sided AE 10065780 a muscular weakness AE that has a reduction in the strength of the muscles on the left side of the body. CTCAE: E12455 NCIt: C78455 MW, YH muscle weakness lower limb AE 10065776 MW, YH CTCAE: E12459 NCIt: C78456 a muscular weakness AE that has a reduction in the strength of the lower limb muscles. muscle weakness right-sided AE 10065794 CTCAE: E12463 MW, YH NCIt: C78457 a muscular weakness AE that has a reduction in the strength of the muscles on the right side of the body. muscle weakness trunk AE 10065795 a muscular weakness AE that has a reduction in the strength of the trunk muscles. MW, YH NCIt: C78458 CTCAE: E12467 muscle weakness upper limb AE 10065895 CTCAE: E12471 MW, YH NCIt: C78459 a muscular weakness AE that has a reduction in the strength of the upper limb muscles. musculoskeletal deformity AE 10065783 MW, YH NCIt: C78488 a musculoskeletal and connective tissue AE that has a malformation of the musculoskeletal system. CTCAE: E12481 nail discoloration AE 10028691 NCIt: C78492 CTCAE: E13661 MW, YH a nail AE that has a change in the color of the nail plate. nail loss AE 10049281 NCIt: C78494 MW, YH a nail AE that has loss of all or a portion of the nail. CTCAE: E13663 nail ridging AE 10062283 a nail AE that has vertical or horizontal ridges on the nails. CTCAE: E13666 NCIt: C78499 MW, YH neck soft tissue necrosis AE 10065781 CTCAE: E12497 a necrosis AE that has a necrotic process occurring in the soft tissues of the neck. NCIt: C78502 MW, YH nipple deformity AE 10065823 MW, YH CTCAE: E13138 a female reproductive system AE that has a malformation of the nipple. NCIt: C78503 ovarian hemorrhage AE 10065763 a hemorrhage AE that has bleeding from the ovary. NCIt: C78511 MW, YH CTCAE: E13145 ovarian rupture AE 10033279 MW, YH a female reproductive system AE that is tearing or disruption of the ovarian tissue. NCIt: C78513 CTCAE: E13151 ovulation pain AE 10033314 a pain AE that has marked discomfort sensation in one side of the abdomen between menstrual cycles, around the time of the discharge of the ovum from the ovarian follicle. MW, YH CTCAE: E13157 NCIt: C78514 pelvic floor muscle weakness AE 10064026 MW, YH a muscular weakness AE that has a reduction in the strength of the muscles of the pelvic floor. NCIt: C78524 CTCAE: E13161 pelvic soft tissue necrosis AE 10065793 CTCAE: E12516 MW, YH a necrosis AE that has a necrotic process occurring in the soft tissues of the pelvis. NCIt: C78525 penile pain AE 10034310 MW, YH NCIt: C78527 CTCAE: E13171 a pain AE that has marked discomfort sensation in the penis. personality change AE 10034719 NCIt: C78548 CTCAE: E12942 a psychiatric disorder AE that has a conspicuous change in a person's behavior and thinking. MW, YH pharyngeal fistula AE 10034825 NCIt: C78551 MW, YH CTCAE: E13454 a fistula AE that has an abnormal communication between the pharynx and another organ or anatomic site. pharyngeal mucositis AE 10065881 an inflammation AE that has an inflammation involving the mucous membrane of the pharynx. CTCAE: E13466 NCIt: C78553 MW, YH pharyngeal necrosis AE 10065706 CTCAE: E13472 a necrosis AE that has a necrotic process occurring in the pharynx. MW, YH NCIt: C78554 pharyngeal stenosis AE 10050028 NCIt: C78555 MW, YH CTCAE: E13476 a respiratory system AE that has a narrowing of the pharyngeal airway. prostatic hemorrhage AE 10055325 NCIt: C78572 CTCAE: E13181 MW, YH a hemorrhage AE that has bleeding from the prostate gland. prostatic obstruction AE 10055026 MW, YH a prostatic disorder AE that has compression of the urethra secondary to enlargement of the prostate gland. This results in voiding difficulties (straining to void, slow urine stream, and incomplete emptying of the bladder). CTCAE: E13187 NCIt: C78573 prostatic pain AE 10036968 a pain AE that has a sensation of marked discomfort in the prostate gland. NCIt: C78574 CTCAE: E13191 MW, YH psychosis AE 10037234 MW, YH NCIt: C78576 a psychiatric disorder AE that has personality change, impaired functioning, and loss of touch with reality. It may be a manifestation of schizophrenia, bipolar disorder or brain tumor. CTCAE: E12954 pulmonary fistula AE 10065873 a fistula AE that has an abnormal communication between the lung and another organ or anatomic site. CTCAE: E13533 MW, YH NCIt: C78577 radiculitis AE 10061928 MW, YH an inflammation AE that has inflammation involving a nerve root. Patients experience marked discomfort radiating along a nerve path because of spinal pressure on the connecting nerve root. NCIt: C78581 CTCAE: E12786 recurrent laryngeal nerve palsy AE 10038130 NCIt: C78592 CTCAE: E12792 MW, YH a recurrent alsy AE that occurs at the laryngeal nerve. renal colic AE 10038419 NCIt: C78593 CTCAE: E13024 a renal calculus AE that has paroxysmal and severe flank marked discomfort radiating to the inguinal area. Often, the cause is the passage of kidney stones. MW, YH renal hemorrhage AE 10038463 MW, YH a hemorrhage AE that has bleeding from the kidney. CTCAE: E13028 NCIt: C78594 retinoic acid syndrome AE 10038921 NCIt: C78597 MW, YH CTCAE: E13554 a syndrome AE that has weight gain, dyspnea, pleural and pericardial effusions, leukocytosis and/or renal failure originally described in patients treated with all-trans retinoic acid. scoliosis AE 10039722 CTCAE: E12521 NCIt: C78603 a bone disorder AE that has a malformed, lateral curvature of the spine. MW, YH scrotal pain AE 10039757 NCIt: C78607 a pain AE that has marked discomfort sensation in the scrotal area. MW, YH CTCAE: E13201 sinus pain AE 10040747 CTCAE: E12810 a pain AE that has marked discomfort in the face, between the eyes, or upper teeth originating from the sinuses. NCIt: C78609 MW, YH skin induration AE 10051837 CTCAE: E13724 MW, YH an induration AE that has an area of hardness in the skin. NCIt: C78611 soft tissue necrosis lower limb AE 10065777 NCIt: C78620 CTCAE: E12525 MW, YH a necrosis AE that has a necrotic process occurring in the soft tissues of the lower extremity. soft tissue necrosis upper limb AE 10065778 MW, YH a necrosis AE that has a necrotic process occurring in the soft tissues of the upper extremity. CTCAE: E12530 NCIt: C78621 spermatic cord hemorrhage AE 10065762 NCIt: C78623 MW, YH a hemorrhage AE that has bleeding from the spermatic cord. CTCAE: E13205 spermatic cord obstruction AE 10065805 NCIt: C78624 MW, YH a male reproductive system AE that has blockage of the normal flow of the contents of the spermatic cord. CTCAE: E13211 superficial soft tissue fibrosis AE 10065798 a connective tissue disorder AE that has fibrotic degeneration of the superficial soft tissues. NCIt: C78633 MW, YH CTCAE: E12535 testicular hemorrhage AE 10055347 MW, YH NCIt: C78635 a hemorrhage AE that has bleeding from the testis. CTCAE: E13221 testicular pain AE 10043345 MW, YH a pain AE that has a sensation of marked discomfort in the testis. CTCAE: E13227 NCIt: C78636 tracheal fistula AE 10065787 MW, YH a fistula AE that hasan abnormal communication between the trachea and another organ or anatomic site. CTCAE: E13583 NCIt: C78641 tracheal mucositis AE 10065900 an inflammation AE that has an inflammation involving the mucous membrane of the trachea. MW, YH NCIt: C78644 CTCAE: E13589 tracheal stenosis AE 10050816 NCIt: C78646 CTCAE: E13595 a respiratory system AE that has a narrowing of the trachea. MW, YH tumor pain AE 10045158 a pain AE that has marked discomfort from a neoplasm that may be pressing on a nerve, blocking blood vessels, inflamed or fractured from metastasis. MW, YH CTCAE: E12565 NCIt: C78656 unequal limb length AE 10065738 NCIt: C78657 a musculoskeletal and connective tissue AE that hasa discrepancy between the lengths of the lower or upper extremities. MW, YH CTCAE: E12545 urine discoloration AE 10046628 MW, YH an urine abnormality AE that has a change in the color of the urine. CTCAE: E13065 NCIt: C78678 uterine fistula AE 10065811 a fistula AE that has an abnormal communication between the uterus and another organ or anatomic site. NCIt: C78685 CTCAE: E13231 MW, YH uterine obstruction AE 10065928 MW, YH an urinary system AE that has blockage of the uterine outlet. CTCAE: E13243 NCIt: C78693 uterine pain AE 10046809 NCIt: C78694 MW, YH a pain AE that has a sensation of marked discomfort in the uterus. CTCAE: E13247 vaginal dryness AE 10046904 MW, YH NCIt: C78699 a female reproductive system AE that has an uncomfortable feeling of itching and burning in the vagina. CTCAE: E13254 vaginal obstruction AE 10065817 CTCAE: E13276 NCIt: C78700 a female reproductive system AE that has blockage of vaginal canal. MW, YH vaginal pain AE 10046937 MW, YH CTCAE: E13280 a pain AE that has a sensation of marked discomfort in the vagina. NCIt: C78701 vaginal perforation AE 10065818 CTCAE: E13284 NCIt: C78702 a female reproductive system AE that has a rupture in the vaginal wall. MW, YH vaginismus AE 10046947 CTCAE: E13295 NCIt: C78703 a female reproductive system AE that hasinvoluntary spasms of the pelvic floor muscles, resulting in pathologic tightness of the vaginal wall during penetration such as during sexual intercourse. MW, YH visceral arterial ischemia AE 10054692 NCIt: C78712 an ischemia AE that has a decrease in blood supply due to narrowing or blockage of a visceral (mesenteric) artery. MW, YH CTCAE: E13843 body odor AE 10005901 a skin AE that has an abnormal body smell resulting from the growth of bacteria on the body. MW, YH CTCAE: E13614 NCIt: C79542 bronchial fistula AE 10006437 NCIt: C79543 MW, YH a fistula AE that has an abnormal communication between the bronchus and another organ or anatomic site. CTCAE: E13322 extrapyramidal disorder AE 10015832 NCIt: C79593 CTCAE: E12658 MW, YH a nervous system AE that has an abnormal, repetitive, involuntary muscle movements, frenzied speech and extreme restlessness. hypertrichosis AE 10020864 MW, YH CTCAE: E13649 a hair growth abnormal AE that has hair density or length beyond the accepted limits of normal in a particular body region, for a particular age or race. NCIt: C79597 lactation disorder AE 10061261 NCIt: C79606 a female reproductive system AE that has disturbances of milk secretion. It is not necessarily related to pregnancy that is observed in females and can be observed in males. CTCAE: E13129 MW, YH laryngeal stenosis AE 10023862 MW, YH CTCAE: E13427 a respiratory system AE that has a narrowing of the laryngeal airway. NCIt: C79608 meningismus AE 10027198 MW, YH CTCAE: E12722 a nervous system AE that has neck stiffness, headache, and photophobia resulting from irritation of the cerebral meninges. NCIt: C79694 phantom pain AE 10056238 MW, YH CTCAE: E12774 a pain AE that has marked discomfort related to a limb or an organ that is removed from or is not physically part of the body. NCIt: C79703 scalp pain AE 10049120 NCIt: C79716 a pain AE that has marked discomfort sensation in the skin covering the top and the back of the head. CTCAE: E13704 MW, YH unintended pregnancy AE 10045542 CTCAE: E12872 a pregnancy AE that has an unexpected pregnancy at the time of conception. NCIt: C79801 MW, YH urinary tract obstruction AE 10061574 MW, YH CTCAE: E13052 an urinary system AE that has blockage of the normal flow of contents of the urinary tract. NCIt: C79805 vaginal fistula AE 10065813 CTCAE: E13258 NCIt: C79847 a fistula AE that has an abnormal communication between the vagina and another organ or anatomic site. MW, YH urinary fistula AE 10065368 MW, YH NCIt: C79850 CTCAE: E13034 a fistula AE that has an abnormal communication between any part of the urinary system and another organ or anatomic site. azoospermia AE 10003883 a male reproductive system AE that has laboratory test results that indicate complete absence of spermatozoa in the semen. CTCAE: E13067 MW, YH NCIt: C80076 chronic kidney disease AE 10064848 MW, YH CTCAE: E12988 a renal failure AE that has gradual and usually permanent loss of kidney function resulting in renal failure. NCIt: C80078 concentration impairment AE 10010250 NCIt: C80081 MW, YH a behavior and neurological AE that has a deterioration in the ability to concentrate. CTCAE: E12621 fetal growth retardation AE 10054746 MW, YH NCIt: C80083 a fetal disorder AE that has inhibition of fetal growth resulting in the inability of the fetus to achieve its potential weight. CTCAE: E12857 premature menopause AE 10036601 MW, YH a menstrual disorder AE that has ovarian failure before the age of 40. Symptoms include hot flashes, night sweats, mood swings and a decrease in sex drive. NCIt: C80099 CTCAE: E13179 leukemia secondary to oncology chemotherapy AE 10048293 NCIt: C80691 a tumor AE that has leukemia arising as a result of the mutagenic effect of chemotherapy agents. CTCAE: E12549 MW, YH bronchopleural fistula AE 10053481 MW, YH NCIt: C80694 CTCAE: E13340 a fistula AE that has an abnormal communication between a bronchus and the pleural cavity. urinary tract pain AE 10062225 CTCAE: E13058 NCIt: C83493 a pain AE that has a sensation of marked discomfort in the urinary tract. MW, YH breast atrophy AE 10006179 MW, YH a female reproductive system AE that has underdevelopment of the breast. NCIt: C83494 CTCAE: E13069 medical procedure YH, SS a medical intervention that refers to any series of pre-defined steps that should be followed to achieve a desired result. WEB: http://www.wisegeekhealth.com/what-is-the-difference-between-a-surgery-and-a-procedure.htm Grade 1 lymphedema AE CTCAE: E13803 a hymphedema AE that has trace thickening or faint discoloration YH, MW Grade 2 lymphedema AE YH, MW CTCAE: E13804 a hymphedema AE that has marked discoloration; leathery skin texture; papillary formation; limiting instrumental ADL Grade 1 superior vena cava syndrome AE CTCAE: E13820 a superior vena cava syndrome AE that has asymptomatic; incidental finding of SVC thrombosis YH, MW Grade 2 superior vena cava syndrome AE a superior vena cava syndrome AEthat has symptomatic; medical intervention indicated (e.g., anticoagulation, radiation or chemotherapy) CTCAE: E13821 YH, MW Grade 3 superior vena cava syndrome AE a superior vena cava syndrome AE that has severe symptoms; multi-modality intervention indicated (e.g., anticoagulation, chemotherapy, radiation, stenting) YH, MW CTCAE: E13822 Grade 4 superior vena cava syndrome AE a superior vena cava syndrome AE that has life-threatening consequences; urgent multi-modality intervention indicated (e.g., lysis, thrombectomy, surgery) CTCAE: E13823 YH, MW Grade 1 thromboembolic event AE a thromboembolic event AE that has venous thrombosis (e.g., superficial thrombosis) YH, MW CTCAE: E13826 Grade 2 thromboembolic event AE a thromboembolic event AE that has venous thrombosis (e.g., uncomplicated deep vein thrombosis), medical intervention indicated YH, MW CTCAE: E13827 Grade 3 thromboembolic event AE YH, MW CTCAE: E13828 a thromboembolic event AE that has thrombosis (e.g., uncomplicated pulmonary embolism [venous], non-embolic cardiac mural [arterial] thrombus), medical intervention indicated Grade 4 thromboembolic event AE a thromboembolic event AE that has life-threatening (e.g., pulmonary embolism, cerebrovascular event, arterial insufficiency); hemodynamic or neurologic instability; urgent intervention indicated CTCAE: E13829 YH, MW Grade 2 visceral arterial ischemia AE a visceral arterial ischemia AE that has brief (<24 hrs) episode of ischemia managed medically and without permanent deficit YH, MW CTCAE: E13844 Grade 3 visceral arterial ischemia AE CTCAE: E13845 a visceral arterial ischemia AE that has prolonged (>=24 hrs) or recurring symptoms and/or invasive intervention indicated YH, MW Grade 1 menopause AE YH, MW a menopause AE that the menopause occurres at age 46 - 53 years of age CTCAE: E13751 Grade 2 menopause AE a menopause AE that the menopause occurres at age 40 - 45 years of age CTCAE: E13752 YH, MW Grade 3 menopause AE CTCAE: E13753 a menopause AE that the menopause occurres before age 40 years of age YH, MW Grade 1 body odor AE a body odor AE that has mild odor; physician intervention not indicated; self care interventions YH, MW CTCAE: E13615 Grade 2 body odor AE CTCAE: E13616 YH, MW a body odor AE that has pronounced odor; psychosocial impact; patient seeks medical intervention Grade 1 bullous dermatitis AE YH, MW CTCAE: E13618 a bullous AE that has asymptomatic; blisters covering <10% BSA Grade 2 bullous dermatitis AE YH, MW a bullous AE that has blisters covering 10 - 30% BSA; painful blisters; limiting instrumental ADL CTCAE: E13619 Grade 3 bullous dermatitis AE YH, MW a bullous AE that has blisters covering >30% BSA; limiting self care ADL CTCAE: E13620 Grade 4 bullous dermatitis AE CTCAE: E13621 YH, MW a bullous AE that has blisters covering >30% BSA; associated with fluid or electrolyte abnormalities; ICU care or burn unit indicated Grade 2 erythroderma AE YH, MW an erythroderma AE that has erythema covering >90% BSA without associated symptoms; limiting instrumental ADL CTCAE: E13634 Grade 3 erythroderma AE an erythroderma AE that has erythema covering >90% BSA with associated symptoms (e.g., pruritus or tenderness); limiting self care ADL CTCAE: E13635 YH, MW Grade 4 erythroderma AE YH, MW an erythroderma AE that has erythema covering >90% BSA with associated fluid or electrolyte abnormalities; ICU care or burn unit indicated CTCAE: E13636 Grade 1 fat atrophy AE a fat atrophy AE that is covering <10% BSA and asymptomatic YH, MW CTCAE: E13639 Grade 2 fat atrophy AE a fat atrophy AE that is covering 10 - 30% BSA and associated with erythema or tenderness; limiting instrumental ADL CTCAE: E13640 YH, MW Grade 3 fat atrophy AE CTCAE: E13641 a fat atrophy AE that is covering >30% BSA; associated with erythema or tenderness; limiting self-care ADL YH, MW Grade 1 hirsutism AE a hirsutism AE that is In women, increase in length, thickness or density of hair in a male distribution that the patient is able to camouflage by periodic shaving, bleaching, or removal of hair YH, MW CTCAE: E13643 Grade 2 hirsutism AE a hirsutism AE that In women, increase in length, thickness or density of hair in a male distribution that requires daily shaving or consistent destructive means of hair removal to camouflage; associated with psychosocial impact YH, MW CTCAE: E13644 Grade 1 hypertrichosis AE a hypertrichosis AE that has increased in length, thickness or density of hair. The patient is either able to camouflage by periodic shaving or removal of hairs or is not concerned enough about the overgrowth to use any form of hair removal YH, MW CTCAE: E13650 Grade 2 hypertrichosis AE CTCAE: E13651 YH, MW a hypertrichosis AE that has increased in length, thickness or density of hair at least on the usual exposed areas of the body [face (not limited to beard/moustache area) plus/minus arms] that requires frequent shaving or use of destructive means of hair removal to camouflage; associated with psychosocial impact Grade 3 hypohidrosis AE a hypertrichosis AE that has increased in body temperature; limiting self care ADL CTCAE: E13654 YH, MW Grade 4 hypohidrosis AE YH, MW a hypertrichosis AE that has heat stroke CTCAE: E13655 Grade 1 lipohypertrophy AE a lipohypertrophy AE that has asymptomatic and covering <10% BSA CTCAE: E13658 YH, MW Grade 2 lipohypertrophy AE YH, MW CTCAE: E13659 a lipohypertrophy AE that covers 10 - 30% BSA and associated tenderness; limiting instrumental ADL Grade 3 lipohypertrophy AE YH, MW a lipohypertrophy AE that covers >30% BSA and associated tenderness and narcotics or NSAIDs indicated; lipohypertrophy; limiting self care ADL CTCAE: E13660 Grade 1 nail loss AE a nail loss AE that has asymptomatic separation of the nail bed from the nail plate or nail loss CTCAE: E13664 YH, MW Grade 2 nail loss AE YH, MW CTCAE: E13665 a nail loss AE that has symptomatic separation of the nail bed from the nail plate or nail loss; limiting instrumental ADL Grade 1 rash acneiform AE CTCAE: E13695 a rash acneiform AE that has papules and/or pustules covering <10% BSA, which may or may not be associated with symptoms of pruritus or tenderness YH, MW Grade 2 rash acneiform AE YH, MW CTCAE: E13696 a rash acneiform AE that has papules and/or pustules covering 10 - 30% BSA, which may or may not be associated with symptoms of pruritus or tenderness; associated with psychosocial impact; limiting instrumental ADL Grade 3 rash acneiform AE a rash acneiform AE that has papules and/or pustules covering >30% BSA, which may or may not be associated with symptoms of pruritus or tenderness; limiting self care ADL; associated with local superinfection with oral antibiotics indicated YH, MW CTCAE: E13697 Grade 4 rash acneiform AE CTCAE: E13698 a rash acneiform AE that has papules and/or pustules covering any % BSA, which may or may not be associated with symptoms of pruritus or tenderness and are associated with extensive superinfection with IV antibiotics indicated; life-threatening consequences YH, MW Grade 1 rash maculo-papular AE CTCAE: E13701 YH, MW a rash maculopapular AE that has macules/papules covering <10% BSA with or without symptoms (e.g., pruritus, burning, tightness) Grade 2 rash maculo-papular AE YH, MW a rash maculopapular AE that has macules/papules covering 10 - 30% BSA with or without symptoms (e.g., pruritus, burning, tightness); limiting instrumental ADL CTCAE: E13702 Grade 3 rash maculo-papular AE CTCAE: E13703 a rash maculopapular AE that has macules/papules covering >30% BSA with or without associated symptoms; limiting self care ADL YH, MW Grade 1 skin induration AE YH, MW a skin induration AE that has mild induration, able to move skin parallel to plane (sliding) and perpendicular to skin (pinching up) CTCAE: E13725 Grade 2 skin induration AE YH, MW CTCAE: E13726 a skin induration AE that has moderate induration, able to slide skin, unable to pinch skin; limiting instrumental ADL Grade 3 skin induration AE CTCAE: E13727 YH, MW a skin induration AE that has severe induration, unable to slide or pinch skin; limiting joint movement or orifice (e.g., mouth, anus); limiting self care ADL Grade 4 skin induration AE a skin induration AE that has generalized; associated with signs or symptoms of impaired breathing or feeding YH, MW CTCAE: E13728 Grade 2 bronchial fistula AE CTCAE: E13324 a bronchial fistula AE that has symptomatic; tube thoracostomy or medical management indicated; limiting instrumental ADL YH, MW Grade 3 bronchial fistula AE YH, MW CTCAE: E13325 a bronchial fistula AE that has severe symptoms; limiting self care ADL; endoscopic or operative intervention indicated (e.g., stent or primary closure) Grade 4 bronchial fistula AE YH, MW a bronchial fistula AE that has life-threatening consequences; urgent operative intervention with thoracoplasty, chronic open drainage or multiple thoracotomies indicated CTCAE: E13326 Grade 2 bronchial obstruction AE CTCAE: E13330 YH, MW a bronchial obstruction AE that has symptomatic (e.g., mild wheezing); endoscopic evaluation indicated; radiographic evidence of atelectasis/lobar collapse; medical management indicated (e.g., steroids, bronchodilators) Grade 3 bronchial obstruction AE a bronchial obstruction AE that has shortness of breath with stridor; endoscopic intervention indicated (e.g., laser, stent placement) CTCAE: E13331 YH, MW Grade 2 bronchial stricture AE YH, MW CTCAE: E13336 a bronchial stricture AE that AE symptomatic (e.g., rhonchi or wheezing) but without respiratory distress; medical intervention indicated (e.g., steroids, bronchodilators) Grade 3 bronchial stricture AE CTCAE: E13337 a bronchial stricture AE that AE shortness of breath with stridor; endoscopic intervention indicated (e.g., laser, stent placement) YH, MW Grade 3 bronchopleural fistula AE YH, MW CTCAE: E13343 a bronchopleural fistula AE that has severe symptoms; limiting self care ADL; endoscopic or operative intervention indicated (e.g., stent or primary closure) Grade 4 bronchopleural fistula AE CTCAE: E13344 a bronchopleural fistula AE that has life-threatening consequences; urgent operative intervention with thoracoplasty, chronic open drainage or multiple thoracotomies indicated YH, MW Grade 2 laryngeal fistula AE a laryngeal fistula AE that has symptomatic; tube thoracostomy or medical management indicated; limiting instrumental ADL YH, MW CTCAE: E13401 Grade 3 laryngeal fistula AE a laryngeal fistula AE that has severe symptoms; limiting self care ADL; endoscopic or operative intervention indicated (e.g., stent or primary closure) YH, MW CTCAE: E13402 Grade 4 laryngeal fistula AE YH, MW a laryngeal fistula AE that has life-threatening consequences; urgent operative intervention indicated (e.g., thoracoplasty, chronic open drainage or multiple thoracotomies) CTCAE: E13403 Grade 1 laryngeal hemorrhage AE a laryngeal hemorrhage AE that has mild cough or trace hemoptysis; laryngoscopic findings YH, MW CTCAE: E13406 Grade 1 laryngeal inflammation AE a laryngeal inflammation AE that has mild sore throat; raspy voice YH, MW CTCAE: E13412 Grade 2 laryngeal inflammation AE YH, MW a laryngeal inflammation AE that has moderate sore throat; analgesics indicated CTCAE: E13413 Grade 3 laryngeal inflammation AE CTCAE: E13414 a laryngeal inflammation AE that has severe throat pain; endoscopic intervention indicated YH, MW Grade 1 laryngeal mucositis AE YH, MW a laryngeal mucositis AE that has endoscopic findings only; mild discomfort with normal intake CTCAE: E13416 Grade 2 laryngeal mucositis AE CTCAE: E13417 a laryngeal mucositis AE that has moderate discomfort; altered oral intake YH, MW Grade 3 laryngeal mucositis AE CTCAE: E13418 YH, MW a laryngeal mucositis AE that has severe pain; severely altered eating/swallowing; medical intervention indicated Grade 4 laryngeal mucositis AE CTCAE: E13419 YH, MW a laryngeal mucositis AE that has life-threatening airway compromise; urgent intervention indicated (e.g., tracheotomy or intubation) Grade 2 laryngeal obstruction AE a laryngeal obstruction AE that has symptomatic (e.g., noisy airway breathing), but causing no respiratory distress; medical management indicated (e.g., steroids); limiting instrumental ADL YH, MW CTCAE: E13423 Grade 3 laryngeal obstruction AE a laryngeal obstruction AE that has limiting self care ADL; stridor; endoscopic intervention indicated (e.g., stent, laser) CTCAE: E13424 YH, MW Grade 2 laryngeal stenosis AE CTCAE: E13429 YH, MW a laryngeal stenosis AE that has symptomatic (e.g., noisy airway breathing), but causing no respiratory distress; medical management indicated (e.g., steroids) Grade 3 laryngeal stenosis AE CTCAE: E13430 YH, MW a laryngeal stenosis AE that has limiting self care ADL; stridor; endoscopic intervention indicated (e.g., stent, laser) Grade 2 laryngopharyngeal dysesthesia AE a laryngopharyngeal dysesthesia AE that has moderate symptoms; mild anxiety, but no dyspnea; short duration of observation and or anxiolytic indicated; limiting instrumental ADL YH, MW CTCAE: E13435 Grade 3 laryngopharyngeal dysesthesia AE YH, MW a laryngopharyngeal dysesthesia AE that has severe symptoms; dyspnea and swallowing difficulty; limiting self care ADL CTCAE: E13436 Grade 2 laryngospasm AE YH, MW CTCAE: E13440 a laryngospasm AE that has transient episode; intervention not indicated Grade 3 laryngospasm AE CTCAE: E13441 a laryngospasm AE that has recurrent episodes; noninvasive intervention indicated (e.g., breathing technique, pressure point massage) YH, MW Grade 4 laryngospasm AE a laryngospasm AE that has persistent or severe episodes associated with syncope; urgent intervention indicated (e.g., fiberoptic laryngoscopy, intubation, botox injection) CTCAE: E13442 YH, MW Grade 2 pharyngeal fistula AE YH, MW CTCAE: E13456 a pharyngeal fistula AE that has symptomatic; tube thoracostomy or medical intervention indicated; limiting instrumental ADL Grade 3 pharyngeal fistula AE CTCAE: E13457 a pharyngeal fistula AE that has severe symptoms; limiting self care ADL; endoscopic or operative intervention indicated (e.g., stent or primary closure) YH, MW Grade 1 pharyngeal mucositis AE a pharyngeal mucositis AE that has endoscopic findings only; minimal symptoms with normal oral intake; mild pain but analgesics not indicated CTCAE: E13467 YH, MW Grade 2 pharyngeal mucositis AE a pharyngeal mucositis AE that has moderate pain and analgesics indicated; altered oral intake; limiting instrumental ADL CTCAE: E13468 YH, MW Grade 3 pharyngeal mucositis AE CTCAE: E13469 a pharyngeal mucositis AE that has severe pain; unable to adequately aliment or hydrate orally; limiting self care ADL YH, MW Grade 3 pharyngeal necrosis AE CTCAE: E13473 YH, MW a pharyngeal necrosis AE that has inability to aliment adequately by GI tract; tube feeding or TPN indicated; radiologic, endoscopic, or operative intervention indicated Grade 2 pharyngeal stenosis AE CTCAE: E13478 YH, MW a pharyngeal stenosis AE that has symptomatic (e.g., noisy airway breathing), but causing no respiratory distress; medical management indicated (e.g., steroids); limiting instrumental ADL Grade 3 pharyngeal stenosis AE YH, MW a pharyngeal stenosis AE that has limiting self care ADL; stridor; endoscopic intervention indicated (e.g., stent, laser) CTCAE: E13479 Grade 4 pharyngeal stenosis AE a pharyngeal stenosis AE that has life-threatening airway compromise; urgent intervention indicated (e.g., tracheotomy or intubation) YH, MW CTCAE: E13480 Grade 2 pulmonary fistula AE CTCAE: E13535 a pulmonary fistula AE that has symptomatic; tube thoracostomy or medical management indicated; limiting instrumental ADL YH, MW Grade 3 pulmonary fistula AE a pulmonary fistula AE that has limiting self care ADL; endoscopic stenting or operative intervention indicated CTCAE: E13536 YH, MW Grade 1 retinoic acid syndrome AE a retinoic acid syndrome AE that has fluid retention; <3 kg of weight gain; intervention with fluid restriction and/or diuretics indicated YH, MW CTCAE: E13555 Grade 1 sleep apnea AE a sleep apnea AE that has snoring and nocturnal sleep arousal without apneic periods CTCAE: E13567 YH, MW Grade 2 sleep apnea AE YH, MW a sleep apnea AE that has moderate apnea and oxygen desaturation; excessive daytime sleepiness; medical evaluation indicated; limiting instrumental ADL CTCAE: E13568 Grade 3 sleep apnea AE YH, MW CTCAE: E13569 a sleep apnea AE that has oxygen desaturation; associated with hypertension; medical intervention indicated; limiting self care ADL Grade 4 sleep apnea AE a sleep apnea AE that has cardiovascular or neuropsychiatric symptoms; urgent operative intervention indicated CTCAE: E13570 YH, MW Grade 2 tracheal fistula AE CTCAE: E13585 YH, MW a tracheal fistula AE that has symptomatic; tube thoracostomy or medical intervention indicated; limiting instrumental ADL Grade 3 tracheal fistula AE a tracheal fistula AE that has severe symptoms; limiting self care ADL; endoscopic or operative intervention indicated (e.g., stent or primary closure) YH, MW CTCAE: E13586 Grade 4 tracheal fistula AE YH, MW CTCAE: E13587 a tracheal fistula AE that has life-threatening consequences; urgent operative intervention indicated (e.g., thoracoplasty, chronic open drainage or multiple thoracotomies) Grade 1 tracheal mucositis AE CTCAE: E13590 YH, MW a tracheal mucositis AE that has endoscopic findings only; minimal hemoptysis, pain, or respiratory symptoms Grade 3 tracheal mucositis AE YH, MW a tracheal mucositis AE that has severe pain; hemorrhage or respiratory symptoms; limiting self care ADL CTCAE: E13592 Grade 2 tracheal stenosis AE CTCAE: E13597 YH, MW a tracheal stenosis AE that has symptomatic (e.g., noisy airway breathing), but causing no respiratory distress; medical management indicated (e.g., steroids) Grade 3 tracheal stenosis AE YH, MW CTCAE: E13598 a tracheal stenosis AE that has stridor or respiratory distress limiting self care ADL; endoscopic intervention indicated (e.g., stent, laser) Grade 4 tracheal stenosis AE CTCAE: E13599 a tracheal stenosis AE that has life-threatening airway compromise; urgent intervention indicated (e.g., tracheotomy or intubation) YH, MW Grade 3 azoospermia AE an azoospermia AE that has absence of sperm in ejaculate CTCAE: E13068 YH, MW Grade 3 breast atrophy AE A breast atrophy AE that has asymmetry >1/3 of breast volume; severe atrophy YH, MW CTCAE: E13072 Grade 1 ejaculation disorder AE an ejaculation disorder AE that has diminished ejaculation CTCAE: E13086 YH, MW Grade 2 ejaculation disorder AE YH, MW CTCAE: E13087 an ejaculation disorder AE that has anejaculation or retrograde ejaculation Grade 1 genital edema AE CTCAE: E13112 a genital edema AE that has mild swelling or obscuration of anatomic architecture on close inspection YH, MW Grade 2 genital edema AE YH, MW CTCAE: E13113 a genital edema AE that has readily apparent obscuration of anatomic architecture; obliteration of skin folds; readily apparent deviation from normal anatomic contour Grade 3 genital edema AE CTCAE: E13114 a genital edema AE that has lymphorrhea; gross deviation from normal anatomic contour; limiting self care ADL YH, MW Grade 1 gynecomastia AE YH, MW CTCAE: E13116 a gynecomastia AE that has asymptomatic breast enlargement Grade 2 gynecomastia AE CTCAE: E13117 a gynecomastia AE that has symptomatic (e.g., pain or psychosocial impact) YH, MW Grade 1 hematosalpinx AE CTCAE: E13120 YH, MW a hematosalpinx AE that has minimal bleeding identified on imaging study or laparoscopy; intervention not indicated Grade 1 irregular menstruation AE CTCAE: E13126 YH, MW an irregular menstruation AE that has intermittent menses with skipped menses for no more than 1 to 3 months Grade 2 irregular menstruation AE an irregular menstruation AE that has intermittent menses with skipped menses for more than 4 to 6 months YH, MW CTCAE: E13127 Grade 3 irregular menstruation AE YH, MW an irregular menstruation AE that has persistent amenorrhea for more than 6 months CTCAE: E13128 Grade 1 lactation disorder AE CTCAE: E13130 YH, MW a lactation disorder AE that has mild changes in lactation, not significantly affecting production or expression of breast milk Grade 2 lactation disorder AE YH, MW CTCAE: E13131 a lactation disorder AE that has changes in lactation, significantly affecting breast production or expression of breast milk Grade 1 nipple deformity AE CTCAE: E13139 a nipple deformity AE that has asymptomatic; asymmetry with slight retraction and/or thickening of the nipple areolar complex YH, MW Grade 2 nipple deformity AE CTCAE: E13140 a nipple deformity AE that has symptomatic; asymmetry of nipple areolar complex with moderate retraction and/or thickening of the nipple areolar complex YH, MW Grade 1 oligospermia AE CTCAE: E13142 YH, MW an oligospermia AE requires sperm concentration >48 million/mL or motility >68% Grade 2 oligospermia AE YH, MW CTCAE: E13143 an oligospermia AE requires sperm concentration 13 - 48 million/mL or motility 32 - 68% Grade 3 oligospermia AE CTCAE: E13144 an oligospermia AE requires sperm concentration <13 million/mL or motility <32% YH, MW Grade 2 testicular disorder AE CTCAE: E13217 YH, MW a testicular disorder AE that has symptomatic but not interfering with urination or sexual activities; intervention not indicated; limiting instrumental ADL Grade 3 testicular disorder AE a testicular disorder AE that has severe symptoms; interfering with urination or sexual function; limiting self care ADL; intervention indicated CTCAE: E13218 YH, MW Grade 1 vaginal discharge AE a vaginal discharge AE that has mild vaginal discharge (greater than baseline for patient) CTCAE: E13252 YH, MW Grade 2 vaginal discharge AE a vaginal discharge AE that has moderate to heavy vaginal discharge; use of perineal pad or tampon indicated YH, MW CTCAE: E13253 Grade 2 bladder spasm AE YH, MW CTCAE: E12986 a bladder spasm AE that has antispasmodics indicated Grade 3 bladder spasm AE YH, MW a bladder spasm AE that has hospitalization indicated CTCAE: E12987 Grade 1 chronic kidney disease AE CTCAE: E12989 a chronic kidney disease AE that requires eGFR (estimated Glomerular Filtration Rate) or CrCl (creatinine clearance) <LLN - 60 ml/min/1.73 m2 or proteinuria 2+ present; urine protein/creatinine >0.5 YH, MW Grade 2 chronic kidney disease AE YH, MW CTCAE: E12990 a chronic kidney disease AE that requires eGFR or CrCl 59 - 30 ml/min/1.73 m2 Grade 3 chronic kidney disease AE CTCAE: E12991 a chronic kidney disease AE that requires eGFR or CrCl 29 - 15 ml/min/1.73 m2 YH, MW Grade 4 chronic kidney disease AE YH, MW CTCAE: E12992 a chronic kidney disease AE that requires eGFR or CrCl <15 ml/min/1.73 m2; dialysis or renal transplant indicated Grade 1 cystitis noninfective AE a cystitis noninfective AE that has microscopic hematuria; minimal increase in frequency, urgency, dysuria, or nocturia; new onset of incontinence YH, MW CTCAE: E12995 Grade 2 cystitis noninfective AE a cystitis noninfective AE that has moderate hematuria; moderate increase in frequency, urgency, dysuria, nocturia or incontinence; urinary catheter placement or bladder irrigation indicated; limiting instrumental ADL CTCAE: E12996 YH, MW Grade 3 cystitis noninfective AE CTCAE: E12997 a cystitis noninfective AE that has gross hematuria; transfusion, IV medications or hospitalization indicated; elective endoscopic, radiologic or operative intervention indicated YH, MW Grade 1 proteinuria AE a proteinuria AE that requires 1+ proteinuria; urinary protein <1.0 g/24 hrs YH, MW CTCAE: E13009 Grade 2 proteinuria AE YH, MW CTCAE: E13010 a proteinuria AE that requires Grade 3 proteinuria AE CTCAE: E13011 a proteinuria AE that requires YH, MW Grade 1 renal calculi AE YH, MW CTCAE: E13019 a renal calculi AE that has asymptomatic or mild symptoms; occasional use of nonprescription analgesics indicated Grade 2 renal calculi AE a renal calculi AE that has symptomatic; oral antiemetics indicated; around the clock nonprescription analgesics or any oral narcotic analgesics indicated CTCAE: E13020 YH, MW Grade 3 renal calculi AE YH, MW a renal calculi AE that has hospitalization indicated; IV intervention (e.g., analgesics, antiemetics); elective endoscopic or radiologic intervention indicated CTCAE: E13021 Grade 2 urinary fistula AE CTCAE: E13035 YH, MW an urinary fistula AE that has noninvasive intervention indicated; urinary or suprapubic catheter placement indicated Grade 3 urinary fistula AE YH, MW CTCAE: E13036 an urinary fistula AE that has limiting self care ADL; elective radiologic, endoscopic or operative intervention indicated; permanent urinary diversion indicated Grade 2 urinary tract obstruction AE an urinary tract obstruction AE that has symptomatic but no hydronephrosis, sepsis or renal dysfunction; urethral dilation, urinary or suprapubic catheter indicated CTCAE: E13054 YH, MW Grade 3 urinary tract obstruction AE YH, MW an urinary tract obstruction AE that has symptomatic and altered organ function (e.g., hydronephrosis, or renal dysfunction); elective radiologic, endoscopic or operative intervention indicated CTCAE: E13055 Grade 1 mania AE CTCAE: E12937 YH, MW a mania AE that has mild manic symptoms (e.g., elevated mood, rapid thoughts, rapid speech, decreased need for sleep) Grade 2 mania AE CTCAE: E12938 YH, MW a mania AE that has moderate manic symptoms (e.g., relationship and work difficulties; poor hygiene) Grade 3 mania AE YH, MW a mania AE that has severe manic symptoms (e.g., hypomania; major sexual or financial indiscretions); hospitalization not indicated CTCAE: E12939 Grade 2 fetal growth retardation AE a fetal growth retardation AE that has <10% percentile of weight for gestational age YH, MW CTCAE: E12858 Grade 3 fetal growth retardation AE a fetal growth retardation AE that has <5% percentile of weight for gestational age CTCAE: E12859 YH, MW Grade 4 fetal growth retardation AE a fetal growth retardation AE that has <1% percentile of weight for gestational age CTCAE: E12860 YH, MW Grade 1 premature delivery AE CTCAE: E12868 YH, MW a premature delivery AE that has delivery of a liveborn infant at >34 to 37 weeks gestation Grade 2 premature delivery AE a premature delivery AE that has delivery of a liveborn infant at >28 to 34 weeks gestation CTCAE: E12869 YH, MW Grade 3 premature delivery AE YH, MW a premature delivery AE that has delivery of a liveborn infant at 24 to 28 weeks gestation CTCAE: E12870 Grade 4 premature delivery AE CTCAE: E12871 YH, MW a premature delivery AE that has delivery of a liveborn infant at 24 weeks of gestation or less Grade 1 spasticity AE a spasticity AE that has mild or slight increase in muscle tone CTCAE: E12821 YH, MW Grade 2 spasticity AE a spasticity AE that has moderate increase in muscle tone and increase in resistance through range of motion CTCAE: E12822 YH, MW Grade 3 spasticity AE a spasticity AE that has severe increase in muscle tone and increase in resistance through range of motion YH, MW CTCAE: E12823 Grade 4 spasticity AE YH, MW a spasticity AE that has life-threatening; unable to move active or passive range of motion CTCAE: E12824 Grade 3 treatment related secondary malignancy AE CTCAE: E12562 YH, MW a treatment related secondary malignancy AE that has non life-threatening secondary malignancy Grade 4 treatment related secondary malignancy AE a treatment related secondary malignancy AE that has acute life-threatening secondary malignancy; blast crisis in leukemia YH, MW CTCAE: E12563 Grade 2 abdominal soft tissue necrosis AE YH, MW an abdominal soft tissue necrosis AE that has local wound care; medical intervention indicated (e.g., dressings or topical medications) CTCAE: E12370 Grade 3 abdominal soft tissue necrosis AE CTCAE: E12371 an abdominal soft tissue necrosis AE that has operative debridement or other invasive intervention indicated (e.g. tissue reconstruction, flap or grafting) YH, MW Grade 1 fibrosis deep connective tissue AE YH, MW a fibrosis deep connective tissue AE that has mild induration, able to move skin parallel to plane (sliding) and perpendicular to skin (pinching up) CTCAE: E12409 Grade 2 fibrosis deep connective tissue AE a fibrosis deep connective tissue AE that has moderate induration, able to slide skin, unable to pinch skin; limiting instrumental ADL CTCAE: E12410 YH, MW Grade 3 fibrosis deep connective tissue AE YH, MW a fibrosis deep connective tissue AE that has severe induration; unable to slide or pinch skin; limiting joint or orifice movement (e.g. mouth, anus); limiting self care ADL CTCAE: E12411 Grade 4 fibrosis deep connective tissue AE a fibrosis deep connective tissue AE that has generalized; associated with signs or symptoms of impaired breathing or feeding CTCAE: E12412 YH, MW Grade 1 growth suppression AE YH, MW CTCAE: E12423 a growth suppression AE that has reduction in growth velocity by 10 - 29% ideally measured over the period of a year Grade 2 growth suppression AE CTCAE: E12424 YH, MW a growth suppression AE that has reduction in growth velocity by 30 - 49% ideally measured over the period of a year or 0 - 49% reduction in growth from the baseline growth curve Grade 3 growth suppression AE CTCAE: E12425 YH, MW a growth suppression AE that has reduction in growth velocity of >=50% ideally measured over the period of a year Grade 2 head soft tissue necrosis AE a head soft tissue necrosis AE that has local wound care; medical intervention indicated (e.g., dressings or topical medications) YH, MW CTCAE: E12427 Grade 3 head soft tissue necrosis AE CTCAE: E12428 a head soft tissue necrosis AE that has operative debridement or other invasive intervention indicated (e.g., tissue reconstruction, flap or grafting) YH, MW Grade 1 joint range of motion decreased cervical spine AE CTCAE: E12440 a joint range of motion decreased cervical spine AE that has mild restriction of rotation or flexion between 60 - 70 degrees YH, MW Grade 2 joint range of motion decreased cervical spine AE a joint range of motion decreased cervical spine AE that has rotation <60 degrees to right or left; <60 degrees of flexion YH, MW CTCAE: E12441 Grade 3 joint range of motion decreased cervical spine AE CTCAE: E12442 YH, MW a joint range of motion decreased cervical spine AE that has ankylosed/fused over multiple segments with no C-spine rotation Grade 1 joint range of motion decreased lumbar spine AE CTCAE: E12444 YH, MW a joint range of motion decreased lumbar spine AE that has stiffness; difficulty bending to the floor to pick up a very light object but able to do athletic activity Grade 2 joint range of motion decreased lumbar spine AE YH, MW a joint range of motion decreased lumbar spine AE that has pain with range of motion (ROM) in lumbar spine; requires a reaching aid to pick up a very light object from the floor CTCAE: E12445 Grade 3 joint range of motion decreased lumbar spine AE CTCAE: E12446 YH, MW a joint range of motion decreased lumbar spine AE that requires <50% lumbar spine flexion; associated with symptoms of ankylosis or fused over multiple segments with no L-spine flexion (e.g., unable to reach to floor to pick up a very light object) Grade 2 neck soft tissue necrosis AE YH, MW a neck soft tissue necrosis AE that has local wound care; medical intervention indicated (e.g., dressings or topical medications) CTCAE: E12498 Grade 3 neck soft tissue necrosis AE CTCAE: E12499 YH, MW a neck soft tissue necrosis AE that has operative debridement or other invasive intervention indicated (e.g., tissue reconstruction, flap or grafting) Grade 2 pelvic soft tissue necrosis AE YH, MW CTCAE: E12517 a pelvic soft tissue necrosis AE that has local wound care; medical intervention indicated (e.g., dressings or topical medications) Grade 3 pelvic soft tissue necrosis AE YH, MW a pelvic soft tissue necrosis AE that has operative debridement or other invasive intervention indicated (e.g., tissue reconstruction, flap or grafting) CTCAE: E12518 Grade 1 scoliosis AE CTCAE: E12522 a scoliosis AE that requires <20 degrees; clinically undetectable YH, MW Grade 2 scoliosis AE CTCAE: E12523 a scoliosis AE that requires >20 - 45 degrees; visible by forward flexion; limiting instrumental ADL YH, MW Grade 3 scoliosis AE a scoliosis AE that requires >45 degrees; scapular prominence in forward flexion; operative intervention indicated; limiting self care ADL; disabling CTCAE: E12524 YH, MW Grade 2 soft tissue necrosis lower limb AE YH, MW CTCAE: E12526 a soft tissue necrosis lower limb AE that has local wound care; medical intervention indicated (e.g., dressings or topical medications) Grade 3 soft tissue necrosis lower limb AE CTCAE: E12527 a soft tissue necrosis lower limb AE that has operative debridement or other invasive intervention indicated (e.g., tissue reconstruction, flap or grafting) YH, MW Grade 2 soft tissue necrosis upper limb AE YH, MW a soft tissue necrosis upper limb AE that has local wound care; medical intervention indicated (e.g., dressings or topical medications) CTCAE: E12531 Grade 3 soft tissue necrosis upper limb AE CTCAE: E12532 a soft tissue necrosis upper limb AE that has operative debridement or other invasive intervention indicated (e.g., tissue reconstruction, flap or grafting) YH, MW Grade 1 superficial soft tissue fibrosis AE a Superficial soft tissue fibrosis AE that has mild induration, able to move skin parallel to plane (sliding) and perpendicular to skin (pinching up) YH, MW CTCAE: E12536 Grade 2 superficial soft tissue fibrosis AE CTCAE: E12537 a Superficial soft tissue fibrosis AE that has moderate induration, able to slide skin, unable to pinch skin; limiting instrumental ADL YH, MW Grade 3 superficial soft tissue fibrosis AE CTCAE: E12538 a Superficial soft tissue fibrosis AE that has severe induration; unable to slide or pinch skin; limiting joint or orifice movement (e.g., mouth, anus); limiting self care ADL YH, MW Grade 4 superficial soft tissue fibrosis AE CTCAE: E12539 a superficial soft tissue fibrosis AE that has generalized; associated with signs or symptoms of impaired breathing or feeding YH, MW Grade 1 trismus AE YH, MW CTCAE: E12542 a trismus AE that has decreased ROM (range of motion) without impaired eating Grade 2 trismus AE a trismus AE that has decreased ROM requiring small bites, soft foods or purees YH, MW CTCAE: E12543 Grade 3 trismus AE a trismus AE that has decreased ROM with inability to adequately aliment or hydrate orally YH, MW CTCAE: E12544 Grade 1 unequal limb length AE YH, MW An unequal limb length AE that has mild length discrepancy <2 cm CTCAE: E12546 Grade 2 unequal limb length AE CTCAE: E12547 An unequal limb length AE that has moderate length discrepancy 2 - 5 cm; shoe lift indicated; limiting instrumental ADL YH, MW Grade 3 unequal limb length AE YH, MW CTCAE: E12548 An unequal limb length AE that has severe length discrepancy >5 cm; limiting self care ADL; disabling; operative intervention indicated Grade 1 alkalosis AE a alkalosis AE that requires pH >normal, but <=7.5 CTCAE: E12248 YH, MW Grade 3 alkalosis AE CTCAE: E12249 a alkalosis AE that requires pH >7.5 YH, MW Grade 2 glucose intolerance AE CTCAE: E12266 a glucose intolerance AE that has symptomatic; dietary modification or oral agent indicated YH, MW Grade 3 glucose intolerance AE YH, MW CTCAE: E12267 a glucose intolerance AE that has severe symptoms; insulin indicated Grade 1 hypermagnesemia AE a hypermagnesemia AE that requires >ULN - 3.0 mg/dL; >ULN - 1.23 mmol/L YH, MW CTCAE: E12289 Grade 3 hypermagnesemia AE YH, MW a hypermagnesemia AE that requires >3.0 - 8.0 mg/dL; >1.23 - 3.30 mmol/L CTCAE: E12290 Grade 4 hypermagnesemia AE YH, MW CTCAE: E12291 a hypermagnesemia AE that requires >8.0 mg/dL; >3.30 mmol/L; life-threatening consequences Grade 1 hypernatremia AE CTCAE: E12294 YH, MW a hypernatremia AE that requires >ULN - 150 mmol/L Grade 2 hypernatremia AE a hypernatremia AE that requires >150 - 155 mmol/L YH, MW CTCAE: E12295 Grade 3 hypernatremia AE CTCAE: E12296 a hypernatremia AE that requires >155 - 160 mmol/L; hospitalization indicated YH, MW Grade 4 hypernatremia AE YH, MW CTCAE: E12297 a hypernatremia AE that requires >160 mmol/L; life-threatening consequences Grade 1 hypokalemia AE a hypokalemia AE that requires <LLN - 3.0 mmol/L YH, MW CTCAE: E12328 Grade 2 hypokalemia AE CTCAE: E12329 YH, MW a hypokalemia AE that requires <LLN - 3.0 mmol/L; symptomatic; intervention indicated Grade 3 hypokalemia AE CTCAE: E12330 a hypokalemia AE that requires <3.0 - 2.5 mmol/L; hospitalization indicated YH, MW Grade 4 hypokalemia AE a hypokalemia AE that requires <2.5 mmol/L; life-threatening consequences YH, MW CTCAE: E12331 Grade 1 hyponatremia AE CTCAE: E12340 a hyponatremia AE that requires <LLN - 130 mmol/L YH, MW Grade 3 hyponatremia AE a hyponatremia AE that requires <130 - 120 mmol/L CTCAE: E12341 YH, MW Grade 4 hyponatremia AE YH, MW a hyponatremia AE that requires <120 mmol/L; life-threatening consequences CTCAE: E12342 Grade 2 obesity AE CTCAE: E12362 an obesity AE that requires BMI 25 - 29.9 kg/m2 YH, MW Grade 3 obesity AE YH, MW an obesity AE that requires BMI 30 - 39.9 kg/m2 CTCAE: E12363 Grade 4 obesity AE CTCAE: E12364 an obesity AE that requires BMI >=40 kg/m2 YH, MW Grade 3 flushing AE YH, MW CTCAE: E13774 a flushing AE that has symptomatic, associated with hypotension and/or tachycardia; limiting self care ADL Grade 2 hematoma AE a hematoma AE that requires minimally invasive evacuation or aspiration YH, MW CTCAE: E13777 Grade 3 hematoma AE a hematoma AE that requires transfusion, radiologic, endoscopic, or elective operative intervention YH, MW CTCAE: E13778 Grade 1 hypertension AE an hypertension AE that has prehypertension (systolic BP 120 - 139 mm Hg or diastolic BP 80 - 89 mm Hg) CTCAE: E13786 YH, MW Grade 2 hypertension AE CTCAE: E13787 YH, MW an hypertension AE that for Adult: has stage 1 hypertension (systolic BP 140 - 159 mm Hg or diastolic BP 90 - 99 mm Hg); medical intervention indicated; recurrent or persistent (>=24 hrs); symptomatic increase by >20 mm Hg (diastolic) or to >140/90 mm Hg if previously WNL; monotherapy indicated; for Pediatric: recurrent or persistent (>=24 hrs) BP >ULN; monotherapy indicated. Grade 3 hypertension AE an hypertension AE that for Adult has Stage 2 hypertension (systolic BP >=160 mm Hg or diastolic BP >=100 mm Hg); medical intervention indicated; more than one drug or more intensive therapy than previously used indicated; for Pediatric: Same as adult. CTCAE: E13788 YH, MW Grade 4 hypertension AE CTCAE: E13789 YH, MW an hypertension AE that for Adult has life-threatening consequences (e.g., malignant hypertension, transient or permanent neurologic deficit, hypertensive crisis); urgent intervention indicated; for Pediatric: Same as adult Grade 2 peripheral ischemia AE YH, MW CTCAE: E13811 a peripheral ischaemia AE that has brief (<24 hrs) episode of ischemia managed non-surgically and without permanent deficit Grade 3 peripheral ischemia AE a peripheral ischaemia AE that has a recurring or prolonged (>=24 hrs) and/or invasive intervention indicated YH, MW CTCAE: E13812 Grade 3 vasculitis AE YH, MW a vasculitis AE that shows severe symptoms, medical intervention indicated (e.g., steroids) CTCAE: E13840 Grade 4 vasculitis AE CTCAE: E13841 a vasculitis AE that shows threatening; evidence of peripheral or visceral ischemia; urgent intervention indicated YH, MW Grade 1 alopecia AE an alopecia AE that has hair loss of <50% of normal for that individual that is not obvious from a distance but only on close inspection; a different hair style may be required to cover the hair loss but it does not require a wig or hair piece to camouflage YH, MW CTCAE: E13612 Grade 2 alopecia AE YH, MW an alopecia AE that has hair loss of >=50% normal for that individual that is readily apparent to others; a wig or hair piece is necessary if the patient desires to completely camouflage the hair loss; associated with psychosocial impact CTCAE: E13613 Grade 1 dry skin AE YH, MW CTCAE: E13624 a dry skin AE that is coverying <10% BSA and no associated erythema or pruritus Grade 2 dry skin AE a dry skin AE that is coverying 10 - 30% BSA and associated with erythema or pruritus; limiting instrumental ADL CTCAE: E13625 YH, MW Grade 3 dry skin AE CTCAE: E13626 a dry skin AE that is coverying >30% BSA and associated with pruritus; limiting self care ADL YH, MW Grade 1 erythema multiforme AE an erythema multiforme AE that has target lesions covering <10% BSA and not associated with skin tenderness CTCAE: E13628 YH, MW Grade 2 erythema multiforme AE YH, MW CTCAE: E13629 an erythema multiforme AE that has target lesions covering 10 - 30% BSA and associated with skin tenderness Grade 3 erythema multiforme AE YH, MW an erythema multiforme AE that has target lesions covering >30% BSA and associated with oral or genital erosions CTCAE: E13630 Grade 4 erythema multiforme AE CTCAE: E13631 an erythema multiforme AE that has target lesions covering >30% BSA; associated with fluid or electrolyte abnormalities; ICU care or burn unit indicated YH, MW Grade 1 hyperhidrosis AE CTCAE: E13646 a hyperhidros AE that shows limited to one site (palms, soles, or axillae); self care interventions YH, MW Grade 2 hyperhidrosis AE YH, MW a hyperhidros AE that has Involving >1 site; patient seeks medical intervention; associated with psychosocial impact CTCAE: E13647 Grade 3 hyperhidrosis AE CTCAE: E13648 YH, MW a hyperhidros AE that has Generalized involving sites other than palms, soles, or axillae; associated with electrolyte/hemodynamic imbalance Grade 1 palmar-plantar erythrodysesthesia syndrome AE CTCAE: E13673 YH, MW a palmar-plantar erythrodysesthesia syndrome AE that has minimal skin changes or dermatitis (e.g., erythema, edema, or hyperkeratosis) without pain Grade 2 palmar-plantar erythrodysesthesia syndrome AE CTCAE: E13674 YH, MW a palmar-plantar erythrodysesthesia syndrome AE that has skin changes (e.g., peeling, blisters, bleeding, edema, or hyperkeratosis) with pain; limiting instrumental ADL Grade 3 palmar-plantar erythrodysesthesia syndrome AE YH, MW CTCAE: E13675 a palmar-plantar erythrodysesthesia syndrome AE that has severe skin changes (e.g., peeling, blisters, bleeding, edema, or hyperkeratosis) with pain; limiting self care ADL Grade 1 periorbital edema AE CTCAE: E13677 YH, MW a periorbital edema AE that has soft or non-pitting Grade 2 periorbital edema AE YH, MW a periorbital edema AE that has indurated or pitting edema; topical intervention indicated CTCAE: E13678 Grade 3 periorbital edema AE CTCAE: E13679 a periorbital edema AE that has edema associated with visual disturbance; increased intraocular pressure, glaucoma or retinal hemorrhage; optic neuritis; diuretics indicated; operative intervention indicated YH, MW Grade 1 photosensitivity AE CTCAE: E13681 a photosensitivity reaction AE that has painless erythema and erythema covering <10% BSA YH, MW Grade 2 photosensitivity AE a photosensitivity reaction AE that has tender erythema covering 10 - 30% BSA YH, MW CTCAE: E13682 Grade 3 photosensitivity AE a photosensitivity reaction AE that has erythema covering >30% BSA and erythema with blistering; photosensitivity; oral corticosteroid therapy indicated; pain control indicated (e.g., narcotics or NSAIDs) CTCAE: E13683 YH, MW Grade 1 pruritus AE CTCAE: E13687 YH, MW a pruritus AE that has mild or localized; topical intervention indicated Grade 2 pruritus AE YH, MW CTCAE: E13688 a pruritus AE that has intense or widespread; intermittent; skin changes from scratching (e.g., edema, papulation, excoriations, lichenification, oozing/crusts); oral intervention indicated; limiting instrumental ADL Grade 3 pruritus AE a pruritus AE that has intense or widespread; constant; limiting self care ADL or sleep; oral corticosteroid or immunosuppressive therapy indicated YH, MW CTCAE: E13689 Grade 1 purpura AE a purpura AE that has combined area of lesions covering <10% BSA YH, MW CTCAE: E13691 Grade 2 purpura AE CTCAE: E13692 YH, MW a purpura AE that has combined area of lesions covering 10 - 30% BSA; bleeding with trauma Grade 3 purpura AE a purpura AE that has combined area of lesions covering >30% BSA; spontaneous bleeding YH, MW CTCAE: E13693 Grade 1 skin atrophy AE YH, MW CTCAE: E13715 a skin atrophy AE that has covering <10% BSA; associated with telangiectasias or changes in skin color Grade 2 skin atrophy AE YH, MW CTCAE: E13716 a skin atrophy AE that has covering 10 - 30% BSA; associated with striae or adnexal structure loss Grade 3 skin atrophy AE YH, MW CTCAE: E13717 a skin atrophy AE that has covering >30% BSA; associated with ulceration Grade 1 skin hyperpigmentation AE YH, MW a skin hyperpigmentation AE that has hyperpigmentation covering <10% BSA; no psychosocial impact CTCAE: E13719 Grade 2 skin hyperpigmentation AE a skin hyperpigmentation AE that has hyperpigmentation covering >10% BSA; associated psychosocial impact YH, MW CTCAE: E13720 Grade 1 skin hypopigmentation AE CTCAE: E13722 a skin hypopigmentation AE that has hypopigmentation or depigmentation covering <10% BSA; no psychosocial impact YH, MW Grade 2 skin hypopigmentation AE CTCAE: E13723 a skin hypopigmentation AE that has hypopigmentation or depigmentation covering >10% BSA; associated psychosocial impact YH, MW Grade 3 stevens-Johnson syndrome AE a stevens-johnson syndrome AE that has skin sloughing covering <10% BSA with associated signs (e.g., erythema, purpura, epidermal detachment and mucous membrane detachment) YH, MW CTCAE: E13737 Grade 4 stevens-Johnson syndrome AE a stevens-johnson syndrome AE that has skin sloughing covering 10 - 30% BSA with associated signs (e.g., erythema, purpura, epidermal detachment and mucous membrane detachment) CTCAE: E13738 YH, MW Grade 1 telangiectasia AE YH, MW a telangiectasia AE that has telangiectasias covering <10% BSA CTCAE: E13741 Grade 2 telangiectasia AE CTCAE: E13742 a telangiectasia AE that has telangiectasias covering >10% BSA; associated with psychosocial impact YH, MW Grade 4 toxic epidermal necrolysis AE YH, MW a toxic epidermal necrolysis AE that has skin sloughing covering >=30% BSA with associated symptoms (e.g., erythema, purpura, or epidermal detachment) CTCAE: E13744 Grade 1 urticaria AE CTCAE: E13747 YH, MW an urticaria AE that has urticarial lesions covering <10% BSA; topical intervention indicated Grade 2 urticaria AE CTCAE: E13748 YH, MW an urticaria AE that has urticarial lesions covering 10 - 30% BSA; oral intervention indicated Grade 3 urticaria AE CTCAE: E13749 an urticaria AE that has urticariallesions covering >30% BSA; IV intervention indicated YH, MW Grade 2 aspiration AE CTCAE: E13312 YH, MW an aspiration AE that has altered eating habits; coughing or choking episodes after eating or swallowing; medical intervention indicated (e.g., suction or oxygen) Grade 3 aspiration AE YH, MW an aspiration AE that has dyspnea and pneumonia symptoms (e.g., aspiration pneumonia); hospitalization indicated; unable to aliment orally CTCAE: E13313 Grade 2 atelectasis AE CTCAE: E13318 an atelectasis AE that has symptomatic (e.g., dyspnea, cough); medical intervention indicated (e.g., chest physiotherapy, suctioning); bronchoscopic suctioning YH, MW Grade 3 atelectasis AE an atelectasis AE that has oxygen indicated; hospitalization or elective operative intervention indicated (e.g., stent, laser) YH, MW CTCAE: E13319 Grade 2 chylothorax AE a chylothorax AE that has symptomatic; thoracentesis or tube drainage indicated YH, MW CTCAE: E13360 Grade 3 chylothorax AE CTCAE: E13361 YH, MW a chylothorax AE that has severe symptoms; elective operative intervention indicated Grade 2 epistaxis AE an epistaxis AE that has moderate symptoms; medical intervention indicated (e.g., nasal packing, cauterization; topical vasoconstrictors) YH, MW CTCAE: E13376 Grade 3 hiccups AE YH, MW CTCAE: E13383 a Hiccups AE that has interfering with sleep; limiting self care ADL Grade 1 hoarseness AE a hoarseness AE that has mild or intermittent voice change; fully understandable; self-resolves YH, MW CTCAE: E13385 Grade 2 hoarseness AE YH, MW CTCAE: E13386 a hoarseness AE that has Moderate or persistent voice changes; may require occasional repetition but understandable on telephone; medical evaluation indicated Grade 3 hoarseness AE CTCAE: E13387 a hoarseness AE that has severe voice changes including predominantly whispered speech YH, MW Grade 2 hypoxia AE CTCAE: E13389 YH, MW a hypoxia AE that has decreased oxygen saturation with exercise (e.g., pulse oximeter <88%); intermittent supplemental oxygen Grade 3 hypoxia AE YH, MW a hypoxia AE that has decreased oxygen saturation at rest (e.g., pulse oximeter <88% or PaO2 <=55 mm Hg) CTCAE: E13390 Grade 4 hypoxia AE CTCAE: E13391 a hypoxia AE that has life-threatening airway compromise; urgent intervention indicated (e.g., tracheotomy or intubation) YH, MW Grade 3 laryngeal edema AE a laryngeal edema AE that has stridor; respiratory distress; hospitalization indicated CTCAE: E13396 YH, MW Grade 4 laryngeal edema AE a laryngeal edema AE that has life-threatening airway compromise; urgent intervention indicated (e.g., tracheotomy or intubation) YH, MW CTCAE: E13397 Grade 2 pleural effusion AE YH, MW a pleural effusion AE that has symptomatic; intervention indicated (e.g., diuretics or limited therapeutic thoracentesis) CTCAE: E13488 Grade 3 pleural effusion AE a pleural effusion AE that has symptomatic with respiratory distress and hypoxia; surgical intervention including chest tube or pleurodesis indicated CTCAE: E13489 YH, MW Grade 1 pleural hemorrhage AE YH, MW CTCAE: E13493 a pleural hemorrhage AE that has asymptomatic; mild hemorrhage confirmed by thoracentesis Grade 2 pleural hemorrhage AE a pleural hemorrhage AE that has symptomatic or associated with pneumothorax; chest tube drainage indicated YH, MW CTCAE: E13494 Grade 3 pleural hemorrhage AE a pleural hemorrhage AE that has >1000 ml of blood evacuated; persistent bleeding (150-200 ml/hr for 2 - 4 hr); persistent transfusion indicated; elective operative intervention indicated CTCAE: E13495 YH, MW Grade 3 pneumonitis AE YH, MW CTCAE: E13505 a pneumonitis AE that has severe symptoms; limiting self care ADL; oxygen indicated Grade 4 pneumonitis AE CTCAE: E13506 a pneumonitis AE that has life-threatening respiratory compromise; urgent intervention indicated (e.g., tracheotomy or intubation) YH, MW Grade 2 pneumothorax AE a pneumothorax AE that has symptomatic; intervention indicated (e.g., tube placement without sclerosis) YH, MW CTCAE: E13510 Grade 3 pneumothorax AE CTCAE: E13511 YH, MW a pneumothorax AE that has sclerosis and/or operative intervention indicated; hospitalization indicated Grade 1 productive cough AE YH, MW a productive cough AE that has occasional/minimal production of sputum with cough CTCAE: E13518 Grade 2 productive cough AE CTCAE: E13519 YH, MW a productive cough AE that has moderate sputum production; limiting instrumental ADL Grade 3 productive cough AE YH, MW CTCAE: E13520 a productive cough AE that has persistent or copious production of sputum; limiting self care ADL Grade 1 pulmonary edema AE CTCAE: E13522 YH, MW a pulmonary edema AE that has radiologic findings only; minimal dyspnea on exertion Grade 2 pulmonary edema AE YH, MW a pulmonary edema AE that has moderate dyspnea on exertion; medical intervention indicated; limiting instrumental ADL CTCAE: E13523 Grade 3 pulmonary edema AE CTCAE: E13524 YH, MW a pulmonary edema AE that has severe dyspnea or dyspnea at rest; oxygen indicated; limiting self care ADL Grade 4 pulmonary edema AE CTCAE: E13525 YH, MW a pulmonary edema AE that has life-threatening respiratory compromise; urgent intervention or intubation with ventilatory support indicated Grade 1 pulmonary fibrosis AE YH, MW a pulmonary fibrosis AE that has mild hypoxemia; radiologic pulmonary fibrosis <25% of lung volume CTCAE: E13528 Grade 2 pulmonary fibrosis AE CTCAE: E13529 a pulmonary fibrosis AE that has moderate hypoxemia; evidence of pulmonary hypertension; radiographic pulmonary fibrosis 25 - 50% YH, MW Grade 3 pulmonary fibrosis AE YH, MW CTCAE: E13530 a pulmonary fibrosis AE that has severe hypoxemia; evidence of right-sided heart failure; radiographic pulmonary fibrosis >50 - 75% Grade 4 pulmonary fibrosis AE YH, MW a pulmonary fibrosis AE that has life-threatening consequences (e.g., hemodynamic/pulmonary complications); intubation with ventilatory support indicated; radiographic pulmonary fibrosis >75% with severe honeycombing CTCAE: E13531 Grade 1 pulmonary hypertension AE a pulmonary hypertension AE that has minimal dyspnea; findings on physical exam or other evaluation YH, MW CTCAE: E13540 Grade 2 pulmonary hypertension AE a pulmonary hypertension AE that has moderate dyspnea, cough; requiring evaluation by cardiac catheterization and medical intervention YH, MW CTCAE: E13541 Grade 3 pulmonary hypertension AE YH, MW CTCAE: E13542 a pulmonary hypertension AE that has severe symptoms, associated with hypoxemia, right heart failure; oxygen indicated Grade 4 pulmonary hypertension AE CTCAE: E13543 a pulmonary hypertension AE that has life-threatening airway consequences; urgent intervention indicated (e.g., tracheotomy or intubation) YH, MW Grade 1 sinus disorder AE YH, MW CTCAE: E13561 a sinus disorder AE that has asymptomatic mucosal crusting; blood-tinged secretions Grade 2 sinus disorder AE CTCAE: E13562 a sinus disorder AE that has symptomatic stenosis or edema/narrowing interfering with airflow; limiting instrumental ADL YH, MW Grade 3 sinus disorder AE CTCAE: E13563 YH, MW a sinus disorder AE that has stenosis with significant nasal obstruction; limiting self care ADL Grade 4 sinus disorder AE CTCAE: E13564 YH, MW a sinus disorder AE that has necrosis of soft tissue or bone; urgent operative intervention indicated Grade 3 sore throat AE CTCAE: E13578 a sore throat AE that has Severe pain; limiting self care ADL; limiting ability to swallow YH, MW Grade 3 stridor AE YH, MW CTCAE: E13580 a stridor AE that has respiratory distress limiting self care ADL; medical intervention indicated Grade 4 stridor AE a stridor AE that has life-threatening airway compromise; urgent intervention indicated (e.g., tracheotomy or intubation) CTCAE: E13581 YH, MW Grade 1 voice alteration AE YH, MW CTCAE: E13602 a voice alteration AE that has mild or intermittent change from normal voice Grade 2 voice alteration AE a voice alteration AE that has moderate or persistent change from normal voice; still understandable CTCAE: E13603 YH, MW Grade 3 voice alteration AE YH, MW a voice alteration AE that has severe voice changes including predominantly whispered speech; may require frequent repetition or face-to-face contact for understandability; may require assistive technology CTCAE: E13604 Grade 1 wheezing AE CTCAE: E13606 YH, MW a wheezing AE that has detectable airway noise with minimal symptoms Grade 3 wheezing AE YH, MW CTCAE: E13608 a wheezing AE that has severe respiratory symptoms limiting self care ADL; oxygen therapy or hospitalization indicated Grade 2 menorrhagia AE CTCAE: E13134 YH, MW a menorrhagia AE that has moderate symptoms; medical intervention indicated (e.g., hormones) Grade 3 menorrhagia AE a menorrhagia AE that has severe; transfusion indicated; surgical intervention indicated (e.g., hysterectomy) CTCAE: E13135 YH, MW Grade 1 acute kidney injury AE YH, MW an acute kidney injury AE that has creatinine level increase of >0.3 mg/dL; creatinine 1.5 - 2.0 x above baseline CTCAE: E12974 Grade 2 acute kidney injury AE CTCAE: E12975 an acute kidney injury AE that has creatinine 2 - 3 x above baseline YH, MW Grade 3 acute kidney injury AE YH, MW an acute kidney injury AE that has creatinine >3 x baseline or >4.0 mg/dL; hospitalization indicated CTCAE: E12976 Grade 2 hematuria AE CTCAE: E13002 YH, MW a hematuria AE that has symptomatic; urinary catheter or bladder irrigation indicated; limiting instrumental ADL Grade 3 hematuria AE CTCAE: E13003 YH, MW a hematuria AE that has gross hematuria; transfusion, IV medications or hospitalization indicated; elective endoscopic, radiologic or operative intervention indicated; limiting self care ADL Grade 1 urinary incontinence AE an urinary incontinence AE that has occasional (e.g., with coughing, sneezing, etc.), pads not indicated YH, MW CTCAE: E13043 Grade 2 urinary incontinence AE YH, MW CTCAE: E13044 an urinary incontinence AE that has spontaneous; pads indicated; limiting instrumental ADL Grade 3 urinary incontinence AE an urinary incontinence AE that has Intervention indicated (e.g., clamp, collagen injections); operative intervention indicated; limiting self care ADL YH, MW CTCAE: E13045 Grade 1 urinary retention AE an urinary retention AE that has urinary, suprapubic or intermittent catheter placement not indicated; able to void with some residual YH, MW CTCAE: E13047 Grade 2 urinary retention AE an urinary retention AE that has placement of urinary, suprapubic or intermittent catheter placement indicated; medication indicated CTCAE: E13048 YH, MW Grade 3 urinary retention AE YH, MW CTCAE: E13049 an urinary retention AE that has elective operative or radiologic intervention indicated; substantial loss of affected kidney function or mass Grade 1 suicidal ideation AE YH, MW a suicidal ideation AE that has increased thoughts of death but no wish to kill oneself CTCAE: E12965 Grade 2 suicidal ideation AE CTCAE: E12966 YH, MW a suicidal ideation AE that has suicidal ideation with no specific plan or intent Grade 3 suicidal ideation AE YH, MW CTCAE: E12967 a suicidal ideation AE that has specific plan to commit suicide without serious intent to die which may not require hospitalization Grade 4 suicidal ideation AE CTCAE: E12968 a suicidal ideation AE that has specific plan to commit suicide with serious intent to die which requires hospitalization YH, MW Grade 3 suicide attempt AE YH, MW a suicide attempt AE that has suicide attempt or gesture without intent to die which may not require hospitalization CTCAE: E12970 Grade 4 suicide attempt AE a suicide attempt AE that has suicide attempt with intent to die which requires hospitalization YH, MW CTCAE: E12971 Grade 3 aphonia AE CTCAE: E12590 YH, MW an aphonia AE that has voicelessness; unable to speak Grade 1 depressed level of consciousness AE CTCAE: E12626 a depressed level of consciousness AE that has decreased level of alertness YH, MW Grade 2 depressed level of consciousness AE CTCAE: E12627 YH, MW a depressed level of consciousness AE that has Sedation; slow response to stimuli; limiting instrumental ADL Grade 3 depressed level of consciousness AE a depressed level of consciousness AE that is difficult to arouse YH, MW CTCAE: E12628 Grade 1 dysgeusia AE YH, MW a dysgenusia AE that has altered taste but no change in diet CTCAE: E12644 Grade 2 dysgeusia AE YH, MW CTCAE: E12645 a dysgenusia AE that has altered taste with change in diet (e.g., oral supplements); noxious or unpleasant taste; loss of taste Grade 1 leukoencephalopathy AE CTCAE: E12713 YH, MW a leukoencephalopathy AE that has asymptomatic; small focal T2/FLAIR hyperintensities; involving periventricular white matter or <1/3 of susceptible areas of cerebrum +/- mild increase in subarachnoid space (SAS) and/or mild ventriculomegaly Grade 2 leukoencephalopathy AE YH, MW CTCAE: E12714 a leukoencephalopathy AE that has moderate symptoms; focal T2/FLAIR hyperintensities, involving periventricular white matter extending into centrum semiovale or involving 1/3 to 2/3 of susceptible areas of cerebrum +/- moderate increase in SAS and/or moderate ventriculomegaly Grade 3 leukoencephalopathy AE CTCAE: E12715 YH, MW a leukoencephalopathy AE that has severe symptoms; extensive T2/FLAIR hyperintensities, involving periventricular white matter involving 2/3 or more of susceptible areas of cerebrum +/- moderate to severe increase in SAS and/or moderate to severe ventriculomegaly Grade 4 leukoencephalopathy AE a leukoencephalopathy AE that has life-threatening consequences; extensive T2/FLAIR hyperintensities, involving periventricular white matter involving most of susceptible areas of cerebrum +/- moderate to severe increase in SAS and/or moderate to severe ventriculomegaly YH, MW CTCAE: E12716 Grade 1 myelitis AE CTCAE: E12733 a myelitis AE that has asymptomatic; mild signs (e.g., Babinski's reflex or Lhermitte's sign) YH, MW Grade 2 myelitis AE YH, MW a myelitis AE that has moderate weakness or sensory loss; limiting instrumental ADL CTCAE: E12734 Grade 3 myelitis AE CTCAE: E12735 YH, MW a myelitis AE that has severe weakness or sensory loss; limiting self care ADL Grade 2 presyncope AE CTCAE: E12779 YH, MW a presyncope AE that has present (e.g., near fainting) Grade 1 seizure AE YH, MW a seizure AE that has brief partial seizure; no loss of consciousness CTCAE: E12805 Grade 2 seizure AE a seizure AE that has brief generalized seizure CTCAE: E12806 YH, MW Grade 3 seizure AE CTCAE: E12807 a seizure AE that has multiple seizures despite medical intervention YH, MW Grade 4 seizure AE CTCAE: E12808 a seizure AE that has life-threatening; prolonged repetitive seizures YH, MW Grade 1 somnolence AE CTCAE: E12815 YH, MW a somnolence AE that has mild but more than usual drowsiness or sleepiness Grade 2 somnolence AE CTCAE: E12816 YH, MW a somnolence AE that has moderate sedation; limiting instrumental ADL Grade 3 somnolence AE YH, MW a somnolence AE that has obtundation or stupor CTCAE: E12817 Grade 3 syncope AE a syncope AE that has fainting; orthostatic collapse CTCAE: E12833 YH, MW Grade 1 arthritis AE CTCAE: E12379 YH, MW an arthritis AE that has mild pain with inflammation, erythema, or joint swelling Grade 2 arthritis AE an arthritis AE that has moderate pain associated with signs of inflammation, erythema, or joint swelling; limiting instrumental ADL CTCAE: E12380 YH, MW Grade 3 arthritis AE YH, MW an arthritis AE that has severe pain associated with signs of inflammation, erythema, or joint swelling; irreversible joint damage; disabling; limiting self care ADL CTCAE: E12381 Grade 1 joint range of motion decreased AE YH, MW a joint range of motion decreased AE that requires <=25% loss of ROM (range of motion); decreased ROM limiting athletic activity CTCAE: E12436 Grade 2 joint range of motion decreased AE CTCAE: E12437 a joint range of motion decreased AE that requires >25 - 50% decrease in ROM; limiting instrumental ADL YH, MW Grade 3 joint range of motion decreased AE a joint range of motion decreased AE that requires >50% decrease in ROM; limiting self care ADL; disabling CTCAE: E12438 YH, MW Grade 1 osteoporosis AE YH, MW CTCAE: E12509 an osteoporosis AE that has radiologic evidence of osteoporosis or Bone Mineral Density (BMD) t-score -1 to -2.5 (osteopenia); no loss of height or intervention indicated Grade 2 osteoporosis AE YH, MW an osteoporosis AE that has BMD t-score <-2.5; loss of height <2 cm; anti-osteoporotic therapy indicated; limiting instrumental ADL CTCAE: E12510 Grade 3 osteoporosis AE CTCAE: E12511 an osteoporosis AE that has loss of height >=2 cm; hospitalization indicated; limiting self care ADL YH, MW Grade 1 acidosis AE YH, MW CTCAE: E12238 an acidosis AE that has pH <normal, but >=7.3 Grade 3 acidosis AE an acidosis AE that has pH <7.3 CTCAE: E12239 YH, MW Grade 1 anorexia AE an anorexia AE that has loss of appetite without alteration in eating habits YH, MW CTCAE: E12253 Grade 2 anorexia AE CTCAE: E12254 an anorexia AE that has oral intake altered without significant weight loss or malnutrition; oral nutritional supplements indicated YH, MW Grade 3 anorexia AE YH, MW CTCAE: E12255 an anorexia AE that has associated with significant weight loss or malnutrition (e.g., inadequate oral caloric and/or fluid intake); tube feeding or TPN indicated Grade 1 dehydration AE YH, MW CTCAE: E12259 a dehydration AE that has increased oral fluids indicated; dry mucous membranes; diminished skin turgor Grade 2 dehydration AE YH, MW a dehydration AE that requires IIV fluids indicated <24 hrs CTCAE: E12260 Grade 1 hypercalcemia AE a hypercalcemia AE that has corrected serum calcium of >ULN - 11.5 mg/dL; >ULN - 2.9 mmol/L; Ionized calcium >ULN - 1.5 mmol/L CTCAE: E12271 YH, MW Grade 2 hypercalcemia AE a hypercalcemia AE that has corrected serum calcium of >11.5 - 12.5 mg/dL; >2.9 - 3.1 mmol/L; Ionized calcium >1.5 - 1.6 mmol/L; symptomatic YH, MW CTCAE: E12272 Grade 3 hypercalcemia AE CTCAE: E12273 YH, MW a hypercalcemia AE that has corrected serum calcium of >12.5 - 13.5 mg/dL; >3.1 - 3.4 mmol/L; Ionized calcium >1.6 - 1.8 mmol/L; hospitalization indicated Grade 4 hypercalcemia AE a hypercalcemia AE that has corrected serum calcium of >13.5 mg/dL; >3.4 mmol/L; Ionized calcium >1.8 mmol/L; life-threatening consequences CTCAE: E12274 YH, MW Grade 1 hyperglycemia AE YH, MW CTCAE: E12277 a hypeglycemia AE that has fasting glucose value >ULN - 160 mg/dL; Fasting glucose value >ULN - 8.9 mmol/L Grade 2 hyperglycemia AE CTCAE: E12278 a hypeglycemia AE that has fasting glucose value >160 - 250 mg/dL; Fasting glucose value >8.9 - 13.9 mmol/L YH, MW Grade 3 hyperglycemia AE YH, MW a hypeglycemia AE that has >250 - 500 mg/dL; >13.9 - 27.8 mmol/L; hospitalization indicated CTCAE: E12279 Grade 4 hyperglycemia AE CTCAE: E12280 a hypeglycemia AE that has >500 mg/dL; >27.8 mmol/L; life-threatening consequences YH, MW Grade 1 hyperkalemia AE CTCAE: E12283 YH, MW a hyperkalemia AE that requires >ULN - 5.5 mmol/L Grade 2 hyperkalemia AE a hyperkalemia AE that requires >5.5 - 6.0 mmol/L YH, MW CTCAE: E12284 Grade 3 hyperkalemia AE CTCAE: E12285 YH, MW a hyperkalemia AE that requires >6.0 - 7.0 mmol/L; hospitalization indicated Grade 4 hyperkalemia AE YH, MW CTCAE: E12286 a hyperkalemia AE that requires >7.0 mmol/L; life-threatening consequences Grade 1 hypertriglyceridemia AE a hypertriglyceridemia AE that requires 150 mg/dL - 300 mg/dL; 1.71 mmol/L - 3.42 mmol/L YH, MW CTCAE: E12300 Grade 2 hypertriglyceridemia AE a hypertriglyceridemia AE that requires >300 mg/dL - 500 mg/dL; >3.42 mmol/L - 5.7 mmol/L YH, MW CTCAE: E12301 Grade 3 hypertriglyceridemia AE CTCAE: E12302 a hypertriglyceridemia AE that requires >500 mg/dL - 1000 mg/dL; >5.7 mmol/L - 11.4 mmol/L YH, MW Grade 4 hypertriglyceridemia AE a hypertriglyceridemia AE that requires >1000 mg/dL; >11.4 mmol/L; life-threatening consequences YH, MW CTCAE: E12303 Grade 1 hyperuricemia AE CTCAE: E12306 a hyperuricemia AE that requires >ULN - 10 mg/dL (0.59 mmol/L) without physiologic consequences YH, MW Grade 3 hyperuricemia AE CTCAE: E12307 a hyperuricemia AE that requires >ULN - 10 mg/dL (0.59 mmol/L) with physiologic consequences YH, MW Grade 4 hyperuricemia AE CTCAE: E12308 a hyperuricemia AE that requires >10 mg/dL; >0.59 mmol/L; life-threatening consequences YH, MW Grade 1 hypoalbuminemia AE a hypoalbuminemia AE that requires NCI<LLN - 3 g/dL; <LLN - 30 g/L CTCAE: E12311 YH, MW Grade 2 hypoalbuminemia AE YH, MW a hypoalbuminemia AE that requires NCI<3 - 2 g/dL; <30 - 20 g/L CTCAE: E12312 Grade 3 hypoalbuminemia AE a hypoalbuminemia AE that requires NCI<2 g/dL; <20 g/L CTCAE: E12313 YH, MW Grade 1 hypocalcemia AE YH, MW CTCAE: E12317 a hypocalcemia AE that requires corrected serum calcium of <LLN - 8.0 mg/dL; <LLN - 2.0 mmol/L; Ionized calcium <LLN - 1.0 mmol/L Grade 2 hypocalcemia AE YH, MW CTCAE: E12318 a hypocalcemia AE that requires corrected serum calcium of <8.0 - 7.0 mg/dL; <2.0 - 1.75 mmol/L; Ionized calcium <1.0 - 0.9 mmol/L; symptomatic Grade 3 hypocalcemia AE CTCAE: E12319 a hypocalcemia AE that requires corrected serum calcium of <7.0 - 6.0 mg/dL; <1.75 - 1.5 mmol/L; Ionized calcium <0.9 - 0.8 mmol/L; hospitalization indicated YH, MW Grade 4 hypocalcemia AE CTCAE: E12320 a hypocalcemia AE that requires corrected serum calcium of <6.0 mg/dL; <1.5 mmol/L; Ionized calcium <0.8 mmol/L; life-threatening consequences YH, MW Grade 1 hypoglycemia AE CTCAE: E12323 YH, MW a hypoglycernia AE that requires <LLN - 55 mg/dL; <LLN - 3.0 mmol/L Grade 2 hypoglycemia AE a hypoglycernia AE that requires <55 - 40 mg/dL; <3.0 - 2.2 mmol/L CTCAE: E13874 YH, MW Grade 3 hypoglycemia AE a hypoglycernia AE that requires <40 - 30 mg/dL; <2.2 - 1.7 mmol/L YH, MW CTCAE: E12324 Grade 4 hypoglycemia AE a hypoglycernia AE that requires <30 mg/dL; <1.7 mmol/L; life-threatening consequences; seizures CTCAE: E12325 YH, MW Grade 1 hypomagnesemia AE CTCAE: E12334 YH, MW a hypomagnesemia AE that requires <LLN - 1.2 mg/dL; <LLN - 0.5 mmol/L Grade 2 hypomagnesemia AE YH, MW a hypomagnesemia AE that requires <1.2 - 0.9 mg/dL; <0.5 - 0.4 mmol/L CTCAE: E12335 Grade 3 hypomagnesemia AE CTCAE: E12336 YH, MW a hypomagnesemia AE that requires <0.9 - 0.7 mg/dL; <0.4 - 0.3 mmol/L Grade 4 hypomagnesemia AE a hypomagnesemia AE that requires <0.7 mg/dL; <0.3 mmol/L; life-threatening consequences YH, MW CTCAE: E12337 Grade 1 hypophosphatemia AE CTCAE: E12345 a hypophosphatemia AE that requires <LLN - 2.5 mg/dL; <LLN - 0.8 mmol/L YH, MW Grade 2 hypophosphatemia AE a hypophosphatemia AE that requires <2.5 - 2.0 mg/dL; <0.8 - 0.6 mmol/L YH, MW CTCAE: E12346 Grade 3 hypophosphatemia AE a hypophosphatemia AE that requires <2.0 - 1.0 mg/dL; <0.6 - 0.3 mmol/L YH, MW CTCAE: E12347 Grade 4 hypophosphatemia AE CTCAE: E12348 YH, MW a hypophosphatemia AE that requires <1.0 mg/dL; <0.3 mmol/L; life-threatening consequences behavior abnormal quality YH, JX a behavioral quality where the behavior in an organism is abnormal. WEB: https://en.wikipedia.org/wiki/Abnormality_(behavior) asystole AE 10003586 CTCAE: E10077 WEB: http://www.cardiachealth.org/asystole-and-pulseless-electrical-activity Asystole is the absence of electrical activity in the heart, as evidenced by a flat line on an EKG. Cardiac arrest is a more general term for conditions where the heart is not circulating blood. Ventricular fibrillation (V-fib) or pulseless Ventricular tachycardia (V-tach) are examples of EKG rhythms which also will produce cardiac arrest, but are not asystole. Pulseless electrical activity (PEA) is another catch-all where there is an otherwise survivable EKG, but no blood is circulating. This can be caused by trauma to the heart, or tremendous blood loss, among other reasons. See: https://answers.yahoo.com/question/index?qid=20081027100243AAy0yt4 a cardiac arrest AE where there is no discernible electrical activity on the ECG monitor. YH, MW NCit:C50479 asystole keratitis AE 10023332 WEB: http://www.mayoclinic.org/diseases-conditions/keratitis/basics/definition/con-20035288 MW, YH NCIT: C26805 CTCAE: E10397 an eye inflammation AE that occurs at the corneal area. eye infection AE 10015929 CTCAE: E11391 MW, YH WEB: https://www.nlm.nih.gov/medlineplus/eyeinfections.html an infection AE where one or two eyes get infected by bacteria, fungi, or viruses. NCIT: C45372 appendicitis AE 10003011 CTCAE: E11292 MW, YH an inflammation AE that shows inflammation at the location of appendix. NCIt: C35145 electrocardiogram QT corrected interval prolonged AE 10014383 WEB: http://lifeinthefastlane.com/ecg-library/basics/qt_interval/ NCIt: C71034 MW, YH CTCAE: E12146 UMLS: C0855333 an electrocardiogram QT prolonged AE that estimates the QT interval at a heart rate of 60 bpm. dermatitis radiation AE 10061103 a skin AE that has an outcome of injury to the skin and underlying tissues from exposure to a large external dose of radiation CTCAE: E11675 NCIt: C0034561 WEB: http://www.dermnetnz.org/reactions/radiation-dermatitis.html MW, YH cardiac troponin I increased AE 10007612 a troponin AE which indicates increased levels of cardiac troponin I in a biological specimen MW, YH CTCAE: E12116 NCIt: C78230 growth accelerated AE 10018746 CTCAE: E10317 MW, YH NCIt: C83495 a musculoskeletal or connective tissue AE that has greater growth than expected for age. postoperative thoracic procedure complication AE 10056745 a surgery AE that has the finding of a previously undocumented problem that occurs after a thoracic procedure. CTCAE: E11909 NCIt: C78567 MW, YH uterine perforation AE 10046810 MW, YH CTCAE: E12028 a uterine AE that has a rupture in the uterine wall. NCIt: C50793 fallopian tube perforation AE 10065790 MW, YH a female reproductive system AE that has the finding of rupture of the fallopian tube wall. CTCAE: E11697 NCIt: C78294 adrenal insufficiency AE 10001367 MW, YH NCIt: C26691 CTCAE: E10298 an endocrine system AE that occurs when the adrenal cortex does not produce enough of the hormone cortisol and in some cases, the hormone aldosterone. It may be due to a disorder of the adrenal cortex as in Addison's disease or primary adrenal insufficiency. cushingoid AE 10011655 CTCAE: E10304 MW, YH NCIt: C37938 an endocrine system AE that has signs and symptoms that resemble Cushing's disease or syndrome: buffalo hump obesity, striations, adiposity, hypertension, diabetes, and osteoporosis, usually due to exogenous corticosteroids. delayed puberty AE 10012205 NCIt: C62587 an endocrine system AE that has unusually late sexual maturity. CTCAE: E10308 MW, YH hyperparathyroidism AE 10020705 an endocrine system AE that has an increase in production of parathyroid hormone by the parathyroid glands. This results in hypercalcemia (abnormally high levels of calcium in the blood). CTCAE: E10319 NCIt: C48259 MW, YH hypoparathyroidism AE 10021041 NCIt: C78350 an endocrine system AE that has a decrease in production of parathyroid hormone by the parathyroid glands. CTCAE: E10328 MW, YH virilization AE 10047488 MW, YH an endocrine system AE that has inappropriate masculinization occurring in a female or prepubertal male. CTCAE: E10343 NCIt: C79859 precocious puberty AE 10058084 CTCAE: E10340 NCIt: C79704 an endocrine system AE that has unusually early development of secondary sexual features; the onset of sexual maturation begins usually before age 8 for girls and before age 9 for boys. MW, YH seroma AE 10040102 NCIt: C50739 MW, YH CTCAE: E11938 a medical intervention site AE that has the finding of tumor-like collection of serum in the tissues. stomal ulcer AE 10042127 a medical intervention site AE that has a circumscribed, inflammatory and necrotic erosive lesion on the jejunal mucosal surface close to the anastomosis site following a gastroenterostomy procedure. NCIt: C79766 CTCAE: E11965 MW, YH intestinal stoma site bleeding AE 10049468 MW, YH CTCAE: E11764 a medical intervention site AE that has a finding of blood leakage from the intestinal stoma. NCIt: C78371 pancreatic anastomotic leak AE 10050457 NCIt: C78518 CTCAE: E11891 a medical intervention site AE that has the finding of leakage due to breakdown of a pancreatic anastomosis (surgical connection of two separate anatomic structures). MW, YH biliary anastomotic leak AE 10050458 CTCAE: E11654 MW, YH NCIt: C78183 a medical intervention site AE that has the finding of leakage of bile due to breakdown of a biliary anastomosis (surgical connection of two separate anatomic structures). intestinal stoma leak AE 10059094 CTCAE: E11759 a medical intervention site AE that has the finding of blockage of the normal flow of the contents of the intestinal stoma. MW, YH NCIt: C78370 intestinal stoma leak AE 10059095 CTCAE: E11753 a medical intervention site AE that has the finding of leakage of contents from an intestinal stoma (surgically created opening on the surface of the body). MW, YH NCIt: C78369 vascular access complication AE 10062169 a medical intervention site AE that has the finding of a previously undocumented problem related to the vascular access site. MW, YH CTCAE: E12046 NCIt: C78709 pharyngeal anastomotic leak AE 10065705 NCIt: C78550 CTCAE: E11897 a medical intervention site AE that has the finding of leakage due to breakdown of a pharyngeal anastomosis (surgical connection of two separate anatomic structures). MW, YH prolapse of intestinal stoma AE 10065745 CTCAE: E11914 MW, YH NCIt: C78570 a medical intervention site AE that has the finding of protrusion of the intestinal stoma (surgically created opening on the surface of the body) above the abdominal surface. urostomy site bleeding AE 10065748 NCIt: C78682 CTCAE: E12011 MW, YH a medical intervention site AE that has the finding of bleeding from the urostomy site. tracheostomy site bleeding AE 10065749 MW, YH CTCAE: E11981 a medical intervention site AE that has the finding of blood leakage from the tracheostomy site. NCIt: C78648 fallopian tube anastomotic leak AE 10065788 a medical intervention site AE that has the finding of leakage due to breakdown of a fallopian tube anastomosis (surgical connection of two separate anatomic structures). NCIt: C78292 CTCAE: E11691 MW, YH bladder anastomotic leak AE 10065802 MW, YH CTCAE: E11660 a medical intervention site AE that has the finding of leakage of urine due to breakdown of a bladder anastomosis (surgical connection of two separate anatomic structures). NCIt: C78206 kidney anastomotic leak AE 10065803 NCIt: C78406 CTCAE: E11879 MW, YH a medical intervention site AE that has the finding of leakage of urine due to breakdown of a kidney anastomosis (surgical connection of two separate anatomic structures). ureteric anastomotic leak AE 10065814 MW, YH NCIt: C78662 CTCAE: E11987 a medical intervention site AE that has the finding of leakage due to breakdown of a ureteral anastomosis (surgical connection of two separate anatomic structures). urethral anastomotic leak 10065815 a medical intervention site AE that has the finding of leakage due to breakdown of a urethral anastomosis (surgical connection of two separate anatomic structures). MW, YH NCIt: C78667 CTCAE: E11993 prolapse of urostomy AE 10065822 NCIt: C78571 CTCAE: E11920 a medical intervention site AE that has the finding of displacement of the urostomay MW, YH gastrointestinal anastomotic leak 10065879 CTCAE: E11715 NCIt: C78318 a medical intervention site AE that has the finding of leakage due to breakdown of a gastrointestinal anastomosis (surgical connection of two separate anatomic structures). MW, YH urostomy leak AE 10065882 CTCAE: E11999 NCIt: C78679 MW, YH a medical intervention site AE that has the finding of leakage of contents from a urostomy. urostomy obstruction AE 10065883 MW, YH CTCAE: E12005 NCIt: C78680 a medical intervention site AE that has the finding of blockage of the urostomy. urostomy stenosis AE 10065885 NCIt: C78683 a medical intervention site AE that has the finding of narrowing of the opening of a urostomy. CTCAE: E12017 MW, YH uterine anastomotic leak AE 10065886 MW, YH NCIt: C78684 CTCAE: E12022 a medical intervention site AE that has the finding of leakage due to breakdown of a uterine anastomosis (surgical connection of two separate anatomic structures). vaginal anastomotic leak AE 10065887 CTCAE: E12034 a medical intervention site AE that has the finding of leakage due to breakdown of a vaginal anastomosis (surgical connection of two separate anatomic structures). MW, YH NCIt: C78698 vas deferens anastomotic leak AE 10065888 MW, YH a medical intervention site AE that has the finding of leakage due to breakdown of a vas deferens anastomosis (surgical connection of two separate anatomic structures). NCIt: C78704 CTCAE: E12040 large intestinal anastomotic leak AE 10065891 NCIt: C78408 MW, YH a medical intervention site AE that has the finding of leakage due to breakdown of an anastomosis (surgical connection of two separate anatomic structures) in the large intestine. CTCAE: E11885 small intestinal anastomotic leak AE 10065892 MW, YH CTCAE: E11942 a medical intervention site AE that has the finding of leakage due to breakdown of an anastomosis (surgical connection of two separate anatomic structures) in the small bowel. NCIt: C78612 gastric anastomotic leak AE 10065893 MW, YH a medical intervention site AE that has the finding of leakage due to breakdown of a gastric anastomosis (surgical connection of two separate anatomic structures). CTCAE: E11709 NCIt: C78310 rectal anastomotic leak AE 10065894 MW, YH CTCAE: E11932 NCIt: C78583 a medical intervention site AE that has the finding of leakage due to breakdown of a rectal anastomosis (surgical connection of two separate anatomic structures). spermatic cord anastomotic leak AE 10065897 NCIt: C78622 CTCAE: E11948 MW, YH a medical intervention site AE that has the finding of leakage due to breakdown of a spermatic cord anastomosis (surgical connection of two separate anatomic structures). stenosis of gastrointestinal stoma AE 10065898 NCIt: C78628 CTCAE: E11960 MW, YH a medical intervention site AE that has the finding of narrowing of the gastrointestinal stoma (surgically created opening on the surface of the body). esophageal anastomotic leak AE 10065961 MW, YH CTCAE: E11681 NCIt: C78270 a medical intervention site AE that has the finding of leakage due to breakdown of an esophageal anastomosis (surgical connection of two separate anatomic structures). bladder infection AE 10005047 NCIt: C26738 MW, YH an infection AE that has an infectious process involving the bladder. CTCAE: E11309 cervicitis infection AE 10008330 MW, YH CTCAE: E11337 an infection AE that has an infectious process involving the uterine cervix. NCIt: C78360 encephalitis infection AE 10014594 NCIt: C79550 CTCAE: E11365 an infection AE that has an infectious process involving the brain tissue. MW, YH encephalomyelitis infection AE 10014621 NCIt: C79551 MW, YH CTCAE: E11369 an infection AE that has an infectious process involving the brain and spinal cord tissues. endocarditis infective AE 10014678 CTCAE: E11373 an infection AE that has an infectious process involving the endocardial layer of the heart. MW, YH NCIt: C78265 gum infection AE 10018784 MW, YH CTCAE: E11400 NCIt: C78329 an infection AE that has an infectious process involving the gums. infective myositis AE 10021918 NCIt: C26984 MW, YH an infection AE that has an infectious process involving the skeletal muscles. CTCAE: E11421 joint infection AE 10023216 an infection AE that has an infectious process involving a joint. MW, YH NCIt: C78402 CTCAE: E11426 kidney infection AE 10023424 MW, YH NCIt: C34965 an infection AE that has an infectious process involving the kidney. CTCAE: E11431 otitis externa AE 10033072 an infection AE that has an infectious process involving the outer ear and ear canal. Contributory factors include excessive water exposure (swimmer's ear infection) and cuts in the ear canal. Symptoms include fullness, itching, swelling and marked discomfort in the ear and ear drainage. NCIt: C3299 CTCAE: E11472 MW, YH salivary gland infection AE 10039413 NCIt: C78601 MW, YH an infection AE that has an infectious process involving the salivary gland. CTCAE: E11550 wound infection AE 10048038 an infection AE that has an infectious process involving the wound. MW, YH CTCAE: E11635 NCIt: C45234 tooth infection AE 10048762 an infection AE that has an infectious process involving a tooth. MW, YH NCIt: C78639 CTCAE: E11594 prostate infection AE 10050662 MW, YH NCIt: C27615 an infection AE that has an infectious process involving the prostate gland. CTCAE: E11540 lymph gland infection AE 10050823 NCIt: C26821 an infection AE that has an infectious process involving the lymph nodes. MW, YH CTCAE: E11449 pancreas infection AE 10051741 MW, YH CTCAE: E11487 an infection AE that has an infectious process involving the pancreas. NCIt: C78517 urethral infection AE 10052298 MW, YH NCIt: C78671 CTCAE: E11609 an infection AE that has an infectious process involving the urethra. ovarian infection AE 10055005 NCIt: C78512 CTCAE: E11482 MW, YH an infection AE that has an infectious process involving the ovary. abdominal infection AE 10056519 an infection AE that has an infectious process involving the abdominal cavity. CTCAE: E11282 NCIt: C35669 MW, YH hepatic infection AE 10056522 NCIt: C78339 an infection AE that has an infectious process involving the liver. MW, YH CTCAE: E11406 phlebitis infective AE 10056627 CTCAE: E11530 NCIt: C78558 an infection AE that has an infectious process involving the vein. Clinical manifestations include erythema, marked discomfort, swelling, and induration along the course of the infected vein. MW, YH peritoneal infection AE 10057262 MW, YH CTCAE: E11521 an infection AE that has an infectious process involving the peritoneum. NCIt: C78540 mediastinal infection AE 10057483 an infection AE that has an infectious process involving the mediastinum. MW, YH CTCAE: E11454 NCIt: C26827 pelvic infection AE 10058674 an infection AE that has an infectious process involving the pelvic cavity. MW, YH NCIt: C3889 CTCAE: E11501 esophageal infection AE 10058804 an infection AE that has an infectious process involving the esophagus. CTCAE: E11386 MW, YH NCIt: C78277 enterocolitis infectious AE 10058838 MW, YH CTCAE: E11381 an infection AE that has an infectious process involving the small and large intestines. NCIt: C80513 rhinitis infective AE 10059827 CTCAE: E11548 NCIt: C78599 MW, YH an infection AE that has an infectious process involving the nasal mucosal. bone infection AE 10061017 NCIt: C26839 MW, YH CTCAE: E11314 an infection AE that has an infectious process involving the bones. pleural infection AE 10061351 CTCAE: E11535 MW, YH an infection AE that has an infectious process involving the pleura. NCIt: C78563 anorectal infection AE 10061640 CTCAE: E11286 NCIt: C78174 MW, YH an infection AE that has an infectious process involving the anal area and the rectum. biliary tract infection AE 10061695 CTCAE: E11305 MW, YH NCIt: C26718 an infection AE that has an infectious process involving the biliary tract. penile infection AE 10061912 an infection AE that has an infectious process involving the penis. NCIt: C78526 MW, YH CTCAE: E11506 splenic infection AE 10062112 MW, YH an infection AE that has an infectious process involving the spleen. CTCAE: E11584 NCIt: C78627 scrotal infection AE 10062156 NCIt: C78606 CTCAE: E11555 an infection AE that has an infectious process involving the scrotum. MW, YH uterine infection AE 10062233 MW, YH NCIt: C26764 an infection AE that has an infectious process involving the endometrium. It may extend to the myometrium and parametrial tissues. CTCAE: E11619 gallbladder infection AE 10062632 NCIt: C78306 an infection AE that has an infectious process involving the gallbladder. CTCAE: E11396 MW, YH stoma site infection AE 10064505 an infection AE that has an infectious process involving a stoma (surgically created opening on the surface of the body). CTCAE: E11588 MW, YH NCIt: C78629 arteritis infective AE 10065744 NCIt: C34399 CTCAE: E11301 MW, YH an infection AE that has an infectious process involving an artery. duodenal infection AE 10065752 MW, YH an infection AE that has an infectious process involving the duodenum. NCIt: C78258 CTCAE: E11360 lip infection AE 10065755 MW, YH NCIt: C78434 an infection AE that has an infectious process involving the lips. CTCAE: E11440 cecal infection AE 10065761 an infection AE that has an infectious process involving the cecum. CTCAE: E11333 MW, YH NCIt: C78235 mucosal infection AE 10065764 MW, YH NCIt: C78454 an infection AE that has an infectious process involving a mucosal surface. CTCAE: E11462 cranial nerve infection AE 10065765 an infection AE that has an infectious process involving a cranial nerve. CTCAE: E11352 NCIt: C78248 MW, YH peripheral nerve infection AE 10065766 CTCAE: E11516 an infection AE that has an infectious process involving the peripheral nerves. MW, YH NCIt: C27589 small intestine infection AE 10065771 NCIt: C78618 CTCAE: E11574 MW, YH an infection AE that has an infectious process involving the small intestine. vulval infection AE 10065772 MW, YH NCIt: C78716 an infection AE that has an infectious process involving the vulva. CTCAE: E11629 anal pain AE 10002167 NCIt: C78172 CTCAE: E10486 a pain AE that has a sensation of marked discomfort in the anal region. MW, YH gallbladder pain AE 10017638 a pain AE that has a sensation of marked discomfort in the gallbladder region. CTCAE: E11204 MW, YH NCIt: C78304 gastrointestinal pain AE 10017999 MW, YH CTCAE: E10755 a pain AE that has a sensation of marked discomfort in the gastrointestinal region. NCIt: C78320 hepatic pain AE 10019705 MW, YH CTCAE: E11224 NCIt: C78341 a pain AE that has a sensation of marked discomfort in the liver region. lip pain AE 10024561 MW, YH CTCAE: E10857 NCIt: C79684 a pain AE that has a sensation of marked discomfort of the lip. rectal pain AE 10038072 a pain AE that has a sensation of marked discomfort in the rectal region. MW, YH NCIt: C78587 CTCAE: E10977 stomach pain AE 10042112 MW, YH NCIt: C78630 a pain AE that has a sensation of marked discomfort in the stomach. CTCAE: E11044 non-cardiac chest pain AE 10062501 CTCAE: E11163 NCIt: C78504 a chest pain AE that has discomfort in the chest unrelated to a heart disorder. MW, YH tracheal obstruction AE 10044291 NCIt: C78645 CTCAE: E11975 MW, YH a respiratory system AE that has the finding of blockage of the lumen of the trachea. colonic hemorrhage AE 10009998 NCIt: C78240 a hemorrhage AE that has bleeding from the colon. CTCAE: E10533 MW, YH esophageal hemorrhage AE 10015384 MW, YH a hemorrhage AE that has bleeding from the esophagus. CTCAE: E10645 NCIt: C78271 esophageal varices hemorrhage AE 10015453 a hemorrhage AE that has bleeding from esophageal varices. NCIt: C78282 CTCAE: E10682 MW, YH hepatic hemorrhage AE 10019678 CTCAE: E11215 MW, YH NCIt: C78338 a hemorrhage AE that has bleeding from the liver. oral hemorrhage AE 10030980 NCIt: C79699 MW, YH CTCAE: E10898 a hemorrhage AE that has bleeding from the mouth. pancreatic hemorrhage AE 10033626 NCIt: C78521 MW, YH CTCAE: E10920 a hemorrhage AE that has bleeding from the pancreas. retroperitoneal hemorrhage AE 10038981 MW, YH CTCAE: E10998 a hemorrhage AE that has bleeding from the retroperitoneal area. NCIt: C26944 lower gastrointestinal hemorrhage AE 10051746 a hemorrhage AE that has bleeding from the lower gastrointestinal tract (small intestine, large intestine, and anus). CTCAE: E10861 MW, YH NCIt: C78438 duodenal hemorrhage AE 10055242 CTCAE: E10588 NCIt: C78257 MW, YH a hemorrhage AE that has bleeding from the duodenum. ileal hemorrhage AE 10055287 CTCAE: E10783 MW, YH NCIt: C78353 a hemorrhage AE that has bleeding from the ileal wall. intra-abdominal hemorrhage AE 10055291 a hemorrhage AE that has bleeding in the abdominal cavity. MW, YH NCIt: C78372 CTCAE: E10817 jejunal hemorrhage AE 10055300 CTCAE: E10828 NCIt: C78397 MW, YH a hemorrhage AE that has bleeding from the jejunal wall. postoperative hemorrhage AE 10055322 NCIt: C34938 a hemorrhage AE that has the finding of bleeding occurring after a surgical procedure. MW, YH CTCAE: E11903 tracheal hemorrhage AE 10062548 CTCAE: E11969 a hemorrhage AE that has the finding of bleeding from the trachea. MW, YH NCIt: C78642 cecal hemorrhage AE 10065747 MW, YH CTCAE: E10511 a hemorrhage AE that has bleeding from the cecum. NCIt: C78234 anal stenosis AE 10002176 CTCAE: E10490 an anus AE that has a narrowing of the lumen of the anal canal. NCIt: C78173 MW, YH biliary fistula AE 10004665 NCIt: C79540 CTCAE: E11179 MW, YH a digestive system AE that has an abnormal communication between the bile ducts and another organ or anatomic site. bloating AE 10005265 MW, YH NCIt: C78213 CTCAE: E10508 a digestive system AE that has subject-reported feeling of uncomfortable fullness of the abdomen. colonic fistula AE 10009995 a digestive system AE that has an abnormal communication between the large intestine and another organ or anatomic site. MW, YH CTCAE: E10527 NCIt: C78239 colonic obstruction AE 10010000 MW, YH a digestive system AE that has blockage of the normal flow of the intestinal contents in the colon. CTCAE: E10539 NCIt: C78241 colonic perforation AE 10010001 a digestive system AE that has a rupture in the colonic wall. NCIt: C78242 MW, YH CTCAE: E10545 colonic ulcer AE 10010006 CTCAE: E10556 MW, YH a digestive system AE that has a circumscribed, inflammatory and necrotic erosive lesion on the mucosal surface of the colon. NCIt: C78244 duodenal fistula AE 10013828 CTCAE: E10582 MW, YH a duodenum AE that has an abnormal communication between the duodenum and another organ or anatomic site. NCIt: C78256 duodenal obstruction AE 10013830 MW, YH NCIt: C79548 a duodenum AE that has blockage of the normal flow of stomach contents through the duodenum. CTCAE: E10594 duodenal perforation AE 10013832 MW, YH NCIt: C78259 CTCAE: E10600 a duodenum AE that has a rupture in the duodenal wall. esophageal obstruction AE 10015387 an esophagus AE that has blockage of the normal flow of the contents in the esophagus. CTCAE: E10655 MW, YH NCIt: C78279 esophageal ulcer AE 10015451 NCIt: C26950 an esophagus AE that has a circumscribed, inflammatory and necrotic erosive lesion on the mucosal surface of the esophageal wall. CTCAE: E10676 MW, YH gallbladder fistula AE 10017631 a digestive system AE that has an abnormal communication between the gallbladder and another organ or anatomic site. MW, YH NCIt: C78305 CTCAE: E11189 gallbladder obstruction AE 10017636 MW, YH a digestive system AE that has blockage of the normal flow of the contents of the gallbladder. NCIt: C78308 CTCAE: E11198 gastric perforation AE 10017815 a gastrointestinal perforation AE that occurs in the stomach wall. MW, YH NCIt: C78316 CTCAE: E10716 gastrointestinal fistula AE 10017877 MW, YH CTCAE: E10749 NCIt: C78319 a gastrointestinal disoder AE that has an abnormal communication between any part of the gastrointestinal system and another organ or anatomic site. gastroparesis AE 10018043 CTCAE: E10759 NCIt: C80512 a gastric AE that has an incomplete paralysis of the muscles of the stomach wall resulting in delayed emptying of the gastric contents into the small intestine. MW, YH ileal stenosis AE 10021307 MW, YH NCIt: C78356 a digestive system AE that has a narrowing of the lumen of the ileum. CTCAE: E10800 ileal ulcer AE 10021309 a digestive system AE that has a circumscribed, inflammatory and necrotic erosive lesion on the mucosal surface of the ileum. NCIt: C78357 MW, YH CTCAE: E10806 jejunal perforation AE 10023174 NCIt: C78399 MW, YH a digestive system AE that has a rupture in the jejunal wall. CTCAE: E10840 jejunal stenosis AE 10023176 CTCAE: E10845 a digestive system AE that has a narrowing of the lumen of the jejunum. MW, YH NCIt: C78400 jejunal ulcer AE 10023177 MW, YH a digestive system AE that has a circumscribed, inflammatory and necrotic erosive lesion on the mucosal surface of the jejunum. NCIt: C78401 CTCAE: E10851 malabsorption AE 10025476 NCIt: C3214 a digestive system AE that has inadequate absorption of nutrients in the small intestine. Symptoms include abdominal marked discomfort, bloating and diarrhea. MW, YH CTCAE: E10867 obstruction gastric AE 10029957 a digestive system AE that has blockage of the normal flow of the contents in the stomach. MW, YH NCIt: C78505 CTCAE: E10882 perforation bile duct AE 10034405 CTCAE: E11234 NCIt: C78528 a digestive system AE that has a rupture in the wall of the extrahepatic or intrahepatic bile duct. MW, YH rectal fistula AE 10038062 MW, YH a digestive system AE that has an abnormal communication between the rectum and another organ or anatomic site. NCIt: C79713 CTCAE: E10949 rectal perforation AE 10038073 MW, YH NCIt: C78588 CTCAE: E10981 a digestive system AE that has a rupture in the rectal wall. rectal stenosis AE 10038079 CTCAE: E10986 MW, YH a digestive system AE that has a narrowing of the lumen of the rectum. NCIt: C78589 rectal ulcer AE 10038080 CTCAE: E10992 a digestive system AE that has a circumscribed, inflammatory and necrotic erosive lesion on the mucosal surface of the rectum. NCIt: C78590 MW, YH salivary gland fistula AE 10039411 a digestive system AE that has an abnormal communication between a salivary gland and another organ or anatomic site. NCIt: C79715 CTCAE: E11009 MW, YH small intestinal perforation AE 10041103 a digestive system AE that has a rupture in the small intestine wall. NCIt: C78616 MW, YH CTCAE: E11027 pancreatic fistula AE 10049192 MW, YH CTCAE: E10914 a digestive system AE that has an abnormal communication between the pancreas and another organ or anatomic site. NCIt: C79701 duodenal stenosis AE 10050094 CTCAE: E10605 MW, YH NCIt: C78260 a duodenum AE that has a narrowing of the lumen of the duodenum. bile duct stenosis AE 10051341 MW, YH NCIt: C78182 a digestive system AE that has a narrowing of the lumen of the bile duct. CTCAE: E11173 gastric necrosis AE 10051886 CTCAE: E10712 NCIt: C78314 MW, YH a gastric disorder AE that has a necrotic process occurring in the gastric wall. pancreatic necrosis AE 10058096 NCIt: C78522 a digestive system AE that has a necrotic process occurring in the pancreas. CTCAE: E10926 MW, YH gallbladder necrosis AE 10059446 MW, YH a digestive system AE that has a necrotic process occurring in the gallbladder. NCIt: C78307 CTCAE: E11195 gastric stenosis AE 10061970 a gastric disorder AE that has a narrowing of the lumen of the stomach. CTCAE: E10721 MW, YH NCIt: C78317 enterovesical fistula AE 10062570 a digestive system AE that has an abnormal communication between the urinary bladder and the intestine. MW, YH NCIt: C78266 CTCAE: E10633 pancreatic duct stenosis AE 10065703 a digestive system AE that has a narrowing of the lumen of the pancreatic duct. MW, YH NCIt: C78519 CTCAE: E10908 peritoneal necrosis AE 10065704 a digestive system AE that has a necrotic process occurring in the peritoneum. CTCAE: E10939 MW, YH NCIt: C78543 rectal obstruction AE 10065707 CTCAE: E10971 NCIt: C78586 MW, YH a digestive system AE that has blockage of the normal flow of the intestinal contents in the rectum. gastrointestinal stoma necrosis 10065712 a gastrointestinal disoder AE that has the finding of a necrotic process occurring in the gastrointestinal tract stoma. MW, YH NCIt: C78321 CTCAE: E11721 gastric fistula AE 10065713 NCIt: C79595 CTCAE: E10700 MW, YH a gastric disorder AE that has an abnormal communication between the stomach and another organ or anatomic site. jejunal fistula AE 10065719 MW, YH CTCAE: E10822 a digestive system AE that has an abnormal communication between the jejunum and another organ or anatomic site. NCIt: C78396 anal necrosis AE 10065722 NCIt: C78171 CTCAE: E10482 an anus AE that has a necrotic process occurring in the anal region. MW, YH esophageal necrosis AE 10065727 MW, YH an esophagus AE that has a necrotic process occurring in the esophageal wall. CTCAE: E10651 NCIt: C78278 ileal fistula AE 10065728 NCIt: C78352 MW, YH CTCAE: E10777 a digestive system AE that has an abnormal communication between the ileum and another organ or anatomic site. ileal obstruction AE 10065730 MW, YH NCIt: C78354 CTCAE: E10789 a digestive system AE that has blockage of the normal flow of the intestinal contents in the ileum. jejunal obstruction AE 10065732 a digestive system AE that has blockage of the normal flow of the intestinal contents in the jejunum. NCIt: C78398 MW, YH CTCAE: E10834 esophageal fistula AE 10065851 NCIt: C79574 MW, YH CTCAE: E10639 an esophagus AE that has an abnormal communication between the esophagus and another organ or anatomic site. dry eye AE 10013774 NCIt: C34553 CTCAE: E10363 an eye AE that has dryness of the cornea and conjunctiva. MW, YH flashing lights AE 10016757 an eye AE that has a sudden or brief burst of light. MW, YH NCIt: C50568 CTCAE: E10384 floaters AE 10016778 an eye AE that has an individual seeing spots before their eyes. The spots are shadows of opaque cell fragments in the vitreous humor or lens. NCIt: C37955 CTCAE: E10388 MW, YH night blindness AE 10029404 CTCAE: E10401 MW, YH NCIt: C34850 an eye AE that has an inability to see clearly in dim light. retinal tear AE 10038897 MW, YH CTCAE: E10425 NCIt: C50732 an eye AE that has a small laceration of the retina, this occurs when the vitreous separates from the retina. Symptoms include flashes and floaters. retinal vascular disorder AE 10038901 CTCAE: E10429 an eye AE that has pathological retinal blood vessels that adversely affects vision. NCIt: C35170 MW, YH vitreous hemorrhage AE 10047656 an eye AE that has blood extravasation into the vitreous humor. NCIt: C50469 CTCAE: E10447 MW, YH watering eyes AE 10047848 NCIt: C78717 MW, YH an eye AE that has excessive tearing in the eyes; it can be caused by overproduction of tears or impaired drainage of the tear duct. CTCAE: E10452 optic nerve disorder AE 10061322 NCIt: C79698 an eye AE that has involvement of the optic nerve (second cranial nerve). CTCAE: E10406 MW, YH scleral disorder AE 10061510 CTCAE: E10437 NCIt: C79717 MW, YH an eye AE that has involvement of the sclera of the eye. vestibular disorder AE 10047386 CTCAE: E10295 NCIt: C27166 an ear AE that has dizziness, imbalance, nausea, and vision problems. MW, YH external ear pain AE 10065785 MW, YH an ear pain AE that has a sensation of marked discomfort in the external ear region. NCIt: C78285 CTCAE: E10272 constrictive pericarditis AE 10010783 CTCAE: E10120 NCIt: C78246 MW, YH a cardiovascular AE that has a thickened and fibrotic pericardial sac; these fibrotic changes impede normal myocardial function by restricting myocardial muscle action. sick sinus syndrome AE 10040639 NCIt: C62244 MW, YH CTCAE: E10202 a cardiovascular AE that has a dysrhythmia with alternating periods of bradycardia and atrial tachycardia accompanied by syncope, fatigue and dizziness. pericardial tamponade AE 10053565 a cardiovascular AE that has an increase in intrapericardial pressure due to the collection of blood or fluid in the pericardium. NCIt: C50481 MW, YH CTCAE: E10177 tricuspid valve disease AE 10061389 MW, YH CTCAE: E10224 NCIt: C78649 a cardiovascular AE that has a defect in tricuspid valve function or structure. mitral valve disease AE 10061532 a cardiovascular AE that has a defect in mitral valve function or structure. NCIt: C78446 MW, YH CTCAE: E10134 pulmonary valve disease AE 10061541 a cardiovascular AE that has a defect in pulmonary valve function or structure. NCIt: C78579 CTCAE: E10186 MW, YH aortic valve disease AE 10061589 CTCAE: E10071 MW, YH NCIt: C78650 a cardiovascular AE that has a defect in aortic valve function or structure. tooth discoloration AE 10044031 CTCAE: E11052 a bone AE that has a change in tooth hue or tint. MW, YH NCIt: C80112 neck edema AE 10054482 MW, YH an edema AE that has swelling due to an accumulation of excessive fluid in the neck. CTCAE: E11159 NCIt: C78501 edema trunk AE 10058720 CTCAE: E11090 MW, YH NCIt: C78263 an edema AE that has swelling due to excessive fluid accumulation in the trunk area. proctitis AE 10036774 CTCAE: E10943 MW, YH NCIt: C38011 an inflammation AE that has inflammation of the rectum. rectal mucositis AE 10063190 NCIt: C78584 an inflammation AE that has inflammation of the mucous membrane of the rectum MW, YH CTCAE: E10961 anal mucositis AE 10065721 MW, YH CTCAE: E10476 NCIt: C78170 an inflammation AE that has inflammation of the mucous membrane of the anus. external ear inflammation AE 10065837 an inflammation AE that has inflammation, swelling and redness to the outer ear and ear canal. NCIt: C79601 MW, YH CTCAE: E10266 middle ear inflammation AE 10065838 MW, YH an inflammation AE that has inflammation (physiologic response to irritation), swelling and redness to the middle ear. NCIt: C34885 CTCAE: E10281 death neonatal AE 10011912 NCIt: C80082 MW, YH CTCAE: E11078 a death AE that has cessation of life occurring during the first 28 days of life. ankle fracture AE 10002544 NCIt: C26989 CTCAE: E11640 a fracture AE that has a break in the continuity of the ankle bone. Symptoms include marked discomfort, swelling and difficulty moving the affected leg and foot. MW, YH hip fracture AE 10020100 CTCAE: E11726 a fracture AE that has the finding of traumatic injury to the hip in which the continuity of either the femoral head, femoral neck, intertrochanteric or subtrochanteric regions is broken. NCIt: C26794 MW, YH spinal fracture AE 10041569 NCIt: C80516 a fracture AE that has the finding of traumatic injury to the spine in which the continuity of a vertebral bone is broken. MW, YH CTCAE: E11954 wrist fracture AE 10048049 a fracture AE that has the finding of traumatic injury to the wrist joint in which the continuity of a wrist bone is broken. MW, YH CTCAE: E12069 NCIt: C80517 bronchial infection AE 10055078 a lung infection AE that has an infectious process involving the bronchi. NCIt: C2911 MW, YH CTCAE: E11323 CPK increased AE 10011268 MW, YH a muscle enzyme level increased AE that has the finding based on laboratory test results that indicate an increase in levels of creatine phosphokinase in a blood specimen. CTCAE: E12132 NCIt: C78247 radiation recall reaction (dermatologic) AE 10037767 CTCAE: E11926 MW, YH a recall phenomenon AE that has the finding of acute skin inflammatory reaction caused by drugs, especially chemotherapeutic agents, for weeks or months following radiotherapy. The inflammatory reaction is confined to the previously irradiated skin and the symptoms disappear after the removal of the pharmaceutical agent. NCIt: C78580 CD4 lymphocytes decreased AE 10007839 MW, YH NCIt: C78233 CTCAE: E12122 an immunology and allergy investigation result abnormal AE that has the finding based on laboratory test results that indicate an decrease in levels of CD4 lymphocytes in a blood specimen. vital capacity abnormal AE 10047580 CTCAE: E12220 NCIt: C78715 a respiratory and pulmonary investigation result abnormal AE that has the finding based on pulmonary function test results that indicate an abnormal vital capacity (amount of exhaled after a maximum inhalation) when compared to the predicted value. MW, YH carbon monoxide diffusing capacity decreased AE 10065906 MW, YH CTCAE: E12112 a respiratory and pulmonary investigation result abnormal AE that has the finding based on lung function test results that indicate a decrease in the lung capacity to absorb carbon monoxide. NCIt: C78229 blood antidiuretic hormone abnormal AE 10005332 CTCAE: E12092 NCIt: C78214 an endocrine investigation result abnormal AE that has the finding based on laboratory test results that indicate abnormal levels of antidiuretic hormone in the blood specimen. MW, YH blood corticotrophin decreased AE 10005452 an endocrine investigation result abnormal AE that has the finding based on laboratory test results that indicate an decrease in levels of corticotrophin in a blood specimen. CTCAE: E12101 MW, YH NCIt: C78215 blood gonadotrophin abnormal AE 10005561 NCIt: C78216 MW, YH an endocrine investigation result abnormal AE that has the finding based on laboratory test results that indicate abnormal levels of gonadotrophin hormone in a blood specimen. CTCAE: E12105 blood prolactin abnormal AE 10005778 an endocrine investigation result abnormal AE that has the finding based on laboratory test results that indicate abnormal levels of prolactin hormone in a blood specimen. CTCAE: E12109 NCIt: C78217 MW, YH growth hormone abnormal AE 10018748 NCIt: C78327 an endocrine investigation result abnormal AE that has the finding based on laboratory test results that indicate abnormal levels of growth hormone in a biological specimen. MW, YH CTCAE: E12166 pancreatic enzymes decreased AE 10062646 MW, YH NCIt: C78520 CTCAE: E12203 an enzyme investigation result abnormal AE that has the finding based on laboratory test results that indicate an decrease in levels of pancreatic enzymes in a biological specimen. fibrinogen decreased AE 10016596 MW, YH NCIt: C78300 a hematology investigation result abnormal AE that has the finding based on laboratory test results that indicate an decrease in levels of fibrinogen in a blood specimen. CTCAE: E12151 haptoglobin decreased AE 10019150 NCIt: C78330 a hematology investigation result abnormal with the finding based on laboratory test results that indicate an decrease in levels of haptoglobin in a blood specimen. CTCAE: E12169 MW, YH acute coronary syndrome AE 10051592 MW, YH NCIt: C53652 a coronary heart disease AE that has signs and symptoms related to acute ischemia of the myocardium secondary to coronary artery disease. The clinical presentation covers a spectrum of heart diseases from unstable angina to myocardial infarction. CTCAE: E10066 eyelid function disorder AE 10061145 CTCAE: E10380 MW, YH an eyelid disorder AE that has impaired eyelid function. NCIt: C78288 aortic injury AE 10002899 CTCAE: E11644 MW, YH NCIt: C35623 an injury AE that has the finding of damage to the aorta. arterial injury AE 10003162 an injury AE that has the finding of damage to an artery CTCAE: E11648 MW, YH NCIt: C35401 injury to carotid artery AE 10022161 CTCAE: E11730 MW, YH NCIt: C79599 an injury AE that has the finding of damage to the carotid artery. injury to inferior vena cava AE 10022213 MW, YH CTCAE: E11734 an injury AE that has the finding of damage to the inferior vena cava. NCIt: C78363 injury to superior vena cava AE 10022356 CTCAE: E11741 an injury AE that has the finding of damage to the superior vena cava. MW, YH NCIt: C78365 intraoperative gastrointestinal injury AE 10065825 MW, YH CTCAE: E11798 an injury AE that has the finding of damage to the gastrointestinal system during a surgical procedure. NCIt: C78380 intraoperative arterial injury AE 10065826 CTCAE: E11770 an injury AE that has the finding of damage to an artery during a surgical procedure. MW, YH NCIt: C78375 intraoperative hepatobiliary injury AE 10065827 an injury AE that has the finding of damage to the hepatic parenchyma and/or biliary tract during a surgical procedure. CTCAE: E11814 MW, YH NCIt: C78382 intraoperative urinary injury AE 10065828 NCIt: C78391 CTCAE: E11867 MW, YH an injury AE that has the finding of damage to the urinary system during a surgical procedure. intraoperative musculoskeletal injury AE 10065829 MW, YH CTCAE: E11820 an injury AE that has the finding of damage to the musculoskeletal system during a surgical procedure. NCIt: C78383 intraoperative neurological injury AE 10065830 CTCAE: E11826 MW, YH an injury AE that has the finding of damage to the nervous system during a surgical procedure. NCIt: C78384 intraoperative breast injury AE 10065831 NCIt: C78376 MW, YH CTCAE: E11776 an injury AE that has the finding of damage to the breast parenchyma during a surgical procedure. intraoperative respiratory injury AE 10065832 CTCAE: E11850 NCIt: C78388 an injury AE that has the finding of damage to the respiratory system during a surgical procedure. MW, YH intraoperative endocrine injury AE 10065834 CTCAE: E11792 an injury AE that has the finding of damage to the endocrine gland during a surgical procedure. MW, YH NCIt: C78379 intraoperative reproductive tract injury AE 10065840 CTCAE: E11844 an injury AE that has the finding of damage to the reproductive organs during a surgical procedure. MW, YH NCIt: C78387 intraoperative ocular injury AE 10065841 NCIt: C78385 CTCAE: E11832 an injury AE that has the finding of damage to the eye during a surgical procedure. MW, YH lintraoperative head and neck injury AE 10065842 MW, YH CTCAE: E11804 NCIt: C78381 an injury AE that has the finding of damage to the head and neck during a surgical procedure. intraoperative cardiac injury AE 10065843 CTCAE: E11782 an injury AE that has the finding of damage to the heart during a surgical procedure. MW, YH NCIt: C78377 intraoperative ear injury AE 10065844 CTCAE: E11786 MW, YH NCIt: C78378 an injury AE that has the finding of damage to the ear during a surgical procedure. intraoperative renal injury AE 10065845 CTCAE: E11838 an injury AE that has the finding of damage to the kidney during a surgical procedure. NCIt: C78386 MW, YH intraoperative skin injury AE 10065846 MW, YH NCIt: C78389 an injury AE finding of damage to the skin during a surgical procedure. CTCAE: E11856 intraoperative splenic injury AE 10065847 NCIt: C78390 CTCAE: E11862 an injury AE that has the finding of damage to the spleen during a surgical procedure. MW, YH intraoperative venous injury AE 10065848 CTCAE: E11873 MW, YH an injury AE that has the finding of damage to a vein during a surgical procedure. NCIt: C78392 injury to jugular vein AE 10065849 an injury AE that has the finding of damage to the jugular vein. CTCAE: E11737 NCIt: C78364 MW, YH appendicitis perforated AE 10003012 NCIt: C78178 CTCAE: E11296 an appendicitis AE that has acute inflammation to the vermiform appendix caused by a pathogenic agent with gangrenous changes resulting in the rupture of the appendiceal wall. The appendiceal wall rupture causes the release of inflammatory and bacterial contents from the appendiceal lumen into the abdominal cavity. MW, YH cardiac troponin T increased 10007613 CTCAE: E12119 MW, YH NCIt: C78231 a troponin AE which indicates increased levels of cardiac troponin T in a biological specimen conjunctivitis infective AE 10010742 an eye infection AE that has an infectious process involving the conjunctiva. Clinical manifestations include pink or red color in the eyes. CTCAE: E11342 MW, YH NCIt: C35704 endophthalmitis AE 10014801 an eye infection AE that has an infectious process involving the internal structures of the eye. NCIt: C34586 MW, YH CTCAE: E11377 periorbital infection AE 10051472 CTCAE: E11511 MW, YH an eye infection AE that has an infectious process involving the orbit of the eye. NCIt: C78531 corneal infection AE 10061788 MW, YH CTCAE: E11347 NCIt: C26805 an eye infection AE that has an infectious process involving the cornea. Grade 1 fatigue AE a fatigue AE that has fatigue relieved by rest CTCAE: E11099 MW, YH Grade 2 fatigue AE MW, YH a fatigue AE that has fatigue not relieved by rest; limiting instrumental activities of daily living CTCAE: E11100 Grade 3 fatigue AE a fatigue AE that has fatigue not relieved by rest, limiting self care activities of daily living CTCAE: E11101 MW, YH Grade 2 myocardial infarction AE MW, YH a myocardial infarction AE that has asymptomatic and cardiac enzymes minimally abnormal and no evidence of ischemic ECG changes CTCAE: E10153 Grade 3 myocardial infarction AE a myocardial infarction AE that has severe symptoms; cardiac enzymes abnormal; hemodynamically stable; ECG changes consistent with infarction CTCAE: E10154 MW, YH Grade 3 pancreatitis AE a pancreatitis AE that has enzyme elevation or radiologic findings only CTCAE: E10931 MW, YH Grade 3 pancreatitis AE CTCAE: E10932 a pancreatitis AE that has severe pain; vomiting; medical intervention indicated (e.g., analgesia, nutritional support) MW, YH Grade 1 activated partial thromboplastin time prolonged AE an activated partial thromboplastin time prolonged AE that is greater than the upper limit of normal to 1.5 times the upper limit of normal CTCAE: E12074 MW, YH Grade 2 activated partial thromboplastin time prolonged AE an activated partial thromboplastin time prolonged AE that is 1.5-2.5 times the upper limit of normal MW, YH CTCAE: E12075 Grade 3 activated partial thromboplastin time prolonged AE an activated partial thromboplastin time prolonged AE that is greater than 2.5 times the upper limit of normal; hemorrhage CTCAE: E12076 MW, YH Grade 1 alanine aminotransferase level increased AE MW, YH CTCAE: E12078 an alanine aminotransferase level increased AE that is greater than the upper limit of normal to 3 times the upper limit of normal Grade 2 alanine aminotransferase level increased AE an alanine aminotransferase level increased AE that is greater than 3 to 5 times the upper limit of normal CTCAE: E12079 MW, YH Grade 3 alanine aminotransferase level increased AE an alanine aminotransferase level increased AE that is greater than 5 to 20 times the upper limit of normal MW, YH CTCAE: E12080 Grade 4 alanine aminotransferase level increased AE an alanine aminotransferase level increased AE that is greater than 20 times the upper limit of normal CTCAE: E12081 MW, YH Grade 2 anal ulcer AE CTCAE: E10498 MW, YH an anal ulcer AE that is symptomatic; altered GI function Grade 3 anal ulcer AE an anal ulcer AE that has severely altered GI function; TPN indicated; elective operative or endoscopic intervention indicated; disabling CTCAE: E10499 MW, YH Grade 3 atrial flutter AE CTCAE: E10090 an atrial flutter AE that has symptomatic and incompletely controlled medically, or controlled with device (e.g., pacemaker), or ablation MW, YH Grade 2 otitis media AE MW, YH an otitis media AE that is localized; local intervention indicated (e.g., topical antibiotic, antifungal, or antiviral) CTCAE: E11478 Grade 3 otitis media AE CTCAE: E11479 an otitis media AE where IV antibiotic, antifungal, or antiviral intervention indicated; radiologic or operative intervention indicated MW, YH Grade 1 pericarditis AE CTCAE: E10181 MW, YH a pericarditis AE that has asymptomatic, ECG or physical findings (e.g., rub) consistent with pericarditis Grade 2 pericarditis AE CTCAE: E10182 MW, YH a pericarditis AE that has symptomatic pericarditis (e.g., chest pain) Grade 3 pericarditis AE MW, YH a pericarditis AE that has pericarditis with physiologic consequences (e.g., pericardial constriction) CTCAE: E10183 Grade 2 pharyngitis AE a pharyngitis AE that is localized; local intervention indicated (e.g., topical antibiotic, antifungal, or antiviral) CTCAE: E11526 MW, YH Grade 3 pharyngitis AE MW, YH CTCAE: E11527 a pharyngitis AE where IV antibiotic, antifungal, or antiviral intervention indicated; radiologic or operative intervention indicated Grade 1 fever AE MW, YH a fever AE that has 38.0 - 39.0 degrees C (100.4 - 102.2 degrees F) CTCAE: E11103 Grade 2 fever AE CTCAE: E11104 a fever AE that has greater than 39.0 - 40.0 degrees C (102.3 - 104.0 degrees F) MW, YH Grade 3 fever AE a fever AE that has greater than 40.0 degrees C (greater than104.0 degrees F) for less than or equal to 24 hrs CTCAE: E11105 MW, YH Grade 4 fever AE a fever AE that has greater than 40.0 degrees C (greater than104.0 degrees F) for more than 24 hrs CTCAE: E11106 MW, YH Grade 1 injection-site adverse event MW, YH CTCAE: E11139 an injection-site adverse event characterized by tenderness with or without associated symptoms (e.g., warmth, erythema, itching) Grade 2 injection-site adverse event CTCAE: E11140 an injection-site adverse event characterized by pain; lipodystrophy; edema; phlebitis MW, YH Grade 3 injection-site adverse event MW, YH an injection-site adverse event characterized by ulceration or necrosis; severe tissue damage; operative intervention indicated CTCAE: E11141 Grade 3 leukocytosis AE CTCAE: E10049 a leukocyte cell number increased AE where leukocytes are greater than 100,000/mm3 MW, YH Grade 4 leukocytosis AE MW, YH CTCAE: E10050 a leukocyte cell number increased AE that has clinical manifestations of leucostasis; urgent intervention indicated Grade 1 leukocyte cell number decreased AE CTCAE: E12233 MW, YH a leukocyte cell number decreased AE that is less than the lower limit of normal - 3000/mm3; less than the lower limit of normal - 3.0 x 10e9 /L Grade 2 leukocyte cell number decreased AE CTCAE: E12234 a leukocyte cell number decreased AE that is less than 3000 - 2000/mm3; less than 3.0 - 2.0 x 10e9 /L MW, YH Grade 3 leukocyte cell number decreased AE MW, YH a leukocyte cell number decreased AE that is less than 2000 - 1000/mm3; less than 2.0 - 1.0 x 10e9 /L CTCAE: E12235 Grade 4 leukocyte cell number decreased AE CTCAE: E12236 MW, YH a leukocyte cell number decreased AE that is less than 1000/mm3; less than 1.0 x 10e9 /L Grade 1 malaise AE a malaise AE that has uneasiness or lack of well being CTCAE: E11153 MW, YH Grade 2 malaise AE CTCAE: E11154 MW, YH a malaise AE that has uneasiness or lack of well being; limiting instrumental activities of daily living Grade 1 chills AE MW, YH a chills AE that has mild sensation of cold; shivering; chattering of teeth CTCAE: E11075 Grade 2 chills AE CTCAE: E11076 A chills AE that has moderate tremor of the entire body; narcotics indicated MW, YH Grade 3 chills AE MW, YH a chills AE that has severe or prolonged, not responsive to narcotics CTCAE: E11077 Grade 1 edema face AE CTCAE: E11083 an edema face AE that has localized facial edema MW, YH Grade 3 meningitis AE CTCAE: E11459 MW, YH a meningitis AE where IV antibiotic, antifungal, or antiviral intervention indicated; radiologic or operative intervention indicated; focal neurologic deficit Grade 2 serum sickness AE CTCAE: E11278 a serum sickness AE that has moderate arthralgia; fever, rash, urticaria, antihistamines indicated MW, YH Grade 3 serum sickness AE a serum sickness AE that has severe arthralgia or arthritis; extensive rash; steroids or IV fluids indicated MW, YH CTCAE: E11279 Grade 2 urinary tract infection AE CTCAE: E11615 MW, YH a urinary tract infection AE that is localized; local intervention indicated (e.g., topical antibiotic, antifungal, or antiviral) Grade 3 urinary tract infection AE a urinary tract infection AE where IV antibiotic, antifungal, or antiviral intervention indicated; radiologic or operative intervention indicated MW, YH CTCAE: E11616 Grade 2 laryngitis AE a laryngitis AE that has moderate symptoms; oral intervention indicated (e.g., antibiotic, antifungal, antiviral) MW, YH CTCAE: E11436 Grade 3 laryngitis AE CTCAE: E11437 a laryngitis AE where IV antibiotic, antifungal, or antiviral intervention indicated; radiologic or operative intervention indicated MW, YH Grade 1 dry mouth AE CTCAE: E10579 MW, YH a dry mouth AE that is symptomatic (e.g., dry or thick saliva) without significant dietary alteration; unstimulated saliva flow greater than0.2 ml/min Grade 2 dry mouth AE CTCAE: E10580 MW, YH a dry mouth AE that has moderate symptoms; oral intake alterations (e.g., copious water, other lubricants, diet limited to purees and/or soft, moist foods); unstimulated saliva 0.1 to 0.2 ml/min Grade 3 dry mouth AE MW, YH a dry mouth AE that has the inability to adequately aliment orally; tube feeding or TPN indicated; unstimulated saliva <0.1 ml/min CTCAE: E10581 Grade 2 pustular rash AE a pustular rash AE that is localized; local intervention indicated (e.g., topical antibiotic, antifungal, or antiviral) CTCAE: E11546 MW, YH Grade 3 pustular rash AE CTCAE: E11547 MW, YH a pustular rash AE where IV antibiotic, antifungal, or antiviral intervention indicated; radiologic or operative intervention indicated Grade 2 flatulence AE CTCAE: E10699 MW, YH a flatulence AE that has moderate; persistent; psychosocial sequelae Grade 1 weight loss AE MW, YH a weight loss AE that is 5 to less than 10% from baseline; intervention not indicated CTCAE: E12229 Grade 2 weight loss AE a weight loss AE that is 10 - less than 20% from baseline; nutritional support indicated CTCAE: E12230 MW, YH Grade 3 weight loss AE MW, YH a weight loss AE that is greater than or equal to 20% from baseline; tube feeding or TPN indicated CTCAE: E12231 Grade 1 abnormal gait AE CTCAE: E11113 an abnormal gait AE that has mild change in gait (e.g., wide-based, limping or hobbling) MW, YH Grade 2 abnormal gait AE CTCAE: E11114 an abnormal gait AE that has moderate change in gait (e.g., wide-based, limping or hobbling); assistive device indicated; limiting instrumental activities of daily living MW, YH Grade 1 anemia AE MW, YH CTCAE: E10011 an anemia AE where hemoglobin (Hgb) is less than the lower limit of normal (LLN), which is 10.0 g/dL, 6.2 mmol/L, or 100 g/L. Grade 2 anemia AE CTCAE: E10012 an anemia AE where hemoglobin (Hgb) is less than 10.0-8.0 g/dL, 6.2 -4.9 mmol/L, or 100 - 80 g/L. MW, YH Grade 3 anemia AE MW, YH an anemia AE where hemoglobin (Hgb) is less than 8.0 g/dL, 4.9 mmol/L, or 80 g/L. CTCAE: E10013 Grade 2 sinusitis AE a sinusitis AE that is localized; local intervention indicated (e.g., topical antibiotic, antifungal, or antiviral) CTCAE: E11564 MW, YH Grade 3 sinusitis AE CTCAE: E11565 MW, YH a sinusitis AE where IV antibiotic, antifungal, or antiviral intervention indicated; radiologic, endoscopic, or operative intervention indicated Grade 1 allergy AE an allergy AE that has transient flushing or rash, drug fever <38 degrees C (<100.4 degrees F); intervention not indicated MW, YH CTCAE: E11249 Grade 2 allergy AE MW, YH CTCAE: E11250 an allergy AE where intervention or infusion interruption indicated; responds promptly to symptomatic treatment (e.g., antihistamines, NSAIDS, narcotics); prophylactic medications indicated for less than or equal to 24 hrs Grade 3 allergy AE CTCAE: E11251 an allergy AE that is prolonged (e.g., not rapidly responsive to symptomatic medication and/or brief interruption of infusion); recurrence of symptoms following initial improvement; hospitalization indicated for clinical sequelae (e.g., renal impairment, pulmonary infiltrates) MW, YH Grade 1 dysphagia AE a dysphagia AE that is symptomatic, able to eat regular diet CTCAE: E10622 MW, YH Grade 2 dysphagia AE CTCAE: E10623 a dysphagia AE that is symptomatic and altered eating/swallowing MW, YH Grade 3 dysphagia AE a dysphagia AE that has severely altered eating/swallowing; tube feeding or TPN or hospitalization indicated MW, YH CTCAE: E10624 Grade 1 platelet count decreased AE MW, YH CTCAE: E12208 a platelet count decreased AE that is less than the lower limit of normal - 75,000/mm3; less than the lower limit of normal - 75.0 x 10e9 /L Grade 2 platelet count decreased AE a platelet count decreased AE that is less than 75,000 - 50,000/mm3; less than 75.0 - 50.0 x 10e9 /L MW, YH CTCAE: E12209 Grade 3 platelet count decreased AE MW, YH CTCAE: E12210 a platelet count decreased AE that is less than 50,000 - 25,000/mm3; less than 50.0 - 25.0 x 10e9 /L Grade 4 platelet count decreased AE a platelet count decreased AE that is less than 25,000/mm3; less than 25.0 x 10e9 /L CTCAE: E12211 MW, YH Grade 1 vomiting AE CTCAE: E11069 a vomiting AE that has 1 - 2 episodes (separated by 5 minutes) in 24 hrs MW, YH Grade 2 vomiting AE a vomiting AE that has 3 - 5 episodes (separated by 5 minutes) in 24 hrs CTCAE: E11070 MW, YH Grade 3 vomiting AE MW, YH CTCAE: E11071 a vomiting AE that has 6 or more episodes (separated by 5 minutes) in 24 hrs; tube feeding, TPN or hospitalization indicated Grade 1 constipation AE CTCAE: E10563 a constipation AE that has occasional or intermittent symptoms; occasional use of stool softeners, laxatives, dietary modification, or enema MW, YH Grade 2 constipation AE CTCAE: E10564 MW, YH a constipation AE that has persistent symptoms with regular use of laxatives or enemas; limiting instrumental activities of daily living Grade 3 constipation AE a constipation AE that has obstipation with manual evacuation indicated; limiting self care activities of daily living CTCAE: E10565 MW, YH Grade 2 lymphocyte count increased AE CTCAE: E12196 MW, YH a lymphocyte count increased AE that is greater than 4000/mm3 - 20,000/mm3 Grade 3 lymphocyte count increased AE MW, YH a lymphocyte count increased AE that is greater than 20,000/mm3 CTCAE: E12197 Grade 2 hypothermia AE a hypothermia AE that has 35 - greater than 32 degrees C; 95 - greater than 89.6 degrees F MW, YH CTCAE: E11123 Grade 3 hypothermia AE CTCAE: E11124 MW, YH a hypothermia AE that has 32 - greater than 28 degrees C; 89.6 - greater than 82.4 degrees F Grade 4 hypothermia AE CTCAE: E11125 MW, YH a hypothermia AE that has less than or equal to 28 degrees C; 82.4 degrees F; life-threatening consequences (e.g., coma, hypotension, pulmonary edema, acidemia, ventricular fibrillation) Grade 1 hematoma AE MW, YH a hematoma AE that is localized or in a dependent area CTCAE: E11667 Grade 2 hematoma AE CTCAE: E11668 MW, YH a hematoma AE that is generalized Grade 1 aspartate aminotransferase level increased AE an aspartate aminotransferase level increased AE that is greater than the upper limit of normal to 3 times the upper limit of normal CTCAE: E12088 MW, YH Grade 2 aspartate aminotransferase level increased AE MW, YH CTCAE: E12089 an aspartate aminotransferase level increased AE that is greater than 3 to 5 times the upper limit of normal Grade 3 aspartate aminotransferase level increased AE an aspartate aminotransferase level increased AE that is greater than 5 to 20 times the upper limit of normal MW, YH CTCAE: E12090 Grade 4 aspartate aminotransferase level increased AE an aspartate aminotransferase level increased AE that is greater than 20 times the upper limit of normal MW, YH CTCAE: E12091 Grade 3 atrial fibrillation AE CTCAE: E10084 MW, YH an atrial fibrillation AE that has symptomatic and incompletely controlled medically, or controlled with device (e.g., pacemaker), or ablation Grade 1 blood alkaline phosphatase increased AE a blood alkaline phosphatase increased AE that is greater than the upper limit of normal to 2.5 times the upper limit of normal CTCAE: E12083 MW, YH Grade 2 blood alkaline phosphatase increased AE CTCAE: E12084 a blood alkaline phosphatase increased AE that is greater than 2.5 to 5 times the upper limit of normal MW, YH Grade 3 blood alkaline phosphatase increased AE CTCAE: E12085 MW, YH a blood alkaline phosphatase increased AE that is greater than 5 to 20 times the upper limit of normal Grade 4 blood alkaline phosphatase increased AE CTCAE: E12086 MW, YH a blood alkaline phosphatase increased AE that is greater than 20 times the upper limit of normal Grade 1 blood amylase level increased AE a blood amylase level increased AE that is greater than the upper limit of normal - 1.5 times the upper limit of normal CTCAE: E12213 MW, YH Grade 2 blood amylase level increased AE MW, YH CTCAE: E12214 a blood amylase level increased AE that is greater than 1.5 - 2.0 times the upper limit of normal Grade 3 blood amylase level increased AE a blood amylase level increased AE that is greater than 2.0 - 5.0 times the upper limit of normal MW, YH CTCAE: E12215 Grade 4 blood amylase level increased AE CTCAE: E12216 MW, YH a blood amylase level increased AE that is greater than 5.0 times the upper limit of normal Grade 1 blood bilirubin level increased AE CTCAE: E12097 MW, YH a blood bilirubin level increased AE that is greater than the upper limit of normal to 1.5 times the upper limit of normal Grade 2 blood bilirubin level increased AE a blood bilirubin level increased AE that is greater than 1.5 to 3 times the upper limit of normal MW, YH CTCAE: E12098 Grade 3 blood bilirubin level increased AE MW, YH a blood bilirubin level increased AEgreater than3.0 - 10.0 x upper limit of normal CTCAE: E12099 Grade 4 blood bilirubin level increased AE CTCAE: E12100 a blood bilirubin level increased AE that is greater than 10 times the upper limit of normal MW, YH Grade 1 blood cholesterol increased AE a blood cholesterol increased AE that is greater than the upper limit of normal to 300 mg/dL; greater than the upper limit of normal to 7.75 mmol/L MW, YH CTCAE: E12128 Grade 2 blood cholesterol increased AE MW, YH CTCAE: E12129 a blood cholesterol increased AE that is greater than 300 - 400 mg/dL; greater than 7.75 - 10.34 mmol/L Grade 3 blood cholesterol increased AE MW, YH CTCAE: E12130 a blood cholesterol increased AE that is greater than 400 - 500 mg/dL; greater than 10.34 - 12.92 mmol/L Grade 4 blood cholesterol increased AE CTCAE: E12131 a blood cholesterol increased AE that is greater than 500 mg/dL; greater than 12.92 mmol/L MW, YH Grade 1 blood creatinine level increased AE CTCAE: E12138 a blood creatinine level increased AE that is greater than 1 - 1.5 times the baseline; greater than the upper limit of normal - 1.5 times the upper limit of normal MW, YH Grade 2 blood creatinine level increased AE a blood creatinine level increased AE that is greater than 1.5 - 3.0 times the baseline; greater than 1.5 - 3.0 times the upper limit of normal MW, YH CTCAE: E12139 Grade 3 blood creatinine level increased AE MW, YH CTCAE: E12140 a blood creatinine level increased AE that is greater than 3.0 times the baseline; greater than 3.0 - 6.0 times the upper limit of normal Grade 4 blood creatinine level increased AE CTCAE: E12141 a blood creatinine level increased AE that is greater than 6.0 times the upper limit of normal MW, YH Grade 1 bone marrow depression AE MW, YH a bone marrow depression AE categorized as mildly hypocellular or less than or equal to 25% reduction from normal cellularity for age CTCAE: E10023 Grade 2 bone marrow depression AE a bone marrow depression AE categorized as moderately hypocellular or greater than 25 to less than 50% reduction from normal cellularity for age CTCAE: E10024 MW, YH Grade 3 bone marrow depression AE CTCAE: E10025 MW, YH a bone marrow depression AE cateogirzed as severely hypocellular or greater than 50 to less than or equal to 75% reduction cellularity from normal for age Grade 4 bone marrow depression AE a bone marrow depression AE categorized as aplastic persistent for longer than 2 weeks CTCAE: E10026 MW, YH Grade 2 breast infection AE MW, YH CTCAE: E11319 a breast infection AE that has local infection with moderate symptoms; oral intervention indicated (e.g., antibiotic, antifungal, antiviral) Grade 3 breast infection AE a breast infection AE that has severe infection; axillary adenitis; IV antibacterial, antifungal, or antiviral intervention indicated CTCAE: E11320 MW, YH Grade 1 cardiac failure AE a cardiac failure AE that is asymptomatic with laboratory (e.g., BNP [B-Natriuretic Peptide ]) or cardiac imaging abnormalities CTCAE: E10125 MW, YH Grade 2 cardiac failure AE a cardiac failure AE that has symptoms with mild to moderate activity or exertion CTCAE: E10126 MW, YH Grade 3 cardiac failure AE a cardiac failure AE that has severe with symptoms at rest or with minimal activity or exertion; intervention indicated MW, YH CTCAE: E10127 Grade 4 cardiac failure AE MW, YH CTCAE: E10128 a cardiac failure AE that has life-threatening consequences; urgent intervention indicated (e.g., continuous IV therapy or mechanical hemodynamic support) Grade 2 cataract AE a cataract AE that is symptomatic; moderate decrease in visual acuity (20/40 or better) CTCAE: E10352 MW, YH Grade 3 cataract AE MW, YH a cataract AE that is symptomatic with marked decrease in visual acuity (worse than 20/40 but better than 20/200); operative intervention indicated (e.g., cataract surgery) CTCAE: E10353 Grade 4 cataract AE a cataract AE that is characterized by blindness (20/200 or worse) in the affected eye CTCAE: E10354 MW, YH Grade 2 catheter related infection AE CTCAE: E11329 a catheter related infection AE that is localized; local intervention indicated; oral intervention indicated (e.g., antibiotic, antifungal, antiviral) MW, YH Grade 3 catheter related infection AE MW, YH a catheter related infection AE where IV antibiotic, antifungal, or antiviral intervention indicated; radiologic or operative intervention indicated CTCAE: E11330 Grade 2 colitis AE a colitis AE that has abdominal pain; mucus or blood in stool CTCAE: E10523 MW, YH Grade 3 colitis AE CTCAE: E10524 MW, YH a colitis AE that has severe abdominal pain; change in bowel habits; medical intervention indicated; peritoneal signs Grade 1 cytokine release syndrome AE CTCAE: E11265 a cytokine release syndrome AE that has a mild reaction; infusion interruption not indicated; intervention not indicated MW, YH Grade 2 cytokine release syndrome AE a cytokine release syndrome AE where therapy or infusion interruption indicated but responds promptly to symptomatic treatment (e.g., antihistamines, NSAIDS, narcotics, IV fluids); prophylactic medications indicated for less than or equal to 24 hrs MW, YH CTCAE: E11266 Grade 3 cytokine release syndrome AE MW, YH a cytokine release syndrome AEthat is prolonged (e.g., not rapidly responsive to symptomatic medication and/or brief interruption of infusion); recurrence of symptoms following initial improvement; hospitalization indicated for clinical sequelae (e.g., renal impairment, pulmonary infiltrates) CTCAE: E11267 Grade 1 dental caries AE a dental caries AE that has one or more dental caries, not involving the root CTCAE: E10569 MW, YH Grade 2 dental caries AE MW, YH a dental caries AE that has dental caries involving the root CTCAE: E10570 Grade 3 dental caries AE CTCAE: E10571 a dental caries AE that has dental caries resulting in pulpitis or periapical abscess or resulting in tooth loss MW, YH Grade 3 device related infection AE a device related infection AE where IV antibiotic, antifungal, or antiviral intervention indicated; radiologic or operative intervention indicated MW, YH CTCAE: E11357 Grade 2 disseminated intravascular coagulation AE a disseminated intravascular coagulation AE that has laboratory findings with no bleeding CTCAE: E10029 MW, YH Grade 3 disseminated intravascular coagulation AE MW, YH a disseminated intravascular coagulation AE that has laboratory findings and bleeding CTCAE: E10030 Grade 2 ejection fraction decreased AE CTCAE: E12143 MW, YH an ejection fraction decreased AE where the resting ejection fraction (EF) 50 - 40%; 10 - 19% drop from baseline Grade 3 ejection fraction decreased AE MW, YH CTCAE: E12144 an ejection fraction decreased AE where the resting ejection fraction (EF) 39 - 20%; greater than 20% drop from baseline Grade 4 ejection fraction decreased AE CTCAE: E12145 MW, YH an ejection fraction decreased AE where the resting ejection fraction (EF) less than 20% Grade 1 electrocardiogram qt prolonged AE MW, YH CTCAE: E12147 an electrocardiogram qt prolonged AE where the QTc 450 - 480 ms Grade 2 electrocardiogram qt prolonged AE MW, YH CTCAE: E12148 an electrocardiogram qt prolonged AE where the QTc 481 - 500 ms Grade 3 electrocardiogram qt prolonged AE an electrocardiogram qt prolonged AE where the QTc is greater than or equal to 501 ms on at least two separate ECGs CTCAE: E12149 MW, YH Grade 4 electrocardiogram qt prolonged AE CTCAE: E12150 an electrocardiogram qt prolonged AE where the QTc is greater than or equal to 501 or greater than 60 ms change from baseline and Torsade de pointes or polymorphic ventricular tachycardia or signs/symptoms of serious arrhythmia MW, YH Grade 2 enterocolitis AE MW, YH an enterocolitis AE that has abdominal pain; mucus or blood in stool CTCAE: E10629 Grade 3 enterocolitis AE MW, YH CTCAE: E10630 an enterocolitis AE that has severe or persistent abdominal pain; fever; ileus; peritoneal signs Grade 1 fall AE a fall AE that is minor with no resultant injuries; intervention not indicated CTCAE: E11688 MW, YH Grade 3 fall AE a fall AE where hospitalization indicated MW, YH CTCAE: E11690 Grade 3 febrile neutropenia AE CTCAE: E10034 a febrile neutropenia AE categorized as anC less than 1000/mm3 with a single temperature of greater than 38.3 degrees C (101 degrees F) or a sustained temperature of greater than or equal to 38 degrees C (100.4 degrees F) for more than one hour. MW, YH Grade 1 forced expiratory volume decreased AE MW, YH CTCAE: E12157 a forced expiratory volume decreased AE where FEV1% (percentages of observed FEV1 and FVC related to their respective predicted values) 99 - 70% predicted Grade 2 forced expiratory volume decreased AE MW, YH CTCAE: E12158 a forced expiratory volume decreased AE where FEV1 60 - 69% Grade 3 forced expiratory volume decreased AE MW, YH a forced expiratory volume decreased AE where FEV1 50 - 59% CTCAE: E12159 Grade 4 forced expiratory volume decreased AE CTCAE: E12160 a forced expiratory volume decreased AE where FEV1 is less than or equal to 49% MW, YH Grade 2 fracture AE CTCAE: E11705 a fracture AE that is symptomatic but non-displaced; immobilization indicated MW, YH Grade 3 fracture AE CTCAE: E11706 MW, YH a fracture AE that has severe symptoms; displaced or open wound with bone exposure; disabling; operative intervention indicated Grade 1 gamma-glutamyltransferase level increased AE MW, YH CTCAE: E12162 a gamma-glutamyltransferase level increased AE that is greater than the upper limit of normal - 2.5 times upper limit of normal Grade 2 gamma-glutamyltransferase level increased AE CTCAE: E12163 MW, YH a gamma-glutamyltransferase level increased AE that is greater than 2.5 - 5.0 times the upper limit of normal Grade 3 gamma-glutamyltransferase level increased AE CTCAE: E12164 a gamma-glutamyltransferase level increased AE that is greater than 5.0 - 20.0 times the upper limit of normal MW, YH Grade 4 gamma-glutamyltransferase level increased AE MW, YH a gamma-glutamyltransferase level increased AE that is greater than 20.0 times the upper limit of normal CTCAE: E12165 Grade 2 gastric ulcer AE a gastric ulcer AE that is symptomatic; altered GI function; medical intervention indicated; limiting instrumental activities of daily living CTCAE: E10729 MW, YH Grade 3 gastric ulcer AE MW, YH a gastric ulcer AE that has severely altered GI function; TPN indicated; elective operative or endoscopic intervention indicated; limiting self care activities of daily living; disabling CTCAE: E10730 Grade 2 gastritis AE CTCAE: E10735 MW, YH a gastritis AE that is symptomatic; altered GI function; medical intervention indicated Grade 3 gastritis AE MW, YH a gastritis AE that has severely altered eating or gastric function; TPN or hospitalization indicated CTCAE: E10736 Grade 1 hemolytic uremic syndrome AE a hemolytic uremic syndrome AE that has evidence of RBC destruction (schistocytosis) without clinical consequences MW, YH CTCAE: E10044 Grade 3 hemolytic uremic syndrome AE MW, YH CTCAE: E10045 a hemolytic uremic syndrome AE that has laboratory findings with clinical consequences (e.g., renal insufficiency, petechiae) Grade 4 hemolytic uremic syndrome AE MW, YH CTCAE: E10046 a hemolytic uremic syndrome AE that has life-threatening consequences, (e.g., CNS hemorrhage or thrombosis/embolism or renal failure) Grade 3 hemorrhoidal hemorrhage AE MW, YH CTCAE: E10770 a hemorrhoidal hemorrhage AE where transfusion, radiologic, endoscopic, or elective operative intervention indicated Grade 3 hepatic failure AE MW, YH CTCAE: E11212 a hepatic failure AE that has asterixis; mild encephalopathy; limiting self care activities of daily living Grade 4 hepatic failure AE CTCAE: E11213 a hepatic failure AE that has moderate to severe encephalopathy; coma; life-threatening consequences MW, YH Grade 3 hepatitis viral AE CTCAE: E11412 a hepatitis viral AE that has symptomatic liver dysfunction; fibrosis by biopsy; compensated cirrhosis; reactivation of chronic hepatitis MW, YH Grade 4 hepatitis viral AE a hepatitis viral AE that has decompensated liver function (e.g., ascites, coagulopathy, encephalopathy, coma) CTCAE: E11413 MW, YH Grade 2 ileus AE MW, YH an ileus AE that is symptomatic; altered GI function; bowel rest indicated CTCAE: E10813 Grade 3 ileus AE an ileus AE that has severely altered GI function; TPN indicated CTCAE: E10814 MW, YH Grade 1 infusion related reaction AE an infusion related reaction AE that has mild transient reaction; infusion interruption not indicated; intervention not indicated CTCAE: E11128 MW, YH Grade 2 infusion related reaction AE an infusion related reaction AE where therapy or infusion interruption indicated but responds promptly to symptomatic treatment (e.g., antihistamines, NSAIDS, narcotics, IV fluids); prophylactic medications indicated for less than or equal to 24 hrs MW, YH CTCAE: E11129 Grade 3 infusion related reaction AE MW, YH an infusion related reaction AE that is prolonged (e.g., not rapidly responsive to symptomatic medication and/or brief interruption of infusion); recurrence of symptoms following initial improvement; hospitalization indicated for clinical sequelae CTCAE: E11130 Grade 2 infusion site extravasation AE an infusion site extravasation AE that has erythema with associated symptoms (e.g., edema, pain, induration, phlebitis) MW, YH CTCAE: E11134 Grade 3 infusion site extravasation AE CTCAE: E11135 MW, YH an infusion site extravasation AE that has ulceration or necrosis; severe tissue damage; operative intervention indicated Grade 1 irritability AE an irritability AE that has mild; easily consolable MW, YH CTCAE: E11145 Grade 2 irritability AE an irritability AE that has moderate; limiting instrumental activities of daily living; increased attention indicated CTCAE: E11146 MW, YH Grade 3 irritability AE MW, YH an irritability AE that has severe abnormal or excessive response; limiting self care activities of daily living; inconsolable CTCAE: E11147 Grade 3 left venticular systolic dysfuction AE CTCAE: E10131 a left ventricular dysfunction AE that has symptomatic due to drop in ejection fraction responsive to intervention MW, YH Grade 4 left ventricular systolic dysfuction AE MW, YH a left ventricular dysfunction AE chracterized as refractory or poorly controlled heart failure due to drop in ejection fraction; intervention such as ventricular assist device, intravenous vasopressor support, or heart transplant indicated CTCAE: E10132 Grade 1 lipase increased AE a lipase increased AE that is greater than the upper limit of normal - 1.5 times upper limit of normal CTCAE: E12186 MW, YH Grade 2 lipase increased AE MW, YH a lipase increased AE that is greater than 1.5 - 2.0 times upper limit of normal CTCAE: E12187 Grade 3 lipase increased AE a lipase increased AE that is greater than 2.0 - 5.0 times upper limit of normal CTCAE: E12188 MW, YH Grade 4 lipase increased AE a lipase increased AE that is greater than 5.0 times upper limit of normal MW, YH CTCAE: E12189 Grade 1 localized edema AE a localized edema AE that has localized to dependent areas, no disability or functional impairment MW, YH CTCAE: E11149 Grade 2 lung infection AE MW, YH a lung infection AE that has moderate symptoms; oral intervention indicated (e.g., antibiotic, antifungal, antiviral) CTCAE: E11445 Grade 3 lung infection AE MW, YH a lung infection AE where IV antibiotic, antifungal, or antiviral intervention indicated; radiologic, endoscopic, or operative intervention indicated CTCAE: E11446 Grade 1 lymphocyte count decreased AE a lymphocyte count decreased AE that is less than the lower limit of normal - 800/mm3; less than the lower limit of normal - 0.8 x 10e9 /L CTCAE: E12191 MW, YH Grade 2 lymphocyte count decreased AE MW, YH CTCAE: E12192 a lymphocyte count decreased AE that is less than 800 - 500/mm3; less than 0.8 - 0.5 x 10e9 /L Grade 3 lymphocyte count decreased AE MW, YH CTCAE: E12193 a lymphocyte count decreased AE that is less than 500 - 200/mm3; less than 0.5 - 0.2 x 10e9 /L Grade 4 lymphocyte count decreased AE MW, YH CTCAE: E12194 a lymphocyte count decreased AE that is less than 200/mm3; less than 0.2 x 10e9 /L Grade 1 myocarditis AE a myocarditis AE that has asymptomatic with laboratory (e.g., BNP [B-Natriuretic Peptide ]) or cardiac imaging abnormalities MW, YH CTCAE: E10158 Grade 2 myocarditis AE MW, YH CTCAE: E10159 a myocarditis AE that has symptoms with mild to moderate activity or exertion Grade 3 myocarditis AE CTCAE: E10160 a myocarditis AE that has severe with symptoms at rest or with minimal activity or exertion; intervention indicated MW, YH Grade 4 myocarditis AE MW, YH a myocarditis AE that has life-threatening consequences; urgent intervention indicated (e.g., continuous IV therapy or mechanical hemodynamic support) CTCAE: E10161 Grade 1 neutrophil count decreased AE CTCAE: E12199 a neutrophil count decreased AE that is less than the lower limit of normal - 1500/mm3; less than the lower limit of normal - 1.5 x 10e9 /L MW, YH Grade 2 neutrophil count decreased AE CTCAE: E12200 MW, YH a neutrophil count decreased AE that is less than 1500 - 1000/mm3; less than 1.5 - 1.0 x 10e9 /L Grade 3 neutrophil count decreased AE MW, YH a neutrophil count decreased AE that is less than 1000 - 500/mm3; less than 1.0 - 0.5 x 10e9 /L CTCAE: E12201 Grade 4 neutrophil count decreased AE CTCAE: E12202 a neutrophil count decreased AE that is less than 500/mm3; less than 0.5 x 10e9 /L MW, YH Grade 2 esophageal stenosis AE MW, YH an esophageal stenosis AE that is symptomatic; altered GI function CTCAE: E10672 Grade 3 esophageal stenosis AE CTCAE: E10673 MW, YH an esophageal stenosis AE that has severely altered GI function; tube feeding; hospitalization indicated; elective operative intervention indicated Grade 2 esophagitis AE CTCAE: E10689 MW, YH an esophagitis AE that is symptomatic; altered eating/swallowing; oral supplements indicated Grade 3 esophagitis AE CTCAE: E10690 an esophagitis AE that has severely altered eating/swallowing; tube feeding, TPN or hospitalization indicated MW, YH Grade 2 oral cavity fistula AE MW, YH CTCAE: E10890 an oral cavity fistula AE that is symptomatic; altered GI function Grade 3 oral cavity fistula AE an oral cavity fistula AE that has severely altered GI function; TPN or hospitalization indicated; elective operative intervention indicated MW, YH CTCAE: E10891 Grade 2 papilledema AE a papilloedema AE that has a symptomatic decline in vision; visual field defect present sparing the central 20 degrees CTCAE: E10413 MW, YH Grade 3 papilledema AE MW, YH CTCAE: E10414 a papilloedema AE that has a marked visual field defect (worse than 20/40 but better than 20/200) Grade 4 papilledema AE a papilloedema AE that has blindness (20/200 or worse) in the affected eye CTCAE: E10415 MW, YH Grade 2 pericardial effusion AE MW, YH CTCAE: E10173 a pericardial effusion AE that has asymptomatic effusion size small to moderate Grade 3 pericardial effusion AE CTCAE: E10174 a pericardial effusion AE that has effusion with physiologic consequences MW, YH Grade 2 portal hypertension AE MW, YH CTCAE: E11239 a portal hypertension AE that has decreased portal vein flow Grade 3 portal hypertension AE CTCAE: E11240 a portal hypertension AE that has reversal/retrograde portal vein flow; associated with varices and/or ascites MW, YH Grade 1 dermatitis radiation AE MW, YH CTCAE: E11676 a dermatitis radiation AE that has faint erythema or dry desquamation Grade 2 dermatitis radiation AE MW, YH a dermatitis radiation AE that has moderate to brisk erythema; patchy moist desquamation, mostly confined to skin folds and creases; moderate edema CTCAE: E11677 Grade 3 dermatitis radiation AE MW, YH CTCAE: E11678 a dermatitis radiation AE that has moist desquamation in areas other than skin folds and creases; bleeding induced by minor trauma or abrasion Grade 4 dermatitis radiation AE CTCAE: E11679 MW, YH a dermatitis radiation AE that has life-threatening consequences; skin necrosis or ulceration of full thickness dermis; spontaneous bleeding from involved site; skin graft indicated Grade 3 rectal hemorrhage AE a rectal hemorrhage AE where transfusion, radiologic, endoscopic, or elective operative intervention indicated MW, YH CTCAE: E10958 Grade 1 skin infection AE CTCAE: E11569 MW, YH a skin infection AE that is localized, local intervention indicated Grade 2 skin infection AE a skin infection AE where oral intervention indicated (e.g., antibiotic, antifungal, antiviral) CTCAE: E11570 MW, YH Grade 3 skin infection AE a skin infection AE where IV antibiotic, antifungal, or antiviral intervention indicated; radiologic or operative intervention indicated MW, YH CTCAE: E11571 Grade 2 small intestinal obstruction AE CTCAE: E11023 MW, YH a small intestinal obstruction AE that is symptomatic; altered GI function; limiting instrumental activities of daily living Grade 2 small intestinal stenosis AE MW, YH a small intestinal stenosis AE that is symptomatic; altered GI function CTCAE: E11034 Grade 3 small intestinal stenosis AE CTCAE: E11035 a small intestinal stenosis AE that is symptomatic and severely altered GI function; tube feeding, TPN or hospitalization indicated; non-emergent operative intervention indicated MW, YH Grade 2 soft tissue infection AE MW, YH CTCAE: E11580 a soft tissue infection AE that is localized; local intervention indicated (e.g., topical antibiotic, antifungal, or antiviral) Grade 3 soft tissue infection AE a soft tissue infection AE where IV antibiotic, antifungal, or antiviral intervention indicated; radiologic or operative intervention indicated CTCAE: E11581 MW, YH Grade 3 gastric hemorrhage AE CTCAE: E10709 MW, YH a gastric hemorrhage AE where transfusion, radiologic, endoscopic, or elective operative intervention indicated Grade 2 tracheitis AE a tracheitis AE that has moderate symptoms; oral intervention indicated (e.g., antibiotic, antifungal, antiviral) MW, YH CTCAE: E11600 Grade 3 tracheitis AE a tracheitis AE where IV antibiotic, antifungal, or antiviral intervention indicated; radiologic, endoscopic, or operative intervention indicated CTCAE: E11601 MW, YH Grade 3 upper gastrointestinal hemorrhage AE MW, YH CTCAE: E11065 an upper gastrointestinal hemorrhage AE where transfusion, radiologic, endoscopic, or elective operative intervention indicated Grade 3 urine output decreased AE a urine output decreased AE that has oliguria (less than 80 ml in 8 hr) CTCAE: E12218 MW, YH Grade 4 urine output decreased AE MW, YH a urine output decreased AE that has anuria (less than 240 ml in 24 hr) CTCAE: E12219 Grade 2 vaginal infection AE CTCAE: E11625 MW, YH a vaginal infection AE that is localized; local intervention indicated (e.g., topical antibiotic, antifungal, or antiviral) Grade 3 vaginal infection AE MW, YH a vaginal infection AE where IV antibiotic, antifungal, or antiviral intervention indicated; radiologic or operative intervention indicated CTCAE: E11626 Grade 2 venous injury AE CTCAE: E12053 MW, YH a venous injury AE that is symptomatic (e.g., claudication); repair or revision not indicated Grade 3 venous injury AE a venous injury AE that has severe symptoms; limiting self care activities of daily living; repair or revision indicated; disabling MW, YH CTCAE: E12054 Grade 4 venous injury AE CTCAE: E12055 MW, YH a venous injury AE that has life-threatening consequences; evidence of end organ damage; urgent operative intervention indicated Grade 1 weight increased AE CTCAE: E12225 a weight increased AE that is 5 - less than 10% from baseline MW, YH Grade 2 weight increased AE a weight increased AE that is 10 - less than 20% from baseline CTCAE: E12226 MW, YH Grade 3 weight increased AE CTCAE: E12227 a weight increased AE that is greater than or equal to 20% from baseline MW, YH Grade 3 Wolff-Parkinson-White syndrom AE CTCAE: E10247 MW, YH a wolff-parkinson-white syndrome AE that is symptomatic and incompletely controlled medically or controlled with procedure Grade 1 wound complication AE CTCAE: E12058 a wound complication AE that has incisional separation of less than or equal to 25% of wound, no deeper than superficial fascia MW, YH Grade 2 wound complication AE MW, YH a wound complication AE that has incisional separation greater than 25% of wound; local care indicated CTCAE: E12059 Grade 3 wound complication AE a wound complication AE that has hernia without evidence of strangulation; fascial disruption/dehiscence; primary wound closure or revision by operative intervention indicated CTCAE: E12060 MW, YH Grade 4 wound complication AE MW, YH a wound complication AE that has hernia with evidence of strangulation; major reconstruction flap, grafting, resection, or amputation indicated CTCAE: E12061 Grade 1 wound dehiscence AE CTCAE: E12064 MW, YH a wound dehiscence AE that has incisional separation of less than or equal to 25% of wound, no deeper than superficial fascia Grade 2 wound dehiscence AE MW, YH CTCAE: E12065 a wound dehiscence AE that has incisional separation greater than 25% of wound with local care; asymptomatic hernia or symptomatic hernia without evidence of strangulation Grade 3 wound dehiscence AE CTCAE: E12066 a wound dehiscence AE that has fascial disruption or dehiscence without evisceration; primary wound closure or revision by operative intervention indicated MW, YH Grade 4 wound dehiscence AE MW, YH a wound dehiscence AE that has life-threatening consequences; symptomatic hernia with evidence of strangulation; fascial disruption with evisceration; major reconstruction flap, grafting, resection, or amputation indicated CTCAE: E12067 Grade 3 multi-organ failure AE a multi-organ failure AE chracterized by shock with azotemia and acid-base disturbances; significant coagulation abnormalities CTCAE: E11156 MW, YH Grade 4 multi-organ failure AE CTCAE: E11157 a multi-organ failure AE that has life-threatening consequences (e.g., vasopressor dependent and oliguric or anuric or ischemic colitis or lactic acidosis) MW, YH Grade 3 restrictive cardiomyopathy AE MW, YH a restrictive cardiomyopathy AE that has symptomatic heart failure or other cardiac symptoms, responsive to intervention CTCAE: E10193 Grade 4 restrictive cardiomyopathy AE a restrictive cardiomyopathy AE that has refractory heart failure or other poorly controlled cardiac symptoms MW, YH CTCAE: E10194 Grade 3 atrioventricular block complete AE MW, YH CTCAE: E10095 a complete atrioventricular block AE that has symptomatic and incompletely controlled medically, or controlled with device (e.g., pacemaker) Grade 3 Mobitz type I block AE CTCAE: E10149 MW, YH a Mobitz type I block AE that has symptomatic and incompletely controlled medically, or controlled with device (e.g., pacemaker) Grade 3 Mobitz type II atrioventricular block AE MW, YH a Mobitz type II block AE that has symptomatic and incompletely controlled medically, or controlled with device (e.g., pacemaker) CTCAE: E10143 Grade 1 hemoglobin level increased AE a hemoglobin level increased AE where the increase is greater than 0 - 2 gm/dL above upper limit of normal or above baseline if baseline is above upper limit of normal MW, YH CTCAE: E12172 Grade 2 hemoglobin level increased AE MW, YH CTCAE: E12173 a hemoglobin level increased AE where the increase is greater than 2 - 4 gm/dL above the upper limit of normal or above baseline if baseline is above upper limit of normal Grade 3 hemoglobin level increased AE CTCAE: E12174 MW, YH a hemoglobin level increased AE where the increase is greater than 4 gm/dL above the upper limit of normal or above baseline if baseline is above upper limit of normal Grade 1 right ventricular dysfuction AE MW, YH a right ventricular dysfunction AE that has asymptomatic with laboratory (e.g., BNP [B-Natriuretic Peptide ]) or cardiac imaging abnormalities CTCAE: E10197 Grade 2 right ventricular dysfuction AE CTCAE: E10198 a right ventricular dysfunction AE that has symptoms with mild to moderate activity or exertion MW, YH Grade 3 right ventricular dysfuction AE CTCAE: E10199 a right ventricular dysfunction AE that has severe symptoms, associated with hypoxemia, right heart failure; oxygen indicated MW, YH Grade 4 right ventricular dysfunction AE a right ventricular dysfunction AE that has life-threatening consequences; urgent intervention indicated (e.g., ventricular assist device); heart transplant indicated CTCAE: E10200 MW, YH Grade 3 intraoperative hemorrhage AE a Intraoperative hemorrhage AE where postoperative radiologic, endoscopic, or operative intervention indicated MW, YH CTCAE: E11811 Grade 2 uveitis AE MW, YH an uveitis AE that has anterior uveitis; medical intervention indicated CTCAE: E10444 Grade 3 uveitis AE MW, YH CTCAE: E10445 an uveitis AE that has posterior or pan-uveitis Grade 4 uveitis AE CTCAE: E10446 MW, YH an uveitis AE that has blindness (20/200 or worse) in the affected eye Grade 2 retinopathy AE a retinopathy AE that is symptomatic with moderate decrease in visual acuity (20/40 or better); limiting instrumental activities of daily living CTCAE: E10434 MW, YH Grade 3 retinopathy AE a retinopathy AE that is symptomatic with marked decrease in visual acuity (worse than 20/40); disabling; limiting self care activities of daily living CTCAE: E10435 MW, YH Grade 4 retinopathy AE MW, YH CTCAE: E10436 a retinopathy AE that has blindness (20/200 or worse) in the affected eye Grade 1 hearing loss AE CTCAE: E10277 MW, YH a hearing loss AE for adults enrolled on a Monitoring Program (on a 1, 2, 3, 4, 6 and 8 kHz audiogram): Threshold shift of 15 - 25 dB averaged at 2 contiguous test frequencies in at least one ear. Adults not enrolled in Monitoring Program: subjective change in hearing in the absence of documented hearing loss. Pediatric (on a 1, 2, 3, 4, 6 and 8 kHz audiogram): Threshold shift greater than20 dB at 8 kHz in at least one ear. Grade 2 hearing loss AE a hearing loss AE for adults enrolled in Monitoring Program (on a 1, 2, 3, 4, 6 and 8 kHz audiogram): Threshold shift of greater than25 dB averaged at 2 contiguous test frequencies in at least one ear. Adults not enrolled in Monitoring Program: hearing loss but hearing aid or intervention not indicated; limiting instrumental activities of daily living. Pediatric (on a 1, 2, 3, 4, 6 and 8 kHz audiogram): Threshold shift greater than20 dB at 4 kHz and above in at least one ear. CTCAE: E10278 MW, YH Grade 3 hearing loss AE CTCAE: E10279 MW, YH a hearing loss AE for adults enrolled in Monitoring Program (on a 1, 2, 3, 4, 6 and 8 kHz audiogram): Threshold shift of greater than25 dB averaged at 3 contiguous test frequencies in at least one ear; therapeutic intervention indicated. Adults not enrolled in Monitoring Program: hearing loss with hearing aid or intervention indicated; limiting self care activities of daily living. Pediatric (on a 1, 2, 3, 4, 6 and 8 kHz audiogram): hearing loss sufficient to indicate therapeutic intervention, including hearing aids; threshold shift greater than20 dB at 3 kHz and above in at least one ear; additional speech-language related services indicated. Grade 4 hearing loss AE CTCAE: E10280 a hearing loss AE for adults: Decrease in hearing to profound bilateral loss (absolute threshold greater than80 dB HL at 2 kHz and above); non-servicable hearing. Pediatric: Audiologic indication for cochlear implant and additional speech-language related services indicated. MW, YH Grade 1 international normalized ratio increased AE CTCAE: E12176 MW, YH a international normalized ratio increased AE that is greater than 1 - 1.5 times the upper limit of normal; greater than 1 - 1.5 times above baseline if on anticoagulation Grade 2 international normalized ratio increased AE MW, YH CTCAE: E12177 a international normalized ratio increased AE that is greater than 1.5 - 2.5 times the upper limit of normal; greater than 1.5 - 2.5 times above baseline if on anticoagulation Grade 3 international normalized ratio increased AE a international normalized ratio increased AE that is greater than 2.5 times the upper limit of normal; greater than 2.5 times above baseline if on anticoagulation MW, YH CTCAE: E12178 Grade 1 fecal incontinence AE a fecal incontinence AE that has occasional use of pads required MW, YH CTCAE: E10694 Grade 2 fecal incontinence AE a fecal incontinence AE that has daily use of pads required CTCAE: E10695 MW, YH Grade 3 fecal incontinence AE CTCAE: E10696 MW, YH a fecal incontinence AE that has severe symptoms; elective operative intervention indicated Grade 1 thrombotic thrombocytopenic purpura AE a thrombotic thrombocytopenic purpura AE that has evidence of RBC destruction (schistocytosis) without clinical consequences CTCAE: E10062 MW, YH Grade 3 thrombotic thrombocytopenic purpura AE MW, YH a thrombotic thrombocytopenic purpura AE charaterized by laboratory findings with clinical consequences (e.g., renal insufficiency, petechiae) CTCAE: E10063 Grade 4 thrombotic thrombocytopenic purpura AE MW, YH a thrombotic thrombocytopenic purpura AE that has life-threatening consequences, (e.g., CNS hemorrhage or thrombosis/embolism or renal failure) CTCAE: E10064 Grade 1 glaucoma AE a glaucoma AE that has elevated intraocular pressure (EIOP) with single topical agent for intervention; no visual field deficit CTCAE: E10393 MW, YH Grade 2 glaucoma AE MW, YH a glaucoma AE that has elevated intraocular pressure causing early visual field deficits; multiple topical or oral agents indicated; limiting instrumental activities of daily living CTCAE: E10394 Grade 3 glaucoma AE MW, YH a glaucoma AE that has elevated intraocular pressure causing marked visual field deficits (e.g., involving both superior and inferior visual fields); operative intervention indicated; limiting self care activities of daily living CTCAE: E10395 Grade 4 glaucoma AE a glaucoma AE that has blindness (20/200 or worse) in the affected eye CTCAE: E10396 MW, YH Grade 3 anaphylaxis AE MW, YH CTCAE: E11255 an anaphylaxis AE that has symptomatic bronchospasm, with or without urticaria; parenteral intervention indicated; allergy-related edema/angioedema; hypotension Grade 2 retinal detachment AE a retinal detachment AE that has exudative and visual acuity 20/40 or better MW, YH CTCAE: E10422 Grade 3 retinal detachment AE MW, YH CTCAE: E10423 a retinal detachment AE that has rhegmatogenous or exudative detachment; operative intervention indicated; decline in vision (worse than 20/40 but better than 20/200) Grade 4 retinal detachment AE a retinal detachment AE that has blindness (20/200 or worse) in the affected eye CTCAE: E10424 MW, YH Grade 1 hemolysis AE MW, YH CTCAE: E10038 a hemolysis AE that has laboratory evidence of hemolysis only (e.g., direct antiglobulin test; DAT; Coombs'; schistocytes; decreased haptoglobin) Grade 2 hemolysis AE a hemolysis AE that has evidence of hemolysis and greater than or equal to 2 gm decrease in hemoglobin. MW, YH CTCAE: E10039 Grade 3 hemolysis AE MW, YH a hemolysis AE where transfusion or medical intervention is indicated (e.g., steroids) CTCAE: E10040 Grade 2 anal fistula AE MW, YH CTCAE: E10466 an anal fistula AE that is symptomatic; altered GI function Grade 3 anal fistula AE MW, YH an anal fistula AE that has severely altered GI function; tube feeding, TPN or hospitalization indicated; elective operative intervention indicated CTCAE: E10467 Grade 3 atrial tachycardia AE MW, YH CTCAE: E10169 an atrial tachycardia AE where IV medication is indicated Grade 4 atrial tachycardia AE CTCAE: E10170 an atrial tachycardia AE that has life-threatening consequences; incompletely controlled medically; cardioversion indicated MW, YH Grade 3 cholecystitis AE MW, YH a cholecystitis AE that has severe symptoms; radiologic, endoscopic or elective operative intervention indicated CTCAE: E11186 Grade 1 autoimmune disorder AE an autoimmune disorder AE that is asymptomatic; serologic or other evidence of autoimmune reaction, with normal organ function; intervention not indicated MW, YH CTCAE: E11259 Grade 2 autoimmune disorder AE an autoimmune disorder AE that has evidence of autoimmune reaction involving a non-essential organ or function (e.g., hypothyroidism) MW, YH CTCAE: E11260 Grade 3 autoimmune disorder AE CTCAE: E11261 an autoimmune disorder AE that has autoimmune reactions involving major organ (e.g., colitis, anemia, myocarditis, kidney) MW, YH Grade 1 spleen disorder AE a spleen disorder AE that has incidental findings (e.g., Howell-Jolly bodies); mild degree of thrombocytosis and leukocytosis CTCAE: E10057 MW, YH Grade 2 spleen disorder AE CTCAE: E10058 a spleen disorder AE when prophylactic antibiotics are indicated MW, YH Grade 2 burn AE CTCAE: E11671 a burn AE that requires medical intervention; minimal debridement indicated MW, YH Grade 3 burn AE CTCAE: E11672 a burn AE that requires moderate to major debridement or reconstruction indicated MW, YH Grade 1 papulopustular rash AE MW, YH a papulopustular rash AE that has papules and/or pustules covering less than 10% body surface area which may or may not be associated with symptoms of pruritus or tenderness CTCAE: E11492 Grade 2 papulopustular rash AE CTCAE: E11493 a papulopustular rash AE that has papules and/or pustules covering 10-30% body surface area, which may or may not be associated with symptoms of pruritus or tenderness; associated with psychosocial impact; limiting instrumental activities of daily living MW, YH Grade 3 papulopustular rash AE MW, YH a papulopustular rash AE that has papules and/or pustules covering greater than 30% body surface area, which may or may not be associated with symptoms of pruritus or tenderness; limiting self-care activities of daily living; associated with local superinfection with oral antibiotics indicated CTCAE: E11494 Grade 4 papulopustular rash AE a papulopustular rash AE that has papules and/or pustules covering any % body surface area, which may or may not be associated with symptoms of pruritus or tenderness and are associated with extensive superinfection with IV antibiotics indicated; life-threatening consequences CTCAE: E11495 MW, YH Grade 2 acute coronary syndrome AE CTCAE: E10067 MW, YH an acute coronary syndrome AE that has symptomatic, progressive angina; cardiac enzymes normal; hemodynamically stable Grade 3 acute coronary syndrome AE an acute coronary syndrome AE that has symptomatic, unstable angina and/or acute myocardial infarction, cardiac enzymes abnormal, hemodynamically stable CTCAE: E10068 MW, YH Grade 4 acute coronary syndrome AE CTCAE: E10069 an acute coronary syndrome AE that has symptomatic, unstable angina and/or acute myocardial infarction, cardiac enzymes abnormal, hemodynamically unstable MW, YH Grade 1 aortic valve disease AE an aortic valve disease AE that has asymptomatic valvular thickening with or without mild valvular regurgitation or stenosis by imaging CTCAE: E10072 MW, YH Grade 2 aortic valve disease AE an aortic valve disease AE that has symptomatic; moderate regurgitation or stenosis by imaging MW, YH CTCAE: E10073 Grade 3 aortic valve disease AE CTCAE: E10074 an aortic valve disease AE that has symptomatic; severe regurgitation or stenosis by imaging; symptoms controlled with medical intervention MW, YH Grade 4 aortic valve disease AE CTCAE: E10075 MW, YH an aortic valve disease AE that has life-threatening consequences; urgent intervention indicated (e.g., valve replacement, valvuloplasty) Grade 1 asystole AE MW, YH CTCAE: E10078 an asystole AE that has periods of asystole; non-urgent medical management indicated Grade 3 constrictive pericarditis AE a constrictive pericarditis AE that has symptomatic heart failure or other cardiac symptoms, responsive to intervention MW, YH CTCAE: E10121 Grade 4 constrictive pericarditis AE CTCAE: E10122 MW, YH a constrictive pericarditis AE that has refractory heart failure or other poorly controlled cardiac symptoms Grade 1 mitral valve disease AE a mitral valve disease AE that has asymptomatic valvular thickening with or without mild valvular regurgitation or stenosis by imaging CTCAE: E10135 MW, YH Grade 2 mitral valve disease AE MW, YH CTCAE: E10136 a mitral valve disease AE that has asymptomatic; moderate regurgitation or stenosis by imaging Grade 3 mitral valve disease AE a mitral valve disease AE that has symptomatic; severe regurgitation or stenosis by imaging; symptoms controlled with medical intervention MW, YH CTCAE: E10137 Grade 4 mitral valve disease AE MW, YH CTCAE: E10138 a mitral valve disease AE that has life-threatening consequences; urgent intervention indicated (e.g., valve replacement, valvuloplasty) Grade 1 pulmonary valve disease AE a pulmonary valve disease AE that has asymptomatic valvular thickening with or without mild valvular regurgitation or stenosis by imaging MW, YH CTCAE: E10187 Grade 2 pulmonary valve disease AE MW, YH a pulmonary valve disease AE that has asymptomatic; moderate regurgitation or stenosis by imaging CTCAE: E10188 Grade 3 pulmonary valve disease AE MW, YH CTCAE: E10189 a pulmonary valve disease AE that has symptomatic; severe regurgitation or stenosis by imaging; symptoms controlled with medical intervention Grade 4 pulmonary valve disease AE CTCAE: E10190 MW, YH a pulmonary valve disease AE that has life-threatening consequences; urgent intervention indicated (e.g., valve replacement, valvuloplasty) Grade 1 tricuspid valve disease AE a tricuspid valve disease AE that has asymptomatic valvular thickening with or without mild valvular regurgitation or stenosis MW, YH CTCAE: E10225 Grade 2 tricuspid valve disease AE a tricuspid valve disease AE that is asymptomatic; moderate regurgitation or stenosis by imaging MW, YH CTCAE: E10226 Grade 3 tricuspid valve disease AE a tricuspid valve disease AE that is symptomatic; severe regurgitation or stenosis; symptoms controlled with medical intervention CTCAE: E10227 MW, YH Grade 4 tricuspid valve disease AE CTCAE: E10228 MW, YH a tricuspid valve disease AE that has life-threatening consequences; urgent intervention indicated (e.g., valve replacement, valvuloplasty) Grade 1 external ear inflammation AE CTCAE: E10267 an external ear inflammation AE that has external otitis with erythema or dry desquamation MW, YH Grade 2 external ear inflammation AE an external ear inflammation AE that has external otitis with moist desquamation, edema, enhanced cerumen or discharge; tympanic membrane perforation; tympanostomy MW, YH CTCAE: E10268 Grade 3 external ear inflammation AE an external ear inflammation AE that has external otitis with mastoiditis; stenosis or osteomyelitis; necrosis of soft tissue or bone MW, YH CTCAE: E10269 Grade 4 external ear inflammation AE an external ear inflammation AE where urgent operative intervention indicated MW, YH CTCAE: E10270 Grade 1 middle ear inflammation AE CTCAE: E10282 MW, YH a middle ear inflammation AE that has serous otitis Grade 2 middle ear inflammation AE MW, YH CTCAE: E10283 a middle ear inflammation AE that has serous otitis, medical intervention indicated Grade 3 middle ear inflammation AE MW, YH a middle ear inflammation AE that has mastoiditis; necrosis of canal soft tissue or bone CTCAE: E10284 Grade 2 delayed puberty AE CTCAE: E10309 a delayed puberty AE that has no breast development by age 13 yrs for females; testes volume of <3 cc or no Tanner Stage 2 development by age 14.5 yrs for males MW, YH Grade 3 delayed puberty AE a delayed puberty AE that has no breast development by age 14 yrs for females; no increase in testes volume or no Tanner Stage 2 by age 16 yrs for males; hormone replacement indicated MW, YH CTCAE: E10310 Grade 2 growth accelerated AE CTCAE: E10318 a growth accelerated AE that has greater than or equal to +2 SD (standard deviation) above mid parental height or target height MW, YH Grade 1 precocious puberty AE MW, YH a precocious puberty AE that has physical signs of puberty with no biochemical markers for females younger than 8 years and males younger than 9 years CTCAE: E10341 Grade 2 precocious puberty AE CTCAE: E10342 a precocious puberty AE that has physical signs and biochemical markers of puberty for females younger than 8 years and males younger than 9 years MW, YH Grade 3 corneal ulcer AE MW, YH a corneal ulcer AE that has limiting self care activities of daily living declining vision (worse than 20/40 but better than 20/200) CTCAE: E10361 Grade 4 corneal ulcer AE CTCAE: E10362 MW, YH a corneal ulcer AE that has perforation or blindness (20/200 or worse) in the affected eye Grade 1 dry eye AE MW, YH a dry eye AE that is asymptomatic; clinical or diagnostic observations only; mild symptoms relieved by lubricants CTCAE: E10364 Grade 3 dry eye AE MW, YH CTCAE: E10366 a dry eye AE that has a decrease in visual acuity (<20/40); limiting self care activities of daily living Grade 3 keratitis AE CTCAE: E10399 MW, YH a keratitis AE that has a decline in vision (worse than 20/40 but better than 20/200); limiting self care activities of daily living Grade 4 keratitis AE MW, YH a keratitis AE that has perforation or blindness (20/200 or worse) in the affected eye CTCAE: E10400 Grade 4 night blindness AE a night blindness AE that has blindness (20/200 or worse) in the affected eye CTCAE: E10405 MW, YH Grade 2 optic nerve disorder AE MW, YH an optic nerve disorder AE that has limiting vision of the affected eye (20/40 or better) CTCAE: E10408 Grade 3 optic nerve disorder AE an optic nerve disorder AE that has limiting vision in the affected eye (worse than 20/40 but better than 20/200) CTCAE: E10409 MW, YH Grade 4 optic nerve disorder AE MW, YH an optic nerve disorder AE that has blindness (20/200 or worse) in the affected eye CTCAE: E10410 Grade 2 retinal tear AE a retinal tear AE where laser therapy or pneumopexy indicated CTCAE: E10426 MW, YH Grade 3 retinal tear AE a retinal tear AE where vitroretinal surgical repair indicated CTCAE: E10427 MW, YH Grade 4 retinal tear AE CTCAE: E10428 a retinal tear AE that has blindness (20/200 or worse) in the affected eye MW, YH Grade 2 retinal vascular disorder AE MW, YH a retinal vascular disorder AE where topical medication indicated CTCAE: E10430 Grade 3 retinal vascular disorder AE a retinal vascular disorder AE where intravitreal medication; operative intervention indicated MW, YH CTCAE: E10431 Grade 2 scleral disorder AE MW, YH a scleral disorder AE that is symptomatic, limiting instrumental activities of daily living; moderate decrease in visual acuity (20/40 or better) CTCAE: E10439 Grade 3 scleral disorder AE MW, YH a scleral disorder AE that is symptomatic, limiting self care activities of daily living; marked decrease in visual acuity (worse than 20/40) CTCAE: E10440 Grade 4 scleral disorder AE CTCAE: E10441 a scleral disorder AE that has blindness (20/200 or worse) in the affected eye MW, YH Grade 3 vitreous hemorrhage AE MW, YH CTCAE: E10450 a vitreous hemorrhage AE that has limiting self care activities of daily living; vitrectomy indicated Grade 4 vitreous hemorrhage AE CTCAE: E10451 a vitreous hemorrhage AE that has blindness (20/200 or worse) in the affected eye MW, YH Grade 3 anal necrosis AE MW, YH an anal necrosis AE where TPN or hospitalization indicated; radiologic, endoscopic, or operative intervention indicated CTCAE: E10483 Grade 2 anal stenosis AE CTCAE: E10492 an anal stenosis AE that is symptomatic; altered GI function MW, YH Grade 3 anal stenosis AE an anal stenosis AE that is symptomatic and severely altered GI function; non-emergent operative intervention indicated; TPN or hospitalization indicated MW, YH CTCAE: E10493 Grade 1 bloating AE a bloating AE that has no change in bowel function or oral intake CTCAE: E10509 MW, YH Grade 2 bloating AE MW, YH a bloating AE that is symptomatic, decreased oral intake; change in bowel function CTCAE: E10510 Grade 2 cecal hemorrhage AE MW, YH CTCAE: E10513 a cecal hemorrhage AE that has moderate symptoms; medical intervention or minor cauterization indicated Grade 3 cecal hemorrhage AE MW, YH CTCAE: E10514 a cecal hemorrhage AE where transfusion, radiologic, endoscopic, or elective operative intervention indicated Grade 2 colonic fistula AE CTCAE: E10529 a colonic fistula AE that is symptomatic; altered GI function MW, YH Grade 3 colonic fistula AE MW, YH CTCAE: E10530 a colonic fistula AE that has severely altered GI function; bowel rest, TPN or hospitalization indicated; elective operative intervention indicated Grade 3 colonic hemorrhage AE CTCAE: E10536 a colonic hemorrhage AE where transfusion, radiologic, endoscopic, or elective operative intervention indicated MW, YH Grade 2 colonic obstruction AE CTCAE: E10541 a colonic obstruction AE that is symptomatic; altered GI function MW, YH Grade 2 colonic ulcer AE a colonic ulcer AE that is symptomatic; altered GI function MW, YH CTCAE: E10558 Grade 3 colonic ulcer AE CTCAE: E10559 a colonic ulcer AE that has severely altered GI function; TPN indicated; elective operative or endoscopic intervention indicated; disabling MW, YH Grade 2 duodenal fistula AE a duodenal fistula AE that is symptomatic; altered GI function MW, YH CTCAE: E10584 Grade 3 duodenal fistula AE a duodenal fistula AE that has severely altered GI function; tube feeding, TPN or hospitalization indicated; elective operative intervention indicated MW, YH CTCAE: E10585 Grade 3 duodenal hemorrhage AE a duodenal hemorrhage AE where transfusion, radiologic, endoscopic, or elective operative intervention indicated MW, YH CTCAE: E10591 Grade 2 duodenal obstruction AE a duodenal obstruction AE that is symptomatic; altered GI function CTCAE: E10596 MW, YH Grade 2 duodenal stenosis AE MW, YH a duodenal stenosis AE that is symptomatic; altered GI function CTCAE: E10607 Grade 3 duodenal stenosis AE CTCAE: E10608 a duodenal stenosis AE that has severely altered GI function; tube feeding; hospitalization indicated; elective operative intervention indicated MW, YH Grade 2 esophageal fistula AE an esophageal fistula AE that is symptomatic; altered GI function CTCAE: E10641 MW, YH Grade 3 esophageal fistula AE an esophageal fistula AE that has severely altered GI function; tube feeding, TPN or hospitalization indicated; elective operative intervention indicated MW, YH CTCAE: E10642 Grade 3 esophageal hemorrhage AE MW, YH an esophageal hemorrhage AE where transfusion, radiologic, endoscopic, or elective operative intervention indicated CTCAE: E10648 Grade 3 esophageal necrosis AE an esophageal necrosis AE that has inability to aliment adequately by GI tract; radiologic, endoscopic, or operative intervention indicated MW, YH CTCAE: E10652 Grade 2 esophageal obstruction AE MW, YH an esophageal obstruction AE that is symptomatic; altered GI function; limiting instrumental activities of daily living CTCAE: E10657 Grade 2 esophageal ulcer AE MW, YH CTCAE: E10678 an esophageal ulcer AE that is symptomatic; altered GI function; limiting instrumental activities of daily living Grade 3 esophageal ulcer AE an esophageal ulcer AE that has severely altered GI function; TPN indicated; elective operative or endoscopic intervention indicated; limiting self care activities of daily living; disabling CTCAE: E10679 MW, YH Grade 3 esophageal varices hemorrhage AE CTCAE: E10684 an esophageal varices hemorrhage AE where transfusion, radiologic, endoscopic, or elective operative intervention indicated MW, YH Grade 2 gastric fistula AE CTCAE: E10702 a gastric fistula AE that is symptomatic; altered GI function MW, YH Grade 3 gastric fistula AE a gastric fistula AE that has severely altered GI function; bowel rest; tube feeding, TPN or hospitalization indicated; elective operative intervention indicated MW, YH CTCAE: E10703 Grade 3 gastric necrosis AE a gastric necrosis AE that has inability to aliment adequately by GI tract; radiologic, endoscopic, or operative intervention indicated CTCAE: E10713 MW, YH Grade 2 gastric stenosis AE MW, YH a gastric stenosis AE that is symptomatic; altered GI function CTCAE: E10723 Grade 3 gastric stenosis AE CTCAE: E10724 a gastric stenosis AE that has severely altered GI function; tube feeding; hospitalization indicated; elective operative intervention indicated MW, YH Grade 2 gastrointestinal fistula AE a gastrointestinal fistula AE that is symptomatic; altered GI function CTCAE: E10751 MW, YH Grade 3 gastrointestinal fistula AE MW, YH a gastrointestinal fistula AE that has severely altered GI function; tube feeding, TPN or hospitalization indicated CTCAE: E10752 Grade 1 gastroparesis AE a gastroparesis AE that has mild nausea, early satiety and bloating, able to maintain caloric intake on regular diet CTCAE: E10760 MW, YH Grade 2 gastroparesis AE MW, YH a gastroparesis AE that has moderate symptoms; able to maintain nutrition with dietary and lifestyle modifications; may need pharmacologic intervention CTCAE: E10761 Grade 3 gastroparesis AE CTCAE: E10762 a gastroparesis AE that has weight loss; refractory to medical intervention; unable to maintain nutrition orally MW, YH Grade 2 ileal fistula AE an ileal fistula AE that is symptomatic; altered GI function MW, YH CTCAE: E10779 Grade 3 ileal fistula AE CTCAE: E10780 an ileal fistula AE that has severely altered GI function; TPN or hospitalization indicated; elective operative intervention indicated MW, YH Grade 3 ileal hemorrhage AE CTCAE: E10786 MW, YH an ileal hemorrhage AE where transfusion, radiologic, endoscopic, or elective operative intervention indicated Grade 2 ileal obstruction AE MW, YH an ileal obstruction AE that is symptomatic; altered GI function; limiting instrumental activities of daily living CTCAE: E10791 Grade 2 ileal stenosis AE an ileal stenosis AE that is symptomatic; altered GI function CTCAE: E10802 MW, YH Grade 3 ileal stenosis AE CTCAE: E10803 an ileal stenosis AE that has severely altered GI function; tube feeding or hospitalization indicated; elective operative intervention indicated MW, YH Grade 2 ileal ulcer AE CTCAE: E10808 an ileal ulcer AE that is symptomatic; altered GI function MW, YH Grade 3 ileal ulcer AE MW, YH an ileal ulcer AE that has severely altered GI function; TPN indicated; elective operative or endoscopic intervention indicated; disabling CTCAE: E10809 Grade 3 intra-abdominal hemorrhage AE CTCAE: E10819 an intra-abdominal hemorrhage AE where transfusion, radiologic, endoscopic, or elective operative intervention indicated MW, YH Grade 2 jejunal fistula AE MW, YH a jejunal fistula AE that is symptomatic; altered GI function CTCAE: E10824 Grade 3 jejunal fistula AE CTCAE: E10825 a jejunal fistula AE that has severely altered GI function; TPN or hospitalization indicated; elective operative intervention indicated MW, YH Grade 3 jejunal hemorrhage AE MW, YH CTCAE: E10831 ajejunal hemorrhage AE where transfusion, radiologic, endoscopic, or elective operative intervention indicated Grade 2 jejunal obstruction AE CTCAE: E10836 a jejunal obstruction AE that is symptomatic; altered GI function; limiting instrumental activities of daily living MW, YH Grade 2 jejunal stenosis AE MW, YH a jejunal stenosis AE that is symptomatic; altered GI function CTCAE: E10847 Grade 3 jejunal stenosis AE MW, YH CTCAE: E10848 a jejunal stenosis AE that has severely altered GI function; tube feeding or hospitalization indicated; elective operative intervention indicated Grade 2 jejunal ulcer AE a jejunal ulcer AE that is symptomatic; altered GI function CTCAE: E10853 MW, YH Grade 3 jejunal ulcer AE CTCAE: E10854 a jejunal ulcer AE that has severely altered GI function; TPN indicated; elective operative or endoscopic intervention indicated; disabling MW, YH Grade 3 lower gastrointestinal hemorrhage AE CTCAE: E10864 a lower gastrointestinal hemorrhage AE where transfusion, radiologic, endoscopic, or elective operative intervention indicated MW, YH Grade 2 malabsorption AE MW, YH a malabsorption AE where altered diet; oral intervention indicated CTCAE: E10868 Grade 3 malabsorption AE CTCAE: E10869 a malabsorption AE that has inability to aliment adequately; TPN indicated MW, YH Grade 2 obstruction gastric AE an obstruction gastric AE that is symptomatic; altered GI function; limiting instrumental activities of daily living MW, YH CTCAE: E10884 Grade 3 oral hemorrhage AE CTCAE: E10901 an oral hemorrhage AE where transfusion, radiologic, endoscopic, or elective operative intervention indicated MW, YH Grade 2 pancreatic duct stenosis AE CTCAE: E10910 MW, YH a pancreatic duct stenosis AE that is symptomatic; altered GI function Grade 3 pancreatic duct stenosis AE a pancreatic duct stenosis AE that has severely altered GI function; tube feeding or hospitalization indicated; elective operative intervention indicated CTCAE: E10911 MW, YH Grade 2 pancreatic fistula AE MW, YH CTCAE: E10916 a pancreatic fistula AE that is symptomatic; altered GI function Grade 3 pancreatic fistula AE MW, YH a pancreatic fistula AE that has severely altered GI function; tube feeding or TPN or hospitalization indicated; elective operative intervention indicated CTCAE: E10917 Grade 3 pancreatic hemorrhage AE MW, YH a pancreatic hemorrhage AE where transfusion, radiologic, endoscopic, or elective operative intervention indicated CTCAE: E10923 Grade 3 pancreatic necrosis AE MW, YH CTCAE: E10927 a pancreatic necrosis AE where tube feeding or TPN indicated; radiologic, endoscopic, or operative intervention indicated Grade 3 peritoneal necrosis AE a peritoneal necrosis AE where tube feeding or TPN indicated; radiologic, endoscopic, or operative intervention indicated MW, YH CTCAE: E10940 Grade 1 proctitis AE CTCAE: E10944 MW, YH a proctitis AE that has rectal discomfort, intervention not indicated Grade 2 proctitis AE CTCAE: E10945 a proctitis AE that has symptoms (e.g., rectal discomfort, passing blood or mucus); medical intervention indicated; limiting instrumental activities of daily living MW, YH Grade 3 proctitis AE MW, YH a proctitis AE that has severe symptoms; fecal urgency or stool incontinence; limiting self care activities of daily living CTCAE: E10946 Grade 2 rectal fistula AE a rectal fistula AE that is symptomatic; altered GI function CTCAE: E10951 MW, YH Grade 3 rectal fistula AE MW, YH CTCAE: E10952 a rectal fistula AE that has severely altered GI function; TPN or hospitalization indicated; elective operative intervention indicated Grade 2 rectal obstruction AE MW, YH a rectal obstruction AE that is symptomatic; altered GI function; limiting instrumental activities of daily living CTCAE: E10973 Grade 2 rectal stenosis AE MW, YH a rectal stenosis AE that is symptomatic; altered GI function CTCAE: E10988 Grade 3 rectal stenosis AE MW, YH a rectal stenosis AE that has severely altered GI function; tube feeding or hospitalization indicated; elective operative intervention indicated CTCAE: E10989 Grade 2 rectal ulcer AE CTCAE: E10994 a rectal ulcer AE that is symptomatic; altered GI function (e.g. altered dietary habits, vomiting, diarrhea) MW, YH Grade 3 rectal ulcer AE MW, YH CTCAE: E10995 a rectal ulcer AE that has severely altered GI function; TPN indicated; elective operative or endoscopic intervention indicated; disabling Grade 3 retroperitoneal hemorrhage AE CTCAE: E11000 a retroperitoneal hemorrhage AE where transfusion, medical, radiologic, endoscopic, or elective operative intervention indicated MW, YH Grade 2 salivary gland fistula AE MW, YH a salivary gland fistula AE that is symptomatic; altered GI function; tube feeding indicated CTCAE: E11011 Grade 3 salivary gland fistula AE CTCAE: E11012 a salivary gland fistula AE that has severely altered GI function; hospitalization indicated; elective operative intervention indicated MW, YH Grade 1 tooth discoloration AE MW, YH a tooth discoloration AE that has surface stains CTCAE: E11053 Grade 1 edema limbs AE an edema limbs AE that has 5 - 10% inter-limb discrepancy in volume or circumference at point of greatest visible difference; swelling or obscuration of anatomic architecture on close inspection CTCAE: E11087 MW, YH Grade 2 edema limbs AE an edema limbs AE that has more than 10 to 30% inter-limb discrepancy in volume or circumference at point of greatest visible difference; readily apparent obscuration of anatomic architecture; obliteration of skin folds; readily apparent deviation from normal anatomic contour; limiting instrumental activities of daily living MW, YH CTCAE: E11088 Grade 3 edema limbs AE CTCAE: E11089 MW, YH an edema limbs AE that has more than 30% inter-limb discrepancy in volume; gross deviation from normal anatomic contour; limiting self care activities of daily living Grade 1 edema trunk AE MW, YH CTCAE: E11091 an edema trunk AE that has swelling or obscuration of anatomic architecture on close inspection Grade 2 edema trunk AE MW, YH CTCAE: E11092 an edema trunk AE that has readily apparent obscuration of anatomic architecture; obliteration of skin folds; readily apparent deviation from normal anatomic contour; limiting instrumental activities of daily living Grade 3 edema trunk AE MW, YH CTCAE: E11093 an edema trunk AE that has gross deviation from normal anatomic contour; limiting self care activities of daily living Grade 2 neck edema AE A neck edema AE that has moderate neck edema; slight obliteration of anatomic landmarks; limiting instrumental activities of daily living MW, YH CTCAE: E11161 Grade 3 neck edema AE CTCAE: E11162 a neck edema AE that has generalized neck edema (e.g., difficulty in turning neck); limiting self care activities of daily living MW, YH Grade 2 bile duct stenosis AE MW, YH a bile duct stenosis AE that is symptomatic; altered GI function; IV fluids indicated <24 hrs CTCAE: E11175 Grade 3 bile duct stenosis AE CTCAE: E11176 MW, YH a bile duct stenosis AE that has severely altered GI function; radiologic, endoscopic or elective operative intervention indicated Grade 3 biliary fistula AE MW, YH CTCAE: E11181 a biliary fistula AE that has severely altered GI function; TPN indicated; endoscopic intervention indicated; elective operative intervention indicated Grade 3 gallbladder fistula AE a gallbladder fistula AE that is symptomatic or severely altered GI function; TPN indicated; radiologic, endoscopic or elective operative intervention indicated MW, YH CTCAE: E11192 Grade 2 gallbladder obstruction AE CTCAE: E11200 a gallbladder obstruction AE that is symptomatic; altered GI function; IV fluids indicated <24 hrs MW, YH Grade 3 gallbladder obstruction AE a gallbladder obstruction AE that is symptomatic and severely altered GI function; tube feeding, TPN or hospitalization indicated; non-emergent operative intervention indicated CTCAE: E11201 MW, YH Grade 3 hepatic hemorrhage AE a hepatic hemorrhage AE where transfusion indicated MW, YH CTCAE: E11218 Grade 3 perforation bile duct AE MW, YH a perforation bile duct AE where radiologic, endoscopic or elective operative intervention indicated CTCAE: E11235 Grade 3 abdominal infection AE an abdominal infection AE where IV antibiotic, antifungal, or antiviral intervention indicated; radiologic or operative intervention indicated MW, YH CTCAE: E11283 Grade 1 anorectal infection AE MW, YH an anorectal infection AE that is localized; local intervention indicated CTCAE: E11287 Grade 2 anorectal infection AE CTCAE: E11288 an anorectal infection AE where oral intervention indicated (e.g., antibiotic, antifungal, antiviral) MW, YH Grade 3 anorectal infection AE MW, YH an anorectal infection AE where IV antibiotic, antifungal, or antiviral intervention indicated; radiologic, endoscopic, or operative intervention indicated CTCAE: E11289 Grade 3 appendicitis AE an appendicitis AE where IV antibiotic, antifungal, or antiviral intervention indicated; radiologic or operative intervention indicated MW, YH CTCAE: E11293 Grade 3 arteritis infective AE CTCAE: E11302 MW, YH an arteritis infective AE where IV antibiotic, antifungal, or antiviral intervention indicated; radiologic or operative intervention indicated Grade 3 biliary tract infection AE MW, YH a biliary tract infection AE where IV antibiotic, antifungal, or antiviral intervention indicated; radiologic or operative intervention indicated CTCAE: E11306 Grade 2 bladder infection AE CTCAE: E11310 MW, YH a bladder infection AE where oral intervention indicated (e.g., antibiotic, antifungal, antiviral) Grade 3 bladder infection AE CTCAE: E11311 a bladder infection AE where IV antibiotic, antifungal, or antiviral intervention indicated; radiologic, endoscopic, or operative intervention indicated MW, YH Grade 3 bone infection AE a bone infection AE where IV antibiotic, antifungal, or antiviral intervention indicated; radiologic or operative intervention indicated MW, YH CTCAE: E11315 Grade 2 bronchial infection AE MW, YH a bronchial infection AE that has moderate symptoms; oral intervention indicated (e.g., antibiotic, antifungal, antiviral) CTCAE: E11324 Grade 3 bronchial infection AE a bronchial infection AE where IV antibiotic, antifungal, or antiviral intervention indicated; radiologic, endoscopic, or operative intervention indicated CTCAE: E11325 MW, YH Grade 3 cecal infection AE CTCAE: E11334 a cecal infection AE where IV antibiotic, antifungal, or antiviral intervention indicated; radiologic, endoscopic, or operative intervention indicated MW, YH Grade 2 cervicitis infection AE CTCAE: E11338 MW, YH a cervicitis infection AE that is localized; local intervention indicated (e.g., topical antibiotic, antifungal, or antiviral) Grade 3 cervicitis infection AE MW, YH a cervicitis infection AE where IV antibiotic, antifungal, or antiviral intervention indicated; radiologic or operative intervention indicated CTCAE: E11339 Grade 2 conjunctivitis infective AE a conjunctivitis infective AE that is localized; local intervention indicated (e.g., topical antibiotic, antifungal, or antiviral) CTCAE: E11343 MW, YH Grade 3 conjunctivitis infective AE a conjunctivitis infective AE where IV antibiotic, antifungal, or antiviral intervention indicated; radiologic or operative intervention indicated CTCAE: E11344 MW, YH Grade 2 corneal infection AE CTCAE: E11348 a corneal infection AE that is localized; local intervention indicated (e.g., topical antibiotic, antifungal, or antiviral) MW, YH Grade 3 corneal infection AE MW, YH CTCAE: E11349 a corneal infection AE where IV antibiotic, antifungal, or antiviral intervention indicated; radiologic or operative intervention indicated Grade 3 cranial nerve infection AE a cranial nerve infection AE where IV antibiotic, antifungal, or antiviral intervention indicated; radiologic or operative intervention indicated CTCAE: E11353 MW, YH Grade 2 duodenal infection AE CTCAE: E11361 a duodenal infection AE that has moderate symptoms; medical intervention indicated (e.g., oral antibiotics) MW, YH Grade 3 duodenal infection AE MW, YH CTCAE: E11362 a duodenal infection AE where IV antibiotic, antifungal, or antiviral intervention indicated; radiologic or operative intervention indicated Grade 3 encephalitis infection AE MW, YH CTCAE: E11366 an encephalitis infection AE where IV antibiotic, antifungal, or antiviral intervention indicated; severe changes in mental status; self-limited seizure activity; focal neurologic abnormalities Grade 3 encephalomyelitis infection AE MW, YH an encephalomyelitis infection AE when IV antibiotic, antifungal, or antiviral intervention indicated; radiologic or operative intervention indicated CTCAE: E11370 Grade 3 endocarditis infective AE an endocarditis infective AE when IV antibiotic, antifungal, or antiviral intervention indicated; radiologic or operative intervention indicated MW, YH CTCAE: E11374 Grade 4 endophthalmitis AE CTCAE: E11380 an endophthalmitis AE that has blindness (20/200 or worse) MW, YH Grade 2 enterocolitis infectious AE MW, YH an enterocolitis infectious AE that has the passage of more than 3 unformed stools per 24 hrs or duration of illness longer than 48 hrs; moderate abdominal pain CTCAE: E11382 Grade 3 enterocolitis infectious AE CTCAE: E11383 an enterocolitis infectious AE where IV antibiotic, antifungal, or antiviral intervention indicated; radiologic, endoscopic, or operative intervention indicated; profuse watery diarrhea with signs of hypovolemia; bloody diarrhea; fever; severe abdominal pain; hospitalization indicated MW, YH Grade 2 esophageal infection AE MW, YH CTCAE: E11387 an esophageal infection AE where local intervention indicated (e.g., oral antibiotic, antifungal, antiviral) Grade 3 esophageal infection AE MW, YH an esophageal infection AE where IV antibiotic, antifungal, or antiviral intervention indicated; radiologic or operative intervention indicated CTCAE: E11388 Grade 2 eye infection AE MW, YH CTCAE: E11392 an eye infection AE that is localized; local intervention indicated (e.g., topical antibiotic, antifungal, or antiviral) Grade 3 eye infection AE an eye infection AE where IV antibiotic, antifungal, or antiviral intervention indicated; radiologic or operative intervention indicated CTCAE: E11393 MW, YH Grade 4 eye infection AE MW, YH an eye infection AE that has life-threatening consequences; urgent intervention indicated; enucleation CTCAE: E11394 Grade 3 gallbladder infection AE a gallbladder infection AE where IV antibiotic, antifungal, or antiviral intervention indicated; radiologic, endoscopic, or operative intervention indicated MW, YH CTCAE: E11397 Grade 1 gum infection AE MW, YH a gum infection AE where local therapy indicated (swish and swallow) CTCAE: E11401 Grade 2 gum infection AE MW, YH a gum infection AE that has moderate symptoms; oral intervention indicated (e.g., antibiotic, antifungal, antiviral) CTCAE: E11402 Grade 3 gum infection AE a gum infection AE where IV antibiotic, antifungal, or antiviral intervention indicated; radiologic or operative intervention indicated CTCAE: E11403 MW, YH Grade 3 hepatic infection AE CTCAE: E11407 MW, YH a hepatic infection AE where IV antibiotic, antifungal, or antiviral intervention indicated; radiologic or operative intervention indicated Grade 2 infective myositis AE MW, YH a infective myositis AE that is localized; local intervention indicated (e.g., topical antibiotic, antifungal, or antiviral) CTCAE: E11422 Grade 3 infective myositis AE MW, YH CTCAE: E11423 a infective myositis AE where IV antibiotic, antifungal, or antiviral intervention indicated; radiologic or operative intervention indicated Grade 2 joint infection AE a joint infection AE that is localized; local intervention indicated; oral intervention indicated (e.g., antibiotic, antifungal, antiviral); needle aspiration indicated (single or multiple) CTCAE: E11427 MW, YH Grade 3 joint infection AE MW, YH a joint infection AE where arthroscopic intervention indicated (e.g., drainage) or arthrotomy (e.g., open surgical drainage) CTCAE: E11428 Grade 3 kidney infection AE a kidney infection AE where IV antibiotic, antifungal, or antiviral intervention indicated; radiologic, endoscopic, or operative intervention indicated CTCAE: E11432 MW, YH Grade 1 lip infection AE a lip infection AE that is localized, local intervention indicated MW, YH CTCAE: E11441 Grade 2 lip infection AE a lip infection AE where oral intervention indicated (e.g., antibiotic, antifungal, antiviral) CTCAE: E11442 MW, YH Grade 3 lip infection AE CTCAE: E11443 a lip infection AE where IV antibiotic, antifungal, or antiviral intervention indicated; radiologic or operative intervention indicated MW, YH Grade 2 lymph gland infection AE MW, YH a lymph gland infection AE that is localized; local intervention indicated (e.g., topical antibiotic, antifungal, or antiviral) CTCAE: E11450 Grade 3 lymph gland infection AE CTCAE: E11451 a lymph gland infection AE where IV antibiotic, antifungal, or antiviral intervention indicated; radiologic or operative intervention indicated MW, YH Grade 3 mediastinal infection AE MW, YH a mediastinal infection AE where IV antibiotic, antifungal, or antiviral intervention indicated; radiologic or operative intervention indicated CTCAE: E11455 Grade 1 mucosal infection AE CTCAE: E11463 MW, YH a mucosal infection AE that is localized, local intervention indicated Grade 2 mucosal infection AE a mucosal infection AE where oral intervention indicated (e.g., antibiotic, antifungal, antiviral) MW, YH CTCAE: E11464 Grade 3 mucosal infection AE a mucosal infection AE where IV antibiotic, antifungal, or antiviral intervention indicated; radiologic or operative intervention indicated CTCAE: E11465 MW, YH Grade 1 nail infection AE MW, YH CTCAE: E11469 a nail infection AE that is localized, local intervention indicated Grade 2 nail infection AE a nail infection AE where oral intervention indicated (e.g., antibiotic, antifungal, antiviral) CTCAE: E11470 MW, YH Grade 3 nail infection AE a nail infection AE where IV antibiotic, antifungal, or antiviral intervention indicated; radiologic or operative intervention indicated MW, YH CTCAE: E11471 Grade 2 otitis externa AE CTCAE: E11473 an otitis externa AE that is localized; local intervention indicated (e.g., topical antibiotic, antifungal, or antiviral) MW, YH Grade 3 otitis externa AE an otitis externa AE where IV antibiotic, antifungal, or antiviral intervention indicated; radiologic or operative intervention indicated CTCAE: E11474 MW, YH Grade 2 ovarian infection AE MW, YH an ovarian infection AE that is localized; local intervention indicated (e.g., topical antibiotic, antifungal, or antiviral) CTCAE: E11483 Grade 3 ovarian infection AE an ovarian infection AE where IV antibiotic, antifungal, or antiviral intervention indicated; radiologic or operative intervention indicated CTCAE: E11484 MW, YH Grade 3 pancreas infection AE MW, YH a pancreas infection AE where IV antibiotic, antifungal, or antiviral intervention indicated; radiologic or operative intervention indicated CTCAE: E11488 Grade 1 paronychia AE a paronychia AE that has nail fold edema or erythema; disruption of the cuticle CTCAE: E11498 MW, YH Grade 2 paronychia AE CTCAE: E11499 a paronychia AE where localized intervention indicated; oral intervention indicated (e.g., antibiotic, antifungal, antiviral); nail fold edema or erythema with pain; associated with discharge or nail plate separation; limiting instrumental activities of daily living MW, YH Grade 3 paronychia AE a paronychia AE where surgical intervention or IV antibiotics indicated; limiting self care activities of daily living CTCAE: E11500 MW, YH Grade 2 pelvic infection AE MW, YH CTCAE: E11502 a pelvic infection AE that has moderate symptoms; oral intervention indicated (e.g., antibiotic, antifungal, antiviral) Grade 3 pelvic infection AE a pelvic infection AE where IV antibiotic, antifungal, or antiviral intervention indicated; radiologic or operative intervention indicated CTCAE: E11503 MW, YH Grade 2 penile infection AE MW, YH CTCAE: E11507 a penile infection AE that is localized; local intervention indicated (e.g., topical antibiotic, antifungal, or antiviral) Grade 3 penile infection AE CTCAE: E11508 a penile infection AE where IV antibiotic, antifungal, or antiviral intervention indicated; radiologic or operative intervention indicated MW, YH Grade 2 periorbital infection AE MW, YH CTCAE: E11512 a periorbital infection AE that is localized; local intervention indicated (e.g., topical antibiotic, antifungal, or antiviral) Grade 3 periorbital infection AE MW, YH CTCAE: E11513 a periorbital infection AE where IV antibiotic, antifungal, or antiviral intervention indicated; radiologic or operative intervention indicated Grade 2 peripheral nerve infection AE a peripheral nerve infection AE that is localized; local intervention indicated (e.g., topical antibiotic, antifungal, or antiviral) MW, YH CTCAE: E11517 Grade 3 peripheral nerve infection AE MW, YH CTCAE: E11518 a peripheral nerve infection AE where IV antibiotic, antifungal, or antiviral intervention indicated; radiologic or operative intervention indicated Grade 3 peritoneal infection AE CTCAE: E11522 MW, YH a peritoneal infection AE where IV antibiotic, antifungal, or antiviral intervention indicated; radiologic, endoscopic, or operative intervention indicated Grade 2 phlebitis infective AE MW, YH a phlebitis infective AE that is localized; local intervention indicated (e.g., topical antibiotic, antifungal, or antiviral) CTCAE: E11531 Grade 3 phlebitis infective AE a phlebitis infective AE where IV antibiotic, antifungal, or antiviral intervention indicated; radiologic or operative intervention indicated CTCAE: E11532 MW, YH Grade 2 pleural infection AE MW, YH CTCAE: E11536 a pleural infection AE that is localized; local intervention indicated (e.g., topical antibiotic, antifungal, or antiviral) Grade 3 pleural infection AE a pleural infection AE where IV antibiotic, antifungal, or antiviral intervention indicated; radiologic, endoscopic, or operative intervention indicated MW, YH CTCAE: E11537 Grade 2 prostate infection AE CTCAE: E11541 MW, YH a prostate infection AE that has moderate symptoms; oral intervention indicated (e.g., antibiotic, antifungal, antiviral) Grade 3 prostate infection AE CTCAE: E11542 MW, YH a prostate infection AE where IV antibiotic, antifungal, or antiviral intervention indicated; radiologic, endoscopic, or operative intervention indicated Grade 2 rhinitis infective AE MW, YH a rhinitis infective AE that is localized; local intervention indicated (e.g., topical antibiotic, antifungal, or antiviral) CTCAE: E11549 Grade 2 salivary gland infection AE a salivary gland infection AE that has moderate symptoms; oral intervention indicated (e.g., antibiotic, antifungal, antiviral) MW, YH CTCAE: E11551 Grade 3 salivary gland infection AE CTCAE: E11552 MW, YH a salivary gland infection AE where IV antibiotic, antifungal, or antiviral intervention indicated; radiologic or operative intervention indicated Grade 2 scrotal infection AE CTCAE: E11556 MW, YH a scrotal infection AE that is localized; local intervention indicated (e.g., topical antibiotic, antifungal, or antiviral) Grade 3 scrotal infection AE a scrotal infection AE where IV antibiotic, antifungal, or antiviral intervention indicated; radiologic or operative intervention indicated CTCAE: E11557 MW, YH Grade 2 small intestine infection AE a small intestine infection AE that has moderate symptoms; oral intervention indicated (e.g., antibiotic, antifungal, antiviral) MW, YH CTCAE: E11575 Grade 3 small intestine infection AE a small intestine infection AE where IV antibiotic, antifungal, or antiviral intervention indicated; radiologic or operative intervention indicated CTCAE: E11576 MW, YH Grade 3 splenic infection AE CTCAE: E11585 MW, YH a splenic infection AE where IV antibiotic, antifungal, or antiviral intervention indicated; radiologic or operative intervention indicated Grade 1 stoma site infection AE CTCAE: E11589 a stoma site infection AE that is localized, local intervention indicated MW, YH Grade 2 stoma site infection AE a stoma site infection AE where oral intervention indicated (e.g., antibiotic, antifungal, antiviral) CTCAE: E11590 MW, YH Grade 3 stoma site infection AE a stoma site infection AE where IV antibiotic, antifungal, or antiviral intervention indicated; radiologic, endoscopic, or operative intervention indicated CTCAE: E11591 MW, YH Grade 2 tooth infection AE MW, YH a tooth infection AE that is localized; local intervention indicated (e.g., topical antibiotic, antifungal, or antiviral) CTCAE: E11595 Grade 3 tooth infection AE MW, YH CTCAE: E11596 a tooth infection AE where IV antibiotic, antifungal, or antiviral intervention indicated; radiologic or operative intervention indicated Grade 2 upper respiratory infection AE an upper respiratory infection AE that has moderate symptoms; oral intervention indicated (e.g., antibiotic, antifungal, antiviral) CTCAE: E11605 MW, YH Grade 3 upper respiratory infection AE CTCAE: E11606 an upper respiratory infection AE where IV antibiotic, antifungal, or antiviral intervention indicated; radiologic, endoscopic, or operative intervention indicated MW, YH Grade 2 urethral infection AE MW, YH CTCAE: E11610 a urethral infection AE that is localized; local intervention indicated (e.g., topical antibiotic, antifungal, or antiviral) Grade 3 urethral infection AE a urethral infection AE where IV antibiotic, antifungal, or antiviral intervention indicated; radiologic, endoscopic, or operative intervention indicated MW, YH CTCAE: E11611 Grade 2 uterine infection AE MW, YH a uterine infection AE that has moderate symptoms; oral intervention indicated (e.g., antibiotic, antifungal, antiviral) CTCAE: E11620 Grade 3 uterine infection AE a uterine infection AE where IV antibiotic, antifungal, or antiviral intervention indicated; radiologic or operative intervention indicated MW, YH CTCAE: E11621 Grade 1 vulval infection AE MW, YH CTCAE: E11630 a vulval infection AE that is localized, local intervention indicated Grade 2 vulval infection AE A vulval infection AE where oral intervention indicated (e.g., antibiotic, antifungal, antiviral) MW, YH CTCAE: E11631 Grade 3 vulval infection AE MW, YH CTCAE: E11632 a vulval infection AE where IV antibiotic, antifungal, or antiviral intervention indicated; radiologic or operative intervention indicated Grade 2 wound infection AE a wound infection AE that is localized; local intervention indicated (e.g., topical antibiotic, antifungal, or antiviral) CTCAE: E11636 MW, YH Grade 3 wound infection AE a wound infection AE where IV antibiotic, antifungal, or antiviral intervention indicated; radiologic or operative intervention indicated CTCAE: E11637 MW, YH Grade 1 ankle fracture AE an ankle fracture AE that is mild; non-surgical intervention indicated MW, YH CTCAE: E11641 Grade 2 ankle fracture AE MW, YH CTCAE: E11642 an ankle fracture AE that is limiting instrumental activities of daily living; operative intervention indicated Grade 3 ankle fracture AE an ankle fracture AE that is limiting self care activities of daily living; elective surgery indicated MW, YH CTCAE: E11643 Grade 3 aortic injury AE an aortic injury AE that has severe symptoms; limiting self care activities of daily living; disabling; repair or revision indicated MW, YH CTCAE: E11645 Grade 4 aortic injury AE an aortic injury AE that has life-threatening consequences; evidence of end organ damage; urgent operative intervention indicated MW, YH CTCAE: E11646 Grade 2 arterial injury AE CTCAE: E11650 an arterial injury AE that is symptomatic (e.g., claudication); repair or revision not indicated MW, YH Grade 3 arterial injury AE an arterial injury AE that has severe symptoms; limiting self care activities of daily living; disabling; repair or revision indicated MW, YH CTCAE: E11651 Grade 4 arterial injury AE an arterial injury AE that has life-threatening consequences; evidence of end organ damage; urgent operative intervention indicated MW, YH CTCAE: E11652 Grade 3 biliary anastomotic leak AE CTCAE: E11657 MW, YH a biliary anastomotic leak AE that has severe symptoms; radiologic, endoscopic or elective operative intervention indicated Grade 3 bladder anastomotic leak AE a bladder anastomotic leak AE that has severe symptoms; radiologic, endoscopic or elective operative intervention indicated MW, YH CTCAE: E11663 Grade 3 esophageal anastomotic leak AE MW, YH CTCAE: E11684 an esophageal anastomotic leak AE that has severe symptoms; radiologic, endoscopic or elective operative intervention indicated Grade 3 fallopian tube anastomotic leak AE MW, YH CTCAE: E11694 a fallopian tube anastomotic leak AE that has severe symptoms; radiologic, endoscopic or elective operative intervention indicated Grade 4 fallopian tube perforation AE MW, YH a fallopian tube perforation AE that has life-threatening consequences; urgent operative intervention indicated (e.g., organ resection) CTCAE: E11701 Grade 3 gastric anastomotic leak AE CTCAE: E11712 MW, YH a gastric anastomotic leak AE that has severe symptoms; radiologic, endoscopic or elective operative intervention indicated Grade 3 gastrointestinal anastomotic leak CTCAE: E11718 a gastrointestinal anastomotic leak AE that has severe symptoms; radiologic, endoscopic or elective operative intervention indicated MW, YH Grade 2 gastrointestinal stoma necrosis MW, YH a gastrointestinal stoma necrosis AE that is a superficial necrosis; intervention not indicated CTCAE: E11722 Grade 2 hip fracture AE CTCAE: E11727 MW, YH a hip fracture AE that has a hairline fracture; mild pain; limiting instrumental activities of daily living; non-surgical intervention indicated Grade 3 hip fracture AE MW, YH a hip fracture AE that has severe pain; hospitalization or intervention indicated for pain control (e.g., traction); operative intervention indicated CTCAE: E11728 Grade 4 hip fracture AE CTCAE: E11729 a hip fracture AE that has life-threatening consequences; symptoms associated with neurovascular compromise MW, YH Grade 3 injury to carotid artery AE MW, YH CTCAE: E11731 an injury to carotid artery AE that has severe symptoms; limiting self care activities of daily living (e.g., transient cerebral ischemia); repair or revision indicated Grade 3 injury to jugular vein AE CTCAE: E11738 an injury to jugular vein AE that is symptomatic limiting self care activities of daily living; disabling; repair or revision indicated MW, YH Grade 3 injury to superior vena cava AE CTCAE: E11744 MW, YH an injury to superior vena cava AE that has severe symptoms; limiting self care activities of daily living; disabling; repair or revision indicated Grade 4 injury to superior vena cava AE a injury to superior vena cava AE that has life-threatening consequences; evidence of end organ damage; urgent operative intervention indicated MW, YH CTCAE: E11745 Grade 3 intestinal stoma leak AE MW, YH an intestinal stoma leak AE that has severe symptoms; radiologic, endoscopic or elective operative intervention indicated CTCAE: E11756 Grade 3 intestinal stoma leak AE an intestinal stoma leak AE that has severe symptoms; IV fluids, tube feeding, or TPN indicated greater than or equal to 24 hrs; elective operative intervention indicated MW, YH CTCAE: E11761 Grade 1 intestinal stoma site bleeding AE an intestinal stoma site bleeding AE that has minimal bleeding identified on clinical exam; intervention not indicated MW, YH CTCAE: E11765 Grade 3 intestinal stoma site bleeding AE an intestinal stoma site bleeding AE that has severe bleeding; transfusion indicated; radiologic or endoscopic intervention indicated CTCAE: E11767 MW, YH Grade 1 intraoperative arterial injury AE an intraoperative arterial injury AE where primary repair of injured organ/structure indicated CTCAE: E11771 MW, YH Grade 2 intraoperative arterial injury AE MW, YH an intraoperative arterial injury AE where partial resection of injured organ/structure indicated CTCAE: E11772 Grade 3 intraoperative arterial injury AE MW, YH an intraoperative arterial injury AE where complete resection or reconstruction of injured organ/structure indicated; disabling CTCAE: E11773 Grade 1 intraoperative breast injury AE MW, YH CTCAE: E11777 an intraoperative breast injury AE where primary repair of injured organ/structure indicated Grade 2 intraoperative breast injury AE an intraoperative breast injury AE where partial resection of injured organ/structure indicated CTCAE: E11778 MW, YH Grade 3 intraoperative breast injury AE MW, YH CTCAE: E11779 an intraoperative breast injury AE where complete resection or reconstruction of injured organ/structure indicated; disabling Grade 3 intraoperative cardiac injury AE an intraoperative cardiac injury AE where primary repair of injured organ/structure indicated MW, YH CTCAE: E11783 Grade 1 intraoperative ear injury AE CTCAE: E11787 MW, YH an intraoperative ear injury AE where primary repair of injured organ/structure indicated Grade 2 intraoperative ear injury AE CTCAE: E11788 MW, YH an intraoperative ear injury AE where partial resection of injured organ/structure indicated Grade 3 intraoperative ear injury AE an intraoperative ear injury AE where complete resection of injured organ/structure indicated; disabling (e.g., impaired hearing; impaired balance) MW, YH CTCAE: E11789 Grade 1 intraoperative endocrine injury AE an intraoperative endocrine injury AE where primary repair of injured organ/structure indicated MW, YH CTCAE: E11793 Grade 2 intraoperative endocrine injury AE an intraoperative endocrine injury AE where partial resection of injured organ/structure indicated CTCAE: E11794 MW, YH Grade 3 intraoperative endocrine injury AE MW, YH CTCAE: E11795 an intraoperative endocrine injury AE where complete resection or reconstruction of injured organ/structure indicated; disabling Grade 1 intraoperative gastrointestinal injury AE MW, YH CTCAE: E11799 an intraoperative gastrointestinal injury AE where primary repair of injured organ/structure indicated Grade 2 intraoperative gastrointestinal injury AE MW, YH CTCAE: E11800 an intraoperative gastrointestinal injury AE where partial resection of injured organ/structure indicated Grade 3 intraoperative gastrointestinal injury AE CTCAE: E11801 MW, YH an intraoperative gastrointestinal injury AE where complete resection or reconstruction of injured organ/structure indicated; disabling Grade 1 lintraoperative head and neck injury AE CTCAE: E11805 a lintraoperative head and neck injury AE where primary repair of injured organ/structure indicated MW, YH Grade 2 lintraoperative head and neck injury AE a lintraoperative head and neck injury AE where partial resection of injured organ/structure indicated MW, YH CTCAE: E11806 Grade 3 lintraoperative head and neck injury AE CTCAE: E11807 a lintraoperative head and neck injury AE where complete resection or reconstruction of injured organ/structure indicated; disabling MW, YH Grade 1 intraoperative hepatobiliary injury AE an intraoperative hepatobiliary injury AE where primary repair of injured organ/structure indicated MW, YH CTCAE: E11815 Grade 2 intraoperative hepatobiliary injury AE CTCAE: E11816 an intraoperative hepatobiliary injury AE where partial resection of injured organ/structure indicated MW, YH Grade 3 intraoperative hepatobiliary injury AE MW, YH CTCAE: E11817 an intraoperative hepatobiliary injury AE where complete resection or reconstruction of injured organ/structure indicated; disabling Grade 1 intraoperative musculoskeletal injury AE MW, YH CTCAE: E11821 an intraoperative musculoskeletal injury AE where primary repair of injured organ/structure indicated Grade 2 intraoperative musculoskeletal injury AE CTCAE: E11822 MW, YH an intraoperative musculoskeletal injury AE where partial resection of injured organ/structure indicated Grade 3 intraoperative musculoskeletal injury AE an intraoperative musculoskeletal injury AE where complete resection or reconstruction of injured organ/structure indicated; disabling CTCAE: E11823 MW, YH Grade 1 intraoperative neurological injury AE MW, YH CTCAE: E11827 an intraoperative neurological injury AE where primary repair of injured organ/structure indicated Grade 2 intraoperative neurological injury AE an intraoperative neurological injury AE where partial resection of injured organ/structure indicated CTCAE: E11828 MW, YH Grade 3 intraoperative neurological injury AE CTCAE: E11829 an intraoperative neurological injury AE where complete resection or reconstruction of injured organ/structure indicated; disabling MW, YH Grade 1 intraoperative ocular injury AE an intraoperative ocular injury AE where primary repair of injured organ/structure indicated MW, YH CTCAE: E11833 Grade 2 intraoperative ocular injury AE an intraoperative ocular injury AE where partial resection of injured organ/structure indicated CTCAE: E11834 MW, YH Grade 3 intraoperative ocular injury AE CTCAE: E11835 an intraoperative ocular injury AE where complete resection or reconstruction of injured organ/structure indicated; disabling MW, YH Grade 1 intraoperative renal injury AE CTCAE: E11839 MW, YH an intraoperative renal injury AE where primary repair of injured organ/structure indicated Grade 2 intraoperative renal injury AE an intraoperative renal injury AE where partial resection of injured organ/structure indicated MW, YH CTCAE: E11840 Grade 3 intraoperative renal injury AE an intraoperative renal injury AE where complete resection or reconstruction of injured organ/structure indicated; disabling CTCAE: E11841 MW, YH Grade 1 intraoperative reproductive tract injury AE an intraoperative reproductive tract injury AE where primary repair of injured organ/structure indicated MW, YH CTCAE: E11845 Grade 2 intraoperative reproductive tract injury AE an intraoperative reproductive tract injury AE where partial resection of injured organ/structure indicated CTCAE: E11846 MW, YH Grade 3 intraoperative reproductive tract injury AE MW, YH an intraoperative reproductive tract injury AE where complete resection or reconstruction of injured organ/structure indicated; disabling CTCAE: E11847 Grade 1 intraoperative respiratory injury AE an intraoperative respiratory injury AE where primary repair of injured organ/structure indicated CTCAE: E11851 MW, YH Grade 2 intraoperative respiratory injury AE CTCAE: E11852 MW, YH an intraoperative respiratory injury AE where partial resection of injured organ/structure indicated Grade 3 intraoperative respiratory injury AE CTCAE: E11853 MW, YH an intraoperative respiratory injury AE where complete resection or reconstruction of injured organ/structure indicated; disabling Grade 1 intraoperative skin injury AE an intraoperative skin injury AE where primary repair of injured organ/structure indicated CTCAE: E11857 MW, YH Grade 2 intraoperative skin injury AE CTCAE: E11858 an intraoperative skin injury AE where partial resection of injured organ/structure indicated MW, YH Grade 3 intraoperative skin injury AE CTCAE: E11859 MW, YH an intraoperative skin injury AE where complete resection or reconstruction of injured organ/structure indicated; disabling Grade 2 intraoperative splenic injury AE CTCAE: E11863 MW, YH an intraoperative splenic injury AE where primary repair of injured organ/structure indicated Grade 3 intraoperative splenic injury AE an intraoperative splenic injury AE where resection or reconstruction of injured organ/structure indicated; disabling MW, YH CTCAE: E11864 Grade 1 intraoperative urinary injury AE MW, YH CTCAE: E11868 an intraoperative urinary injury AE where primary repair of injured organ/structure indicated Grade 2 intraoperative urinary injury AE CTCAE: E11869 MW, YH an intraoperative urinary injury AE where partial resection of injured organ/structure indicated Grade 3 intraoperative urinary injury AE MW, YH CTCAE: E11870 an intraoperative urinary injury AE where complete resection or reconstruction of injured organ/structure indicated; disabling Grade 1 intraoperative venous injury AE an intraoperative venous injury AE where primary repair of injured organ/structure indicated CTCAE: E11874 MW, YH Grade 2 intraoperative venous injury AE CTCAE: E11875 an intraoperative venous injury AE where partial resection of injured organ/structure indicated MW, YH Grade 3 intraoperative venous injury AE an intraoperative venous injury AE where complete resection or reconstruction of injured organ/structure indicated; disabling MW, YH CTCAE: E11876 Grade 3 kidney anastomotic leak AE CTCAE: E11882 a kidney anastomotic leak AE that has severe symptoms; radiologic, endoscopic or elective operative intervention indicated MW, YH Grade 3 large intestinal anastomotic leak AE CTCAE: E11888 a large intestinal anastomotic leak AE that has severe symptoms; radiologic, endoscopic or elective operative intervention indicated MW, YH Grade 3 pancreatic anastomotic leak AE a pancreatic anastomotic leak AE that has severe symptoms; radiologic, endoscopic or elective operative intervention indicated CTCAE: E11894 MW, YH Grade 3 pharyngeal anastomotic leak AE a pharyngeal anastomotic leak AE that has severe symptoms; radiologic, endoscopic or elective operative intervention indicated MW, YH CTCAE: E11900 Grade 2 postoperative hemorrhage AE CTCAE: E11905 a postoperative hemorrhage AE that has moderate bleeding; radiologic, endoscopic, or operative intervention indicated MW, YH Grade 3 postoperative hemorrhage AE MW, YH a postoperative hemorrhage AE where transfusion indicated of greather than or equal to 2 units (10 cc/kg for pediatrics) pRBCs beyond protocol specification; urgent radiologic, endoscopic, or operative intervention indicated CTCAE: E11906 Grade 2 postoperative thoracic procedure complication AE a postoperative thoracic procedure complication AE when the patient is extubated within 24 - 72 hrs postoperatively MW, YH CTCAE: E11910 Grade 3 postoperative thoracic procedure complication AE MW, YH CTCAE: E11911 a postoperative thoracic procedure complication AE when the patient is extubated more than 72 hrs postoperatively, but before tracheostomy indicated Grade 3 postoperative thoracic procedure complication AE CTCAE: E11912 MW, YH a postoperative thoracic procedure complication AE that has life-threatening airway compromise; urgent intervention indicated (e.g., tracheotomy or intubation) Grade 1 prolapse of intestinal stoma AE a prolapse of intestinal stoma AE that is asymptomatic; reducible MW, YH CTCAE: E11915 Grade 2 prolapse of intestinal stoma AE MW, YH CTCAE: E11916 a prolapse of intestinal stoma AE that is recurrent after manual reduction; local irritation or stool leakage; difficulty to fit appliance; limiting instrumental activities of daily living Grade 2 prolapse of urostomy AE a prolapse of urostomy AE treated with local care or maintenance; minor revision indicated MW, YH CTCAE: E11922 Grade 3 prolapse of urostomy AE CTCAE: E11923 a prolapse of urostomy AE that has dysfunctional stoma; elective operative intervention or major stomal revision indicated MW, YH Grade 1 radiation recall reaction (dermatologic) AE CTCAE: E11927 a radiation recall reaction (dermatologic) AE that has faint erythema or dry desquamation MW, YH Grade 2 radiation recall reaction (dermatologic) AE MW, YH CTCAE: E11928 a radiation recall reaction (dermatologic) AE that has moderate to brisk erythema; patchy moist desquamation, mostly confined to skin folds and creases; moderate edema Grade 3 radiation recall reaction (dermatologic) AE CTCAE: E11929 MW, YH a radiation recall reaction (dermatologic) AE that has moist desquamation in areas other than skin folds and creases; bleeding induced by minor trauma or abrasion Grade 4 radiation recall reaction (dermatologic) AE CTCAE: E11930 a radiation recall reaction (dermatologic) AE that has life-threatening consequences; skin necrosis or ulceration of full thickness dermis; spontaneous bleeding from involved site; skin graft indicated MW, YH Grade 3 rectal anastomotic leak AE CTCAE: E11935 a rectal anastomotic leak AE that has severe symptoms; radiologic, endoscopic or elective operative intervention indicated MW, YH Grade 2 seroma AE a seroma AE that is symptomatic; simple aspiration indicated MW, YH CTCAE: E11940 Grade 3 seroma AE a seroma AE that is symptomatic, elective radiologic or operative intervention indicated CTCAE: E11941 MW, YH Grade 3 small intestinal anastomotic leak AE CTCAE: E11945 a small intestinal anastomotic leak AE that has severe symptoms; radiologic, endoscopic or elective operative intervention indicated MW, YH Grade 3 spermatic cord anastomotic leak AE MW, YH a spermatic cord anastomotic leak AE that has severe symptoms; radiologic, endoscopic or elective operative intervention indicated CTCAE: E11951 Grade 1 spinal fracture AE a spinal fracture AE that has mild back pain; nonprescription analgesics indicated MW, YH CTCAE: E11955 Grade 2 spinal fracture AE CTCAE: E11956 MW, YH a spinal fracture AE that has moderate back pain; prescription analgesics indicated; limiting instrumental activities of daily living Grade 3 spinal fracture AE a spinal fracture AE that has severe back pain; hospitalization or intervention indicated for pain control (e.g., vertebroplasty); limiting self care activities of daily living; disability MW, YH CTCAE: E11957 Grade 4 spinal fracture AE MW, YH CTCAE: E11958 a spinal fracture AE that has life-threatening consequences; symptoms associated with neurovascular compromise Grade 2 stenosis of gastrointestinal stoma AE a stenosis of gastrointestinal stoma AE that is symptomatic; IV fluids indicated <24 hrs; manual dilation at bedside MW, YH CTCAE: E11961 Grade 3 stenosis of gastrointestinal stoma AE CTCAE: E11962 MW, YH a stenosis of gastrointestinal stoma AE that has severely altered GI function; tube feeding, TPN or hospitalization indicated; elective operative intervention indicated Grade 3 tracheal hemorrhage AE CTCAE: E11972 a tracheal hemorrhage AE that has severe bleeding; transfusion indicated; radiologic or endoscopic intervention indicated MW, YH Grade 1 tracheal obstruction AE MW, YH CTCAE: E11976 a tracheal obstruction AE that has partial asymptomatic obstruction on examination (e.g., visual, radiologic or endoscopic) Grade 2 tracheal obstruction AE CTCAE: E11977 MW, YH a tracheal obstruction AE that is symptomatic (e.g., noisy airway breathing), no respiratory distress; medical intervention indicated (e.g., steroids); limiting instrumental activities of daily living Grade 3 tracheal obstruction AE CTCAE: E11978 MW, YH a tracheal obstruction AE that has stridor; radiologic or endoscopic intervention indicated (e.g., stent, laser); limiting self care activities of daily living Grade 4 tracheal obstruction AE CTCAE: E11979 a tracheal obstruction AE that has life-threatening airway compromise; urgent intervention indicated (e.g., tracheotomy or intubation) MW, YH Grade 3 tracheostomy site bleeding AE a tracheostomy site bleeding AE that has severe bleeding; transfusion indicated; radiologic or endoscopic intervention indicated CTCAE: E11984 MW, YH Grade 3 ureteric anastomotic leak AE an ureteric anastomotic leak AE that has severe symptoms; radiologic, endoscopic or elective operative intervention indicated MW, YH CTCAE: E11990 Grade 3 urethral anastomotic leak CTCAE: E11996 MW, YH an urethral anastomotic leak AE that has severe symptoms; radiologic, endoscopic or elective operative intervention indicated Grade 3 urostomy leak AE MW, YH a urostomy leak AESevere symptoms; radiologic, endoscopic or elective operative intervention indicated CTCAE: E12002 Grade 2 urostomy obstruction AE a urostomy obstruction AE that is symptomatic; dilation or endoscopic repair or stent placement indicated MW, YH CTCAE: E12007 Grade 3 urostomy site bleeding AE MW, YH a urostomy site bleeding AE that has severe bleeding; transfusion indicated; radiologic or endoscopic intervention indicated CTCAE: E12014 Grade 2 urostomy stenosis AE a urostomy stenosis AE that is symptomatic but no hydronephrosis, no sepsis or no renal dysfunction; dilation or endoscopic repair or stent placement indicated CTCAE: E12018 MW, YH Grade 3 urostomy stenosis AE MW, YH a urostomy stenosis AE that is symptomatic (e.g., hydronephrosis, or renal dysfunction); elective operative intervention indicated CTCAE: E12019 Grade 3 uterine anastomotic leak AE a uterine anastomotic leak AE that has severe symptoms; radiologic, endoscopic or elective operative intervention indicated CTCAE: E12025 MW, YH Grade 3 vaginal anastomotic leak AE CTCAE: E12037 MW, YH a vaginal anastomotic leak AE that has severe symptoms; radiologic, endoscopic or elective operative intervention indicated Grade 3 vas deferens anastomotic leak AE CTCAE: E12043 a vas deferens anastomotic leak AE that has severe symptoms; radiologic, endoscopic or elective operative intervention indicated MW, YH Grade 2 vascular access complication AE CTCAE: E12047 MW, YH a vascular access complication AE that has device dislodgement, blockage, leak, or malposition; device replacement indicated Grade 3 vascular access complication AE MW, YH A vascular access complication AE that has deep vein or cardiac thrombosis; intervention indicated (e.g., anticoagulation, lysis, filter, invasive procedure) CTCAE: E12048 Grade 4 vascular access complication AE a vascular access complication AE that has embolic event including pulmonary embolism or life-threatening thrombus CTCAE: E12049 MW, YH Grade 3 blood antidiuretic hormone abnormal AE MW, YH CTCAE: E12095 a blood antidiuretic hormone abnormal AE where hospitalization indicated Grade 3 blood corticotrophin decreased AE a blood corticotrophin decreased AE where hospitalization indicated CTCAE: E12104 MW, YH Grade 1 carbon monoxide diffusing capacity decreased AE MW, YH a carbon monoxide diffusing capacity decreased AE that is 3 - 5 units below lower limit of normal; for follow-up, a decrease of 3 - 5 units (ml/min/mm Hg) below the baseline value CTCAE: E12113 Grade 2 carbon monoxide diffusing capacity decreased AE a carbon monoxide diffusing capacity decreased AE that is 6 - 8 units below lower limit of normal; for follow-up, an asymptomatic decrease of greater than 5 - 8 units (ml/min/mm Hg) below the baseline value CTCAE: E12114 MW, YH Grade 3 carbon monoxide diffusing capacity decreased AE CTCAE: E12115 MW, YH a carbon monoxide diffusing capacity decreased AE that is an asymptomatic decrease of greater than 8 units drop; greater than 5 units drop along with the presence of pulmonary symptoms (e.g. , greater than Grade 2 hypoxia or greater than Grade 2 or higher dyspnea) Grade 1 cardiac troponin I increased AE a cardiac troponin I increased AE that has levels above the upper limit of normal and below the level of myocardial infarction as defined by the manufacturer CTCAE: E12117 MW, YH Grade 3 cardiac troponin I increased AE MW, YH CTCAE: E12118 a cardiac troponin I increased AE that has levels consistent with myocardial infarction as defined by the manufacturer Grade 1 cardiac troponin T increased AE a cardiac troponin T increased AE that has levels above the upper limit of normal and below the level of myocardial infarction as defined by the manufacturer CTCAE: E12120 MW, YH Grade 3 cardiac troponin T increased AE MW, YH a cardiac troponin T increased AE that has levels consistent with myocardial infarction as defined by the manufacturer CTCAE: E12121 Grade 1 CD4 lymphocytes decreased AE MW, YH a CD4 lymphocytes decreased AE that is less than the lower limit of normal to 500/mm3 or 0.5 x 10e9 /L CTCAE: E12123 Grade 2 CD4 lymphocytes decreased AE CTCAE: E12124 MW, YH a CD4 lymphocytes decreased AE that is less than 500 - 200/mm3; less than 0.5 - 0.2 x 10e9 /L Grade 3 CD4 lymphocytes decreased AE MW, YH a CD4 lymphocytes decreased AE that is less than 200 - 50/mm3; less than 0.2 x 0.05 - 10e9 /L CTCAE: E12125 Grade 4 CD4 lymphocytes decreased AE CTCAE: E12126 MW, YH a CD4 lymphocytes decreased AE that is less than 50/mm3; less than 0.05 x 10e9 /L Grade 1 CPK increased AE MW, YH a CPK increased AE that is greater than the upper limit of normal to 2.5 times the upper limit of normal CTCAE: E12133 Grade 2 CPK increased AE CTCAE: E12134 a CPK increased AE that is greater than 2.5 -5 times the upper limit of normal MW, YH Grade 3 CPK increased AE CTCAE: E12135 a CPK increased AE that is greater than 5 to 10 times the upper limit of normal MW, YH Grade 4 CPK increased AE a CPK increased AE that is greater than 10 times the upper limit of normal CTCAE: E12136 MW, YH Grade 1 fibrinogen decreased AE a fibrinogen decreased AE that is less than 1.0 - 0.75 times the lower limit of normal or less than 25% decrease from baseline MW, YH CTCAE: E12152 Grade 2 fibrinogen decreased AE MW, YH a fibrinogen decreased AE that is less than 0.75 - 0.5 times the lower limit of normal or 25 - less than 50% decrease from baseline CTCAE: E12153 Grade 3 fibrinogen decreased AE a fibrinogen decreased AE that is less than 0.5 - 0.25 times the lower limit of normal or 50 - less than 75% decrease from baseline CTCAE: E12154 MW, YH Grade 4 fibrinogen decreased AE MW, YH a fibrinogen decreased AE that is less than 0.25 times the lower limit of normal or 75% decrease from baseline or absolute value less than 50 mg/dL CTCAE: E12155 Grade 1 haptoglobin decreased AE a haptoglobin decreased AE that is less than the lower limit of normal MW, YH CTCAE: E12170 Grade 1 pancreatic enzymes decreased AE CTCAE: E12204 a pancreatic enzymes decreased AE that is less than the lower limit of normal and asymptomatic MW, YH Grade 2 pancreatic enzymes decreased AE a pancreatic enzymes decreased AE that has an increase in stool frequency, bulk, or odor; steatorrhea MW, YH CTCAE: E12205 Grade 3 pancreatic enzymes decreased AE MW, YH CTCAE: E12206 a pancreatic enzymes decreased AE that has sequelae of absorption deficiency Grade 1 vital capacity abnormal AE CTCAE: E12221 MW, YH a vital capacity abnormal AE that has 90 - 75% of predicted value Grade 2 vital capacity abnormal AE CTCAE: E12222 MW, YH a vital capacity abnormal AE that is less than 75 - 50% of predicted value; limiting instrumental activities of daily living Grade 3 vital capacity abnormal AE a vital capacity abnormal AE that is less than 50% of predicted value; limiting self care activities of daily living CTCAE: E12223 MW, YH esophagus AE YH, MW a digestive system AE that occurs at esophagus 食道副作用 anus AE a digestive system AE that occurs at anus YH, MW duodenum AE a digestive system AE that occurs at duodenum MW, YH Grade 1 cognitive disturbance AE MW, YH a cognitive disturbance AE that has mild cognitive disability; not interfering with work/school/life performance; specialized educational services/devices not indicated CTCAE: E12618 Grade 2 cognitive disturbance AE a cognitive disturbance AE that has moderate cognitive disability; interfering with work/school/life performance but capable of independent living; specialized resources on part time basis indicated MW, YH CTCAE: E12619 Grade 3 cognitive disturbance AE MW, YH a cognitive disturbance AE that has severe cognitive disability; significant impairment of work/school/life performance CTCAE: E12620 uterine AE JX, YH a female reproductive system AE that occurs in the uterus WEB: https://en.wikipedia.org/wiki/Uterus female reproduction system inflammation AE YH, JX an inflammation AE which occurs in the female reproduction system palsy AE A paralysis AE accompanied by involuntary tremors. 麻痹 KY, YH WEB: https://en.oxforddictionaries.com/definition/palsy WEB: https://en.wikipedia.org/wiki/Palsy Grade 1 diarrhea AE CTCAE: E10573 MW, EO a diarrhea AE that has 4 stools per day over baseline; mild increase in ostomy output compared to baseline. Grade 2 diarrhea AE CTCAE: E10574 MW, EO a diarrhea AE that has increased of 4 - 6 stools per day over baseline; moderate increase in ostomy output compared to baseline. Grade 3 diarrhea AE CTCAE: E10575 MW, EO a diarrhea AE that has increased of >=7 stools per day over baseline; incontinence; hospitalization indicated; severe increase in ostomy output compared to baseline; limiting self care ADL Grade 1 nausea AE CTCAE: E10879 MW, EO a nausea AE that has Loss of appetite without alteration in eating habits Grade 2 nausea AE CTCAE: E10880 MW, EO a nausea AE that has oral intake decreased without significant weight loss, dehydration or malnutrition Grade 3 nausea AE CTCAE: E10881 MW, EO a nausea AE that has inadequate oral caloric or fluid intake; tube feeding, TPN, or hospitalization indicated ulcer A disorder material entity that forms an open sore on the skin or a mucous membrane, accompanied by the disintegration of tissue. https://en.wikipedia.org/wiki/Ulcer YH Grade 3 duodenal ulcer AE A duodenal ulcer AE that alters GI function and requiresTPN indicated; elective operative or endoscopic intervention indicated; limiting self care ADL. CTCAE: E10614 anal hemorrhage AE 10055226 NCIt: C78168 An anus AE that bleed from the anal region. CTCAE: E10470 Grade 2 anal hemorrhage AE An anal hemorrhage AE that has moderate symptoms; medical intervention or minor cauterization indicated. CTCAE: E10472 Grade 3 anal hemorrhage AE An anal hemorrhage AE that has transfusion, radiologic, endoscopic, or elective operative intervention indicated. CTCAE: E10473 colonic stenosis AE 10010004 CTCAE: E10550 NCIt: C78243 A gastrointestinal disorder AE that has a narrowing of the lumen of the colon. Grade 2 colonic stenosis AE CTCAE: E10552 A colonic stenosis AE that altered GI function. Grade 3 colonic stenosis AE CTCAE: E10553 A colonic stenosis AE that alters GI function and requires tube feeding or hospitalization. esophageal perforation AE 10055472 CTCAE: E10665 An esophagus AE that has a rupture in the wall of the esophagus. NCIt: C50693 Grade 2 mucosal inflammation AE A mucosal inflammation AE that has moderate pain which is not interfering with oral intake but modified diet indicated. CTCAE: E10874 Grade 3 mucosal inflammation AE CTCAE: E10875 A mucosal inflammation AE that is interfering with oral intake. oral dysesthesia AE 10054520 A dysesthesia AE that has burning or tingling sensation on the lips, tongue or entire mouth. NCIt: C62545 CTCAE: E10894 Grade 3 Oral dysesthesia AE An oral dysesthesia AE that has disabling pain, requires tube feeding and TPN. CTCAE: E10897 Grade 2 Oral dysesthesia AE An oral dysesthesia AE that has m oderate pain and is interfering with oral intake. CTCAE: E10896 Grade 1 Oral dysesthesia AE An oral dysesthesia AE that has mild discomfort but is not interfering with oral intake. CTCAE: E10895 Grade 3 periodontal disease AE CTCAE: E10938 A periodontal disease AE that has spontaneous bleeding, severe bone loss with or without tooth loss and osteonecrosis of maxilla or mandible. Grade 2 periodontal disease AE CTCAE: E10937 A periodontal disease AE that has moderate gingival recession or gingivitis, multiple sites of bleeding on probing and moderate bone loss. Grade 1 periodontal disease AE A periodontal disease AE that has gingival recession or gingivitis, limited bleeding on probing and mild local bone loss. CTCAE: E10936 rectal necrosis AE 10065709 CTCAE: E10967 NCIt: C78585 A necrosis AE that there the ecrotic process occurring in the rectal wall. Grade 3 rectal necrosis AE A rectal necrosis AE that requires tube feeding or TPN indicated; radiologic, endoscopic, or operative intervention indicated. CTCAE: E10968 salivary duct inflammation AE 10056681 An inflammation AE that has inflammation of the salivary duct. CTCAE: E10470 NCIt: C78600 Grade 3 salivary duct inflammation AE CTCAE: E11006 A salivary duct inflammation AE that has acute salivary gland necrosis; severe secretion-induced symptoms (e.g., thick saliva/oral secretions or gagging); tube feeding or TPN indicated; limiting self care ADL; disabling Grade 2 salivary duct inflammation AE A salivary duct inflammation AE that has thick, ropy, sticky saliva; markedly altered taste; alteration in diet indicated; secretion-induced symptoms; limiting instrumental ADL CTCAE: E11005 Grade 1 salivary duct inflammation AE A salivary duct inflammation AE that has slightly thickened saliva; slightly altered taste (e.g., metallic) CTCAE: E11004 small intestinal mucositis AE 10065710 NCIt: C78613 An inflammation AE that has inflammation of the mucous membrane of the small intestine. CTCAE: E11015 Grade 3 small intestinal mucositis AE CTCAE: E11018 A small intestinal mucositis AE that has severe pain and is interfering with oral intake; tube feeding, TPN or hospitalization indicated. Grade 3 small intestine ulcer AE CTCAE: E11041 A small intestine ulcer AE that has altered GI function, requires TPN indicated. Elective operative or endoscopic intervention indicated; limiting self care ADL; disablingoperative intervention Grade 2 small intestine ulcer AE CTCAE: E11040 A small intestine ulcer AE that has altered GI function. tooth development disorder AE 10044030 CTCAE: E11048 A tooth disorder AE that has a pathological process of the teeth occurring during tooth development. NCIt: C35596 Grade 3 tooth development disorder AE CTCAE: E11051 A tooth development disorder AE that has maldevelopment with impairment not surgically correctable. Grade 2 tooth development disorder AE A tooth development disorder AE that has impairment correctable with oral surgery CTCAE: E11050 Grade 1 tooth development disorder AE A tooth development disorder AE that has hypoplasia of tooth or enamel. CTCAE: E11049 Grade 3 cecitis AE CTCAE: E11059 A digestive system AE that has abdominal pain, fever, change in bowel habits with ileus and peritoneal signs. planned process 'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.) 6/11/9: Edited at workshop. Used to include: is initiated by an agent Bjoern Peters Injecting mice with a vaccine in order to test its efficacy branch derived A processual entity that realizes a plan which is the concretization of a plan specification. This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call) planned process disorder A material entity which is clinically abnormal and part of an extended organism. Disorders are the physical basis of disease. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf bodily process Albert Goldfain creation date: 2009-06-23T11:53:49Z pathological bodily process Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf A bodily process that is clinically abnormal. creation date: 2009-06-23T11:54:29Z behavioral quality An organismal quality inhering in a bearer by virtue of the bearer's behavior aggregate of the responses or reactions or movements in a given situation. PATO:0000186 PATO:0001722 behavioural quality quality physical quality A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities. PATO:0001018 PATO:0002079 Wikipedia:Physical_property quality relational physical quality process quality A quality which inheres in an process. PATO:0001236 PATO:0001239 PATO:0001240 See comments of relational quality of a physical entity. quality quality of a process quality of occurrent quality of process relational quality of occurrent physical object quality A quality which inheres in a continuant. PATO:0001237 PATO:0001238 PATO:0001241 Relational qualities are qualities that hold between multiple entities. Normal (monadic) qualities such as the shape of a eyeball exist purely as a quality of that eyeball. A relational quality such as sensitivity to light is a quality of that eyeball (and connecting nervous system) as it relates to incoming light waves/particles. monadic quality of a continuant monadic quality of an object monadic quality of continuant multiply inhering quality of a physical entity quality quality of a continuant quality of a single physical entity quality of an object quality of continuant snap:Quality organismal quality A quality that inheres in an entire organism or part of an organism. PATO:0001995 quality nose BTO:0000840 CALOHA:TS-2037 EHDAA2:0001274 EHDAA:1502 EMAPA:16542 EV:0100037 EV:0100370 FMA:46472 GAID:77 MA:0000281 MAT:0000139 MESH:D009666 MIAA:0000139 OpenCyc:Mx4rvViCbJwpEbGdrcN5Y29ycA Organ that is the specialized structure of the face that contains olfactory neurons. The peripheral olfactory organ is paired[ZFA:0000047]. TAO:0000047 The olfactory organ of vertebrates, consisting of nares, olfactory epithelia and the structures and skeletal framework of the nasal cavity. UBERON:0000004 UMLS:C0028429 ZFA:0000047 a protuberance in vertebrates that houses the nostrils, or nares, which admit and expel air for respiration in conjunction with the mouth. Behind the nose are the olfactory mucosa and the sinuses. Behind the nasal cavity, air next passes through the pharynx, shared with the digestive system, and then into the rest of the respiratory system. In humans, the nose is located centrally on the face; on most other mammals, it is on the upper tip of the snout[WP]. GO: The nose is the specialized structure of the face that serves as the organ of the sense of smell and as part of the respiratory system. Includes the nasi externus (external nose) and cavitas nasi (nasal cavity)[Wikipedia:Nose]. galen:Nose nasal sac nasus nose olfactory apparatus peripheral olfactory organ proboscis the organ that is specialized for smell and is part of the respiratory system the structure of the nose varies across vertebrates. In tetrapods the nose is part of the respiratory system.[PMID:25312359] uberon islet of Langerhans A primitive exocrine pancreas can be found in holocephalan cartilaginous fish; a pancreatic duct directly ending in the gut lumen is connected to a glandular structure made of exocrine cells and associated with cell islets, which comprises three different hormone-producing cell types: insulin, somatostatin and glucagon (Yui and Fujita, 1986) AAO:0010406 Anatomical structure which consists of glands developed from pancreatic ducts in the larvae and secrete insulin.[AAO] BTO:0000991 CALOHA:TS-0741 EFO:0000856 EMAPA:32927 EV:0100130 FMA:16016 GAID:324 MA:0000127 MAT:0000076 MESH:D007515 MIAA:0000076 Mammals, birds, reptiles and amphibians have a pancreas with similar histology and mode of development, while in some fish, the islet cells are segregated as Brockmann bodies.[well established][VHOG] UBERON:0000006 UMLS:C0022131 VHOG:0000646 XAO:0000159 island of Langerhans island of pancreas islets of langerhans pancreatic insula pancreatic islet the clusters of hormone-producing cells that are scattered throughout the pancreas uberon peripheral nervous system (...) specific vertebrate traits within the chordate phylum such as skeletal tissues, PNS, and spectacular head and brain development, are linked to the NC (neural crest) and its derivatives.[well established][VHOG] A major division of the nervous system that contains nerves which connect the central nervous system (CNS) with sensory organs, other organs, muscles, blood vessels and glands. AAO:0000429 BAMS:PNS BILA:0000081 BTO:0001028 CALOHA:TS-0808 EFO:0000891 EHDAA2:0001445 EHDAA:2893 EMAPA:16665 EV:0100335 FBbt:00005098 FMA:9903 GAID:715 MA:0000218 MAT:0000338 MESH:D017933 MIAA:0000338 Nervous structures including ganglia outside of the central nervous system. Kimmel et al, 1995.[TAO] PNS Part of nervous system in which nerves extend throughout the body outside of the brain and spinal cord.[AAO] TAO:0000142 The peripheral nervous system (PNS) is the part of the nervous system connected to the CNS which contains cranial nerves III - XII, spinal, peripheral and autonomic nerves. (CUMBO) UBERON:0000010 UMLS:C0206417 UMLS:C1305921 VHOG:0000399 XAO:0000178 ZFA:0000142 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=247 lateral part of the basal amygdalar nucleus lateral part of the basolateral nucleus nucleus amygdalae basalis, pars lateralis nucleus amygdaloideus basalis, pars lateralis magnocellularis nucleus basalis lateralis amygdalae pars peripherica pars peripherica; systema nervosum periphericum systema nervosum periphericum uberon zone of skin (...) it is well-established that neural crest cells contribute to both the dermal skeleton (craniofacial bone, teeth, and the caudal fin rays of teleosts) and the integument, including craniofacial dermis and all pigment cells outside the retina (...).[well established][VHOG] Any portion of the organ that covers that body and consists of a layer of epidermis and a layer of dermis. EHDAA2:0001844 EHDAA:6530 EMAPA:17525 EV:0100152 FMA:86166 GAID:933 MA:0000151 MAT:0000284 MESH:D012867 MIAA:0000284 Note the distinction between the entire skin of the body, of which there is only 1 in an organism, and zones of skin, of which there can be many. Examples: skin of knee OpenCyc:Mx4rvVjX3ZwpEbGdrcN5Y29ycA UBERON:0000014 VHOG:0000860 portion of skin region of skin skin skin region skin zone uberon we assume that mouse, HOG and GAID all mean zone of skin when they say skin. We also choose skin as an exact synonym, as it is more intuitive anatomical boundary A non-material anatomical entity of two dimensions. Anatomical boundaries are contiguous structures. AEO:0000192 CARO:0000010 Except in the case of abstracted fiat boundaries such as the midline plane of an organism, all 2D anatomical entities have a 3 dimensional projection. For example, the surface of the shell of a muscle has a distinct shape that projects into the third dimension. Note that boundaries are 2D structures. They have no thickness - and so can not be sites of gene expression or gene product localisation. For this, use boundary region terms. FMA:50705 UBERON:0000015 uberon endocrine pancreas BTO:0000650 CALOHA:TS-1302 EFO:0002542 EMAPA:35305 EV:0100129 FMA:16018 In the hagfish and lampreys (our most primitive vertebrate species of today), the first sign of 'a new organ' is found as collections of endocrine cells around the area of the bile duct connection with the duodenum. These endocrine organs are composed of 99% beta cells and 1% somatostatin-producing delta cells. Compared to the more primitive protochordates (e.g. amphioxus), this represents a stage where all previously scattered insulin-producing cells of the intestinal tissue have now quantitatively migrated to found a new organ involved in sensing blood glucose rather than gut glucose. Only later in evolution, the beta cells are joined by exocrine tissue and alpha cells (exemplified by the rat-, rabbit- and elephant-fishes). Finally, from sharks and onwards in evolution, we have the islet PP-cell entering to complete the pancreas.[well established][VHOG] MA:0001582 TAO:0001260 The part of the pancreas that acts as an endocrine gland, consisting of the islets of Langerhans, which secrete insulin and other hormones. [TFD][VHOG] The part of the pancreas that is part of the endocrine system and is made up of islet cells, which produce insulin, glucagon and somatostatin. The zebrafish endocrine pancreas is composed of small groups of islet cells that are distributed throughout the exocrine pancreas. The islet cells produce insulin, glucagon and somatostatin.[TAO] UBERON:0000016 VHOG:0000049 ZFA:0001260 create a separate class for distributed pancreas, eg cyclostomes? endocrine and exocrine pancreas are not co-associated in hagfishes or lampreys endocrine pancreas endocrine part of pancreas islets of Langerhans part of pancreas pars endocrina pancreatis uberon exocrine pancreas AAO:0010407 BTO:0000434 CALOHA:TS-1241 EMAPA:35328 EV:0100093 FMA:16017 In the hagfish and lampreys (our most primitive vertebrate species of today), the first sign of 'a new organ' is found as collections of endocrine cells around the area of the bile duct connection with the duodenum. These endocrine organs are composed of 99% beta cells and 1% somatostatin-producing delta cells. Compared to the more primitive protochordates (e.g. amphioxus), this represents a stage where all previously scattered insulin-producing cells of the intestinal tissue have now quantitatively migrated to found a new organ involved in sensing blood glucose rather than gut glucose. Only later in evolution, the beta cells are joined by exocrine tissue and alpha cells (exemplified by the rat-, rabbit- and elephant-fishes). Finally, from sharks and onwards in evolution, we have the islet PP-cell entering to complete the pancreas.[well established][VHOG] MA:0002415 TAO:0001249 The exocrine pancreas is composed of acinar epithelial cells and ductal epithelium that manufacture the proteolytic enzymes and bicarbonate required for digestion.[TAO] The part of the pancreas that acts as an exocrine gland, consisting of the pancreatic acini, which produce pancreatic juice and secrete it into the intestine to aid in protein digestion. [TFD][VHOG] The part of the pancreas that is part of the exocrine system and which produces and store zymogens of digestive enzymes, such as chymotrypsinogen and trypsinogen in the acinar cells [GO]. UBERON:0000017 UMLS:C0553695 VHOG:0000048 XAO:0000137 ZFA:0001249 exocrine component of pancreas exocrine pancreas exocrine part of pancreas pars exocrina pancreatis uberon camera-type eye A cavitated compound organ that transduces light waves into neural signals.[TAO] AAO:0010340 An organ of sight that includes the camera-type eyeball and supporting structures such as the lacrimal apparatus, the conjunctiva, the eyelid. BTO:0004688 EHDAA2:0000484 EHDAA:936 EMAPA:16198 FMA distinguishes Eye (subdivision of face) which has its parts an Eyeball (organ), as well as other structures, and the orbit of skull. MA includes eyelid, conjunctiva and lacrimal apparatus as part of MA:eye - consistent with FMA - so we can infer that MA:eye is more like FMA:eye than FMA:eyeball. For other AOs this distinction is less meaningful - e.g. ZFA has no eyelid; XAO has no eyelid, but it has conjuctiva, which is considered part of the xao:eye. GO considers eyelid development part of eye development. See also notes on optic nerve - XAO, AAO and BTO consider this part of the eye. MA considers the eye muscles part of the eye, whereas FMA has a class 'orbital content' for this FMA:54448 MA:0000261 OpenCyc:Mx8Ngx4rwKSh9pwpEbGdrcN5Y29ycB4rvVil5pwpEbGdrcN5Y29ycB4rvViTvpwpEbGdrcN5Y29ycA TAO:0000107 The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG] UBERON:0000019 UMLS:C0015392 UMLS:C1280202 VHOG:0000275 XAO:0000179 ZFA:0000107 camera-type eye plus associated structures eye eyes orbital part of face orbital region regio orbitalis uberon vertebrate eye sense organ AEO:0000094 An organ that is capable of transducing sensory stimulus to the nervous system. BSA:0000121 BTO:0000202 CALOHA:TS-2043 EHDAA2:0001824 EHDAA:500 EMAPA:16192 EMAPA:35955 FBbt:00005155 GAID:63 HAO:0000930 MA:0000017 MESH:D012679 Sinnesorgan UBERON:0000020 UMLS:C0935626 VHOG:0001407 WBbt:0006929 organ of sense organ system organ of sensory organ system organ of sensory system sense organ system organ sensillum sensor sensory organ sensory organ system organ sensory system organ uberon tube Any hollow cylindrical anatomical structure containing a lumen through which substances are transported. UBERON:0000025 anatomical tube duct galen:Tube not every anatomical conduit is a tube - for example, a bone foramen is an opening in the bone, and there is no distinct separate tube structure. Tubes may transport large mixed objects (for example, a bolus of food in the digestive tube) or they may transport the secretions of a single gland (for example, gland ducts) tubular uberon appendage AEO:0000193 An appendage is an external body part, or natural prolongation, that protrudes from an organism's body, such as a vertebrate's limbs[BILA][BILA:0000018]. BILA:0000018 BTO:0001492 CARO:0010003 EFO:0000799 EHDAA2:0003193 EV:0100155 FBbt:00007000 HAO:0000144 MAT:0000023 MESH:D005121 MIAA:0000023 Major subdivision of an organism that protrudes from the body[DOS, CARO]. OpenCyc:Mx4rvViC-JwpEbGdrcN5Y29ycA Organ or organ part that is attached to the body of an organism. For example a limb[GO, modified][GO:0048736]. UBERON:0000026 UMLS:C0598782 VSAO:0000075 XAO:0000218 appendages appendicular extremitaet extremity limbs/digits/tail this is currently a subtype of organism subdivision - which would exclude feathers uberon head AAO:0010335 AEO:0000106 BILA:0000115 BTO:0000282 CALOHA:TS-0436 EFO:0000964 EHDAA2:0003106 EMAPA:31858 FBbt:00000004 FMA:7154 GAID:61 HAO:0000397 MA:0000023 MAT:0000294 MESH:D006257 MIAA:0000294 OpenCyc:Mx4rEOLm4rgPEdmAAAACs6hRjg OpenCyc:Mx4rvVi6YJwpEbGdrcN5Y29ycA Organism subdivision that is the part of the body consisting of the cranial and pharyngeal regions.[AAO] Organism subdivision which is the part of the body which consists of the cranial and pharygeal regions.[TAO] SPD:0000016 TAO:0001114 TGMA:0000002 The head is the anterior-most division of the body [GO]. UBERON:0000033 UMLS:C0018670 VHOG:0001644 Vertebrate evolution has been characterized by a fresh and vast array of cranial structures that collectively form the head.[well established][VHOG] WBbt:0005739 XAO:0003024 ZFA:0001114 adult head cephalic area galen:Head head (volume) uberon serous membrane A multi-tissue structure that is comprised of a secretory epithelial layer and a connective tissue layer.[TAO] FMA:9581 GAID:19 MESH:D012704 TAO:0005425 UBERON:0000042 UMLS:C0036760 ZFA:0005425 a smooth membrane consisting of a thin layer of cells which excrete serous fluid. Serous membranes line and enclose several body cavities, known as serous cavities, where they secrete a lubricating fluid which reduces friction from muscle movement. Serosa is not to be confused with adventitia, a connective tissue layer which binds together structures rather than reducing friction between them. Each serous membrane is composed of a secretory epithelial layer and a connective tissue layer underneath. The epithelial layer, known as mesothelium, consists of a single layer of avascular flat nucleated cells (cuboidal epithelium) which produce the lubricating serous fluid. This fluid has a consistency similar to thin mucus. These cells are bound tightly to the underlying connective tissue. The connective tissue layer provides the blood vessels and nerves for the overlying secretory cells, and also serves as the binding layer which allows the whole serous membrane to adhere to organs and other structures.[WP] in FMA, SM = mesothelium + connective tissue. It excludes the cavity. Serous sac = SM + cavity. Note that the SM is a subtype of wall in FMA. multi-tissue structure that is comprised of a secretory epithelial layer (mesothelium) and a connective tissue layer. serosa tunica serosa uberon wall of serous sac tendon AEO:0000091 BTO:0001356 CALOHA:TS-1021 Dense regular connective tissue that connects muscle to bone.[VSAO] Dense regular connective tissue that connects muscle to bone[VSAO]. EHDAA2:0003091 EMAPA:35854 EV:0100149 FMA:9721 GAID:276 MA:0000115 MESH:D013710 OpenCyc:Mx4rvVjefJwpEbGdrcN5Y29ycA Phylogenetically, tendinous tissue first appears in the invertebrate chordate Branchiostoma as myosepta. This two-dimensional array of collagen fibers is highly organized, with fibers running along two primary axes. In hagfish the first linear tendons appear and the myosepta have developed specialized regions with unidirectional fiber orientation - a linear tendon within the flat sheet of myoseptum.[well established][VHOG] UBERON:0000043 UMLS:C0039508 VHOG:0001286 VSAO:0000073 XAO:0000173 ZFA:0005647 galen:Tendon in FMA, tendon is an organ component that with parts dense-irregular-connective-tissue of tendon and dense-irregular-connective-tissue of tendon sheath; we follow VSAO in making it a subtype of the former. In VSAO tendons connect muscle to bone; in WP the def states integument (e.g. auricular muscles) - but JB confirms this is not actually tendon but aponeurosis sinew tendo uberon ganglion A biological tissue mass, most commonly a mass of nerve cell bodies. A ganglion is a cluster of neurons. It is part of a nervous system. It may include glial cells. The neurons are arranged in a specific constellation: neuronal somata are concentrated at the surface, thus forming a cell cortex, and neurites are concentrated in the centre of the ganglion to form the neuropil. A ganglion is a distinct unit but several ganglia may be anterio-posteriorly joined by connectives or transversally by commissures AAO:0010426 AEO:0000135 BAMS:G BTO:0000497 CALOHA:TS-0397 Cranial sensory placodes are focused areas of the head ectoderm of vertebrates that contribute to the development of the cranial sense organs and their associated ganglia. Placodes have long been considered a key character of vertebrates, and their evolution is proposed to have been essential for the evolution of an active predatory lifestyle by early vertebrates.[well established][VHOG] EFO:0000899 EHDAA2:0003135 EHDAA:2897 EHDAA:4662 EHDAA:5621 EHDAA:918 EMAPA:32846 EV:0100372 FBbt:00005137 FMA:5884 MA:0002406 MAT:0000207 MAT:0000343 MESH:D005724 MIAA:0000207 MIAA:0000343 Portion of tissue that contains cell bodies of neurons and is located outside the central nervous system.[AAO] Structures containing a collection of nerve cell bodies. (Source: BioGlossary, www.Biology-Text.com)[TAO] Subdivision of nervous system which primarily consists of cell bodies of neurons located outside the neuraxis (brain and spinal cord. Examples: spinal ganglion, trigeminal ganglion, superior cervical ganglion, celiac ganglion, inferior hypogastric (pelvic) ganglion (adapted from Foundational Model of Anatomy)[NIFSTD:nlx_anat_100302]. TAO:0000190 TGMA:0001016 TODO - check vert vs invert. Other species: Any of a number of aggregations of neurons, glial cells and their processes, surrounded by a glial cell and connective tissue sheath (plural: ganglia). // Subdivision of neural tree (organ) which primarily consists of cell bodies of neurons located outside the neuraxis (brain and spinal cord); together with a nucleus and its associated nerve, it constitutes a neural tree (organ). Examples: spinal ganglion, trigeminal ganglion, superior cervical ganglion, celiac ganglion, inferior hypogastric (pelvic) ganglion. // a cluster of nerve cells and associated glial cells (nuclear location) // Portion of tissue that contains cell bodies of neurons and is located outside the central nervous system. UBERON:0000045 UMLS:C0017067 VHOG:0000156 WBbt:0005189 XAO:0000209 ZFA:0000190 ganglia ganglionic neural ganglion uberon simple eye An eye with one concave chamber. Note that 'simple' does not imply a reduced level of complexity or acuity. TGMA:0000729 UBERON:0000047 uberon vessel A tubular structure that contains, conveys body fluid, such as blood or lymph. UBERON:0000055 uberon ureter AAO:0010254 Anatomical structure consisting of long narrow duct which carries urine from the kidney to the urinary bladder.[AAO] BTO:0001409 CALOHA:TS-1084 EFO:0000930 EHDAA2:0002139 EHDAA:9341 EMAPA:17950 EV:0100097 FMA:9704 GAID:438 MA:0000378 MAT:0000120 MESH:D014513 MIAA:0000120 Muscular duct that propels urine from the kidneys to the urinary bladder, or related organs. OpenCyc:Mx4rvhmm6JwpEbGdrcN5Y29ycA The duct of amniotes that carries urine from a metanephric kidney to the urinary bladder. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-29, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG] The first embryonic hint of a metanephros is the formation of the metanephric duct that appears as a ureteric diverticulum arising at the base of preexisting mesonephric duct. The ureteric diverticulum grows dorsally into the posterior region of the nephric ridge. Here it enlarges and stimulates the growth of metanephric tubules that come to make up the metanephric kidney. The metanephros becomes the adult kidney of amniotes, and the metanephric duct is usually called the ureter.[well established][VHOG] UBERON:0000056 UMLS:C0041951 VHOG:0000605 XAO:0000144 galen:Ureter in humans, consists of adventitial, muscular and mucoa layers metanephric duct uberon ureteral ureteric urethra BTO:0001426 CALOHA:TS-1132 EFO:0000931 EMAPA:30901 EV:0100099 FMA:19667 GAID:390 In human males, the urethra travels through the penis, and carries semen as well as urine. In females, the urethra is shorter and emerges above the vaginal opening. MA:0000379 MAT:0000121 MESH:D014521 MIAA:0000121 OpenCyc:Mx4rvVjkypwpEbGdrcN5Y29ycA UBERON:0000057 UMLS:C0041967 VHOG:0001264 XAO:0000153 galen:Urethra the fibromuscular tubular canal through which urine is discharged from the bladder to the exterior via the external urinary meatus; in males, the urethra is joined by the ejaculatory ducts and serves as a passageway for semen during ejaculation, as well as a canal for urine during voiding; in females, the urethra is shorter and emerges above the vaginal opening uberon urethral duct A tube shaped portion of tissue lined with epithelial cells that collects secretions and routes them to their destination[ZFA:0005171]. A tubular structure that transports secreted or excreted substances. AAO:0011123 FBbt:00100314 FMA:30320 Most ducts, but not all, are exocrine gland ducts. Some ontologies classify structures such as the oviduct here. TAO:0005171 UBERON:0000058 UMLS:C0687028 XAO:0004000 ZFA:0005171 anatomical duct ducts exocrine duct exocrine gland duct galen:Duct uberon large intestine A subdivision of the digestive tract that connects the small intestine to the cloaca or anus. Lacks or has few villi[Kardong]. AAO:0010396 BTO:0000706 CALOHA:TS-1306 EFO:0000840 EMAPA:19252 EV:0100077 FMA:7201 GAID:306 Intestinal surface area also is increased in amphibians and reptiles by internal folds and occasionally by a few villi. The intestine can be divided into a small intestine and a slightly wider large intestine.[well established][VHOG] MA:0000333 MESH:A03.492.411.495 MIAA:0000046 OpenCyc:Mx4rvVkF5pwpEbGdrcN5Y29ycA UBERON:0000059 UMLS:C0021851 VHOG:0000054 XAO:0000131 galen:LargeIntestine intestinum crassum uberon anatomical wall EMAPA:25036 FMA:82482 Organ component adjacent to an organ cavity and which consists of a maximal aggregate of organ component layers. UBERON:0000060 UBERON:0009915 galen:Wall in FMA, serosa is a wall organ wall uberon wall wall of organ anatomical structure AAO:0010825 AEO:0000003 BILA:0000003 CARO:0000003 EHDAA2:0003003 EMAPA:0 FBbt:00007001 FMA:67135 GAID:781 HAO:0000003 MA:0003000 MESH:D000825 Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome. TAO:0000037 TGMA:0001823 UBERON:0000061 VHOG:0001759 WBbt:0000100 XAO:0003000 ZFA:0000037 biological structure connected biological structure uberon organ Anatomical structure that performs a specific function or group of functions [WP]. CARO v1 does not include a generic 'organ' class, only simple and compound organ. CARO v2 may include organ, see https://github.com/obophenotype/caro/issues/4 CARO:0020004 EFO:0000634 EMAPA:35949 ENVO:01000162 FMA:67498 MA:0003001 OpenCyc:Mx4rv5XMb5wpEbGdrcN5Y29ycA OpenCyc:Mx4rwP3iWpwpEbGdrcN5Y29ycA Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions. UBERON:0000062 UMLS:C0178784 WBbt:0003760 anatomical unit body organ element uberon organ subunit A part of an organ that constitutes a distinct modular sub-unit. In some cases, the organ may also contain other sub-units of identical or similar types, in other cases this may be a distinct entity. FMA distinguishes segment from zone by whether the fiat boundaries are fixed/anchored (segments) or floating (zone). It's not completely clear how to apply this distinction FMA:86140 Organ region with one or more anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyeball. Organ region with one or more fixed or anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyebal. UBERON:0000063 organ region with fixed fiat boundary organ segment segment of organ uberon organ part A multicellular structure that is a part of an organ. AAO:0011124 EFO:0000635 FMA:82472 UBERON:0000064 cardinal organ part currently defined in a very broad sense, may be replaced by more specific classes in the future regional part of organ uberon respiratory tract Anatomical structure that is part of the respiratory system. In mammals consists of upper and lower tracts EHDAA2:0001606 EHDAA:1568 EHDAA:2219 EMAPA:16737 FMA:265130 OpenCyc:Mx4rvvM--pwpEbGdrcN5Y29ycA UBERON:0000065 VHOG:0000393 uberon fully formed stage BTO:0001043 BilaDO:0000004 EFO:0001272 FBdv:00005369 The stage of development at which the animal is fully formed, including immaturity and maturity. Includes both sexually immature stage, and adult stage. UBERON:0000066 WBls:0000041 XtroDO:0000084 adult stage fully formed animal stage juvenile-adult stage uberon embryo stage part A stage that is part of the embryo stage. UBERON:0000067 embryonic stage part uberon embryo stage A life cycle stage that starts with fertilization and ends with the fully formed embryo. BilaDO:0000002 EV:0300001 FBdv:00005289 FMA:72652 HsapDv:0000002 MmusDv:0000002 OGES:000000 OGES:000022 UBERON:0000068 WBls:0000003 WBls:0000092 WBls:0000102 XAO:1000012 embryogenesis embryonic stage uberon death stage End of the life of an organism. UBERON:0000071 XAO:0000437 XtroDO:0000085 death ncit:Death is an outcome uberon proximo-distal subdivision of respiratory tract An section of a respiratory tract. EMAPA:16737 FMA:45660 MA:0000434 MA:0000434 has subclasses upper and lower, so it corresponds to a segment of the tract, rather than the tract as a whole UBERON:0000072 respiratory tract subdivision of respiratory tract uberon regional part of nervous system 2009-06-18T09:00:04Z Any part or collection of parts of the central or peripheral nervous system. Parts may span both CNS and PNS. Melissa Haendel UBERON:0000073 UMLS:C1518256 part of nervous system uberon subdivision of skeletal system Anatomical cluster consisting of the skeletal elements and articular elements that are part of an individual subdivision of the organism. FMA:85544 UBERON:0000075 UBERON:0010322 UMLS:C1519343 galen:ComplexSkeletalStructure skeletal system part skeletal system subdivision uberon external ectoderm (or external ectoderm) forms the following structures: Skin Epithelium of the mouth and nasal cavity saliavary glands, and glands of mouth and nasal cavity Enamel - as a side note dentin and dental pulp are formed from ectomesenchyme which is derived from ectoderm Epithelium of pineal and pituitary glands Lens and cornea of the eye Apical ectodermal ridge inducing development of the limb buds of the embryo. Sensory receptors in epidermis EHDAA2:0001968 EHDAA:1494 EHDAA:350 EHDAA:4784 EHDAA:4790 EHDAA:4796 EHDAA:7860 EMAPA:16096 FMA:87656 The surface (external) layer of ectoderm which begins to proliferate shortly after separation from the neuroectoderm. UBERON:0000076 UMLS:C1515087 merge with non-neural. In vertebrates, the ectoderm has three parts: external ectoderm (also known as surface ectoderm), the neurectoderm (neural crest, and neural tube) surface (external) ectoderm surface ectoderm uberon mixed endoderm/mesoderm-derived structure An anatomical structure that develops from the endoderm and the mesoderm. Grouping term for query purposes. Notes that the developmental relationships are being refined such that most structures should develop in whole from at most one layer, but may have contributions from multiple UBERON:0000077 uberon male reproductive system BTO:0000082 By far, sexual reproduction is the more common pattern among living vertebrate forms and its widespread occurrence suggests that it is the plesiomorphic, or primitive, reproductive mode among the vertebrates.[well established][VHOG] CALOHA:TS-1310 EFO:0000970 EHDAA2:0001054 EHDAA:8136 EMAPA:17968 EV:0100101 FBbt:00004927 FMA:45664 GAID:386 HAO:0000505 MA:0000396 MESH:D005837 OpenCyc:Mx4rvViCepwpEbGdrcN5Y29ycA TGMA:0000634 The organs associated with producing offspring in the gender that produces spermatozoa. UBERON:0000079 UMLS:C0017422 UMLS:C1963704 VHOG:0000725 WBbt:0008423 XAO:0000155 genitalia of male organism male genital organ male genital system male genital tract male genitalia male genitals male organism genitalia male organism reproductive system male reproductive tract reproductive system of male organism systema genitale masculinum uberon mesonephros A kidney formed of nephric tubules arising in the middle region of the nephric ridge; a transient embryonic stage that replaces the pronephros, but is itself replaced by the adult metanephros [in mammals; in fishes and amphibians it is the adult kidney]. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Kardong_KV, Vertebrates:_Comparative_Anatomy, p.745][VHOG] AAO:0010384 As the pronephros regresses, the archinephric duct induces the sequential differentiation of tubules in the more caudal parts of the nephric ridge. (...) Tubules that differentiate in the middle part of the nephric ridge form a kidney called the mesonephros. This kidney functions in the embryos and larvae of all vertebrates. (...) In all vertebrate embryos, the kidney begins with the differentiation of a few renal tubules from the anterior end of the nephric ridge overlying the pericardial cavity. (...) This early-developing embryonic kidney is called the pronephros.[well established][VHOG] BTO:0001542 By contrast to the pronephros, the histological features of the mammalian mesonephros, with its primitive glomeruli, suggest that it probably functions as a primitive kidney, and is involved in the production of much of the amniotic fluid. Within the two mesonephroi, one located on either side of the dorsal mesentery of the hindgut, a substantial number (in the region of about 40 or more) of cranio-caudally segmented mesonephric tubules are formed. It has, however, been suggested that only the most rostrally located 4-6 pairs of mesonephric tubules drain into the mesonephric portion of the nephric duct. This is now seen to extend along the length of the mesonephroi, being located towards their lateral sides. The mesonephros is also retained over a considerably longer period than the pronephros, but gradually undergoes regression in a cranio-caudal direction. While the rostral part displays clear evidence of regression its more caudal part appears to display evidence of functional activity. Within the medial part of the mesonephros, vesicles are formed, although no glomeruli are formed there in this species. It is, however, difficult to believe that the relatively enormous mesonephroi do not have an excretory role in the mouse, only serving as a base for gonadal differentiation. In the human embryo, the medial part of the mesonephric tubules enlarges, become invaginated by capillaries, and form glomeruli. These then take on an excretory role. In the mouse, the mesonephric ducts appear to be patent throughout their length[GUDMAP, modified] CALOHA:TS-0624 EFO:0000928 EHDAA2:0001130 EHDAA:1581 EHDAA:5903 EMAPA:16744 EMAPA:27644 FMA:72171 GAID:1308 In mammals, the mesonephros is the second of the three embryonic kidneys to be established and exists only transiently. In fish and amphibians, the mesonephros will form the mature kidney MESH:D001755 Organ that is the definitive adult kidney. It replaces the earlier pronephros, which degenerates as the mesonephros becomes functional in feeding stage tadpoles.[AAO] TAO:0000529 The second stage of the kidney. It serves as the main excretory organ of aquatic vertebrates and as a temporary embryonic kidney in higher vertebrates. It is composed of the mesonephric duct (also called the Wolffian duct), mesonephric tubules, and associated capillary tufts. A single tubule and its associated capillary tuft is called a mesonephric excretory unit; these units are similar in structure and function to nephrons of the adult kidney. The mesonephros is derived from intermediate mesoderm in the vertebrate embryo. UBERON:0000080 UMLS:C0025492 VHOG:0000038 Wolffian body XAO:0000141 ZFA:0000529 amphibian adult kidney corpus Wolffi mesonephric mesonephric kidney mesonephroi middle kidney opisthonephros opisto nephros opistonephros uberon metanephros A kidney formed of nephric tubules arising in the posterior region of the nephric ridge and drained by a ureter; replaces the embryonic pronephros and mesonephros [in mammals]. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Kardong_KV, Vertebrates:_Comparative_Anatomy, p.745][VHOG] BTO:0001543 During the fifth week of gestation, the mesonephric duct develops an outpouching, the ureteric bud, near its attachment to the cloaca. This bud, also called the metanephrogenic diverticulum, grows posteriorly and towards the head of the embryo. The elongated stalk of the ureteric bud, the metanephric duct, later forms the ureter. As the cranial end of the bud extends into the intermediate mesoderm, it undergoes a series of branchings to form the collecting duct system of the kidney. It also forms the major and minor calyces and the renal pelvis EHDAA2:0001137 EHDAA:3089 EHDAA:5911 EMAPA:17207 EMAPA:17373 FMA:72172 In mammals, the metanephros is the excretory organ of the fetus, which develops into the mature kidney and is formed from the rear portion of the nephrogenic cord. The metanephros is an endocrine and metabolic organ that filters the blood and excretes the end products of body metabolism in the form of urine[GO] TODO check developmental relationships The ureteric diverticulum grows dorsally into the posterior region of the nephric ridge. Here it enlarges and stimulates the growth of metanephric tubules that come to make up the metanephric kidney. The metanephros becomes the adult kidney of amniotes.[well established][VHOG] UBERON:0000081 UMLS:C0231049 VHOG:0000039 definite kidney definitive kidney hind kidney metanephric metanephric kidney metanephron uberon mesonephric tubule A mesonephric tubule is an epithelial tube that is part of the mesonephros[GO]. Genital ridge that is next to the mesonephros[WP]. AAO:0010389 Any of the renal tubules composing the mesonephros. In mammals they function as excretory structures during the early embryonic development but are later incorporated into the reproductive system. [TFD][VHOG] As the pronephros regresses, the archinephric duct induces the sequential differentiation of tubules in the more caudal parts of the nephric ridge. (...) Tubules that differentiate in the middle part of the nephric ridge form a kidney called the mesonephros. This kidney functions in the embryos and larvae of all vertebrates.[well established][VHOG] EHDAA2:0001134 EMAPA:27588 EMAPA:27659 TODO check UBERON:0000083 VHOG:0000500 XAO:0000148 renal tubules tubuli mesonephrici uberon ureteric bud An epithelial swelling on the Wolffian duct that elongates to invade the adjacent metanephric mesenchyme[MP] BTO:0001646 EHDAA2:0002140 EHDAA:3091 EHDAA:5917 EMAPA:17209 EMAPA:17376 Outgrowth of the mesonephric duct that penetrates the metanephric mesoderm and forms the ureter, renal pelvis, major and minor calyces and collecting ducts. [Embryology, See_Dudek_RW_and_Fix_JD, Third_Edition_(2004)_Philadelphia:_Lippincott_William_and_Wilkins, p.137][VHOG] Outgrowth of the mesonephric duct that penetrates the metanephric mesoderm and forms the ureter, renal pelvis, major and minor calyces and collecting ducts[VHOG:0000541]. The first embryonic hint of a metanephros is the formation of the metanephric duct that appears as a ureteric diverticulum arising at the base of preexisting mesonephric duct. The ureteric diverticulum grows dorsally into the posterior region of the nephric ridge. Here it enlarges and stimulates the growth of metanephric tubules that come to make up the metanephric kidney. The metanephros becomes the adult kidney of amniotes, and the metanephric duct is usually called the ureter.[well established][VHOG] UBERON:0000084 UMLS:C1284058 VHOG:0000541 diverticulum diverticulum metanephricum gemma ureterica metanephric bud metanephric diverticulum uberon ureteric ampulla ureteric diverticulum post-embryonic stage BilaDO:0000003 In birds, the postnatal stage begins when the beak penetrates the shell (i.e., external pipping) (Brown et al. 1997) OGES:000010 OGES:000014 OGES:000024 UBERON:0000092 WBls:0000022 WBls:0000093 WBls:0000103 post-hatching stage postembryonic postembryonic stage stage succeeding embryo, including mature structure uberon membrane organ 2009-07-30T05:19:13Z FMA:7145 Nonparenchymatous organ that primarily consists of dense connective tissue organized into a sheet which interconnects two or more organs, separates two or more body spaces from one another, or surrounds an organ or body part. Examples: interosseous membrane of forearm, obturator membrane, tympanic membrane, fibrous pericardium, fascia lata, dura mater. [FMA] UBERON:0000094 cjm membrane membrane of organ uberon life cycle An entire span of an organism's life, commencing with the zygote stage and ending in the death of the organism. FBdv:00000000 HsapDv:0000001 MmusDv:0000001 OGES:000011 UBERON:0000104 entire life cycle entire lifespan life lifespan ncithesaurus:Life uberon life cycle stage A spatiotemporal region encompassing some part of the life cycle of an organism. BILS:0000105 EFO:0000399 FBdv:00007012 FMA:24120 HsapDv:0000000 MmusDv:0000000 OlatDv:0000010 PdumDv:0000090 UBERON:0000105 WBls:0000002 XAO:1000000 ZFS:0000000 ZFS:0100000 developmental stage ncithesaurus:Developmental_Stage stage the WBls class 'all stages' belongs here as it is the superclass of other WBls stages this class represents a proper part of the life cycle of an organism. The class 'life cycle' should not be placed here uberon we map the ZFS unknown stage here as it is logically equivalent to saying *some* life cycle stage zygote stage 1-cell stage A stage at which the organism is a single cell produced by means of sexual reproduction. As in all metazoans, eumetazoan development begins with a fertilized egg, or zygote.[well established][VHOG] BILS:0000106 BilaDO:0000005 EFO:0001322 EHDAA:27 EMAPA:16033 FBdv:00005288 PdumDv:0000100 UBERON:0000106 VHOG:0000745 XAO:1000001 ZFS:0000001 fertilized egg stage fertilized egg stage one cell stage one-cell stage uberon zygote zygotum cleavage stage BILS:0000107 BilaDO:0000006 EFO:0001290 FBdv:00000054 MESH:A16.254.270 MmusDv:0000004 OGES:000015 OGES:000020 PdumDv:0000200 The first few specialized divisions of an activated animal egg; Stage consisting of division of cells in the early embryo. The zygotes of many species undergo rapid cell cycles with no significant growth, producing a cluster of cells the same size as the original zygote. The different cells derived from cleavage are called blastomeres and form a compact mass called the morula. Cleavage ends with the formation of the blastula. UBERON:0000107 XAO:1000004 ZFS:0000046 uberon blastula stage An early stage of embryonic development in animals. It is produced by cleavage of a fertilized ovum and consists of a spherical layer of around 128 cells surrounding a central fluid-filled cavity called the blastocoel. The blastula follows the morula and precedes the gastrula in the developmental sequence. BILS:0000108 BilaDO:0000007 EFO:0001282 HsapDv:0000006 MmusDv:0000007 OGES:000003 OGES:000016 OGES:000021 OpenCyc:Mx4rEetFnKP2EdqAAAACs4vPlg UBERON:0000108 WBls:0000005 XAO:1000003 ZFS:0000045 consider adding a preceding stage 'morula stage' as part of cleavage uberon gastrula stage A stage defined by complex and coordinated series of cellular movements that occurs at the end of cleavage during embryonic development of most animals. The details of gastrulation vary from species to species, but usually result in the formation of the three primary germ layers, ectoderm, mesoderm and endoderm. BILS:0000109 BilaDO:0000008 EFO:0001296 FBdv:00005317 HsapDv:0000010 MmusDv:0000013 OGES:000004 OGES:000019 UBERON:0000109 WBls:0000010 XAO:1000005 ZFS:0000047 blastocystis trilaminaris stage trilaminar blastocyst stage trilaminar blastoderm stage trilaminar disk stage trilaminar germ stage trilaminar stage uberon neurula stage BILS:0000110 BilaDO:0000009 HsapDv:0000012 MmusDv:0000017 Staged defined by the formation of a tube from the flat layer of ectodermal cells known as the neural plate. This will give rise to the central nervous system. UBERON:0000110 XAO:1000006 uberon organogenesis stage A stage at which the ectoderm, endoderm, and mesoderm develop into the internal organs of the organism. BILS:0000111 BilaDO:0000010 HsapDv:0000015 MmusDv:0000018 OGES:000005 OGES:000032 UBERON:0000111 segmentation stage uberon respiratory tube A tube in the respiratory system. Examples: bronchus, bronchiole, trachea. FMA:12224 UBERON:0000117 in GO lung development is part of respiratory tube development. This can lead to inconsistencies with other ontologies, e.g. VT. The GO structure may be better represented by a tree of tubes (see the FMA class) respiratory conducting tube segment of tracheobronchial tree segment of tracheobronchial tree tracheobronchial tree segment uberon lung bud BTO:0001643 EHDAA2:0004089 Structure derived from foregut that becomes a lung[GO]. UBERON:0000118 UMLS:C1514420 UMLS:C1514897 clarify successors - include bronchi? gemma pulmonalis gemma respiratoria lung bud primary lung bud respiratory diverticulum uberon neuron projection bundle A fasciculated bundle of neuron projections (GO:0043005), largely or completely lacking synapses. CARO:0001001 FBbt:00005099 UBERON:0000122 UBERON:0005163 funiculus nerve fiber bundle neural fiber bundle uberon neural nucleus A spatially aggregated collection of nerve cell bodies in the CNS, consisting of one or more subpopulations that share cell type, chemical phenotype, and connections, and including nearby cells that share the same cell type, chemical phenotype, and connections. (CUMBO) AEO:0000136 Anatomical structure consisting of a discrete aggregate of neuronal soma[GO][GO_REF:0000021]. FMA:83686 Proposed CUMBO def from MM: A subcortical part of the nervous system consisting of a relatively compact group of cells that is distinguishable histologically that share a commonality of cytoarchitecture, chemoarchitecturel and connectivity. (comments: I put in 'subcortical' because I don't think we consider either the cerebellar cortex or cerebral cortex to be nuclei. Some people distinguish between a nucleus and a laminar structure (see Wikipedia definition). However, there are structures identified as nuclei that are laminar, e.g., lateral geniculate nucleus, although they are not laminated in all species. Also, I put in 'relatively compact' and 'distiguishable by histology' because we have groups of cells, e.g., cholinergic cell groups, doparminergic cell groups that are related on the 3 criteria but which we don't tend to consider nuclei because they don't occupy an easily defined territory. But all is open to debate. UBERON:0000125 nervous system nucleus neuraxis nucleus neuronal nucleus nucleus nucleus of CNS nucleus of neuraxis uberon cranial nerve nucleus FMA:54501 Nucleus that receives projections from or contains neurons that send projections through one of the cranial nerves UBERON:0000126 cranial neural nucleus nucleus nervi cranialis nucleus of cranial nerve uberon anterior region of body UBERON:0000153 uberon posterior region of body UBERON:0000154 uberon membranous layer A thin sheet or layer of pliable tissue, serving as a covering or envelope of a part, as the lining of a cavity, as a partition or septum, or to connect two structures. FMA:30322 FMA:82500 MESH:D008566 UBERON:0000158 membrane membranous organ component uberon intestine AAO:0000246 ANISEED:1235303 BSA:0000093 BTO:0000648 CALOHA:TS-0490 EFO:0000834 EMAPA:32874 EMAPA:35180 EV:0100071 FMA:7199 GAID:295 In zebrafish, No stomach, small intestine, or large intestine can be distinguished. However, differences can be found in the morphology of the mucosa columnar epithelial cells and the number of goblet cells, suggesting functional differentiation. The intestine has numerous folds that become progressively shorter in a rostral-to-caudal direction. Proportionally, these folds are significantly larger than the finger-like intestinal villi of mammals and other amniotes (Wallace et al. 2005). Columnar-shaped absorptive enterocytes are the most numerous in the zebrafish intestinal epithelium. Goblet cells are the second most populous epithelial cell type. MA:0000328 MA:0001524 MESH:A03.492.411 MIAA:0000043 Portion of the alimentary canal bounded anteriorly by the pyloric sphincter and posteriorly by the cloacal sphincter.[AAO] Segment of the alimentary canal extending from the stomach to the anus and, in humans and other mammals, consists of two segments, the small intestine and the large intestine. TAO:0001338 The tract of the alimentary canal. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] This class is probably too inclusive UBERON:0000160 UMLS:C0021853 VHOG:0000056 WBbt:0005772 XAO:0000129 ZFA:0001338 bowel galen:Intestine intestinal intestinal tract uberon orifice Anatomical conduit that connects two adjacent body spaces (or a body space with the space surrounding the organism)[FMA,modified]. FMA:3724 UBERON:0000161 anatomical orifice anatomical ostium hilum in FMA, this is an anatomical conduit *space*, rather than anatomical conduit ostium uberon cloaca A cloaca is apparently a primitive vertebrate feature because it occurs in most primitive gnathostomes and persists in the embryos of almost all vertebrates.[well established][VHOG] A common passage for fecal, urinary, and reproductive discharge in most lower vertebrates as well as the terminal end of the hindgut before division into rectum, bladder, and genital primordia in mammalian embryos. [TFD][VHOG] AAO:0000095 Anatomical structure which is the common receptacle for the alimentary canal, Wolffian ducts, oviducts, and the bladder.[AAO] Common chamber into which the intestines and excretory system opens. Arises during development in all vertebrates, but in many it becomes subdivided, lost or incorporated into other structures GAID:1206 Human beings only have an embryonic cloaca, which is split up into separate tracts during the development of the urinary and reproductive organs MESH:D002988 UBERON:0000162 UMLS:C0008987 VHOG:0001186 XAO:0000244 ZFA:0005781 adding df link to embryonic cloaca leads to a cycle in uberon-simple, as cloaca is a suberclass of embryonic cloaca cloacal cloacal chamber hindgut endoderm and proctodeal ectoderm. uberon vent embryonic cloaca EHDAA2:0000256 EHDAA:4895 EMAPA:27573 EMAPA:27638 UBERON:0000163 cloaca endoderm-lined chamber that develops as pouch-like dilation of the caudal end of the hindgut and receives the allantois ventrally and two mesonephric ducts laterally; caudally it ends blindly at the cloacal membrane formed by the union of proctodeal (anal pit) ectoderm and cloacal endoderm, with no intervening mesoderm[MP]. this class represents the embryonic form of the cloaca, as found in both mammals and non-mammals. uberon primitive urogenital sinus EHDAA2:0004060 EHDAA:5029 EHDAA:5919 EMAPA:17211 EMAPA:17379 In mammals the lowly monotremes still have a cloaca. Higher types have done away with this structure and have a separate anal outlet for the rectum. The monotreme cloaca shows the initiation of this subdivision. The cloaca has such includes only the distal part, roughly comparable to the proctodeum. The more proximal part is divided into (1) a large dorsal passage into which the intestine opens, the coprodeum, and (2) a ventral portion, the urodeum with which the bladder connects. (...) the development of the placental mammals recapitulates in many respects the phylogenetic story. In the sexually indifferent stage of placental mammal there is a cloaca. While the indifferent stage still persists, a septum develops, and extends out to the closing membrane. This divides the cloaca into two chambers: a coprodeum continuous with the gut above, and a urodeum or urogenital sinus below.[well established][VHOG] The ventral part of the cloaca after its separation from the rectum, giving rise to the lower part of the bladder in both sexes, to the prostatic portion of the male urethra, and to the urethra and vestibule in the female. [TFD][VHOG] UBERON:0000164 UGS UMLS:C0231057 VHOG:0000414 fetal UGS sinus urogenitalis the term 'urogenital sinus' may refer to the primitive urogenital sinus present as a transient developmental structure in most mammals or it may refer to a condition in which an unseptated cloaca persists in animals longer than normal the ventral part of the cloaca remaining after septation of the rectum, which further develops into part of the bladder, part of the prostatic part of the male urethra and the urethra and vestibule in females uberon urogenital sinus mouth AAO:0010355 BTO:0001090 BTO:0004698 CALOHA:TS-1315 Cavity in which food is initially ingested and generally contains teeth, tongue and glands.[AAO] EFO:0000825 EHDAA2:0001326 EHDAA:542 EMAPA:16262 FBbt:00003126 FMA:49184 GAID:75 MA:0000341 MA:0002474 MAT:0000038 MESH:D009055 MIAA:0000038 Molecular and developmental cell lineage data suggest that the acoel mouth opening is homologous to the mouth of protostomes and deuterostomes and that the last common ancestor of the Bilateria (the 'urbilaterian') had only this single digestive opening.[well established][VHOG] OpenCyc:Mx4rvVidh5wpEbGdrcN5Y29ycA TADS:0000040 TAO:0000547 TAO:0000590 TGMA:0000131 The proximal portion of the digestive tract, containing the oral cavity and bounded by the oral opening. In vertebrates, this extends to the pharynx and includes gums, lips, tongue and parts of the palate. Typically also includes the teeth, except where these occur elsewhere (e.g. pharyngeal jaws) or protrude from the mouth (tusks). UBERON:0000165 VHOG:0000280 VHOG:0000812 XAO:0003029 ZFA:0000547 ZFA:0000590 adult mouth cavital oralis cavitas oris cavum oris galen:Mouth in FMA, the tongue, palate etc are part of the mouth which is itself a subdivision of the face. ZFA includes a separate class 'oral region' which is part of the mouth, but excludes tongue and lips mouth cavity oral oral region oral vestibule regio oralis rima oris some AOs place this as developing from the stomodeum but we weaken this to developmental contribution, as the mouth includes non-ectodermal derivatives stoma stomatodaeum trophic apparatus uberon vestibule of mouth vestibulum oris oral opening (...) mouth development is very similar in protostomes and 'basal' deuterostomes, whereas the chordate mouth seems to develop at a new position. Recent data for echinoderms and hemichordates further suggest that this change in mouth position may result from change in the influence of a conserved ectodermal patterning system on mouth development. It has been suggested that the mouths of vertebrates and urochordates may constitute a 'new' mouth.[well established][VHOG] FMA:59806 The orifice that connects the mouth to the exterior of the body. UBERON:0000166 mouth oral fissure oral orifice oral part of face uberon proximal-distal subdivision of colon A section dividing a colon along a proximal-distal axis. FMA:222905 UBERON:0000168 segment of colon uberon pair of lungs 1 1 1 1 FMA:68877 OpenCyc:Mx4rvVjKy5wpEbGdrcN5Y29ycA The pair of anatomical structures comprised of a left lung and right lung. UBERON:0000170 lungs lungs pair pulmones set of lungs uberon respiration organ EMAPA:17607 Organ that functions in gaseous exchange between an organism and its environment. In plants, microorganisms, and many small animals, air or water makes direct contact with the organism's cells or tissue fluids, and the processes of diffusion supply the organism with dioxygen (O2) and remove carbon dioxide (CO2). In larger animals the efficiency of gaseous exchange is improved by specialized respiratory organs, such as lungs and gills, which are ventilated by breathing mechanisms. SPD:0000428 TGMA:0001247 UBERON:0000171 apparatus respiratorius organ breathing organ gas exchange organ organ of apparatus respiratorius organ of respiratory system respiratory organ respiratory system organ uberon excreta A portion of organism substance that is the product of an excretion process that will be eliminated from the body. An excretion process is elimination by an organism of the waste products that arise as a result of metabolic activity AEO:0000184 BTO:0000491 EHDAA2_RETIRED:0003184 ENVO:02000022 FMA:9674 UBERON:0000174 UBERON:0000324 UBERON:0007550 excreted substance excretion galen:Excretion portion of excreted substance uberon waste substance blood A complex mixture of cells suspended in a liquid matrix that delivers nutrients to cells and removes wastes. (Source: BioGlossary, www.Biology-Text.com)[TAO] A fluid that is composed of blood plasma and erythrocytes. AAO:0000046 BTO:0000089 CALOHA:TS-0079 EFO:0000296 EHDAA2:0000176 EHDAA:418 EMAPA:16332 ENVO:02000027 EV:0100047 FMA:9670 GAID:965 Highly specialized circulating tissue consisting of several types of cells suspended in a fluid medium known as plasma.[AAO] MA:0000059 MESH:D001769 MIAA:0000315 OpenCyc:Mx4rvVjI8JwpEbGdrcN5Y29ycA Recent findings strongly suggest that the molecular pathways involved in the development and function of blood cells are highly conserved among vertebrates and various invertebrates phyla. (...) There is now good reason to believe that, in vertebrates and invertebrates alike, blood cell lineages diverge from a common type of progenitor cell, the hemocytoblast.[well established][VHOG] TAO:0000007 This class excludes blood analogues, such as the insect analog of blood. See UBERON:0000179 haemolymphatic fluid. UBERON:0000178 UMLS:C0005767 VHOG:0000224 XAO:0000124 ZFA:0000007 galen:Blood portion of blood relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO] uberon vertebrate blood whole blood haemolymphatic fluid 2009-04-08T04:38:19Z CARO:0000081 Circulating fluid that is part of the hemolymphoid system. Blood, lymph, interstitial fluid or its analogs. UBERON:0000179 blood or blood analog circulating fluid cjm uberon blastula BILA:0000059 BTO:0000128 GAID:1294 MESH:A16.254.270.274 OGEM:000006 OpenCyc:Mx4rEetFnKP2EdqAAAACs4vPlg Organism at the blastula stage - an early stage of embryonic development in animals. It is produced by cleavage of a fertilized ovum and consists of a spherical layer of around 128 cells surrounding a central fluid-filled cavity called the blastocoel. The blastula follows the morula and precedes the gastrula in the developmental sequence. TODO - check relationship with epiblast. Note in FMA this is not a subclass of embryo, but in uberon embryo is the whole organism from zygote onwards and thus includes the blastula UBERON:0000307 UBERON:0007011 blastosphere blastula embryo uberon breast BTO:0000149 CALOHA:TS-2083 EV:0100124 FMA:9601 GAID:33 MESH:D001940 OpenCyc:Mx4rvVjV7ZwpEbGdrcN5Y29ycA The breasts of a female primate's body contain the mammary glands, which secrete milk used to feed infants. Both men and women develop breasts from the same embryological tissues. However, at puberty female sex hormones, mainly estrogens, promote breast development, which does not happen with men. As a result women's breasts become more prominent than men's. The upper ventral region of an animal's torso. UBERON:0000310 UMLS:C0006141 galen:Breast mamma mammary part of chest mammary region uberon duodenal mucosa A mucosa that is part of a duodenum [Automatically generated definition]. BTO:0000367 CALOHA:TS-0213 Doudenal mucosa Duodenal mucous membrane EMAPA:27235 FMA:14942 MA:0003207 UBERON:0000320 UBERON:0003348 duodenum mucosa mucosa of duodenum mucous membrane of duodenum uberon gastric gland BTO:0000503 EMAPA:27181 FMA:14919 The branched tubular glands found in the mucosa of the fundus and body of the stomach which contain parietal cells that secrete hydrochloric acid and zymogenic cells that produce pepsin. UBERON:0000325 uberon gut wall BTO:0000547 FMA:45653 The wall of the digestive tract. This encompasses all parts of the digestive tract with the exception of the lumen (cavity). UBERON:0000328 We model the digestive tract as consisting of two parts: the wall and the lumen. digestive tract wall uberon wall of alimentary tract wall of digestive tract wall of gut throat BTO:0000828 FMA:228738 In anatomy, the throat is the anterior part of the neck, in front of the vertebral column. It consists of the pharynx and larynx. An important feature of the throat is the epiglottis, a flap which separates the esophagus from the trachea and prevents inhalation of food or drink. The throat contains various blood vessels, various pharyngeal muscles, the trachea (windpipe) and the esophagus. The hyoid bone and the clavicle are the only bones located in the throat of mammals. It is sometimes considered a synonym for fauces. [WP,unvetted]. OpenCyc:Mx4rwQtO_JwpEbGdrcN5Y29ycA The hyoid bone and the clavicle are the only bones located in the throat of mammals. UBERON:0000341 UMLS:C0230069 gula gular uberon mucosa A lining of mostly endodermal origin, covered in epithelium, which is involved in absorption and secretion. They line various body cavities that are exposed to the external environment and internal organs. It is at several places continuous with skin: at the nostrils, the lips, the ears, the genital area, and the anus. The sticky, thick fluid secreted by the mucous membranes and gland is termed mucus. The term mucous membrane refers to where they are found in the body and not every mucous membrane secretes mucus[WP] AEO:0000199 BTO:0000886 CALOHA:TS-2031 EHDAA2_RETIRED:0003234 EV:0100382 FMA has mucosa vs region of mucosa; these are subtypes of Mucosa: Mucosa of gallbladder, tongue, .... The following are subtypes of Region of mucosa: Mucosa of zone of stomach, trachea, bronchus, dorsum of tongue.... Depends on whether the covered area is an organ or organ component. Uberon does not regard organ vs organ component as crucial distinction and thus collapses these into a single class deliberately FMA:85355 FMA:85358 GAID:297 MESH:D009092 OpenCyc:Mx4rvmKNOpwpEbGdrcN5Y29ycA UBERON:0000344 UMLS:C0026724 galen:Mucosa mucosa of organ mucosa of organ part mucosal mucosal region mucous membrane organ mucosa region of mucosa tunica mucosa uberon parenchyma EHDAA:3015 EHDAA:3905 EHDAA:3999 EHDAA:4005 EHDAA:6899 EHDAA:6903 EHDAA:6994 EHDAA:8086 EHDAA:9182 EHDAA:9190 EHDAA:9196 EHDAA:9202 Early in development the mammalian embryo has three distinct layers: ectoderm (external layer), endoderm (internal layer) and in between those two layers the middle layer or mesoderm. The parenchyma of most organs is of ectodermal (brain, skin) or endodermal origin (lungs, gastrointestinal tract, liver, pancreas). The parenchyma of a few organs (spleen, kidneys, heart) is of mesodermal origin. The stroma of all organs is of mesodermal origin FMA:45732 UBERON:0000353 UMLS:C0933845 functional part of an organ in the body. This is in contrast to the stroma, which refers to the structural tissue of organs, being exactly, connective tissues. parenchymal the FMA definition is more restrictive, and limits this to solid organs. This would seem to cause problems for the lung parenchyma, except FMA classifies Lung as solid rather than cavitated uberon musculature of body AAO:0000307 Anatomical system that consists of the muscles of the body.[VSAO] BILA:0000088 BTO:0001369 BTO:0001485 EFO:0000801 EMAPA:35578 FBbt:00005069 FMA:72954 MA:0002888 MAT:0000025 MIAA:0000025 The subdivision of the musculoskeletal system that consists of all the muscles of the body[VSAO, modified]. UBERON:0000383 VSAO:0000033 XAO:0004042 consider whether this should be restricted to skeletal musculature. See https://github.com/obophenotype/uberon/issues/77 muscle system muscle system of body muscular system musculature system muskelsystem set of all muscles set of muscles of body uberon vertebrate muscular system we place the MA term musculature here, rather than under uberon:musculature, as this seems more appropriate given the structure of MA serous gland A gland in which the principal secretory cells are serous secreting cells. BTO:0001837 FMA:62889 UBERON:0000409 glands that secrete watery albuminous material that often contains enzymes[MP:0008052]. uberon mucous gland A gland in which the principal secretory cells are mucus secreting cells. AAO:0010601 BTO:0001979 FMA:62888 In frogs and salamanders, this is the smaller of the two types of gland, the other being the granular (poison) gland. In these species the mucous gland is a cluster of cells that release secretion into a common duct[Kardong] UBERON:0000414 glandula mucosa muciparous gland mucous secreting gland mucus gland mucus-secreting gland uberon bodily secretion A portion of organism substance that is produced by exocrine glands. AEO:0001005 BTO has two distunct classes, with exocrine glandular secretion a subtype of secretion - however, all examples in BTO directly under secretion appear to be exocrine gland secretions BTO:0002977 BTO:0002979 EMAPA:36535 FMA:9675 MA:0002504 MESH:D012634 UBERON:0000456 UBERON:0006540 UMLS:C1516992 exocrine gland fluid exocrine gland fluid or secretion exocrine gland fluid/secretion exocrine gland secretion external secretion galen:Secretion secreted substance secretion uberon organism substance AAO:0010839 AEO:0000004 BILA:0000004 CALOHA:TS-2101 CARO:0000004 EHDAA2:0003004 EMAPA:35178 FBbt:00007019 FMA:9669 HAO:0000004 MA:0002450 Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body. SPD:0000008 TAO:0001487 TGMA:0001824 UBERON:0000463 VHOG:0001726 XAO:0004001 ZFA:0001487 body fluid or substance body substance galen:BodySubstance organism substance portion of body substance portion of organism substance uberon anatomical space AAO:0010110 AEO:0000005 BILA:0000005 CARO:0000005 EHDAA2:0003005 FBbt:00007017 FMA:5897 HAO:0000005 Non-material anatomical entity of three dimensions, that is generated by morphogenetic or other physiologic processes; is surrounded by one or more anatomical structures; contains one or more organism substances or anatomical structures. TAO:0001668 TGMA:0001825 UBERON:0000464 UMLS:C0524461 VHOG:0001728 XAO:0003190 ZFA:0001643 anatomical spaces lumen lumen space space uberon material anatomical entity AAO:0010264 AEO:0000006 Anatomical entity that has mass. BILA:0000006 CARO:0000006 EHDAA2:0003006 FBbt:00007016 FMA:67165 HAO:0000006 TAO:0001836 TGMA:0001826 UBERON:0000465 VHOG:0001721 uberon immaterial anatomical entity AAO:0010265 AEO:0000007 Anatomical entity that has no mass. BILA:0000007 CARO:0000007 EHDAA2:0003007 FBbt:00007015 FMA:67112 HAO:0000007 TAO:0001835 TGMA:0001827 UBERON:0000466 VHOG:0001727 immaterial physical anatomical entity uberon anatomical system AAO:0000007 AEO:0000011 BILA:0000011 BSA:0000049 CALOHA:TS-2088 CARO:0000011 EHDAA2:0003011 EHDAA:392 EMAPA:16103 EV:0100000 FBbt:00004856 FMA:7149 HAO:0000011 MA:0000003 Multicellular, connected anatomical structure that has multiple organs as parts and whose parts work together to achieve some shared function. OpenCyc:Mx4rCWM0QCtDEdyAAADggVbxzQ TAO:0001439 TGMA:0001831 UBERON:0000467 UMLS:C0460002 VHOG:0001725 WBbt:0005746 WBbt:0005763 XAO:0003002 ZFA:0001439 anatomical systems body system connected anatomical system galen:AnatomicalSystem organ system system uberon multicellular organism AAO:0010026 AEO:0000191 Anatomical structure that is an individual member of a species and consists of more than one cell. BILA:0000012 BSA:0000038 BTO:0000042 CARO:0000012 EFO:0002906 EHDAA2:0003103 EHDAA2:0003191 EHDAA:1 EHDAA:9178 EMAPA:25765 EV:0100016 FBbt:00000001 FMA:256135 HAO:0000012 Koerper TADS:0000001 TAO:0001094 TGMA:0001832 TODO - split body and mc organism? body continues after death stage UBERON:0000468 VHOG:0000671 WBbt:0007833 XAO:0003004 ZFA:0001094 animal body galen:Organism multi-cellular organism ncithesaurus:Whole_Organism organism organismal uberon whole body whole organism compound organ component AAO:0010017 AEO:0000019 BILA:0000019 CARO:0000019 EHDAA2:0003019 HAO:0000019 Multi-tissue structure that is part of a compound organ. TAO:0001489 TGMA:0001835 UBERON:0000471 XAO:0003039 ZFA:0001489 compound organ components this class was introduced for consistency with CARO, however, it has yet to be used in this or other ontologies. It may be retired in the future uberon female reproductive system BTO:0000083 By far, sexual reproduction is the more common pattern among living vertebrate forms and its widespread occurrence suggests that it is the plesiomorphic, or primitive, reproductive mode among the vertebrates.[well established][VHOG] CALOHA:TS-1303 EFO:0000969 EHDAA2:0000506 EHDAA:8116 EMAPA:17959 EV:0100110 FBbt:00004864 FMA:45663 GAID:364 HAO:0000324 MA:0000381 MESH:D005836 MIAA:0000028 OpenCyc:Mx4rvVipTZwpEbGdrcN5Y29ycA TGMA:0000635 The organs and associated structures associated with bearing offspring in a female animal. UBERON:0000474 UMLS:C0700038 VHOG:0000726 WBbt:0006748 WikipediaCategory:Female_reproductive_system XAO:0000156 female genital system female genital tract female genitalia female genitals female organism genitalia female organism reproductive system female reproductive tract genitalia of female organism gynaecological tissue reproductive system of female organism systema genitale femininum uberon organism subdivision AAO:0010053 AEO:0000032 Anatomical structure which is a subdivision of a whole organism, consisting of components of multiple anatomical systems, largely surrounded by a contiguous region of integument. BILA:0000032 CALOHA:TS-2084 CARO:0000032 EFO:0000808 EHDAA2:0003032 EMAPA:36031 FBbt:00007009 FMA:7153 HAO:0000032 MA:0002433 MAT:0000293 MESH:D001829 MIAA:0000293 OpenCyc:Mx4rvViAHJwpEbGdrcN5Y29ycA Reflects CARO2. todo - check the inclusion of FMA 'cardinal body part here', and check child terms for consistency TAO:0001308 TGMA:0001840 UBERON:0000475 UMLS:C0229962 VHOG:0001758 XAO:0003013 ZFA:0001308 anatomic region body part body region cardinal body part galen:BodyPart uberon acellular anatomical structure AAO:0010268 AEO:0000040 Anatomical structure that consists of cell parts and cell substances and together does not constitute a cell or a tissue. BILA:0000040 CARO:0000040 EHDAA2:0003040 FBbt:00007013 FMA:63863 HAO:0000040 TAO:0000382 TGMA:0001841 UBERON:0000476 XAO:0003162 ZFA:0000382 acellular anatomical structures uberon anatomical cluster AAO:0010009 AEO:0000041 Anatomical group that has its parts adjacent to one another. BILA:0000041 CARO:0000041 EHDAA2:0003041 FBbt:00007277 FMA:49443 HAO:0000041 TADS:0000605 TAO:0001478 TGMA:0001842 UBERON:0000477 VHOG:0001737 Will be obsoleted in CARO v2 [https://github.com/obophenotype/caro/issues/3] XAO:0003160 ZFA:0001478 uberon tissue AAO:0000607 AAO:0010054 AEO:0000043 BILA:0000043 CALOHA:TS-2090 CARO:0000043 EHDAA2:0003043 EMAPA:35868 FBbt:00007003 FMA:9637 HAO:0000043 MA:0003002 MESH:D014024 Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation. TAO:0001477 TGMA:0001844 UBERON:0000479 UMLS:C0040300 VHOG:0001757 WBbt:0005729 XAO:0003040 ZFA:0001477 changed label and definition to reflect CARO2 galen:Tissue portion of tissue simple tissue tissue portion uberon multi-tissue structure AAO:0010048 AEO:0000055 Anatomical structure that has as its parts two or more portions of tissue of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona-fide boundaries from other distinct structural units of different types. BILA:0000055 CARO:0000055 EHDAA2:0003055 FBbt:00007010 HAO:0000055 TAO:0001488 TGMA:0001847 UBERON:0000481 VHOG:0001762 XAO:0003037 ZFA:0001488 multi-tissue structures uberon epithelium AAO:0000144 AAO:0010055 AEO:0000066 BILA:0000066 BTO:0000416 CALOHA:TS-0288 CARO:0000066 EHDAA2:0003066 EMAPA:32738 FBbt:00007005 FMA:9639 GAID:402 HAO:0000066 MA:0003060 MESH:D004848 Portion of tissue, that consists of one or more layers of epithelial cells connected to each other by cell junctions and which is underlain by a basal lamina. Examples: simple squamous epithelium, glandular cuboidal epithelium, transitional epithelium, myoepithelium[CARO]. TAO:0001486 The two basic types of metazoan tissue are epithelial and connective. The simplest metazoans, and developmental stages of many primitive invertebrates, consist solely of these two layers. Thus, epithelial and connective tissues may be the primary (original) tissues of metazoans, and both are important in the functional organization of animals.[well established][VHOG] UBERON:0000483 UMLS:C0014609 VHOG:0000387 XAO:0003045 ZFA:0001486 epithelial epithelial tissue portion of epithelium uberon simple columnar epithelium AAO:0010063 AEO:0000068 BILA:0000068 CARO:0000068 EHDAA2_RETIRED:0003068 FBbt:00007027 FMA:45567 HAO:0000068 TAO:0001496 UBERON:0000485 UMLS:C0836135 Unilaminar epithelium, which consists of a single layer of columnar cells. Examples: ciliated columnar epithelium, gastric epithelium, microvillus columnar epithelium.[FMA] XAO:0004008 ZFA:0001496 columnar epithelium columnar epithlium epithelium simplex columnare simple columnar epithelia simple columnar epithelium uberon multilaminar epithelium AAO:0010059 AEO:0000069 BILA:0000069 BTO:0002074 CARO:0000069 EHDAA2:0003069 Epithelium that consists of more than one layer of epithelial cells.[CARO] Epithelium which consists of more than one layer of epithelial cells that may or may not be in contact with a basement membrane. Examples: keratinized stratified squamous epithelium, ciliated stratified columnar epithelium.[FMA] FMA:45562 HAO:0000069 TAO:0001494 UBERON:0000486 UMLS:C0682575 XAO:0004006 ZFA:0001494 laminated epithelium stratified epithelium uberon simple squamous epithelium AAO:0010066 AEO:0000070 BILA:0000070 BTO:0002073 CARO:0000070 EHDAA2:0003070 FMA:45565 HAO:0000070 TAO:0001498 UBERON:0000487 UMLS:C0836133 Unilaminar epithelium that consists of a single layer of squamous cells.[CARO] Unilaminar epithelium which consists of a single layer of squamous cells. Examples: pulmonary alveolar epithelium, endothelium.[FMA] XAO:0004010 ZFA:0001498 epithelium simplex squamosum simple squamous epithelia uberon cavitated compound organ AAO:0010016 AEO:0000072 BILA:0000072 CARO:0000072 Compound organ that contains one or more macroscopic anatomical spaces. EHDAA2:0003072 FMA:55671 HAO:0000072 TAO:0001490 TGMA:0001857 UBERON:0000489 VHOG:0001730 XAO:0003165 ZFA:0001490 cavitated compound organs cavitated organ this class was introduced for consistency with CARO, however, it has yet to be used in this or other ontologies. It may be retired in the future uberon unilaminar epithelium AAO:0010062 AEO:0000073 BILA:0000073 BTO:0002073 CARO:0000073 EHDAA2:0003073 Epithelium that consists of a single layer of epithelial cells.[CARO] Epithelium which consists of a single layer of epithelial cells. Examples: endothelium, mesothelium, glandular squamous epithelium.[FMA] FMA:45561 HAO:0000073 TAO:0001495 UBERON:0000490 UMLS:C0682574 XAO:0004007 ZFA:0001495 consider adding disjointness axiom between unilaminar and multilaminar - but note that this will render EHDAA2:0003244 (chorionic trophoblast) unsatisfiable simple epithelium uberon unilaminar epithelia mucus CALOHA:TS-2144 ENVO:02000040 FMA:66938 GAID:1164 MESH:D009093 Mucus is a bodily fluid consisting of a slippery secretion of the lining of the mucous membranes in the body. It is a viscous colloid containing antiseptic enzymes (such as lysozyme) and immunoglobulins. Mucus is produced by goblet cells in the mucous membranes that cover the surfaces of the membranes. It is made up of mucins and inorganic salts suspended in water. OpenCyc:Mx4rvVjHq5wpEbGdrcN5Y29ycA UBERON:0000912 UMLS:C0026727 galen:Mucus mucoid mucous uberon thoracic segment of trunk EMAPA:35862 FMA:259209 MA:0000022 Subdivision of trunk that lies between the head and the abdomen. UBERON:0000915 anterior subdivision of trunk note that we use the slightly verbose term 'thoracic segment of trunk' to avoid confusuon with insect thorax. todo - taxonomic constraints. Also, in FMA 'thorax' is a synonym for chest thorax uberon upper body upper trunk abdomen BTO:0000020 CALOHA:TS-0001 EFO:0000968 EMAPA:35102 EV:0100011 FMA:9577 GAID:16 MA:0000029 MAT:0000298 MESH:A01.047 MIAA:0000298 OpenCyc:Mx4rvVjgyZwpEbGdrcN5Y29ycA The subdivision of the vertebrate body between the thorax and pelvis. The ventral part of the abdomen contains the abdominal cavity and visceral organs. The dorsal part includes the abdominal section of the vertebral column. UBERON:0000916 Vertebrate specific. In arthropods 'abdomen' is the most distal section of the body which lies behind the thorax or cephalothorax. If need be we can introduce some grouping class abdominal abdominopelvic region abdominopelvis adult abdomen belly celiac celiac region galen:Abdomen uberon embryo AAO:0011035 AEO:0000169 Anatomical entity that comprises the organism in the early stages of growth and differentiation that are characterized by cleavage, the laying down of fundamental tissues, and the formation of primitive organs and organ systems. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant. BILA:0000056 BSA:0000039 BTO:0000379 CALOHA:TS-0229 EFO:0001367 EHDAA2:0000002 EHDAA2_RETIRED:0003236 EHDAA:38 EMAPA:16039 FBbt:00000052 FMA:69068 GAID:963 MAT:0000226 MESH:D004622 MIAA:0000019 OGEM:000001 Obsoleted in ZFA. Note that embryo is not classified as an embryonic structure - an embryonic structure is only the parts of an embryo OpenCyc:Mx4rwP1ceZwpEbGdrcN5Y29ycA UBERON:0000922 UMLS:C0013935 VHOG:0001766 XAO:0000113 ZFA:0000103 developing organism developmental tissue embryonic embryonic organism uberon germ layer A layer of cells produced during the process of gastrulation during the early development of the animal embryo, which is distinct from other such layers of cells, as an early step of cell differentiation. The three types of germ layers are the endoderm, ectoderm, and mesoderm. AAO:0000480 BILA:0000035 BTO:0000556 Classically the germ layers are ectoderm, mesoderm and endoderm. Alternatively: primary = ectoderm, endoderm; secondary=mesoderm; tertiary=dorsal mesoderm, NC[https://github.com/obophenotype/uberon/wiki/The-neural-crest] EMAPA:36033 FBbt:00000110 FMA:69069 GAID:1303 MESH:A16.254.425 TAO:0001122 The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] UBERON:0000923 UMLS:C0920502 UMLS:C1708239 VHOG:0001223 XAO:0003011 ZFA:0001122 embryonic germ layer embryonic germ layers embryonic tissue germinal layer primary germ layer uberon ectoderm AAO:0000137 BILA:0000036 BTO:0000315 CALOHA:TS-0216 EFO:0000414 EHDAA2:0000428 EMAPA:16069 EV:0100003 FBbt:00000111 FMA:69070 GAID:1304 MAT:0000155 MAT:0000173 MESH:A16.254.425.273 MIAA:0000173 Primary germ layer that is the outer of the embryo's three germ layers and gives rise to epidermis and neural tissue. Primary germ layer that is the outer of the embryonic germ layers and gives rise to epidermis and neural tissue.[AAO] TAO:0000016 The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] UBERON:0000924 UMLS:C0013574 VHOG:0000153 XAO:0000001 ZFA:0000016 ectodermal embryonic ectoderm uberon endoderm AAO:0000139 BILA:0000038 BTO:0000800 CALOHA:TS-0273 EFO:0002545 EHDAA2:0000436 EMAPA:16062 EV:0100005 FBbt:00000125 FMA:69071 GAID:1305 MAT:0000175 MESH:A16.254.425.407 MIAA:0000175 Primary germ layer that lies remote from the surface of the embryo and gives rise to internal tissues such as gut. TAO:0000017 The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] UBERON:0000925 UMLS:C0014144 VHOG:0000154 XAO:0000090 ZFA:0000017 endodermal entoderm uberon mesoderm AAO:0000304 BILA:0000037 BTO:0000839 CALOHA:TS-0623 EFO:0001981 EHDAA2:0001128 EHDAA:124 EHDAA:160 EHDAA:168 EHDAA:183 EMAPA:16083 EV:0100006 FBbt:00000126 FMA:69072 GAID:522 MAT:0000174 MESH:A16.254.425.660 MIAA:0000174 Primary germ layer that is the middle of the embryonic germ layers.[AAO] TAO:0000041 The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] The middle germ layer of the embryo, between the endoderm and ectoderm. UBERON:0000926 UBERON:0003263 UMLS:C0025485 VHOG:0000152 XAO:0000050 ZFA:0000041 embryonic mesoderm entire mesoderm mesodermal mesodermal mantle sponges do not seem to have a mesoderm and accordingly Amphimedon lacks transcription factors involved in mesoderm development (Fkh, Gsc, Twist, Snail)[http://www.nature.com/nature/journal/v466/n7307/full/nature09201.html]. Mesoderm may not be homologous across verteberates uberon stomodeum Anterior part of the embryonic alimentary canal formed as an invagination of the ectoderm; the future mouth.[TAO] Anterior part of the embryonic digestive tract that develops into a mouth. The stomodeum includes as parts an invagination of the ectoderm and the stomodeal cavity. BTO:0004224 EHDAA2:0001929 EMAPA:16263 FBbt:00000439 FMA:295846 TAO:0001290 TGMA:0000135 This class groups together disparate structures as all being the anterior part of the early metazoan digestive tract and precursor of the mouth. However, the developmental processes vary, so this class may be split in future. E.g. in mammals it is a rostral depression surrounded by prominences. Outgrowth of the prominences produces a stomodeal cavity. UBERON:0000930 UMLS:C1514977 XAO:0000269 ZFA:0001290 consider indicating location. e.g. anterior. Note some AOs place this as part of oral opening, but it's not clear when this structure comes into existence mouth pit mouth primordium oral ectoderm oral pit primitive oral cavity stomatodeum stomodaeum stomodeal stomodeal-hypophyseal primordium the primordial mouth region of the developing head, initially a midline ectodermal depression between the forebrain bulge (cranially) and the heart bulge (caudally) and between the maxillary and mandibular components of the first pharyngeal arch; the stomodeum is separated from the anterior end of the foregut by the buccopharyngeal membrane; the mouth is developed partly from the stomodeum, and partly from the floor of the anterior portion of the foregut; the lips, teeth, and gums are formed from the walls of the stomodeum, but the tongue is developed in the floor of the pharynx uberon proctodeum AAO:0011087 An inward fold on the surface of the embryonic ectoderm that develops into part of the anal passage.[TAO] EHDAA2:0000121 EMAPA:25038 FBbt:00000123 Inward fold on the surface of the embryonic ectoderm that develops into an ectodermal terminal part of the digestive tract. Inward fold on the surface of the embryonic ectoderm that develops into part of the anal passage.[AAO] TAO:0000066 UBERON:0000931 UMLS:C0231054 VHOG:0000139 XAO:0001019 ZFA:0000066 amnioproctodeal invagination anal pit anus porus embryonic proctodaeum proctodaeum proctodeal removed WBbt:0006795 'proctodeum' - junction between the alimentary and genital tracts in the male. uberon stomach AAO:0000579 ANISEED:1235297 An expanded region of the vertebrate alimentary tract that serves as a food storage compartment and digestive organ. A stomach is lined, in whole or in part by a glandular epithelium. BTO:0001307 CALOHA:TS-0980 EFO:0000837 EHDAA2:0001915 EHDAA:2993 EMAPA:17021 EV:0100070 FMA:7148 GAID:293 It appears that the stomach has an ancient origin. The stomach first appears in the fish lineage. The prevertebrate chordates do not have a true stomach, whereas the cartilaginous and bony fish do. Although most fish do have a true stomach, some fish species appear to have lost the stomach secondarily. The remaining vertebrate lineages do have a true stomach (at least in the adult animal), although there is great variation in the size and shape of the stomach.[well established][VHOG] MA:0000353 MAT:0000051 MESH:A03.492.766 MIAA:0000051 OpenCyc:Mx4rvVjlqpwpEbGdrcN5Y29ycA Portion of alimentary canal with increased circular and longitudinal smooth muscle. Bounded posteriorly by the pyloric sphincter. Mucosal lining has increased folding.[AAO] TAO:0002121 UBERON:0000945 UMLS:C0038351 VHOG:0000408 Ventricular We restrict this to the vertebrate specific structure - see the grouping class 'food storage organ' for analogous structures in other species. Teleosts: Zebrafish is functionally stomach-less, but may retain ontogenic footprint. Although the precise shape and size of the stomach varies widely among different vertebrates, the relative positions of the oesophageal and duodenal openings remain relatively constant. As a result, the organ always curves somewhat to the left before curving back to meet the pyloric sphincter. However, lampreys, hagfishes, chimaeras, lungfishes, and some teleost fish have no stomach at all, with the oesophagus opening directly into the intestine. The gastric lining is usually divided into two regions, an anterior portion lined by fundic glands, and a posterior with pyloric glands. Cardiac glands are unique to mammals, and even then are absent in a number of species. The distributions of these glands vary between species, and do not always correspond with the same regions as in man. Furthermore, in many non-human mammals, a portion of the stomach anterior to the cardiac glands is lined with epithelium essentially identical to that of the oesophagus. Ruminants, in particular, have a complex stomach, the first three chambers of which are all lined with oesophageal mucosa XAO:0000128 anterior intestine galen:Stomach gaster mesenteron stomach chamber uberon ventriculus aorta AAO:0010213 All amniotes have a broadly similar arrangement to that of humans, albeit with a number of individual variations. In fish, however, there are two separate vessels referred to as aortas. The ventral aorta carries de-oxygenated blood from the heart to the gills; part of this vessel forms the ascending aorta in tetrapods (the remainder forms the pulmonary artery). A second, dorsal aorta carries oxygenated blood from the gills to the rest of the body, and is homologous with the descending aorta of tetrapods. The two aortas are connected by a number of vessels, one passing through each of the gills. Amphibians also retain the fifth connecting vessel, so that the aorta has two parallel arches BTO:0000135 CALOHA:TS-0046 EFO:0000265 EMAPA:18601 EV:0100027 FMA:3734 GAID:469 MA:0000062 MAT:0000035 MESH:D001011 MIAA:0000035 OpenCyc:Mx4rvVjvTpwpEbGdrcN5Y29ycA The main artery of the circulatory system which carries oxygenated blood from the heart to all the arteries of the body except those of the lungs.[AAO] The main trunk of the systemic arterial system that carries blood from the heart to all the organs and other structures of the body, bringing oxygenated blood to all parts of the body in the systemic circulation This class is currently a mixed bag, encompassing (1) the entirety of the mammalian aorta together with (2) the developmental and phylogenetic homologs of its segments: the ventral aorta and dorsal aortae. UBERON:0000947 UMLS:C0003483 VHOG:0001523 When vertebrates first appeared, they must have possessed a ventral and dorsal aorta with aortic arches between them.[well established][VHOG] XAO:0003010 aortic arteria maxima dorsal aorta galen:Aorta trunk of aortic tree trunk of systemic arterial tree uberon heart A myogenic muscular circulatory organ found in the vertebrate cardiovascular system composed of chambers of cardiac muscle. It is the primary circulatory organ. AAO:0010210 As noted, the hearts of birds and mammals have four chambers that arises from the two chambers (atrium and ventricle) of the fish heart.[well established][VHOG] BILA:0000020 BTO:0000562 Blood pumping organ composed of four chambers: sinus venosus, atrium, cardiac ventricle and bulbus arteriosus.[TAO] CALOHA:TS-0445 EFO:0000815 EHDAA2:0000738 EHDAA:420 EMAPA:16105 EV:0100018 FMA:7088 GAID:174 Herz@de MA:0000072 MAT:0000036 MESH:D006321 MIAA:0000036 OpenCyc:Mx4rvVjvDpwpEbGdrcN5Y29ycA Part of the circulatory system responsible for pumping blood; composed of three chambers--two atria and one ventricle.[AAO] TAO:0000114 Taxon notes:" the ascidian tube-like heart lacks chambers....The ascidian heart is formed after metamorphosis as a simple tube-like structure with a single-layered myoepithelium that is continuous with a single-layered pericar- dial wall. It lacks chambers and endocardium.... The innovation of the chambered heart was a key event in vertebrate evolution, because the chambered heart generates one-way blood flow with high pressure, a critical requirement for the efficient blood supply of large-body vertebrates... all extant vertebrates have hearts with two or more chambers (Moorman and Christoffels 2003)" http://dx.doi.org/10.1101/gad.1485706 UBERON:0000948 UMLS:C0018787 VHOG:0000276 XAO:0000064 ZFA:0000114 branchial heart cardiac cardium chambered heart galen:Heart relationship type change: differentiates_from lateral plate mesoderm (AAO:0010574) CHANGED TO: develops_from lateral plate mesoderm (UBERON:0003081)[AAO] uberon vertebrate heart endocrine system AAO:0010279 Anatomical system containing glands which regulates bodily functions though the secretion of hormones.[AAO] Anatomical system that consists of the glands and parts of glands that produce endocrine secretions and help to integrate and control bodily metabolic activity. CALOHA:TS-1301 EFO:0002969 EHDAA2:0002224 EMAPA:35306 EV:0100128 FBbt:00005068 FMA:9668 GAID:439 MA:0000012 MESH:D004703 Multicellular organisms have complex endocrine systems, allowing responses to environmental stimuli, regulation of development, reproduction, and homeostasis. Nuclear receptors (NRs), a metazoan-specific family of ligand-activated transcription factors, play central roles in endocrine responses, as intermediates between signaling molecules and target genes. The NR family includes ligand-bound and orphan receptors, that is, receptors with no known ligand or for which there is no ligand Pocket. Understanding NR evolution has been further improved by comparison of several completed genomes, particularly those of deuterostomes and ecdysozoans. In contrast, evolution of NR ligands is still much debated. One hypothesis proposes that several independent gains and losses of ligand-binding ability in NRs occurred in protostomes and deuterostomes. A second hypothesis, pertaining to the NR3 subfamily (vertebrate steroid hormone receptors and estrogen related receptor), proposes that before the divergence of protostomes and deuterostomes, there was an ancestral steroid receptor (AncSR) that was ligand-activated and that orphan receptors secondarily lost the ability to bind a ligand. (...) Our analysis reveals that steroidogenesis has been independently elaborated in the 3 main bilaterian lineages (...).[well established][VHOG] TAO:0001158 UBERON:0000949 UMLS:C0014136 VHOG:0000098 XAO:0000158 ZFA:0001158 endocrine endocrine glandular system endocrine system systema endocrinum uberon brain (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2).[well established][VHOG] AAO:0010478 ABA:Brain BAMS:Br BAMS:Brain BILA:0000135 BTO:0000142 CALOHA:TS-0095 Cavitated compound organ which is comprised of gray and white matter and surrounds the cerebral ventricular system.[TAO] DHBA:10155 EFO:0000302 EHDAA2:0000183 EHDAA:2641 EHDAA:6485 EMAPA:16894 EV:0100164 FBbt:00005095 FMA:50801 GAID:571 HBA:4005 MA:0000168 MAT:0000098 MESH:D001921 MIAA:0000098 OpenCyc:Mx4rvVjT65wpEbGdrcN5Y29ycA PBA:3999 Part of the central nervous system situated within the cranium and composed of both nerve cell bodies and nerve fibers.[AAO] TAO:0000008 The brain is the center of the nervous system in all vertebrate, and most invertebrate, animals. Some primitive animals such as jellyfish and starfish have a decentralized nervous system without a brain, while sponges lack any nervous system at all. In vertebrates, the brain is located in the head, protected by the skull and close to the primary sensory apparatus of vision, hearing, balance, taste, and smell[WP]. The part of the central nervous system contained within the cranium, comprising the forebrain, midbrain, hindbrain, and metencephalon. It is derived from the anterior part of the embryonic neural tube (or the encephalon). Does not include retina. (CUMBO) UBERON:0000955 UMLS:C0006104 UMLS:C1269537 VHOG:0000157 XAO:0000010 ZFA:0000008 encephalon galen:Brain http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=21 requires review for applicability to invertebrate structures, e.g. synganglion suprasegmental levels of nervous system suprasegmental structures synganglion the brain uberon cornea AAO:0010344 BTO:0000286 CALOHA:TS-0171 Compared to terrestial animals, the cornea of zebrafish is relatively flat. It consists of nonpigmented, stratified squamous nonkeratinizing epithelial cells, attached to a thick basement membrane that is considered to be analogous to the Bowman's membrane in mammals. In fish, and aquatic vertebrates in general, the cornea plays no role in focusing light, since it has virtually the same refractive index as water EFO:0000377 EHDAA2:0000316 EHDAA:10199 EMAPA:17161 EV:0100341 FMA:58238 GAID:892 MA:0000266 MESH:D003315 OpenCyc:Mx4rvViBa5wpEbGdrcN5Y29ycA TAO:0000640 UBERON:0000964 UMLS:C0010031 VHOG:0000164 XAO:0000180 ZFA:0000640 cornea of camera-type eye corneal corneas the transparent anterior portion of the fibrous coat of the eye that serves as the chief refractory structure tunica cornea uberon lens of camera-type eye AAO:0010348 BTO:0000723 CALOHA:TS-0545 EHDAA:9057 EMAPA:17838 EV:0100343 FMA:58241 MA:0000275 MAT:0000141 MESH:A09.371.509 MIAA:0000141 OpenCyc:Mx4rvVj0fZwpEbGdrcN5Y29ycA RETIRED_EHDAA2:0000975 TAO:0000035 The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG] The lens is avascular and nourished by diffusion from the aqueous and vitreous This class excludes compound eye corneal lenses. Transparent part of camera-type eye that helps to refract light to be focused on the retina. UBERON:0000965 UMLS:C0023317 VHOG:0000169 XAO:0000008 ZFA:0000035 camera-type eye lens crystalline lens eye lens lens lens crystallina lenses ocular lens uberon retina AAO:0010352 BAMS:R BTO:0001175 CALOHA:TS-0865 Currently this class encompasses only verteberate AOs but could in theory also include cephalopod - we may want to make a more specific class for vertebrate retina. note that this class excludes ommatidial retinas, as the retina must be part of an eyeball. Use the parent class photoreceptor array / light-sensitive tissue for arthropods EFO:0000832 EHDAA2:0001627 EHDAA:4757 EMAPA:17168 EV:0100348 FMA:58301 GAID:755 MA:0000276 MAT:0000142 MBA:304325711 MESH:D012160 MIAA:0000142 NIFSTD_RETIRED:birnlex_1156 Netzhaut OpenCyc:Mx4rvViTfpwpEbGdrcN5Y29ycA TAO:0000152 The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG] The portion of the eye developing from the optic primordium and including the neural retina and the retinal pigment layer. Kimmel et al, 1995.[TAO] The retina is the innermost layer or coating at the back of the eyeball, which is sensitive to light and in which the optic nerve terminates. UBERON:0000966 UMLS:C0035298 UMLS:C1278894 VHOG:0000229 XAO:0000009 ZFA:0000152 inner layer of eyeball retina of camera-type eye retinal retinas tunica interna of eyeball uberon eye An organ that detects light. BILA:0000017 BTO:0000439 CALOHA:TS-0309 EFO:0000827 EV:0100336 FBbt:00005162 GAID:69 MAT:0000140 MESH:D005123 MIAA:0000140 Note that whilst this is classified as an organ, it is in fact more of a unit composed of different structures: in Drosophila, it includes the interommatidial bristle as a part; we consider here the vertebrate eye to include the eyeball/eye proper as a part, with the eye having as parts (when present): eyelids, conjuctiva, OpenCyc:Mx4rvViTvpwpEbGdrcN5Y29ycA This class encompasses a variety of light-detecting structures from different phyla with no implication of homology, from the compound insect eye to the vertebrate camera-type eye (distinct classes are provided for each) UBERON:0000970 light-detecting organ ocular optic uberon visual apparatus neck AEO:0000108 An organism subdivision that extends from the head to the pectoral girdle, encompassing the cervical vertebral column. BTO:0000420 CALOHA:TS-2045 EFO:0000967 EHDAA2:0003108 EMAPA:35587 FMA:7155 GAID:86 MA:0000024 MAT:0000297 MESH:D009333 MIAA:0000297 OpenCyc:Mx4rvVjLF5wpEbGdrcN5Y29ycA UBERON:0000974 UMLS:C0027530 cervical collum galen:Neck neck (volume) true necks are considered to be present when the pectoral girdle is separate from the skull - Tiktaalik is the earliest known fish to have a true neck. uberon leg BTO:0000721 CALOHA:TS-2206 EFO:0001411 EHDAA2:0000972 EHDAA:5151 EHDAA:6176 EHDAA:8289 EMAPA:17489 GAID:49 MA:0000047 MESH:D035002 Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG] OpenCyc:Mx4rvViYzZwpEbGdrcN5Y29ycA The portion of the hindlimb that contains both the stylopod and zeugopod. The term leg can mean: [1] an appendage on which an animal walks [2] the entire hindlimb of a tetrapod [3] the segment of a human leg between knee and ankle (cf FMA) [4] the region of a hindlimb include the stylopod and zeugopod, but excluding the autopod. We define this class as [4], and thus 'leg' is compltely analagous to 'arm'. For [1], see the class 'locomotive weight-bearing appendage'. For [2] we use 'hindlimb'. For UBERON:0000978 VHOG:0000345 lower extremity tetrapod leg uberon we use the less open to misinterpretation 'hindlimb zeugopod'. Editor note: currently declared as overlapping foot, as AOs disagree over whether some ankle parts are in the leg or foot skeletal joint AEO:0000182 Anatomical cluster that consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[VSAO] Anatomical cluster that consists of two or more adjacent skeletal structures, which may be interconnected by various types of tissue[VSAO]. Anatomical cluster which consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[TAO] BTO:0001686 CALOHA:TS-2023 EFO:0000948 EMAPA:35456 FMA:7490 GAID:102 MA:0000319 MAT:0000188 MESH:D007596 MIAA:0000188 OpenCyc:Mx4rvVjjdpwpEbGdrcN5Y29ycA RETIRED_EHDAA2:0003182 TAO:0000367 UBERON:0000982 UMLS:C0022417 VHOG:0001276 VSAO:0000101 XAO:0000171 ZFA:0001596 articular joint articulation galen:Joint joint joints uberon reproductive system AAO:0010258 Anatomical system that has as its parts the organs concerned with reproduction. Anatomical system which consists of organs and tissues associated with sexual reproduction of the organism.[AAO] Arguably, one of the most important aspects of urbilaterian organogenesis would have been gonadogenesis, since Urbilateria must have successfully generated gametes and developed a strategy for extrusion and fertilization, in order to be the ancestor of all living Bilateria.[well established][VHOG] BILA:0000103 BTO:0000081 CALOHA:TS-1318 EFO:0000809 EHDAA2:0001603 EHDAA:5923 EMAPA:17381 EV:0100100 FBbt:00004857 FMA:7160 GAID:363 Geschlechtsorgan HAO:0000374 HAO:0000895 MA:0000326 MIAA:0000305 OpenCyc:Mx4rvVja4ZwpEbGdrcN5Y29ycA TAO:0000632 UBERON:0000990 UMLS:C1261210 VHOG:0000182 WBbt:0005747 XAO:0000142 ZFA:0000632 animal reproductive system consider splitting genitalia from reproductive system genital system genital tract genitalia organa genitalia reproductive tissue reproductive tract systemata genitalia uberon gonad AAO:0000213 Anatomical structure which produces gametes as well as certain sex hormones controlled by the pituitary gonadotropins.[AAO] BILA:0000123 BSA:0000079 BTO:0000534 EMAPA:16857 EMAPA:17383 Examination of different vertebrate species shows that the adult gonad is remarkably similar in its morphology across different phylogenetic classes. Surprisingly, however, the cellular and molecular programs employed to create similar organs are not evolutionarily conserved.[uncertain][VHOG] FBbt:00004858 FMA xref is a 'general anatomical term' FMA:18250 GAID:368 HAO:0000379 MA:0002420 MESH:D006066 OpenCyc:Mx4rwQvdiZwpEbGdrcN5Y29ycA Reproductive organ that produces and releases eggs (ovary) or sperm (testis). TAO:0000413 The part of the reproductive system that produces and releases eggs (ovary) or sperm (testis).[TAO] UBERON:0000991 UMLS:C0018067 VHOG:0000397 WBbt:0005175 XAO:0003146 ZFA:0000413 gonada gonadal gonads uberon female gonad (...) while it is likely that Urbilateria lacked a complex somatic reproductive system, it is at present impossible to speculate on whether or not it possessed a true gonad, let alone any other somatic adaptations for reproduction (reference 1); Examination of different vertebrate species shows that the adult gonad is remarkably similar in its morphology across different phylogenetic classes. Surprisingly, however, the cellular and molecular programs employed to create similar organs are not evolutionarily conserved (reference 2).[uncertain][VHOG] AAO:0000371 BILA:0000125 BSA:0000080 BTO:0000975 CALOHA:TS-0730 EFO:0000973 EHDAA2:0001360 EHDAA:8124 EMAPA:17962 EV:0100111 Either of paired female reproductive organs involved in production of ova and female sex hormones.[AAO] FBbt:00004865 FMA:7209 Female reproductive organ.[TAO] GAID:367 MA:0000384 MESH:D010053 MIAA:0000125 OpenCyc:Mx4rvVi9QJwpEbGdrcN5Y29ycA Ovaries of some kind are found in the female reproductive system of many animals that employ sexual reproduction, including invertebrates. However, they develop in a very different way in most invertebrates than they do in vertebrates, and are not truly homologous. Many of the features found in human ovaries are common to all vertebrates, including the presence of follicular cells, tunica albuginea, and so on. However, many species produce a far greater number of eggs during their lifetime than do humans, so that, in fish and amphibians, there may be hundreds, or even millions of fertile eggs present in the ovary at any given time. In these species, fresh eggs may be developing from the germinal epithelium throughout life. Corpora lutea are found only in mammals, and in some elasmobranch fish; in other species, the remnants of the follicle are quickly resorbed by the ovary. In birds, reptiles, and monotremes, the egg is relatively large, filling the follicle, and distorting the shape of the ovary at maturity. Amphibians and reptiles have no ovarian medulla; the central part of the ovary is a hollow, lymph-filled space. The ovary of teleosts is also often hollow, but in this case, the eggs are shed into the cavity, which opens into the oviduct. Although most normal female vertebrates have two ovaries, this is not the case in all species. In birds and platypuses, the right ovary never matures, so that only the left is functional. In some elasmobranchs, the reverse is true, with only the right ovary fully developing. In the primitive jawless fish, and some teleosts, there is only one ovary, formed by the fusion of the paired organs in the embryo TAO:0000403 UBERON:0000992 UMLS:C0029939 VHOG:0000251 XAO:0000258 ZFA:0000403 female organism genitalia gonad female organism genitalia gonada female organism reproductive system gonad female organism reproductive system gonada female reproductive system gonad female reproductive system gonada genitalia of female organism gonad genitalia of female organism gonada gonad of female organism genitalia gonad of female organism reproductive system gonad of female reproductive system gonad of genitalia of female organism gonad of reproductive system of female organism gonada of female organism genitalia gonada of female organism reproductive system gonada of female reproductive system gonada of genitalia of female organism gonada of reproductive system of female organism ovarian ovaries ovarium ovary ovum-producing ovary reproductive system of female organism gonad reproductive system of female organism gonada the gonad of a female organism which contains germ cells uberon oviduct A passage through which ova leave the maternal body or pass to an organ communicating with the exterior of the body. [TFD][VHOG] A tube or collection of tubes in an animal from the ovaries to the outside of the body. AAO:0010533 BSA:0000083 BTO:0000980 EFO:0000974 EMAPA:18984 GAID:366 In all remaining vertebrates (i.e., coelacanths, lungfishes, amphibians, reptiles, birds, and mammals), the oviduct arises in ontogeny as a longitudinal, groovelike invagination of the coelomic epithelium on the lateral surface of the mesonephros.[well established][VHOG] MAT:0000126 MESH:D010057 MIAA:0000126 TAO:0000560 The only female vertebrates to lack oviducts are the jawless fishes. In these species, the single fused ovary releases eggs directly into the body cavity. The fish eventually extrudes the eggs through small genital pores towards the rear of the body[WP] UBERON:0000993 UMLS:C0029954 VHOG:0001136 XAO:0003052 ZFA:0000560 female reproductive tracts in birds divided into infundibulum, magnum, isthmus, uterus, and vagina ovarian duct ovarian tube oviducts sometimes oviduct is used interchangeably with follaopian tube. Here they are different - the oviduct connects the gonad to the outside in a variety of animals. The mammal-class fallopian tube is derived from the mullerian duct and connects the gonads/infubdibulum to the uterus tuba uterina tuba uterinae tubular parts of female reproductive system uberon uterine tube uterus An infundibulum, uterine tube, uterus, and vagina also differentiate along the oviducts of eutherian mammals.[well established][VHOG] BTO:0001424 CALOHA:TS-1102 EFO:0000975 EMAPA:29915 EV:0100113 FMA:17558 GAID:172 MA:0000389 MAT:0000127 MESH:D014599 MIAA:0000127 Most animals that lay eggs, such as birds and reptiles, have an oviduct instead of a uterus. In monotremes, mammals which lay eggs and include the platypus, either the term uterus or oviduct is used to describe the same organ, but the egg does not develop a placenta within the mother and thus does not receive further nourishment after formation and fertilization. Marsupials have two uteruses, each of which connect to a lateral vagina and which both use a third, middle 'vagina' which functions as the birth canal. Marsupial embryos form a choriovitelline 'placenta' (which can be thought of as something between a monotreme egg and a 'true' placenta), in which the egg's yolk sac supplies a large part of the embryo's nutrition but also attaches to the uterine wall and takes nutrients from the mother's bloodstream. OpenCyc:Mx4rvViojJwpEbGdrcN5Y29ycA The hollow muscular organ in female mammals in which the blastocyst normally becomes embedded and in which the developing embryo and fetus is nourished. Its cavity opens into the vagina below and into a uterine tube on either side. [TFD][VHOG] Two uteruses usually form initially in a female fetus, and in placental mammals they may partially or completely fuse into a single uterus depending on the species. In many species with two uteruses, only one is functional. Humans and other higher primates such as chimpanzees, along with horses, usually have a single completely fused uterus, although in some individuals the uteruses may not have completely fused [Wikipedia:Uterus] UBERON:0000995 UMLS:C0042149 VHOG:0001137 galen:Uterus the female muscular organ of gestation in which the developing embryo or fetus is nourished until birth uberon uterine vagina 'The distal end of the oviducts differentiates as a vagina in Metatheria and Eutheria.' Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective, Third Edition (2001) Orlando Fla.: Harcourt College Publishers, p.688 A fibromuscular tubular tract leading from the uterus to the exterior of the body in female placental mammals and marsupials, or to the cloaca in female birds, monotremes, and some reptiles[WP]. BTO:0000243 CALOHA:TS-1103 EFO:0000976 EMAPA:18986 EV:0100117 FMA:19949 GAID:381 MA:0000394 MAT:0000128 MESH:D014621 MIAA:0000128 OpenCyc:Mx4rvVj1B5wpEbGdrcN5Y29ycA Organ with organ cavity which connects the cervical canal of uterus to the vestibule of vagina.[FMA] The distal end of the oviducts differentiates as a vagina in Metatheria and Eutheria.[well established][VHOG] The genital canal in the female, leading from the opening of the vulva to the cervix of the uterus. [TFD][VHOG] UBERON:0000996 UMLS:C0042232 VHOG:0001138 distal oviductal region distal portion of oviduct galen:Vagina uberon vaginae vaginal skin epidermis (...) outer epithelia in all metazoan animals are homologous. (...) The ancestor of all metazoans likely had an epidermis with a basal extracellular matrix (ECM), an apical extracellular glycocalyx, and one cilium with a striated rootlet per cell.[well established][VHOG] A cellular, multilayered epithelium derived from the ectoderm. Zebrafish epidermis consists only of living cells unlike terrestrial vertebrates in which dead, keratinized cells are present. Le Guellec et al, 2004.[TAO] AAO:0000143 BTO:0000404 CALOHA:TS-0283 EFO:0000954 EMAPA:17528 EV:0100153 FMA:70596 GAID:932 MA:0000153 MAT:0000154 MESH:D004817 MIAA:0000154 TAO:0000105 The outer epithelial layer of the external integument of the body that is derived from the embryonic epiblast.[AAO] The outer epithelial layer of the skin that is superficial to the dermis. UBERON:0001003 UMLS:C0014520 VHOG:0000077 XAO:0000028 ZFA:0000105 Zebrafish epidermis consists only of living cells unlike terrestrial vertebrates in which dead, keratinized cells are present. In terrestrial vertebrates the epidermis often forms an outer keratinized or cornified layer, the stratum corneum. Interaction between the epideris and dermis gives rise to feathers (birds), hair and mammary glands (mammals), teeth and scales (placoid: chondrichthyans; cosmoids, ganoid, cycloid in bony fishes). epidermal epidermis relationship loss: subclass external integument structures (AAO:0000961)[AAO] skin uberon vertebrate epidermis respiratory system AAO:0000541 Atmungssystem BTO:0000203 CALOHA:TS-1319 EFO:0000804 EHDAA2:0001604 EHDAA:2203 EMAPA:16727 EV:0100036 FMA:7158 Functional system which consists of structures involved in respiration. GAID:78 MA:0000327 MAT:0000030 MESH:D012137 MIAA:0000030 OpenCyc:Mx4rvVjzFJwpEbGdrcN5Y29ycA TAO:0000272 The anatomical system in which the exchange of oxygen and carbon dioxide between the organism and its environment.[AAO] There is no doubt that the primitive pattern of vertebrate air-breathing is the buccal pulse pump found in actinopterygian fishes.[well established][VHOG] UBERON:0001004 UMLS:C0035237 VHOG:0000202 XAO:0000117 ZFA:0000272 apparatus respiratorius apparatus respiratorius respiratory system systema respiratorium uberon respiratory airway An airway through which respiratory air passes in organisms. FMA:265130 This class generically groups trachea and analagous structures throughout metazoa. Consider renaming, as the term could be taken to mean lumen of tracheal system (e.g. in SNOMED). As a grouping class this is quite vague, as it is not clear where the airway begins and ends UBERON:0001005 airway airways uberon digestive system AAO:0000129 An anatomical system consisting of the alimentary canal and digestive glands responsible for intake, absorption, digestion and excretion of food.[AAO] Anatomical system that has as its parts the organs devoted to the ingestion, digestion, and assimilation of food and the discharge of residual wastes. BILA:0000082 BTO:0000058 CALOHA:TS-1293 EFO:0000793 EV:0100056 FBbt:00005055 FMA:7152 GAID:278 MA:0002431 MAT:0000018 MESH:D004064 MIAA:0000018 TADS:0000170 TAO:0000339 UBERON:0001007 WBbt:0005748 XAO:0000125 ZFA:0000339 alimentary system alimentary tract digestive galen:DigestiveSystem gastrointestinal system gut many anatomy ontologies consider gastrointestinal system synonymous with digestive system. here we follow MA in dividing digestive system into gastrointestinal and hepatobiliary. hepatobiliary includes the liver and biliary tract. species-specific AO classes are categorized according to whether liver is included. For example, XAO includes liver as part of XAO:0000125 alimentary system, so we assume this class is the more generic class ncithesaurus:Digestive_System uberon renal system AAO:0010257 An anatomical system which consists of organs and tissues which produce, store, and excrete urine.[AAO] BILA:0000015 BTO:0001244 BTO:0003092 CALOHA:TS-1323 EFO:0000803 EHDAA2:0001601 EHDAA:5901 EMAPA:17366 EV:0100095 Evolution of vertebrate renal anatomy appears quite conservative when compared, for example, to evolution of respiratory and cardiovascular systems in vertebrates. Major anatomical changes in vertebrates kidneys separate those of birds and mammals from kidneys of lower vertebrates. General increase in animal size from fish to mammals is reflected by an increase in total number of nephrons per kidney, rather than by constant change in tubular dimensions.[well established][VHOG] FBbt:00005056 FMA:7159 GAID:391 In humans, the renal system comprises a pair of kidneys, a pair of ureters, urinary bladder, urethra, sphincter muscle and associated blood vessels In various sources such as Encyclopedia Britannica, the excretory and urinary systems are indeed the same system (see wikipedia talk page); we merge two BTO classes here MA:0000325 MAT:0000027 MESH:D014551 MIAA:0000027 TADS:0000162 TAO:0000163 The renal system in an anatomical system that maintains fluid balance and contributes to electrolyte balance, acid/base balance, and disposal of nitrogenous waste products.. This definition is inclusive of the organs of the vertebrate renal system, as well as the Malpighian tubules of insects, and allows for future incorporation of structures such as the antennal glands of crustaceans UBERON:0001008 UMLS:C1508753 VHOG:0000723 WBbt:0005736 XAO:0000143 ZFA:0000163 excretory system galen:UrinaryTract renal or urinary system renal system renal/urinary system systema urinaria systema urinarium uberon urinary system urinary tract circulatory system AAO:0000959 Anatomical system of ion binding, a pumping mechanism, and an efficient vascular system; consisting of the blood, heart, and blood and lymph vessels, respectively.[AAO] CALOHA:TS-2103 FBbt:00005057 OpenCyc:Mx4rvVjzG5wpEbGdrcN5Y29ycA UBERON:0001009 VHOG:0001248 We should divest ourselves of the view that earlier vertebrate groups were 'on their way' to becoming mammals, as clearly they were not such visionaries. Neither were their systems 'imperfect' as earlier anatomists thought. Instead, their circulatory systems served them well to address the ecological demands arising from their lifestyles.[well established][VHOG] organ system that passes nutrients (such as amino acids and electrolytes), gases, hormones, blood cells, etc. to and from cells in the body to help fight diseases and help stabilize body temperature and pH to maintain homeostasis[WP]. systema cardiovasculare the cardiovascular system and the lymphatic system are parts of the circulatory system uberon adipose tissue AAO:0000001 AEO:000020 Adipose tissue is unique to vertebrates. It is found in mostmammals, birds, reptiles and amphibians, and a variety is found in some species of fish. Furthermore, in insects the fat body found in larvae as well as in adults shares some homology with adipose tissue.[well established][VHOG] BTO:0001487 CALOHA:TS-0013 Connective tissue in which fat is stored.[TAO] EFO:0000790 EHDAA2:0003120 EMAPA:35112 EV:0100381 FMA:20110 GAID:920 In humans, adipose tissue is located beneath the skin (subcutaneous fat), around internal organs (visceral fat), in bone marrow (yellow bone marrow) and in breast tissue. Adipose tissue is found in specific locations, which are referred to as adipose depots. Adipose tissue contains several cell types, with the highest percentage of cells being adipocytes, which contain fat droplets. Other cell types include fibroblasts, macrophages, and endothelial cells. Adipose tissue contains many small blood vessels.; Mice have eight major adipose depots, four of which are within the abdominal cavity. The paired gonadal depots are attached to the uterus and ovaries in females and the epididymis and testes in males; the paired retroperitoneal depots are found along the dorsal wall of the abdomen, surrounding the kidney, and, when massive, extend into the pelvis. The mesenteric depot forms a glue-like web that supports the intestines, and the omental depot, which originates near the stomach and spleen, and, when massive, extends into the ventral abdomen. MA:0000009 MAT:0000015 MESH:D000273 MIAA:0000015 OpenCyc:Mx4rvVjc_ZwpEbGdrcN5Y29ycA Portion of connective tissue composed of adipocytes enmeshed in areolar tissue TAO:0002134 Tissue that contains adipocytes, used for cushioning, thermal insulation, lubrication (primarily in the pericardium) and energy storage.[AAO] UBERON:0001013 UMLS:C0001527 VHOG:0001284 XAO:0003049 ZFA:0005345 adipose adipose bodyfat fat fat tissue fatty depot fatty tissue galen:FattyTissue in FMA this is dense irregular connective tissue relationship loss: subclass connective tissue proper (AAO:0000099)[AAO] uberon musculature A subdivision of the muscular system corresponding to a subdisivision of an organism. AAO:0011066 BTO:0000887 EFO:0001949 EMAPA:32715 EMAPA:35577 FMA:32558 In FMA this is classified as a set of organs. ZFA musculature system has subtypes, so it is classified here. WBbt muscular system has subtypes so it goes here. Note that we use the MA term set of skeletal muscles here as it seems most appropriate (*not* MA:musculature). AAO is generally confused here. MA:0000165 OpenCyc:Mx4rvVjmr5wpEbGdrcN5Y29ycA TAO:0000548 UBERON:0001015 UMLS:C0026845 VSAO:0005038 WBbt:0005737 ZFA:0000548 muscle group muscle system muscles muscles set musculature musculature system musculi set of muscles set of skeletal muscles uberon nervous system A regulatory system of the body that consists of neurons and neuroglial cells. The nervous system is divided into two parts, the central nervous system (CNS) and the peripheral nervous system (PNS). (Source: BioGlossary, www.Biology-Text.com)[TAO] AAO:0000324 Anatomical system consisting of nerve bodies and nerve fibers which regulate the response of the body to external and internal stimuli.[AAO] BILA:0000079 BTO:0001484 CALOHA:TS-1313 EFO:0000802 EHDAA2:0001246 EHDAA:826 EMAPA:16469 EV:0100162 FBbt:00005093 FMA:7157 GAID:466 MA:0000016 MAT:0000026 MESH:D009420 MIAA:0000026 Nervous systems evolved in the ancestor of Eumetazoa.[well established][VHOG] OpenCyc:Mx4rvViT_pwpEbGdrcN5Y29ycA TAO:0000396 The nervous system is an organ system containing predominantly neuron and glial cells. In bilaterally symmetrical organism, it is arranged in a network of tree-like structures connected to a central body. The main functions of the nervous system are to regulate and control body functions, and to receive sensory input, process this information, and generate behavior [CUMBO]. UBERON:0001016 UMLS:C0027763 VHOG:0000402 WBbt:0005735 XAO:0000177 ZFA:0000396 nerve net nervous neural neurological system systema nervosum uberon central nervous system (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2); Taken together, our data make a very strong case that the complex molecular mediolateral architecture of the developing trunk CNS (central nervous system), as shared between Platynereis and vertebrates, was already present in their last common ancestor, Urbilateria. The concept of bilaterian nervous system centralization implies that neuron types concentrate on one side of the trunk, as is the case in vertebrates and many invertebrates including Platynereis, where they segregate and become spatially organized (as opposed to a diffuse nerve net). Our data reveal that a large part of the spatial organization of the annelid and vertebrate CNS was already present in their last common ancestor, which implies that Urbilateria had already possessed a CNS (reference 3).[well established][VHOG] AAO:0000090 BAMS:CNS BILA:0000080 BTO:0000227 CALOHA:TS-0150 CNS EFO:0000908 EHDAA2:0000225 EHDAA:828 EMAPA:16470 EMAPA:16754 EV:0100163 FBbt:00005094 FMA:55675 GAID:570 MA:0000167 MAT:0000457 MESH:D002490 OpenCyc:Mx4rvzYt3pwpEbGdrcN5Y29ycA Part of the nervous system which includes the brain and spinal cord.[AAO] TAO:0000012 The brain and spinal cord. Kimmel et al, 1995.[TAO] The central nervous system (CNS) is the part of the nervous system which includes the brain, spinal cord, and nerve cell layer of the retina (CUMBO). The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the neural tube derivatives: the brain and spinal cord. In invertebrates it includes central ganglia plus nerve cord. UBERON:0001017 UMLS:C0927232 VHOG:0000293 XAO:0000215 ZFA:0000012 cerebrospinal axis neuraxis systema nervosum centrale uberon nerve A portion of tissue which is a fasiculated group of axons.[TAO] AAO:0011070 AEO:0000137 An enclosed, cable-like bundle of axons in the peripheral nervous system originating in a nerve root in the central nervous system (or a condensed nervous structure) connecting with peripheral structures. BAMS:n BSA:0000098 BTO:0000925 BTO:0001027 CALOHA:TS-0772 EHDAA2:0003137 EHDAA:2851 EHDAA:3776 EHDAA:4657 EMAPA:32808 EMAPA:32815 EV:0100371 FBbt:00005105 FMA:65132 FMA:65239 GAID:747 GAID:758 MA:0000217 MA:0000228 MESH:D010525 OpenCyc:Mx4rwP3lkpwpEbGdrcN5Y29ycA TAO:0007009 UBERON:0001021 UMLS:C0027740 UMLS:C0031119 VHOG:0000901 XAO:0000204 XAO:0003047 ZFA:0007009 galen:Nerve nerves nervous neural subtree peripheral nerve uberon sensory system AAO:0000555 An early step in the evolution of neural crest, therefore, may have been the origin of a specific dorsal neural cell population contributing to sensory processing; this would predate the divergence of the amphioxus and vertebrate lineages.[well established][VHOG] Anatomical system that overlaps the nervous system and is responsible for receiving and processing sensory information. BAMS:SEN BILA:0000099 EFO:0000805 EHDAA2:0003094 EMAPA:16192 FBbt:00005827 FMA:75259 MA:0002442 MAT:0000031 MIAA:0000031 TAO:0000282 UBERON:0001032 VHOG:0001674 XAO:0003194 ZFA:0000282 note the distinct between entire sensory system and individual system. this reconciles is_a and part_of distinctions between ssAOs organa sensuum organa sensuum sense organ subsystem sense organs sense organs set sensory organ system sensory subsystem sensory systems set of sense organs uberon gustatory system AAO:0010577 BILA:0000143 EFO:0000830 FMA:7194 MA:0002446 MAT:0000275 MIAA:0000275 TAO:0001101 The sensory system for the sense of taste. The sensory system for the sense of taste[NIFSTD:nlx_anat_090803]. The sensory system used for the sense of taste.[AAO] UBERON:0001033 XAO:0003197 ZFA:0001101 gustatory gustatory organ system in ZFA and MA this is a subtype of sensory system. we should change sensory system to disambiguate parts and wholes taste system uberon foregut AAO:0011042 Anterior subdivision of a digestive tract. BILA:0000085 BTO:0000507 EHDAA2:0000557 EHDAA:520 EMAPA:16548 FBbt:00005379 FMA:45616 MA:0001526 Note we define this generically to include invertebrates (partly for consistency with GO), but the class may be split in future. In vertebrates the term may refer to a developmental structure TGMA:0001014 The anterior portion of the primitive digestive tube of the embryo that lies cephalic to the junction of the yolk stalk, consists of endodermal tissue, and gives rise to the the pharynx, lower respiratory system, esophagus, stomach, duodenum proximal to the biliary tract, liver, pancreas, biliary tract, and gall bladder. The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG] UBERON:0001041 UMLS:C0231051 VHOG:0000285 XAO:0000232 praeenteron proenteron uberon chordate pharynx (...) the earliest vertebrates possessed unjointed internal and external branchial arches, and musculature encircling the pharynx.[well established][VHOG] A funnel-shaped fibromuscular tube that conducts food to the ESOPHAGUS, and air to the LARYNYX and LUNGS. It is located posterior to the NASAL CAVITY; ORAL CAVITY; and LARYNX, and extends from the SKULL BASE to the inferior border of the CRICOID CARTILAGE anteriorly and to the inferior border of the C6 vertebra posteriorly. It is divided into the NASOPHARYNX; OROPHARYNX; and HYPOPHARYNX (laryngopharynx)[MESH:A03.867]. A portion of the respiratory and digestive tracts; its distal limit is the superior part of the esophagus and it connects the nasal and oral cavities with the esophagus and larynx; it contains the valleculae and the pyriform recesses; its upper limits are the nasal cavity and cranial base.[FEED]. AAO:0000967 Anatomical cavity bounded by the derivatives of the branchial arches.[AAO] BTO:0001049 CALOHA:TS-0785 Consider generalizing to deuterostome pharynx EFO:0000836 EHDAA2:0001458 EHDAA:2947 EMAPA:16706 EV:0100065 FMA:46688 GAID:155 MA/FMA pharynx not part of digestive/alimentary system, we are consistent with this scheme MA:0000432 MESH:A03.867 OpenCyc:Mx4rvViv7ZwpEbGdrcN5Y29ycA Swollen region of the anterior foregut, posterior to the mouth and anterior to the liver; its walls form the jaws and gills. Kimmel et al, 1995.[TAO] Swollen region of the anterior foregut, posterior to the mouth and anterior to the liver; its walls form the jaws and gills[ZFA:0000056, ZFIN:ZDB-PUB-961014-576]. TAO:0000056 The portion of the alimentary canal between the mouth and the oesophagus. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] UBERON:0001042 UMLS:C0031354 VHOG:0000462 XAO:0003227 ZFA:0000056 galen:Pharynx pharynx relationship type change: part_of_proxy respiratory system (AAO:0000541) CHANGED TO: develops_from respiratory system (UBERON:0001004)[AAO] relationship type change: part_of_proxy respiratory system (AAO:0000541) CHANGED TO: part_of respiratory system (UBERON:0001004)[AAO] uberon esophagus AAO:0000145 ANISEED:1235301 Anterior end of the alimentary canal lined with smooth muscle. Bounded anteriorly by a constriction in the pharynx. Bounded posteriorly by and increase in circular and/or longitudinal smooth muscle associated with the stomach.[AAO] BTO:0000959 CALOHA:TS-0700 EFO:0000835 EHDAA2:0001285 EHDAA:2937 EMAPA:16833 EV:0100069 FMA:7131 GAID:291 MA:0000352 MAT:0000048 MESH:A03.365 MIAA:0000048 OpenCyc:Mx4rvVj9Q5wpEbGdrcN5Y29ycA TAO:0000204 The few structural specializations in (adult lampreys) pharynx include complex valves on the external gill openings that direct the tidal flow, and the division of the ancestral pharynx into an oesophagus and a respiratory pharynx.[well established][VHOG] Tube that connects the pharynx to the stomach. In mammals, the oesophagus connects the buccal cavity with the stomach. The stratified squamous non-keratinised epithelium lining the buccal cavity is continued through the pharynx down into the oesophagus. The lowest part of the oesophagus (ca. 2 cm) is lined with gastric mucosa and covered by peritoneum. The main body of the oesophagus is lined with small, simple mucous glands. Each gland opens into the lumen by a long duct which pierces the muscularis mucosae (Wilson and Washington, 1989). A sphincter is situated at the point where the oesophagus enters the stomach to prevent gastro-oesophageal reflux, i.e. to prevent acidic gastric contents from reaching stratified epithelia of the oesophagus, where they can cause inflammation and irritation (Wilson and Washington, 1989; Brown et al., 1993). UBERON:0001043 UMLS:C0014876 VHOG:0000450 XAO:0000127 ZFA:0000204 esophageal esophagus NOT part of gut in MA. part of gut in ZFA. part_of gut (via UGIT) in FMA. Consider splitting. Interspecies: The human oesophagus is 25 cm long and has a diameter of ca. 2 cm. Only little information was found on the oesophagus in rat, rabbit and pig. The oesophagus of rat (75 x 2 mm) and rabbit has no mucous glands and the cardia of the stomach has a well-developed sphincter, which prevents them from vomiting (Hebel and Stromberg, 1988; Manning et al., 1994). Morphologically the oesophagus is similar in man and pig; both are omnivores and have a non-keratinised epithelium, submucous glands and similar membrane enzymes. Like in humans, pigs can suffer from reflux oesophagitis and stress ulceration of the oesophagus. The pig oesophagus may therefore be a good model for investigation compared to the human oesophagus (Christie et al., 1995) galen:Esophagus gullet oesophagus uberon midgut BILA:0000086 BTO:0000863 EFO:0001950 EHDAA2:0001185 EHDAA:983 EMAPA:16255 FBbt:00005383 FMA:45617 In humans: originates from the foregut at the opening of the bile duct into the duodenum and continues through the small intestine and much of the large intestine until the transition to the hindgut about two-thirds of the way through the transverse colon MA:0001564 Middle subdivision of a digestive tract[CJM]. In vertebrates: The middle part of the alimentary canal from the stomach, or entrance of the bile duct, to, or including, the large intestine[GO]. Note we define this generically to include invertebrates (partly for consistency with GO), but the class may be split in future. We may explicitly make this a developmental class TGMA:0001036 The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG] UBERON:0001045 UMLS:C0231052 VHOG:0000290 XAO:0000103 in FMA this represents an embryonic region. mesenteron uberon hindgut AAO:0011052 BILA:0000087 BTO:0000510 EHDAA2:0000779 EHDAA:975 EMAPA:16715 FBbt:00005384 FMA:45618 MA:0001527 Note we define this generically to include invertebrates (partly for consistency with GO), but the class may be split in future (vertebrates have some contribution from NC - https://github.com/obophenotype/uberon/wiki/The-neural-crest). We may explicitly make this a developmental class TGMA:0001020 The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG] The caudalmost subdivision of a digestive tract. UBERON:0001046 UMLS:C0231053 VHOG:0000459 XAO:0000104 in FMA this class has no children. In MA it has a single child hindgut epithelium metenteron the caudal portion of the primitive digestive tube of the embryo uberon primordium AEO:0000171 BTO:0001886 EFO:0001652 EHDAA2:0003171 FBbt:00005495 FMA:86589 MAT:0000482 Primordia are populations of contiguous cells that are morphologically distinct and already correspond in extent to a later organ/tissue[FBbt, Hartenstein, V. (2004)]. UBERON:0001048 UMLS:C0678727 XAO:0003043 bud future organ placode primordia rudiment uberon neural tube (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] AAO:0010617 BTO:0001057 CALOHA:TS-2371 DHBA:10154 EHDAA2:0001254 EHDAA:2869 EHDAA:908 EMAPA:16164 EMAPA:16530 EMAPA:16757 FMA:293882 Hollow epithelial tube on dorsal side of the embryo that develops into the central nervous system.[AAO] In the developing vertebrate, the neural tube is the embryo's precursor to the central nervous system, which comprises the brain and spinal cord. The neural groove gradually deepens as the neural folds become elevated, and ultimately the folds meet and coalesce in the middle line and convert the groove into a closed tube, the neural tube or neural canal (which strictly speaking is the center of the neural tube), the ectodermal wall of which forms the rudiment of the nervous system. [WP,unvetted]. MAT:0000069 MIAA:0000069 TAO:0001135 The dorsal tubular structure in the vertebrate embryo that develops into the brain and spinal cord. [TFD][VHOG] The mature structure of the neural tube exists when the tube has been segmented into the forebrain, midbrain, hindbrain and spinal cord regions. In addition neural crest has budded away from the epithelium UBERON:0001049 UMLS:C0231024 VHOG:0000307 XAO:0003204 ZFA:0001135 neural primordium presumptive central nervous system tubus neuralis uberon rectum AAO:0010401 BTO:0001158 CALOHA:TS-1180 EFO:0000848 EHDAA2:0001592 EHDAA:5836 EMAPA:17896 EV:0100081 FMA:14544 GAID:311 In the lungfish, sharks and rays the rectum opens into the cloaca which also receives wastes (urine) from the kidneys and material from the reproductive organs. In bony fish the rectum reaches the outside environment through the anus, which is normally situated just in front the urinary and reproductive openings. However in some fish the digestive tract may be curled back on itself, and in the Electric Eel (Electrophorus electricus) the anus is situated in the fish's throat. -- http://www.earthlife.net/fish/digestion.html MA:0000336 MAT:0000050 MESH:A03.492.411.495.767 MIAA:0000050 OpenCyc:Mx4rvVjaU5wpEbGdrcN5Y29ycA The terminal portion of the large intestine between the ileo-pelvic colon and the anus. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] UBERON:0001052 UMLS:C0034896 VHOG:0001751 XAO:0000238 galen:Rectum intestinum rectum rectal rectal sac terminal portion of intestine terminal portion of large intestine the terminal portion of the intestinal tube, terminating with the anus uberon anatomical entity AAO:0010841 AEO:0000000 BILA:0000000 Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species. CARO:0000000 EHDAA2:0002229 FBbt:10000000 FBbt_root:00000000 FMA:62955 HAO:0000000 MA:0000001 TAO:0100000 TGMA:0001822 UBERON:0001062 UMLS:C1515976 XAO:0000000 ZFA:0100000 uberon ventral pancreatic duct A duct joining the pancreas to the common bile duct to supply pancreatic juices which aid in digestion provided by the exocrine pancreas. The pancreatic duct joins the common bile duct just prior to the ampulla of Vater, after which both ducts perforate the medial side of the second portion of the duodenum at the major duodenal papilla. BTO:0002362 EHDAA2:0001396 EHDAA:6905 EMAPA:17510 FMA:16003 GAID:337 MA:0000126 MESH:D010183 RETIRED_EHDAA2:0002177 These data show that ducts within the zebrafish pancreas originally arise in situ from isolated progenitor cells rather than arising from reiterative branching of the pancreatic epithelium. This process of pancreatic duct formation in zebrafish may be analogous to the mechanism of duct formation in the mammalian mammary and salivary glands. (...) A related mechanism of duct formation has also been proposed to occur within the mammalian pancreatic epithelium.[uncertain][VHOG] UBERON:0001064 UBERON:0005627 UMLS:C0030288 Upon reaching its final destination, the ventral pancreatic bud fuses with the much larger dorsal pancreatic bud. At this point of fusion, the main ducts of the ventral and dorsal pancreatic buds fuse, forming the duct of Wirsung, the main pancreatic duct. VHOG:0000256 canal of Wirsung chief pancreatic duct duct of Wirsung ductus pancreatis ventralis hepaticopancreatic duct in EHDAA2 this is an epithelium, in FMA the wall consists of epithelium and connective tissue main pancreatic duct pancreatic duct uberon urine BTO:0001419 CALOHA:TS-1092 EFO:0001939 EMAPA:36554 ENVO:00002047 Excretion that is the output of a kidney FMA:12274 GAID:1189 MA:0002545 MAT:0000058 MESH:D014556 MIAA:0000058 OpenCyc:Mx4rvVjGppwpEbGdrcN5Y29ycA UBERON:0001088 UMLS:C0042036 galen:Urine kidney excreta from some taxa (e.g. in aves) may not be liquid uberon synovial fluid BTO:0001339 CALOHA:TS-0996 ENVO:02000039 FMA:12277 GAID:265 MA:0002544 MESH:D013582 Portion of organism substance that is a clear fluid that occupies the space in synovial joints.[TAO] TAO:0005154 Transudate contained in the synovial cavity of joints, and in the cavity of tendon sheaths and bursae. UBERON:0001090 UMLS:C0039097 ZFA:0005154 galen:SynovialFluid joint fluid uberon lobe of liver EMAPA:18306 FMA:13361 MA:0000360 Traditional gross anatomy divided the liver into four lobes based on surface features. The falciform ligament is visible on the front (anterior side) of the liver. This divides the liver into a left anatomical lobe, and a right anatomical lobe. UBERON:0001113 UMLS:C0447541 hepatic lobe liver lobe lobus hepatis some work needs to be done to ensure the child terms of this class have correct isa/partof placement. in MA they are subclasses, in FMA they are parts uberon right lobe of liver 2nd lobe EHDAA2:0001008 EHDAA:4001 EMAPA:18311 FMA:13362 MA:0000363 Portion of the liver which develops on the fish's right side adjacent to the gall bladder.[TAO] TAO:0005173 The right lobe is much larger than the left; the proportion between them being as six to one. It occupies the right hypochondrium, and is separated from the left lobe on its upper surface by the falciform ligament; on its under and posterior surfaces by the left sagittal fossa; and in front by the umbilical notch. It is of a somewhat quadrilateral form, its under and posterior surfaces being marked by three fossæ: the porta and the fossæ for the gall-bladder and inferior vena cava, which separate its left part into two smaller lobes; the quadrate and caudate lobes. [WP,unvetted]. This class was created automatically from a combination of ontologies UBERON:0001114 UMLS:C0227481 VHOG:0001424 ZFA:0005173 gall bladder lobe liver right lobe lobus hepaticus dexter lobus hepatis dexter right hepatic lobe right liver lobe second lobe uberon left lobe of liver EHDAA2:0001000 EHDAA:3995 EMAPA:18307 FMA:13363 MA:0000361 Portion of the liver which develops on the fish's left side.[TAO] TAO:0005172 The left lobe is smaller and more flattened than the right. It is situated in the epigastric and left hypochondriac regions. Its upper surface is slightly convex and is moulded on to the diaphragm; its under surface presents the gastric impression and omental tuberosity. [WP,unvetted]. This class was created automatically from a combination of ontologies UBERON:0001115 UMLS:C0227486 VHOG:0001423 ZFA:0005172 left hepatic lobe left liver lobe liver left lobe lobus hepaticus sinister lobus hepatis sinister uberon cardiac muscle tissue AAO:0010245 AEO:0000142 BILA:0000134 BTO:0000199 CALOHA:TS-0440 EHDAA2:0003142 EMAPA:32688 FMA:14068 Muscle tissue composed of cardiac muscle cells, forming the muscles of the heart[ZFA,modified]. TAO:0005280 UBERON:0001133 UBERON:0007096 ZFA:0005280 cardiac muscle cardiac muscle muscle tissue cardiac muscle textus muscularis cardiac musculature check relationship with myocardium. part_of in MA - but we also have a more specific class 'cardiac muscle tissue of myocardium'. Check ncit galen:CardiacMuscle galen:CardiacMuscleTissue heart muscle muscle tissue heart muscle textus muscularis heart myocardium muscle tissue heart myocardium textus muscularis muscle of heart muscle tissue muscle of heart textus muscularis muscle tissue of cardiac muscle muscle tissue of heart muscle muscle tissue of heart myocardium muscle tissue of muscle of heart muscle tissue of myocardium myocardium muscle tissue myocardium textus muscularis ncithesaurus:Heart_Muscle textus muscularis of cardiac muscle textus muscularis of heart muscle textus muscularis of heart myocardium textus muscularis of muscle of heart textus muscularis of myocardium uberon skeletal muscle tissue EMAPA:32716 FMA:14069 MA:0002439 Muscle tissue that consists primarily of skeletal muscle fibers. Muscle, composed of long cylindrical, multinucleated cells that attaches to the skeleton via tendons.[TAO] TODO - add skeletal muscle organ? See GO:0060538 skeletal muscle organ development. Todo - group FBbt:00005073 - somatic muscle. This result implies the following views in terms of evolutionary differentiation: (1) Arthropod striated muscle and vertebrate skeletal and cardiac muscles share a common ancestor. In other words, they did not evolve independently (...) (5) The divergence of vertebrate skeletal and cardiac muscles/vertebrate smooth muscle and nonmuscle is at least before that of vertebrates/arthropods. In other words, emergence of skeletal and cardiac musle type tissues preceded the vertebrate/arthropod divergence (ca. 700 MYA).[well established][VHOG] Tissue which consists of skeletal muscle fibers surrounded by endomysium. Examples: Skeletal muscle tissue of biceps, Skeletal muscle tissue of diaphragm[FMA] UBERON:0001134 UMLS:C0242692 skeletal muscle skeletal muscle system somatic muscle uberon smooth muscle tissue (...) the first bilateral animals possessed only smooth muscles with the molecular repertoire necessary to build a striated muscle. (...) it is more parsimonious to regard striated muscle cells as a sister cell type to the smooth muscle cells. In this scenario, striated and smooth muscles would have arisen in the stem lineage that led to the Nephrozoa (i.e. all Bilateria exclusive the acoelomorphs) (Hejnol et al., 2009), from an 'acoel-like' smooth muscle, by segregation and divergence of functions and through differential recruitment of additional genes[well established][VHOG] A non-striated muscle that is composed of spindle-shaped cells. Smooth muscle usually is organized into sheets that line cavitated organs.[TAO] AAO:0010244 AEO:0000141 BTO:0001260 CALOHA:TS-0943 EFO:0000889 EHDAA2:0003141 EMAPA:32717 EV:0100378 FBbt:00003525 FMA:14070 GAID:167 GO uses visceral and smooth interchangeably. However visceral can also be used in the sense of the viscera. Many fly annotations to smooth muscle terms. If we want to be inclusive of insects have to have a general definition of tissue that includes cells. Involuntary muscle tissue consisting of uninucleate spindle-shaped fibers.[AAO] MA:0000166 MAT:0000303 MESH:D009130 MIAA:0000303 Muscle tissue which is unstriated, composed primarily of smooth muscle fibers surrounded by a reticulum of collagen and elastic fibers. Smooth muscle differs from striated muscle in the much higher actin/myosin ratio, the absence of conspicuous sarcomeres and the ability to contract to a much smaller fraction of its resting length[GO]. OpenCyc:Mx4rvvSS3pwpEbGdrcN5Y29ycA TAO:0005274 UBERON:0001135 UMLS:C1267092 VHOG:0001246 WBbt:0005781 XAO:0000175 ZFA:0005274 galen:SmoothMuscle galen:SmoothMuscleTissue involuntary muscle non-striated muscle smooth muscle textus muscularis levis; textus muscularis nonstriatus textus muscularis nonstriatus uberon visceral muscle visceral muscle tissue mesothelium AEO:0000111 BTO:0002422 CALOHA:TS-1183 EHDAA2_RETIRED:0003111 EHDAA:2331 EHDAA:2349 EHDAA:295 EHDAA:6073 EHDAA:640 EHDAA:646 EMAPA:32856 FMA:14074 MA:0000565 Simple squamous epithelium of mesodermal origin which lines serous membranes. Examples: mesothelium of pleura, mesothelium of peritoneum[FMA]. http://en.wikipedia.org/wiki/ The mesothelium is a membrane that forms the lining of several body cavities: the pleura (thoracal cavity), peritoneum (abdominal cavity including the mesentery) and pericardium (heart sac). Mesothelial tissue also surrounds the male internal reproductive organs (the tunica vaginalis testis) and covers the internal reproductive organs of women (the tunica serosa uteri). UBERON:0001136 UMLS:C0086610 uberon dorsum A major subdivision of an organism that is the entire part of the organism dorsal to a horizontal plane and bounded on one side by the same transverse plane. In vertebrares this includes the vertebral column.. BTO:0001713 CALOHA:TS-2223 EFO:0001405 FMA:14181 GAID:30 In humans, called the back, a large posterior area of the human body, rising from the top of the buttocks to the back of the neck and the shoulders. It is the surface opposite to the chest, its height being defined by the vertebral column (commonly referred to as the spine or backbone) and its breadth being supported by the ribcage and shoulders. The spinal canal runs through the spine and provides nerves to the rest of the body MESH:A01.176 OpenCyc:Mx4rvVkEU5wpEbGdrcN5Y29ycA UBERON:0001137 UMLS:C0004600 back back of body proper dorsal dorsal part of organism galen:Back uberon cystic duct Duct that connects the gall bladder and the common bile duct.[TAO] EHDAA2:0000333 EHDAA:3045 EMAPA:16841 FMA:14539 GAID:290 MA:0000355 MESH:A03.159.183.419 OpenCyc:Mx4rveBeC5wpEbGdrcN5Y29ycA TAO:0005166 The duct of the gallbladder which joins the common hepatic duct, thus forming the common biliary duct. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] UBERON:0001152 UMLS:C0010672 VHOG:0000213 ZFA:0005166 ductus cysticus galen:CysticDuct the tubular structure that conducts gall bladder contents from the gall bladder to the common bile duct uberon caecum A cecum is present in most amniote species, and also in lungfish, but not in any living species of amphibian. In reptiles, it is usually a single median structure, arising from the dorsal side of the large intestine. Birds typically have two paired ceca, as, unlike other mammals, do hyraxes. Most mammalian herbivores have a relatively large cecum, hosting a large number of bacteria, which aid in the enzymatic breakdown of plant materials such as cellulose; in many species, it is considerably wider than the colon. In contrast, obligatory carnivores, whose diets contain little or no plant material, have a reduced cecum, which is often partially or wholly replaced by the vermiform appendix. Many fish have a number of small outpocketings, called pyloric ceca, along their intestine; despite the name they are not homologous with the cecum of amniotes, and their purpose is to increase the overall area of the digestive epithelium.[2] Some invertebrates, such as squid,[3] may also have structures with the same name, but these have no relationship with those of vertebrates. A pouch in the digestive tract that connects the ileum with the ascending colon of the large intestine. It is separated from the ileum by the ileocecal valve, and is the beginning of the large intestine. It is also separated from the colon by the cecocolic junction. BTO:0000166 CALOHA:TS-0122 EFO:0000850 EHDAA2:0000206 EHDAA:3913 EMAPA:35197 EV:0100397 FMA:14541 GAID:307 Kardong: in some herbivorous lizards, a cecum is present between small and large intestines MA:0000334 MESH:A03.492.411.495.209 MIAA:0000288 OpenCyc:Mx4rve6u4JwpEbGdrcN5Y29ycA UBERON:0001153 UMLS:C0007531 VHOG:0001559 blind intestine blindgut caeca caecal caecum ceca cecum galen:Cecum intestinum caecum intestinum crassum caecum intestinum crassum cecum uberon vermiform appendix A blind-ended tube connected to the cecum, from which it develops embryologically[WP]. A comparative anatomical approach reveals three apparent morphotypes of the cecal appendix, as well as appendix-like structures in some species that lack a true cecal appendix. Cladistic analyses indicate that the appendix has evolved independently at least twice (at least once in diprotodont marsupials and at least once in Euarchontoglires), shows a highly significant (P < 0.0001) phylogenetic signal in its distribution, and has been maintained in mammalian evolution for 80 million years or longer.[well established][VHOG] BTO:0000084 CALOHA:TS-1267 EFO:0000849 EHDAA2:0000588 EMAPA:35140 EV:0100076 EV:0100080 FMA:14542 GAID:308 MA:0001540 MAT:0000287 MESH:A03.492.411.495.209.290 MIAA:0000287 OpenCyc:Mx4rvVjGgJwpEbGdrcN5Y29ycA Organ with organ cavity which is continuous proximally with the cecum and distally terminates in the tip of the appendix. Examples: There is only one appendix[FMA:14542]. UBERON:0001154 UMLS:C0003617 VHOG:0001306 apex of caecum apex of cecum appendiceal appendix appendix vermiformis appendix vermiformis caecal appendix cecal appendix galen:AppendixVermiformis uberon vermix colon AAO:0010400 Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[uncertain][VHOG] BTO:0000269 CALOHA:TS-0158 EFO:0000361 EMAPA:18939 EV:0100079 FMA:14543 GAID:309 In mammals, the colon consists of four sections: the ascending colon, the transverse colon, the descending colon, and the sigmoid colon[WP] In zebrafish, the posterior intestine has short longitudinally arranged epithelial folds which are similar to the colon of higher vertebrates[ZFIN] Last portion of the large intestine before it becomes the rectum. MA:0000335 MAP:0000001 MAT:0000526 MESH:A03.492.411.495.356 OpenCyc:Mx4rvgLEM5wpEbGdrcN5Y29ycA TAO:0000706 TODO - abstract this such that it legitimately covers all vertebrates The last portion of the digestive system, it extracts water and salt from solid wastes before they are eliminated from the body.[AAO] The posterior intestine has short longitudinally arranged epithelial folds which are similar to the colon of higher vertebrates. Wallace et al, 2005.[TAO] UBERON:0001155 UMLS:C0009368 VHOG:0000648 XAO:0000243 ZFA:0000706 colonic galen:Colon hindgut it extracts water and salt from solid wastes before they are eliminated from the body[WP] large bowel posterior intestine uberon ascending colon BTO:0000270 CALOHA:TS-0057 EFO:0000843 EMAPA:35151 FMA:14545 MA:0001541 MAT:0000311 MIAA:0000311 OpenCyc:Mx4rv3H0FZwpEbGdrcN5Y29ycA Section of colon which is distal to the cecum and proximal to the transversecolon.[FMA,modified] UBERON:0001156 UMLS:C0227375 colon ascendens galen:AscendingColon in MA, this is a subclass of colon spiral colon uberon transverse colon BTO:0000272 CALOHA:TS-2052 EFO:0000844 EMAPA:35880 FMA:14546 MA:0001543 MAT:0000312 MIAA:0000312 OpenCyc:Mx4rvg7qyJwpEbGdrcN5Y29ycA The proximal-distal subdivision of colon that runs transversely across the upper part of the abdomen, from the right to the left colic flexure. Continuous with the descending colon[BTO,modified]. UBERON:0001157 UMLS:C0227386 colon transversum galen:TransverseColon uberon descending colon BTO:0000641 CALOHA:TS-2010 EFO:0000845 EMAPA:35285 FMA:14547 MA:0001542 MAT:0000313 MIAA:0000313 OpenCyc:Mx4rwHsNhpwpEbGdrcN5Y29ycA The portion of the colon between the left colic flexure and the sigmoid colon at the pelvic brim; the portion of the descending colon lying in the left iliac fossa is sometimes called the iliac colon. UBERON:0001158 UMLS:C0227389 colon descendens galen:DescendingColon uberon sigmoid colon BTO:0000645 CALOHA:TS-2044 EFO:0000846 EMAPA:36391 FMA:14548 MAT:0000314 MESH:A03.492.411.495.356.668 MIAA:0000314 OpenCyc:Mx4rwHX_-5wpEbGdrcN5Y29ycA The part of the large intestine that is closest to the rectum and anus. It forms a loop that averages about 40 cm. in length, and normally lies within the pelvis, but on account of its freedom of movement it is liable to be displaced into the abdominal cavity. UBERON:0001159 UMLS:C0227391 UMLS:C0682612 colon sigmoideum galen:SigmoidColon pelvic colon sigmoid colon sigmoid flexure uberon body of stomach BTO:0000505 EMAPA:35810 FMA:14560 MA:0002559 The body of stomach is the part of the stomach that lies between the fundus above and the pyloric antrum below; its boundaries are poorly defined[GO]. UBERON:0001161 UMLS:C0227230 corpus gastricum corpus gastricum (ventriculare) corpus ventriculare corpus ventriculi galen:GastricCorpus gastric body gastric corpus stomach body uberon we include this as zone of stomach even though it is not distinguished by gland type pyloric antrum BTO:0001732 EFO:0002555 EMAPA:17891 FMA:14579 GAID:332 MA:0001624 MESH:A03.492.766.716 UBERON:0001165 UMLS:C0034193 antrum antrum of Willis antrum of stomach antrum pylori antrum pyloricum galen:PyloricAntrum gastric antrum stomach antrum stomach pyloric antrum the area at the bottom of the stomach on the caudal side of the pyloric canal that contains gastrin-producing G cells, which stimulate acid production, and the luminal pH-sensitive population of somatostatin-producing D cells uberon pylorus Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[uncertain][VHOG] BTO:0001146 EHDAA2:0001580 EHDAA:4860 EMAPA:17631 FMA:14581 GAID:333 MA:0002560 MESH:A03.492.766.799 The orifice which allows the passage from the stomach into the intestine. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] UBERON:0001166 UMLS:C0034196 VHOG:0000420 We follow Kardong in defining stomach regions by glands galen:Pylorus pars pylorica pars pylorica gastricae pyloric pyloric part of stomach pyloric region stomach pyloric region the stomach tissue region surrounding and controlling the distal outlet of the stomach, which opens into the duodenum uberon valvula pylori wall of stomach EMAPA:35826 FMA:14582 MA:0002692 UBERON:0001167 anatomical wall of stomach anatomical wall of ventriculus galen:WallOfStomach gastric wall stomach anatomical wall stomach wall the layered structure that makes up the stomach, typiclly consists of a serous coat, a muscular coat, a mucous membrane, and other tissue layers in between uberon ventriculus anatomical wall ventriculus wall wall of ventriculus wall of small intestine An anatomical wall that is part of a small intestine [Automatically generated definition]. EMAPA:35785 FMA:14615 MA:0002696 UBERON:0001168 UMLS:C1519375 anatomical wall of small bowel anatomical wall of small intestine small bowel anatomical wall small bowel wall small intestinal wall small intestine anatomical wall small intestine wall uberon wall of small bowel portal lobule FMA:14653 MA:0002498 The triangular region on the periphery of the liver lobules that contain a bile duct and a terminal branch of the hepatic artery and portal vein, and may also include a lymphatic vessel. UBERON:0001171 UMLS:C0682620 uberon hepatic acinus EMAPA:35497 FMA:14654 MA:0002496 The functional unit of the liver, consisting of a mass of hepatocytes from adjacent liver lobules aligned around the hepatic arterioles and portal venules just as they anastomose into sinusoids. UBERON:0001172 UMLS:C0227519 liver acinus portal acinus uberon biliary tree A complex network of conduits that begins with the canals of Hering (intralobar bile duct) and progressively merges into a system of interlobular, septal, and major ducts which then coalesce to form the extrahepatic bile ducts, which finally deliver bile to the intestine, and in some species to the gallbladder. AAO:0011020 EMAPA:35172 FMA:14665 Hollow tree organ, the organ parts of which consist of the bile ducts.[AAO] The path in many species is as follows: Bile canaliculi -> Canals of Hering (intralobar bile duct) -> interlobular bile ducts -> intrahepatic bile ducts -> left and right hepatic ducts merge to form -> common hepatic duct *exits liver* and joins -> cystic duct (from gall bladder) forming -> common bile duct -> joins with pancreatic duct -> forming ampulla of Vater -> enters duodenum [WP] UBERON:0001173 UMLS:C0005423 XAO:0000455 biliary tract uberon common bile duct Digestive system duct that collects bile from the hepatic bile duct and the cystic duct.[TAO] EHDAA2:0000303 EHDAA:3981 EMAPA:17201 FMA:14667 GAID:282 MA:0001631 MESH:D003135 TAO:0005165 The duct formed by the union of the common hepatic and cystic ducts. [Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier, adapted_from_Dorian_AF][VHOG] UBERON:0001174 UMLS:C0009437 VHOG:0000214 ZFA:0005165 ductus choledochus ductus choledochus (biliaris) galen:CommonBileDuct the part of the biliary tree formed by the union of the cystic duct and the common hepatic duct uberon common hepatic duct EMAPA:19101 FMA:14668 GAID:286 MA:0002660 MESH:D006500 Predominantly extrahepatic bile duct which is formed by the junction of the right and left hepatic ducts, which are predominantly intrahepatic, and, in turn, joins the cystic duct to form the common bile duct[GAID]. The common hepatic duct is the duct formed by the convergence of the right hepatic duct (which drains bile from the right functional lobe of the liver) and the left hepatic duct (which drains bile from the left functional lobe of the liver). The common hepatic duct then joins the cystic duct coming from the gallbladder to form the common bile duct[WP]. TODO - MA distinguishes between bile duct, hepatic duct, common bile duct and common hepatic duct. in FMA hepatic duct and common hepatic duct are the same. Common is part of extra-hepatic part The duct which conveys the bile from the liver and unites with the cystic duct to form the common bile duct. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] UBERON:0001175 UMLS:C0019149 VHOG:0000220 ductus hepaticus communis hepatic duct uberon right hepatic duct EHDAA2:0001727 EHDAA:3992 EMAPA:32797 FMA:14669 MA:0001639 The duct that drains bile from the right half of the liver and joins the left hepatic duct to form the common hepatic duct. The duct which drains bile from the right half of the liver and unites with the left hepatic duct to form the common hepatic duct. [adapted_from_http://www.medterms.com/script/main/art.asp?articlekey=26032][VHOG] UBERON:0001176 UMLS:C0227557 VHOG:0000217 ductus hepaticus dexter uberon left hepatic duct EHDAA2:0000941 EHDAA:3990 EMAPA:32795 FMA:14670 MA:0001638 The duct that drains bile from the left half of the liver and joins the right hepatic duct to form the common hepatic duct. The duct which drains bile from the left half of the liver and unites with the right hepatic duct to form the common hepatic duct. [adapted_from_http://www.medterms.com/script/main/art.asp?articlekey=26032][VHOG] UBERON:0001177 UMLS:C0227560 VHOG:0000218 ductus hepaticus sinister uberon hepatic artery An artery that supplies the liver. Artery that supplies blood to the liver.[TAO] BTO:0004307 EMAPA:17859 FMA:14769 GAID:496 MA:0001963 MESH:D006499 OpenCyc:Mx4rvzKtFpwpEbGdrcN5Y29ycA TAO:0005161 UBERON:0001193 UMLS:C0019145 ZFA:0005161 arteria hepatica arteria hepatica propria currently defined in a generic fashion. galen:HepaticArtery uberon mucosa of stomach BTO:0001308 CALOHA:TS-0404 EMAPA:35817 FMA:14907 GAID:321 MA:0002683 MESH:A03.492.766.440 Magenschleimhaut OpenCyc:Mx8NhB4rvcD6KJwpEbGdrcN5Y29ycB4rvmKNOpwpEbGdrcN5Y29ycB4rvVj5FpwpEbGdrcN5Y29ycB4rvVjlqpwpEbGdrcN5Y29ycA The gastric mucosa is the mucous membrane layer of the stomach which contains the glands and the gastric pits. In men it is about 1 mm thick and its surface is smooth, soft, and velvety. It consists of epithelium, lamina propria, and the muscularis mucosae. In its fresh state, it is of a pinkish tinge at the pyloric end and of a red or reddish-brown color over the rest of its surface. In infancy it is of a brighter hue, the vascular redness being more marked. It is thin at the cardiac extremity, but thicker toward the pylorus. During the contracted state of the organ it is thrown into numerous plaits or rugae, which, for the most part, have a longitudinal direction, and are most marked toward the pyloric end of the stomach, and along the greater curvature. These folds are entirely obliterated when the organ becomes distended. When examined with a lens, the inner surface of the mucous membrane presents a peculiar honeycomb appearance from being covered with funnel-like depressions or foveolae of a polygonal or hexagonal form, which vary from 0.12 to 0.25 mm. in diameter. These are the ducts of the gastric glands, and at the bottom of each may be seen one or more minute orifices, the openings of the gland tubes. Gastric glands are simple or branched tubular glands that emerge on the deeper part of the gastric foveola, inside the gastric areas and outlined by the folds of the mucosa. There are three types of glands: cardiac glands (in the proximal part of the stomach), oxyntic glands (the dominating type of gland), and pyloric glands. The cardiac glands mainly contain mucus producing cells. The bottom part of the oxyntic glands is dominated by zymogen (chief) cells that produce pepsinogen (an inactive precursor of the pepsin enzyme). Parietal cells, which secrete hydrochloric acid are scattered in the glands, with most of them in the middle part. The upper part of the glands consist of mucous neck cells; in this part the dividing cells are seen. The pyloric glands contain mucus-secreting cells. Several types of endocrine cells are found in all regions of the gastric mucosa. In the pyloric glands contain gastrin producing cells (G cells); this hormone stimulates acid production from the parietal cells. ECL (enterochromaffine-like) cells, found in the oxyntic glands release histamine, which also is a powerful stimulant of the acid secretion. The A cells produce glucagon, which mobilizes the hepatic glycogen, and the enterochromaffin cells that produce serotonin, which stimulates the contraction of the smooth muscles. The surface of the mucous membrane is covered by a single layer of columnar epithelium . This epithelium commences very abruptly at the cardiac orifice, where there is a sudden transition from the stratified epithelium of the esophagus. The epithelial lining of the gland ducts is of the same character and is continuous with the general lining of the stomach. [WP,unvetted][Wikipedia:Gastric_mucosa]. The mucosal layer that lines the stomach. UBERON:0001199 UMLS:C0017136 galen:GastricMucosa gastric mucosa gastric mucous membrane mucosa of organ of stomach mucosa of organ of ventriculus mucosa of ventriculus mucous membrane of stomach mucous membrane of ventriculus organ mucosa of stomach organ mucosa of ventriculus stomach mucosa stomach mucosa of organ stomach mucous membrane stomach organ mucosa tunica mucosa (gaster) tunica mucosa gastricae tunica mucosa gastris uberon ventriculus mucosa ventriculus mucosa of organ ventriculus mucous membrane ventriculus organ mucosa pyloric sphincter (...) the adult Xenopus stomach exhibits both glandular and aglandular regions and a distinct pyloric sphincter similar to that of the amniotic vertebrates (...).[uncertain][VHOG] A strong ring of smooth muscle at the end of the pyloric canal which lets food pass from the stomach to the duodenum. It receives sympathetic innervation from the celiac ganglion[WP]. AAO:0011093 EMAPA:19251 FMA:14916 MA:0002952 OpenCyc:Mx4rvly2ZZwpEbGdrcN5Y29ycA UBERON:0001202 UMLS:C0227238 VHOG:0001466 XAO:0000457 pyloric valve uberon mucosa of small intestine A mucosa that is part of a small intestine [Automatically generated definition]. BTO:0001259 CALOHA:TS-0941 EMAPA:35780 FMA:14933 MA:0002686 UBERON:0001204 UMLS:C0227261 mucosa of organ of small bowel mucosa of organ of small intestine mucosa of small bowel mucous membrane of small bowel mucous membrane of small intestine organ mucosa of small bowel organ mucosa of small intestine small bowel mucosa small bowel mucosa of organ small bowel mucous membrane small bowel organ mucosa small intestinal mucosa small intestine mucosa small intestine mucosa of organ small intestine mucous membrane small intestine organ mucosa tunica mucosa (intestinum tenue) tunica mucosa intestini tenuis uberon renal pelvis A funnel shaped proximal portion of the ureter that is formed by convergence of the major calices [MP]. CALOHA:TS-2230 EMAPA:17948 FMA:15575 GAID:426 In this ontology, the renal pelvis is represented as the area of part-overlap between the kidney and the ureter MA:0000374 MESH:D007682 UBERON:0001224 UMLS:C0227666 galen:RenalPelvis kidney pelvis p. renallis pelvis of ureter pyelum uberon intestinal mucosa BTO:0000642 EMAPA:35440 FMA:15695 GAID:296 MA:0001537 MESH:A03.492.411.369 The innermost membrane of the four coats of the intestinal wall, the other three being the submucosa, muscular layers, and serosa. (Berk et al., Gastroenterology, 4th ed, v.3, p1479) UBERON:0001242 UMLS:C0021839 bowel mucosa bowel mucosa of organ bowel mucous membrane bowel organ mucosa intestine mucosa intestine mucosa of organ intestine mucous membrane intestine organ mucosa mucosa of bowel mucosa of intestine mucosa of organ of bowel mucosa of organ of intestine mucous membrane of bowel mucous membrane of intestine organ mucosa of bowel organ mucosa of intestine tunica mucosa intestini uberon anus BTO:0001680 CALOHA:TS-2005 EV:0100082 FBbt:00003148 FMA:15711 GAID:312 In the lungfish, sharks and rays the rectum opens into the cloaca which also receives wastes (urine) from the kidneys and material from the reproductive organs. In bony fish the rectum reaches the outside environment through the anus, which is normally situated just in front the urinary and reproductive openings. However in some fish the digestive tract may be curled back on itself, and in the Electric Eel (Electrophorus electricus) the anus is situated in the fish's throat. -- http://www.earthlife.net/fish/digestion.html MA:0000331 MESH:A03.492.411.495.767.288 OpenCyc:Mx4rvVjaEZwpEbGdrcN5Y29ycA Orifice at the opposite end of an animal's digestive tract from the mouth. Its function is to expel feces, unwanted semi-solid matter produced during digestion, which, depending on the type of animal, may be one or more of: matter which the animal cannot digest, such as bones; food material after all the nutrients have been extracted, for example cellulose or lignin; ingested matter which would be toxic if it remained in the digestive tract; and dead or excess gut bacteria and other endosymbionts. TADS:0000066 TGMA:0001279 UBERON:0001245 UMLS:C0003461 WBbt:0005364 anal anal opening anal orifice galen:Anus opening of terminal part of digestive tract proctodeum uberon interlobular bile duct FMA:15767 MA:0002668 The canals that carry bile in the liver between the intralobular ducts and the biliary ductules; interlobular bile ducts are part of the interlobular portal triad. UBERON:0001246 UMLS:C0227515 interlobular ductule uberon urinary bladder A saccular organ in which urine accumulates before discharge from the body. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-29, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG] AAO:0000623 Anatomical structure which consists of a membranous sac used to temporarily store urine until it is excreted from the body.[AAO] BTO:0001418 CALOHA:TS-1090 EFO:0000290 EHDAA2:0000174 EHDAA:9328 EMAPA:18321 EV:0100098 FMA:15900 GAID:0000004 In tetrapods, the urinary bladder arises as an outpocketing of the cloaca. (...) The tetrapod urinary bladder appears first among amphibians and is present in Sphenodon, turtles, most lizards, ostriches among birds, and all mammals.[well established][VHOG] MA:0000380 MAT:0000122 MESH:A05.810.161 MIAA:0000122 OpenCyc:Mx4rvVjMmZwpEbGdrcN5Y29ycA The urinary bladder evolved in tetrapods. Birds to not possess a true urinary bladder, although Palaeognathae have an undifferentiated cloacal outpocketing that serves a similar function[https://github.com/obophenotype/uberon/issues/454] UBERON:0001255 UMLS:C0005682 VHOG:0000740 XAO:0000154 bladder distensible musculomembranous organ situated in the anterior part of the pelvic cavity in which urine collects before excretion[MP]. galen:UrinaryBladder uberon urocyst vesica vesica urinaria vesical wall of intestine An anatomical wall that is part of a intestine [Automatically generated definition]. BTO:0000647 EMAPA:35181 EMAPA:35444 FMA:15949 MA:0001525 MA:0002693 UBERON:0001262 UMLS:C1708548 anatomical wall of bowel anatomical wall of intestine bowel anatomical wall bowel wall bowel wall intestinal wall intestine anatomical wall intestine wall uberon wall of bowel we place two MA classes here due to the official ncit2ma mapping to intestinal wall tissue; not clear how bowel and intestine are different pancreatic acinus EMAPA:35651 FMA:16011 MA:0002417 The secretory units of the exocrine pancreas, where fluid containing digestive enzymes is produced; consists of a group of secretory cells surrounding a luminal space that connects to the pancreatic duct. UBERON:0001263 UMLS:C0227578 acinus pancreaticus pancreas acinus pancreatic acinar pancreatic acini uberon pancreas AAO:0010112 An endoderm derived structure that produces precursors of digestive enzymes and blood glucose regulating enzymes[GO]. As a secretory organ serving exocrine and endocrine functions, the pancreas is specific to the vertebrates[PMID:16417468] Hagfishes and lampreys are unique in the complete separation of their endocrine pancreas (islet or- gan) and their exocrine pancreas (50). The endocrine and exocrine pancreas are coassociated in crown gnathostomes (50). In Branchiostoma and Ciona, there is no diverticulum as there is in hagfishes, lampreys, and gnathostomes, only dispersed insulin-secreting cells in the walls of the gastrointestinal tract (51, 52) BTO:0000988 CALOHA:TS-0736 EFO:0000855 EHDAA2:0001367 EHDAA:6893 EMAPA:17503 EV:0100092 FMA:7198 GAID:334 In the hagfish and lampreys (our most primitive vertebrate species of today), the first sign of 'a new organ' is found as collections of endocrine cells around the area of the bile duct connection with the duodenum. These endocrine organs are composed of 99% beta cells and 1% somatostatin-producing delta cells. Compared to the more primitive protochordates (e.g. amphioxus), this represents a stage where all previously scattered insulin-producing cells of the intestinal tissue have now quantitatively migrated to found a new organ involved in sensing blood glucose rather than gut glucose. Only later in evolution, the beta cells are joined by exocrine tissue and alpha cells (exemplified by the rat-, rabbit- and elephant-fishes). Finally, from sharks and onwards in evolution, we have the islet PP-cell entering to complete the pancreas.[well established][VHOG] MA:0000120 MAT:0000075 MESH:D010179 MIAA:0000075 OpenCyc:Mx4rvVimZZwpEbGdrcN5Y29ycA Organ which secretes a fluid containing enzymes that aid in the digestion of food.[AAO] TAO:0000140 The mature pancreas of higher vertebrates and mammals comprises two major functional units: the exocrine pancreas, which is responsible for the production of digestive enzymes to be secreted into the gut lumen, and the endocrine pancreas, which has its role in the synthesis of several hormones with key regulatory functions in food uptake and metabolism. The exocrine portion constitutes the majority of the mass of the pancreas, and contains only two different cell types, the secretory acinar cells and the ductular cells. The endocrine portion, which comprises only 1-2% of the total mass, contains five different cell types, which are organized into mixed functional assemblies referred to as the islets of Langerhans The zebrafish does not have a discrete pancreas. Exocrine pancreatic tissue can be found scattered along the intestinal tract. The acinar structure of the exocrine pancreas is very similar to that of mammals and comprises cells with a very dark, basophilic cytoplasm UBERON:0001264 UMLS:C0030274 VHOG:0000050 XAO:0000136 ZFA:0000140 galen:Pancreas pancreatic uberon pelvic girdle region FMA:16581 Subdivision of lower limb or fin which links the limb/fin to the body[FMA,modified]. There is only one instance of the pelvic girdle region per organism.[VSAO] The organism subdivision that includes the pelvic girdle skeleton and associated soft tissue. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). Examples: There are only two instances in an organism, right and left pectoral girdle regions. UBERON:0001271 UMLS:C0684083 VSAO:0000304 girdle - pelvic pelvic girdle this class describes the subdivision of the limb/fin, NOT the skeleton within. See also: skeleton of pectoral girdle (UBERON:0007831). See also comments on obo-anatomy mail list. Note that even though the class includes soft tissue it is more restrictive than 'pelvis' which also includes structures in cavities etc. TODO this needs to be better documented uberon epithelium of stomach BTO:0000500 CALOHA:TS-2068 EHDAA2:0001918 EMAPA:17023 FMA:17091 MA:0001610 The epithelial layer of the stomach . UBERON:0001276 VHOG:0001433 epithelial tissue of stomach epithelial tissue of ventriculus epithelium of ventriculus gastric epithelium in FMA this is classified as simple columnar, MA divides this into squamous and glandular stomach epithelial tissue stomach epithelium uberon ventriculus epithelial tissue ventriculus epithelium portal triad A multi-organ-part structure that consists of three vessels of the portal lobule including the bile duct, a terminal branch of the hepatic artery and portal vein, and may also include a lymphatic vessel FMA:17523 MA:0002499 The misnomer 'portal triad' traditionally has included only the first three structures, and was named before lymphatic vessels were discovered in the structure. It can refer both to the largest branch of each of these vessels running inside the hepatoduodenal ligament, and to the smaller branches of these vessels inside the liver. UBERON:0001279 UMLS:C0227514 trias hepatica trias hepatica uberon liver parenchyma AAO:0010405 EHDAA2:0001004 EHDAA:2201 EMAPA:17203 FMA:17540 MA:0000366 The functional units of the liver including the lobules. UBERON:0001280 UBERON:0003223 VHOG:0000539 XAO:0000454 hepatic parenchyma hepatic parenchyme liver parenchyme parenchyma of liver the (liver) tubular structure (dual layered parenchyma) appears to be conserved among all embryonic vertebrates (...) it is not unlikely that all vertebrate livers share the same fundamental functional unit.[well established][VHOG] uberon intralobular bile duct FMA:17545 MA:0002669 Note that this is part of the intrahepatic bile duct in MA, as this class is more alike the tree in FMA. Note also that SCT has canal of Hering and Entire IBduct as the only sibling terms under 'Structure of intralobular bile duct' (i.e. the CoH is the only part of the entire IBduct) UBERON:0001282 UMLS:C0227517 canal of Hering canal of Herring canals of Hering cholangiole duct of Herring ductus interlobularis bilifer intrahepatic bile ductule the tubules located between the bile canaliculi and interlobular bile ducts near the outer edge of a classic liver lobule uberon anal region Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[uncertain][VHOG] EFO:0000847 EHDAA2:0000122 EHDAA:2931 EMAPA:16831 MA:0000329 MAT:0000042 MIAA:0000042 The anus and surrounding regions. Encompasses both internal and external regions, where present UBERON:0001353 UMLS:C0230120 VHOG:0000395 WBbt:0006919 posterior posterior end of organism uberon skeletal system AAO:0000566 Anatomical system consisting of multiple elements and tissues that provides physical support.[TAO] Anatomical system that is a multi-element, multi-tissue anatomical cluster that consists of the skeleton and the articular system. Anatomical system that is a multi-element, multi-tissue anatomical cluster that consists of the skeleton and the articular system.[VSAO] BTO:0001486 By taking a holistic approach, integration of the evidence from molecular and developmental features of model organisms, the phylogenetic distribution in the 'new animal phylogeny' and the earliest fossilized remains of mineralized animal skeletons suggests independent origins of the skeleton at the phylum level.[debated][VHOG] CALOHA:TS-1320 EFO:0000806 EHDAA2:0003168 EMAPA:35773 FMA:23881 GO defines skeletal system very generically: The skeleton is the bony framework of the body in vertebrates (endoskeleton) or the hard outer envelope of insects (exoskeleton or dermoskeleton) GO:0001501; however, all annotations are to vertebrates MA:0000018 OpenCyc:Mx4rvVi1rpwpEbGdrcN5Y29ycA Skelettsystem System that provides physical support to the organism.[AAO] TAO:0000434 UBERON:0001434 UMLS:C0037253 VHOG:0001254 VSAO:0000027 XAO:0003060 ZFA:0000434 https://github.com/obophenotype/uberon/wiki/The-skeletal-system set of all bones and joints skeletal skeleton system uberon hindlimb skeleton AAO:0000217 EHDAA2:0002226 EMAPA:32633 FMA:24144 Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG] OpenCyc:Mx4rvZcKkZwpEbGdrcN5Y29ycA Skeletal structure of the paired, posterior appendages.[AAO] Subdivision of skeleton consisting of all skeletal elements in an hindlimb region. TOOD - find a home for: FMA:24140 UBERON:0001441 VHOG:0001255 VSAO:0000152 XAO:0003062 bones of lower limb free lower limb skeleton hind limb skeleton hind-limb skeleton hindlimb skeleton lower limb skeleton ossa membri inferioris relationship type change: differentiates_from lateral plate mesoderm (AAO:0010574) CHANGED TO: develops_from lateral plate mesoderm (UBERON:0003081)[AAO] set of bones of lower limb skeleton of free lower limb skeleton of lower limb uberon chest BTO:0001368 CALOHA:TS-1039 EFO:0000965 EV:0100010 FMA:24216 present in FMA1, but gone in subsequent versions FMA:9576 GAID:91 MA:0000031 MAT:0000295 MESH:A01.911 MIAA:0000295 OpenCyc:Mx4rvVikFZwpEbGdrcN5Y29ycA Subdivision of trunk proper, which is demarcated from the neck by the plane of the superior thoracic aperture and from the abdomen internally by the inferior surface of the diaphragm and externally by the costal margin and associated with the thoracic vertebral column and ribcage and from the back of the thorax by the external surface of the posterolateral part of the rib cage, the anterior surface of the thoracic vertebral column and the posterior axillary lines; together with the abdomen and the perineum, it constitutes the trunk proper[FMA]. UBERON:0001443 UMLS:C0817096 UMLS:C1527391 anterolateral part of thorax front of thorax galen:Chest galen:Thorax pectoral pectus thoracic thoracic body wall thorax uberon ventral part of thoracic region subdivision of head FMA:24218 UBERON:0001444 XAO:0000040 head region head subdivision region of head uberon skeleton of pes EHDAA2:0002228 FMA:24222 Subdivision of skeleton that is the collection of all skeletal elements in a pes, which is the distal section of the posterior hindlimb skeleton consisting of the mesopodium, the metapodium and the acropodium (e.g. including the ankle, sole, and toes)[Phenoscape]. UBERON:0001445 VSAO:0005021 foot region skeleton foot skeleton here 'pes' includes both the ankle region, metatarsals and acropodial region https://github.com/obophenotype/uberon/wiki/Skeleton-partonomy-Design-Pattern pedal skeleton pes pes skeleton posterior autopodium posterior autopodium skeleton set of bones of foot skeleton of foot uberon face A subdivision of the head that has as parts the layers deep to the surface of the anterior surface, including the mouth, eyes, and nose (when present). In vertebrates, this includes the facial skeleton and structures superficial to the facial skeleton (cheeks, mouth, eyeballs, skin of face, etc). BTO:0003369 CALOHA:TS-2216 EMAPA:32763 FMA:24728 GAID:64 HAO:0000316 MA:0002473 MESH:D005145 OpenCyc:Mx4rvVi5GZwpEbGdrcN5Y29ycA Subdivision of head which consists of the viscerocranium and all layers superficial to it. Examples: There is only one face. The area that extends from the median ocellus to the oral foramen[HAO]. The face develops from outward growth of tissue located rostral to the cranium & pharynx. The lower jaw and most of the upper jaw are formed by growth of the first pharyngeal (branchial) arch. The upper incisor region and the nose and forehead (frontal region) are formed from tissue located rostral to the neural tube (frontonasal prominence) UBERON:0001456 UMLS:C0015450 facia/facies facial galen:Face uberon visage hip BTO:0001457 CALOHA:TS-2226 EFO:0001929 EHDAA2:0000783 EHDAA:5153 EHDAA:6178 EMAPA:17490 FMA:24964 GAID:47 MA:0000045 MESH:D006615 OpenCyc:Mx4rvVjhy5wpEbGdrcN5Y29ycA See notes for shoulder. in BTO this is part of the abdomen - this creates an inconsistency if limb and abdomen are spatially disjoint The hip region is located lateral to the gluteal region (i.e. the buttock), inferior to the iliac crest, and overlying the greater trochanter of the thigh bone. In adults, three of the bones of the pelvis have fused into the hip bone which forms part of the hip region. The hip joint, scientifically referred to as the acetabulofemoral joint (art. coxae), is the joint between the femur and acetabulum of the pelvis and its primary function is to support the weight of the body in both static (e.g. standing) and dynamic (e.g. walking or running) postures. [WP,modified]. The pelvic girdle is never joined by contributions of dermal bone. From its first appearance in placoderms, the pelvic girdle is exclusively endoskeletal. It arose from pterygiophores, perhaps several times, in support of the fin.[well established][VHOG] UBERON:0001464 UMLS:C0019552 VHOG:0000346 coxa coxal galen:Hip hip region regio coxae uberon bone element AAO:0000047 AEO:0000082 Also called osseous tissue, (Latin: os). Is a type of hard endoskeletal connective tissue found in many vertebrate animals. Bone is the main tissue of body organs that support body structures, protect internal organs, (in conjunction with muscles) facilitate movement; and are involved with cell formation, calcium metabolism, and mineral storage.[AAO] BTO:0000140 CALOHA:TS-0088 EFO:0000298 EHDAA2:0003082 EMAPA:32782 ENVO:00002039 EV:0100140 FMA:30317 FMA:5018 GAID:92 MA:0001459 MAT:0000299 MIAA:0000299 OpenCyc:Mx4rvViDlpwpEbGdrcN5Y29ycA OpenCyc:Mx4rvVkCG5wpEbGdrcN5Y29ycA Portion of tissue which is calcified connective tissue making up the structural elements of the skeletal system.[TAO] Skeletal element that is composed of bone tissue. Skeletal element that is composed of bone tissue.[VSAO] TAO:0001514 The 'new animal phylogeny' reveals that many of the groups known to biomineralize sit among close relatives that do not, and it favours an interpretation of convergent or parallel evolution for biomineralization in animals. (...) Whether this 'biomineralization toolkit'of genes reflects a parallel co-option of a common suite of genes or the inheritance of a skeletogenic gene regulatory network from a biomineralizing common ancestor remains an open debate.[debated][VHOG] UBERON:0001474 UMLS:C0262950 VHOG:0001190 VSAO:0000057 XAO:0000169 ZFA:0001514 bone bone element bone organ bones galen:Bone relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO] uberon articular capsule An articular capsule (or joint capsule) is an envelope surrounding a synovial joint. [WP,unvetted]. FMA:34836 GAID:263 MA:0001519 MESH:D017746 UBERON:0001484 UMLS:C0206207 capsula articularis capsulae articulares check ncita fibrous capsule of joint galen:JointCapsule joint capsule joint fibrous capsule uberon digestive tract A tube extending from the mouth to the anus. AAO:0010023 BILA:0000083 BTO:0000511 BTO:0000545 EHDAA2:0000726 EHDAA:518 EMAPA:16247 FBbt:00003125 FMA also has a term 'gastrointestinal tract', but this includes the liver. FMA:45615 MA:0000917 OpenCyc:Mx4rvVi0GpwpEbGdrcN5Y29ycA TAO:0000112 TGMA:0001819 The alimentary or digestive tract, and associated organs.[TAO] The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG] UBERON:0001555 UMLS:C0017189 VHOG:0000309 WBbt:0005743 ZFA:0000112 alimentary canal alimentary tract digestive canal digestive tube enteric tract galen:AlimentaryTract gut gut tube uberon we following Kardong in naming the entire tube from mouth to anus the alimentary canal. Kardong calls the portion of this tract that excludes buccal cavity and pharynx the 'alimentary canal', consider adding an extra class for this we place the MA and EMAPA class here, although the intent is probably a smaller region. See https://github.com/obophenotype/uberon/issues/509 lower urinary tract FMA:45659 MA:0002636 Subdivision of urinary system which consists of the urinary bladder and the urethra. UBERON:0001556 galen:LowerUrinaryTract uberon upper respiratory tract EHDAA2:0002136 EMAPA:17669 FMA:45661 MA:0000442 OpenCyc:Mx4rtT2HwgJMEdyAAADggVbxzQ Some specify that the glottis (vocal cords) is the defining line between the upper and lower respiratory tracts;[2] yet even others make the line at the cricoid cartilage. The FMA includes nose, nasopharynx, oropharynx and larynx[WP] The segment of the respiratory tract that starts proximally with the nose and ends distally with the cricoid cartilage, before continuing to the trachea. UBERON:0001557 VHOG:0000406 uberon lower respiratory tract EHDAA2:0001036 EMAPA:16738 FMA:45662 MA:0000435 OpenCyc:Mx4rQRqjUgAKEdyHxgDggVfs8g The segment of the respiratory tract that starts proximally with the trachea and includes all distal structures including the lungs[WP,modified] UBERON:0001558 VHOG:0000382 uberon ciliary muscle BTO:0000654 Bowman`s muscles EMAPA:35240 FMA:49151 MA:0001269 The ciliary muscle is a ring of smooth muscle in the middle layer of the eye that controls the eye's accommodation for viewing objects at varying distances and regulates the flow of aqueous humour through Schlemm's canal. [WP,unvetted]. UBERON:0001605 UMLS:C0559230 ciliaris musculus ciliaris musculus ciliarus uberon coronary artery An artery that supplies the myocardium. BTO:0000290 CALOHA:TS-0176 EFO:0002551 EMAPA:19160 EMAPA:25968 EV:0100383 FMA:49893 MA:0002453 OpenCyc:Mx4rvoL56ZwpEbGdrcN5Y29ycA UBERON:0001621 UMLS:C0205042 VHOG:0001557 ZFA:0005812 coronary arterial tree coronary vessel galen:CoronaryArtery uberon muscle organ AAO:0011066 EMAPA:32715 EV:0100146 FMA:5022 GAID:131 It seems clear that the metazoan ancestor inherited from its unicellular descendants an actin cytoskeleton and motor-proteins of the myosin superfamily. Within metazoans, these two molecules were arranged into effective contractile units, the muscles. The basic trends for muscle evolution are already expressed in the diploblastic taxa.[well established][VHOG] MA:0000015 OpenCyc:Mx4rv2kf-5wpEbGdrcN5Y29ycA Organ consisting of a tissue made up of various elongated cells that are specialized to contract and thus to produce movement and mechanical work[GO]. Portion of tissue composed of contractile fibers.[TAO] TAO:0005145 UBERON:0001630 VHOG:0001245 XAO:0000172 ZFA:0005145 galen:Muscle muscle muscular uberon artery AAO:0010211 AEO:0000208 An epithelial tube or tree of tibes that transports blood away from the heart[modified from AEO definition]. BTO:0000573 CALOHA:TS-0054 EFO:0000814 EHDAA2:0000143 EHDAA2:0003253 EMAPA:35147 EV:0100026 FMA:50720 GAID:468 MA:0000064 MAT:0000034 MESH:D001158 MIAA:0000034 Note that in FMA an artery is a tree, whereas AEO/JB defines it as a tube; FMA includes a separate class for what it calls the trunk. Classification in this ontology may currently (Jan 2012) represent a mix of both schemes, although we are gradually revising in the direction of the AEO scheme. OpenCyc:Mx4rvVjknZwpEbGdrcN5Y29ycA Part of the circulatory system composed of blood vessels which carry oxygenated blood away from the heart to the rest of the body.[AAO] TAO:0000005 The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] UBERON:0001637 UMLS:C0003842 VHOG:0001251 XAO:0000114 ZFA:0000005 arterial arterial subtree arterial system arterial tree organ part arterial vessel arteries galen:Artery uberon vein AAO:0010212 AEO:0000209 Any of the tubular branching vessels that carry blood from the capillaries toward the heart. BTO:0000234 CALOHA:TS-1108 EFO:0000816 EHDAA2:0003254 EMAPA:35906 EV:0100031 FMA:50723 GAID:492 MA:0000067 MAT:0000037 MESH:D014680 MIAA:0000037 OpenCyc:Mx4rvVjkWpwpEbGdrcN5Y29ycA Part of the circulatory system composed of blood vessels which carry blood from other organs, tissues, and cells to the heart.[AAO] TAO:0000082 TODO - check with MA - vein vs venous blood vessel The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] UBERON:0001638 UMLS:C0042449 VHOG:0001743 XAO:0000115 ZFA:0000082 galen:Vein uberon vascular element vena venae venous subtree venous tree organ part venous vessel ear AAO:0011014 BTO:0000368 Both vertebrate and invertebrate auditory organs are thought to have evolved from primitive mechanosensors, but the nature of the ancestral structure and the evolutionary trajectories followed in distinct animal lineages remain unknown. In particular, we do not know how many types of mechanosensor existed in the protostome-deuterostome ancestor from which insects and vertebrates evolved or whether the PDA had an auditory organ.[well established][VHOG] CALOHA:TS-1165 EFO:0000826 EHDAA2:0000423 EHDAA:502 EMAPA:16193 EV:0100353 FMA:52780 GAID:62 MA:0000236 MAT:0000138 MESH:D004423 MIAA:0000138 OpenCyc:Mx4rvViXS5wpEbGdrcN5Y29ycA OpenCyc:Mx4rvVjL05wpEbGdrcN5Y29ycA Sense organ in vertebrates that is specialized for the detection of sound, and the maintenance of balance. Includes the outer ear and middle ear, which collect and transmit sound waves; and the inner ear, which contains the organs of balance and (except in fish) hearing. Also includes the pinna, the visible part of the outer ear, present in some mammals. The organ of hearing and of equilibrium. [TFD][VHOG] UBERON:0001690 UMLS:C0013443 UMLS:C0521421 VHOG:0000330 XAO:0000189 auditory apparatus auricular auris galen:Ear uberon nail A horn-like keratin structure covering the dorsal aspect of the terminal phalanges of fingers and toes[WP]. A primate's nail consists of the unguis alone; the subunguis has disappeared BTO:0001719 CALOHA:TS-2034 EFO:0000956 EMAPA:35580 EV:0100159 FMA:54326 GAID:1320 MA:0002703 MAT:0000158 MESH:D009262 MIAA:0000158 OpenCyc:Mx4rvVjJv5wpEbGdrcN5Y29ycA The nails of humans and the claws are moth are highly similar. Both species have a proximal nail fold, cuticle, nail matrix, nail bed, nail plate, and hyponychium. Distinguishing features are the shape of the nail and the presence of an extended hyponychium in the mouse [PMC3579226] UBERON:0001705 UMLS:C0027342 Use this class for both the nails of primates and the homologous claws of mammals such as mouse. VHOG:0001361 XAO:0003103 claw galen:Nail nail/claw talon uberon eyelid A fold of skin that covers and protects part of the eyeball. Examples: upper eyelid, lower eyelid, nictitating membrane BTO:0002241 Consider adding 'eye surface', like MA EHDAA2:0000487 EHDAA:9037 EMAPA:17829 EV:0100338 FMA divides this into skin, fascia, conjunctiva FMA:54437 GAID:72 In humans the upper and lower eyelid consists of the following layers, starting anteriorly: (1) skin, (2) a layer of subcutaneous connective tissue, (3) a layer of striated muscle fibres of the orbicularis muscle, (4) a layer of submuscular connective tissue, (5) a fibrous layer, including the tarsal plates, (6) a layer of smooth muscle, (7) the palpebral conjunctiva. MA:0000268 MESH:D005143 OpenCyc:Mx4rvVi4m5wpEbGdrcN5Y29ycA UBERON:0001711 UMLS:C0015426 VHOG:0000016 blephara blepharic blepharon eye lid palpebra palpebrae palpebral uberon cranial ganglion BTO:0000106 EFO:0000902 EMAPA:16659 FMA:54502 Ganglion which is located in the head.[TAO] MA:0000213 MA:0000214 MAT:0000200 MIAA:0000200 TAO:0000013 UBERON:0001714 UBERON:0003213 UBERON:0026601 VHOG:0000076 XAO:0000027 ZFA:0000013 cranial ganglia cranial ganglion cranial ganglion part of peripheral nervous system cranial ganglion/nerve cranial nerve ganglion cranial neural ganglion cranial neural tree organ ganglion ganglion of cranial nerve ganglion of cranial neural tree organ head ganglion presumptive cranial ganglia the groups of nerve cell bodies associated with the twelve cranial nerves uberon larynx (In anura) a dorsal pair of arytenoid cartilages (...), which support vocal cords, and a ventral pair (often fused) of cricoid cartilage (...). These cartilages are regarded as derivatives of posterior visceral arches of ancestors. Together they constitute the larynx, a structure characteristic of tetrapods. (...) (In mammals) Paired arytenoid cartilages help support and control the vocal cords. The cricoid cartilage is single. Two additional cartilages are present that are lacking in other vertebrates: a large ventral thyroid cartilage (...) and a cartilage in the epiglottis.[well established][VHOG] A continuation of the pharynx that is involved in breathing, sound production, and protecting the trachea against food aspiration. AAO:0000268 An anatomical cluster consisting of the epiglottus, the arytenoid cartilages, the thyroid cartilage, the cricoid cartilage and the muscles, membranes, and ligaments connecting them, and also of the mucosal covering these structures.[FEED] Anatomical structure consisting of a narrowly triangular chamber supported by a series of semicircular cartilages in which part of the sound-production system is located.[AAO] BTO:0001208 CALOHA:TS-0532 EFO:0000838 EHDAA2:0004063 EMAPA:18333 EV:0100039 FMA:55097 GAID:108 Kehlkopf@ge MA:0000414 MAT:0000187 MESH:D007830 MIAA:0000187 OpenCyc:Mx4rvViOnZwpEbGdrcN5Y29ycA UBERON:0001737 UMLS:C0023078 VHOG:0001279 XAO:0003081 galen:Larynx laryngeal uberon vagus nerve 10n AAO:0010475 BAMS:10n BAMS:Xn BTO:0003472 CN-X Cranial nerve that branches into the lateral (to body sense organs) and the intestino-accessorial (to the skin, muscles of shoulder, hyoid, larynx, gut, lungs, and heart). EFO:0002549 FMA:5731 GAID:721 HBA:9337 MA:0001106 MBA:917 MESH:D014630 Nerve consisting of branchiomotor and visceral efferent fibers which branch and innervate the smooth muscles and glands of the heart, lungs, esophagus, and stomach as well as some throat muscles. Sensory fibers supply mucosa of the mouth and pharynx.[AAO] OpenCyc:Mx4rviHk2ZwpEbGdrcN5Y29ycA TAO:0000453 UBERON:0001759 UMLS:C0042276 UMLS:C1305910 VHOG:0000737 Vagus nerve [X] We conclude this section by listing some of the many synapomorphies of craniates, including (...) (5) cranial nerves (...) (reference 1); Phylogenetically, the cranial nerves are thought to have evolved from dorsal and ventral nerves of a few anterior spinal nerves that became incorporated into the braincase. Dorsal and ventral nerves fuse in the trunk but not in the head, and they produce two series: dorsal cranial nerves (V, VII, IX, and X) and ventral cranial nerves (III, IV, VI, and XIII) (reference 2).[well established][VHOG] XAO:0003097 ZFA:0000453 cranial nerve X galen:VagusNerve http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=702 nerve X nervus vagus nervus vagus [x] pneuomgastric nerve tenth cranial nerve uberon vagal nerve vagus vagus X nerve vagus nerve or its root vagus nerve tree uvea CALOHA:TS-2228 EMAPA:35901 FMA:58103 GAID:912 MA:0002480 MESH:D014602 TODO - check child terms, isa vs partof. See also MA:0001284 ! tunica vasculosa plexus UBERON:0001768 UMLS:C0042160 pars iridica retinae the pigmented middle of the three concentric layers that make up an eye, consisting of the iris, ciliary body and choroid[WP,edited]. tunica vasculatis oculi tunica vasculosa bulbi tunica vasculosa of eyeball uberon uvea uveal uveal tract vascular layer of eyeball iris AAO:0010347 BTO:0000653 CALOHA:TS-0491 EFO:0004245 EMAPA:19154 EV:0100345 FMA:58235 GAID:917 MA:0000273 MESH:D007498 OpenCyc:Mx4rvVjbppwpEbGdrcN5Y29ycA TAO:0001238 The avian iris and ciliary body undergoes a transition from smooth-to-striated muscle during embryonic development [doi:dx.doi.org/10.1006/dbio.1998.9019] The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG] The opaque muscular contractile diaphragm suspended in the aqueous humour in front of the lens of the eye. The organ is perforated by the pupil and continues peripherally with the ciliary body. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] UBERON:0001769 UMLS:C0022077 VHOG:0000101 XAO:0000185 ZFA:0001238 anterior uvea irides iridial irises the adjustable membrane, composed of the stroma and pigmented epithelium, located just in front of the crystalline lens within the eye uberon corneal epithelium BTO:0000287 CALOHA:TS-0173 EFO:0001917 EHDAA2:0000319 EMAPA:17162 FMA:58263 GAID:895 In Humans: It consists of several layers of cells. The cells of the deepest layer are columnar; then follow two or three layers of polyhedral cells, the majority of which are prickle cells similar to those found in the stratum mucosum of the cuticle. Lastly, there are three or four layers of squamous cells, with flattened nuclei In zebrafish: nonpigmented, stratified squamous nonkeratinizing epithelial cells, attached to a thick basement membrane that is considered to be analogous to the Bowman's membrane in mammals MA:0001243 MESH:D019573 Portion of tissue comprised of four to six layers of nonkeratinized, stratified squamous cells and represents approximately 60% of the thickness of the cornea.[TAO] TAO:0002187 UBERON:0001772 UMLS:C0459875 ZFA:0001683 anterior corneal epithelium anterior endothelium of cornea cornea epithelial tissue cornea epithelium e. anterius corneae endothelium anterius corneae endothelium camerae anterioris bulbi endothelium corneale epithelial tissue of cornea epithelium anterius (cornea) epithelium anterius corneae epithelium corneæ anterior layer epithelium of cornea epithelium posterius corneae external epithelium of cornea the smooth stratified squamous epithelium that covers the outer surface of the cornea uberon sclera AAO:0010354 BTO:0001606 Disease notes: implicated in rheumatoid arthritis. EMAPA:19027 EV:0100342 FMA:58269 GAID:911 MA:0000280 MESH:D012590 Majority derives from NC that surrounds optic cup of neurectoderm; a small temporal portion develops from the mesoderm that contributes to striated extra-ocular muscles and vascular endothelia[Rada&Johnson]. Opaque fibrous outer layer of the eyeball[ZFA,Kardong,WP]. OpenCyc:Mx4rv7yR55wpEbGdrcN5Y29ycA Seko et al demonstrate chondrogenic potential and identify this as connective tissue[doi:10.1371/journal.pone.0003709]. The sclera, also known as the white part of the eye, is the opaque (usually white, though certain animals, such as horses and lizards, can have black sclera), fibrous, protective, outer layer of the eye containing collagen and elastic fiber. It is derived from the neural crest. In children, it is thinner and shows some of the underlying pigment, appearing slightly blue. In the elderly, however, fatty deposits on the sclera can make it appear slightly yellow. The sclera forms the posterior five sixths of the connective tissue coat of the globe. It is continuous with the dura mater and the cornea, and maintains the shape of the globe, offering resistance to internal and external forces, and provides an attachment for the extraocular muscle insertions. The sclera is perforated by plenty of nerves and vessels passing through the posterior scleral foramen, the hole that is formed by the optic nerve. At the optic disk the outer two-thirds of the sclera continues with the dura mater (outer coat of the brain) via the dural sheath of the optic nerve. The inner third joins with some choroidal tissue to form a plate (lamina cribrosa) across the optic nerve with perforations through which the optic fibers (fasciculi). The thickness of the sclera varies from 1mm at the posterior pole to 0.3 mm just behind the rectus muscle insertions. The sclera's blood vessels are mainly on the surface, and together with the conjunctiva (which lies on top) This is a thin layer covering the sclera. Along with the vessels of the conjunctiva, those of the sclera renders the inflamed eye bright red. [WP,unvetted][Wikipedia:Sclera]. The tough, usually white, outer coat of the eyeball, covering all the posterior surface and continuous anteriorly with the cornea. [TFD][VHOG] UBERON:0001773 UMLS:C0036410 VHOG:0001274 XAO:0000183 ZFA:0005563 continuous with the dura mater and the cornea; The sclera forms the posterior five-sixths of the connective tissue coat of the globe. in fish, reptiles and monotremes the connective tissue of the sclera is skeletal scleral scleral capsule uberon ciliary body AAO:0010341 BTO:0000260 CALOHA:TS-0694 EMAPA:19065 EV:0100346 FMA:58295 GAID:916 MA:0000264 MESH:D002924 The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG] UBERON:0001775 UMLS:C0008779 VHOG:0000102 XAO:0000186 anterior uvea ciliary bodies corpus ciliare ocular ciliary body the thickened portion of the vascular tunic, which lies between the choroid and the iris, composed of ciliary muscle and ciliary processes uberon optic choroid BTO:0001829 CALOHA:TS-2054 EMAPA:19077 EV:0100347 FMA:58298 GAID:913 MA:0000263 MESH:D002829 MP treats posterior uvea and optic choroid as distinct TAO:0005229 UBERON:0001776 UMLS:C0008520 VHOG:0001568 ZFA:0005229 check choroid vs choroid layer; check ZFA/TAO placement - no homology assertion in VHOG. Note this is entirely in the posterior region of eyeball in ZFA chorioid choroid choroid coat choroidal choroidea choroidea eye choroid optic choroid posterior uvea uberon vascular layer containing connective tissue, of the eye lying between the retina and the sclera. The choroid provides oxygen and nourishment to the outer layers of the retina. Along with the ciliary body and iris, the choroid forms the uveal tract[WP]. spinal nerve AAO:0011101 Any of the paired nerves emerging from the spinal cord, each attached to the cord by two roots: ventral and dorsal, and passing out between the vertebrae. [TFD][VHOG] BAMS:spin BTO:0000870 EHDAA2:0001898 EMAPA:16989 FMA:5858 GAID:841 MA:0000233 MESH:D013127 OpenCyc:Mx4rwK_iFJwpEbGdrcN5Y29ycA UBERON:0001780 UMLS:C0037941 VHOG:0000824 XAO:0003101 backbone nerve nerve of backbone nerve of spinal column nerve of spine nerve of vertebral column nervi spinales spinal column nerve spinal nerve tree spinal nerves spine nerve the any of the paired peripheral nerves formed by the union of the dorsal and ventral spinal roots from each spinal cord segment[MP,modified] uberon vertebral column nerve layer of retina AAO:0010353 Any of the layers that make up the retina[MP]. EMAPA:35742 FMA:58617 MA does not treat internal/external limiting memranes as layers - these are classified as laminae. Here we follow other ontologies in grouping with other layers. MA also treats retinal pigment epithelium and neural retina epithelium as distinct from the layers. We follow ontologies such as FMA and ZFA in first dividing into pigmented and neural layers - these are also classified as layers, giving us over the usual 10 layers MA:0001319 UBERON:0001781 UMLS:C0459649 XAO:0000266 retina layer retina neuronal layer retinal layer retinal neuronal layer uberon cranial nerve AAO:0000108 BAMS:cran BTO:0001104 Cranial nerves are nerves that emerge directly from the brain, in contrast to spinal nerves, which emerge from segments of the spinal cord. EHDAA2:0000323 EMAPA:17264 FMA:5865 GAID:802 HBA:9299 MA:0000215 MBA:967 MESH:D003391 OpenCyc:Mx4rvWvJVpwpEbGdrcN5Y29ycA See https://github.com/obophenotype/mouse-anatomy-ontology/issues/6 TAO:0000641 Twelve pairs of cranial nerves exit/enter the cranium through openings in the skull. The nerves contain efferent axons with motor and glandular functions, as well as afferent axons from cranial ganglia with sensory functions. The nerves are numbered in a rostral to caudal sequence, with the exception of the lateral line nerves.[TAO] UBERON:0001785 UMLS:C0010268 UMLS:C1269897 VHOG:0000279 We conclude this section by listing some of the many synapomorphies of craniates, including (...) (5) cranial nerves (...).[well established][VHOG] XAO:0000429 XAO:0003089 ZFA:0000641 classified as neural tree organ, not nerve in FMA. CN II poses a challenge here as it is not strictly a nerve, yet is expected to be classified under CN. cranial nerves cranial neural tree organ nervus cranialis uberon anterior segment of eyeball EMAPA:36594 FMA:58865 MA:0002484 MESH:D000869 UBERON:0001801 UMLS:C0003153 ZFA:0005566 anterior eye segment anterior segment eye anterior segment of eye anterior segment of the eye any of the parts of the eye that lie in front of, or ventral to, the lens (inclusive) eye anterior segment segmentum anterius (bulbus oculi) segmentum anterius bulbi oculi uberon posterior segment of eyeball EMAPA:36595 FMA:58868 MA:0002485 UBERON:0001802 UMLS:C0278450 ZFA:0005567 any of the parts of the eye that lie in back of, or dorsal to, the lens (but not inclusive) eye posterior segment posterior eye segment posterior segment eye posterior segment of eye posterior segment of the eye segmentum posterius (bulbus oculi) segmentum posterius bulbi oculi uberon lip BTO:0001647 CALOHA:TS-0558 EMAPA:32839 FMA:59816 GAID:76 MA:0000343 MESH:D008046 One of the two fleshy folds which surround the opening of the mouth. OpenCyc:Mx4rvVi4U5wpEbGdrcN5Y29ycA Surface structure that is one of the two fleshy folds surrounding the opening of the mouth.[TAO] TAO:0007006 UBERON:0001833 UMLS:C0023759 VHOG:0000677 ZFA:0007006 galen:Lip labia oris labial lips uberon forebrain AAO:0010147 BAMS:FB BAMS:Forebrain BTO:0000478 CALOHA:TS-0380 DHBA:10156 DMBA:15566 EFO:0000909 EHDAA2:0000556 EHDAA:3470 EMAPA:16895 FB FMA:61992 In craniate embryos, neural expression of Distal-less-related genes is exclusively in the forebrain (...). Because the major neural expression domain of amphioxus AmphiDll is in the anterior three-fourths of the cerebral vesicle, we suggest that this region of the neural tube is homologous to parts of the craniate forebrain. This conclusion is strongly supported by three-dimensional, computer-assisted reconstruction of the neural tube of amphioxus based on serial transmission electron microscopy. At the neuroanatomical level, a number of detailed homologies are indicated between the anterior three-fourths of the amphioxus cerebral vesicle and the diencephalic region of the craniate forebrain. If one assumes that the amphioxus condition fairly represents the nervous system of the proximate ancestor of the craniates, one can suggest that they evolved from a creature that had the beginnings of a forebrain.[well established][VHOG] MA:0000170 MAT:0000105 MESH:D016548 MIAA:0000105 Most anterior of the three regions of the brain consisting of the telencephalon and diencephalon.[AAO] TAO:0000109 The most anterior region the brain including both the telencephalon and diencephalon. The most anterior region the brain including both the telencephalon and diencephalon. Kimmel et al, 1995.[TAO] UBERON:0001890 UMLS:C0085140 VHOG:0000383 XAO:0000011 ZFA:0000109 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=27 prosencephalic prosencephalon relationship loss: develops_from forebrain neural tube (TAO:0007041)[TAO] uberon midbrain AAO:0010149 BAMS:MES BM:MB BTO:0000138 CALOHA:TS-0630 DHBA:10648 DMBA:16649 EFO:0000919 EHDAA2:0001162 EHDAA:3694 EMAPA:16974 EV:0100242 FMA:61993 Fine structural, computerized three-dimensional (3D) mapping of cell connectivity in the amphioxus nervous system and comparative molecular genetic studies of amphioxus and tunicates have provided recent insights into the phylogenetic origin of the vertebrate nervous system. The results suggest that several of the genetic mechanisms for establishing and patterning the vertebrate nervous system already operated in the ancestral chordate and that the nerve cord of the proximate invertebrate ancestor of the vertebrates included a diencephalon, midbrain, hindbrain, and spinal cord.[well established][VHOG] HBA:9001 MA:0000207 MAT:0000106 MB MBA:313 MESH:D008636 MIAA:0000106 Middle part of the brain composed of the optic tectum and penducular region.[AAO] OpenCyc:Mx4rvsBUqpwpEbGdrcN5Y29ycA RETIRED_EHDAA2:0001104 TAO:0000128 The brain region between the forebrain anteriorly and the hindbrain posteriorly, including the tectum dorsally and the midbrain tegmentum ventrally. Kimmel et al, 1995.[TAO] The midbrain is the middle division of the three primary divisions of the developing chordate brain or the corresponding part of the adult brain (in vertebrates, includes a ventral part containing the cerebral peduncles and a dorsal tectum containing the corpora quadrigemina and that surrounds the aqueduct of Sylvius connecting the third and fourth ventricles)[GO]. UBERON:0001891 UMLS:C0025462 VHOG:0000069 XAO:0000014 ZFA:0000128 developmental relationships need revised http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=462 mesencephalic mesencephalon part of brainstem in ABA - we reject this in favor of ISBN10:0471888893 which has an implicit overlaps relationships uberon telencephalon AAO:0010479 BAMS:CB BAMS:CH BAMS:IV BAMS:Tel BM:Tel BTO:0000239 CALOHA:TS-1018 DHBA:10158 EFO:0000912 EHDAA2:0001982 EMAPA:16652 EMAPA:16910 EV:0100165 FMA:62000 From an evolutionary standpoint, the telencephalon is the most recent brain structure: the amphioxus does not have this structure as a morphological entity. Overt telencephalon is present in the hagfish and lamprey to receive numerous input fibers from various parts of the CNS, similar to gnathostomes.[well established][VHOG] GAID:621 HBA:4007 In mammals the cortex covers almost the whole of the cerebral hemispheres. In ray-finned fishes the inner surfaces of the lateral and ventral regions of the cerebrum bulge up into the ventricles. In the amniotes, the cerebrum becomes increasingly large and complex. In reptiles, the paleopallium is much larger than in amphibians, and its growth has pushed the basal nuclei into the central regions of the cerebrum. In the most primitive living vertebrates, the hagfishes and lampreys, the cerebrum is a relatively simple structure receiving nerve impulses from the olfactory bulb. MA:0000183 MAT:0000421 MBA:567 MESH:D013687 MIAA:0000421 Organ component of neuraxis that has as its parts the cerebral cortex, cerebral white matter, basal ganglia, septum and fornix, as well as subcortical gray and white matter structures[FMA:62000]. PBA:128011350 Part of the forebrain consisting of paired olfactory bulbs and cerebral hemispheres. Part of the forebrain consisting of paired olfactory bulbs and cerebral hemispheres.[AAO] TAO:0000079 The anterior and dorsal forebrain neuromere, includes the olfactory bulb. Kimmel et al, 1995.[TAO] The cerebrum of birds has evolved along different lines to that of mammals, although they are similarly enlarged, by comparison with reptiles. However, this enlargement is largely due to the basal ganglia, with the other areas remaining relatively primitive in structure. UBERON:0001893 UMLS:C0039452 VHOG:0000283 XAO:0000012 ZFA:0000079 cerebral cerebrum dolphins are the only species (other than humans) to have cerebra accounting for as much as 2 percent of their body weight. endbrain http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=31 relationship loss: develops_from presumptive telencephalon (TAO:0000571)[TAO] supratentorial region telenencephalic uberon metencephalon Anterior part of the hindbrain ventral to the cerebellum[NIFSTD:birnlex_965]. BAMS:Met BTO:0000673 CALOHA:TS-2029 DHBA:10655 EHDAA2:0001149 EHDAA:5498 EMAPA:17071 FMA:62003 GAID:594 HBA:4833 MA:0000197 MESH:D020540 Rostral segment of the hindbrain that has as its parts the pons (where present) and the cerebellum[WP,modified]. The anterior of two brain vesicles formed by specialization of the rhombencephalon in the developing embryo. It gives rise to cerebellum and pons. [TFD][VHOG] The early development of most vertebrate brains is similar (...). The zebrafish neural tube follows the same basic differentiation pattern as the mammalian neural tube (reference 1); The brain develops from three embryonic enlargements of the neural tube, which later differentiate into five regions. A forebrain differentiates into telencephalon and diencephalon. The midbrain, or mesencephalon, remains undivided. The hindbrain divides into the metencephalon and myelencephalon. Cavities within the brain enlarge to form a series of interconnected ventricles (reference 2).[well established][VHOG] UBERON:0001895 UMLS:C0376353 UMLS:C1516904 VHOG:0000741 epencephalon epencephalon-2 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=543 the terms metencephalon and myelencephalon are only meaningful in mammals and birds[Neuroanatomy of the Zebrafish Brain]. In zebrafish, with the exception of the cerebellum, the ventral remainder of the metencephalon can be separated only arbitrarily from the more caudal myelencephalic portion of the medulla oblongata and thus these are not distinguished in ZFA[ZFA]. uberon medulla oblongata AAO:0010486 BAMS:MY BAMS:Md BM:Me BTO:0000041 CALOHA:TS-0607 Classical anatomical studies subdivided the vertebrate rhombencephalon into pons and medulla oblongata. (...) The medulla oblongata appears therefore as a tagma, that is, a group of segmental units (pseudorhombomeres, in this case) sharing some morphological and molecular characteristics, and in some aspects different from the segmental units present in adjoining brain regions, pons and spinal cord.[well established][VHOG] DMBA:17352 EFO:0000924 EHDAA2:0001088 EHDAA:7588 EMAPA:17550 EV:0100275 FMA:62004 GAID:590 MA:0000206 MAT:0000111 MAT:0000367 MBA:354 MESH:D008526 MIAA:0000111 OpenCyc:Mx4rvVjxSJwpEbGdrcN5Y29ycA OpenCyc:Mx4rwCqnXJwpEbGdrcN5Y29ycA Organ component of neuraxis that has as its parts the medullary reticular formation, inferior olivary complex and cochlear nuclear complex, among other structures[FMA]. The medulla oblongata lies directly above the spinal cord and controls vital autonomic functions such as digestion, breathing and the control of heart rate[GO]. Posterior portion of the hindbrain which controls respiration, heartbeat, digestion, and swallowing as well as some locomotor responses.[AAO] TAO:0000545 The posterior region of the brain that is continuous with the spinal cord. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-17, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG] UBERON:0001896 UMLS:C0025148 UMLS:C1269575 VHOG:0000181 XAO:0003100 ZFA:0000545 bulb bulbus http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=698 medulla medulla oblonzata metepencephalon uberon midbrain tegmentum 'tegmentum' is used generically for the ventral part of the brainstem (ISBN10:0471888893). We use the label 'midbrain tegmentum' to denote the midbrain structure. In NIFSTD tegmentum is a composite structure and there is a separate class for midbrain tegmentum and pontine tegmentum BAMS:MTg BTO:0003388 DHBA:12195 EFO:0000921 EHDAA2:0004475 EMAPA:18215 FMA:62393 HBA:9002 MA:0000212 MAT:0000452 MTg TAO:0000160 Together, our results reveal a shared basic organization in the tegmental domains of the diencephalon and midbrain of developing lamprey, indicating early appearance of the domain in vertebrate phylogeny.[well established][VHOG] UBERON:0001943 UMLS:C0039441 VHOG:0001367 Ventral part of the midbrain, separated from the hindbrain by the isthmus[ISBN10:0471888893]. Subdivision of the midbrain lying anterior to the tectum and posterior to the substantia nigra and cerebral peduncle[FMA] The part of the midbrain extending from the substantia nigra to the cerebral aqueduct in a horizontal section of the midbrain. It forms the floor of the midbrain that surrounds the cerebral aqueduct[WP]. XAO:0004271 ZFA:0000160 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=491 mesencephalic tegmentum tegmentum tegmentum mesencephali tegmentum mesencephalicum tegmentum of midbrain uberon blood plasma BTO:0000131 CALOHA:TS-0800 EFO:0001905 EMAPA:35690 FMA:62970 GAID:1178 MA:0002501 MAT:0000052 MESH:D010949 MIAA:0000052 OpenCyc:Mx4rEg4ZYrIbEduAAAAOpmP6tw The liquid component of blood, in which erythrocytes are suspended. UBERON:0001969 UMLS:C0032105 blood plasm plasma portion of blood plasma portion of plasma uberon bile BTO:0000121 CALOHA:TS-1172 ENVO:02000023 FMA:62971 GAID:1157 In many species, bile is stored in the gallbladder and upon eating is discharged into the duodenum. MA:0002513 MESH:D001646 UBERON:0001970 UMLS:C0005388 aids the process of digestion of lipids in the small intestine bile salts function to emulsify dietary fats and facilitate their intestinal absorption elimination of cholesterol fel galen:Bile gall major excretory route for potentially harmful exogenous lipophilic substances many hormones and pheromones are excreted in bile, and contribute to growth and development of the intestine in some species and provide attractants for the weaning of non-human vertebrates protects the organism from enteric infections by excreting immune globulin A (IgA), inflammatory cytokines, and stimulating the innate immune system in the intestine uberon vital aqueous secretion of the liver that is formed by hepatocytes and modified down stream by absorptive and secretory properties of the bile duct epithelium. venule BTO:0002626 EMAPA:35917 FMA:63130 MA:0000071 MESH:A07.231.432.952 Multi-tissue structure part of the blood vasculature formed by the anastomosis of capillaries. Venules carry blood toward the heart.[TAO] One of the minute vessels that collect deoxygenated blood from the capillary plexuses returns it to the veins TAO:0005315 UBERON:0001979 UMLS:C0042520 VHOG:0001765 ZFA:0005315 uberon venula arteriole AAO:0010253 BTO:0001997 EMAPA:35146 FMA:63182 MA:0000063 MESH:D001160 Multi-tissue structure part of the blood vasculature, feeds into capillaries. Arterioles carry blood away from the heart.[TAO] Small, terminal branch of an artery which generally connects to capillaries.[AAO] TAO:0002138 The smallest division of the artery located between the muscular arteries and the capillaries[GO]. UBERON:0001980 UMLS:C0003847 VHOG:0001763 ZFA:0005255 arteriola uberon blood vessel A vessel through which blood circulates in the body. AAO:0011004 AEO:0000207 Any of the vessels through which blood circulates in the body. [XAO:0001011_][VHOG] Any of the vessels through which blood circulates in the body.[AAO] BTO:0001102 CALOHA:TS-0080 EFO:0000817 EHDAA2:0003252 EHDAA:240 EMAPA:32743 EMAPA:35993 FMA:50722 FMA:63183 FMA:63183 Blood vessel is categorized as 'general anatomical term'. Suggestion to map to region of vascular tree from Terry H at JAX GAID:169 MA:0000060 MAT:0000393 MESH:D001808 OpenCyc:Mx4rvVjxlpwpEbGdrcN5Y29ycA TAO:0002137 The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] UBERON:0001981 UMLS:C0005847 VHOG:0001250 XAO:0001011 ZFA:0005314 annelids have blood vessels, but this class is not applicable to annelids. consider adopting the EMAPA superclass 'vascular element', which includes microvasculature (e.g. capillaries), vascular plexus region of vascular tree organ uberon vas sanguineum vascular element vascular tree organ region capillary AAO:0010252 Any of the smallest blood vessels connecting arterioles with venules. Any of the tiny blood vessels connecting the arterioles to the venules.[AAO] BTO:0002045 CALOHA:TS-2006 EFO:0001906 EMAPA:35198 EV:0100035 FMA:63194 MA:0000065 MESH:A07.231.432.410 OpenCyc:Mx4rvWEU-5wpEbGdrcN5Y29ycA TAO:0005250 The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] UBERON:0001982 UMLS:C0935624 VHOG:0001253 XAO:0000116 ZFA:0005250 blood capillary capillaries lack tunica media and tunica adventitia; only the endothelial wall of the tunica intima belongs capillary vessel not all sources agree capillary is a blood vessel - consider adopting EMAPA superclass of vascular element uberon portal vein A vein that conducts blood from the digestive organs, spleen, pancreas, and gallbladder to the liver[BTO]. BTO:0001792 CALOHA:TS-0814 EHDAA2:0001485 EHDAA:6510 EMAPA:17349 FMA:66645 GAID:540 MA:0002198 MESH:D011169 OpenCyc:Mx4rv_bem5wpEbGdrcN5Y29ycA UBERON:0002017 UMLS:C0032718 VHOG:0000656 XAO:0000392 galen:PortalVein portal venous tree organ part uberon gray matter A nervous system structure composed primarily of nerve cell bodies (somas). May also include dendrites and the initial unmyelinated portion of axons. AEO:0001012 EHDAA2:0003136 EHDAA2_RETIRED:0004658 FMA:67242 HBA:4006 MA:0001112 Multi-tissue comprised of neurons, dendrites, axon terminals, glial cells, and capillaries.[TAO] OpenCyc:Mx4rwDdKMpwpEbGdrcN5Y29ycA TAO:0002197 UBERON:0002020 UMLS:C0018220 VHOG:0001768 ZFA:0001681 gray mater gray matter gray matter of neuraxis grey matter grey matter of neuraxis grey substance grisea neuronal grey matter substantia grisea uberon hindbrain AAO:0010150 BAMS:HB BTO:0000672 CALOHA:TS-0457 DHBA:10653 DMBA:16808 EFO:0000923 EHDAA2:0000746 EHDAA:3514 EHDAA:6487 EMAPA:16916 FMA:67687 Fine structural, computerized three-dimensional (3D) mapping of cell connectivity in the amphioxus nervous system and comparative molecular genetic studies of amphioxus and tunicates have provided recent insights into the phylogenetic origin of the vertebrate nervous system. The results suggest that several of the genetic mechanisms for establishing and patterning the vertebrate nervous system already operated in the ancestral chordate and that the nerve cord of the proximate invertebrate ancestor of the vertebrates included a diencephalon, midbrain, hindbrain, and spinal cord.[well established][VHOG] MA:0000195 MAT:0000107 MBA:1065 MESH:D012249 MIAA:0000107 Posterior part of the brain consisting of the cerebellum and medulla oblongata.[AAO] TAO:0000029 The most posterior of the three principal regions of the brain, forming the rhombencephalon and all or most of the metencephalon. Kimmel et al, 1995.[TAO] The most posterior of the three principal regions of the brain. In mammals and birds the hindbrain is divided into a rostral metencephalon and a caudal myelencephalon. In zebrafish, with the exception of the cerebellum, the ventral remainder of the metencephalon can be separated only arbitrarily from the more caudal myelencephalic portion of the medulla oblongata (From: Neuroanatomy of the Zebrafish Brain)[ZFA]. Organ component of neuraxis that has as its parts the pons, cerebellum and medulla oblongata[FMA]. UBERON:0002028 UMLS:C0035507 UMLS:C1522180 VHOG:0000070 XAO:0000015 ZFA:0000029 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=540 in MA, brainstem and hindbrain and part-of siblings under brain, consistent with FMA and NIF. See also notes for cerebellum. We weaken the relation in ABA to overlaps relationship loss: develops_from hindbrain neural tube (TAO:0007043)[TAO] rhombencephalic rhombencephalon uberon striated muscle tissue AAO:0010762 AEO:0000140 CALOHA:TS-2047 EHDAA2:0003140 EMAPA:36390 FMA:67905 MA:0002438 Muscle tissue that contains fibers that are divided by transverse bands into striations. OpenCyc:Mx4rwAoze5wpEbGdrcN5Y29ycA UBERON:0002036 UMLS:C1331262 Voluntary muscle tissue arranged in bundles of fibers.[AAO] WBbt:0005779 galen:StriatedMuscle striated muscle uberon cerebellum AAO:0010485 BAMS:CB BAMS:Cb BM:CB BTO:0000232 CALOHA:TS-0125 DHBA:10656 Dorsal part of the hindbrain that coordinates muscle movement, posture, and balance.[AAO] EFO:0000327 EHDAA2:0000232 EMAPA:17787 EV:0100293 FMA:67944 GAID:595 HBA:4696 However, although the lamprey possesses a region comparable to the cerebellum and display expression of LjFgf8/17 at the MHB (midbrain hindbrain boundary), it does not have Purkinje cells and cerebellar nuclei, as well as components of the rhombic lip-derived cerebellar and pre-cerebellar systems. It is noteworthy that the latter structures require specific expression of Pax6 in the rhombic lip of the gnathostome hindbrain. Interestingly, the lamprey rhombic lip does not express Pax6. Thus, it is tempting to speculate that in vertebrate evolution the rostral hindbrain is incapable of differentiating into the cerebellum before the co-option of Pax6 in that region. In other words, cerebellum has been brought about as an evolutionary innovation in gnathostomes, based on exaptation of MHB, rhombic lip, and some regulatory gene expression already present in the vertebrate common ancestor.[well established][VHOG] MA:0000198 MAT:0000110 MBA:512 MESH:D002531 MIAA:0000110 OpenCyc:Mx4rvl1eipwpEbGdrcN5Y29ycA Part of the metencephalon that lies in the posterior cranial fossa behind the brain stem. It is concerned with the coordination of movement[MESH]. A large dorsally projecting part of the brain concerned especially with the coordination of muscles and the maintenance of bodily equilibrium, situated between the brain stem and the back of the cerebrum , and formed in humans of two lateral lobes and a median lobe[BTO]. Brain structure derived from the anterior hindbrain, and perhaps including posterior midbrain. The cerebellum plays a role in somatic motor function, the control of muscle tone, and balance[ZFA]. Specialized brain region derived from the dorsal metencephalon (anterior hindbrain, and perhaps including posterior midbrain) and becoming distinctive late in the segmentation period. Kimmel et al, 1995.[TAO] TAO:0000100 The absence of a cerebellum in hagfishes and lampreys appears to be the only exception [to the rule that vertebrates possess the same number of brain divisions]. Both hagfishes and lampreys do possess a thin band of cells located medial to the lateral line centers of the medulla (Ronan and Northcutt, 1998), which has been interpreted as a primitive cerebellum (Larsell, 1967), but more recent experimental studies (Kishida et al., 1987; Weigle and Northcutt, 1998) fail to support Larsell's claim[http://icb.oxfordjournals.org/content/42/4/743.full] UBERON:0002037 UMLS:C0007765 UMLS:C1268981 VHOG:0000024 XAO:0003098 ZFA:0000100 almost all AOs agree that the cerebellum is part of the hindbrain (sometimes specifically part of the metencephalon, which, when present, is part of the hindbrain). However, ABA has cerebellum and brain stem as partof siblings, with the hindbrain part of the brainstem cerebellar corpus cerebelli epencephalon-1 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=643 infratentorial region parencephalon uberon thyroid gland (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (2) a groove in the pharyngeal floor known as the endostyle, or a thyroid gland derived from part of the endostyle (...).[well established][VHOG] A two-lobed endocrine gland found in all vertebrates, located in front of and on either side of the trachea in humans, and producing various hormones, such as triiodothyronine and calcitonin[BTO]. AAO:0010544 BTO:0001379 CALOHA:TS-1047 EFO:0000861 EHDAA2:0002028 EHDAA:2148 EHDAA:2975 EMAPA:17068 EV:0100133 Either of paired structures located in the throat which develop from the ventral wall of the pharynx and excretes hormones involved in the morphological and functional changes during metamorphosis as well as influencing other tissues.[AAO] FMA:9603 GAID:465 In fish, it is usually located below the gills and is not always divided into distinct lobes. However, in some teleosts, patches of thyroid tissue are found elsewhere in the body, associated with the kidneys, spleen, heart, or eyes In larval lampreys, the thyroid originates as an exocrine gland, secreting its hormones into the gut, and associated with the larva's filter-feeding apparatus. In the adult lamprey, the gland separates from the gut, and becomes endocrine, but this path of development may reflect the evolutionary origin of the thyroid. For instance, the closest living relatives of vertebrates, the tunicates and Amphioxus, have a structure very similar to that of larval lampreys, and this also secretes iodine-containing compounds (albeit not thyroxine) In tetrapods, the thyroid is always found somewhere in the neck region. In most tetrapod species, there are two paired thyroid glands - that is, the right and left lobes are not joined together. However, there is only ever a single thyroid gland in most mammals, and the shape found in humans is common to many other species MA:0000129 MAT:0000081 MESH:D013961 MIAA:0000081 OpenCyc:Mx4rvVjLT5wpEbGdrcN5Y29ycA UBERON:0002046 UMLS:C0040132 VHOG:0000418 XAO:0000162 galen:ThyroidGland glandula thyroidea thyroid uberon lung AAO:0000275 AAO:0010567 BTO:0000763 CALOHA:TS-0568 EFO:0000934 EHDAA2:0001042 EHDAA:1554 EHDAA:2205 EMAPA:16728 EV:0100042 Either of two organs which allow gas exchange absorbing oxygen from inhaled air and releasing carbon dioxide with exhaled air.[AAO] FMA:7195 GAID:345 Lungs had already developed as paired ventral pockets from the intestine in the ancestor of Osteognathostomata. (...) In actinopterygian fishes, apart from Cladistia, the ventral intestinal pocket migrates dorsally and becomes the swim-bladder, a mainly hydrostatical organ (reference 1); Comparative transcriptome analyses indicate molecular homology of zebrafish swimbladder and Mammalian lung (reference 2).[well established][VHOG] MA:0000415 MAT:0000135 MESH:D008168 MIAA:0000135 OpenCyc:Mx4rvVjKy5wpEbGdrcN5Y29ycA Respiration organ that develops as an oupocketing of the esophagus. Snakes and limbless lizards typically possess only the right lung as a major respiratory organ; the left lung is greatly reduced, or even absent. Amphisbaenians, however, have the opposite arrangement, with a major left lung, and a reduced or absent right lung [WP] UBERON:0002048 UMLS:C0024109 VHOG:0000310 XAO:0000119 galen:Lung pulmo pulmonary respiration organ in all air-breathing animals, including most tetrapods, a few fish and a few snails. In mammals and the more complex life forms, the two lungs are located in the chest on either side of the heart. Their principal function is to transport oxygen from the atmosphere into the bloodstream, and to release carbon dioxide from the bloodstream into the atmosphere. This exchange of gases is accomplished in the mosaic of specialized cells that form millions of tiny, exceptionally thin-walled air sacs called alveoli. // Avian lungs do not have alveoli as mammalian lungs do, they have Faveolar lungs. They contain millions of tiny passages known as para-bronchi, connected at both ends by the dorsobronchi uberon vasculature An interconnected tubular multi-tissue structure contains fluid that is actively transported around the organism[ZFA]. Examples: vasculature of lung, vasculature of face. BTO:0003718 FMA:69050 TAO:0005249 UBERON:0002049 ZFA:0005249 see also: vascular system. Consider merging? uberon vascular vascular network embryonic structure AAO:0000138 Anatomical structure that is part of an embryo. Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[AAO] Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[TAO] Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[VSAO] BILA:0000034 BTO:0000174 CALOHA:TS-2110 EFO:0000461 FBbt:00004208 FMA:69067 GAID:407 MESH:D004628 RETIRED_EHDAA2:0003169 TAO:0001105 UBERON:0002050 UMLS:C0013948 VSAO:0000178 XAO:0003042 ZFA:0001105 developing embryonic structure developing structure embryonale Struktur embryonic anatomical structure embryonic structures in FMA embryo is_a embryonic structure uberon dermis A collagenous layer of the skin subjacent to the epidermis and covering the hypodermis. It contains various types of cells (e.g. fibroblasts, pigment cells, nerve, blood vessels and scales. Le Guellec et al, 2004.[TAO] AAO:0000128 BTO:0000294 CALOHA:TS-2076 Consider adding a layer-of-skin grouping class for all skin layers EFO:0000953 EMAPA:17527 EV:0100154 FMA:70323 GAID:1321 MA:0000152 MAT:0000153 MESH:D020405 MIAA:0000153 TAO:0001119 The dermis is a layer of skin between the epidermis (with which it makes up the skin) and subcutaneous tissues, and is composed of two layers, the papillary and reticular dermis[WP]. UBERON:0002067 UMLS:C0011646 VHOG:0000108 When approaching controversies surrounding skin evolution, we need to remember that the skin consists of two layers, an epidermis and a dermis, not a single evolving structure. (...) It is little wonder that controversies about homology exist. If we think of the epidermis, the dermis, and their interactions as an evolving unit, then their specialized products (hair, feathers, and reptilian scales) are broadly homologous.[well established][VHOG] XAO:0000217 ZFA:0001119 corium cutis dermal uberon vertebrate dermis hypodermis A layer separating the inner face of the dermis from the subjacent muscle cells. It is covered on both sides by a basement membrane. It contains pigment cells. Le Guellec et al, 2004.[TAO] A layer separating the inner face of the dermis from the subjacent muscle cells. It is covered on both sides by a basement membrane. It contains pigment cells[FMA:70544]. BTO has 'subcutis', as part of dermis. We follow FMA in having distinct classes for hypodermis and superficial fascia, and including these as part of the non-skin intgeument. BTO:0001314 CALOHA:TS-2366 FMA:70544 Lowermost layer of the integumentary system in vertebrates. Types of cells that are found in the hypodermis are fibroblasts, adipose cells, and macrophages. It is derived from the mesoderm, but unlike the dermis, it is not derived from the dermatome region of the mesoderm. The hypodermis is used mainly for fat storage[WP]. TAO:0001136 UBERON:0002072 UMLS:C0278403 ZFA:0001136 hypoderm hypodermal sub-tegumental tissue subcutaneous subcutaneous tissue subcutaneus subcutis subtegumental tissue superficial fascia tela subcutanea uberon vertebrate hypodermis viscus AAO:0010386 An internal organ of the body; especially: one (as the heart, liver, or intestine) located in the great cavity of the trunk proper.[AAO] An organ that is located within the body cavity (or in its extension, in the scrotum); it consists of organ parts that are embryologically derived from endoderm, splanchnic mesoderm or intermediate mesoderm; together with other organs, the viscus constitutes the respiratory, gastrointestinal, urinary, reproductive and immune systems, or is the central organ of the cardiovascular system. Examples: heart, lung, esophagus, kidney, ovary, spleen. BTO:0001491 EHDAA:512 EMAPA:16245 FMA:7085 MA:0000019 MESH:D014781 Organsystem@ge RETIRED_EHDAA2:0002201 UBERON:0002075 UMLS:C0042779 XAO:0003034 general anatomical term in FMA. Note that we place the MA class here temporarily, although properly systems should be distinguished from organs. splanchnic tissue uberon viscera visceral organ visceral organ system visceral tissue cardiac ventricle A chamber of the heart that receives blood from one or more atria and pumps it by muscular contraction into the arteries.[AAO] AAO:0010249 BTO:0000862 CALOHA:TS-0444 Cardiac chamber through which blood leaves the heart. EFO:0000317 EHDAA2:0004164 EHDAA:1912 EMAPA:17331 EV:0100020 FMA:7100 GAID:568 In the primitive vertebrate heart the four chambers are: 1. Sinus venosus (...) 2. Atrium (...) 3. Ventricle (...) 4. Conus arteriosus (...)[well established][VHOG] MA:0000091 MAT:0000497 MESH:D006352 One of four heart chambers.[TAO] OpenCyc:Mx4rvVjj1pwpEbGdrcN5Y29ycA TAO:0000009 UBERON:0002082 UMLS:C0018827 VHOG:0000435 XAO:0003193 ZFA:0000009 galen:Ventricle heart ventricle lower chamber of heart uberon ventricle ventricle of heart heart left ventricle A cardiac ventricle that is in the left side of the heart. BTO:0001629 CALOHA:TS-0439 EHDAA2:0002178 EMAPA:17337 FMA:7101 In mammals continuous with aorta MA:0000092 OpenCyc:Mx4rtW8v46gEEdudWQACs5b6Bw OpenCyc:Mx8Ngh4rvgIFoJwpEbGdrcN5Y29ycB4rvVjj1pwpEbGdrcN5Y29ycA The vertebrate heart initially forms as a tube from a population of precursor cells termed the first heart field (FHF). Cells from the adjacent second heart field (SHF) are then progressively added to the developing heart. In avian and mammalian hearts, the FHF contributes mainly to the left ventricle, whereas the SHF gives rise to the outflow tract and large portions of the right ventricle and atria. Both fields arise from common mesodermal progenitors, although the detailed lineage relationships between FHF and SHF remain uncertain.[well established][VHOG] Thick-walled muscular chamber constituting the left border and apex of the heart. It receives oxygenated blood from the left atrium through the mitral orifice and send it off into the aorta. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] UBERON:0002084 UMLS:C0225897 VHOG:0000718 cardiac left ventricle galen:LeftVentricle https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern left cardiac ventricle left ventricle left ventricle of heart uberon ventriculus sinister cordis postcranial axial skeleton AAO:0000034 EFO:0000942 EHDAA2:0000161 EHDAA:5049 EMAPA:17214 FMA:71221 MA:0002986 MAT:0000148 MIAA:0000148 Skeletal subdivision of the central body axis including vertebrae, notochord, ribs, and sternum.[VSAO] TAO:0000317 The axial musculoskeletal system represents the plesiomorphic locomotor engine of the vertebrate body, playing a central role in locomotion. In craniates, the evolution of the postcranial skeleton is characterized by two major transformations. First, the axial skeleton became increasingly functionally and morphologically regionalized. Second, the axial-based locomotion plesiomorphic for craniates became progressively appendage-based with the evolution of extremities in tetrapods.[well established][VHOG] The axial skeleton is formed by the vertebral column, a metameric, semi-flexible, arched bar located in the dorsal part of the trunk, and is formed by a series of cartilaginous or bony vertebrae. It provides suspension for the appendicular skeleton and protection for the spinal nerve cord.[AAO] The post-cranial structural components forming the long axis of the vertebrate body; usually consists of the notochord, vertebrae, ribs, supraneurals, intermuscular bones, and unpaired median fins.[TAO] The post-cranial subdivision of skeleton structural components forming the long axis of the vertebrate body; in Danio, consisting of the notochord, vertebrae, ribs, supraneurals, intermuscular bones, and unpaired median fins; in human consists of the bones of the vertebral column, the thoracic cage and the pelvis[ZFA+FMA]. UBERON:0002090 VHOG:0000317 VSAO:0000093 XAO:0003073 ZFA:0000317 axial skeleton http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton post-cranial axial skeleton previous some AOs had used the term 'axial skeleton' to include the skull. This is being resolved (see tracker items above). Status: MA - fixed. uberon appendicular skeleton AAO:0000747 EFO:0000951 EMAPA:32729 FMA:71222 MA:0000290 MAT:0000278 MIAA:0000278 Skeletal subdivision consisting of all the skeletal elements in the pectoral and pelvic appendage complexes.[VSAO] Skeletal system that consists of the paired fins (pectoral or pelvic fins).[TAO] Subdivision of skeleton which which consists of all the skeletal elements in in the pectoral and pelvic appendage complexes[cjm]. The pectoral and pelvic girdles, which articulate with the axial skeleton, together with their associated limbs, the forelimbs and hind limbs, form the appendicular skeleton.[AAO] UBERON:0002091 UMLS:C0222646 VHOG:0001666 VSAO:0000076 XAO:0003166 appendicular skeleton entire appendicular skeleton https://github.com/obophenotype/uberon/wiki/Appendages-and-the-appendicular-skeleton ontologies differ in whether they treat the term appendicular skeleton as being the entire set of bones in the limbs, or whether the fore and hind limbs/fins are treated as seperate appendicular skeletons. Here we follow FMA, and treat the appendicular skeleton as the sum total of skeletal elements in the organism (this is evidenced by the fact that in FMA, skeleton of left/right upper/lower limb is part_of a appendicular skeleton, and subtypes of 'subdivision of appendicular skeleton'). We have separate classes such as 'skeleton of limb', and 'skeleton of hindlimb' for the 4 parts of the appendicular skeleton. In future the ZFA/TAO classes may be moved. paired fin skeleton skeleton appendiculare uberon skin of body BTO:0001253 CALOHA:TS-0934 EFO:0000962 EHDAA2:0001844 EMAPA:17525 FMA:7163 MA uses the term skin to refer to what is called here: zone of skin MESH:D012867 MFMO:0000099 OpenCyc:Mx4rvVjX3ZwpEbGdrcN5Y29ycA The organ covering the body that consists of the dermis and epidermis. UBERON:0002097 UMLS:C1123023 XAO:0000023 consider 'integumentary system' for invertebrates entire integument entire skin galen:Skin integument integumental organ pelt skin skin organ uberon trunk AAO:0010339 BILA:0000116 BTO:0001493 CALOHA:TS-1071 EFO:0000966 EMAPA:31857 FMA:7181 MA:0000004 MAT:0000296 MIAA:0000296 OpenCyc:Mx4rvVkJjpwpEbGdrcN5Y29ycA Organism subdivision that is the part of the body posterior to the head and anterior to the tail.[AAO] Organism subdivision which is the part of the body posterior to the cervical region (or head, when cervical region not present) and anterior to the caudal region. Includes the sacrum when present. Organism subdivision which is the part of the body posterior to the head and anterior to the tail.[TAO] Rumpf TAO:0001115 UBERON:0002100 UMLS:C0460005 XAO:0000054 XAO:0003025 ZFA:0001115 galen:Trunk thoracolumbar region torso trunk region uberon limb A paired appendage that is evolved from a paired fin. The extent of this structure includes autopod, stylopod and zeugopod regions when present, but excludes the girdle and its parts. AAO:0010336 AEO:0000172 CALOHA:TS-0552 EFO:0000876 EHDAA2:0003172 EHDAA:1697 EHDAA:8273 EMAPA:16405 FMA:24875 GAID:36 MA:0000007 MAT:0000090 MIAA:0000090 Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG] OpenCyc:Mx4rvn1uSZwpEbGdrcN5Y29ycA Organism subdivision that has as its parts the jointed appendages used for locomotion and manipulation.[AAO] UBERON:0002101 UMLS:C0015385 VHOG:0000336 VSAO:0000121 XAO:0003027 extremities extremity flipper free limb galen:Extremity limb sensu vertebrata pentadactyl limb tetrapod limb uberon hindlimb A (free) limb that is connected to a pelvic girdle region. The extent of this structure includes autopod, stylopod and zeugopod regions when present, but excludes the pelvic girdle and its parts. AAO:0000219 BTO:0002345 CALOHA:TS-2215 EFO:0000883 EHDAA2:0001033 EHDAA:6094 EMAPA:17458 EV:0100015 FMA:24879 GAID:1221 GAID:38 Lower limb, which connects the pes with the pelvic girdle.[AAO] MA:0000026 MAT:0000395 MESH:D006614 MIAA:0000395 Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG] UBERON:0002103 UMLS:C0023216 UMLS:C1522391 VHOG:0000337 VSAO:0000150 XAO:0003031 crural free lower limb free part of lower limb galen:LowerExtremity hind limb hind-limb hindlimb inferior member lower extremity lower limb membrum inferius membrum inferius note that this corresponds to FMA:'free lower limb' (a limb segment), NOT 'lower limb'. Both MA and FMA consider shoulder (and shoulder bones) part of upper limb. Note that AAO class probably refers to skeleton pelvic appendage uberon visual system AAO:0000632 BILA:0000140 EMAPA:36003 FMA:7191 MA:0002444 OpenCyc:Mx4rvViCtpwpEbGdrcN5Y29ycA TAO:0001127 The sensory system subserving the sense of vision. The sensory system used for sight.[AAO] UBERON:0002104 UBERON:0007036 UMLS:C0587900 XAO:0003198 ZFA:0001127 photosensory system uberon visual organ system vestibulo-auditory system AAO:0000631 EMAPA:36002 FMA:78500 Sensory system responsible for the perception of spatial orientation and auditory stimuli. TAO:0001138 The sensory system used for balance and hearing.[AAO] UBERON:0002105 XAO:0003195 ZFA:0001138 auditory organ system auditory system auditory/vestibular system uberon vestibuloauditory system vestibuloauditory system liver AAO:0010111 All vertebrates possess a liver (reference 1); Later in craniate evolution, an anterior gill arch was transformed into jaws, and many new types of feeding subsequently evolved.(...) A liver evolved that, among its many functions, stores considerable energy as glycogen or lipid (reference 2).[well established][VHOG] An exocrine gland which secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes[GO]. An organ sometimes referred to as a liver is found associated with the digestive tract of the primitive chordate Amphioxus. However, this is an enzyme secreting gland, not a metabolic organ, and it is unclear how truly homologous it is to the vertebrate liver. The zebrafish liver differs from the mammalian liver in that the hepatocytes are not clearly organized in cords or lobules and the typical portal triads are not apparent. In addition, the zebrafish liver does not have Kuppfer cells. Furthermore, a clear distinction can be made between the male and female liver in the adult zebrafish. The female hepatocytes are very basophilic (Figure 15c) as a result of the production of vitellogenin (Van der Ven et al. 2003). BTO:0000759 CALOHA:TS-0564 EFO:0000887 EHDAA2:0000997 EHDAA:2197 EMAPA:16846 EV:0100089 FMA:7197 GAID:288 MA:0000358 MAT:0000097 MESH:D008099 MIAA:0000097 Only ZFA considers this part_of immune system - we weaken this to an overlaps relation, as in general it's only a subset of cells that have clear immune function. OpenCyc:Mx4rvVimppwpEbGdrcN5Y29ycA Organ which secretes bile and participates in formation of certain blood proteins.[AAO] TAO:0000123 The liver is found in all vertebrates, and is typically the largest visceral organ. Its form varies considerably in different species, and is largely determined by the shape and arrangement of the surrounding organs. Nonetheless, in most species it is divided into right and left lobes; exceptions to this general rule include snakes, where the shape of the body necessitates a simple cigar-like form. The internal structure of the liver is broadly similar in all vertebrates. UBERON:0002107 UMLS:C0023884 VHOG:0000257 XAO:0000133 ZFA:0000123 galen:Liver hepatic iecur jecur relationship type change: differentiates_from endoderm (AAO:0000139) CHANGED TO: develops_from endoderm (UBERON:0000925)[AAO] secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes[GO]. uberon small intestine AAO:0010397 BTO:0000651 CALOHA:TS-0942 EFO:0000841 EMAPA:32834 EV:0100072 FMA:7200 GAID:313 Intestinal surface area also is increased in amphibians and reptiles by internal folds and occasionally by a few villi. The intestine can be divided into a small intestine and a slightly wider large intestine.[well established][VHOG] MA:0000337 MAT:0000047 MESH:A03.492.411.620 MIAA:0000047 OpenCyc:Mx4rvVjlIJwpEbGdrcN5Y29ycA Subdivision of digestive tract that connects the stomach to the large intestine and is where much of the digestion and absorption of food takes place (with the exception of ruminants). The mammalian small intestine is long and coiled and can be differentiated histologically into: duodenum, jejunem, ileum[WP,cjm,Kardong]. TAO:0001323 The terminal region of the mid intestine is comprised of specialized enterocytes that appear to play a role in mucosal immunity. Wallace et al, 2005.[TAO] UBERON:0002108 UMLS:C0021852 VHOG:0000055 XAO:0000130 ZFA:0001323 anterior intestine galen:SmallIntestine intestinum tenue mid intestine small bowel small intestine uberon gall bladder AAO:0010114 An organ that aids digestion and stores bile produced by the liver[WP]. BTO:0000493 CALOHA:TS-0394 EFO:0000853 EHDAA2:0000699 EHDAA:8062 EMAPA:17202 EV:0100090 FMA:7202 MA:0000356 MAT:0000072 MESH:D005704 MIAA:0000072 Membranous muscular sac in which the bile from the liver remains stored until it is required. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] OpenCyc:Mx4rvVkGr5wpEbGdrcN5Y29ycA Organ attached to the liver which stores bile and empties into the duodenum via the bile duct as needed for digestion.[AAO] Rats do not have a gallbladder, but produce bile. The bile flows directly from the liver through the (hepatic) bile duct into the small intestine (Hebel and Stromberg, 1988) TAO:0000208 The presence of a gallbladder appears to be a primitive trait. It is found in most fish and all adult reptiles and amphibians and has been well conserved in mammals, for the most part.[well established][VHOG] UBERON:0002110 UMLS:C0016976 VHOG:0000221 XAO:0000135 ZFA:0000208 galen:Gallbladder gall bladder gallbladder relationship type change: differentiates_from endoderm (AAO:0000139) CHANGED TO: develops_from endoderm (UBERON:0000925)[AAO] uberon vesica biliaris vesica fellea kidney A paired organ of the urinary tract which has the production of urine as its primary function. AAO:0000250 BTO:0000671 CALOHA:TS-0510 EFO:0000929 EMAPA:17373 EV:0100096 FMA:7203 GAID:423 MA:0000368 MAT:0000119 MESH:D007668 MIAA:0000119 One of either of a pair of structures lying on either side of the dorsal aorta in which fluid balance is regulated and waste is excreted out in the form of urine.[AAO] OpenCyc:Mx4rvVjlYpwpEbGdrcN5Y29ycA UBERON:0002113 UMLS:C0022646 XAO:0003267 galen:Kidney renal reniculate kidney uberon duodenum AAO:0010402 BTO:0000365 CALOHA:TS-0214 EFO:0000851 EMAPA:18852 EV:0100073 FMA:7206 GAID:284 In fish, the divisions of the small intestine are not as clear, and the terms anterior intestine or proximal intestine may be used instead of duodenum. In humans, the duodenum is a hollow jointed tube about 10-15 inches (25-38 centimetres) long connecting the stomach to the jejunum. It begins with the duodenal bulb and ends at the ligament of Treitz. MA:0000338 MAT:0000044 MESH:A03.492.411.620.270 MIAA:0000044 OpenCyc:Mx4rv4LJDpwpEbGdrcN5Y29ycA The first part of the small intestine. At the junction of the stomach and the duodenum the alimentary canal is inflected. The duodenum first goes anteriorly for a short distance, turns dorsally, and eventually caudally, thus it is a U-shaped structure with two horizontal sections (a ventral and a dorsal one). The fixed portion of the small intestine deeply lodged in the posterior wall of the abdomen and extending from the pylorus to the beginning of the jejunum. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] UBERON:0002114 UMLS:C0013303 VHOG:0000052 XAO:0000236 duodenal galen:Duodenum proximal intestine uberon upper intestine pronephros A kidney formed of nephric tubules arising in the anterior region of the nephric ridge; forms only as a transient embryonic structure. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Kardong_KV, Vertebrates:_Comparative_Anatomy, p.748][VHOG] AAO:0011089 BTO:0001541 EFO:0000927 EHDAA2:0001570 EHDAA:1017 EMAPA:16579 FMA:72170 In all vertebrate embryos, the kidney begins with the differentiation of a few renal tubules from the anterior end of the nephric ridge overlying the pericardial cavity. (...) This early-developing embryonic kidney is called the pronephros.[well established][VHOG] In mammals, the pronephros is the first of the three embryonic kidneys to be established and exists only transiently. In lower vertebrates such as fish and amphibia, the pronephros is the fully functional embryonic kidney and is indispensible for larval life[GO]. MAT:0000117 MIAA:0000117 Once the more complex mesonephros forms the pronephros undergoes apoptosis in amphibians. In fishes the nephron degenerates but the organ remains and becomes a component of the immune system[Wikipedia:Pronephros]. // TODO - check developmental relationships. Note that we previously include the ZFA/XAO terms under the more specific 'pronephric kidney', but these are now merged. TODO GCI: relationship: capable_of GO:0030104 Organ that serves as a transient kidney, providing osmoregulation during early developmental stages and then degenerating during metamorphosis.[AAO] TAO:0000151 The embryonic kidney, present at the level of the third somite, is composed of two glomeruli fused at the midline, two pronephric tubules, and paired bilateral pronephric ducts that modify the composition of the blood filtrate before delivering it to the cloaca for excretion.Kimmel et al, 1995.[TAO] UBERON:0002120 UBERON:0005794 UMLS:C0231048 VHOG:0000037 XAO:0002000 ZFA:0000151 archinephron embryonic kidney pronephric pronephric kidney pronephron uberon right lung EHDAA2:0001730 EHDAA:4969 EMAPA:17661 FMA:7309 Lung which consists of the right upper lobe, middle lobe and right lower lobe.[FMA] Lungs had already developed as paired ventral pockets from the intestine in the ancestor of Osteognathostomata.[well established][VHOG] MA:0000426 OpenCyc:Mx8Ngh4rvgHsHZwpEbGdrcN5Y29ycB4rvVjKy5wpEbGdrcN5Y29ycA UBERON:0002167 UMLS:C0225706 VHOG:0000301 https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern uberon left lung EHDAA2:0000943 EHDAA:4947 EMAPA:17653 FMA:7310 Lung which consists of the left upper lobe and left lower lobe.[FMA] Lungs had already developed as paired ventral pockets from the intestine in the ancestor of Osteognathostomata.[well established][VHOG] MA:0000425 OpenCyc:Mx8Ngh4rvgIFoJwpEbGdrcN5Y29ycB4rvVjKy5wpEbGdrcN5Y29ycA UBERON:0002168 UMLS:C0225730 VHOG:0000618 https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern uberon bronchus BTO:0001340 CALOHA:TS-1229 EFO:0000932 EMAPA:32689 EV:0100041 Each of the two primary divisions of the trachea leading respectively into the right and the left lung. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] FMA:7409 GAID:346 In humans, the main bronchus is histologically identical to trachea; 2ary and 3ary bronchi are not; epithelium becomes simple columnar, goblet cell number decreases, elastic fibers in lamina propria increases, distribution more uniform. Muscular layer between mucosa and submucosa appears. cartilage rings become discontinuous plates connected by fibrous connective tissue MA:0000436 MAT:0000133 MESH:D001980 MIAA:0000133 UBERON:0002185 UMLS:C0006255 VHOG:0000262 XAO:0000121 bronchi bronchial bronchial tissue bronchial trunk the upper conducting airways of the lung; these airways arise from the terminus of the trachea uberon hemolymphoid system Anatomical cluster consisting of the hematopoietic system and the lymphoid system, or its analogs. CALOHA:TS-2018 EHDAA2:0004615 EMAPA:18765 FMA:74562 MA:0000013 UBERON:0002193 haemolymphoid system hematolymphoid system lymphomyeloid complex uberon integument AAO:0000239 Anatomical system that protects the body from damage, comprising the skin and its appendages.[AAO] BTO:0000634 FMA:74657 Hautsystem@de Surface structure that is the outer protective covering of the body.[VSAO] TAO:0000368 The dermis, epidermis and hypodermis. The outer protective barrier that separates the animal from its aquatic environment. Le Guellec et al, 2004.[TAO] UBERON:0002199 VSAO:0000029 ZFA:0000368 dermal system dermis plus epidermis plus hypodermis dermoid system galen:Integument in FMA intergument = skin+superficial fascia(hypodermis), skin=dermis+epidermis+hair_nail. Note that the definition provided here excludes the more general sense of the term 'integument' used in invertebrates; consider 'integumental system'. Note that the VSAO class appears to include adnexa by its definition. integumental integumentary integumentum commune skin skin and subcutaneous tissue skin plus hypodermis tegument the integument uberon vertebrate integument vasculature of head EFO:0003656 FMA:74710 TAO:0001267 UBERON:0002200 Vasculature that is part of a head [Automatically generated definition]. XAO:0004152 ZFA:0001267 adult head vascular network adult head vasculature cranial vasculature head vascular network head vasculature uberon vascular network of adult head vascular network of head vasculature of adult head vasculature of trunk A vasculature that is part of a trunk [Automatically generated definition]. FMA:74712 TAO:0005024 UBERON:0002201 ZFA:0005024 torso vascular network torso vasculature trunk vascular network trunk vasculature uberon vascular network of torso vascular network of trunk vasculature of torso vasculature of eye FMA:74743 TAO:0007057 UBERON:0002203 Vasculature that is part of the eye region. ZFA:0007057 eye vascular network eye vasculature not part of the eye in ZFA. Note this changed to a blood vessel in ZFA ocular blood vessel ocular vasculature optic vasculature uberon vascular network of eye musculoskeletal system AAO:0010546 Anatomical system that consists of the muscular and skeletal systems. Anatomical system that provides locomotion and physical support to the organism.[AAO] CALOHA:TS-1311 EMAPA:32714 EV:0100139 FMA:7482 GAID:98 MA:0002418 MESH:D009141 OpenCyc:Mx4rQRpVNgAKEdyHxgDggVfs8g There are more than 50,000 extant vertebrate species, representing over 500 million years of evolution. During that time, the vertebrate musculoskeletal systems have adapted to aquatic, terrestrial, fossorial, and arboreal lifestyles, while simultaneously retaining functionally integrated axial and appendicular skeletal systems.[well established][VHOG] UBERON:0002204 UMLS:C0026860 VHOG:0001275 VSAO:0000031 XAO:0000168 musculo-skeletal system musculoskeletal uberon synovial joint AEO:0000183 CALOHA:TS-2138 EHDAA2:0003183 FMA:7501 Is a joint that is located at the point of contact of articulating bones allowing movement. The joint has a capsule containing synovial fluid surrounding the articulating bone surfaces.[TAO] Joint in which the articulating bones or cartilages are connected by an articular capsule which encloses a synovial membrane and a synovial cavity. Examples: Temporomandibular joint, knee joint.[FMA] MA:0000322 OpenCyc:Mx4rv2bBV5wpEbGdrcN5Y29ycA TAO:0005153 UBERON:0002217 ZFA:0005153 articulatio synoviale diarthrodial joints diarthroses diarthrosis diarthrosis joint galen:SynovialJoint uberon thoracic cavity EMAPA:36497 FMA:7565 GAID:93 In many species, the diaphragm separates thoracic and abdominal cavities MA:0000032 MESH:A01.911.800 OpenCyc:Mx4rmvyleLfEEduAAAACs6hRXg OpenCyc:Mx4rvhU_TpwpEbGdrcN5Y29ycA The part of the coelemic cavity lumen that is enclosed by the walls of the thorax. UBERON:0002224 UMLS:C0230139 cavitas thoracis cavity of chest cavity of thorax chest cavity pectoral cavity space of thoracic compartment thoracic lumen uberon spinal cord (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2).[well established][VHOG] AAO:0010151 BAMS:SP BAMS:Spinal BM:SpC BTO:0001279 CALOHA:TS-0953 DHBA:12890 DMBA:17651 EFO:0000110 EHDAA2:0001255 EHDAA:2863 EMAPA:17577 EV:0100316 FMA:7647 GAID:695 MA:0000216 MAT:0000183 MESH:D013116 MIAA:0000183 OpenCyc:Mx4rvVjjk5wpEbGdrcN5Y29ycA Part of the central nervous system located in the vertebral canal continuous with and caudal to the brain; demarcated from brain by plane of foramen magnum. It is composed of an inner core of gray matter in which nerve cells predominate, and an outer layer of white matter in which myelinated nerve fibers predominate, and surrounds the central canal. (CUMBO) Part of the central nervous system which descends from the hindbrain within the vertebral column.[AAO] SpC TAO:0000075 TODO - add superclass to unify with VNC? UBERON:0002240 UMLS:C0037925 VHOG:0000601 XAO:0000020 ZFA:0000075 cerebro-cerebellar fissure cerebrocerebellar fissure fissura cerebro-cerebellaris fissura cerebrocerebellaris http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=22 medulla spinalis spinal cord structure spinal medulla uberon olfactory organ AAO:0010180 An olfactory organ overlaps with the olfactory system, because some parts of the nose (e.g. nasal skeleton) are parts of the skeletal system, which is spatially disjoint An organ that houses olfactory neurons and is responsible for the sense of smell. Examples include the vertebrate nose and the Drosophila dorsal organ. BTO:0001772 FBbt:00005158 FMA:77659 UBERON:0002268 VHOG:0000287 XAO:0000273 fma general anatomical term. xao has no subtypes (but Johnstons organ develops from this). An olfactory organ overlaps with the olfactory system, because some parts of the nose (e.g. nasal skeleton) are parts of the skeletal system, which is spatially disjoint main olfactory organ olfactory neuroepithelium olfactory organ olfactory sense organ olfactory sensory organ organ olfactus organum olfactorium primary olfactory organ uberon biliary system FMA:79646 GAID:279 MA:0001273 MESH:D001659 Organ system subdivision that consists of the organs and ducts that are involved in the production and transportation of bile. In most species this is the gallbladder and the bile ducts (biliary tree). UBERON:0002294 biliary apparatus biliary tract uberon brainstem 'brainstem' is a loose term that sometimes refers to the ventral parts o the brain except for any part of the telencephalon - sometimes it includes the diencephalon or subpallial telencephalon structures (ISBN10:0471888893). Here we use it in a more restriced sense, to include only the medulla oblongata, pons (when present) and the midbrain tegmentum (following the ZFA definitions). BAMS:BS BTO:0000146 CALOHA:TS-0093 EFO:0001962 EMAPA:32678 EV:0100241 FMA:79876 MA:0000169 MBA:343 MESH:D001933 Multi-tissue structure that has as its parts the medulla oblongata of the hindbrain and the tegmentum of the midbrain.[TAO] Multi-tissue structure that has as its parts the medulla oblongata of the hindbrain and the tegmentum of the midbrain[ZFA,adopted][ZFA:0001707]. Stalk-like part of the brain that includes amongst its parts the medulla oblongata of the hindbrain and the tegmentum of the midbrain[ZFA,MP,generalized]. TAO:0002156 UBERON:0002298 UMLS:C0006121 VHOG:0001457 ZFA:0001707 accessory medullary lamina of pallidum brain stem http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=236 lamella pallidi incompleta lamina medullaris accessoria lamina medullaris incompleta pallidi lamina pallidi incompleta the stalk-like part of the brain that comprises the midbrain (aka mesencephalon), the pons (aka pons Varolii), and the medulla oblongata, and connects the cerebral hemispheres with the cervical spinal cord[MP] truncus encephali truncus encephalicus uberon nucleus of brain A neural nucleus that is part of the brain. EMAPA:35185 FMA:83840 MA:0000811 UBERON:0002308 UMLS:C1706993 ZFA:0005575 brain nuclei brain nucleus uberon coelemic cavity lumen AEO:0000186 Anatomical space, part of the trunk that contains the pericardial and pleuroperitoneal cavities[ZFA]. BTO:0001707 EHDAA2:0000267 FBbt:00005060 FMA:85006 In mammals it forms the peritoneal, pleural, and pericardial cavities RETIRED_EHDAA2:0003186 TAO:0001438 The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities. The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities[BTO]. UBERON:0000169 UBERON:0002323 UMLS:C0333343 ZFA:0001438 body cavity celom check the FMA placement here; ncit placement of body cavity here probably not correct coelom coelome coelomic cavity coelomic cavity lumen galen:BodyCavity hemocoel main body cavity space of body compartment uberon ventral body cavity notochord (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (3) a stiff, longitudinal rod of turgid cells along the dorsal part of the body that is called a notochord (...).[well established][VHOG] A flexible rod-shaped body found in embryos of all chordates. It is composed of cells derived from the mesoderm and defines the primitive axis of the embryo. In some chordates, it persists throughout life as the main axial support of the body, while in most vertebrates it becomes the nucleus pulposus of the intervertebral disc. The notochord is found ventral to the neural tube. AAO:0000327 Avascular multi-tissue structure composed of large vacuolated epithelial cells (chordablasts) and perichordal fibrous tissue.[VSAO] BTO:0001768 CALOHA:TS-0690 EHDAA2:0001277 EHDAA:1241 EHDAA:6021 EMAPA:16191 EV:0100002 FMA:85521 GAID:1311 In between vertebra the notochord becomes the nucleus pulposus, under it degenerates, and at anterior end in some species its tissue merges with some of the cranial bones.. Some organisms retain a post-embryonic notochord. MAT:0000281 MESH:A16.254.610 Rod-like principal supportive element of the embryo and larva, present in the midline just ventral to the neural tube, and differentiating during the segmentation period to form large vacuolated epithelial cells and a surrounding a sheath of fibrous and elastic layers. Layering of the sheath may differ in structure, thickness and development among groups; in cypriniforms there are actually three very thin layers to the sheath. A functional, well developed notochord is present throughout life in certain basal fish groups but not in cypriniforms. Kimmel et al, 1995.[TAO] Slender rod of fibrous connective tissue surrounding a core of fluid-filled cells of mesodermal origin; it lies above the gut and directly beneath the spinal cord. The notochord is present during early development and in a few cases it is retained through life; however, usually the notochord is replaced by the vertebral column.[AAO] TAO:0000135 The notochord appears early in embryogeny and plays an important role in promoting or organizing the embryonic development of nearby structures. In most adult chordates the notochord disappears or becomes highly modified. In some non-vertebrate chordates and fishes the notochord persists as a laterally flexible but incompressible skeletal rod that prevents telescopic collapse of the body during swimming[TOLWEB] UBERON:0002328 UMLS:C0028439 VHOG:0000199 VSAO:0000032 XAO:0000055 ZFA:0000135 embryonic notocord notochorda notochordal notocord relationship type change: differentiates_from mesoderm (AAO:0000304) CHANGED TO: develops_from mesoderm (UBERON:0000926)[AAO] uberon somite (...) cephalocordates and craniates belong to a group known as Somitichordata. Somitichordate synapomorphies include (1) somites (...) (reference 1); The idea that the last common ancestor of bilaterian animals (Urbilateria) was segmented has been raised recently on evidence coming from comparative molecular embryology (reference 2).[well established][VHOG] AAO:0010569 AEO:0001015 BTO:0001558 EHDAA2:0003436 EHDAA:366 EHDAA:699 EMAPA:31169 FMA:85522 GAID:1306 MAT:0000068 MESH:A16.254.425.660.750 MIAA:0000068 Post-cranial axial segments which form sclerotome and dermomyotome.[AAO] Somites are spheres of epithelial cells that form sequentially along the anterior-posterior axis of the embryo through mesenchymal to epithelial transition of the presomitic mesoderm. TAO:0000155 UBERON:0002329 UMLS:C0376449 Undifferentiated mesodermal components of early trunk or tail segments or metameres, derived from paraxial mesoderm; forms myotomes, sclerotomes and perhaps dermatomes. Kimmel et al, 1995.[TAO] VHOG:0000191 When the somite becomes segmented from the segmental plate, it is composed of an epithelial sac enclosing mesenchymal somitocoel cells. Thereafter the somite differentiates into two parts, the ventro-medial mesenchymal sclerotome and the dorso-lateral epithelial dermomyotome. This change in the epithelial somite depends on surrounding tissue [PMID:15906248] XAO:0000058 ZFA:0000155 currently classified as an epithelial vesicle, consistent with EHDAA2 and https://github.com/obophenotype/uberon/wiki/The-neural-crest. Consider making 'somitic mesoderm' a separate term and correlate with regionalization processes. Consider moving ZFA term to 'trunk somite' as it is part of the trunk epimere epimere mesoderm epithelial somite mesodermal cluster relationship loss: develops_from paraxial mesenchyme (TAO:0000942)[TAO] relationship type change: OBO_REL:part_of trunk (TAO:0001115) CHANGED TO: develops_from trunk (UBERON:0002100)[TAO] relationship type change: part_of paraxial mesoderm (AAO:0010568) CHANGED TO: develops_from paraxial mesoderm (UBERON:0003077)[AAO] somites somitic somitic mesoderm somitus uberon exocrine system Anatomical system that consists of the glands and parts of glands that produce exocrine secretions and help to integrate and control bodily metabolic activity. Exocrine glands are glands that secrete their products (hormones) into ducts (duct glands). They are the counterparts to endocrine glands, which secrete their products (hormones) directly into the bloodstream (ductless glands) or release hormones (paracrines) that affect only target cells nearby the release site. [Wikipedia]. CALOHA:TS-2057 EHDAA2:0002225 EMAPA:35329 FMA:85539 MA:0002411 UBERON:0002330 UMLS:C1516995 WikipediaCategory:Exocrine_system exocrine glandular system uberon neural crest A cell population arising from the dorsolateral aspect of the central nervous system primordium during the segmentation period, and later migrating along stereotyped pathways to give rise to a diverse and well-defined set of cell types including pigment cells, peripheral neurons and glia, and head cartilage. Kimmel et al, 1995.[TAO] A specialized region of ectoderm found between the neural ectoderm (neural plate) and non-neural ectoderm and composed of highly migratory pluripotent cells that delaminate in early embryonic development from the dorsal neural tube and give rise to an astounding variety of differentiated cell types[MP]. A well developed neural crest population is present in lampreys (Horigome et al. 1999 ; Tomsa & Langeland, 1999) and gnathostomes. chordate fossils from the early Cambrian (Yunnanozoan and Haikouella) with apparent neural-crest derived structures (pharyngeal denticles and pharyngeal skeletons resembling the striped mucocartilage of the branchial bars in lamprey ammocoete larvae), suggests that neural crest arose very early in vertebrate evolution (Chen et al. 1999; Holland & Chen, 2001). The invertebrate chordates apparently lack defini- tive neural crest. One marker of migrating neural crest in some vertebrates, the antibody HNK1, does not recognize any cells in amphioxus embryos (Holland, unpublished). Even so, in both amphioxus and tunicates, cells at the edges of the neural plate and adjacent nonneural ectoderm share some properties of neural crest[PMID:11523831] AAO:0010578 BTO:0001764 CALOHA:TS-0676 EHDAA2:0004419 EMAPA:32737 FMA:86666 GAID:1310 Gene notes: Many factors and genes, such as Pax3 (Tremblay et al., 1995), slug (Nieto et al., 1994), AP-2 (Zhang et al., 1996; Schorle et al., 1996), and Wnt-1/3a (Ikeya et al., 1997) are expressed in the dorsal most region of the neural tube, and have been shown to be involved in the generation of neural crest cells. MAT:0000066 MESH:A16.254.600 MIAA:0000066 Migratory cell population which delaminates from neural tube, borders surface ectoderm and neural ectoderm, and gives rise to many different tissue types.[AAO] NC TAO:0000045 UBERON:0002342 UMLS:C0027789 VHOG:0000057 We conclude that the neural crest is a vertebrate novelty, but that neural crest cells and their derivatives evolved and diversified in a step-wise fashion - first by elaboration of neural plate border cells, then by the innovation or co-option of new or ancient metazoan cell fates.[well established][VHOG] XAO:0000048 ZFA:0000045 consider including subclasses for pre- and post- migratory (e.g. sheets/paths/streams). crista neuralis neural crest material uberon neurectoderm (...) the ability of ectoderm to produce neuronal cells is a general metazoan feature.[well established][VHOG] AAO:0011074 BILA:0000039 CALOHA:TS-1212 EHDAA2:0001248 EHDAA:1498 EHDAA:255 EMAPA:16073 EV:0100004 Embryonic ectoderm that gives rise to nervous tissue. FBbt:00001061 FMA:87657 MAT:0000176 MIAA:0000176 TAO:0001120 UBERON:0002346 UMLS:C1518271 VHOG:0000150 XAO:0000042 ZFA:0001120 epithelium tubi neuralis; neuroectoderma neuaral ectoderm neural ectoderm neurectodermal neuroectoderm presumptive central nervous system uberon ventral neurogenic region we prefer neurectoderm to neural ectoderm since placodal ectoderm is not classified here myocardium AAO:0010410 BSA:0000089 BTO:0000901 CALOHA:TS-0440 EFO:0000819 EHDAA2:0004150 EMAPA:32688 EV:0100022 FMA:9462 GAID:173 MA:0000164 MAT:0000453 MESH:D009206 OpenCyc:Mx4ro36AFrCvEduAAAAOpmP6tw RETIRED_EHDAA2:0001220 Robust muscular tunic of the heart which forms the basic part of its walls. Its external surface is covered by the pericardium and its internal one by the endocardium. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] TAO:0001319 TODO - check 'Myocardum proper' in FMA. We superclass the more generic class for now. FMA has is_a muscle layer - should we add this? ZFA and BTO both have is_a 'cardiac muscle' (tissue?). But in U we also follow FMA and have cardiac muscle tissue of myocardium (there is also Fibrocollagenous connective tissue of myocardium), which would be identical (see issue-10). Note that GO also treats left/right ventricular cardiac muscle tissue synonymous with ventricular myocardium The middle layer of the heart, consisting of cardiac muscle.[AAO] UBERON:0002349 UMLS:C0027061 VHOG:0000083 XAO:0000065 ZFA:0001319 cardiac muscle galen:Myocardium heart muscle heart myocardium muscle of heart myocardial the middle layer of the heart, comprised mainly of striated cardiac muscle fibers uberon conducting system of heart EFO:0003909 EHDAA2 divides the system from the tissue EHDAA2:0004185 EMAPA:35428 EV:0100025 FMA:9476 MA:0000094 MESH:D006329 TAO:0005063 The cardiac conduction system consists of specialized cardiomyocytes that regulate the frequency of heart beat[GO] The fish heart displays clear polarity of contraction in a posterior-to-anterior direction. The contraction waves originate in the sinus venosus and terminate in the conus arteriosus. The nodal phenotype persists in the inflow region of the heart, varying from the venosinus to the sinoatrial junctional areas in different species . Similar to the mammalian situation, pacemaker tissue with a lower intrinsic rhythmicity is also found at the atrioventricular junction.[uncertain][VHOG] UBERON:0002350 VHOG:0001271 ZFA:0005063 cardiac conducting system cardiac conduction system cardiac impulse conducting system cardionector central conduction system complexus stimulans cordis heart conduction system impulse conducting system systema conducente cordis uberon sinoatrial node BTO:0004358 EHDAA2:0004184 EMAPA:35772 FMA:9477 GAID:561 Koch's node MA:0000097 MESH:D012849 OpenCyc:Mx4rOhejDGMcEd2AAABQjYGu0g SA nodal muscle tissue SA node TAO:0005069 The part of the cardiac conduction system that controls the timing of heart muscle contraction. It relays electrical signals to the AV node[GO]. Subdivision of conducting system of heart at the junction of the right atrium and the superior vena cava, around the sinoatrial nodal branch of right coronary artery and is continuous with the internodal tract[FMA]. UBERON:0002351 UMLS:C0037189 WP:Heart states: "The SA node is found in all amniotes but not in more primitive vertebrates. In these animals, the muscles of the heart are relatively continuous and the sinus venosus coordinates the beat which passes in a wave through the remaining chambers. Indeed, since the sinus venosus is incorporated into the right atrium in amniotes, it is likely homologous with the SA node. In teleosts, with their vestigial sinus venosus, the main centre of coordination is, instead, in the atrium.". Note however that ZFA has SA node. ZFA:0005069 cardiac pacemaker node of Keith-Flack nodus sinuatrialis nodus sinuatrialis sinoatrial node sinu-atrial node sinuatrial nodal muscle tissue sinuatrial node sinus node sinus node of Keith and Flack uberon pelvic region of trunk BTO:0001006 CALOHA:TS-2227 EFO:0002805 EMAPA:35931 EV:0100012 FMA:9578 GAID:87 MA and FMA differ in what they consider to be parts of the pelvis. MA includes ureter, urethra, urinary bladder, reproductive organs MA:0000030 MESH:A01.673 OpenCyc:Mx4rvVjiTJwpEbGdrcN5Y29ycA The lower segment of the trunk, inferioposterior to the abdomen proper, in the transition area between the trunk and the lower limbs. UBERON:0002355 UMLS:C0030797 galen:Pelvis lesser pelvis pelvic pelvic region pelvis pelvis region true pelvis uberon meninx BTO:0000144 CALOHA:TS-1177 EFO:0000867 EMAPA:32660 EV:0100312 FMA:9589 GAID:687 In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] MA:0001113 MAT:0000113 MESH:D008578 Membrane covering the brain and spinal cord. It is represented by a single layer in fishes, two in amphibians, reptiles and birds and three in mammals (named dura mater, arachnoid and pia mater). [TFD][VHOG] Membrane organ that surrounds the brain and the spinal cord. Not consider part of the CNS/neuraxis in FMA OpenCyc:Mx4rwDOl8JwpEbGdrcN5Y29ycA TAO:0001355 UBERON:0002360 UMLS:C0025285 VHOG:0001295 Whereas cyclostomes and fishes only have a single envelope called the primitive meninx, amphibians have two layers, consisting of an outer dura mater which is extremely dense and protective, and a pia-arachnoid or secondary meninx which is more delicate and vascular. Mammals have three meninges: pia mater (which follows all the convolutions of the brain and is the most interior), the arachnoid layer (which is delicate and sends strands to the pia mater), and the dura mater (the outer, more protective meninx). ZFA:0001355 layer of meninges meningeal meningeal layer meninx primitiva uberon exocrine gland A gland that secretes products (excluding hormones and other chemical messengers) into ducts (duct glands) which lead directly into the external environment[WP]. Typical exocrine glands include sweat glands, salivary glands, mammary glands, stomach, liver, pancreas AEO:0000097 BTO:0000765 CALOHA:TS-2012 Currently this is logically defined by the system it belongs to, but a better system may be base this on presence/absence of ducts. However, the dual nature of the liver should be taken into consideration here. Consider adding subclasses EHDAA2:0003097 EMAPA:35327 FMA:9596 GAID:34 MA:0002564 MESH:D005088 UBERON:0002365 UMLS:C0015282 ducted gland glandula exocrina uberon prostate gland BTO:0001129 CALOHA:TS-0828 EFO:0000858 EMAPA:19287 EV:0100104 FMA:9600 GAID:392 MA:0000404 MAT:0000078 MESH:D011467 MIAA:0000078 OpenCyc:Mx4rv6trqZwpEbGdrcN5Y29ycA TODO - FMA treats the gland as part of the prostate - see also FMA:74119. The prostate gland is a partly muscular, partly glandular body that is situated near the base of the mammalian male urethra and secretes an alkaline viscid fluid which is a major constituent of the ejaculatory fluid. UBERON:0002367 UMLS:C0033572 VHOG:0001261 galen:ProstateGland male prostate prostata prostate prostatic uberon endocrine gland AEO:0000098 BTO:0001488 CALOHA:TS-1300 EHDAA2:0003098 EMAPA:35999 Endocrine glands are glands of the endocrine system that secrete their products directly into the circulatory system rather than through a duct.[WP, modified]. FMA:9602 GAID:335 MA:0002563 MESH:D004702 OpenCyc:Mx4rvbkiRZwpEbGdrcN5Y29ycA UBERON:0002368 UMLS:C0014133 ductless gland ductless gland glandula endocrina glandulae endocrinae uberon bone marrow AAO:0011007 BTO:0000141 BTO:0000829 CALOHA:TS-0087 EFO:0000868 EMAPA:32760 EV:0100046 FMA:9608 GAID:1287 In adults, marrow in large bones produces new blood cells[Wikipedia:Bone_marrow] MA:0000134 MAT:0000084 MESH:D001853 MIAA:0000084 OpenCyc:Mx4rvVm-FpwpEbGdrcN5Y29ycA TODO - create superclass for bone marrow / head kidney. both are portions of tissue in the hematopoetic system. also consider adding as subclass of zone of bone organ for consistency with FMA. See also: Leydig and epigonal organs The bone marrow is the hematopoietic organ in all vertebrates but fishes, in which hematopoiesis occurs in the kidney.[well established][VHOG] UBERON:0002371 UMLS:C0005953 VHOG:0001218 XAO:0000123 galen:BoneMarrow medulla of bone medulla ossea medulla ossium the soft tissue that fills the cavities of bones uberon connective tissue AAO:0000098 BTO:0000421 Bindegewebe CALOHA:TS-2009 EFO:0000952 EMAPA:35251 FMA:9640 GAID:100 MA also has set of connective tissues MA:0000011 MAT:0000301 MESH:D003238 MIAA:0000301 One of the four types of tissue in traditional classifications. It is largely a category of exclusion rather than one with a precise definition, but there are certain characteristics shared by all or most tissues in this category, such as involvement in structure and support, derived from mesoderm, and characterized largely by the traits of non-living tissue.[AAO] OpenCyc:Mx4rv-aBgZwpEbGdrcN5Y29ycA Portion of tissue that consists of mesodermally derived cells and intercellular matrix comprised of protein fibers and carbohydrates, which supports, ensheathes and binds together other tissues.[TAO] TAO:0001641 Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance. Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance.[VSAO] UBERON:0002384 UMLS:C0009780 VSAO:0000017 XAO:0001017 ZFA:0001632 galen:ConnectiveTissue portion of connective tissue textus connectivus uberon muscle tissue AAO:0000306 AEO:0000122 CALOHA:TS-0642 EHDAA2:0003122 EMAPA:32715 FMA:9641 MA:0002437 MESH:D009132 Muscle tissue is a contractile tissue made up of actin and myosin fibers[GO]. One of the four types of tissue in traditional classifications. Tissue that contains cells with contractile filaments that move past each other and change the size of the cell. Muscle tissue also is separated into three distinct categories.[AAO] UBERON:0002385 UMLS:C2328219 Vertebrate muscle is categorized into three major muscle types defined by their structural and functional properties: skeletal, cardiac and smooth. In Dmel the counterparts are somatic, heart/cardiac and visceral. Here we take a cell type based approach. galen:MuscleTissue muscular tissue portion of muscle tissue textus muscularis uberon pes BTO:0000476 CALOHA:TS-0377 EFO:0003065 EHDAA2:0000546 EMAPA:17459 FMA:9664 GAID:40 MA:0000044 MESH:D005528 OpenCyc:Mx4rvVi-k5wpEbGdrcN5Y29ycA UBERON:0002387 UMLS:C0016504 VHOG:0000350 distal portion of the hind limb, including tarsal region, metatarsal region and digits. foot galen:Foot hind foot hind limb autopodium hind paw hind-paw hindfeet hindfoot hindfoot of quadruped hindlimb autopod hindlimb autopodium hindlimb distal free limb segment hindpaw pedal pes terminal segment of free lower limb uberon hematopoietic system AAO:0011002 Anatomical system that consists of the blood and blood forming tissues.[AAO] Anatomical system that is involved in the production of hematopoietic cells. BTO:0000570 Blutbildungssystem CALOHA:TS-0449 EFO:0000798 EMAPA:35402 EV:0100045 FMA:9667 GAID:1008 In humans this is primarily the bone marrow, spleen, tonsils, and lymph nodes MA:0002434 MAT:0000022 MESH:D006413 MIAA:0000022 TAO:0005023 UBERON:0002390 UMLS:C0018957 VHOG:0001624 XAO:0000122 ZFA:0005023 Zebrafish developmental hematopoiesis shows close correspondence to the development of the mammalian hematopoietic system and is regulated by conserved molecular pathways.[well established][VHOG] haematological system haematopoietic system haemopoietic system hematological system hematolymphoid system hematopoietic hemopoietic system organa haemopoietica uberon bile duct (...) the amphibian liver has characteristics in common with both fish and terrestrial vertebrates. (...) The histological structure of the liver is similar to that in other vertebrates, with hepatocytes arranged in clusters and cords separated by a meshwork of sinusoids and the presence of the traditional triad of portal venule, hepatic arteriole, and bile duct.[well established][VHOG] A duct that carries bile from the liver to the intestine. AAO:0011019 Any of the ducts that form the biliary tree, carrying bile from the liver to the small intestine. Any of the excretory ducts in the liver that convey bile between the liver and the intestine. [TFD][VHOG] BTO:0000122 CALOHA:TS-0075 EHDAA2:0000741 EMAPA:35171 EV:0100091 FMA:9706 GAID:280 MA:0000354 MESH:D001652 OpenCyc:Mx4rvdCds5wpEbGdrcN5Y29ycA TAO:0001100 UBERON:0002394 UMLS:C0005400 VHOG:0000212 XAO:0000134 ZFA:0001100 bile tube biliary duct gall duct hepatic duct uberon we place the ZFA class here as this fits its textual definition and child nodes. We may recommend a label change for ZFA immune system AAO:0011003 Anatomical system that protects the body from foreign substances, cells, and tissues by producing the immune response and that includes especially the thymus, spleen, lymphoid tissue, lymphocytes including the B cells and T cells, and antibodies. BILA:0000104 FMA:9825 GAID:328 MA:0002711 MESH:D007107 OpenCyc:Mx4rvWNkm5wpEbGdrcN5Y29ycA TAO:0001159 The antibody-based immune system defined by the presence of the major histocompatibility complex (MHC), T cell receptor (TCR), B cell receptor (BCR) or recombination activating genes (RAGs) is known beginning from jawed fishes.[well established][VHOG] UBERON:0002405 UMLS:C0020962 VHOG:0001247 XAO:0003152 ZFA:0001159 uberon integumental system (...) the integument of many tetrapods is reinforced by a morphologically and structurally diverse assemblage of skeletal elements. These elements are widely understood to be derivatives of the once all-encompassing dermal skeleton of stem-gnathostomes (...).[well established][VHOG] AEO:0000154 BILA:0000118 CALOHA:TS-1299 CARO:0002001 Connected anatomical system that forms a barrier between an animal and its environment. In vertebrates, the integumental system consists of the epidermis, dermis plus associated glands and adnexa such as hair and scales. In invertebrates, the integumental system may include cuticle. EFO:0000807 EHDAA2:0000836 EHDAA2_RETIRED:0003154 EHDAA:6520 EMAPA:17524 EV:0100151 FBbt:00004969 FMA:72979 HAO:0000421 MA:0000014 MAT:0000033 MESH:D034582 MIAA:0000033 TADS:0000108 UBERON:0002416 UBERON:0007029 UMLS:C0037267 VHOG:0000403 XAO:0000176 body surface dermal system external covering of organism galen:Surface integumentary system integumentum commune organism surface surface uberon abdominal segment of trunk EMAPA:35104 FMA:259211 MA:0000021 The abdominal segment of the torso. UBERON:0002417 abdomen/pelvis/perineum lower body lower trunk lumbar region uberon cartilage tissue A type of dense connective tissue. It is composed of cells called chondrocytes which are dispersed in a firm gel-like ground substance, called the matrix. Cartilage is avascular (contains no blood vessels) and nutrients are diffused through the matrix. Cartilage is found in the joints, the rib cage, the ear, the nose, in the throat and between intervertebral disks. It makes up virtually the entire skeleton in chondrichthyes.[AAO] AAO:0000060 AEO:0000087 BTO:0000206 EFO:0000949 EHDAA2:0003087 EMAPA:32730 EV:0100141 FMA:37377 GAID:99 MA:0000104 MAT:0000189 MESH:D002356 MIAA:0000189 OpenCyc:Mx4rvVjeOZwpEbGdrcN5Y29ycA Phylogenetic analysis suggests that cartilage arose independently in cnidarians, hemichordates, vertebrates, arthropods, annelids, brachiopods, and molluscs - or a common ancestor of brachiopods and molluscs (...). Analyses of cartilage as a tissue and of the development of invertebrate cartilages are consistent with homology between invertebrate and vertebrate cartilage. From the discussion above, it will be clear that understanding genetic changes underlying cartilage evolution is key to determining whether the multiple origins of cartilage represent parallel evolution.[well established][VHOG] Portion of tissue which is connective tissue composed of collagen and/or elastin fibers and chondrocytes. Cartilage is avascular and provides both skeletal functions and a framework upon which bone is deposited.[TAO] Previous: "A portion of connective tissue dominated by extracellular matrix containing collagen type II and large amounts of proteoglycan, particularly chondroitin sulfate[GO]. Regular connective tissue, which consists of chondrocytes and related cells, the intercellular matrix of which is chondrified. Examples: hyaline cartilage, fibrocartilage, elastic cartilage[FMA]. an avascular supporting and articular skeletal tissue. It also functions as the primary endoskeletal support in vertebrate embryos. Cartilage is deposited by and is composed of chondroblasts and chondrocytes separated by an extracellular matrix, which may or may not mineralize depending on cartilage type, age, or taxon[Hall and Witten]." See also FMA:71500 Set of cartilages, FMA:55107 Cartilage organ, FMA:12264 Articular cartilage. // elements made from cartilage, cartilage-like, or chondroid tissues evolved in invertebrates[H&W] Skeletal tissue that is avascular, rich in glycosaminoglycans (GAGs) and typically includes chondrocytes within isolated lacunae. Cartilage tissue is deposited by chondroblasts. Skeletal tissue that is avascular, rich in glycosaminoglycans (GAGs) and typically includes chondrocytes within isolated lacunae. Cartilage tissue is deposited by chondroblasts.[VSAO] TAO:0001501 UBERON:0002418 UMLS:C0007301 VHOG:0001207 VSAO:0000040 XAO:0000170 ZFA:0005622 cartilage cartilage tissue cartilages cartilaginous tissue chondrogenic tissue galen:Cartilage portion of cartilage tissue relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO] uberon hepatobiliary system AAO:0011056 CALOHA:TS-1308 EFO:0000800 EHDAA2:0000998 EHDAA:2189 EMAPA:16840 EV:0100088 MA:0000324 MAT:0000024 MIAA:0000024 System responsible for the production and movement of bile[ZFIN:curator]. TAO:0000036 The hepaticobiliary system is responsible for metabolic and catabolic processing of small molecules absorbed from the blood or gut, hormones and serum proteins, detoxification, storage of glycogen, triglycerides, metals and lipid soluble vitamins and excretion of bile. Included are the synthesis of albumin, blood coagulation factors, complement, and specific binding proteins. The parts are: liver, bile duct, gall bladder and hepatic duct [GO:0061008] The part of the digestive system that contains the liver and the biliary system UBERON:0002423 UMLS:C1711359 VHOG:0000294 XAO:0000132 ZFA:0000036 hepaticobiliary system liver and biliary system liver/biliary system uberon limb bone A bone that is part of a limb [Automatically generated definition]. EFO:0000945 MAT:0000151 MIAA:0000151 NCITA includes clavicle. MA:'limb bone' is actually a bone of limb or girdle UBERON:0002428 UMLS:C0582791 bone of extremity bone of limb free limb bone the formal definition is very inclusive, and includes sesamoids uberon autopod region BTO:0004359 EFO:0000877 EMAPA:32722 FMA:83015 MA:0002714 MAT:0000091 MIAA:0000091 Naming conventions for pod terms under discussion within phenoscape group; note that this refers to the limb segment, not just the skeleton. Terminal segment of free limb, immediately distal to the zeugopod region. The fully developed autopod consists of the autopod skeleton plus associated structures such as integument, muscle tissue, vasculature etc. The autopod is divided into mesopodial, metapodiual, and acropodial segments. Examples: human hand, mouse paw, human foot UBERON:0002470 UMLS:C0687080 autopod autopodial element autopodial limb segment autopodial segment autopodium autopodium region distal free limb segment distal segment of free limb distal segment of limb manus/pes paw paw/hand/foot/hoof pod uberon zeugopod EFO:0000878 FMA:83016 MA:0002716 MAT:0000092 MIAA:0000092 The middle free limb segment, between the autopod and stylopod segments. Includes as parts the zeugopodial skeleton. Examples: There are two types of zeugopod: forelimb zeugopod (aka forearm), hindlimb zeugopod (aka crus). There exists some controversy about which podial segments are present in some fishes, e.g. if the autopod is not newly evolved in tetrapods, there is a question as to which segments are actually present in basal vertebrate taxa.[PHENOSCAPE:curators] UBERON:0002471 epipodium middle free limb segment middle limb segment middle part of limb middle segment of free limb uberon zeugopod limb segment zeugopodial zeugopodial limb segment zeugopodium zygopod zygopodium stylopod EFO:0000879 FMA:83014 MA:0002717 MAT:0000093 MIAA:0000093 Naming conventions for pod terms under discussion within phenoscape group The proximal free limb segment. Includes as parts the stylopod skeleton. UBERON:0002472 propodium proximal free limb segment proximal part of limb proximal segment of free limb stylopodial stylopodial limb segment stylopodium uberon bone tissue CALOHA:TS-2011 EMAPA:35179 FMA:224804 MA:0002780 MESH:D001842 Skeletal tissue with a collagen-rich extracellular matrix vascularized, mineralized with hydroxyapatite and typically including osteocytes located in lacunae that communicate with one another by cell processes (in canaliculi). Bone is deposited by osteoblasts. Skeletal tissue with a collagen-rich extracellular matrix vascularized, mineralized with hydroxyapatite and typically including osteocytes located in lacunae that communicate with one another by cell processes (in canaliculi). Bone is deposited by osteoblasts.[VSAO] UBERON:0002481 UMLS:C0391978 VSAO:0000047 XAO:0004040 ZFA:0005621 bone calcium tissue galen:BoneTissue mineralized bone tissue osseous tissue osteogenic tissue portion of bone tissue see https://github.com/obophenotype/uberon/issues/27 uberon long bone BTO:0004256 EMAPA:35503 Endochondral_ossification is an essential process during the rudimentary formation of long bones, with the exception of the clavicle[Wikipedia:Endochondral_ossification]. The medial and and lateral ends undergo EO, the mid-portion is formed by a process with features of EO & IO (the process is shared by the mandible)[ISBN:9780397517251] FMA:7474 Long bone is a limb bone that is subcylindrical and has a shaft with periosteum separating the ends of the bones. Long bones are present only in the limbs[VSAO:wd]. MA:0002802 OpenCyc:Mx4rv6axr5wpEbGdrcN5Y29ycA UBERON:0002495 UMLS:C0222647 galen:LongBone os longum uberon endochondral bone AAO:0010776 AEO:0000083 BTO:0002157 EHDAA2:0003083 FMA:24321 Replacement bone that forms within cartilage. Replacement bone that forms within cartilage.[VSAO] TAO:0001591 UBERON:0002513 VSAO:0000145 XAO:0004018 ZFA:0001591 cartilaginous bone endochondral bones https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern ossified chondrogenic bone placement in this class to be inferred some structures, e.g. in ZFA are both intramembrane and endochondral uberon limb segment A major subdivision of a mature or developing limb, including both skeletal elements (or the mesenchyme that gives rise to the skeletal elements) and associated tissues, such as muscle, connective tissue, integument. Examples: autopod region, zeugopod region, stylopod region, metapodial region, arm region. Excludes the limb girdles. FMA has both limb segment and free limb segment, the former includes the girdles. Note that MA uses the term more generally and includes A,S,Z,S+Z(arm/leg), whereas FMA is just A,S,Z FMA:241863 MA:0002889 TODO - align this with the CARO2 class 'appendage segment'; note the FMA class does not appear to require repetition UBERON:0002529 UMLS:C1268195 extremity part free limb segment limb region region of limb segment of limb subdivision of limb uberon gland AAO:0000212 AEO:0000096 BTO:0000522 Druese EFO:0000797 EHDAA2:0003096 EHDAA:2161 EHDAA:4475 EHDAA:6522 EMAPA:18425 FBbt:00100317 FMA:7146 FMA:86294 HAO:0000375 MA:0003038 MAT:0000021 MIAA:0000021 OpenCyc:Mx4rwP3vyJwpEbGdrcN5Y29ycA UBERON:0002530 UBERON:MIAA_0000021 UMLS:C1285092 WikipediaCategory:Glands an organ that functions as a secretory or excretory organ galen:Gland glandula glandular glandular organ uberon paired fin bud An outgrowth on the lateral trunk of the embryo that develops into a paired fin. The fin bud is divided into ectoderm and mesenchyme[cjm, modified from MP]. EFO:0003468 Embryonic surface structure that develops into a paired fin.[ZFA] MAT:0000062 MIAA:0000062 TAO:0001383 UBERON:0002531 VSAO:0000179 ZFA:0001383 fin bud fin buds uberon epiblast (generic) BTO:0004593 FMA:296704 In amniote animal embryology, the epiblast is a tissue type derived either from the inner cell mass in mammals or the blastodisc in birds and reptiles. It lies above the hypoblast. In mammalian embryogenesis, the columnar cells of the epiblast are adjacent to the trophoblast, while the cuboidal cells of the hypoblast are closer to the blastocoele. The epiblast, whilst referred to as the primary ectoderm, differentiates to form all three layers of the trilaminar germ disc in a process called gastrulation[WP]. The outer of the two layers of the blastoderm that form during gastrulation, corresponding to primitive ectoderm during gastrulation and to the definitive ectoderm after gastrulation[ZFA] In pregastrula zebrafish embryos, the epiblast is an inverted cup of cells that sits on top of a large yolk cell. (...) In amniote embryos (mammals and birds), gastrulation initiates in an epithelial layer called the epiblast. Cells in the epiblast undergo an epithelial to mesenchymal transition (EMT), migrate through the primitive streak (PS), and incorporate in the middle (mesoderm) or outer (endoderm) layer. The presumptive definitive endoderm (DE) cells invade and displace an outer layer of extraembryonic tissue cells, the hypoblast in chick and the visceral endoderm (VE) in mouse, which form supporting structures such as the yolk sac.[uncertain][VHOG] MAT:0000067 MIAA:0000067 MP says - tissue that gives rise to the ectoderm, endoderm and mesoderm of the embryo proper. In HOG, epiblast is part of primitive streak/blastpore, which is inconsistent with the MP definition of primitive streak as a ridge of the epiblast. Note that these terms, epiblast and hypoblast, are also used to describe layers of the avian embryonic blastoderm, but the layers so-named seem to be altogether different in these two kinds of vertebrate embryos(CVS). Consider obsoleting this as a grouping class UBERON:0002532 VHOG:0000243 blastocyst ectoblast epiblast epiblastus primitive ectoderm uberon paired fin Fin that is one of a pair located ventrally on the organism. TAO:0002278 UBERON:0002534 VSAO:0000111 ZFA:0005596 artioptérygie@fr nageoire paire@fr pelvic/pectoral fin uberon pharyngeal arch A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down.[well established][VHOG] AAO:0010359 BTO:0001785 EFO:0000959 EHDAA:571 EMAPA:16117 FMA:293015 GAID:1292 MAT:0000242 MESH:A16.254.160 MIAA:0000242 Numbered cranial to caudal. different in mammals. branchial arch = ZFA:0001613 pharyngeal arch 3-7. generally gill arch 1 = pharyngeal arch 3. terminology varies as to whether branchial arch follows gill or pharyngeal numbering One of a series of bony or cartilaginous arches that develop in the walls of the mouth cavity and pharynx of the embryo.[AAO] One of a series of paired bulges that develop along the lateral walls of the foregut. The pharyngeal arches have developmental contributions from endoderm, mesoderm, and neural crest cells and are separated by anterior lateral endoderm out-pockets known as pharyngeal pouches. TAO:0001306 UBERON:0002539 UMLS:C0080322 VHOG:0000155 XAO:0000096 ZFA:0001306 arcus pharyngei branchial arch pharyngeal arches uberon visceral arch digit A subdivision of the autopod that has as part a series of phalanges together with associated vasculature, musculature, integument and nerves. It is continuous with the metapodial subdivision of the autopod, but does not include the metapodials. In species such as humans, fully formed digits are distinct, whereas in other species the digits may be connected by interdigital webbing, or may be completely unseparated (for example, in cetaceans). AAO:0011126 EFO:0000881 EMAPA:32725 FMA:85518 MA:0000690 MAT:0000285 MIAA:0000285 OpenCyc:Mx4rvzLD_ZwpEbGdrcN5Y29ycA Our reinterpretation of the distal fin endoskeleton of Panderichthys removes the final piece of evidence supporting the formerly popular hypothesis that tetrapod digits are wholly new structures without homologues in sarcopterygian fish fins. This hypothesis, which was based partly on the complete absence of plausible digit homologues in Panderichthys (then the closest known relative of tetrapods), has already been called into question by the discovery of digit-like radials in Tiktaalik and the fact that Hox gene expression patterns closely resembling those associated with digit formation in tetrapods occur in the distal fin skeletons of paddlefish and Australian lungfish. Our new data show that Panderichthys is not an anomaly: like Tiktaalik and other fish members of the Tetrapodomorpha, it has distal radials that can be interpreted as digit homologues.[well established][VHOG] UBERON:0002544 UMLS:C0582802 VHOG:0000944 XAO:0003032 acropodial unit digit (phalangeal portion) plus soft tissue digital galen:Digit limb digit this class represents the entire organism subdivision encompassing soft tissue as well as the underlying skeletal framework. The class represents the phalangeal part only - historically the term 'digit' has also been used to represent the unit consisting of a series of phalanges together with a metapodial bone. We may in future relabel this class to avoid confusion with this concept, but the class will continue to represent the phalangeal portion uberon cranial placode AAO:0010466 Comparisons of developmental gene expression suggest that the anterior ectoderm in amphioxus may be homologous to the vertebrate olfactory placode, the only vertebrate placode with primary, not secondary, neurons EFO:0001650 Ectodermal placode that develops in the head into a part of the sensory nervous system. With a few exceptions (lens, adenohypophyseal), cranial placodes are neurogenic. MAT:0000369 MIAA:0000369 The term placode or placodes also applies to developing organs such as teeth, mammary glands, hair follicles, feathers and scales. We include a separate parent class for this. UBERON:0002546 XAO:0000305 cranial placodes placode to avoid confusion, we include neurogenic placode as a subclass. Do not merge. uberon anatomical cavity Anatomical space which contains portions of one or more body substances and is bounded by the internal surface of one maximally connected anatomical structure. Examples: cranial cavity, pharyngeal recess space, nasal cavity, tooth socket, cavity of serous sac, lumen of stomach, lumen of artery, fornix of vagina. FMA:67552 MA:0002447 UBERON:0002553 cavity galen:Cavity uberon regional part of brain Anatomical divisons of the brain according to one or more criteria, e.g. cytoarchitectural, gross anatomy. Parts may be contiguous in 3D or not, e.g., basal ganglia. FMA:55676 UBERON:0002616 UMLS:C0445620 anatomical structure of brain biological structure of brain brain anatomical structure brain biological structure brain part neuraxis segment neuroanatomical region segment of brain uberon olfactory placode A thick plate of cells derived from the neural ectoderm in the head region of the embryo that develops into the olfactory region of the nasal cavity. AAO:0011076 EFO:0003420 EHDAA2:0001232 EHDAA:1504 EMAPA:16543 FMA:293971 Olfactory placodes are the only ectodermal placodes to produce glia, a cell type typically derived from neural crest // Note that NBK53171 classifies this as non-neurogenic TAO:0000048 UBERON:0003050 VHOG:0000186 We conclude this section by listing some of the many synapomorphies of craniates, including (...) (2) neurogenic placodes (...).[well established][VHOG] XAO:0000005 ZFA:0000048 nasal I placode nasal placode olfactory placodes placoda nasalis placoda olfactoria uberon midbrain-hindbrain boundary AAO:0011064 DMBA:16810 EHDAA2:0004395 EHDAA:5789 EMAPA:32857 Lampreys also have an MHB [midbrain hindbrain boundary], expressing a similar repertoire of regulatory gene cognates as in gnathostomes.[well established][VHOG] MHB TAO:0000042 The part of the brain that is the morphological boundary between the midbrain and hindbrain and that is the location of an organizing center which patterns the midbrain and hindbrain primordia of the neural plate. UBERON:0003052 VHOG:0000649 XAO:0000016 ZFA:0000042 consider adding class for organizer. Consider adding separate class for isthmus as a structure isthmic organizer territory isthmo-cerebellar region isthmus isthmus/MHB mid-hindbrain boundary mid-hindbrain junction midbrain hindbrain boundary uberon periderm A temporary epithelium that derives from the outer layer of the ectdoerm and is shed once the inner layer differentiates to form a true epidermis. EHDAA2:0001846 EHDAA:6538 EVL FMA:295662 In mice, the first non-basal layer formed at ~E9.5; it is a temporary structure composed of simple squamous epithelium that serves as the first barrier to the embryo's physical environment, exists throughout the entire keratinocyte stratification process, and sheds off at ~E17, when it is replaced by corneocytes[MP] In some mammals, Eyelid Fusion is thought to be driven by a population of cells which are derived from the periderm, the outermost layer of the developing epidermis Originally the epidermis is one layer thick, in most vertebrates it soon becomes a two-layered structure. The outer layer gives rise to the periderm. The periderm goes through distinct developmental phases and is ultimately sloughed into the amniotic fluid when differentiation of the underlying epidermal layers is complete. The function of the periderm is not known, but is thought to be related to transport/exchange between the fetus and the amniotic fluid (http://courses.washington.edu/hubio567/devbio/periderm.html) TAO:0001185 The outermost epidermal layer covering the fish at embryonic stages; derived from the EVL and thought to eventually be replaced by the superficial stratum of the epidermis. Sometimes used synonymously with EVL. Le Guellec et al, 2004.[TAO] UBERON:0003055 UMLS:C1518973 VHOG:0001680 XAO:0000029 ZFA:0001185 epidermis epithelial layer epidermis outer layer epitrichium periderm relationship type change: OBO_REL:part_of ectoderm (TAO:0000016) CHANGED TO: develops_from ectoderm (UBERON:0000924)[TAO] skin periderm uberon pre-chordal neural plate (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] AAO:0011084 TAO:0007016 The portion of neural plate anterior to the mid-hindbrain junction. UBERON:0003056 VHOG:0001200 XAO:0000045 ZFA:0007016 anterior neural plate uberon chordal neural plate (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] TAO:0007017 The portion of neural plate posterior to the mid-hindbrain junction. UBERON:0003057 VHOG:0001201 XAO:0000046 ZFA:0007017 posterior neural plate uberon presomitic mesoderm AAO:0011086 EFO:0001982 EMAPA:16189 EMAPA:16752 It is reasonable to assume that the proximate invertebrate ancestor of the vertebrates had an amphioxus-like tail bud in its larval stage. This archetypal tail bud would have (...) (3) lacked any component of mesenchyme cells, (4) budded off new mesodermal segments directly, without any intervening zone of presomitic mesoderm (...). Then, early in vertebrate evolution, epithelium-to-mesenchyme interconversions (and the gene networks for effecting them) became prominent features of development. (...) In any case, conspicuous mesenchymal components tended to be added to the vertebrate tail bud itself. In addition, a mesenchymatous presomitic mesoderm (not a part of the tail bud proper) came to intervene between the tail bud and the forming somites.[well established][VHOG] PSM TAO:0000279 UBERON:0003059 Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. Kimmel et al, 1995.[TAO] VHOG:0000559 XAO:0000057 ZFA:0000279 presumptive somite mesoderm segmental plate somitogenic mesoderm somitomeric mesoderm uberon unsegmented mesenchyme unsegmented paraxial mesoderm pronephric duct (...) in all craniates, the archinephric duct develops in embryogeny.[well established][VHOG] AAO:0011088 Duct of the embryonic kidney, present bilaterally ventral to the somites and leading to the anal region where it empties separately from, and just posterior to the anus. Kimmel et al, 1995.[TAO] In mammals, the pronephric duct is the predecessor of the Wolffian duct[WP]. TAO:0000150 The first-formed kidney duct, which drains the kidney of most anamniotes and becomes the ductus deferens of male amniotes. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-3, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG] The pronephric duct collects the filtrate from the pronephric tubules and opens to the exterior of the pronephric kidney[GOC:mtg_kidney_jan10, http://www.ncbi.nlm.nih.gov/pubmed/15647339, XAO:0000063, ZFA:0000150] UBERON:0003060 UMLS:C1283945 VHOG:0000082 XAO:0000063 ZFA:0000150 archinephric duct ductus pronephricus pronephric ducts uberon blood island AAO:0011006 Blood islands are structures in the developing embryo which lead to many different parts of the circulatory system. They primarily derive from plexuses formed from angioblasts. Within them, vacuoles appear through liquefaction of the central part of the syncytium into plasma. The lumen of the blood vessels thus formed is probably intracellular. The flattened cells at the periphery form the endothelium. The nucleated red blood corpuscles develop either from small masses of the original angioblast left attached to the inner wall of the lumen or directly from the flat endothelial cells. In either case the syncytial mass thus formed projects from and is attached to the wall of the vessel. Such a mass is known as a blood island and hemoglobin gradually accumulates within it. Later the cells on the surface round up, giving the mass a mulberry-like appearance. Then the red blood cells break loose and are carried away in the plasma. Such free blood cells continue to divide. Blood islands have been seen in the area vasculosa in the omphalomesenteric vein and arteries, and in the dorsal aorta[WP, unvetted]. EFO:0003489 EHDAA2 distinguishes 3 types, but does not have a superclass. The VHOG class may refer to yolk sac EHDAA:207 Nests of developing blood cells arising late in the segmentation period from the intermediate mass, and located in the anterior-ventral tail, just posterior to the yolk extension. Kimmel et al, 1995.[TAO] Region located on the ventral surface of the developing embryo that is a site of hematopoiesis and that is analogous to the yolk sac blood islands of higher vertebrates.[AAO] Small clusters of mesodermal cells called blood islands mark the embryonic debut of the cardiovascular system (in vertebrates) (reference 1); In birds and mammals, primitive hemangioblasts are extraembryonic, populating the yolk sac as the so-called blood islands (reference 2).[well established][VHOG] TAO:0000094 TE:E5.11.2.0.0.0.4 UBERON:0003061 UMLS:C1511224 VBI VHOG:0000085 XAO:0000067 ZFA:0000094 blood islands caudal hematopoietic tissue posterior ICM posterior blood island relationship loss: part_of intermediate cell mass of mesoderm (TAO:0000033)[TAO] uberon ventral blood island ventral lateral plate mesoderm intermediate mesoderm (...)the mesoderm of a developing vertebrate transitionally differentiates into the following sub-types: Chordamesoderm (also known as axial mesoderm) which later on gives rise to notochord in all chordates, Paraxial mesoderm, Intermediate mesoderm, Lateral plate mesoderm (reference 1); The mesoderm is present in Bilateria, therefore they are sometimes called triploblasts. Ectoderm and endoderm are usually organized as epithelial layers, while mesoderm can be epithelial or a compact, three-dimensional tissue.[well established][VHOG] AAO:0010575 EMAPA:16056 EMAPA:16178 FMA:293147 IM Mesoderm between somite and lateral plate. Traditionally thought to give rise to the urogenital system.[AAO] TAO:0001206 The intermediate mesoderm is located between the lateral mesoderm and the paraxial mesoderm. It develops into the kidney and gonads. UBERON:0003064 UMLS:C1284010 VHOG:0000087 XAO:0000085 ZFA:0001206 all AOs differ in the relationship between this structure and the mesoderm; in ZFA it is a subclass (and this is implied by the GO definition and GO relationships), in AAO it is part of, and in EHDAA2 it develops from the mesoderm (but in EHDAA2 the naming convention is to use 'paraxial mesenchyme', rather than 'paraxial mesoderm'). intermediate mesenchyme intermediate plate intermediate plate mesoderm mesenchyma intermedium uberon pharyngeal arch 2 2 2nd arch 2nd pharyngeal arch 2nd visceral arch A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down. The pharyngeal arches are separated by endodermal outpocketings, the pharyngeal pouches.[well established][VHOG] AAO:0010363 EHDAA2:0000050 EHDAA:611 EMAPA:16272 FMA:293017 TAO:0001596 The second of the series of bony or cartilaginous arches that develop in the walls of the mouth cavity and pharynx of the embryo.[AAO] The second pharyngeal arch will form the hyoid apparatus. The cranial neural crest cells that populate the second pharyngeal arch emerge primarily from rhombomere 4 and will form skeletal elements. UBERON:0003066 VHOG:0000297 XAO:0000098 ZFA:0001611 arcus pharyngeus secundus branchial arch 2 hyoid arch hyoid bars in XAO, develops from visceral pouch 2 pharyngeal arch 2 pharyngeal arches 2 second branchial arch second pharyngeal arch second visceral arch uberon visceral arch 2 axial mesoderm AAO:0011017 EFO:0003647 TAO:0001204 The axial mesoderm includes the prechordal mesoderm and the chordamesoderm. It gives rise to the prechordal plate and to the notochord. The portion of the mesoderm underlying the midline of the embryo. [Gastrulation:_From_cells_to_embryo_(2004)_Cold_Spring_Harbor, Glossary_XV, New_York:_Cold_Spring_Harbor_Laboratory_Press, Stern_CD][VHOG] UBERON:0003068 VHOG:0000107 XAO:0000205 ZFA:0001204 chordamesoderm uberon eye primordium AAO:0011038 EFO:0003541 EHDAA2:0004431 Portion of tissue that is part of the anterior neural keel and will form the optic vesicle[ZFA]. A paired ectodermal placode that becomes invaginated to form the embryonic lens vesicles. TAO:0000570 TODO - check that GO's optic placode is the same as ZFA's eye primordium; we may want to have separate term for ocular primordium precursor. XAO has both optic field and eye primordium. UBERON:0003071 UBERON:0005060 XAO:0000227 XAO:0004090 ZFA:0000570 eye anlage eye field eye placode occular primordium ocular primordium optic field optic placode optic placode of camera-type eye optic placodes optic primordium uberon optic cup (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup.[well established][VHOG] BTO:0005351 EHDAA2:0001303 EHDAA:2912 EMAPA:16674 Multi-tissue structure that is comprised of neural and non-neural epithelial layers which will form the retina and retinal pigmented epithelium of the mature eye[ZFA]. double walled structured formed by expansion and invagination of the distal end of the optic vesicle that develops into the pigmented and sensory layers of the retina while the mouth of the optic cup eventually forms the pupil of the eye[MP]. TAO:0001202 UBERON:0003072 UMLS:C0231109 VHOG:0000167 ZFA:0001202 eye cup eyecup ocular cup ophtalmic cup uberon lens placode (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The optic cup induces the overlying surface ectoderm first to thicken as a lens placode and then to invaginate and form a lens vesicle that differentiates into the lens.[well established][VHOG] A thickened portion of ectoderm which serves as the precursor to the lens. SOX2 and Pou2f1 are involved in its development[WP]. AAO:0011055 Classical transplantation experiments using amphibian embryos suggested that the optic vesicle is the source of lens-inducing signals sufficient to generate lens tissues in competent ectoderm (reviewed in Grainger et al., 1996). More recent findings suggest a multistep model for lens induction. There is now good evidence that lens specification occurs at the neurula stage, before the optic vesicle contact the surface ectoderm, and that neural crest cell migration in the frontonasal region is required to restrict the position of the lens placode (Bailey et al., 2006) EFO:0003494 EHDAA2:0000982 EHDAA:2908 EMAPA:16672 Ectodermal primordium of the lens of the eye. Kimmel et al, 1995.[TAO] FMA:296767 TAO:0000122 UBERON:0003073 UMLS:C1517770 VHOG:0000166 XAO:0000240 ZFA:0000122 lens placodes placoda lentis uberon mesonephric duct (...) in all craniates, the archinephric duct develops in embryogeny.[well established][VHOG] AAO:0000637 Anatomical structure consisting of either of a pair of longitudinal ducts which carry urine and in males, sperm, to the cloaca.[AAO] Consider adding subclasses for male and female specific variants EHDAA2:0001243 EHDAA:1590 EMAPA:16577 GAID:1315 In the male the Wolffian duct persists, and forms for example the epididymis, the ductus deferens, the ejaculatory duct, seminal vesicle and efferent ducts. Leydig's duct MESH:A16.254.940 Paired organ that connects the primitive kidney Wolffian body (or mesonephros) to the cloaca and serves as the anlage for certain male reproductive organs. the Wolffian duct is what remains of the pronephric duct after the atrophy of the pronephros[WP]. In Zebrafish: Duct of the adult kidney (mesonephros), present bilaterally ventral to the somites and leading to the cloacal chamber[ZFA]. TAO:0000546 TODO - mesonephric portion of the nephric duct The first-formed kidney duct, which drains the kidney of most anamniotes and becomes the ductus deferens of male amniotes. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-3, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG] UBERON:0003074 UMLS:C0043204 VHOG:0000082 Wolffian duct XAO:0000242 ZFA:0000546 archinephric duct ductus mesonephricus; ductus Wolffi renal duct uberon neural plate (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] A region of embryonic ectodermal cells that lie directly above the notochord. During neurulation, they change shape and produce an infolding of the neural plate (the neural fold) that then seals to form the neural tube[XAO]. The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium[ZFA] AAO:0011072 BTO:0001765 DHBA:10153 DMBA:15565 EHDAA:346 EHDAA:902 EMAPA:35593 FMA:293879 RETIRED_EHDAA2:0001252 TAO:0000132 The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium. Kimmel et al, 1995.[TAO] UBERON:0003075 UMLS:C0920623 VHOG:0000068 XAO:0000249 ZFA:0000132 lamina neuralis presumptive central nervous system uberon posterior neural tube (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] AAO:0011082 TAO:0007037 UBERON:0003076 VHOG:0001383 XAO:0000250 ZFA:0007037 uberon paraxial mesoderm AAO:0010568 EFO:0003515 EMAPA:16183 EMAPA:16751 FMA:293145 Mesoderm lateral to the neural tube and notochord that is divided into cranial and post-cranial portions. The trunk portions further segment into somites.[AAO] Presently, Cephalochordata, Urochordata, and Vertebrata are placed as subphyla of the phylum Chordata, in which the overall organization of embryonic tissues (dorsal hollow nerve cord, ventral digestive tract, axial notochord, and bilateral paraxial mesoderm) is largely conserved. In contrast, the echinoderms and hemichordates are sister groups of the chordates and they lack the notochord and paraxial mesoderm. Thus, the basic mesodermal organization of vertebrates must have appeared first in the common ancestor of the chordates.[well established][VHOG] TAO:0000255 The paraxial mesoderm is the mesoderm located bilaterally adjacent to the notochord and neural tube[GO] UBERON:0003077 UMLS:C1284009 VHOG:0000114 XAO:0000259 ZFA:0000255 mesoderma paraxiale note that all AOs differ in the relationship between this structure and the mesoderm; in ZFA it is a subclass (and this is implied by the GO definition and GO relationships), in AAO it is part of, and in EHDAA2 it develops from the mesoderm (but in EHDAA2 the naming convention is to use 'paraxial mesenchyme', rather than 'paraxial mesoderm'). Also in ZFA it is part of the trunk whereas this conflicts with the division into head and trunk in ehdaa2 (which we follow here) paraxial mesenchyme somitic mesoderm uberon anterior neural tube (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] AAO:0011012 TAO:0007038 TODO - add grouping class for the anterior end of the neural tube at all stages UBERON:0003080 VHOG:0001384 XAO:0000307 ZFA:0007038 uberon lateral plate mesoderm A ventrolateral zone of amphioxus mesoderm grows down to surround the gut. Homology of this zone to the lateral plate mesoderm of vertebrates is supported by site of origin and fate.[well established][VHOG] AAO:0010574 EHDAA2:0000919 EHDAA:379 EMAPA:16179 FMA:293149 LPM Portion of mesoderm traditionally thought to give rise to limb bones and parts of the girdles.[AAO] Portion of the middle of the three primary germ layers of the embryo that resides on the periphery of the embryo, is continuous with the extra-embryonic mesoderm, splits into two layers enclosing the intra-embryonic coelom, and gives rise to body wall structures[MP]. TAO:0000121 The portion of the mesoderm of the trunk of vertebrate embryos lying lateral to the intermediate mesoderm. [...] [It] subdivides into two plates: one dorsal, called the somatopleure, and one ventral, called the splanchnopleure. [Gastrulation:_From_cells_to_embryo_(2004)_Cold_Spring_Harbor, Glossary_XV, New_York:_Cold_Spring_Harbor_Laboratory_Press, Stern_CD][VHOG] UBERON:0003081 UBERON:0006258 UMLS:C1517749 VHOG:0000118 XAO:0000311 ZFA:0000121 lateral mesoderm lateral plate lateral plate mesenchyme mesoderma laminae lateralis subclass of mesoderm in ZFA. uberon myotome A transitional population of migrating mesenchymal cells that derive from somites and that will become muscle cells. AAO:0011067 AEO:0001018 BTO:0000742 EHDAA2_RETIRED:0003431 EHDAA:1721 EHDAA:1727 EHDAA:1733 EHDAA:1739 EMAPA:32841 FMA:295658 In all vertebrates, the skeletal muscle of the body axis is chiefly derived from an early embryonic compartment, known as the myotome.[well established][VHOG] Portion of the somites giving rise to body wall muscle masses. Kimmel et al, 1995.[TAO] TAO:0001056 The term 'myotome' is also used to describe the muscles served by a single nerve root / spinal segment - consider adding new class, myomere. UBERON:0003082 UMLS:C1513802 VHOG:0001244 XAO:0000315 ZFA:0001056 muscle plate myomere myomeres myotome region myotomes myotomus uberon heart primordium AAO:0011044 BTO:0001887 Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline between 21 and 26 somites to form the heart rudiment or cone. Stainier 2001.[TAO] Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline to form the heart rudiment or cone. TAO:0000028 The fused aspects of ventral mesoderm, which have migrated from either side of the prechordal plate, and fused ventrally, just behind the cement gland. They will give rise to the endocardium at NF stage 27&28.[AAO] UBERON:0003084 UMLS:C1514450 XAO:0000336 ZFA:0000028 cardiac field fused heart primordium relationship loss: develops_from lateral mesoderm (TAO:0001065)[TAO] should probably be merged with heart rudiment. uberon sclerotome AAO:0010571 AEO:0000212 EHDAA2:0003439 EMAPA:31159 FMA:295652 Skeletogenic portion of somites.[AAO] TAO:0001080 The vertebrate sclerotome has no equivalent in amphioxus and is a novelty linked with the evolution of the axial skeleton.[well established][VHOG] UBERON:0003089 UMLS:C0183176 VHOG:0000680 Ventral somitic compartment that is a precursor of the axial skeleton[XAO]. Sclerotomes eventually differentiate into the vertebrae and most of the skull. The caudal (posterior) half of one sclerotome fuses with the rostral (anterior) half of the adjacent one to form each vertebra. From their initial location within the somite, the sclerotome cells migrate medially towards the notochord. These cells meet the sclerotome cells from the other side to form the vertebral body. From this vertebral body, sclerotome cells move dorsally and surround the developing spinal cord, forming the vertebral arch[WP]. XAO:0000397 ZFA:0001080 part_of somite in XAO sclerotomes sclerotomus uberon thyroid primordium AAO:0011106 BTO:0004709 EHDAA2:0002033 EHDAA:952 EMAPA:16361 In all vertebrates the thyroid arises from the ventral aspect of the second pouch Note that we follow EHDAA2 in dividing this into endoderm and mesenchyme. In this ontology we place the broad developmental relationship at this level, and include specific relationships to the pharyngeal endoderm at the level of the endoderm Portion of tissue part of the pharyngeal endoderm that is fated to become thyroid follicle[ZFIN:curator]. TAO:0001081 The initial thyroid precursor, the thyroid primordium, starts as a simple midline thickening and develops to form the thyroid diverticulum. This structure is initially hollow, although it later solidifies and becomes bilobed. The 2 lobes are located on either side of the midline and are connected via an isthmus. UBERON:0003091 UMLS:C1519512 XAO:0000444 ZFA:0001081 thyroid primordia uberon cranial neural crest AAO:0010580 Anterior most portion of the neural crest. Migrates in three highly conserved streams: mandibular, hyoid and branchial.[AAO] CNC EFO:0003645 EHDAA2:0004420 EMAPA:16091 Neural crest that is part of the head.[TAO] TAO:0001194 UBERON:0003099 VHOG:0000063 We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG] XAO:0001001 ZFA:0001194 cephalic neural crest cranial NCC population crista neuralis cranialis head NCC population head crest head neural crest neural crest cells (NCCs) originating in the anterior part of the developing embryo and residing between the mid-diencephalon and the forming hindbrain; cranial NCCs migrate dorsolaterally to form the craniofacial mesenchyme that differentiates into various craniofacial cartilages and bones, cranial neurons, glia, and connective tissues of the face; these cells enter the pharyngeal pouches and arches where they give rise to thymic cells, bones of the middle ear and jaw (mandible), and the odontoblasts of the tooth primordia; like their counterparts in the trunk, cranial NCCs also contribute to the developing peripheral nervous system, along with the pigmented cell (i.e. melanocyte) lineage. uberon female organism AAO:0010030 BILA:0000028 CARO:0000028 FBbt:00007011 FMA:67812 Gonochoristic organism that can produce female gametes. HAO:0000028 TAO:0000303 TGMA:0001839 UBERON:0003100 XAO:0003005 ZFA:0000303 female female human body uberon male organism AAO:0010033 BILA:0000027 CARO:0000027 FBbt:00007004 FMA:67811 Gonochoristic organism that can produce male gametes. HAO:0000027 TAO:0000242 TGMA:0001838 UBERON:0003101 WBbt:0007850 XAO:0003006 ZFA:0000242 male male human body uberon surface structure AAO:0010337 AEO_RETIRED:0000010 Anatomical structure that overlaps the outer epithelial layer and is adjacent to the space surrounding the organism. EHDAA2_RETIRED:0003010 Organism subdivision which is the collection of anatomical structures on the body surface.[ZFA] TAO:0000292 UBERON:0003102 VSAO:0000001 XAO:0003028 ZFA:0000292 anatomical surface feature galen:SurfaceRegion surface feature surface region surface structures uberon compound organ AAO:0010015 AEO:0000024 Anatomical structure that has as its parts two or more multi-tissue structures of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona fide boundaries from other distinct anatomical structures of different types. BILA:0000024 CARO:0000024 EHDAA2:0003024 HAO:0000024 TADS:0000598 TAO:0000496 TGMA:0001837 UBERON:0003103 VHOG:0001723 XAO:0003041 ZFA:0000496 organ this class was introduced for consistency with CARO. However, in this ontology we typically classify organs directly under 'organ' rather than subdividing into compound and simple organs uberon mesenchyme A mesh-like cell arrangement, less compact than an epithelium. Kimmel et al, 1995.[TAO] AAO:0010427 AEO:0000145 BTO:0001393 CALOHA:TS-0620 EHDAA2:0003145 EV:0100007 Portion of tissue consisting of loosely organized undifferentiated mesodermal cells that give rise to such structures as connective tissues, blood, lymphatics, bone, and cartilage.[AAO] Portion of tissue consisting of loosely organized undifferentiated mesodermal cells that give rise to such structures as connective tissues, blood, lymphatics, bone, and cartilage[XAO]. A mesh-like cell arrangement, less compact than an epithelium[ZFA]. The part of the embryonic mesoderm, consisting of loosely packed, unspecialized cells set in a gelatinous ground substance, from which connective tissue, bone, cartilage, and the circulatory and lymphatic systems develop[BTO]. TAO:0000393 UBERON:0003104 UMLS:C0162415 VHOG:0000170 XAO:0003046 ZFA:0000393 mesenchyma mesenchymal mesenchymal tissue mesenchyme tissue portion of mesenchymal tissue portion of mesenchyme tissue the relationship to mesoderm is weaker than develops_from in order to have classes such as 'head mesenchyme from mesoderm' make sense uberon pharyngeal arch 3 3 3rd arch 3rd pharyngeal arch 3rd visceral arch A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down. The pharyngeal arches are separated by endodermal outpocketings, the pharyngeal pouches.[well established][VHOG] AAO:0010365 EHDAA2:0000069 EHDAA:1080 EMAPA:16399 FMA:293029 TAO:0001598 The most anterior, or first, pharygeal/branchial arch, composed of the mandibular process, forming the posterior border of the stomodeum, and the maxillary process anterior to the stomodeum, contains the first aortic arch.[AAO] The third branchial arch contributes to the development of the hyoid bone, stylopharyngeus muscle, inferior parathyroid gland, and thymus. UBERON:0003114 VHOG:0000298 XAO:0000447 ZFA:0001606 branchial arch 1 first branchial arch first gill arch gill arch 1 in XAO, called branchial arch 1 and df VP3 third pharyngeal arch third visceral arch uberon visceral arch 3 pharyngeal arch 6 6 6th arch 6th pharyngeal arch 6th visceral arch A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down. The pharyngeal arches are separated by endodermal outpocketings, the pharyngeal pouches.[well established][VHOG] AAO:0010368 EHDAA2:0004075 EMAPA:32766 FMA:293047 TAO:0001601 The 6th pharyngeal arch. contributes to the development of the sternocleidomastoid and trapezius muscles The forth in a series of paired bars in the wall of the pharynx, within which are formed the forth aortic arch and the cartilage bar of the visceral skeleton, forms and supports the gills.[AAO] UBERON:0003117 UBERON:0004349 VHOG:0001205 XAO:0000453 ZFA:0001609 branchial arch 4 fourth branchial arch gill arch 4 sixth branchial arch sixth pharyngeal arch sixth visceral arch uberon visceral arch 6 trachea AAO:0010140 An elongated tube which carries air to and from the lungs.[AAO] BTO:0001388 CALOHA:TS-1060 EFO:0000935 EHDAA2:0002066 EHDAA:3078 EMAPA:16853 EV:0100040 FMA:7394 GAID:361 In birds, the trachea runs from the pharynx to the syrinx, from which the primary bronchi diverge. Swans have an unusually elongated trachea, part of which is coiled beneath the sternum; this may act as a resonator to amplify sound. In some birds, the cartilagenous rings are complete, and may even be ossified. In amphibians, the trachea is normally extremely short, and leads directly into the lungs, without clear primary bronchi. A longer trachea is, however found in some long-necked salamanders, and in caecilians. While there are irregular cartilagenous nodules on the amphibian trachea, these do not form the rings found in amniotes. The only vertebrate to have lungs, but no trachea, is Polypterus, in which the lungs arise directly from the pharynx. In primitive fishes and most tetrapods, the lungs of adults are usually paired. They lie ventral to the digestive tract and are connected to the outside environment through the trachea.[well established][VHOG] MA:0000441 MAT:0000137 MESH:D014132 MIAA:0000137 OpenCyc:Mx4rvViOX5wpEbGdrcN5Y29ycA The respiratory tube between the larynx and the bronchi. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-29, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG] The trachea is the portion of the airway that attaches to the bronchi as it branches [GO:dph]. UBERON:0003126 UMLS:C0040578 VHOG:0000371 XAO:0000118 cartilaginous trachea in mouse 15-18 C-rings, 15-20 in human. tracheal tracheal tubule uberon vertebrate trachea windpipe reproductive organ An organ involved in reproduction EMAPA:17381 GO uses genitalia for the singular organ MA:0001752 MESH:D005835 OpenCyc:Mx4rwO39aJwpEbGdrcN5Y29ycA TGMA:0000591 UBERON:0003133 UMLS:C0017420 WBbt:0008422 genital organ genitalia reproductive system organ sex organ uberon female reproductive organ A female organ involved in reproduction EMAPA:28540 MA:0000544 UBERON:0003134 female organism reproductive organ female organism reproductive structure female organism reproductive system organ female organism sex organ female reproductive gland/organ female reproductive system organ female sex organ reproductive organ of female organism reproductive structure of female organism reproductive system organ of female organism sex organ of female organism uberon metanephric mesenchyme A mass of intermediate mesodermal cells around the distal end of the ureteric bud that gives rise to nephrons in the metanephric kidney. [TFD][VHOG] EHDAA2:0004062 EHDAA:4041 EHDAA:5021 EHDAA:5915 EMAPA:17208 EMAPA:17375 EMAPA:29990 Genes: The positional specification of the metanephrogenic mesenchyme is negatively regulated by Foxc1 and Foxc2. Next the permanent kidney forming metanephrogenic mesenchyme is specified by Hox11 genes. The competence to respond to ureteric bud inducers is regulated by WT1. GDNF secretion restricted to posterior region by Robo2 and Sprouty1. The receptors for GDNF are synthesized in the nephric ducts and later in ureteric buds [ISBN:9780878932504 "Developmental Biology"] UBERON:0003220 VHOG:0000540 When the ureteric buds emerge from the nephric duct, they enter the metanephrogenic mesenchyme. The ureteric buds induce this mesenchymal tissue to condense around them and differentiate into the nephrons of the mammalian kidney. As this mesenchyme differentiates, it tells the ureteric bud to branch and grow.[well established][VHOG] metanephric blastema metanephric mesoderm metanephrogenic mesenchyme metanephros associated mesenchyme one of the two embryological structures that give rise to the kidney (the other is the ureteric bud). The metanephric blastema mostly develops into nephrons, but can also form parts of the collecting duct system.[WP]. Metanephric mesenchyme is the tissue made up of loosely connected mesenchymal cells in the metanephros[GO] uberon phalanx CALOHA:TS-2211 EMAPA:32614 Endochondral bones that are often elongate and arranged in rows of articulating elements, and form the visible part of the digits. FMA:321661 In primates such as humans and monkeys, the thumb and big toe have two phalanges, while the other fingers and toes consist of three MA:0000304 OpenCyc:Mx4rvolPZpwpEbGdrcN5Y29ycA UBERON:0003221 UMLS:C0222682 VSAO:0000199 digit long bone galen:Phalanx long bone of digit phalange phalangeal phalanges phalanx bone uberon endoderm of foregut An endoderm that is part of a foregut [Automatically generated definition]. EHDAA2:0004568 EHDAA:524 TODO - check UBERON:0003258 foregut endoderm uberon gland of foregut A gland that is part of a foregut [Automatically generated definition]. EHDAA2:0000567 EHDAA:950 EMAPA:16557 UBERON:0003294 VHOG:0000650 foregut gland uberon eye mesenchyme EHDAA2:0000485 EHDAA:2910 EMAPA:16673 Mesenchyme that is part of a developing camera-type eye. TODO - change mesenchyme relationships to precursor_of UBERON:0003314 VHOG:0001084 mesenchyme of eye uberon epithelium of mucosa A layer of epithelial cells on the surface of the mucosa. BTO:0003752 UBERON:0003350 lamina epithelialis mucosa lamina epithelialis mucosae lies on top of lamina propria uberon epithelium of hindgut An epithelium that is part of a hindgut [Automatically generated definition]. EHDAA2:0000782 EMAPA:16717 MA:0003206 UBERON:0003353 epithelial tissue of hindgut hindgut epithelial tissue hindgut epithelium uberon smooth muscle of eye EMAPA:18807 MA:0001268 Not clear if we need this and intra-ocular muscle. See issue #331. MA includes ciliary and iris smooth muscle UBERON:0003386 any of the striated muscles that move the eye and include: superior rectus, inferior rectus, medial rectus, lateral rectus, superior oblique, inferior oblique, retractor bulbi ocular smooth muscle uberon gland of gut A gland that is part of a digestive tract [Automatically generated definition]. EMAPA:18815 MA:0003202 UBERON:0003408 digestive tract gland gland of digestive tract gland of lower gastrointestinal tract gut gland lower gastrointestinal tract gland uberon pelvic appendage bud mesenchyme EHDAA2:0001035 EMAPA:16781 Mesenchyme that is part of a pelvic appendage bud. Mesoderm part of pelvic fin bud.[TAO] TAO:0001386 UBERON:0003412 ZFA:0001386 hindlimb bud mesenchyme leg mesenchyme lower limb bud mesenchyme mesoderm pelvic fin bud pelvic fin bud mesenchyme uberon thoracic cavity vein A vein that is part of a thoracic cavity [Automatically generated definition]. MA:0001903 UBERON:0003479 cavity of chest vein cavity of thorax vein chest cavity vein pectoral cavity vein uberon vein of cavity of chest vein of cavity of thorax vein of chest cavity vein of pectoral cavity vein of thoracic cavity heart blood vessel A blood vessel that is part of a heart [Automatically generated definition]. EMAPA:35397 MA:0002483 UBERON:0003498 blood vessel of heart cardiac blood vessel uberon arterial blood vessel A blood vessel that is part of the arterial system. Includes artery, arteriole and aorta. EMAPA:35144 MA:0000061 UBERON:0003509 only in MA - supertype of artery, arteriole, aorta. uberon trunk blood vessel A blood vessel that is part of a trunk [Automatically generated definition]. MA:0000511 UBERON:0003513 blood vessel of torso blood vessel of trunk torso blood vessel uberon thoracic cavity blood vessel A blood vessel that is part of a thoracic cavity [Automatically generated definition]. MA:0000554 UBERON:0003519 blood vessel of cavity of chest blood vessel of cavity of thorax blood vessel of chest cavity blood vessel of pectoral cavity blood vessel of thoracic cavity cavity of chest blood vessel cavity of thorax blood vessel chest cavity blood vessel pectoral cavity blood vessel uberon brain gray matter A gray matter that is part of a brain [Automatically generated definition]. EMAPA:35184 MA:0000810 UBERON:0003528 UMLS:C1707348 brain grey matter brain grey substance gray matter of brain grey matter of brain grey substance of brain uberon limb long bone A long bone that is part of a limb [Automatically generated definition]. EMAPA:35495 MA:0000298 UBERON:0003606 long bone of limb uberon limb joint Any joint that is part of a (free) limb. EMAPA:36501 FMA:321558 MA:0000691 Most limb joints are synovial, but a few such as the tibiofibular joints are syndesmoses UBERON:0003657 galen:LimbJoint joint of limb joint of limb skeletal system skeletal limb joint uberon extrahepatic bile duct FMA:14678 GAID:281 MA:0002659 MESH:D017734 Passages external to the liver for the conveyance of bile. These include the common bile duct and the common hepatic duct. UBERON:0003703 UMLS:C0206187 bile duct extrahepatic part extrahepatic biliary system includes all the cystic duct, all the common bile duct and the extrahapetic part of the hepatic duct uberon intrahepatic bile duct Duct that collects bile from the bile ductules and connects to the extrahepatic bile duct.[TAO] FMA:15766 GAID:287 MA:0001630 MESH:D001653 Passages within the liver for the conveyance of bile. Includes right and left hepatic ducts even though these may join outside the liver to form the common hepatic duct. TAO:0005169 UBERON:0003704 UMLS:C0005401 ZFA:0005169 bile duct intrahepatic part includes the hepatic duct of the caudate lobe, and the intra- and inter- lobar bile ducts intrahepatic biliary system uberon neural tissue AAO:0000325 AEO:0000123 EHDAA2:0003123 FMA definition includes vasculature FMA:9642 GAID:609 MESH:D009417 One of the four types of tissue in traditional classifications. Cells forming the brain, spinal cord and peripheral nervous system.[AAO] OpenCyc:Mx4rVmfYCsQ_QdeM_bFAeS8NRQ Portion of tissue in the nervous system which consists of neurons and glial cells, and may also contain parts of the vasculature. UBERON:0003714 UMLS:C0027757 nerve tissue nervous tissue portion of neural tissue uberon recurrent laryngeal nerve A branch of the vagus nerve that supplies motor function and sensation to the larynx (voice box). It travels within the endoneurium. It is the nerve of the 6th Branchial Arch. AAO:0010754 Branch of the vagus nerve that separates from the vagus well postcranially, then continues anteriorly to innervate the larynx[AAO:0010754]. FMA:6246 GAID:804 MESH:D012009 UBERON:0003716 VHOG:0001347 inferior laryngeal nerve nervus laryngeus recurrens ramus recurrens recurrent laryngeal nerve from vagus nerve recurrent nerve uberon vagus X nerve recurrent laryngeal branch prostate bud A region of the fetal urogenital sinus epithelium destined to become the prostate[GO]. AR activation releases instructive signals from UGM that acts on UGS epithelium (UGE) to stimulate cell proliferation, form prostate ductal progenitors (prostatic buds), and regulate cell adhesion dynamics to permit prostatic bud outgrowth. There are three phases of prostatic budding: (1) the specification phase, when instructive developmental cues define where buds will form in the UGS, (2) the initiation phase, when prostatic buds begin to form, and (3) the elongation phase, when proliferation, cell adhesion, and cell migration coordinate outgrowth of prostatic buds into UGM. Timing of prostatic bud formation and the quantity and pattern of buds that are formed in the UGS are strictly regulated [3, 4]. The position of prostatic buds as they emerge from the UGS in utero determines the arrangement of prostate ducts in adulthood.[PMID:18977204] EMAPA:36141 UBERON:0003820 prostate ductal progenitor prostate gland bud prostate primordium prostatic bud uberon metapodium bone A bone of the metapodial skeleton MA:0000301 UBERON:0003821 metacarpal or metatarsal bone metacarpal/metatarsal metacarpal/metatarsal bone metapodi bone metapodial bone metapodium bone uberon thoracic segment blood vessel A blood vessel that is part of a thorax [Automatically generated definition]. MA:0000558 UBERON:0003834 blood vessel of thorax thorax blood vessel uberon upper body blood vessel autopod joint A limb joint that is part of an autopod [Automatically generated definition]. EMAPA:35160 MA:0002715 UBERON:0003841 autopod joint of limb autopod limb joint distal free limb segment joint of limb distal free limb segment limb joint joint of limb of autopod joint of limb of distal free limb segment limb joint of autopod limb joint of distal free limb segment paw joint uberon neural tube lumen (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] AAO:0011073 An anatomical space that surrounded_by a neural tube. EHDAA2:0001269 EHDAA:2889 EHDAA:914 EMAPA:16167 EMAPA:16533 UBERON:0003842 UBERON:0005713 VHOG:0001119 XAO:0000252 cavity of neural tube central lumen lumen of neural tube neural lumen neural tube neural lumen neurocoel prosencoel uberon mesencephalic neural crest A neural crest that has_potential_to_developmentally_contribute_to a midbrain. EFO:0003591 EHDAA2:0001101 EHDAA:360 TAO:0000935 UBERON:0003849 VHOG:0000796 We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG] ZFA:0000935 mesencephalic neural crest neural crest midbrain uberon telencephalon neural crest A neural crest that has_potential_to_developmentally_contribute_to a telencephalon. Cranial neural crest that is part of the telencephalon.[TAO] EFO:0003574 RETIRED_EHDAA2:0001991 TAO:0000812 UBERON:0003850 VHOG:0000799 We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG] ZFA:0000812 neural crest telencephalon uberon rhombencephalon neural crest A neural crest that has_potential_to_developmentally_contribute_to a hindbrain. Cranial neural crest that is part of the hindbrain.[TAO] EHDAA2:0001628 EHDAA:362 EMAPA:35747 TAO:0007063 UBERON:0003852 VHOG:0001210 We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG] ZFA:0007063 neural crest hindbrain rhombencephalic neural crest rhombomere neural crest uberon spinal cord neural crest A neural crest that has_potential_to_developmentally_contribute_to a spinal cord. EHDAA:696 EMAPA:16163 EMAPA:16529 EMAPA:16881 UBERON:0003853 VHOG:0001006 We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...)[well established][VHOG] neural crest spinal cord spinal neural crest uberon presumptive ganglion A presumptive structure that has the potential to develop into a ganglion. UBERON:0003869 uberon future coelemic cavity lumen An anatomical cavity that has the potential to develop into a coelemic cavity lumen. UBERON:0003886 body cavity precursor uberon intraembryonic coelom (...) I regard it unlikely that coeloms of all bilaterian animals are comparable and evolved very early. Considering all these questions, few convincing characters concerning the evolution of body cavities remain to be named. (...) A segmental coelom appears to have evolved at least two times, in Annelida and in Myomerata (Acrania and Craniota).[well established][VHOG] EHDAA:251 EMAPA:16088 The part of the coelom in the embryo between the somatopleuric and splanchnopleuric mesoderm; the principal body cavities of the trunk (thoracic, abdominal, and pelvic) arise from this embryonic part of the coelom UBERON:0003887 UMLS:C1512940 VHOG:0000316 consider merging with coelom. TODO - add spatial relationships to halves of LPM. Note the OG places XAO and ZFA coelem terms here. editor note: TODO check ZFA, which appears to be a structure present in adults somatic coelom uberon liver primordium A small endodermal thickening in the foregut adjacent to the transverse septum. Invaginates forming the hepatic diverticulum. AAO:0011058 BTO:0003391 EFO:0002577 EFO:0003428 EHDAA2:0000744 EHDAA:973 EMAPA:16847 TAO:0000124 UBERON:0003894 UMLS:C0734013 UMLS:C1514451 XAO:0003266 ZFA:0000124 consider adding further subdivisions of the endoderm, e.g. ventral foregut. Note we place two EFO classes here, it's not clear how they differ embryological hepatic plate hepatic plate liver bud liver endoderm primordium of the liver uberon retinal neural layer (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG] AAO:0011095 BTO:0000929 CALOHA:TS-0685 EHDAA2:0001253 EHDAA:4763 EMAPA:17171 EMAPA:18590 FMA:58628 MA:0000277 TAO:0000046 The part of the retina that contains neurons and photoreceptor cells[GO]. UBERON:0003902 UMLS:C1518263 VHOG:0000535 XAO:0003216 ZFA:0000046 neural layer of retina neural retina neural retinal epithelium neuroretina stratum nervosum (retina) stratum nervosum retinae uberon epithelial tube AEO:0000114 EHDAA2:0003114 Epithelial tubes transport gases, liquids and cells from one site to another and form the basic structure of many organs and tissues, with tube shape and organization varying from the single-celled excretory organ in Caenorhabditis elegans to the branching trees of the mammalian kidney and insect tracheal system. FBbt:00007474 UBERON:0003914 contrast with a multi-tissue tube, which has as parts both epithelium, connective tissue, possibly muscle layers epithelial or endothelial tube uberon kidney mesenchyme Kidney mesenchyme is the tissue made up of loosely connected mesenchymal cells in the kidney[GO]. UBERON:0003918 check this mesenchyme of kidney uberon venous blood vessel A blood vessel that carries blood from the capillaries toward the heart Compare to: vein EMAPA:35932 FMA:86188 MA:0000066 UBERON:0003920 segment of venous tree organ uberon venous tree organ segment pancreas primordium EFO:0002579 EFO:0003434 EHDAA2:0001382 EHDAA:2163 EMAPA:17066 FMA:79792 TAO:0000254 UBERON:0003921 XAO:0001101 ZFA:0000254 embryonic structure that develops into pancreatic bud. in EHDAA2 this has dorsal and ventral primordia as parts. the buds are part of the primordium, with the ducts developing from the buds; only parenchyma and ducts have contribution from buds pancreatic anlage pancreatic endoderm pancreatic primordium primordial pancreas revisit after standardizing terms 'primordium', 'anlagen', 'bud' uberon pancreatic epithelial bud EFO:0003470 EMAPA:35645 TAO:0001390 The embryonic pancreas develops from two separate anlagen in the foregut epithelium, one dorsal and two ventral pancreatic buds[PMID]. UBERON:0003922 UMLS:C1283285 ZFA:0001390 pancreas epithelium pancreatic anlage pancreatic bud pancreatic buds uberon dorsal pancreatic bud AAO:0011031 EFO:0003465 EHDAA2:0001385 EMAPA:17067 In chick, Xenopus laevis, and the teleost fish Medaka, the pancreas develops from three buds that emerge from the gut tube, two from its ventral aspect, and one from its dorsal aspect. In mouse, although there are initially three buds that arise from the gut tube at the point of contact between the endoderm and the vasculature, the pancreas develops from only two of these buds, one dorsal and one ventral. (...) In this study, we use a transgenic zebrafish line (...). We provide evidence for the existence of two distinct pancreatic anlagen - a ventral anterior bud and a dorsal posterior bud - that join to form the definitive pancreas (reference 1); The pancreas develops from the fusion of distinct endoderm-derived dorsal and ventral diverticula. In humans, by day 35 of development, the ventral pancreatic bud begins to migrate backwards and comes into contact and eventually fuses with the dorsal pancreatic bud during the sixth week of development (reference 2).[well established][VHOG] TAO:0001370 The pancreatic bud that gives rise to the accessory pancreatic duct.[AAO] UBERON:0003923 VHOG:0001428 XAO:0000467 ZFA:0001370 dorsal pancreas anlage dorsal pancreatic anlage pancreas dorsal primordium duct bud pancreas primordium dorsal bud pancreatic bud that gives rise to the accessory pancreatic duct. posterior pancreatic anlage posterior pancreatic bud primary pancreatic bud uberon ventral pancreatic bud AAO:0011111 EFO:0003464 EHDAA2:0001389 EMAPA:17256 In chick, Xenopus laevis, and the teleost fish Medaka, the pancreas develops from three buds that emerge from the gut tube, two from its ventral aspect, and one from its dorsal aspect. In mouse, although there are initially three buds that arise from the gut tube at the point of contact between the endoderm and the vasculature, the pancreas develops from only two of these buds, one dorsal and one ventral. (...) In this study, we use a transgenic zebrafish line (...). We provide evidence for the existence of two distinct pancreatic anlagen - a ventral anterior bud and a dorsal posterior bud - that join to form the definitive pancreas (reference 1); The pancreas develops from the fusion of distinct endoderm-derived dorsal and ventral diverticula. In humans, by day 35 of development, the ventral pancreatic bud begins to migrate backwards and comes into contact and eventually fuses with the dorsal pancreatic bud during the sixth week of development (reference 2).[well established][VHOG] TAO:0001369 The ventral pancreatic bud becomes the head and uncinate process, and comes from the hepatic diverticulum[WP] UBERON:0003924 VHOG:0001429 XAO:0001103 ZFA:0001369 anterior pancreatic anlage anterior pancreatic bud pancreas primordium ventral bud pancreas ventral primordium duct bud pancreatic bud that gives rise to the major pancreatic duct. the ventral pancreas and liver are derived from a common precursor cell population[PMID:16417468]. TODO - add this relationship. uberon ventral pancreas anlage ventral pancreatic anlage digestive system duct A duct that is part of a digestive system [Automatically generated definition]. TAO:0005162 UBERON:0003928 ZFA:0005162 duct of digestive system duct of gastrointestinal system gastrointestinal system duct uberon digestive tract epithelium An epithelium that lines the lumen of the digestive tract. BTO:0000956 EHDAA2:0004567 EMAPA:32928 Epithelium lining the lumen of the gut.[TAO] MA:0003201 TAO:0005123 UBERON:0003929 UMLS:C0836205 XAO:0003200 ZFA:0005123 alimentary tract epithelium digestive tract epithelial tissue epithelial tissue of digestive tract epithelial tissue of gut epithelium of digestive tract epithelium of gut gastrodermis gut epithelial tissue gut epithelium uberon sex gland Any of the organized aggregations of cells that function as secretory or excretory organs and are associated with reproduction. MA:0001751 UBERON:0003937 genitalia gland gland of genitalia gland of reproductive system reproductive gland reproductive system gland uberon internal female genitalia BTO:0003099 FMA:45654 TODO: Relabel. Make distinct organ class. See https://github.com/obophenotype/uberon/issues/547 The internal feminine genital organs, including the ovaries, uterine tubes, uterus, uterine cervix, and vagina. UBERON:0003975 female internal genitalia internal female genital organ internal genitalia of female reproductive system organa genitalia feminina interna uberon dermatome A transitional population of migrating mesenchymal cells that derive from somites and that will become dermal cells. AAO:0011028 AEO:0001017 EHDAA2_RETIRED:0003428 EHDAA:1719 EHDAA:1725 EHDAA:1731 EHDAA:1737 EMAPA:32838 FMA:295656 Not to be confused with 'dermatome segment of skin'. UBERON:0004016 UMLS:C0180383 XAO:0000220 cutis plate dermatomal mesenchyme epimere mesoderm mesenchyma dermatomiale uberon germinal neuroepithelium As the cells adjacent to the lumen continue to divide, the migrating cells form a second layer around the original neural tube. This layer becomes progressively thicker as more cells are added to it from the germinal neuroepithelium. This new layer is called the mantle (or intermediate) zone, and the germinal epithelium is now called the ventricular zone (and, later, the ependyma)[NCBIBook:NBK10047] The single layer of epithelial cells that lines the early neural tube and develops into the nervous system and into the neural crest cells UBERON:0004022 germinal neuroepithelial layer germinal neuroepithelium original neural tube uberon biliary ductule BTO:0002840 In ZFA, Digestive system duct that collects bile from the canaliculus and transports bile through the liver -- (check if the same) // The smallest and the most peripheral branches of the biliary tree consist of a portal part (portal ductule) and an intralobular part (intralobular ductule) One of the fine terminal elements of the bile duct system, leaving the portal canal, and pursuing a course at the periphery of a lobule of the liver[BTO]. the excretory ducts of the liver that connect the interlobular ductules to the right or left hepatic duct[MP] TAO:0005164 UBERON:0004058 ZFA:0005164 bile capillary bile ductule biliary ductule biliary ductule cholangiole ductuli biliferi terminal cholangiole uberon neural tube ventricular layer EMAPA:17152 EMAPA:35362 EMAPA_RETIRED:16783 MA:0003193 The layer of undifferentiated, proliferating cells that line the neural tube lumen The layer of undifferentiated, proliferating cells that line the neural tube lumen that is the immediate transformation of the germinal neuroepithelium UBERON:0004060 consider merging with 'ventricular zone'; note that the MA class probably does not belong here, as this is an embryonic structure ependymal layer neural tube ependymal layer neural tube ependymal zone neural tube ventricular germinal zone neural tube ventricular zone uberon neural tube mantle layer EMAPA:17148 EMAPA:35360 The layer of glia and differentiating neurons that forms as a second layer around the germinal neuroepithium; as this develops it comes to lie between the ventricular and marginal layers and includes the basal and alar plates. Develops into neurons and glia forming a gray matter layer. UBERON:0004061 future brain marginal layer neural tube intermediate zone uberon neural tube marginal layer EMAPA:17151 The outermost layer of the neural tube that consists of axons from the developing mantle layer and will form the white matter UBERON:0004062 brain marginal zone neural tube marginal zone uberon neural tube basal plate AAO:0010561 EFO:0001904 The region of the mantle layer of the neural tube that lies ventral to the sulcus limitans and contains primarily motor neurons and interneurons. UBERON:0004064 UMLS:C1511061 basal plate basal plate of neural tube motor part of neural tube spinal cord basal plate uberon ventral part of neural tube vena cava AAO:0010215 Any of the veins that carries deoxygenated blood from a part of the body into the right atrium of the heart. BTO:0001438 EMAPA:18415 FMA:321896 GAID:547 MA:0000068 MESH:D014684 OpenCyc:Mx4rkJQ4U6gEEdudWQACs5b6Bw UBERON:0004087 UMLS:C0042460 caval vein uberon venae cavae orbital region FMA:260119 The subdivision of the face that includes the eye (eyeball plus adnexa such as eyelids) and the orbit of the skull and associated parts of the face such as the eyebrows, if present UBERON:0004088 content of orbital part of eye eye region in HP covers eyelid, eyebrow. note the FMA class is more narrow though, and is more like eye + muscles + vasculature. The FMA also has FMA:72951 orbital part of eye ocular and peri-ocular region ocular region orbital content orbital part of eye orbital part of face uberon anatomical conduit 2 2 AEO:0000080 Any tube, opening or passage that connects two distinct anatomical spaces. EHDAA2:0003080 FMA has both conduit and conduit space. In EHDAA2 this is a surface feature FMA:242873 UBERON:0004111 foramen foramina opening ostia ostium uberon pharyngeal pouch A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down. The pharyngeal arches are separated by endodermal outpocketings, the pharyngeal pouches.[well established][VHOG] AAO:0011113 An internal pocketing of pharyngeal endoderm that contacts a region of ectoderm (a pharyngeal cleft) and interdigitates in the anterior and posterior directions with the pharyngeal arches. EFO:0003627 EHDAA:1086 EHDAA:1669 EHDAA:579 EHDAA:617 EMAPA also includes a distinct pouch endoderm EMAPA:32752 FMA:293063 Outpocketings of pharyngeal endoderm that interdigitate with the neural crest derived pharyngeal arches. The pouches later fuse with the surface ectoderm to form the gill slits. Crump et al, 2004.[TAO] TAO:0001106 The pouches are polarized structures. For example, whereas the rostral half of each pouch expresses Bmp-7, the caudal half expresses FGF-8 and the dorsal aspect of each pouch is marked via its expression of Pax-1. each pouch has an individual sense of identity. Shh expression is a prominent early feature of the caudal endoderm of the second arch, and individual pouches mark the anterior limits of expression of Hox genes within the pharyngeal endoderm; Hox-a2 has a rostral boundary at the second pouch, Hox-a3 at the third pouch and Hox-a4 at the most caudal pouch[PMID:16313389] UBERON:0004117 UMLS:C0231067 VHOG:0001203 XAO:0000282 ZFA:0001106 branchial pouch pharyngeal pouches uberon visceral pouch visceral pouches endoderm-derived structure An anatomical structure that develops (entirely or partially) from the endoderm. Grouping term for query purposes UBERON:0004119 uberon mesoderm-derived structure An anatomical structure that develops (entirely or partially) from the mesoderm. Grouping term for query purposes UBERON:0004120 uberon ectoderm-derived structure An anatomical structure that develops (entirely or partially) from the ectoderm. Grouping term for query purposes UBERON:0004121 uberon genitourinary system AAO:0000624 Anatomical system that has as its parts the organs concerned with the production and excretion of urine and those concerned with reproduction. Anatomical system that has as its parts the organs concerned with the production and excretion of urine and those concerned with reproduction.[AAO] BILA:0000122 BTO:0003091 EFO:0003864 EHDAA:1013 EMAPA:16367 EV:0100094 FMA:280610 GAID:362 GU tract Kidneys and gonads (of vertebrates) develop from adjacent tissues, and after the excretory or urinary ducts have developed, the reproductive system usually taps into them or their derivatives.[well established][VHOG] MESH:D014566 OpenCyc:Mx4rQRpVMgAKEdyHxgDggVfs8g UBERON:0004122 UG tract UMLS:C0042066 Urogenitalsystem VHOG:0000286 XAO:0000140 galen:GenitoUrinarySystem genito-urinary system genitourinary genitourinary tract relationship type change: differentiates_from intermediate mesoderm (AAO:0010575) CHANGED TO: develops_from intermediate mesoderm (UBERON:0003064)[AAO] uberon urogenital urogenital system urogenital tract optic vesicle (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles.[well established][VHOG] AAO:0011039 EHDAA2:0001320 EMAPA:16540 FMA:293357 Genes: Six3, Pax6, Rx1 are expressed together in the tip of the neural plate [ISBN:9780878932504 "Developmental Biology"]. Development notes: During subsequent develop- ment, the optic vesicle invaginates and becomes a two-layered structure with an inner neural retina and outer retinal pigment epithelium. As soon as the developing optic vesicle makes contact with the overlying ectoderm, it induces the ectoderm to thicken and form the lens placode [PMID:16496288] TAO:0000050 The optic vesicle is the evagination of neurectoderm that precedes formation of the optic cup[GO]. Portion of tissue that is comprised of neuroepitheium which has pinched off from the anterior neural keel and will form the optic cup[ZFA]. UBERON:0004128 UMLS:C0231106 VHOG:0000165 XAO:0000228 ZFA:0000050 evagination eye vesicle ocular vesicle optic vesicles uberon cardiogenic plate (In vertebrates) The embryonic mesoderm is the source of both the cardiogenic plate, giving rise to the future myocardium as well as the endocardium that will line the system on the inner side.[well established][VHOG] EHDAA2:0000215 EMAPA:16106 TODO - check plate vs rudiment vs primordium vs endocardial tube. See XAO The first recognizable structure derived from the heart field UBERON:0004139 VHOG:0000975 cardiac crescent cardiogenic crescent heart rudiment myocardial plate uberon primary heart field A specific region of the lateral mesoderm that will form the primary beating heart tube. In mammals the primary heart field gives rise to the left ventricle. FHF PHF UBERON:0004140 XAO:0004185 first heart field heart field primary heart field this term denotes the primary heart field; GO:0003128 denotes the superclass of primary and secondary: specific region of the lateral mesoderm into the area which will form the primary beating heart tube[GO:0003138] uberon heart tube AAO:0010411 An epithelial tube that will give rise to the mature heart. EFO:0003526 EMAPA:32685 TAO:0000360 UBERON:0004141 XAO:0000337 ZFA:0000360 embryonic heart tube endocardial heart tube endocardial tube the paired, longitudinal, endothelial-lined channels formed from the cardiogenic mesoderm in embryonic development; angiogenic cell clusters (aka angioblastic cords) located in a horse-shoe shape configuration in the cardiogenic plate coalesce to form the right and left endocardial heart tubes which then fuse in cephalo-caudal direction to form a single primitive heart tube. uberon cardiac chamber A cardiac chamber surrounds an enclosed cavity within the heart FMA:7095 OpenCyc:Mx4rmexpjPdAEduAAAAOpmP6tw UBERON:0004151 chamber of heart generic enough to cover FBbt:00003156 heart chamber but this is a cavity. GO defines it as the cavity. TODO - move subclasses. Note this also includes sinus venosus heart chamber uberon septum transversum A thick plate of mesodermal tissue that occupies the space between the thoracic cavity and yolk stalk in the early embryo, forming a transverse partition partially separating the coelomic cavity into thoracic and abdominal portions. It gives rise to the central tendon of the diaphragm. [TFD][VHOG] A thick plate of mesodermal tissue that occupies the space between the thoracic cavity and yolk stalk in the early embryo, forming a transverse partition partially separating the coelomic cavity into thoracic and abdominal portions. It gives rise to the central tendon of the diaphragm[VHOG]. EHDAA2:0001829 EHDAA:736 EMAPA:16318 FMA:295593 In hagfishes a transverse septum extends upward from the ventral body wall posterior to the heart, partly separating an anterior pericardial cavity from a larger peritoneal cavity. (...) These basic relationships have not been modified by urodeles. The small pericardial cavity remains far forward where it is separated by a transverse septum from the principal coelom, which may now be called a pleuroperitoneal cavity because slender lungs are present. (...) The heart (of other tetrapods) is separated from the lungs (and liver if present) by more or less horizontal partitions that have their origin in the embryo as folds on the serous membrane of the right and left lateral body walls. These grow out to join in the midline of the body. They are called lateral mesocardia (birds) or pleuropericardial membranes. Posteriorly they join the transverse septum to form the adult pericardial membrane, or pericardium. (...) In their partitioning of their coelom, embryonic mammals resemble first early fishes (incomplete partition, posterior to heart, consisting of the transverse septum) and then reptiles (pericardium derived from transverse septum and pleuropericardial membranes) Mammals then separate paired pleural cavities from the peritoneal cavity by a diaphragm. The ventral portion of this organ comes from the transverse septum. The dorsal portion is derived from the dorsal mesentery and from still another pair of outgrowths from the lateral body wall, the pleuroperitoneal membranes.[well established][VHOG] The cranial part of the septum transversum gives rise to the central tendon of the diaphragm and is the origin of the myoblasts that invade the pleuroperitoneal folds resulting in the formation of the muscular diaphragm. The caudal part of the septum transversum is invaded by the hepatic diverticulum which divides within it to form the liver and thus gives rise to the ventral mesentery of the foregut. UBERON:0004161 UMLS:C0231004 VHOG:0000019 in EHDAA2 this is divided into mesenchymal portion and hepatic diverticulum transverse septum uberon internal genitalia FMA:45652 TODO: make a subdivision of reproductive system. Relabel. See https://github.com/obophenotype/uberon/issues/547 The internal genitalia are the internal sex organs such as the uterine tube, the uterus and the vagina in female mammals, and the testis, seminal vesicle, ejaculatory duct and prostate in male mammals UBERON:0004175 internal genitalia internal genitals internal reproductive organ internal sex organ uberon external genitalia FMA:45643 TODO: make a subdivision of reproductive system. Relabel. See https://github.com/obophenotype/uberon/issues/547 The external genitalia are the outer sex organs, such as the penis or vulva in mammals UBERON:0004176 external genitalia external reproductive organ external sex organ uberon endodermal part of digestive tract A portions of the gut that is derived from endoderm. EMAPA:32930 UBERON:0004185 endodermal gut gut endoderm uberon eye muscle A muscle that is part of the eye region. AAO:0000156 EMAPA:35335 MA:0000271 OpenCyc:Mx8Ngx4rwKSh9pwpEbGdrcN5Y29ycB4rvViTvpwpEbGdrcN5Y29ycB4rvYA8cJwpEbGdrcN5Y29ycA UBERON:0004277 uberon skeleton AEO:0000168 Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body. Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body.[VSAO] EHDAA2:0001843 EHDAA:5047 EMAPA:17213 FMA:23875 GAID:177 MA:0003006 MAT:0000032 MESH:D012863 MIAA:0000032 OpenCyc:Mx4rvVi1rpwpEbGdrcN5Y29ycA UBERON:0004288 VSAO:0000026 XAO:0004053 galen:Skeleton https://github.com/obophenotype/uberon/wiki/The-skeletal-system set of all bones set of bones of body skeletal uberon dermomyotome AAO:0010572 AEO:0000214 EHDAA2:0003259 EMAPA:31109 Epithelial sheet on the external surface of the somite that gives rise to trunk, muscle and dermis. Within the dermomyotome there is also a medio-lateral difference. The central region makes dermis, the mesenchymal connective tissue of the back skin. The medial region (closest to neural tube) makes epaxial muscle, and the lateral region (furthest from neural tube) makes hypaxial muscle[http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=eurekah&part=A66768]. Epithelial sheet on the external surface of the somite that gives rise to trunk, muscle and dermis.[TAO] FMA:295654 Portion of somites that gives rise to dermis and muscles.[AAO] TAO:0001513 The bilaminar epithelium formed from the myotome and dermatome. Thus, representatives of the agnathan vertebrates, chondrichthyans, and sarcopterygians all have a layer of undifferentiated cells external to the embryonic myotome. In the amniotes, this external cell layer is the dermomyotome. The simplest interpretation of the similar position, morphology, and lack of myosin labeling is that a dermomyotome epithelium is a shared, ancestral vertebrate characteristic.[well established][VHOG] UBERON:0004290 UMLS:C1511786 VHOG:0000676 ZFA:0001513 all but the sclerotome of a mesodermal somite; the primordium of skeletal muscle and, perhaps, of the dermis. dermamyotome dermomyotomes uberon heart rudiment A cone-like structure that is formed when myocardial progenitor cells of the heart field fuse at the midline. The heart rudiment is the first structure of the heart tube. TAO:0000115 The migrating myocardial precursors of the heart rudiment form a cone like structure between 19.5hpf and 22hpf, and eventually telescope out into the primitive heart tube at 24hpf. Stainier 2001.[TAO] UBERON:0004291 ZFA:0000115 heart cone rudimentary heart uberon distal phalanx AAO:0010676 Distal-most phalanx within a digit. EMAPA:35287 In human anatomy, the distal phalanges of the four fingers and toes articulate proximally with the intermediate phalanges at the distal interphalangeal joints (DIP); in the thumb and big toe, with only two phalanges, the distal phalanges articulate proximally with the proximal phalanges. The distal phalanges carry and shape nails and claws and are therefore occasionally referred to as the ungual phalanges. The distal phalanges are cone-shaped in most mammals, including most primates, but relatively wide and flat in humans. MA:0002914 UBERON:0004300 phalanx distalis phalanx distalis terminal phalanx uberon ungual phalanx middle phalanx A phalanx located between proximal and distal phalanges. AAO:0010677 EMAPA:35572 Intermediate phalanges are bones found in the limbs of most vertebrates. In humans, they are the bones of the finger and toe which lie in the middle, between the two wrinkly joints. The thumb and big toe do not have intermediate phalanges. In most other vertebrates, they have a corresponding place in their limbs, whether they be paw, wing, hoof or fin MA:0002915 UBERON:0004301 consider using numbering system, and axioms to the effect that there is a single middle phalanx per finger in humans. This should perhaps be renamed 'intermediate phalanx', leaving the term middle phalanx open for the specific intermediate phalanx of a 3-phalanx digit in some groups such as whales, there are multiple intermediate phalanges intermediate phalanx medial phalanx penultimate phalanx phalanx 2 phalanx II uberon proximal phalanx 1 AAO:0010680 EMAPA:35716 MA:0002916 Proximal phalanges are bones found in the limbs of most vertebrates. In humans, they are the bones at the base of a toe or finger, the prominent, knobby ends of which are often called the knuckles. In other vertebrates, proximal phalanges have a similar placement in the corresponding limbs, be they paw, wing or fin. In many species, they are the longest and thickest phalanx ('finger' bone) Proximal-most phalanx within a digit. UBERON:0004302 phalanx 1 phalanx I proximal-most phalanx uberon primitive streak (...) the blastopore equivalent of chordates (germ ring in fish, marginal zone/blastopore lip in frog and node/primitive streak in chick and mouse) (...) (reference 1); Indeed, the primitive streak has been considered the homologue of the blastopore since the 1870s (reference 2).[well established][VHOG] EHDAA2:0001525 EHDAA:185 EMAPA:16072 FMA:293110 The primitive streak is a structure that forms during the early stages of avian, reptilian and mammalian embryonic development[WP]. the midline ridge of the embryonic epiblast that later develops into mesoderm and endoderm[MP] UBERON:0004341 UMLS:C0033153 VHOG includes a very broad grouping here based on http://www.ncbi.nlm.nih.gov/pubmed/9609826 VHOG:0001202 primitive streak - blastopore - germ ring uberon limb bud AAO:0010375 An outgrowth on the lateral trunk of the embryo that develops into a limb. The limb bud is divided into ectoderm and mesenchyme[cjm, modified from MP]. BTO:0001640 EMAPA:35944 Early outgrowth of presumptive limb.[AAO] FMA:296780 GAID:1307 MESH:A16.254.462 UBERON:0004347 UMLS:C0282505 XAO:0003161 developmentally_induced_by Fgf10, capable of initiating limb forming interactions between endoderm and mesoderm gemmae membrorum limb buds limbbud uberon optic eminence EHDAA:938 EMAPA:16322 RETIRED_EHDAA2:0001308 The embryonic structure that gives rise to the corneal ectoderm UBERON:0004348 VHOG:0001296 uberon apical ectodermal ridge AAO:0010760 AER Distal ectodermal thickening which forms along the anterior-posterior limb axis. Signaling from this region influences proximal-distal patterning of the limb. Structure is missing in some lineages (salamanders, Eleutherodactylus coqui) however morphologically their indistinct distal ectoderm may still be involved in signaling.[AAO] EMAPA:32744 Proliferative region that is part of the developing fin fold or fin.[TAO] TAO:0002146 The AER of tetrapods regresses after specification of skeletal progenitors, the AER of teleosts form an elongating fin fold UBERON:0004356 UMLS:C1516037 XAO:0004121 ZFA:0001702 apical epidermal ridge crista ectodermalis apicalis maintaining mesenchyme in plastic proliferating state; maintaining expression of A-P axis genes; interacting with D-V proteins. Genes: AER induced by Fgf10 in mesenchyme. AER secretes Fgf8, which stimulates mitosis in the mesenchyme causing Fgf10 production - positive feedback loop multilayered ectodermal region at the distal tip of a limb or fin bud necessary for the proper development of the underlying mesenchyme[MP,modified]. Along with the zone of polarizing activity, it is a crucial organizing region during limb development[WP]. note that media, dorsal fins etc have AERs. relationship loss: subclass proliferative region (TAO:0000098)[TAO] uberon paired limb/fin bud An outgrowth on the lateral trunk of the embryo that develops into a limb or paired fin. The limb/fin bud is divided into ectoderm and mesenchyme[cjm, modified from MP]. Genes: In limb buds of chick and mouse, Shh expression is activated as soon as there is a morphological bud, whereas in S. canicula fin buds, consistent with reported data in other cartilaginous fishes, Shh is transcribed late in fin development[PMID:17187056] The tetrapod limb is derived from a posterior part of the fin endoskeleton of elasmobranchs and basal bony fish, the so-called metapterygium, a series of endoskeletal elements that is the first to form in the developing paired fins. (...) In addition, there is an independent endoskeletal element called the protopterygium that develops anterior to the metapterygium in many basal fishes (e.g., the bichir and sturgeon). Teleosts have lost the metapterygium whereas the sarcopterygians, on the other hand, have lost the protopterygium. Sarcopterygians thus develop all their endoskeletal structures from the metapterygium and consequently the tetrapod limb skeleton is derived from the metapterygium.[uncertain][VHOG] UBERON:0004357 VHOG:0001258 limb - fin bud paired appendage bud paired limb/fin bud uberon anterior limiting lamina of cornea A transparent homogeneous acellular layer, 6 to 9 um thick, lying between the basal lamina of the outer layer of stratified epithelium and the substantia propria of the cornea; it is considered to be a basement membrane. Acellular anatomical structure that is the zone of collagen fibers adjacent the basement membrane of the corneal epithelium.[TAO] Bowman's anterior elastic lamina Bowman's layer Bowman's membrane Compared to terrestial animals, the cornea of zebrafish is relatively flat. It consists of nonpigmented, stratified squamous nonkeratinizing epithelial cells, attached to a thick basement membrane that is considered to be analogous to the Bowman's membrane in mammals FMA:58273 MA:0001240 Reichert's membrane TAO:0002155 UBERON:0004370 UMLS:C0229127 ZFA:0001684 anterior elastic lamina anterior limiting lamina anterior limiting lamina of cornea anterior limiting membrane lamina limitans anterior (cornea) lamina limitans anterior corneae uberon bone of free limb or fin A bone that is part of an appendage [Automatically generated definition]. UBERON:0004375 appendage bone bone of appendage bone of free segment of appendicular skeleton uberon skeleton of limb EHDAA2 considers hip and shoulder joints part of limb skeleton. EHDAA2:0002221 EMAPA:32702 Skeletal subdivision that is part of the limb.[VSAO] The collection of all skeletal elements in an individual limb. UBERON:0004381 VSAO:0000300 free limb skeleton limb skeleton set of bones of limb uberon entire sense organ system FMA:78499 Sum of all sensory systems in an organism. UBERON:0004456 note the distinct between entire sensory system and individual system. this reconciles is_a and part_of distinctions between ssAOs sense organ system uberon cardiac muscle tissue of myocardium A portion of cardiac muscle tissue that is part of a myocardium [Automatically generated definition]. EMAPA:32688 FMA:261726 MA:0002441 Note placement of MA class based on parthood relationship UBERON:0004493 uberon anatomical projection A projection or outgrowth of tissue from a larger body or organ. AAO:0010278 Anatomical structure that is a natural outgrowth, projection, or appendage. A process can be part of a bone, cartilage, or tissue.[AAO] Anatomical structure that is a natural outgrowth, projection, or appendage. A process can be part of a bone, cartilage, tissue, fin, scale, etc.[TAO] Anatomical structure that is a natural outgrowth, projection, or appendage. A process can be part of a bone, cartilage, tissue, fin, scale, etc.[VSAO] FMA:67601 HAO:0000822 TAO:0001834 UBERON:0004529 VSAO:0000180 XAO:0004020 anatomical process anatomical protrusion flange flanges galen:Ridge lamella lamellae lamina laminae organ process papilla process process of organ processes processus projection projection projections protrusion ridge ridges shelf shelves should be declared disjoint from organ, but in some ontologies (e.g. ZFA), structures such as neural spines are classified as bones (and hence organs) spine uberon cardiovascular system AAO:0011001 Anatomical system that has as its parts the heart and blood vessels. BILA:0000016 BTO:0000088 CALOHA:TS-1297 CV system EFO:0000791 EHDAA2:0000216 EHDAA:394 EMAPA:16104 EMAPA:16370 EV:0100017 FMA:7161 GAID:467 Herz und Gefaesssystem MA:0000010 MAT:0000016 MESH:D002319 MIAA:0000016 OpenCyc:Mx4rvVjzG5wpEbGdrcN5Y29ycA TAO:0000010 The vessels of the cardiovascular system are as varied as the diverse organs they supply. However, these variations are based on modifications of a fundamental plan of organization common to vertebrates.[well established][VHOG] UBERON:0004535 UMLS:C0007226 VHOG:0000302 WikipediaCategory:Cardiovascular_system XAO:0000100 XAO:0001010 ZFA:0000010 uberon we treat cardiovascular as part of circulatory system, with the latter including other kinds of circulation, including lymph. blood vasculature A vascular network consisting of blood vessels. TAO:0001079 UBERON:0004537 ZFA:0001079 blood system blood vascular network blood vessel system blood vessels set of blood vessels uberon systemic arterial system FMA:45623 The part of the arterial system which carries oxygenated blood away from the heart to the body, and returns deoxygenated blood back to the heart. UBERON:0004571 systemic arterial circulatory system uberon arterial system BTO:0004690 EHDAA2:0000143 EHDAA:396 EMAPA:16201 EMAPA:16371 MA:0002719 The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] The part of the cardiovascular system consisting of all arteries. UBERON:0004572 VHOG:0000273 uberon systemic artery An artery of the systemic circulation, which is the part of the cardiovascular system which carries oxygenated blood away from the heart, to the body, and returns deoxygenated blood back to the heart. FMA:66464 UBERON:0004573 systemic arterial subtree uberon venous system BTO:0004692 EHDAA2:0002171 EHDAA:486 EMAPA:16240 MA:0002720 The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] The part of the cardiovascular system consisting of all venous vessels. In vertebrates with a double circulation, this can be divided into systemic and pulmonary portions. UBERON:0004582 UMLS:C1267406 VHOG:0000277 uberon vein system sphincter muscle A structure, usually a circular muscle, that normally maintains constriction of a natural body passage or orifice and which relaxes as required by normal physiological functioning. FMA class is not a subtype of muscle FMA:75004 UBERON:0004590 UMLS:C1409894 circular muscle sphincter uberon liver lobule EMAPA:35499 FMA:14471 MA:0002494 UBERON:0004647 UMLS:C0227518 hepatic lobule lobules of liver lobuli hepatici lobuli hepatis lobulus hepaticus should not be confused with the anatomic lobes of the liver (caudate lobe, quadrate lobe, left lobe, and right lobe), or any of the functional lobe classification systems.[WP] the polygonal structure of the liver that consists of hepatocytes radiating outward from a hepatic vein uberon paired limb/fin An appendage that is part of a appendage girdle complex. UBERON:0004708 UBERON:0009872 VSAO:0000067 girdle-associated appendage jointed paired lateral appendage limb or fin limb/fin paired appendage pectoral or pelvic appendage pelvic/pectoral appendage this class is the union of the classes limb, pectoral fin and pelvic fin. uberon pelvic appendage Paired appendage that consists of the posterior appendicular skeleton and associated soft and hard tissues, but excludes the pelvic girdle and its associated soft and hard tissues. UBERON:0004709 UBERON:0009876 VSAO:0000126 hindlimb/pelvic fin pelvic appendage pelvic limb/fin posterior appendage posterior limb/fin posterior paired appendage uberon conceptus AEO:0000194 BTO:0003834 EHDAA2 places this as a subtype of organism. This leads to the inference that a conceptus is an embryo (if an embryo is defined as an organism at embryo stage), which eliminates the embryonic + extra-embryonic = conceptus EHDAA2:0000001 EHDAA2:0003235 EMAPA:36040 The embryo and its adnexa (appendages or adjunct parts) or associated membranes (i.e. the products of conception) The conceptus includes all structures that develop from the zygote, both embryonic and extraembryonic. It includes the embryo as well as the embryonic part of the placenta and its associated membranes - amnion, chorion (gestational sac), and yolk sac[WP]. UBERON:0004716 UMLS:C1516779 embryo plus adnexa uberon segmental subdivision of nervous system Any segmental subdivision of a nervous system. Includes metameric developmental segments, such as vertebrates neuromeres. FBbt:00005140 UBERON:0004732 neuromere revisit this after CARO is revised and/or we have defined metameric segment; note that with the additional of an A/P axis constraint this corresponds to what Richter at al call a neuromere (PMID:21062451) uberon segmental subdivision of hindbrain An organ subunit that is part of a hindbrain [Automatically generated definition]. FMA:61998 UBERON:0004733 hindbrain segment segment of hindbrain uberon gastrula BILA:0000060 BTO:0001403 FBbt:00005317 FMA:293108 GAID:1302 MESH:A16.254.412 MIAA:0000179 Organism at the gastrula stage. UBERON:0004734 UBERON:0007012 UMLS:C0017199 UMLS:C1284022 We explicitly merge the NCITA terms here blastocystis trilaminaris gastrula embryo tri-laminar disc tri-laminar disk trilaminar blastocyst trilaminar blastoderm trilaminar disc trilaminar disk trilaminar germ uberon skeletal tissue A specialized form of connective tissue in which the extracellular matrix is firm, providing the tissue with resilience, and/or mineralized and that functions in mechanical and structural support.[VSAO] A specialized form of connective tissue in which the extracellular matrix is firm, providing the tissue with resilience, and/or mineralized and that functions in mechanical and structural support.[VSAO] Four classes of mineralized tissues are found in vertebrates: bone, cartilage, dentine, and enamel. We think of cartilage and bone as skeletal tissues and of enamel and dentine as dental tissues, but enamel and dentine arose evolutionarily together with bone as skeletal tissues in the dermal skeleton (exoskeleton) of early vertebrates. Scales and teeth of sharks are examples of dermal skeletal elements that are still composed of the three ancient components-enamel, dentine, and bone. Cartilage, on the other hand, provided the basis for the second vertebrate skeletal system, the endoskeleton (Smith and Hall, 1990; Hall, 1998a,b). some invertebrate skeletal tissues have surprisingly bone-like features. Examples include chondrocytes interconnected by cell processes in cephalopod cartilages (Cole and Hall, 2004a,b), and the calcium phosphate layer in the shells of brachiopods (Rodland et al., 2003). However, neither bone nor mineralized cartilage have been found in invertebrates. Editors notes: TODO - develops_from MA:0003047 UBERON:0004755 VSAO:0000015 XAO:0004038 ZFA:0005619 uberon skeletal element AAO:0011129 Organ consisting of skeletal tissue. Encompasses whole bones, fused bones, cartilaginious elements, teeth, dermal denticles. Organ entity that is typically involved in mechanical support and may have different skeletal tissue compositions at different stages.[VSAO] Organ entity that may have different tissue compositions at different stages and is typically involved in mechanical support.[TAO] TAO:0001890 UBERON:0004765 VSAO:0000128 XAO:0004012 ZFA:0005494 galen:SkeletalStructure uberon articular system Anatomical system that consists of all the joints of the body. EMAPA:35150 FMA:23878 MA:0003007 UBERON:0004770 VSAO:0000181 joint system set of all joints set of all joints of body set of joints of body uberon gastrointestinal system mucosa A mucosa that is part of a gastrointestinal system. BTO:0000546 BTO:0005568 EMAPA:36591 MA:0001521 The gut mucosa of amphioxus has insulin-secreting cells. http://www.ncbi.nlm.nih.gov/pubmed/16417468 UBERON:0004786 digestive tract mucosa gut mucosa gut mucuous membrane mucosa of gut uberon respiratory tract epithelium BTO:0000419 CALOHA:TS-0023 EMAPA:32827 MA:0001480 UBERON:0004802 VHOG:0000981 airway epithelium epithelial tissue of respiratory tract epithelium of respiratory tract respiratory epithelium respiratory tract epithelial tissue the pseudostratified ciliated epithelium that lines much of the conducting portion of the airway, including part of the nasal cavity and larynx, the trachea, and bronchi uberon respiratory system epithelium An epithelium that is part of a respiratory system [Automatically generated definition]. CALOHA:TS-0023 EMAPA:32826 MA:0001823 UBERON:0004807 VHOG:0000981 apparatus respiratorius epithelial tissue apparatus respiratorius epithelium epithelial tissue of apparatus respiratorius epithelial tissue of respiratory system epithelium of apparatus respiratorius epithelium of respiratory system respiratory system epithelial tissue uberon gastrointestinal system epithelium An epithelium that is part of a digestive system [Automatically generated definition]. EMAPA:32683 MA:0001520 UBERON:0004808 digestive system epithelial tissue digestive system epithelium epithelial tissue of digestive system epithelial tissue of gastrointestinal system epithelium of digestive system epithelium of gastrointestinal system gastrointestinal system epithelial tissue uberon upper respiratory tract epithelium An epithelium that is part of a upper respiratory tract [Automatically generated definition]. EMAPA:35894 MA:0001912 UBERON:0004814 epithelial tissue of upper respiratory tract epithelium of upper respiratory tract uberon upper respiratory tract epithelial tissue kidney epithelium BTO:0000059 CALOHA:TS-0505 EMAPA:35457 MA:0002846 UBERON:0004819 epithelial tissue of kidney epithelium of kidney kidney epithelial tissue renal epithelium the cellular avascular layer of the kidney luminar surfaces uberon splanchnic layer of lateral plate mesoderm AAO:0011102 BILA:0000044 FMA:295568 Layer of lateral plate mesoderm that forms the circulatory system and future gut wall - overlies endoderm[WP]. UBERON:0004872 We group the BILA class here. Considering adding more general class for metazoa grouping cardiogenic successors XAO:0000276 inner layer of lateral plate mesoderm splanchnic mesoderm uberon visceral mesoderm somatopleure A structure created during embryogenesis when the lateral mesoderm splits into two layers - the outer (or somatic) layer becomes applied to the inner surface of the ectoderm, and with it forms the somatopleure.[WP]. EHDAA2:0001847 EHDAA:381 EMAPA:16180 FMA:295566 Gives rise to the paired appendages in jawed vertebrates. a persistent somatopleure through the redistribution and expansion of the lateral plate mesoderm is a synapomorphy for gnathostomes and a critical step in generating a novel developmental module with dramatic evolutionary potentia (Tulenko et al. 2012) http://burkelab.research.wesleyan.edu/current-projects/lamprey/ UBERON:0004874 UMLS:C1519423 VHOG:0000557 sources differ as to whether this is part-of or develops-from the LPM uberon nephrogenic cord A portion of the urogenital ridge which is the source of much of the urinary system[WP]. FMA:72168 UBERON:0004875 UMLS:C1283944 chorda nephrogenica part_of or develops_from urogenital ridge? uberon urogenital fold EHDAA2:0004022 EMAPA:30888 FMA:321919 Less commonly, urogenital fold refers to the fold in the mesonephros which is the precursor of e.g. the suspensory ligament of the ovary. This is the case in older versions of Gray's anatomy[WP] One of of the pair of folds derived from the cloacal folds which give rise to a portion of the external genitalia; in male embryos they close over the urethral plate and fuse to form the spongy (penile) urethra and ventral aspect of the penis, not including the glans; failure of fusion of the urethral folds leads to hypospadias; in female embryos they fuse only anterior to the anus and form the labia minora[MP]. UBERON:0004876 uberon urethral fold urogenital fold urogenital ridge chordamesoderm AAO:0000478 EFO:0003426 Notochord rudiment[ZFIN:ZDB-PUB-961014-576]. TAO:0000091 The central region of trunk mesoderm. This tissue forms the notochord UBERON:0004880 WP treats this as synonym of axial mesoderm. Induces neural tube. Gilbert: contains an anterior head process and the notochord. ZFA:0000091 axial chorda mesoderm chorda mesoderm dorsal mesoderm presumptive notochord uberon urogenital sinus epithelium EHDAA2:0004061 EMAPA:31509 EMAPA:31520 The fetal urogenital sinus (from which the prostate derives) is a simple cylinder of stratified basal epithelium, surrounded by mesenchyme and positioned between the embryonic bladder and pelvic urethra UBERON:0004902 UGE epithelium of urogenital sinus uberon we follow EHDAA2 in dividing the UGS into epithelium and lumen articulation Anatomical cluster that connects two or more adjacent skeletal elements or hardened body parts. FBbt:00005811 UBERON:0004905 joint uberon lower digestive tract FMA:49179 MA class was moved from here. See https://github.com/obophenotype/uberon/issues/509 The region of the digestive tract extending from the beginning of the intestines to the anus[GO - gut definition]. UBERON:0004907 UMLS:C0226875 WP: small intestine, large intestine, anus. Anal canal not part of LGIT according to FMA, but anus is considered part of LGIT according to WP. Duodenum overlaps both U/L galen:LowerGastrointestinalTract gut lower GI tract lower gastrointestinal tract uberon upper digestive tract FMA:49177 The region of the digestive tract extending from the mouth cavity through pharynx esophagus stomach and duodenum. UBERON:0004908 UMLS:C0226874 WP: small intestine, large intestine, anus. Anal canal not part of LGIT according to FMA, but anus is considered part of LGIT according to WP. Duodenum overlaps both U/L. In Galen, entire GI tract excludes esophagus galen:UpperGastrointestinalTract uberon upper GI tract upper gastrointestinal tract biliary bud EHDAA2:0000171 EMAPA:16561 EMAPA_RETIRED:16565 UBERON:0004912 VHOG:0001351 hepatic diverticulum uberon hepatopancreatic ampulla A dilation of the duodenal papilla that is the opening of the juncture of the common bile duct and the main pancreatic duct. Ampulla formed by the union of the pancreatic duct and the common bile duct where they enter the intestine.[TAO] CALOHA:TS-2348 FMA:15076 GAID:283 MESH:A03.159.183.079.300.900 TAO:0005167 UBERON:0004913 UMLS:C0042425 Vater's ampulla ZFA:0005167 ampulla Vaterii ampulla biliaropancreatica ampulla hepatopancreatica ampulla of Vater ampulla of bile duct biliaropancreatic ampulla galen:AmpullaOfVater papilla Vateri papilla duodeni major uberon duodenal papilla EMAPA:18662 FMA:15953 MA:0003107 One of the two small elevations on the mucosa of the duodenum, the major at the entrance of the conjoined pancreatic and common bile ducts and the minor at the entrance of the accessory pancreatic duct. UBERON:0004914 papilla duodenalis papilla duodeni papilla of duodenum uberon subdivision of digestive tract A proximal-distal subdivision of the digestive tract. FBbt:00100315 FMA:71131 UBERON:0004921 alimentary system subdivision intended to denote both embryonic and adult structures. Note the FMA grouping here is not quite correct. intestinal tract segment of intestinal tract subdivision of alimentary system uberon organ component layer A part of a wall of an organ that forms a layer. FMA:82485 UBERON:0004923 uberon mucosa of pylorus A mucosa that is part of a pylorus [Automatically generated definition]. BTO:0004110 EMAPA:27199 FMA:17461 UBERON:0004998 antropyloric mucosa mucosa of organ of pyloric part of stomach mucosa of organ of pylorus mucosa of organ of stomach pyloric region mucosa of pyloric part of stomach mucosa of stomach pyloric region mucous membrane of pyloric part of stomach mucous membrane of pylorus mucous membrane of stomach pyloric region organ mucosa of pyloric part of stomach organ mucosa of pylorus organ mucosa of stomach pyloric region pyloric part of stomach mucosa pyloric part of stomach mucosa of organ pyloric part of stomach mucous membrane pyloric part of stomach organ mucosa pylorus mucosa pylorus mucosa of organ pylorus mucous membrane pylorus organ mucosa stomach pyloric region mucosa stomach pyloric region mucosa of organ stomach pyloric region mucous membrane stomach pyloric region organ mucosa uberon neural groove AAO:0011071 EMAPA:35594 FMA:295624 The median dorsal longitudinal groove formed in the embryo by the neural plate after the appearance of the neural folds. The neural groove is a shallow median groove between the neural folds of an embryo. The neural folds are two longitudinal ridges that are caused by a folding up of the ectoderm in front of the primitive streak of the developing embryo. The groove gradually deepens as the neural folds become elevated, and ultimately the folds meet and coalesce in the middle line and convert the groove into a closed tube, the neural tube or canal, the ectodermal wall of which forms the rudiment of the nervous system. After the coalescence of the neural folds over the anterior end of the primitive streak, the blastopore no longer opens on the surface but into the closed canal of the neural tube, and thus a transitory communication, the neurenteric canal, is established between the neural tube and the primitive digestive tube. The coalescence of the neural folds occurs first in the region of the hind-brain, and from there extends forward and backward; toward the end of the third week the front opening (anterior neuropore) of the tube finally closes at the anterior end of the future brain, and forms a recess which is in contact, for a time, with the overlying ectoderm; the hinder part of the neural groove presents for a time a rhomboidal shape, and to this expanded portion the term sinus rhomboidalis has been applied. Before the neural groove is closed a ridge of ectodermal cells appears along the prominent margin of each neural fold; this is termed the neural crest or ganglion ridge, and from it the spinal and cranial nerve ganglia and the ganglia of the sympathetic nervous system are developed. By the upward growth of the mesoderm the neural tube is ultimately separated from the overlying ectoderm. The cephalic end of the neural groove exhibits several dilatations, which, when the tube is closed, assume the form of three vesicles; these constitute the three primary cerebral vesicles, and correspond respectively to the future fore-brain (prosencephalon), mid-brain (mesencephalon), and hind-brain (rhombencephalon). The walls of the vesicles are developed into the nervous tissue and neuroglia of the brain, and their cavities are modified to form its ventricles. The remainder of the tube forms the medulla spinalis or spinal cord; from its ectodermal wall the nervous and neuroglial elements of the medulla spinalis are developed while the cavity persists as the central canal[Wikipedia:Neural_groove]. UBERON:0005061 UMLS:C0814992 XAO:0000248 uberon neural fold EHDAA2:0001249 EMAPA:16142 EMAPA:16146 EMAPA:16151 EMAPA:16155 EMAPA:16159 EMAPA:16162 EMAPA:16288 EMAPA:16292 EMAPA:16295 EMAPA:16299 EMAPA:16303 EMAPA:16307 EMAPA:16528 FMA:295618 In front of the primitive streak two longitudinal ridges, caused by a folding up of the ectoderm, make their appearance, one on either side of the middle line. These are named the neural folds; they commence some little distance behind the anterior end of the embryonic disk, where they are continuous with each other, and from there gradually extend backward, one on either side of the anterior end of the primitive streak. Also, after differentiation it turns into the neural tubes[Wikipedia:Neural_fold]. One of the two elevated edges of the neural groove[GO,MP]. UBERON:0005062 UMLS:C0814993 XAO:0004087 medullary fold uberon neural rod A solid rod of neurectoderm derived from the neural keel. The neural rod is roughly circular in cross section. Neural rod formation occurs during primary neurulation in teleosts[GO]. An intermediate stage in the development of the central nervous system present during the segmentation period; the neural rod is roughly cylindrical in shape, forms from the neural keel, and is not yet hollowed out into the neural tube[ZFIN]. An intermediate stage in the development of the central nervous system present during the segmentation period; the neural rod is roughly cylindrical in shape, forms from the neural keel, and is not yet hollowed out into the neural tube. Kimmel et al, 1995.[TAO] EFO:0003498 TAO:0000133 UBERON:0005068 ZFA:0000133 neural tube rod uberon metanephric ureteric bud The portion of the ureteric bud tube that contributes to the morphogenesis of the metanephros[GO]. UBERON:0005080 uberon ureter ureteric bud The portion of the ureteric bud that contributes to the morphogenesis of the ureter. The ureter ureteric bud is the initial structure that forms the ureter[GO]. UBERON:0005081 uberon ectodermal placode AEO:0000218 An ectodermal placode is a thickening of the ectoderm that is the primordium of many structures derived from the ectoderm[GO] FMA:293966 UBERON:0005085 With the exception of the adenohypophysis, homologues of the nonneurogenic placodes (e.g. placodes giving rise to the teeth, hair follicles and lens), appear to be lacking in invertebrate chordates. consder adding placodal ectoderm as a distinct class? Also place placodal ectoderm as develops_from ectoderm; need to check taxon-appropriateness epithelial placode in GO, covers optic, otic, olfactory, mammary, hair, tooth, sebaceous. uberon muscle structure EMAPA:32715 FBbt:00005073 FMA:30316 Muscle structures are contractile cells, tissues or organs that are found in multicellular organisms[GO]. UBERON:0005090 in some organisms such as drosophila, muscles can be single cells. This class groups together all discrete muscle elements, from multicellular muscle organs in vertebrates, to individual single-cell muscles in drisophila muscle muscle element musculus uberon kidney rudiment . UBERON:0005095 class added for consistency with GO - consider merging with kidney mesenchyme. kidney anlage uberon mesonephric epithelium An epithelium that is part of a mesonephros [Automatically generated definition]. UBERON:0005103 uberon epithelial bud A bud is a protrusion that forms from an epithelial sheet by localized folding. BTO:0001639 UBERON:0005153 uberon reproductive structure Any anatomical structure that is part of the reproductive system. UBERON:0005156 reproductive system element reproductive system structure uberon epithelial fold An epithelial sheet bent on a linear axis. UBERON:0005157 uberon multi cell part structure A structure consisting of multiple cell components but which is not itself a cell and does not have (complete) cells as a part. AAO:0011000 CARO:0001000 FBbt:00007060 FMA:83115 UBERON:0005162 cell part cluster multi-cell-component structure multi-cell-part structure uberon we go with the FMA classification rather than the CARO one. FMA def: 'Anatomical cluster which has as direct parts cell parts from two or more cells.' hepatic duct A duct that carries bile from the liver to the small intestine.[TAO] A duct that carries bile from the liver to the small intestine[ZFA]. Any portion of the ducts that carry bile from the liver to the common bile duct. This may include both intrahapetic components (parts of left and right hepatic ducts) and extrahapetic components (common hepatic duct, plus hilar portion). EHDAA2:0000741 EHDAA:3049 EMAPA:16843 FMA:71891 MA:0000357 OpenCyc:Mx4rvWo8WJwpEbGdrcN5Y29ycA TODO - MA distinguishes between bile duct, hepatic duct, common bile duct and common hepatic duct. in FMA hepatic duct and common hepatic duct are the same The excretory duct of the liver or one of its branches in the lobes of the liver. [TFD][VHOG] The hepatic duct is the duct that leads from the liver to the bile duct[GO]. UBERON:0005171 UMLS:C0917710 VHOG:0000219 galen:HepaticDuct uberon abdomen element An organ or element that is in the abdomen. Examples: spleen, intestine, kidney, abdominal mammary gland. MA:0000522 UBERON:0005172 abdomen organ uberon abdominal segment element An organ or element that is part of the adbominal segment of the organism. This region can be further subdivided into the abdominal cavity and the pelvic region. MA:0000529 UBERON:0005173 abdominal segment organ uberon dorsal region element An organ or element that part of the dorsum of the organism. Examples: spinal cord, vertebrae, muscles of back. MA:0001901 UBERON:0005174 back organ dorsal region organ uberon trunk region element An organ or element that part of the trunk region. The trunk region can be further subdividied into thoracic (including chest and thoracic cavity) and abdominal (including abdomen and pelbis) regions. MA:0000516 UBERON:0005177 trunk organ uberon thoracic cavity element An organ or element that is in the thoracic cavity. Examples: lung, heart, longus colli. MA:0000557 UBERON:0005178 thoracic cavity organ uberon pelvic region element An organ or element that is part of the pelvic region. Examples: reproductive organs (in some organisms), urinary bladder, bones of the pelvis. MA:0000543 UBERON:0005179 pelvic element pelvis organ pelvis region organ uberon thoracic segment organ An organ that part of the thoracic segment region. This region can be further subdividied chest and thoracic cavity regions. MA:0000563 UBERON:0005181 uberon upper body organ basal plate metencephalon EHDAA2:0001154 EMAPA:17078 The ventral half of the developing neural tube that is the metencephalon. [Chordate_evolution_and_the_origin_of_craniates:_An_old_brain_in_a_new_head._AnaT_Rec_(New_Anat)_(2000)_261(3):_111-125, See_Butler_AB][VHOG] UBERON:0005239 VHOG:0000320 metencephalon basal plate uberon head mesenchyme EFO:0003492 EHDAA2:0000732 EHDAA:179 EMAPA:16098 EMAPA_RETIRED:16269 FMA:76622 Mesoderm that will give rise, along with cranial neural crest cells, to connective tissue, bone and musculature in the head. (Source: BioGlossary, www.Biology-Text.com)[TAO] Portion of primordial embryonic connective tissue of the developing head, consisting of mesenchymal cells supported in interlaminar jelly, that derive mostly from the mesoderm and contribute to head connective tissue, bone and musculature in conjunction with cranial neural crest cells. TAO:0000113 UBERON:0005253 VHOG:0000332 ZFA:0000113 cephalic mesenchyme cranial mesenchyme desmocranium uberon trunk mesenchyme EFO:0003485 EHDAA2:0002092 EHDAA:377 EMAPA:16177 Mesenchyme that is part of a developing trunk. TAO:0000081 UBERON:0005256 VHOG:0000281 ZFA:0000081 trunk and cervical mesenchyme uberon myelencephalon BTO:0000758 CALOHA:TS-0607 CALOHA:TS-2365 DHBA:10662 EHDAA2:0001207 EHDAA:5526 EMAPA:17082 HBA:9512 MA:0000205 The early development of most vertebrate brains is similar (...). The zebrafish neural tube follows the same basic differentiation pattern as the mammalian neural tube (reference 1); The brain develops from three embryonic enlargements of the neural tube, which later differentiate into five regions. A forebrain differentiates into telencephalon and diencephalon. The midbrain, or mesencephalon, remains undivided. The hindbrain divides into the metencephalon and myelencephalon. Cavities within the brain enlarge to form a series of interconnected ventricles (reference 2).[well established][VHOG] The posterior of the two brain vesicles formed by specialization of the rhombencephalon in the developing embryo, it comprises the medulla oblongata. [TFD][VHOG] The posterior part of the developing vertebrate hindbrain or the corresponding part of the adult brain composed of the medulla oblongata and a portion of the fourth ventricle; as well as the glossopharyngeal nerve (CN IX), vagus nerve (CN X), accessory nerve (CN XI), hypoglossal nerve (CN XII), and a portion of the vestibulocochlear nerve (CN VIII).[BTO,WP]. UBERON:0005290 VHOG:0000456 myelencephalon (medulla oblongata) the terms metencephalon and myelencephalon are only meaningful in mammals and birds - Neuroanatomy of the Zebrafish Brain. Note that its not clear if this refers to the developing medulla oblongata - MA (adult) has two distinct classes uberon embryonic tissue A portion of tissue that is part of an embryo. CALOHA:TS-2100 UBERON:0005291 developing tissue portion of embryonic tissue uberon photoreceptor array An array of photoreceptors and any supporting cells found in an eye. FBbt:00004200 UBERON:0005388 light-sensitive tissue uberon transparent eye structure A transparent structure that is part of a visual sense organ, the function of which is to direct or focus light onto a photoreceptor array. UBERON:0005389 directing or focusing light onto light receptors lens uberon male reproductive gland A sex gland that is part of a male reproductive system. BTO:0000080 EMAPA:19285 MA:0000399 UBERON:0005399 accessory sex gland uberon alimentary part of gastrointestinal system All metazoans (with degenerate exceptions) have some sort of digestive cavity with a means of entrance to and exit from it.[well established][VHOG] BTO:0000058 CALOHA:TS-0407 EHDAA2:0000110 EHDAA:514 EMAPA:16246 EV:0100056 FMA:71132 GAID:294 GI tract MA:0000323 MESH:A03.492 The part of the digestive system that excludes the hepatobiliary system. The system that includes the esophagus, stomach, small and large intestine, anus, liver, biliary tract, and pancreas[ncithesaurus:Gastrointestinal_System]. UBERON:0005409 UMLS:C0012240 VHOG:0000412 alimentary system alimentary tract galen:GastrointestinalTract gastro-intestinal system gastrointestinal (GI) tract gastrointestinal system gastrointestinal tract that many anatomy ontologies consider this synonymous with digestive system. here we follow MA in dividing digestive system into gastrointestinal and hepatobiliary. hepatobiliary includes the liver and biliary tract. species-specific AO classes are categorized according to whether liver is included. For example, XAO includes liver as part of XAO:0000125 alimentary system, so we assume this class is the more generic class. We have one entity that is part of both gastrointestinal and hepatobiliary systems: hepatopancreatic ampulla. the decision to split digestive and gastrointestinal in this way may be revisited. As it currently stands, this class more closely aligns what MA calls the alimentary system uberon hindlimb bud A limb bud that develops into a hindlimb. AAO:0010382 EHDAA:2358 EMAPA:16779 Genes: Tbx4 specifies hindlimbs. Wnt8c restricts Fgf10 in chick. MIAA:0000256 RETIRED_EHDAA2:0003197 The bilateral thickening of the ectoderm in the region of the first noticeable at NF stage 47, and innervated by NF stage 51. The hind limb buds develop before the forelimb buds.[AAO] UBERON:0005418 XAO:0003066 hind limb bud leg bud limb bud - hindlimb posterior limb bud uberon pelvic appendage bud A limb bud that develops into a hindlimb or pelvic fin. EFO:0003469 Fin bud that develops into the pelvic fin.[TAO] Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG] TAO:0001384 UBERON:0005420 VHOG:0001260 ZFA:0001384 at this time we have no need to name a more specific 'pelvic fin bud' class, but we may in future hindlimb/pelvic fin bud pelvic fin bud pelvic fin buds uberon developing anatomical structure AEO:0000125 CALOHA:TS-2122 EHDAA2:0003125 FBbt:00007006 FMA:292313 MIAA:0000019 UBERON:0005423 developing structure developmental structure developmental tissue uberon presumptive neural retina (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG] EHDAA2:0001304 EMAPA:16675 Portion of tissue that is the inner layer of the optic cup and will become the neural retina. TAO:0001071 UBERON:0005425 VHOG:0000490 ZFA:0001071 future NR future neural epithelium future neural layer future neural retina future retinal neural layer inner layer optic cup optic cup inner layer presumptive retina presumptive retinas uberon lens vesicle (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The optic cup induces the overlying surface ectoderm first to thicken as a lens placode and then to invaginate and form a lens vesicle that differentiates into the lens.[well established][VHOG] A vesicle formed from the lens pit of the embryo, developing into the crystalline lens. [TFD][VHOG] EHDAA2:0000983 EHDAA:4737 EMAPA:17163 Portion of tissue that gives rise to the lens. TAO:0002205 UBERON:0005426 VHOG:0001163 ZFA:0001679 hollow lens vesicle immature lens lens mass presumptive lens solid lens vesicle the lens of zebrafish (and other teleosts) forms from delamination of cells from the lens placode; thus, there is no formation of a hollow lens vesicle, in contrast to the situation in mammals and birds (Glass and Dahm, 2004) [PMID:16496288] The lens of the zebrafish forms by delamination of lens placodal cells and not through invagination. This results in a solid spherical mass as opposed to a hollow lens vesicle. Detachment of the solid lens vesicle of zebrafish at 24b26 hpf is accomplished in part by apoptosis, similar to mammals uberon corneal primordium Portion of tissue that is part of the eye and gives rise to the mature, fully layered cornea. TAO:0002188 UBERON:0005427 ZFA:0001688 uberon sulcus limitans of neural tube A longitudinal groove in the neural tube wall that divides the neural tube into dorsal (alar) and ventral (basal) halves (dorsal receives input from sensory neurons, ventral effects motor functions); stretches from the mesencephalon caudad[TMD]. BAMS:slim BAMS:slm UBERON:0005478 neural tube lateral wall sulcus limitans sulcus limitans uberon neural tube lateral wall EHDAA2:0001257 EHDAA:2873 EHDAA:912 EMAPA:16532 Portion of tissue on the side of the lumen of the neural tube. TAO:0001435 UBERON:0005496 VHOG:0000513 ZFA:0001435 lateral wall neural tube uberon non-neural ectoderm After gastrulation, neural crest cells are specified at the border of the neural plate and the non-neural ectoderm. EFO:0003643 EHDAA:257 EMAPA:16074 Gene notes: One of the first genes to be expressed in nonneural ectoderm in amphioxus is BMP2/4 (Panopoulou et al. 1998). BMP2/4 homologues appear to have a very ancient role in distinguishing neural from nonneural ectoderm; in Drosophila as well as in amphioxus and vertebrates, BMP2/4 homologues are expressed in nonneural ectoderm and function in distinguishing neural from nonneural ectoderm (Francois & Bier, 1995 ; Sasai et al. 1995 ; Wilson & Hemmati-Brivanlou, 1995; Panopoulou et al. 1998). A change in level of BMP2/4 from very high in nonneural ectoderm to low in neural ectoderm appears to be a key factor in development of neural crest (Baker & Bronner-Fraser,1997a,1997b;Erickson&Reedy,1998;Marchantet al.1998 ;Selleck et al. 1998). Editor note: todo - epidermis? todo - track down EHDAA2 class in new release In the early gastrula of vertebrates, factors from the organizer (e.g. noggin, chordin, and follistatin in Xenopus) antagonize the epidermalizing factor bone morphogenetic protein 4 (BMP4), thus dividing the epiblast into neuroectoderm. In Drosophila, decapentaplegic, the homologue of BMP4, interacts similarly with the protein short gastrulation, the homologue of chordin. Thus, a comparable molecular mechanism for distinguishing non-neural ectoderm from neural ectoderm was probably present in the common ancestor of all bilaterally symmetrical animals.[well established][VHOG] RETIRED_EHDAA2:0001273 TAO:0001178 UBERON:0005497 VHOG:0001372 XAO:0004091 ZFA:0001178 epidermal ectoderm epithelial ectoderm non neural ectoderm surface ectoderm uberon ventral ectoderm primitive heart tube EHDAA2:0001512 EHDAA:424 EHDAA:436 EMAPA:16208 EMAPA:16215 FMA:321916 Multi-tissue structure that arises from the heart rudiment and will become the heart tube. TAO:0000149 UBERON:0005498 ZFA:0000149 early primitive heart tube primitive heart tube uberon gonad primordium EFO:0003651 EHDAA:5927 EMAPA:17204 Immature reproductive tissue that has not undergone final maturation into either testis or ovary.[TAO] Portion of tissue that gives rise to the immature gonad. RETIRED_EHDAA2:0002148 TAO:0001262 UBERON:0005564 WBbt:0008366 ZFA:0001262 future gonad gonadal primordium immature gonad primitive gonad this is a very broad grouping class uberon undifferentiated gonad lung primordium A pair of lateral diverticula just over the liver rudiment representing the primordia of the lungs, formed by the floor of the foregut just anterior to the liver diverticulum. AAO:0011059 EFO:0002578 EMAPA:36007 UBERON:0005597 UBERON:3010717 XAO:0001002 lateral diverticula lung diverticulum lung endoderm uberon extrahepatic part of hepatic duct EMAPA:16844 MA:0001636 UBERON:0005604 VHOG:0000215 extrahepatic part of the hepatic duct hepatic duct extrahepatic part uberon pronephric mesoderm A mesoderm that has the potential to develop into a pronephros. AAO:0011090 EFO:0003479 Portion of tissue that consists of the mesenchymal precursor to the pronephric kidney and that begins to separate from the intermediate mesoderm at NF stage 21 and epithelializes by NF stage 30.[AAO] TAO:0000067 UBERON:0005721 VHOG:0001239 XAO:0000264 ZFA:0000067 pronephric anlage pronephric bulge pronephric mesenchyme pronephric primordium the intermediate mesoderm of the chick embryo acquires its ability to form kidneys through its interactions with the paraxial mesoderm [ISBN:9780878932504 "Developmental Biology", http://www.ncbi.nlm.nih.gov/pubmed/10720431 "Signals from trunk paraxial mesoderm induce pronephros formation in chick intermediate mesoderm"]. These interactions induce the expression of TFs including Lim1, Pax2 and Pax6 that cause the intermediate mesoderm to form the kidney uberon olfactory system A sensory system that is capable of olfacttion (the sensory perception of smell). AAO:0000334 AAO:0000978 BILA:0000144 EFO:0001973 EMAPA:36004 FMA:7190 In mammals, the main olfactory system detects odorants that are inhaled through the nose, where they contact the main olfactory epithelium, which contains various olfactory receptors. These olfactory receptors are membrane proteins of bipolar olfactory receptor neurons in the olfactory epithelium. Rather than binding specific ligands like most receptors, olfactory receptors display affinity for a range of odor molecules. Olfactory neurons transduce receptor activation into electrical signals in neurons. The signals travel along the olfactory nerve, which belongs to the peripheral nervous system. This nerve terminates in the olfactory bulb, which belongs to the central nervous system. The complex set of olfactory receptors on different olfactory neurons can distinguish a new odor from the background environmental odors and determine the concentration of the odor[WP]. MA:0002445 OpenCyc:Mx4rvViw75wpEbGdrcN5Y29ycA TAO:0001149 The olfactory system is the sensory system used for olfaction, or the sense of smell. Most mammals and reptiles have two distinct parts to their olfactory system: a main olfactory system and an accessory olfactory system. The main olfactory system detects volatile, airborne substances, while the accessory olfactory system senses fluid-phase stimuli. Behavioral evidence indicates that most often, the stimuli detected by the accessory olfactory system are pheromones. The olfactory system is often spoken of along with the gustatory system as the chemosensory senses because both transduce chemical signals into perception[WP][Wikipedia:Olfactory_system]. The sensory system used for olfaction (the sense of smell).[AAO] UBERON:0005725 UMLS:C0228065 XAO:0003196 ZFA:0001149 consider splitting into main and accessory. See also: vomeronasal organ uberon we make the relationship to nervous system 'overlaps', as the olfactory system includes e.g. apertures in the cranium that are not part of the nervous system chemosensory system BILA:0000139 UBERON:0005726 uberon pelvic appendage field A limb/fin field that has the potential to develop into a pelvic appendage bud mesenchyme. Embryonic region that develops into the pelvic fin bud.[TAO] TAO:0001454 UBERON:0005730 ZFA:0001454 pelvic appendage field of lateral plate mesoderm pelvic fin field uberon fin field A limb/fin field that has_potential_to_developmentally_contribute_to a paired fin bud. UBERON:0005731 fin field of lateral plate mesoderm uberon paired limb/fin field A ring of cells capable of forming a limb or paired fin[Gilbert,modified]. UBERON:0005732 limb/fin field of lateral plate mesoderm paired limb/fin field uberon we represent the field as being a part of the LPM (consistent with ZFA, Gilbert). As a consequence, the relationship between limb bud (with is ectoderm+mesenchyme) stands in a weaker has_developmental_contribution_from relation to the field - TODO implement this. limb field A ring of cells capable of forming a limb. UBERON:0005733 limb field of lateral plate mesoderm the central portion of the limb field gives rise to the limb proper. mesenchyme cells proliferate from from the somatic layer of limb field lateral plate mesoderm (limb skeletal precursors) and from the somites (limb muscle precursors) . these mesenchymal cells accumulate under the ectedermal tissue to make a limb bud. // The lateral plate mesoderm in the limb field is also special in that it will induce myoblasts to migrate out from the somites and enter the limb bud. No other region of the lateral plate mesoderm will do that (Hayashi and Ozawa 1995) uberon caudal part of nephrogenic cord The metanephros develops from the most caudal part of the nephrogenic cord that is itself derived from the intermediate plate mesoderm. UBERON:0005753 caudal portion of nephrogenic cord caudal region of nephrogenic cord rear part of nephrogenic cord rear portion of nephrogenic cord uberon rostral part of nephrogenic cord The initial renal anlage that develops from the most rostral part of the nephrogenic cord is termed the pronephros. UBERON:0005754 uberon acellular membrane A acellular anatomical structure that is the bounding layer of a anatomical structure. FMA:63871 UBERON:0005764 uberon basement membrane of epithelium AAO:0010596 An acellular membrane that is part of the epithelium, lies adjacent to the epithelial cells, and is the fusion of the the basal lamina and the reticular lamina. FMA:63872 GAID:915 UBERON:0005769 UMLS:C0004799 basement membrane basement membrane of connective tissue membrana basalis this class represents a continuous sheet of basement membrane which can underlie multiple epithelial cells over large regions. In contrast, the GO class 'basal membrane' represents a portion of substance on the scale of a single cell. uberon nephric ridge EHDAA2:0001242 EHDAA:1015 EMAPA:16368 Nephric tubules (nephrons) form embryonically along the nephric ridge. The ridge comprises three regions; anterior, middle and posterior. The functional kidney uses nephrons from only one or two regions of the ridge. A pronephric kidney uses only the nephrons from the anterior region of the ridge. A mesonephric kidney uses only the middle region, a metanephric kidney uses only the posterior region and an opisthonephric kidney uses the middle and posterior regions. TODO - check ridge vs cord vs nephrogenic cord vs blastema UBERON:0005792 VHOG:0001240 nephric cord uberon embryonic uterus FMA:72173 UBERON:0005795 fetal uterus uberon portal system FMA:45628 In the circulatory system of animals, a portal venous system occurs when a capillary bed drains into another capillary bed through veins, without first going through the heart. Both capillary beds and the blood vessels that connect them are considered part of the portal venous system. They are relatively uncommon as the majority of capillary beds drain into veins which then drain into the heart, not into another capillary bed. Portal venous systems are considered venous because the blood vessels that join the two capillary beds are either veins or venules. Examples of such systems include the hepatic portal system and the hypophyseal portal system. Unqualified, 'portal venous system' often refers to the hepatic portal system. For this reason, 'portal vein' most commonly refers to the hepatic portal vein[WP]. MESH:D011168 UBERON:0005806 UMLS:C0226727 portal venous system uberon developing mesenchymal condensation A delimited region of dense mesenchyme within looser mesenchyme. AEO:0000148 EHDAA2_RETIRED:0003148 EHDAA:8979 UBERON:0005856 mesenchyme condensation uberon cartilaginous condensation AEO:0000147 Cell condensation that is an aggregation of mesenchymal cells that are committed to differentiate into chondroblasts and chondrocytes. EHDAA2_RETIRED:0003147 EMAPA:32731 UBERON:0005863 VSAO:0000092 XAO:0004022 cartilage condensation cartilagenous condensation chondrogenic condensation isa cell condensation in VSAO; has_part chondroblast in AEO uberon pre-cartilage condensation A closely packed aggregation of mesenchymal cells just prior to their differentiation into embryonic cartilage. A delimited region of dense mesenchyme within looser mesenchyme whose cells are committed to become chondroblasts. AEO:0000150 EHDAA2:0003150 EMAPA:32736 UBERON:0005866 pre-chondrogenic condensation precartilage condensation precartilagenous condensation prechondrogenic condensation uberon autopodial extension A subdivision of the autopod that corresponds to one or more bones arranged in series branching from the main limb axis. UBERON:0005881 digit or predigit encompasses digits and prepollex. requires review limb outgrowth uberon serous sac EMAPA:16060 FMA:9689 MA:0000005 Organ with organ cavity, which has as parts a serous membrane and a serous cavity . Examples: pleural sac, pericardial sac, tendon sheath, bursa.[FMA] See notes for serous membrane UBERON:0005906 uberon endo-epithelium Epithelium that derives from the endoderm. Examples: urothelium, transitional epithelium of ureter, epithelium of prostatic gland.[FMA] FMA:69065 UBERON:0005911 endoderm-derived epithelium endoepithelium uberon axial skeleton plus cranial skeleton AAO:0000963 EMAPA:17214 EMAPA:18043 MA:0000308 Skeletal subdivision of the central body axis including the cranium, vertebrae, notochord, ribs, and sternum.[VSAO] Subdivision of skeleton which consists of cranial skeleton, set of all vertebrae, set of all ribs and sternum[FMA, modified]. UBERON:0005944 UMLS:C0222645 VSAO:0000056 XAO:0004011 http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton skeleton axiale uberon heart layer The laminar structure of the heart UBERON:0005983 uberon coronary vessel Any of the arteries or veins that supply blood to the heart or return blood from the heart muscles to the circulation MESH:D003331 TODO - change relation from part_of UBERON:0005985 uberon integumentary adnexa Anatomical structure embedded in or located in the integument that is part of the integumental system. Examples: hair, follicles, skin glands, claws, nails, feathers. UBERON:0006003 add subclasses based on resolution of CARO tracker item. Also check: adnexal gland. Note that MP implicitly includes hypodermis. adnexae cutis body hair or bristle skin adnexa skin adnexal structure skin appendage the tissue or structures associated with or embedded in the skin such as hair and hair follicles, sweat glands, sebaceous glands and claws or nails[MP:0010678] uberon multi-limb segment region A collection of two or more connected limb segments. Examples: arm (comprising stylopod and zeugopod regions). UBERON:0006058 uberon rhombic lip DHBA:10664 EHDAA2:0000231 EMAPA:17074 TAO:0001440 The interface between the dorsal neuroepithelium and the roofplate of the fourth ventricle. The source of a number of migratory neuron populations of the hindbrain.[TAO] UBERON:0006215 UBERON:0013163 XAO:0004135 ZFA:0001440 cerebellar anlage cerebellar primordium cerebellum primordium dorsal part of alar plate of metencephalon future cerebellum presumptive cerebellum rostral rhombic lip the posterior section of the developing metencephalon recognized transiently within the vertebrate embryo; the rhombic lip extends posteriorly from the roof of the fourth ventricle to dorsal neuroepithelial cell and can be divided into eight structural units based on rhombomeres 1-8 (r1-r8), recognized at early stages of hindbrain development; producing granule cells and five brainstem nuclei, the rhombic lip plays an important role in developing a complex cerebellar neural system uberon cloacal membrane A membrane that separates the proctodeum and the hindgut in the early embryo. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Vertebrates:_Comparative_Anatomy, p.497, see_Kardong_KV][VHOG] EHDAA2:0000257 EHDAA:214 EHDAA:2933 EMAPA:16832 FMA:295525 In mammals, the cloaca exists as an embryonic structure that undergoes septation to become distinct urethral, anal, and genital orifices.[well established][VHOG] The membrane that covers the embryonic cloaca, formed by the union of proctodeal (anal pit) ectoderm and cloacal endoderm, with no intervening mesoderm; the urorectal septum joins the cloacal membrane and divides it into an anal membrane and a urogenital membrane; the point where the urorectal septum intersects the cloacal membrane is the future site of the perineal body; proliferation of mesoderm and ectoderm around the cloacal membrane produces primordial tissues of the external genitalia in both sexes: the genital tubercle, genital folds, and genital swellings. UBERON:0006217 UMLS:C0231056 VHOG:0001198 embryonic cloacal membrane membrana cloacalis uberon foregut-midgut junction Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[well established][VHOG] An anatomical junctions that overlaps the foregut and midgut. EHDAA2:0000569 EHDAA:526 EMAPA:16363 UBERON:0006235 VHOG:0000291 uberon future brain BAMS:Enc BTO:0004726 EFO:0003431 EHDAA:300 EHDAA:830 EMAPA:16089 EMAPA:16471 FMA:312967 RETIRED_EHDAA2:0000591 TAO:0000146 The embryonic precursor of the brain and the set of mature brain structures that derive from it (CUMBO) The embryonic precursor of the brain. UBERON:0006238 ZFA:0000146 brain rudiment embryonic brain encephalon presumptive brain uberon future forebrain A presumptive structure that has the potential to develop into a forebrain. BAMS:Pros EFO:0003423 EHDAA2:0000661 EHDAA:2643 EMAPA:16640 TAO:0000062 TODO. Add relationships to neural plate (both ZFA and EMAPA time this with the neural plate) UBERON:0006240 ZFA:0000062 future prosencephalon presumptive forebrain presumptive prosencephalon prosencephalon uberon future spinal cord EFO:0003438 EHDAA2:0000674 EHDAA:898 EMAPA:16092 EMAPA:16525 EMAPA:16755 TAO:0000417 UBERON:0006241 ZFA:0000417 presumptive spinal cord presumptive spinal cord neural keel presumptive spinal cord neural plate presumptive spinal cord neural rod uberon gall bladder primordium A sac-like cavity ventral to the liver, lying in the sub-mesodermal space and closed by a thin sheet of ectodermal cells, from which the future gall bladder develops. EHDAA2:0000700 EHDAA:3047 EMAPA:16713 UBERON:0006242 XAO:0004205 uberon notochordal plate EHDAA2:0001278 EHDAA:264 EMAPA:16101 TODO - check ordering; awaiting confirmation from JB The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. [Carson_JL, Dehart_DB, Developmental_Dynamics_(1994)_201:_260-278, Gesteland_K_and_Schoenwolf_GC, Inagaki_T, Morphogenesis_of_the_murine_node_and_notochordal_plate, The_prechordal_plate, Vrablic_T, see_Mueller_F_and_O'Rahilly_R, the_rostral_end_of_the_notochord_and_nearby_median_features_in_staged_human_embryos._Cells_Tissues_Organs_(2003)_173:_1-20_and_Sulik_K][VHOG] UBERON:0006267 UMLS:C1518429 VHOG:0001212 uberon notochordal process A midline cellular cord formed from the migration of mesenchymal cells from the primitive knot EHDAA2:0001279 EHDAA:224 EMAPA:16102 FMA:293135 The notochordal process grows cranially until it reaches the prechordal plate, the future site of the mouth. In this area the ectoderm is attached directly to the endoderm without intervening mesoderm. This area is known as the oropharyngeal membrane, and it will break down to become the mouth. At the other end of the primitive streak the ectoderm is also fused directly to the endoderm; this is known as the cloacal membrane (proctodeum), or primordial anus. UBERON:0006268 UMLS:C1518430 VHOG:0001213 chordamesoderm presumptive notochord uberon future cardiac ventricle EHDAA2:0001531 EMAPA:16233 EMAPA:16350 FMA:71006 Multi-tissue structure that is part of the heart tube and will become the cardiac ventricle. TAO:0002231 The embryonic ventricle or primitive ventricle of the developing heart gives rise to the trabeculated parts of the left and right ventricles. In contrast, the smooth parts of the left and right ventricles originate from the embryological bulbus cordis. The primitive ventricle becomes divided by a septum, the septum inferius or ventricular septum, which grows upward from the lower part of the ventricle, its position being indicated on the surface of the heart by a furrow. Its dorsal part increases more rapidly than its ventral portion, and fuses with the dorsal part of the septum intermedium. For a time an interventricular foramen exists above its ventral portion, but this foramen is ultimately closed by the fusion of the aortic septum with the ventricular septum[WP] UBERON:0006283 UBERON:0010226 ZFA:0001719 early heart ventricle embryonic heart ventricle embryonic ventricle future heart ventricle presumptive cardiac ventricle heart tube primitive ventricle primitive ventricle of heart primordial cardiac ventricle primordial ventricle uberon bodily fluid FMA:280556 GAID:266 Liquid components of living organisms. includes fluids that are excreted or secreted from the body as well as body water that normally is not. MESH:D001826 UBERON:0006314 body fluid fluid galen:BodyFluid uberon renal duct A tube in the kidney that collect and transport urine. TAO:0005289 UBERON:0006553 ZFA:0005289 in ZFA this is defined as part of mesonephros uberon excretory tube A tube that is part of a excretory system. UBERON:0006555 uberon pharynx FBbt:00005380 MAT:0000049 MIAA:0000049 The pharynx is the part of the digestive system immediately posterior to the mouth[GO]. UBERON:0006562 anterior part of foregut branchial currently this is an extremely generic class, encompassing both protostomes and deuterostomes. pharyngeal pharyngeal tube uberon presumptive endoderm AAO:0000471 EFO:0003437 Presumptive structure of the blastula that will develop into endoderm. TAO:0000416 UBERON:0006595 ZFA:0000416 uberon presumptive blood AAO:0000468 EFO:0003439 TAO:0000568 UBERON:0006596 ZFA:0000568 future blood uberon presumptive structure AAO:0000479 Consider merging with anlage Portion of embryonic tissue determined by fate mapping to become a structure. TAO:0001116 UBERON:0006598 ZFA:0001116 future structure presumptive structures uberon presumptive ectoderm AAO:0000470 EFO:0003466 Presumptive structure of the blastula that will develop into ectoderm. TAO:0001376 UBERON:0006601 XAO:0004132 ZFA:0001376 presumptive epidermis uberon presumptive mesoderm AAO:0000476 EFO:0003467 Presumptive structure of the blastula that will develop into mesoderm. TAO:0001377 UBERON:0006603 ZFA:0001377 uberon interphalangeal joint 2 2 A joint that connects one phalanx to another along a proximodistal axis. FMA:42765 Hinge joints between the phalanges of the hand or foot[ncithesaurus:Interphalangeal_Joint]. UBERON:0006658 galen:InterphalangealJoint inter-phalangeal joint inter-phalanx joint uberon mesopodium region Naming conventions for pod terms under discussion within phenoscape group The third segment of the limb, including either the wrist segment (carpus) or the ankle segment (tarsus) UBERON:0006716 carpus/tarsus mesopod mesopodial limb segment mesopodial segment uberon autopodial skeleton Distal section of the limb skeleton, consisting of the anterior autopodium or posterior autopodium.[VSAO] Naming conventions for pod terms under discussion within phenoscape group The collection of all skeletal elements in an autopodium region. UBERON:0006717 VSAO:0005019 autopod skeleton autopodial skeleton autopodium skeletal parts of autopod skeleton of autopod uberon glandular epithelium An epithelium that is composed primarily of secretory cells. BTO:0002991 UBERON:0006799 UMLS:C0682578 UMLS:C1708242 consider splitting epithelium from epithelial tissue uberon surface groove A furrow or an incomplete tube. AEO:0000161 EHDAA2_RETIRED:0003161 UBERON:0006846 groove uberon terminal part of digestive tract FBbt:00005756 The distalmost portion of the digestive tract, derived from the hindgut, and terminating with the anus. UBERON:0006866 WBbt:0005773 rectal part of digestive tract rectum terminal section of digestive tract this class is the superclass of 'rectum', which is currently reserved for the vertebrate structure. May be merged in future. uberon footplate EHDAA2 does not have a single class for footplate, but includes epithelium, mesenchyme and AER EHDAA:5143 EHDAA:6096 EMAPA:17249 FMA:296800 UBERON:0004343 UBERON:0006871 UMLS:C1517291 distal part of hindlimb bud foot disk foot plate the distal elements of the developing limb of vertebrates that will give rise to the pedal appendages (e.g. hand, foot, paw) uberon vasculature of organ A vasculature that is part of a organ. FMA:74612 UBERON:0006876 organ vasculature set of blood vessels of organ uberon lumen of digestive tract An anatomical space that surrounded_by a digestive tract. BTO:0000349 EMAPA:32908 FMA:45677 UBERON:0006909 digestive tract lumen gut cavity gut lumen lumen of alimentary tract lumen of digestive tract lumen of gut uberon squamous epithelium An epithelium characterised by its most superficial layer consisting of squamous epithelial cells. BTO:0002072 FBbt:00007028 (squamous epithelium) A type of epithelium that is made up of flattened cells which are arranged with their long axes in the plane of the epithelium UBERON:0006914 UMLS:C0221909 uberon stomach glandular epithelium A glandular epithelium that lines the stomach. The stomach's glandular epithelium is characterized by the presence of gastric glands. EMAPA:17623 EMAPA:35814 FMA:63458 MA:0002784 UBERON:0006924 epithelium of gastric gland gastric gland epithelium uberon we follow Kardong in treating the glandular epithelium as a distinct entity, and thus as an epithelium which has glands; FMA has 'epithelium of gastric gland', which is part of the gastric gland. digestive gland A gland, such as the liver or pancreas, that secretes into the alimentary canal substances necessary for digestion. AAO:0000130 BTO:0000345 UBERON:0006925 digestive system gland uberon glandular columnar epithelium FMA:64800 Simple columnar epithelium that constitutes the secretory part of a gland. Examples: epithelium of stomach, luminal epithelium of lactiferous duct.[FMA] UBERON:0006929 UMLS:C0225337 uberon stomach glandular region mucosa EMAPA:27167 MA:0001614 UBERON:0006931 stomach glandular region glandular mucous membrane stomach mucosa that is lined with glandular epithelium and part of a stomach glandular region. uberon vascular cord EFO:0003709 TAO:0005077 The vascular cord is the primordial vasculature that will develop into blood vessels by the process of tubulogenesis[GO]. The vascular cord is composed of angioblast or vascular endothelial cells in a solid linear mass called a cord. The cord then undergoes tubulogenesis to form the lumen of the vessels[ZFA]. UBERON:0006965 ZFA:0005077 uberon anatomical surface A two dimensional anatomical structure that is the boundary between an anatomical structure and an anatomical substance, an anatomical space or the organism's environment. Examples include the surface of your skin, the surface of the lining of your gut; the surface of the endothelium of you aorta that is in contact with blood.n AAO:0010270 BILA:0000010 CARO:0001002 EHDAA2:0003192 FMA:24137 ID:0000000 Old definition: 'Non-material anatomical entity of two dimensions, that is demarcated by anatomical lines or points on the external or internal surfaces of anatomical structures.' Note, in the new definition, the space referred to is not necessarily an anatomical space. It may be the outside of an organism. UBERON:0006984 UMLS:C1515977 ZFA:0005594 uberon cardiac mesoderm AAO:0011021 BILA:0000051 EFO:0000315 EHDAA2:0000214 EHDAA:385 FMA:293143 The splanchnic mesoderm in the cardiogenic region where the heart develops; it gives rise to endocardial heart tubes that fuse to form the primordial cardiac tube, the heart primordium[web]. Two migratory heart primordia that move ventrally during the course of neurulation, and then fuse[XAO]. UBERON:0007005 VHOG:0001641 XAO:0000235 cardiogenic mesoderm cardiogenic region consider FBbt:00005541 ! cardiogenic mesoderm heart primordia review EHDAA2 placement uberon cleaving embryo BILA:0000058 Organism at the cleavage stage. UBERON:0007010 uberon presumptive gut BILA:0000084 The endodermal cells generate only the lining of the digestive tube and its glands; mesodermal mesenchyme cells will surround this tube to provide the muscles for peristalsis UBERON:0007026 UMLS:C1514442 embryonic digestive tube future digestive tract future digestive tube future gut primitive gut primordial digestive tube primordial gut uberon primary circulatory organ A hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood or analogs[GO,modified]. FBbt:00003154 Gene notes: Bmp, Nkx, Gata SPD:0000130 TADS:0000147 UBERON:0007100 adult heart dorsal tube heart note we reserve the subclass 'heart' from the vertebrate multi-chambered heart. 'The first heart-like organ is believed to have appeared 500my ago in an ancestral bilaterian'. Amniotes: four-chambered heart. Amphibians: two atria, one ventricle, pulmonary; fish: single atrium and ventricle; amphioxus: tubular, non-striated, closed, unidirectional; ascidians: tubular, striated, open, bidirectional; arthropods: tubular, open; C elegans: contractile pharynx; Cnideria: striated muscle cells associated with gastrodermis uberon pharyngeal pouch 2 2nd arch branchial pouch 2nd arch branchial pouch endoderm 2nd arch pouch endoderm 2nd branchial pouch 2nd pharyngeal pouch endoderm A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down. The pharyngeal arches are separated by endodermal outpocketings, the pharyngeal pouches.[well established][VHOG] A pharyngeal puch that is between the pharyngeal arches 2 and 3. A pouch that is situated between the 2nd and 3rd pharyngeal arch. [ISBN10:0124020607][VHOG] AAO:0011115 Contributes to the middle ear, epithelial lining of Crypts (spaces) of the palatine tonsils, supplied by the facial nerve EFO:0003633 EHDAA2:0000058 EMAPA:16275 EMAPA:16276 FMA:295676 RETIRED_EHDAA2:0000060 Second of the pharyngeal (endodermal) evaginations between the visceral arches from which the Eustachian tube is derived; pouches 2-4 open as gill slits.[AAO] TAO:0001130 UBERON:0005715 UBERON:0007123 UMLS:C0231069 VHOG:0000561 VHOG:0000967 XAO:0000247 ZFA:0001130 pharyngeal pouches 2 second arch pharyngeal pouch second pharyngeal pouch second visceral pouch the dorsal elongation of the second pouch endoderm of all mammals, with the exception of rodents, gives rise to the epithelial lining of palatine tonsils; in rodents, the ventral portion of the second pouch appears to degenerate whereas the remaining part is incorporated into the lateral border of the pharynx; it appears that rodents no longer require tonsils as their function is carried out by the NALT (Nose/Nasal-Associated Lymphoid Tissue) system in the upper respiratory tract. uberon visceral pouch 2 neural keel An intermediate stage (between the neural plate and neural rod) during the early segmentation period in the morphogenesis of the central nervous system primordium; the keel is roughly triangular shaped in cross section. An intermediate stage (between the neural plate and neural rod) during the early segmentation period in the morphogenesis of the central nervous system primordium; the keel is roughly triangular shaped in cross section. Kimmel et al, 1995.[TAO] EFO:0003497 TAO:0000131 UBERON:0007135 ZFA:0000131 presumptive central nervous system uberon tracheobronchial tree FMA:7393 The structure from the trachea, bronchi, and bronchioles that forms the airways that supply air to the lungs. The lining of the tracheobronchial tree consists of ciliated columnar epithelial cells. UBERON:0004102 UBERON:0007196 arbor tracheobronchialis tracheobronchial system uberon mesenchyme derived from head neural crest EFO:0003572 EHDAA2:0000735 EMAPA:16169 EMAPA:16271 EMAPA_RETIRED:16271 Mesenchyme that develops_from a cranial neural crest. TAO:0000787 UBERON:0007213 ZFA:0000787 head mesenchyme from cranial neural crest head mesenchyme from neural crest head neural crest derived mesenchyme uberon pelvic appendage skeleton The collection of all skeletal elements in a pelvic appendage region. UBERON:0007273 uberon presumptive hindbrain BAMS:HB CALOHA:TS-2118 EFO:0003440 EHDAA2:0001630 FMA:295640 TAO:0000569 TODO - unify naming conventions The embryonic rhombencephalon can be subdivided in a variable number of transversal swellings called rhombomeres. Rhombomeres Rh7-Rh4 form the myelencephalon that will give the medulla oblongata. Rhombomeres Rh3-Rh1 form the metencephalon that will form the pons and the cerebellum[NPX:PDR]. The rhombencephalon (or hindbrain) is a developmental categorization of portions of the central nervous system in vertebrates. The rhombencephalon can be subdivided in a variable number of transversal swellings called rhombomeres. In the human embryo eight rhombomeres can be distinguished, from caudal to rostral: Rh7-Rh1 and the isthmus (the most rostral rhombomere). A rare disease of the rhombencephalon, 'rhombencephalosynapsis' is characterized by a missing vermis resulting in a fused cerebellum. Patients generally present with cerebellar ataxia. The caudal rhombencephalon has been generally considered as the initiation site for neural tube closure. UBERON:0007277 ZFA:0000569 embryonic rhombencephalon future hindbrain presumptive rhombencephalon rhombencephalon uberon presumptive midbrain hindbrain boundary EFO:0003446 Embryonic structure that gives rise to the midbrain hindbrain boundary. TAO:0001187 UBERON:0007281 XAO:0004086 ZFA:0001187 presumptive MHB presumptive midbrain-hindbrain boundary uberon presumptive segmental plate A presumptive structure that has the potential to develop into a presomitic mesoderm. EFO:0003421 TAO:0000053 UBERON:0007282 ZFA:0000053 presumptive segmental plates uberon presumptive neural plate A presumptive structure that has the potential to develop into a neural plate. EFO:0003424 Region of the gastrula which gives rise to the neural plate.[TAO] TAO:0000063 UBERON:0007284 ZFA:0000063 consider merging prospective neuroectoderm prospective vegetal ectoderm uberon presumptive paraxial mesoderm A presumptive structure that has the potential to develop into a paraxial mesoderm. EFO:0003443 TAO:0000591 UBERON:0007285 XAO:0004134 ZFA:0000591 future paraxial mesoderm uberon presumptive pronephric mesoderm A presumptive structure that has the potential to develop into a pronephric mesoderm. EFO:0003619 TAO:0001070 UBERON:0007297 ZFA:0001070 nephron primordium uberon pancreatic lobule A dense accumulation of exocrine glands in the pancreas often surrounding islets of Langerhans. FMA:16012 In mice many lobules lack islets, in contrast to other mammals including humans MA:0000721 TODO - check UBERON:0007324 lobulus pancreaticus pancreas lobe pancreatic lobule uberon pancreatic duct A duct that is part of the pancreas and connected to the duodenum. Duct connecting the pancreas with the intestine. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] EHDAA:9194 EMAPA:32952 FMA:10419 MA:0000124 TAO:0001372 These data show that ducts within the zebrafish pancreas originally arise in situ from isolated progenitor cells rather than arising from reiterative branching of the pancreatic epithelium. This process of pancreatic duct formation in zebrafish may be analogous to the mechanism of duct formation in the mammalian mammary and salivary glands. (...) A related mechanism of duct formation has also been proposed to occur within the mammalian pancreatic epithelium.[uncertain][VHOG] UBERON:0007329 VHOG:0000254 ZFA:0001372 duct of pancreas ductus pancreaticus in EHDAA2, the dorsal and ventral ducts are classified as epithelial sacs - review after overhaul of duct/epithelia terms pancreas duct this class groups together accessory (dorsal) and main (ventral) pancreatic ducts uberon outer epithelium BSA:0000073 BTO:0000313 FBbt:00004993 HAO:0000298 TADS:0000109 The epidermis is the entire outer epithelial layer of an animal, it may be a single layer that produces an extracellular material (e.g. the cuticle of arthropods) or a complex stratified squamous epithelium, as in the case of many vertebrate species[GO]. UBERON:0007376 WBbt:0005733 epidermis epidermis (sensu Metazoa) hypoderm hypodermis outer epidermal layer outer epithelial layer this grouping class exists primarily to align with GO - see GO:0008544. uberon stratum compactum AAO:0010600 Portion of the dermis characterized by a well-arranged, plywood-like, collagenous network. Portion of the dermis characterized by a well-arranged, plywood-like, collagenous network. Le Guellec et al, 2004.[TAO] TAO:0001182 UBERON:0007377 ZFA:0001182 connective tissue in the skin is usually diffuse and irregular, although in some species collagen bundles are arranged in a distinct ordered layer in the dermis dermal deep region relationship loss: develops_from collagenous dermal stroma (TAO:0001186)[TAO] uberon enveloping layer of ectoderm EFO:0003425 EVL Originally this tissue is one cell layer thick but in most vertebrates it soon becomes a two layered structure. The outer layer gives rise to the periderm. Outermost layer of cells surrounding the embryo. Outermost monolayer of cells surrounding the embryo that become very flattened in the blastula and give rise to the periderm. Sometimes used synonymously with periderm. Kimmel et al, 1995.[TAO] TAO:0000086 UBERON:0007383 ZFA:0000086 enveloping layer relationship loss: develops_from superficial blastomere (TAO:0001484)[TAO] uberon epithelial sac AEO:0000115 An epithelial tube that is open at one end only. EHDAA2:0003115 UBERON:0007499 uberon epithelial tube open at both ends AEO_RETIRED:0000116 An epithelial tube open at both ends that allows fluid flow. RETIRED_EHDAA2:0003116 UBERON:0007500 uberon epithelial vesicle A closed epithelium with a lumen. AEO:0000119 EHDAA2:0003119 EHDAA2:0003119 UBERON:0007503 uberon dense mesenchyme tissue AEO:0000146 EHDAA2:0003146 EHDAA2:0003146 Mesenchyme with little extracellular matrix. UBERON:0007524 uberon migrating mesenchyme population AEO:0000152 EHDAA2:0003152 EHDAA2:0003152 Mesenchymal cells that are migrating. UBERON:0007530 this class will be an important part of the NC reorganization uberon ciliated columnar epithelium Ciliated columnar epithelium in the pulmonary system is interspersed with goblet cells that secrete mucous to form a mucosal layer apical to the epithelial layer. The rowing-like action of epithelial cilia work in tandem with goblet cells to propel mucus away from the lungs, preventing particulate matter from causing infection[http://www.bio.davidson.edu/people/kabernd/berndcv/lab/epithelialinfoweb/ciliated%20columnar%20epithelium.html] FMA:64798 In humans, Ciliated columnar epithelial cells are found mainly in the tracheal and bronchial regions of the pulmonary system and also in the fallopian tubes of the female reproductive system Simple columnar epithelium in which the luminal side of the cells bears cilia. Examples: epithelium of trachea, epithelium of uterine tube.[FMA] UBERON:0007592 uberon ciliated epithelium Epithelium bearing vibratile cilia on the free surface. UBERON:0007601 uberon layer of synovial tissue A thin, loose vascular connective tissue that makes up the membranes surrounding joints and the sheaths protecting tendons (particularly flexor tendons in the hands and feet) where they pass over bony prominences. Synovial tissue contains synovial cells, which secrete a viscous liquid called synovial fluid; this liquid contains protein and hyaluronic acid and serves as a lubricant and nutrient for the joint cartilage surfaces[BTO]. Synovial tissue can be found in tendons (tissues that connect muscle to bone), bursae (fluid-filled, cushioning sacs found in spaces between tendons, ligaments, and bones), and the cavity (hollow enclosed area) that separates the bones of a freely movable joint, such as the knee or elbow[BTO]. BTO:0001338 CALOHA:TS-0998 FMA:66762 UBERON:0007616 stratum synoviale synovial layer synovial membrane synovial tissue synovium uberon synovial cavity of joint An anatomical cavity that surrounded_by a synovial joint. FMA:11356 UBERON:0007617 articular cavity (synovial joint) cavitas articularis (junctura synovialis) cavity of synovial joint joint cavity synovial cavity uberon pigment epithelium of eye GAID:907 MESH:D010857 UBERON:0007625 epithelial layer of the retina, ciliary body, or iris composed of cells containing pigment granules. eye pigment epithelium uberon future meninx A developing mesenchymal capsule that covers the developing brain and spinal cord and is the precursor of the meningeal cluster. In mammals this gives rise to the arachnoid mater, pia mater and dura mater. In cyclostomes and fishes, the future meninx gives rise to a single meningeal layer, the primitive meninx. EHDAA2:0004453 UBERON:0004065 UBERON:0007645 decide whether to treat the endo and ecto meninx as subtypes or parts of the future meninx meninx primitiva primary meninx primitive meninx primordial meninx the outermost mesenchymal covering of the developing brain and spinal cord that is composed of tough fibrous connective tissue from which the arachnoid mater, pia mater and dura mater are formed[MP:0009726]d uberon anatomical junction 2 An anatomical structure that connects two structures FMA:5898 UBERON:0007651 anatomical junction junction uberon kidney field UBERON:0007687 kidney anlage region of the embryo into the area in which the kidney rudiment will develop. uberon anlage AEO:0000170 Anlagen are populations of contiguous cells, typically arranged in one plane, that are morphologically indistinct, but that already correspond in extent to a later organ/tissue. EFO:0001649 EHDAA2:0003170 FBbt:00005426 UBERON:0007688 developmental field field future organ organ field uberon thyroid diverticulum UBERON:0007689 diverticulum thyroideum endodermal bud derived from the endodermal epithelium of the embryonic pharyngeal floor[MP]. The thyroid diverticulum is the embryological structure from which thyroid follicular cells derive. It grows from the floor of the pharnyx[WP]. saccus thyroideus uberon early pharyngeal endoderm . EFO:0003626 EHDAA2:0001457 EHDAA:962 EMAPA:32754 FMA:293087 TAO:0001104 UBERON:0007690 ZFA:0001104 early pharyngeal arch endoderm pharyngeal arch endoderm pharyngeal endoderm pharyngeal region endoderm relation conflict: ZFA vs EHDAA2. Note EHDAA2 term renamed to 'early PA endoderm' uberon serous fluid Any fluid produced by a serous gland. FMA:20932 UBERON:0007794 serous gland fluid the FMA def is Transudate contained in a serous sac uberon vascular system Anatomical system that consists of all blood and lymph vessels. BTO:0001085 CALOHA:TS-2053 EHDAA2:0004520 EMAPA:35905 Gefaesssystem@ge MA:0002718 The cardiovascular and lymphatic systems, collectively[ncithesaurus:Vascular_System]. UBERON:0007798 UMLS:C0489903 consider merging with vasculature in both MA and BTO, the arterial system and venous sytem are subtypes of the vascular system uberon craniocervical region CALOHA:TS-2356 EV:0100009 FMA:280881 MA:0000006 The anteriormost subdivision of the body that includes the head, jaws, pharyngeal region and the neck (if present). In vertebrates this is the subdivision that includes the cervical vertebrae. UBERON:0007811 UMLS:C0460004 WikipediaCategory:Head_and_neck cephalic area cephalic part of animal cephalic region galen:HeadAndNeck head and neck head or neck uberon appendage girdle region An organism subdivision that encompasses the region containing the pectoral or pelvic girdle. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). An organism subdivision that encompasses the region containing the pectoral or pelvic girdle. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). There are only two instances of appendage girdle regions per organism.[VSAO] FMA:24874 UBERON:0007823 UBERON:0007824 VSAO:0000303 fin girdle fin girdle region girdle girdle region limb girdle limb girdle region this encompasses non-skeletal tissue uberon pelvic girdle skeleton AAO:0000426 AAO:0000768 Anatomical cluster by which the hind limbs are supported and attached to the vertebral column.[AAO] Anatomical cluster that consists of the paired basipterygia which support the pelvic fin.[TAO] EFO:0000947 EHDAA2:0001426 EHDAA:7149 EHDAA:8324 EMAPA:18028 FMA:87592 Girdle skeleton consisting of a set of bones linking the axial series to the hindlimb/fin skeleton and offering anchoring areas for hindlimb/fin and caudal musculature.[VSAO] MAT:0000182 MIAA:0000182 Note that the VSAO and many ontologies use the label 'pelvic girdle' to denote the skeletal region specifically. We place the EHDAA2 class here, note that this includes the pre-cartilage condensation as parts Skeletal subdivision consisting of a set of bones linking the axial series to the hindlimb zeugopodium and offering anchoring areas for hindlimb and caudal musculature. TAO:0000565 The pelvic girdle is never joined by contributions of dermal bone. From its first appearance in placoderms, the pelvic girdle is exclusively endoskeletal. It arose from pterygiophores, perhaps several times, in support of the fin.[well established][VHOG] UBERON:0007832 VHOG:0000305 VSAO:0000155 XAO:0003064 ZFA:0000565 galen:PelvicGirdle need to resolve whether this is a paired structure or a single belt (Paired in FMA - implicitly paired in VSAO) pelvic girdle pelvic girdle skeleton skeletal parts of pelvic girdle skeleton of pelvic girdle uberon cartilage element AAO:0011130 CALOHA:TS-0118 EMAPA:32730 FMA:55107 Skeletal element that is composed of cartilage tissue and may be permanent or transient. TAO still mixes tissue and element UBERON:0007844 VSAO:0000000 XAO:0004013 ZFA:0001501 cartilage cartilage organ cartilaginous element chondrogenic element uberon regular connective tissue Connective tissue, which consists of fibroblasts, the intercellular matrix of which contains a regular network of collagen and elastic fiber bundles. Examples: bone (tissue), cartilage (tissue), dense regular connective tissue. FMA:20103 UBERON:0007845 the connective tissue hierarchy largely follows FMA with definitions from VSAO. Note that in FMA, loose-CT is irregular-CT. This means regular-CT is necessarily equivalent to dense-regular-CT (assuming a JEPD classification). uberon dense regular connective tissue Connective tissue that is dominated by collagen fibres organized into a definitive pattern (e.g., parallel to one another), with comparatively fewer cells (mostly fibroblasts). Connective tissue that is dominated by collagen fibres organized into a definitive pattern (e.g., parallel to one another), with comparatively fewer cells (mostly fibroblasts).[VSAO] FMA:64781 Regular connective tissue, the intercellular matrix of which consists predominantly of collagen fiber bundles arranged in parallel arrays.[FMA] UBERON:0007846 UMLS:C0225333 VSAO:0000050 XAO:0004030 dense fibrous connective tissue dense regular collagenous connective tissue dense regular collagenous tissue regular dense connective tissue typus regularis (textus connectivus collagenosus compactus) uberon lower limb segment A limb segment that is part of a hindlimb. FMA:24877 UBERON:0008784 free lower limb segment free lower limb subdivision segment of free lower limb subdivision of free lower limb uberon pharyngeal arch system A transient embryonic complex that comprises the pharyngeal arches, bulges of tissues of mesoderm and neural crest derivation through which pass nerves and pharyngeal arch arteries. The arches are separated internally by pharyngeal pouches, evaginations of foregut endoderm, and externally by pharyngeal clefts, invaginations of surface ectoderm. The development of the system ends when the stucture it contributes to are forming, which may include (depending on species) the thymus, thyroid, parathyroids, maxilla, mandible, aortic arch, cardiac outflow tract, external and middle ear[GO,modified]. Currently defined in a vertebrate specific manner. The arch system has origins in basal deuterostomes, consider generalizing EHDAA2:0000187 FMA:293041 UBERON:0008814 UMLS:C1519038 pharyngeal apparatus pharyngeal arch region pharyngeal arches and clefts pharyngeal system uberon embryonic head A head that is part of a embryo. CALOHA:TS-0246 FBbt:00000155 FMA:293011 UBERON:0008816 uberon hepatic diverticulum AAO:0011057 An out-pocket of thickened ventral foregut epithelium adjacent to the developing heart. Constitutes the first morphological sign of the embryonic liver. The anterior portion of the hepatic diverticulum gives rise to the liver and intrahepatic biliary tree, while the posterior portion forms the gall bladder and extrahepatic bile ducts. EHDAA2:0000740 EHDAA:1530 The caudal part of the septum transversum is invaded by the hepatic diverticulum which divides within it to form the liver and thus gives rise to the ventral mesentery of the foregut. UBERON:0008835 UMLS:C1512407 XAO:0000101 diverticulum hepaticum in mice, the hepatic diverticulum forms by E9 and expands into an obvious liver bud by E10 liver diverticulum uberon liver bud BTO:0001642 UBERON:0008836 uberon pyloric canal FMA:14580 The short narrow part of the stomach extending from the pyloric antrum to the pyloric sphincter UBERON:0008858 canalis pyloricus canalis pyloricus uberon pyloric gastric gland EMAPA:27211 FMA:14922 The gastric glands in the pyloric region of the stomach; the pyloric glands secrete mucin, which coats the stomach and protects it, and hormones such as gastrin and enkephalin[MP]. UBERON:0008861 UMLS:C0227239 check relationship to pylorus vs antrum glandula pylorica pyloric antrum gland pyloric gland pyloric mucuous gland uberon fin AAO:0010374 AEO:0001004 An external projection of an aquatic animal as a fish used in propelling or guiding the body[BTO]. BTO:0004649 EFO:0000875 MAT:0000087 MESH:D058500 MIAA:0000087 OpenCyc:Mx4rvVjcBZwpEbGdrcN5Y29ycA Surface structure involved in locomotion.[TAO] Surface structure involved in locomotion.[VSAO] TAO:0000108 This class groups together various structures that may have arisen through convergent evolution, including, for example, the dorsal fin of a cetacean UBERON:0008897 VSAO:0000099 XAO:0000002 ZFA:0000108 fins uberon respiratory primordium EHDAA2:0004069 UBERON:0008947 UMLS:C1514898 uberon stomach region An organ part that is part of a stomach. EMAPA:35821 MA:0002561 UBERON:0009034 uberon indifferent gonad A gonad prior to differentiating into a definitive testis or ovary. EHDAA2:0000716 UBERON:0009117 UMLS:C1512703 gonad rudiment typically part of the embryo - however, in male tammar wallabies the gonads are indifferent at the neonatal stage[8827321] uberon entire embryonic mesenchyme EHDAA2:0001113 EHDAA:177 EMAPA:16097 Sum total of mesenchyme in the embryo. UBERON:0003313 UBERON:0009142 consider adding new class (EMAPA:16097) for mesenchyme of embryo (some mesenchyme is extraembryonic - e.g. amnion mesoderm) uberon pharyngeal region of foregut EMAPA:16549 RETIRED_EHDAA2:0001454 UBERON:0009145 pharyngeal region uberon indifferent external genitalia EHDAA2:0004021 UBERON:0009196 uberon nephric duct A nephric duct is a tube that drains a primitive kidney[GO]. EMAPA:28425 EMAPA:28429 UBERON:0009201 pronephric duct or mesonephric duct uberon epithelium of foregut-midgut junction An epithelium that is part of a foregut-midgut junction. EHDAA2:0000573 EMAPA:16564 UBERON:0009497 uberon anal membrane endodermal component An endoderm that is part of a anal region. EHDAA2:0004020 EMAPA:17177 UBERON:0009521 uberon endoderm of foregut-midgut junction An endoderm that is part of a foregut-midgut junction. EHDAA2:0000572 EMAPA:18403 UBERON:0009550 uberon distal segment of digit A segment of a digit containing the distal phalanx, and overlapping the distal interphalangeal joint[CJM]. The digit tip is derived from multiple and distinct embryonic origins, and includes the distal bone with associated marrow cavity and haematopoietic cells, ventral (flexor) and dorsal (extensor) tendons, sweat glands with myoepithelial and luminal secreting cells and associated neurons for innervation, dermis with resident melanocytes and dendritic cells, mesenchyme with resident fibroblasts, skin epidermis with hair follicles, a nail organ composed of six specific parts (the root, nail bed, nail plate, eponychium (cuticle), perionychium and hyponychium). Newborn and adult mice are able to regrow forelimb (finger) and hindlimb (toe) digit tips after their amputation through the distal interphalangeal joint. Regeneration of the digit tip involves the integrated regrowth of multiple tissues within 2-3 months, reaching an external morphology that is cosmetically and functionally similar to normal digits. Most importantly, regeneration of the mouse distal digit shares morphological similarities with clinical cases documenting regrowth of missing distal portions of fingers in both children and adults UBERON:0009551 digit tip distal digit segment tip of digit uberon distal limb integumentary appendage A nail, hoof or claw. MESH:D006724 UBERON:0009564 hoof or claw hoof, claw or nail keratin plate keratin sheath uberon unguis subdivision of trunk FMA:25054 UBERON:0009569 region of trunk trunk subdivision uberon midbrain mantle layer EHDAA2:0001172 EMAPA:16977 UBERON:0009581 VHOG:0000910 mantle layer lateral wall mesencephalon mantle layer lateral wall midbrain midbrain lateral wall mantle layer uberon midbrain hindbrain boundary neural plate MHB neural plate TAO:0007044 TODO - developmental relationships for lines UBERON:0009615 ZFA:0007044 midbrain-hindbrain boundary neural plate uberon presumptive midbrain A presumptive structure that has the potential to develop into a midbrain. BAMS:MES EFO:0003432 EHDAA2:0000615 EMAPA:16140 EMAPA:16472 TAO:0000148 TODO - unify naming conventions UBERON:0009616 ZFA:0000148 early midbrain future midbrain mesencephalon presumptive mesencephalon uberon trunk paraxial mesoderm EHDAA2:0002094 UBERON:0009618 trunk and cervical paraxial mesenchyme trunk paraxial mesenchyme uberon hindbrain nucleus Nucleus located within the hindbrain. TAO:0002177 UBERON:0009662 ZFA:0001658 uberon dorsal pancreas EHDAA2:0001371 UBERON:0009708 pancreatis dorsalis uberon ventral pancreas EHDAA2:0001393 UBERON:0009709 pancreatis ventralis uberon entire pharyngeal arch endoderm EHDAA2:0004621 EMAPA:32754 FMA:293087 UBERON:0009722 pharyngeal arch endoderm uberon limb mesenchyme EMAPA mapping from TH EMAPA:32705 The primordial embryonic connective tissue of the developing limbs, autopods and digits, consisting of mesenchymal cells supported in interlaminar jelly, that derive mostly from the mesoderm and contribute to limb connective tissue, bone and musculature in conjunction with myotome cells. UBERON:0009749 limb mesoderm uberon distal interphalangeal joint An inter-phalangeal joint that connects a distal phalanx to either a medial or proximal phalanx. DIJ joint DIP joint FMA:65024 UBERON:0009768 uberon glandular acinus FMA:55588 The many-lobed berry cluster of cells that is the terminous of a gland where the secretion is produced is acinar in form. UBERON:0009842 acinar acini acinus uberon urogenital sinus mesenchyme Androgen receptor (AR) activation releases instructive signals from UGM that acts on UGS epithelium (UGE) to stimulate cell proliferation, form prostate ductal progenitors (prostatic buds), and regulate cell adhesion dynamics to permit prostatic bud outgrowth EMAPA:31500 EMAPA:31519 Mesenchyme that surrounds primitive urogenital sinus. UBERON:0009845 UGM uberon embryonic cloacal epithelium An epithelium that is part of a embryonic cloaca. EHDAA2:0004585 UBERON:0009846 cloacal epithelium uberon prostate field A specific region of the urogenital sinus epithelium into the area in which the prostate gland will develop. UBERON:0009847 prostate primordium uberon digestive tract diverticulum Branch or outpocketing of the digestive tract. FBbt:00100316 UBERON:0009854 diverticulum of gut intestinal pouch uberon sac UBERON:0009856 diverticulum galen:Diverticulum pouch uberon zone of stomach A division of the stomach. The stomach can be divided based on mucosal histology (glandular epithelium and gastric glands) and the relative position and type of gastric gland. FMA:14558 UBERON:0009870 We follow Kardong in defining stomach regions by gland, but we also include 'body of stomach'. In future we may want to have different partitions of the stomach gastric zone region of stomach section of stomach uberon metapodium region Intermediate segment of the autopod, between the mesopodial region and and acropodial region. Examples: metacarpal region, metatarsal region Naming conventions for pod terms under discussion within phenoscape group UBERON:0009877 cannon region considering adding 'acropodial region' equine cannon region metacarpal or metatarsal part of limb metacarpus/metatarsus metacarpus/metatarsus region metapodial segment metapodium uberon mesopodial skeleton Limb skeleton subdivision consisting of endochondral bones increasing the freedom of movement of the autopodia, and located between zeugopodia and autopodia.[VSAO] The collection of all skeletal elements in a mesopodium. Examples: the tarsal skeleton, the carpal skeleton UBERON:0009878 VSAO:0005022 basipodium basipodium skeleton carpal/tarsal skeleton mesopodial skeleton mesopodium mesopodium skeleton relationship type change: subclass skeletal subdivision (VSAO:0000042) CHANGED TO: distally_connected_to subdivision of skeleton (UBERON:0010912)[VSAO] skeletal parts of mesopodium uberon anterior lateral plate mesoderm ALPM EFO:0003704 TAO:0005041 UBERON:0009881 ZFA:0005041 uberon facial mesenchyme EMAPA:35337 FMA:302884 Mesenchyme that is part of a developing face. UBERON:0009891 face mesenchyme mesenchyme of face uberon lobule FMA:45737 UBERON:0009911 UMLS:C0921005 lobulus todo - provide definition. Clearly distinguish between lobules, lobes and acinar parts of glands (see for example lobule of mammary gland) uberon optic neural crest EHDAA2:0001315 EHDAA:1122 UBERON:0009920 uberon neurogenic placode Cranial ectodermal placode with potential to develop into a component of the nervous system, such as nerves or ganglia. EFO:0003460 Includes: trigeminal, otic, lateral line and epibranchial placodes. TAO:0001309 UBERON:0009955 While some sensory placodes (otic and olfactory) may have homologues in basal chordates (Wada et al., 1998), the so-called neurogenenic placodes (trigeminal, otic, lateral line and epibranchial placodes) appear to have emerged at a later time (Shimeld and Holland, 2000) XAO:0004620 ZFA:0001309 neurogenic placodes placodae neurogenicae uberon multicellular anatomical structure An anatomical structure that has more than one cell as a part. CARO:0010000 FBbt:00100313 UBERON:0010000 multicellular structure uberon cell cluster organ A small cluster of cells of various types which form a discrete structure, largely delimited by a morphological boundary and whose components work together to make the whole structure capable of a specific function. CARO:0010001 Examples include arthropod sensilla. FBbt:00007229 UBERON:0010001 uberon food storage organ An organ of the digestive tract that is capable of retaining and storing food BSA:0000123 TADS:0000172 TGMA:0001041 This is a very broad functionally defined grouping class that collects disparate structures from insects to vertebrates UBERON:0010039 uberon future common hepatic duct An extrahepatic bile duct that has the potential to develop into a common hepatic duct. EHDAA2:0000595 UBERON:0010081 uberon future dermis EHDAA2:0000598 Mesenchyme that has the potential to develop into a dermis. UBERON:0010083 check development uberon future metencephalon A developing anatomical structure that has the potential to develop into a metencephalon. EHDAA2:0000623 UBERON:0010092 uberon future myelencephalon A developing anatomical structure that has the potential to develop into a myelencephalon. EHDAA2:0000640 UBERON:0010096 uberon autopod plate The distal elements of the developing limb of vertebrates that will give rise to the pedal appendages (e.g. manus, pes, paw) UBERON:0010130 limb plate uberon conducting tissue of heart Any portion of cardiac muscle tissue that is part of the conducting system of heart or the Purkinje fibers. EHDAA2:0004528 FMA:83378 UBERON:0010131 specialized conducting tissue of heart specialized muscle tissue of heart uberon male accessory sex gland Any gland, other than the gonad, associated with the genital tract, such as the ampulla of the ductus deferens and the bulbourethral, prostate and vesicular glands of the male. BTO:0004798 UBERON:0010147 male accessory gland uberon protuberance A roughly circular bulge in a surface. AEO:0000205 EHDAA2:0003250 FMA:82506 UBERON:0010188 requires review uberon aortic system EHDAA2:0004512 UBERON:0010191 uberon eyeball of camera-type eye FMA:12513 MIAA:0000283 See notes for camera-type eye The core globe-shaped component of the camera-type eye. UBERON:0010230 VHOG:0001616 bulbus oculi eye eye globe eyeball globe uberon midbrain basal plate DHBA:12322 EFO:0003567 EHDAA2:0004375 Portion of tissue that is dorsolateral to the floor plate and part of the midbrain. TAO:0000761 UBERON:0010285 ZFA:0000761 basal plate midbrain basal plate midbrain region uberon midbrain neural tube Portion of neural tube that gives rise to the midbrain. TAO:0007039 UBERON:0010286 ZFA:0007039 uberon we follow ZFA in temporally dividing midbrain NT from presumptive midbrain, but in future this may be collapsed immature eye Developing anatomical structure that develops into the eyeball and associated structures. Multi-tissue structure that consists of the structures that develop into the retina and lens.[TAO] TAO:0002201 UBERON:0010312 ZFA:0001678 future eye uberon neural crest-derived structure An anatomical structure that develops from the neural crest. Grouping term for query purposes UBERON:0010313 uberon structure with developmental contribution from neural crest An anatomical structure that has some part that develops from the neural crest. Grouping term for query purposes UBERON:0010314 uberon germ layer / neural crest UBERON:0010316 uberon paired limb/fin bud mesenchyme Mesenchyme that is part of a limb/fin bud. UBERON:0010329 uberon endochondral element A skeletal element that has the potential to participate in endochondral ossification, and may participate in intramembranous ossification. UBERON:0010363 VSAO:0000139 XAO:0004017 ZFA:0005620 endochondral replacement element https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern uberon ecto-epithelium Epithelium composed of cells that develops from the ectoderm[FMA,modified]. FMA:69064 UBERON:0010371 ectoderm-derived epithelium uberon pancreas dorsal primordium EHDAA2:0001384 FMA:79793 UBERON:0010375 consider merging with dorsal pancreatic bud. Starts at CS12 in human (EHDAA2, embryology.ch 'bud anlagen') dorsal pancreas uberon pancreas ventral primordium EHDAA2:0001387 FMA:79794 Starts at CS14 in human (EHDAA2) or CS13-14 (embryology.ch 'bud anlagen') UBERON:0010376 uberon ventral pancreas mesenchyme from somatopleure EHDAA2:0001120 Mesenchyme that develops_from a somatopleure. UBERON:0010377 the way this class is defined also includes extraembryonic mesenchyme such as the amniotic mesenchyme; in future this may be restricted to embryonic derivatives uberon ocular surface region EMAPA:35336 MA:0002486 The integrated unit (of the eye) that consists of the conjunctiva, the corneal surface, and the ocular mucosal adnexa including the lid margins and the meibomian gland openings, the lacrimal glands and the lacrimal drainage system, all which are critical to maintain ocular surface integrity and provide protection from external antigens and pathogenic microorganisms. UBERON:0010409 eye surface eye surface region ocular surface uberon ciliary processes FMA:76551 The ciliary processes are formed by the inward folding of the various layers of the choroid, i.e. , the choroid proper and the lamina basalis, and are received between corresponding foldings of the suspensory ligament of the lens. UBERON:0010427 ciliary process ciliary processes ciliary processes set processus ciliares processus ciliares set of ciliary processes uberon pseudostratified columnar epithelium A simple columnar epithelium that looks stratified but is not, because its cells are arranged with their nuclei at different levels. FMA:45572 Pseudostratified epithelia function in secretion or absorption. If a specimen looks stratified but has cilia, then it is a pseudostratified ciliated epithelium, since stratified epithelia do not have cilia. UBERON:0010498 UMLS:C0836138 UMLS:C1514590 glandular in NCIT; we consider the two NCIT terms synonymous uberon pseudostratified ciliated columnar epithelium Epithelium composed of a single layer of cells, appearing as layered because the column-shaped cells vary in height so the nuclei are at different levels. The basal portions of all the cells are in contact with the basement membrane. It lines the respiratory system and the male reproductive tract. The cilia in the respiratory tract are motile, while the stereocilia in the male reproductive tract are immobile. FMA:13146 UBERON:0010499 UMLS:C0506992 epithelium pseudostratificatum columnare ciliatum (trachea et bronchi) uberon microcirculatory vessel A vessel of the microcirculature, lying between the arterioles and venules; includes capillaries (blood and lymphatic), metarterioles and arteriovenous anastomoses. MESH:A07.231.432 TAO:0005251 UBERON:0010523 ZFA:0005251 microcirculatory vessels uberon paired limb/fin segment An appendage segment that is part of a limb/fin. UBERON:0010538 limb/fin segment uberon acropodial skeleton FMA:231315 The subdivision of the skeleton that consists of all the skeletal elements at the distalmost end of the autopodium - i.e. the bones of the digits or their cartilaginous precursors[VSAO,modified]. UBERON:0010543 VSAO:0005028 acropodial skeleton acropodium acropodium skeleton digital skeleton digits skeleton phalangeal skeleton set of phalanges skeletal parts of acropodial region skeletal parts of acropodium skeleton of digits uberon metapodial skeleton Endochondral bone complex located between the mesopodium and the acropodium and consisting of the metacarpals or metatarsals.[VSAO] Subdivision of skeleton that corresponds to metapodium region, between acropodial skeleton and mesopdoial skeleton. UBERON:0010546 VSAO:0005025 metacarpal/metatarsal skeleton metapodial skeleton metapodium metapodium skeleton relationship type change: subclass skeletal subdivision (VSAO:0000042) CHANGED TO: connected_to subdivision of skeleton (UBERON:0010912)[VSAO] relationship type change: subclass skeletal subdivision (VSAO:0000042) CHANGED TO: distally_connected_to subdivision of skeleton (UBERON:0010912)[VSAO] skeletal parts of metapodium skeleton of metapodium uberon phalanx pre-cartilage condensation EMAPA:32720 UBERON:0010700 uberon phalanx cartilage element EMAPA:32721 UBERON:0010701 uberon digit mesenchyme EMAPA:32719 Mesenchyme of the digit region. UBERON:0010702 digital ray uberon appendage girdle complex 2012-04-23T10:46:51Z An organism subdivision that includes both an appendage and its accociated girdle region. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). Anatomical group that consists of the soft and skeletal tissues of the appendicular region of the body and the appendage proper.[VSAO] FMA:7182 It is still called a complex when one of the two parts is missing (?) There are fossil fishes with only an outgrowth (no record of a girdle), including thelodonts (which have a suprabranchial fin) as well as some anaspids which have a distinctive 'paired fin' (with differing published assertions on whether it's homologous to a pec fin or pelvic fin or both or neither). There are many fishes and other vertebrates with only a girdle and no outgrowth.[VSAO] It is still called a complex when one of the two parts is missing (?) There are fossil fishes with only an outgrowth (no record of a girdle), including thelodonts (which have a suprabranchial fin) as well as some anaspids which have a distinctive 'paired fin' (with differing published assertions on whether it's homologous to a pec fin or pelvic fin or both or neither). There are many fishes and other vertebrates with only a girdle and no outgrowth.[VSAO] UBERON:0010707 VSAO:0000214 appendage complex appendage-girdle complex appendage/girdle complex girdle plus limb or fin haendel limb note that the FMA uses the term 'limb' to refer to the entire appendage complex (free limb plus girdle region) uberon pelvic complex Appendage girdle complex that when present, encompasses the pelvic appendage and the pelvic girdle.[VSAO] Appendage girdle complex that when present, encompasses the pelvic appendicular skeleton and the pelvic girdle. FMA:7184 UBERON:0010709 VSAO:0000215 lower limb lower limb and pelvic girdle lower limb and pelvis note that the FMA uses the terms 'upper limb' and 'lower limb' to refer to the entire appendage complex (free limb plus girdle region). Note the MA class 'hindlimb' may also belong here pelvic appendage/girdle complex pelvic girdle plus pelvic limb or fin pelvic girdle plus posterior limb or fin uberon limb skeleton subdivision Skeletal subdivision that is a segment of the limb skeleton. UBERON:0010712 VSAO:0005018 note the distinction between this and skeleton of limb uberon paired fin skeleton Skeletal system that consists of the paired fins (pectoral or pelvic fins).[TAO] Skeletal system that consists of the paired fins (pectoral or pelvic fins).[VSAO] TAO:0000027 The collection of all skeletal elements in a single paired fin. UBERON:0010713 VSAO:0000169 ZFA:0000027 uberon girdle skeleton AAO:0010686 Skeletal subdivision that is part of the appendage girdle region.[VSAO] The subdivision of the skeleton of either the pectoral or pelvic girdle. UBERON:0010719 VSAO:0000302 relationship type change: subclass skeletal subdivision (VSAO:0000042) CHANGED TO: part_of subdivision of skeleton (UBERON:0010912)[VSAO] relationship type change: subclass skeletal subdivision (VSAO:0000042) CHANGED TO: proximally_connected_to subdivision of skeleton (UBERON:0010912)[VSAO] skeleton of girdle uberon bone of appendage girdle complex A bone that is part of an appendage girdle complex (i.e. any bone in a limb, fin or girdle). EMAPA:35494 MA:0000688 UBERON:0010740 bone of extended limb/fin region limb bone uberon meningeal cluster EHDAA2:0004661 EMAPA:32660 FMA:231572 In some primitive organisms, the meningeal cluster includes only the primitive meninx The collection of all meningeal layers that line a central nervous system. UBERON:0010743 cerebral meninges cluster of meninges meningeal meninges uberon subdivision of organism along appendicular axis A major subdivision of an organism that divides an organism along an axis perpedicular to the main body anterior-posterior axis. In vertebrates, this is typically a fin or limb segment. In insects, this includes segments of appendages such as antennae, as well as segments of the insect leg. FBbt:00007018 UBERON:0010758 appendage segment appendicular segment uberon limb cartilage element A skeletal element that is part of a limb and composed of cartilage tissue. UBERON:0010881 uberon limb bone pre-cartilage condensation A skeletal element that is part of a limb and composed of pre-cartilage tissue. UBERON:0010882 uberon subdivision of skeleton Anatomical cluster consisting of the skeletal elements (i.e. bone elements, cartilage elements, cartilage condensations) that are part of an individual subdivision of the organism. Excludes joints. Anatomical cluster consisting of the skeletal elements that are part of the skeleton.[VSAO] FMA:23879 UBERON:0010912 VSAO:0000042 skeletal subdivision subdivision of skeleton (in vivo) uberon nonsynovial joint FMA:7491 Joint in which the articulating bones or cartilages are connected by ligaments or fibrocartilage without an intervening synovial cavity. Examples: sagittal suture, inferior tibiofibular syndesmosis, costochondral joint, pubic symphysis. UBERON:0011134 solid joint uberon axial skeletal system FMA:7483 Subdivision of the skeletal system which consists of the axial skeleton plus associated joints. UBERON:0011137 http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton uberon post-cranial axial skeletal system FMA:302077 Subdivision of the skeletal system which consists of the post-cranial axial skeleton plus associated joints. UBERON:0011138 axial skeletal system http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton uberon synovial limb joint Any synovial joint that is part of a (free) limb. FMA:258776 Most limb joints are synovial, but a few such as the tibiofibular joints are syndesmoses. UBERON:0011139 synovial joint of free limb segment uberon upper urinary tract FMA:45658 Subdivision of urinary system which consists of the kidney and the ureters. UBERON:0011143 galen:UpperUrinaryTract uberon gastrointestinal sphincter A sphincter muscle that is part of the gastrointestinal system UBERON:0011185 UMLS:C1517464 uberon central nervous system cell part cluster A multi cell part structure that is part of a central nervous system. FMA:83143 UBERON:0011215 cell part cluster of neuraxis neuraxis layer uberon organ system subdivision A subdivision of an anatomical system. FBbt:00007330 FMA:67509 UBERON:0011216 uberon intra-ocular muscle AAO:0010038 EMAPA:18808 FMA:49150 Muscles within the eye (bulbus oculi).[AAO] UBERON:0011222 intrinsic muscle of eyeball intrinsic ocular muscle uberon appendicular skeletal system FMA:7484 Skeletal system which consists of the appendicular skeleton plus associated joints.[VSAO] Subdivision of the skeletal system which consists of the appendicular skeleton plus associated joints. UBERON:0011249 VHOG:0001666 VSAO:0000306 https://github.com/obophenotype/uberon/wiki/Appendages-and-the-appendicular-skeleton uberon autopod bone A bone that is part of a autopod region. Note that this incudes the carpal and tarsal bones. UBERON:0011250 https://github.com/obophenotype/uberon/wiki/Skeleton-partonomy-Design-Pattern uberon embryonic skin basal layer EHDAA2:0001845 UBERON:0011272 basal cell layer of skin compare with 'stratum basale of epidermis'. This class is the source for many adult structures - see WP2062. See also: 'enveloping layer of ectoderm' outer epithelium of body uberon paired limb/fin skeleton Skeletal subdivision that is part of the paired limb/fin.[VSAO] The collection of all skeletal elements in an individual limb or fin. UBERON:0011582 VSAO:0000301 limb/fin skeleton skeletal parts of limb/fin skeleton of limb/fin uberon stylopodial skeleton Proximal element of a free limb skeleton consisting of the femur and humerus in the forelimb stylopodium and hindlimb stylopodium respectively[VSAO, modified]. Proximal element of the limb skeleton consisting of the femur and humerus in the forelimb stylopodium and hindlimb stylopodium respectively.[VSAO] UBERON:0011583 VSAO:0005007 mesomere 1 propodial propodial skeleton propodium proximal metapterygial mesomere stylopod stylopodial stylopodium stylopodium skeleton uberon zeugopodial skeleton Section of the forelimb skeleton located between the stylopodium and the autopodium. UBERON:0011584 VSAO:0005010 epipodial skeleton epipodium mesomere 2 mesomere 2 skeleton skeleton of zeugopod uberon zeugopod skeleton zeugopodial zygopodial zygopodium cell condensation Anatomical structure that is an aggregation of similar cells from which cartilages and bones form, and from which chondrogenesis and osteogenesis are initiated during repair and/or regeneration. (Hall and Miyake 1995). UBERON:0011585 VSAO:0000006 XAO:0004021 consider obsoleting, coordinate with VSAO uberon subdivision of organism along main body axis A major subdivision of an organism that divides an organism along its main body axis (typically anterio-posterior axis). In vertebrates, this is based on the vertebral column. Ideally this would be disjoint with analagous class for appendicular axes, but currently 'appendages' like antennae, horns cause a problem UBERON:0011676 axial subdivision of organism body segment main body segment uberon embryonic cardiovascular system A cardiovascular system that is part of a conceptus. EHDAA2:0000216 FMA:305965 UBERON:0011695 conceptus cardiovascular system embryonic circulatory system fetal circulatory system uberon vagus nerve nucleus A cranial nerve nucleus that is associated with a vagus nerve. FMA:54573 UBERON:0011775 nodosal nucleus nucleus of Xth nerve nucleus of vagal X nerve nucleus of vagal nerve nucleus of vagus nerve tenth cranial nerve nucleus uberon vagal X nucleus vagal nucleus vagus nucleus nerve of head region A nerve that is part of a head. UBERON:0011779 cephalic nerve head nerve uberon non-neurogenic ectodermal placode Ectodermal placode that does not develop into a component of the nervous system. UBERON:0011814 uberon irregular connective tissue Connective tissue, which consists of a population of connective tissue cells, the intercellular matrix of which contains an irregular network of collagen and elastic fiber bundles. Examples: areolar tissue, mucoid tissue, connective tissue of peritoneum, connective tissue of fibrous pericardium. FMA:20107 UBERON:0011821 uberon dense irregular connective tissue FMA:20109 Irregular connective tissue is an irregular connective tissue, the intercellular matrix of which contains a dense irregular network of collagen and elastic fiber bundles. Examples: connective tissue of peritoneum, connective tissue of fibrous pericardium. Tissue characterized by a thick, random arrangement of collagen and elastin fibers with very few cells. The majority of the cells are fibroblasts, but mast cells and macrophages may also be seen. It is found in the dermis, periosteum, perichondrium, capsules of organs and sheaths of nerves and muscles[NCIT] UBERON:0011822 UMLS:C0738366 irregular dense connective tissue typus irregularis (textus connectivus collagenosus compactus) uberon dense connective tissue AAO:0000121 Connective tissue in which the fibrous component predominates. The cells, ground substance, and tissue fluid represent a minor component[NCIT] Dense connective tissue is mainly composed of collagen type I. Crowded between the collagen fibers are rows of fibroblasts, fiber-forming cells, that manufacture the fibers. Dense connective tissue forms strong, rope-like structures such as tendons and ligaments. Tendons attach skeletal muscles to bones; ligaments connect bones to bones at joints. Ligaments are more stretchy and contain more elastic fibers than tendons. Dense connective tissue also make up the lower layers of the skin (dermis), where it is arranged in sheets UBERON:0011823 UMLS:C1511770 our OWL definition states that this is differentiated from other connective tissue types by virtue of the fact that the collage fiber component predominates, as opposed to cells and fluid. uberon loose connective tissue FMA:19783 Irregular connective tissue, the intercellular matrix of which contains a sparse irregular network of collagen and elastic fiber bundles. Examples: areolar tissue, neuroglial tissue, mucoid tissue. UBERON:0011825 UMLS:C1253917 textus connectivus collagenosus laxus textus connectivus laxus uberon acinus of exocrine gland An acinus that is part of a exocrine gland. UBERON:0011858 exocrine gland acinus uberon collection of collagen fibrils FMA:63212 MESH:D024022 NIF_Subcellular:sao7547390221 UBERON:0011860 the FMA class specifically refers to ureter uberon anterior uvea Front (ventral) portion of the vascular, pigmentary, or middle coat of the eye, including the ciliary body and the iris. Haller tunica vascula UBERON:0011892 anterior part of uveal tract anterior uveal tract anterior vascular layer of the eyeball anterior vascular tunic of the eye ciliary body and iris tunica vasculosa bulbosa uberon vasculosa oculi ventral uveal tract epimysium Epimysium is a layer of connective tissue which ensheaths the entire muscle. It is composed of dense irregular connective tissue. It is continuous with fascia and other connective tissue wrappings of muscle including the endomysium, and perimysium. It is also continuous with tendons where it becomes thicker and collagenous. FMA:9726 The Epimysium also protects muscles from friction against other muscles and bones UBERON:0011899 UMLS:C0504096 epimysia fascia of muscle organ uberon stomach glandular region A region of the stomach that is lined with glandular epithelium. EMAPA:17623 MA:0001613 UBERON:0011953 UMLS:C0227197 as currently defined, this would include the cardiac antrum; however, the intent may be to exclude the cardiac glands and in mice for this to be part of the region distal to the margo plicatus glandular stomach uberon coelom EHDAA2 distingsuishes between the lumen, the lining, and the 'coelomic cavity', which despire it's name, is not a space - it is the aggregate of space plus lining. EHDAA2:0004731 The aggregate of the coelemic cavity lumen plus the membranes that line the lumen. UBERON:0011997 coelem coelomic coelomic cavity enterocoelom haemocoelom schizocoelom uberon perinatal stage In birds, the paranatal stage starts when the beak penetrates into the air pocket (air cell) between the inner and outer shell membranes The period spanning the range immediately before and after birth UBERON:0012101 paranatal stage uberon segment of autopod UBERON:0012139 uberon digitopodium region A segment of the autopod consisting of both acropodial region and metapodial region, but excluding the mesopodial/basopodial region. UBERON:0012140 acropodium (Wagner) https://github.com/obophenotype/uberon/wiki/Subdivisions-of-the-autopod some sources call this the acropodium. see https://github.com/obophenotype/uberon/wiki/Subdivisions-of-the-autopod uberon skeleton of digitopodium A subdivision of the autopod skeleton consisting of both acropodial skeleon and metapodial skeleton, but excluding the mesopodial/basopodial skeleton. UBERON:0012150 digitopodium https://github.com/obophenotype/uberon/wiki/Subdivisions-of-the-autopod skeleton of digits some sources call this the acropodium. see https://github.com/obophenotype/uberon/wiki/Subdivisions-of-the-autopod uberon columnar epithelium An epithelium that consists of columnar epithelial cells. Columnar epithelia are epithelial cells whose heights are at least four times their width. Columnar epithelia are divided into simple (or unilayered), and the rarer stratified (or multi-layered).[WP, modified] UBERON:0012274 uberon meso-epithelium Epithelium that derives from the mesoderm. [Automatically generated definition]. FMA:86452 UBERON:0012275 mesoderm-derived epithelium mesoepithelium uberon embryonic cloacal fold EHDAA2:0004009 One of the pair of mesenchymal swellings (folds) located on either side of the cloacal membrane during the indifferent stage of embryonic development; cranial to the cloacal membrane the folds unite to form the genital tubercle; caudally the folds are subdivided into urogenital folds anteriorly and anal folds posteriorly UBERON:0012292 We presume this is distinct from AAO:0001003, an external integumentary structure - check with amphibian anatomy ontology developers. AO notes: the text def states mesenchymal swelling, EHDAA2 splits into mesenchymal and epithelial parts cloacal fold uberon fin skeleton Skeletal subdivision consisting of all the skeletal elements in a single fin. UBERON:0012353 skeleton of fin uberon acropodium region The segment of the autopod that is distal to the metapodial region and consists of the digits. UBERON:0012354 acropodial limb segment acropodial region acropodial segment of autopod class refers to an entire limb segment, not just the bones set of digits uberon digitopodium bone A bone that is part of a the digitopodium skeleton - i.e. the acropodial skeleton or the metapodial skeleton. UBERON:0012357 digit bone uberon internal anal region EHDAA2:0004588 UBERON:0012361 uberon hemopoietic tissue Blood-forming tissue, consisting of reticular fibers and cells. Also known as hemopoietic tissue Bone marrow in humans, kidney interstitium in Danio, within a stroma of reticuloendothelial tissue CALOHA:TS-2142 FMA:14073 UBERON:0012429 UMLS:C0229619 bone marrow tissue haemopoietic tissue hematopoietic tissue textus haemopoieticus uberon tunica fibrosa of eyeball FMA:58102 The sclera and cornea form the fibrous tunic of the bulb of the eye; the sclera is opaque, and constitutes the posterior five-sixths of the tunic; the cornea is transparent, and forms the anterior sixth. UBERON:0012430 corneosclera fibrous layer of eyeball fibrous tunic tunica fibrosa uberon external anal region EHDAA2:0004589 UBERON:0012469 uberon skeleton of pelvic complex FMA:24140 The collection of all skeletal elements in a pelvic complex - i.e. the combination of free limb or fin plus pelvic girdle. UBERON:0012476 bones of lower limb lower limb skeleton ossa membri inferioris pelvic complex skeleton set of bones of lower limb skeleton of posterior limb/fin and girdle uberon cloacal epithelium An epithelium that is part of a cloaca. EMAPA:27577 EMAPA:27640 EMAPA:36070 UBERON:0012481 ZFA:0005783 cloacal endoderm cloacal epithelium (cle) (syn: cloacal endoderm) (TS17-TS20): the cloacal epithelium is derived from endoderm and lines the cloacal cavity. It is marked by Shh and Cdh1 and lines the cloacal lumen. The cloacal epithelium gives rise to the urogenital sinus epithelium, hindgut epithelium and the urethral plate epithelium. uberon serous acinus FMA:86279 The secretory unit of a serous gland. The acinar portion is composed of serous secreting cells. UBERON:0013232 acinus of serous gland uberon embryonic urethral groove In humans, the urethral groove is a temporary linear indentation on the underside (ventral side) of the male penis during embryonic development. It typically appears around 8 weeks of gestation and becomes closed into a normal male urethra by the 12th week The precursor of the urethra UBERON:0013241 sulcus urethralis primarius uberon urethral groove urethral sulcus space surrounding organism The space that surrounds an organism. UBERON:0013514 external to organism outside of body uberon subdivision of oviduct A section through the tube or network of tubes that connects the ovaries to the outside of the body. FMA class may only represent the uterine portion FMA:18302 UBERON:0013515 subdivision of fallopian tube subdivision of oviduct subdivision of uterine tube uberon uterine tube zone zone of uterine tube subdivision of tube UBERON:0013522 uberon anatomical conduit space 2 2 An anatomical space which is the lumen of some anatomical conduit and connects two or more spaces together[FMA,modified]. FMA:9338 UBERON:0013686 foramen space uberon main body axis A principle subdivision of an organism that includes all structures along the primary axis, typically the anterior-posterior axis, from head to tail, including structures of the body proper where present (for example, ribs), but excluding appendages. UBERON:0013701 uberon body proper AEO:0000103 BTO:0001489 Cardinal body part, which consists of a maximal set of diverse subclasses of organ and organ part spatially associated with the vertebral column and ribcage. Examples: There is only one body proper[FMA:231424]. EMAPA:36031 FMA:231424 The region of the organism associated with the visceral organs. UBERON:0013702 body uberon whole body integumentary projection Anatomical projection that is part of the integumentl system. UBERON:0013703 skin projection uberon integumentary system layer A organ component layer that is part of a integumental system. UBERON:0013754 layer of skin skin layer uberon venous blood A blood that is part of a vein. FMA:83067 UBERON:0013756 blood in vein portion of venous blood uberon venous blood digestive system element Any of the organs or elements that are part of the digestive system. Examples: tongue, esophagus, spleen, crop, lunge feeding organ, tooth elements. UBERON:0013765 digestive organ digestive system organ uberon great vessel of heart EMAPA:36460 Great vessels is a term used to refer collectively to the large vessels that bring blood to and from the heart. Groupings may vary - typically pulmonary vessels and aorta and vena cavae UBERON:0013768 great vessel great vessel of thorax uberon future telencephalon EHDAA2:0004424 EMAPA:36024 Embryonic structure that gives rise to the telencephalon. TAO:0000571 UBERON:0014371 ZFA:0000571 paired anteriolateral division of the embryonic prosencephalon plus the lamina terminalis from which the olfactory lobes, cerebral cortex, and subcortical nuclei are derived[MP] presumptive telencephalon uberon mesenchyme derived from neural crest EMAPA:32735 FMA:293883 Mesenchyme that develops_from the neural crest[Automatically generated definition]. UBERON:0014387 mesenchyme from neural crest neural crest derived mesenchyme neural crest mesenchyme uberon thoracic skeleton EHDAA2:0002013 FMA:77169 Subdivision of skeletal system that consists of all skeletal elements in the thoracic region of the trunk. In most vertebrates this is the rib cage and sternum. UBERON:0014477 skeleton of thorax thoracic part of axial skeleton thoracic skeleton uberon interlobular duct A duct that is located between lobules, within the thin connective tissue septa that separate lobules. All interlobular ducts are excretory. UBERON:0014716 uberon intralobular duct A duct that is located within a lobule, with no more connective tissue intervening between ducts and secretory units (i.e., acini or tubules) than between adjacent secretory units. Intercalated and striated ducts are intralobular UBERON:0014719 intralobular ductule uberon skeletal muscle organ A muscle organ that consists of skeletal muscle tissue ensheathed in epimysium, that develops from myotome and that is innervated by some somatic motor neuron. Skeletal muscles are typically attached (via a tendon) to a bone but there are exceptions (e.g. intrinsic tongue muscles). AAO:0011099 BTO:0001103 CALOHA:TS-0933 EFO:0000888 EHDAA:5035 EHDAA:5043 EHDAA:5978 EHDAA:5984 EMAPA:35988 EV:0100377 GAID:141 MA:0003148 MAT:0000302 MESH:D018482 MIAA:0000302 OpenCyc:Mx4rv2kf-5wpEbGdrcN5Y29ycA TAO:0005277 UBERON:0014892 VHOG:0000319 XAO:0000174 ZFA:0005277 skeletal muscle uberon primordial vasculature A portion of tissue that will develop into vasculature. EFO:0003708 TAO:0005076 UBERON:0014903 ZFA:0005076 uberon phalanx endochondral element A phalanx bone or its cartilage or pre-cartilage precursor. UBERON:0015023 phalanx element phalanx skeletal element uberon limb endochondral element A limb bone or its cartilage or pre-cartilage precursor. UBERON:0015061 limb bone endochondral element limb bone skeletal element uberon autopod endochondral element A endochondral element that is part of a autopod region. UBERON:0015063 uberon autopod cartilage A autopod endochondral element that is composed primarily of a cartilage tissue. UBERON:0015064 uberon lateral structure Any structure that is placed on one side of the left-right axis of a bilaterian. This class is primarily to implement taxon constraints. It may be removed in the future. UBERON:0015212 uberon circulatory organ A hollow, muscular organ, which, by contracting rhythmically, contributes to the circulation of lymph, blood or analogs. Examples: a chambered vertebrate heart; the tubular peristaltic heart of ascidians; the dorsal vessel of an insect; the lymoh heart of a reptile. SPD:0000130 UBERON:0015228 cardiac pump cardiac structure circulatory vessel heart heart or heart like organ uberon heart plus pericardium MA:0002449 UBERON:0015410 heart/pericardium uberon heterogeneous tissue FMA:62798 UBERON:0015757 portion of heterogeneous tissue uberon eye epithelium A epithelium that is part of a camera-type eye. EMAPA:35957 MA:0003162 UBERON:0015808 uberon foregut epithelium A epithelium that is part of a foregut. EMAPA:32922 MA:0003204 UBERON:0015833 uberon pit AEO:0000204 An roughly circular indentation in a surface. UBERON:0016566 uberon future central nervous system Primordium that develops into the central nervous system UBERON:0016879 UBERON:3000469 future CNS presumptive central nervous system uberon future nervous system AAO:0000477 Primordium that develops into the nervous system UBERON:0016880 UBERON:3000477 presumptive nervous system uberon entire extraembryonic component AEO:0000195 EHDAA2:0000003 EMAPA:16042 The part of the conceptus that may be lost before birth or will be discarded at birth, or when the embryo becomes an independent organism. UBERON:0016887 extra-embryonic component extraembryonic component uberon transitional anatomical structure AEO:0000132 An embryonic anatomical entity that will turn into one or more other anatomical entities, perhaps with other anatomical entities, later in development. UBERON:0016888 uberon developing mesenchymal structure A mesenchyme-derived anatomical entity undergoing a transtion to become another structure. AEO:0001016 UBERON:0017650 uberon abdominal viscera A viscus that is part of a abdomen. FMA:32413 FMA:67355 UBERON:0017672 abdominal viscera abdominal viscera set set of abdominal viscera uberon skeletal musculature Added for consistency with MA EMAPA and EHDAA2. See https://github.com/obophenotype/mouse-anatomy-ontology/issues/104 EHDAA2:0001842 EMAPA:35578 MA:0000165 UBERON:0018254 uberon layer of muscle tissue Any organ component layer that consists of muscle tissue. FMA:45634 NCITA class may refer to smooth muscle only UBERON:0018260 uberon heart vasculature An interconnected tubular multi-tissue structure that contains fluid that is actively transported around the heart. FMA:73747 UBERON:0018674 ZFA:0005811 cardiac vasculature uberon bladder organ A membranous sac in animals that serves as the receptacle of a liquid or contains gas. BTO:0000123 UBERON:0018707 bladder uberon chorioretinal region The part of the eye that consists of both the retina and the optic choroid UBERON:0019207 chorioretina choroid and retina retinachoroid retinachoroidal region uberon sensory organ epithelium EMAPA:35952 MA:0003174 UBERON:0019304 uberon surface of eyeball FMA:58315 UBERON:0022288 surface of region of wall of eyeball uberon nervous system cell part layer Single layer of a laminar structure, identified by different density, arrangement or size of cells and processes arranged in flattened layers or lamina[CUMBO]. UBERON:0022303 lamina layer this is currently used to group some cellular layers that may not strictly conform to the CARO definition of cell-part layer. Consider genericisizing and introducing subtypes for cellular layer, fibrous layer and cell soma layer uberon developing neuroepithelium AEO:0001008 An embryonic or larval epithelium that is committed to form part of the nervous system. BTO:0000314 EHDAA2_RETIRED:0004654 FMA:64807 UBERON:0034705 embryonic neuroepithelium neurepithelium neuroepithelium uberon proliferating neuroepithelium AEO:0001009 An epithelium that is undergoing proliferation to provide large numbers of neuronal cells. UBERON:0034706 uberon differentiating neuroepithelium A neuroepithelium some of whose cells are undergoing terminal differentiation to become neuronal cells. AEO:0001010 UBERON:0034707 uberon cranial neuron projection bundle Any of the cranial nerves, or their central nervous system analogs (the optic tract, the epiphyseal tract). These analogs are not true nerves, and are instead evaginated sensory afferents emanating from the brain UBERON:0034713 cranial nerve fiber bundle cranial nerve fiber tract cranial nerve or tract neuron projection bundle from brain uberon morphological feature A part of an organism or organ that is continuous with its surroundings and distinguished from its surroundings based on morphology. UBERON:0034768 uberon lymphomyeloid tissue FMA:79770 UBERON:0034769 uberon bodily gas Any substance in the body or expelled from the body that is in a gaseous state. FMA:84580 UBERON:0034873 gas in anatomical space portion of gas in anatomical space uberon air in respiratory system Any portion of gas located in a part of the respiratory system that is composed primarily of air. FMA:84581 UBERON:0034874 respiratory air respiratory system air uberon multi organ part structure An multicellular anatomical structure that has subparts of multiple organs as a part. CARO:0020001 UBERON:0034921 anatomical cluster uberon cell cluster A cluster of cells, largely surrounded by a morphological boundary. CARO:0020002 FMA:62807 UBERON:0034922 uberon anatomical collection A collection of anatomical structures that are alike in terms of their morphology or developmental origin. UBERON:0034925 resolve if this should be a subclass of disconnected anatomical group. Some collections (e.g. the skeleton or skull) are arguably connected uberon external soft tissue zone A region or zone on the surface of an organism that encompasses skin and any adnexa, down through muscles and bounded by underlying skeletal support structures. UBERON:0034929 uberon epithelium of biliary system BTO:0001513 The epithelial layer covering the biliary system. This includes the epithelium of the gallbladder (when present) as well as the intrahepatic and extrahepatic bile ducts. UBERON:0034932 biliary epithelium biliary system epithelium biliary tract epithelium uberon zone of organ FMA:55268 UBERON:0034944 organ region with floating fiat boundary organ sector organ zonal region organ zone uberon gas in respiratory system Any portion of gas located in a part of the respiratory system. UBERON:0034947 respiratory gas respiratory system gas uberon epithelial layer of duct UBERON:0034969 duct epithelium ductal epithelium uberon excretory duct UBERON:0035050 uberon left cardiac chamber Any chamber of the left side of the heart FMA:7166 UBERON:0035553 uberon laryngeal nerve Any nerve that innervates the larynx. MESH:A08.800.050.050.925.450 UBERON:0035642 uberon future mouth FMA:293105 The primordial mouth region of the developing head. UBERON:0035804 primitive mouth primordial mouth uberon preplacodal ectoderm Non neural ectoderm that surrounds the presumptive neural plate and gives rise to neurogenic placodes. This class was sourced from an external ontology (teleost_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon ZFA:0007013 teleost_anatomy_curators uberon/phenoscape-anatomy external integument structure Structures of the dermis, epidermis, glands and pigment cells recognizable on the external surfaces of the integument. This class was sourced from an external ontology (amphibian_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon amphibian_anatomy_curators uberon/phenoscape-anatomy digit plus metapodial segment A subdivision of the autopod consisting of digit plus the region incorporating a single metapodial element. These segments are typically repeated along the pre-axiom to post-axial axis. UBERON:5002544 digit digit ( phalanges plus metapodial) plus soft tissue digit digitopodial subdivision digit ray this class represents a series of phalanges plus a metapodial element plus associated soft tissues. Instances of this class typically do not form a distinct unit. uberon individual digit of digitopodial skeleton A subdivision of the skeleton of the autopod consisting of the phalanges of a single digit plus the associated metapodial element. UBERON:5102544 digit digit skeleton this class represents a series of phalanges plus a metapodial element. In comparative anatomy terminology we would call this a 'digit', but the label 'digit' is sometimes used to exclude metapodials and to include soft tissue. This series of elements is hypothesized to be homologous to radials. uberon injection site a medical intervention site that is used for injection of a substance. YH, SS, ZX ready for release pending final vetting axiom holds for all times