John Judkins 2019-01-08 Cristian Cocos Jie Zheng The EuPath ontology is an application ontology developed to encode our understanding of what data is about in the public resources developed and maintained by the Eukaryotic Pathogen Database Bioinformatics Resource Center (EuPathDB; http://eupathdb.org). The EuPath ontology was built based on the Ontology of Biomedical Investigations (OBI) with integration of other OBO ontologies such as PATO, OGMS, DO, etc. as needed for coverage. Currently the EuPath ontology is primarily intended to be used for support of the EuPathDB sites. Terms with EuPath ontology IDs that are not specific to EuPathDB will be submitted to OBO Foundry ontologies for subsequent import and replacement of those terms when they are available. Chris Stoeckert BFO OWL specification label 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. Really of interest to developers only BFO OWL specification label BFO CLIF specification label Relates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2 Person:Alan Ruttenberg Really of interest to developers only BFO CLIF specification label Label used in EuPathDB EuPathDB alternative term definition shown on EuPathDB website EuPathDB definition Label of terms used in Amazonia data dictionary. It is in Spanish. Amazonia data dictionary label (es) English label used in Amazonia project for display on the website Amazonia preferred label (en) Spanish label used in Amazonia project for display on the website Amazonia preferred label (es) label of term used in the ontology ontological label Label of terms used in PRISM data dictionary. It is in English. PRISM data dictionary label (en) English label used in Prism project for display on the website PRISM preferred label (en) Term description provided by Amazonia group Amazonia description Term description provided by PRISM group PRISM description Three options of term type: - category: used for organize the filter in the website, not ontology term - variable: term in the data dictionary of project. Should have mapped ontology term associate with it - value: controlled vocubulary used for annotation of variable in the data dictionary. Should have mapped ontology term associate with it term type specify ICEMR term original from which database resource ID definition of term in ontology ontological definition The order variables will appear in under a given parent term. Left blank if alphabetical order is accepted annotation used for specifing the order of terms displayed on the EuPathDB website display order Label of terms used in Indian data dictionary. It is in English. Indian data dictionary label (en) English label used in Indian project for display on the website Indian preferred label (en) Term description provided by Indian group Indian description Translated English label of terms in Amazonia data dictionary. Amazonia data dictionary label (en) In a data file, there is a column with name 'age'. It mapped to EuPath ontology term 'age at visit'. We can add 'implements variable' annotation with value 'age' to term 'age at visit'. Column header for each variable from the original datasets (use format from datasets, not data dictionary). column header variable The column order of variables in the original data files colOrder The original file name for the data file the variable was found in, or a shortened version of the file name that contains all relevant information to identify the data file. dataFile The highest level parent term (Household, Participant, Observation, Specimen) the variable falls under. category The variable description from the data dictionary. Useful for assigning display labels. To be provided either directly from the data provider in their codebook or filled out by ClinEpi Outreach before handing over to Ontology. codebookDescription All possible responses and their mapped terms for each variable, from the data dictionary. Useful for value mapping. codebookValues Indicate whether variable will be grouped under a multi-filter category. multifilter editor preferred label The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English) PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> editor preferred label editor preferred term editor preferred term 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 PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> example of usage has curation status PERSON:Alan Ruttenberg PERSON:Bill Bug PERSON:Melanie Courtot OBI_0000281 has curation status definition English language definitions of what NCI means by the concept. These are limited to 1024 characters. They may also include information about the definition's source and attribution in a form that can easily be interpreted by software. 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. 2012-04-05: Barry Smith The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. Can you fix to something like: A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. Alan Ruttenberg Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. On the specifics of the proposed definition: We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition definition definition textual definition textual definition editor note 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. PERSON:Daniel Schober GROUP:OBI:<http://purl.obfoundry.org/obo/obi> editor note term editor 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 20110707, MC: label update to term editor and definition modified accordingly. See http://code.google.com/p/information-artifact-ontology/issues/detail?id=115. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> term editor alternative term An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent) PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> alternative term 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 PERSON:Daniel Schober Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition source curator note An administrative note of use for a curator but of no use for a user PERSON:Alan Ruttenberg curator note imported from For external terms/classes, the ontology from which the term was imported PERSON:Alan Ruttenberg PERSON:Melanie Courtot GROUP:OBI:<http://purl.obolibrary.org/obo/obi> imported from elucidation person:Alan Ruttenberg Person:Barry Smith Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms elucidation has associated axiom(nl) Person:Alan Ruttenberg Person:Alan Ruttenberg An axiom associated with a term expressed using natural language has associated axiom(nl) has associated axiom(fol) Person:Alan Ruttenberg Person:Alan Ruttenberg An axiom expressed in first order logic using CLIF syntax has associated axiom(fol) ISA alternative term An alternative term used by the ISA tools project (http://isa-tools.org). Requested by Alejandra Gonzalez-Beltran https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891&atid=886178 Person: Alejandra Gonzalez-Beltran Person: Philippe Rocca-Serra ISA tools project (http://isa-tools.org) ISA alternative term An alternative term used by the National Institute of Allergy and Infectious Diseases (NIAID) Genomic Sequencing Centers for Infectious Diseases (GSCID) and Bioinformatics Resource Centers (BRC). PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group NIAID GSCID-BRC alternative term IEDB alternative term An alternative term used by the IEDB. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IEDB alternative term temporal interpretation temporal interpretation https://code.google.com/p/obo-relations/wiki/ROAndTime Description may include but is not limited to: an abstract, table of contents, reference to a graphical representation of content or a free-text account of the content. An account of the content of the resource. Description Description The present resource may be derived from the Source resource in whole or in part. Recommended best practice is to reference the resource by means of a string or number conforming to a formal identification system. A reference to a resource from which the present resource is derived. Source Source label label 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) this day is part of this year (occurrent parthood) a core relation that holds between a part and its whole 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 Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. part_of part of http://www.obofoundry.org/ro/#OBO_REL:part_of 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) a core relation that holds between a whole and its part 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 Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. has_part has part realized in this disease is realized in this disease course this fragility is realized in this shattering this investigator role is realized in this investigation is realized by realized_in [copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process realized in realizes this disease course realizes this disease this investigation realizes this investigator role this shattering realizes this fragility to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process realizes material may be used for symptom or sign of A relation between a medication material and a disease or symptom that it may treat. may treat A relation between a drug product and (one of) its active ingredient. has active ingredient has measurement unit label has measurement unit label is about This document is about information artifacts and their representations is_about is a (currently) primitive relation that relates an information artifact to an entity. 7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of "mentions" relation. Weaken the is_about relationship to be primitive. We will try to build it back up by elaborating the various subproperties that are more precisely defined. Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic. person:Alan Ruttenberg Smith, Ceusters, Ruttenberg, 2000 years of philosophy is about denotes A person's name denotes the person. A variable name in a computer program denotes some piece of memory. Lexically equivalent strings can denote different things, for instance "Alan" can denote different people. In each case of use, there is a case of the denotation relation obtaining, between "Alan" and the person that is being named. denotes is a primitive, instance-level, relation obtaining between an information content entity and some portion of reality. Denotation is what happens when someone creates an information content entity E in order to specifically refer to something. The only relation between E and the thing is that E can be used to 'pick out' the thing. This relation connects those two together. Freedictionary.com sense 3: To signify directly; refer to specifically 2009-11-10 Alan Ruttenberg. Old definition said the following to emphasize the generic nature of this relation. We no longer have 'specifically denotes', which would have been primitive, so make this relation primitive. g denotes r =def r is a portion of reality there is some c that is a concretization of g every c that is a concretization of g specifically denotes r person:Alan Ruttenberg Conversations with Barry Smith, Werner Ceusters, Bjoern Peters, Michel Dumontier, Melanie Courtot, James Malone, Bill Hogan denotes is quality measurement of m is a quality measurement of q at t when q is a quality there is a measurement process p that has specified output m, a measurement datum, that is about q 8/6/2009 Alan Ruttenberg: The strategy is to be rather specific with this relationship. There are other kinds of measurements that are not of qualities, such as those that measure time. We will add these as separate properties for the moment and see about generalizing later From the second IAO workshop [Alan Ruttenberg 8/6/2009: not completely current, though bringing in comparison is probably important] This one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it "measuring" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail. Werner suggests a solution based on "Magnitudes" a proposal for which we are awaiting details. -- From the second IAO workshop, various comments, [commented on by Alan Ruttenberg 8/6/2009] unit of measure is a quality, e.g. the length of a ruler. [We decided to hedge on what units of measure are, instead talking about measurement unit labels, which are the information content entities that are about whatever measurement units are. For IAO we need that information entity in any case. See the term measurement unit label] [Some struggling with the various subflavors of is_about. We subsequently removed the relation represents, and describes until and only when we have a better theory] a represents b means either a denotes b or a describes describe: a describes b means a is about b and a allows an inference of at least one quality of b We have had a long discussion about denotes versus describes. From the second IAO workshop: An attempt at tieing the quality to the measurement datum more carefully. a is a magnitude means a is a determinate quality particular inhering in some bearer b existing at a time t that can be represented/denoted by an information content entity e that has parts denoting a unit of measure, a number, and b. The unit of measure is an instance of the determinable quality. From the second meeting on IAO: An attempt at defining assay using Barry's "reliability" wording assay: process and has_input some material entity and has_output some information content entity and which is such that instances of this process type reliably generate outputs that describes the input. This one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it "measuring" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail. Werner suggests a solution based on "Magnitudes" a proposal for which we are awaiting details. Alan Ruttenberg is quality measurement of is duration of relates a process to a time-measurement-datum that represents the duration of the process Person:Alan Ruttenberg is duration of provides_service_consumer_with The provides_service_consumer_with relation links the service to its primary process it provides for the consumer (as opposed to secondary processual parts of a service process such as payment or documentation). For example, a 'DNA sequencing service' provides_service_consumer_with 'DNA sequencing' as the essential process performed by the provider for the client. A relation between a service and the primary processual part of the service that is performed by the provider for the consumer. provides_service_consumer_with is_supported_by_data The relation between the conclusion "Gene tpbA is involved in EPS production" and the data items produced using two sets of organisms, one being a tpbA knockout, the other being tpbA wildtype tested in polysacharide production assays and analyzed using an ANOVA. The relation between a data item and a conclusion where the conclusion is the output of a data interpreting process and the data item is used as an input to that process OBI OBI Philly 2011 workshop is_supported_by_data has_specified_input see is_input_of example_of_usage A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of. 8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works. PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Larry Hunter PERSON: Melanie Coutot has_specified_input is_specified_input_of some Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of. Alan Ruttenberg PERSON:Bjoern Peters is_specified_input_of has_specified_output A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of. PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Larry Hunter PERSON: Melanie Courtot has_specified_output is_specified_output_of A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of. Alan Ruttenberg PERSON:Bjoern Peters is_specified_output_of achieves_planned_objective A cell sorting process achieves the objective specification 'material separation objective' This relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process. BP, AR, PPPB branch PPPB branch derived modified according to email thread from 1/23/09 in accordince with DT and PPPB branch achieves_planned_objective has grain the relation of the cells in the finger of the skin to the finger, in which an indeterminate number of grains are parts of the whole by virtue of being grains in a collective that is part of the whole, and in which removing one granular part does not nec- essarily damage or diminish the whole. Ontological Whether there is a fixed, or nearly fixed number of parts - e.g. fingers of the hand, chambers of the heart, or wheels of a car - such that there can be a notion of a single one being missing, or whether, by contrast, the number of parts is indeterminate - e.g., cells in the skin of the hand, red cells in blood, or rubber molecules in the tread of the tire of the wheel of the car. Discussion in Karslruhe with, among others, Alan Rector, Stefan Schulz, Marijke Keet, Melanie Courtot, and Alan Ruttenberg. Definition take from the definition of granular parthood in the cited paper. Needs work to put into standard form PERSON: Alan Ruttenberg PAPER: Granularity, scale and collectivity: When size does and does not matter, Alan Rector, Jeremy Rogers, Thomas Bittner, Journal of Biomedical Informatics 39 (2006) 333-349 has grain supplies A relation between an organisation or person and a material entity who owned or has license to the material entity and there was a legal transfer of ownership or licensing of the material entity to the current owner. GROUP: Relations branch supplies objective_achieved_by This relation obtains between a a objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process. OBI OBI objective_achieved_by is member of organization Relating a legal person or organization to an organization in the case where the legal person or organization has a role as member of the organization. 2009/10/01 Alan Ruttenberg. Barry prefers generic is-member-of. Question of what the range should be. For now organization. Is organization a population? Would the same relation be used to record members of a population JZ: Discussed on May 7, 2012 OBI dev call. Bjoern points out that we need to allow for organizations to be members of organizations. And agreed by the other OBI developers. So, human and organization were specified in 'Domains'. The textual definition was updated based on it. Person:Alan Ruttenberg Person:Helen Parkinson Person:Alan Ruttenberg Person:Helen Parkinson 2009/09/28 Alan Ruttenberg. Fucoidan-use-case is member of organization has organization member Relating an organization to a legal person or organization. See tracker: https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_id=177891&atid=886178 Person: Jie Zheng has organization member has value specification A relation between an information content entity and a value specification that specifies its value. PERSON: James A. Overton OBI has value specification inheres in this fragility inheres in this vase this red color inheres in this apple a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence A dependent inheres in its bearer at all times for which the dependent exists. inheres_in inheres in bearer of this apple is bearer of this red color this vase is bearer of this fragility a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist. bearer_of is bearer of bearer of participates in this blood clot participates in this blood coagulation this input material (or this output material) participates in this process this investigator participates in this investigation a relation between a continuant and a process, in which the continuant is somehow involved in the process participates_in participates in has participant this blood coagulation has participant this blood clot this investigation has participant this investigator this process has participant this input material (or this output material) a relation between a process and a continuant, in which the continuant is somehow involved in the process Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. has_participant http://www.obofoundry.org/ro/#OBO_REL:has_participant has participant concretizes A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process). A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant. concretizes role of this investigator role is a role of this person a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists. is role of role_of role of has role this person has role this investigator role (more colloquially: this person has this role of investigator) a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists. has_role has role derives from this cell derives from this parent cell (cell division) this nucleus derives from this parent nucleus (nuclear division) a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'. derives_from derives from temporal relation move to BFO? Allen A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. temporal relation starts inverse of starts with Chris Mungall Allen starts the relationship between a fraction and the number above the line has numerator the relationship between a fraction and the number below the line (or divisor) has denominator has measurement value has measurement value has specified value A relation between a value specification and a number that quantifies it. A range of 'real' might be better than 'float'. For now we follow 'has measurement value' until we can consider technical issues with SPARQL queries and reasoning. PERSON: James A. Overton OBI has specified value fracture (bone) Fracture burns Burn Foreign body Bacterial infection of skin Tree (organism) Tree shock ICEMR protein array shock Soft tissue injury Animal bite (morphologic abnormality) Animal bite Pyrexia of unknown origin An identifier that denotes a group of organisms or groups of organisms based on common ancestors. genetic clade of organism clade name entity Entity entity Julius Caesar Verdi’s Requiem the Second World War your body mass index 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 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 An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) entity continuant Continuant continuant 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 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]) 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]) (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] continuant occurrent Occurrent occurrent 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 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 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. 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. 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]) Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] occurrent ic IndependentContinuant independent continuant a chair a heart a leg a molecule a spatial region an atom an orchestra. an organism the bottom right portion of a human torso the interior of your mouth A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. 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]) 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]) (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] (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] independent continuant process Process process a process of cell-division, \ a beating of the heart a process of meiosis a process of sleeping the course of a disease the flight of a bird the life of an organism your process of aging. An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. 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]) 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) (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] process disposition Disposition disposition an atom of element X has the disposition to decay to an atom of element Y certain people have a predisposition to colon cancer children are innately disposed to categorize objects in certain ways. the cell wall is disposed to filter chemicals in endocytosis and exocytosis BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type. b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002]) (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] disposition realizable RealizableEntity realizable entity the disposition of this piece of metal to conduct electricity. the disposition of your blood to coagulate the function of your reproductive organs the role of being a doctor the role of this boundary to delineate where Utah and Colorado meet A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances. To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] realizable entity quality Quality quality 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 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]) 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]) (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] (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] quality sdc SpecificallyDependentContinuant specifically dependent continuant 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 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. 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 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. b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n &gt; 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i &lt; j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004]) 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]) 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. (iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004] (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] specifically dependent continuant role Role role John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married. the priest role the role of a boundary to demarcate two neighboring administrative territories the role of a building in serving as a military target the role of a stone in marking a property boundary the role of subject in a clinical trial the student role A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts. BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives. b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] role site Site site Manhattan Canyon) 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 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) 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]) (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] site gdc GenericallyDependentContinuant generically dependent continuant The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity. the pdf file on your laptop, the pdf file that is a copy thereof on my laptop the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule. A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time. b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] generically dependent continuant function p-boundary ProcessBoundary process boundary the boundary between the 2nd and 3rd year of your life. p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001]) Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002]) (forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002] (iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001] process boundary material MaterialEntity material entity 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 the undetached arm of a human being An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. 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. 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]) Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) (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 x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] (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] material entity immaterial ImmaterialEntity immaterial entity 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 immaterial entity liver cell line fibroblast cell line gross anatomical part Anatomical structure that is part of a multicellular organism and is at the gross anatomical level, e.g. above the level of a cell. Included are portions of organism substances such as blood, multi-cell-part structures such as axon tracts, acellular anatomical structures such as hair, and organism subdivisions such as head. Excluded is the whole organism and more granular parts of the organism, such as atoms, molecules, macromolecular complexes and cells. gross anatomical part A triazole-based antifungal agent used for the treatment of esophageal candidiasis, invasive pulmonary aspergillosis, and serious fungal infections caused by Scedosporium apiospermum and Fusarium spp. It is an inhibitor of cytochrome P450 2C9 (CYP2C9) and CYP3A4. voriconazole An optically active form of dopa having L-configuration. Used to treat the stiffness, tremors, spasms, and poor muscle control of Parkinson's disease L-dopa A cinchona alkaloid that is cinchonidine in which the hydrogen at the 6-position of the quinoline ring is substituted by methoxy. quinine An inorganic peroxide consisting of two hydroxy groups joined by a covalent oxygen-oxygen single bond. hydrogen peroxide peptide Amide derived from two or more amino carboxylic acid molecules (the same or different) by formation of a covalent bond from the carbonyl carbon of one to the nitrogen atom of another with formal loss of water. The term is usually applied to structures formed from alpha-amino acids, but it includes those derived from any amino carboxylic acid. X = OH, OR, NH2, NHR, etc. peptide deoxyribonucleic acid High molecular weight, linear polymers, composed of nucleotides containing deoxyribose and linked by phosphodiester bonds; DNA contain the genetic information of organisms. deoxyribonucleic acid molecular entity Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity. We are assuming that every molecular entity has to be completely connected by chemical bonds. This excludes protein complexes, which are comprised of minimally two separate molecular entities. We will follow up with Chebi to ensure this is their understanding as well molecular entity Any substance which when absorbed into a living organism may modify one or more of its functions. The term is generally accepted for a substance taken for a therapeutic purpose, but is also commonly used for abused substances. drug A macrolide antibiotic used to treat potentially life-threatening fungal infections. amphotericin B A substance that kills or slows the growth of microorganisms, including bacteria, viruses, fungi and protozoans. antimicrobial agent An atom of an element that exhibits typical metallic properties, being typically shiny, with high electrical and thermal conductivity. metal atom nucleic acid A macromolecule made up of nucleotide units and hydrolysable into certain pyrimidine or purine bases (usually adenine, cytosine, guanine, thymine, uracil), D-ribose or 2-deoxy-D-ribose and phosphoric acid. nucleic acid ribonucleic acid High molecular weight, linear polymers, composed of nucleotides containing ribose and linked by phosphodiester bonds; RNA is central to the synthesis of proteins. ribonucleic acid macromolecule A macromolecule is a molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. polymer macromolecule An organic cation that consists of 4,4'-bipyridine bearing two N-methyl substituents loctated at the 1- and 1'-positions. paraquat An azole in which the five-membered heterocyclic aromatic skeleton contains three N atoms and two C atoms. triazoles An aminoquinoline that is quinoline which is substituted at position 4 by a [5-(diethylamino)pentan-2-yl]amino group at at position 7 by chlorine. It is used for the treatment of malaria, hepatic amoebiasis, lupus erythematosus, light-sensitive skin eruptions, and rheumatoid arthritis. chloroquine A member of the class of triazoles that is propan-2-ol substituted at position 1 and 3 by 1H-1,2,4-triazol-1-yl groups and at position 2 by a 2,4-difluorophenyl group. It is an antifungal drug used for the treatment of mucosal candidiasis and for systemic infections including systemic candidiasis, coccidioidomycosis, and cryptococcosis. fluconazole A semisynthetic cyclic hexapeptide echinocandin antibiotic which exerts its effect by inhibiting the synthesis of 1,3-beta-D-glucan, an integral component of the fungal cell wall. caspofungin A semisynthetic echinocandin anti-fungal drug. It is active against Aspergillus and Candida species and is used for the treatment of invasive candidiasis. anidulafungin A cyclic hexapeptide echinocandin antibiotic which exerts its effect by inhibiting the synthesis of 1,3-beta-D-glucan, an integral component of the fungal cell wall. It is used as the sodium salt for the treatment of invasive candidiasis, and of aspergillosis in patients who are intolerant of other therapy. micafungin An N-arylpiperazine that is cis-ketoconazole in which the imidazol-1-yl group is replaced by a 1,2,4-triazol-1-yl group and in which the actyl group attached to the piperazine moiety is replaced by a p-[(+-)1-sec-butyl-5-oxo-1,5-dihydro-4H-1,2,4-triazol-4-yl]phenyl group. A potent P-glycoprotein and CYP3A4 inhibitor, it is used as an antifungal drug for the treatment of various fungal infections, including aspergillosis, blastomycosis, candidiasis, chromoblastomycosis, coccidioidomycosis, cryptococcosis, histoplasmosis, and sporotrichosis. itraconazole A racemate composed of (+)-(11R,2'S)- and (-)-(11S,2'R)-enantiomers of mefloquine. An antimalarial agent which acts as a blood schizonticide; its mechanism of action is unknown. mefloquine An N-arylpiperazine that consists of piperazine carrying two 4-substituted phenyl groups at positions 1 and 4. A triazole antifungal drug. posaconazole An N-substituted diamine that is pentane-1,4-diamine substituted by a 6-methoxyquinolin-8-yl group at the N(4) position. It is a drug used in the treatment of malaria and Pneumocystis pneumonia. primaquine cell PMID:18089833.Cancer Res. 2007 Dec 15;67(24):12018-25. "...Epithelial cells were harvested from histologically confirmed adenocarcinomas .." A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane. cell cultured cell A cell in vitro that is or has been maintained or propagated as part of a cell culture. cultured cell A red blood cell. In mammals, mature erythrocytes are biconcave disks containing hemoglobin whose function is to transport oxygen. erythrocyte experimentally modified cell in vitro A cell in vitro that has undergone physical changes as a consequence of a deliberate and specific experimental procedure. experimentally modified cell in vitro white blood cell count respiration rate A disease that involving errors in metabolic processes of building or degradation of molecules. disease of metabolism A disease that is the consequence of the presence of pathogenic microbial agents, including pathogenic viruses, pathogenic bacteria, fungi, protozoa, multicellular parasites, and aberrant proteins known as prions. disease by infectious agent A fungal infectious disease that results_in infection of the keratinized layers located_in skin, located_in hair or located_in nail, which extends deeper into the epidermis, has_material_basis_in Fungi and results_in_formation_of skin lesions. cutaneous mycosis A nervous system disease which is located in a part of the nervous system responsible for processing sensory information that consists of sensory receptors, neural pathways, and parts of the brain involved in sensory perception. Commonly recognized sensory systems are those for vision, hearing, somatic sensation (touch), taste and olfaction (smell). sensory system disease A respiratory system disease which involves the lower respiratory tract. lower respiratory tract disease An opportunistic mycosis that has_material_basis_in Penicillium marneffei, results_in systemic infection and has_symptom fever, has_symptom anemia, has_symptom weight loss, has_symptom lymphadenopathy, has_symptom hepatosplenomegaly, has_symptom respiratory signs, and has_symptom skin lesions. penicilliosis A bacterial infectious disease that results_in infection by bacteria as a result of their presence or activity within the normal, healthy host, and their intrinsic virulence is, in part, a necessary consequence of their need to reproduce and spread. primary bacterial infectious disease A skin disease that is characterized by a rash that results from a variety of causes including bacteria, viruses, toxins, drugs and autoimmune disorders. exanthem An autoimmune hypersensitivity disease that is the abnormal functioning of the immune system that causes your immune system to produce antibodies or T cells against cells and/or tissues in the musculoskeletal system. autoimmune disease of musculoskeletal system An autoimmune hypersensitivity disease that is the abnormal functioning of the immune system that causes your immune system to produce antibodies or T cells against cells and/or tissues in the skin and connective tissue. autoimmune disease of skin and connective tissue A disease of metabolism that has _material_basis_in enzyme deficiency or accumulation of enzymes or toxins which interfere with normal function due to an endocrine organ disease, organ malfunction, inadequate intake, dietary deficiency, or malabsorption. acquired metabolic disease A cheilitis characterized by inflammation of one or both of the corners of the mouth. angular cheilitis An intestinal disease characterized by a protrusion of abdominal cavity contests through the inguinal canal. inguinal hernia A middle ear disease characterized by an inflammation of the mucosal lining of the mastoid antrum and the mastoid air cell system inside the mastoid process. mastoiditis A tooth disease characterized by a localized collection of pus associated with a tooth. dental abscess sensorineural hearing loss A viral infectious disease that results in inflammation located in salivary gland, has material basis in Mumps virus, which is transmitted by droplet spread of saliva or mucus from the mouth, nose, or throat of an infected person, or transmitted by contaminated fomites. The infection has symptom fever, has symptom headache, has symptom muscle aches, has symptom tiredness, has symptom loss of appetite, has symptom swollen and tender salivary glands under the ears or jaw on one or both sides of the face. mumps A parotid disease characterized by the inflammation of one or both parotid glands. parotitis An upper respiratory tract disease which involves inflammation of the tonsils resulting from bacterial (Group A streptococcus) and viral (Epstein-Barr virus, adenovirus) infections. Symptoms include a severe sore throat (which may be experienced as referred pain to the ears), painful/difficult swallowing, coughing, headache, myalgia (muscle aches), fever and chills. Tonsillitis is characterized by signs of red, swollen tonsils which may have a purulent exudative coating of white patches (i.e. pus). Swelling of the cheeks and neck may occur. tonsillitis An upper respiratory tract disease which involves inflammation of the mucous membranes of the nose, throat, eyes, and eustachian tubes with watery then purulent discharge. This is an acute contagious disease caused by rhinoviruses, human parainfluenza viruses, human respiratory syncytial virus, influenza viruses, adenoviruses, enteroviruses, or metapneumovirus. common cold A kidney disease characterized by the failure of the kidneys to adequately filter waste products from the blood. kidney failure A otitis which involves inflammation of the middle ear. otitis media salivary gland disease A viral infectious disease that results in infection located in mouth, has material basis in Human coxsackievirus A16, has material basis in Human enterovirus 71, has material basis in group B coxsackievirus, or has material basis in echoviruses, which are transmitted by ingestion of food contaminated with feces, transmitted by contact with pharyngeal secretions, or transmitted by droplet spread of oronasal secretions. The infection has symptom fever, has symptom sore throat, and has symptom lesions in the back area of the mouth, particularly the soft palate or tonsillar pillars. herpangina tooth disease A lung disease characterized by inadequate gas exchange by the respiratory system. respiratory failure A primary bacterial infectious disease that results in prolonged contraction of skeletal muscle fibers, has material basis in Clostridium tetani, which produces tetanospasmin, a neurotoxin, which is carried to the brain and spinal cord, where it binds irreversibly to receptors inhibiting neurotransmission. Damaged upper motor neurons cannot control reflex responses to afferent sensory stimuli. tetanus A respiratory failure that results from diffuse injury to the endothelium of the lung (as in sepsis, chest trauma, massive blood transfusion, aspiration of the gastric contents, or pneumonia) and is characterized by pulmonary edema with an abnormally high amount of protein in the edematous fluid and by difficult rapid breathing and hypoxemia. ICEMR protein array adult respiratory distress syndrome A lower respiratory tract disease that affects the airways leading into the lungs, which is caused due to inflammation of the bronchi and bronchioles, infection, or blockage. bronchial disease neutropenia marasmus A parasitic protozoa infectious disease characterized as a vector-borne infectious disease caused by the presence of protozoan parasites of the genus Plasmodium in the red blood cells, transmitted from an infected to an uninfected individual by the bite of anopheline mosquitoes, and characterized by periodic attacks of chills and fever that coincide with mass destruction of blood cells and the release of toxic substances by the parasite at the end of each reproductive cycle. malaria An intestinal infectious disease that involves inflammation of the intestines, especially colon, due to chemical irritants, bacteria, protozoa, or parasitic worms, which results in severe diarrhea with passage of mucus and blood. dysentery rectal disease A nail disease characterized by often-tender bacterial or fungal hand infection or foot infection due to either bacteria or fungus (Candida albicans) where the nail and skin meet at the side or the base of a finger or toe nail. The infection can start suddenly (acute paronychia) or gradually (chronic paronychia). Puss is usually present, along with gradual thickening and browning discoloration of the nail plate. paronychia A cystitis characterized by a sudden onset or severe symptoms. acute cystitis A gastrointestinal system disease described as the condition of having frequent loose or liquid bowel movements. Acute diarrhea is a common cause of death in developing countries and the second most common cause of infant deaths worldwide. The loss of fluids through diarrhea can cause severe dehydration which is one cause of death in diarrhea sufferers. Along with water, sufferers also lose dangerous amounts of important salts, electrolytes, and other nutrients. There are at least four types of diarrhea: secretory diarrhea, osmotic diarrhea, motility-related diarrhea, and inflammatory diarrhea. diarrhea A primary bacterial infectious disease that is a communicable systemic illness, has_material_basis_in Salmonella enterica subsp enterica serovar Typhi, which is transmitted_by ingestion of food or water contaminated with the feces of an infected person. The infection has_symptom fever, has_symptom diarrhea, has_symptom prostration, has_symptom headache, has_symptom splenomegaly, has_symptom liver enlargement, has_symptom eruption of rose-colored spots, and has_symptom leukopenia. typhoid fever A disease by infectious agent that is carried out by a parasite which by definition is a pathogen that simultaneously injures and derives sustenance from its host. parasitic infectious disease A malaria that involves neurologic damage resulting from blockage of the blood vessels, caused due to the infection of the red blood cells by Plasmodium species. ICEMR protein array cerebral malaria glossitis A sensory system disease that is located_in the eye or the adnexa of the eye. eye and adnexa disease A primary bacterial infectious disease that is described as an acute, diarrheal illness caused by infection of the intestine with the bacterium Vibrio cholerae, which is characterized by profuse watery diarrhea, vomiting, leg cramps, circulatory collapse and shock. cholera An opportunistic mycosis that involves fungal infection of the mouth, throat, skin, scalp, vagina, fingers, nails, bronchi, lungs, heart and brain by Candida species, of which Candida albicans is the most common. Systemic Candida infections are usually confined to severely immunocompromised persons. candidiasis A skin disease characterized by skin rash notable for pale red, raised and itchy bumps, located_in the upper dermis. urticaria A disease by infectious agent that results_in infection, has_material_basis_in Fungi, which pass the resistance barriers of the human or animal body. fungal infectious disease An autoimmune hypersensitivity disease that involves inflammation or pain in the muscles, joints, or fibrous tissue. rheumatic disease A disease of anatomical entity that located_in the respiratory system which extends from the nasal sinuses to the diaphragm. respiratory system disease A disease of anatomical entity that is located_in the integumentary system comprising the skin and its appendages. integumentary system disease lymphadenitis A disease of anatomical entity that occurs in the muscular and/or skeletal system. musculoskeletal system disease A disease of anatomical entity that is located_in kidney, ureter, bladder and urethra. urinary system disease A bowel dysfunction that is characterized by infrequent or difficult evacuation of feces. constipation dental caries carbuncle An upper respiratory tract disease involving inflammation of the throat or pharynx resulting from bacterial, viral, fungal infections or irritants like pollutants or chemical substances and smoking. The infection is often referred to as "sore throat". The symptoms include pain during swallowing, enlarged tonsils coated with a white discharge, runny nose, cough and slight fever. pharyngitis dyspepsia A gastrointestinal system infectious disease that involves inflammation of the lining of the stomach and small and large intestines, which is caused by viruses, bacteria, or parasites. Chemicals and drugs also cause gastroenteritis. The symptoms include diarrhea, loss of appetite, nausea, vomiting, cramps, and discomfort in the abdomen. gastroenteritis A hematopoietic system disease that is characterized by a decrease in the normal number of red blood cells. anemia A systemic mycosis that results_in fungal infection located_in human body of immunocompromised individuals, has_material_basis_in Fungi. The organisms invade via the respiratory tract, alimentary tract, or intravascular devices. opportunistic mycosis An endocrine system disease that is located_in the pancreas. pancreas disease A skin disease characterized by itchy, erythematous, vesicular, weeping and crusting patches of skin. dermatitis auditory system disease A parasitic infectious disease that is caused by parasitic protozoa which are microorganisms classified as unicellular eukaryotes. parasitic protozoa infectious disease A bronchial disease that is characterized by chronic inflammation and narrowing of the airways, which is caused by a combination of environmental and genetic factors. The disease has_symptom recurring periods of wheezing (a whistling sound while breathing), has_symptom chest tightness, has_symptom shortness of breath, has_symptom mucus production and has_symptom coughing. The symptoms appear due to a variety of triggers such as allergens, irritants, respiratory infections, weather changes, exercise, stress, reflux disease, medications, foods and emotional anxiety. asthma A disease of anatomical entity that is located_in the immune system. immune system disease A lung disease that is an inflammation of the bronchioles, the smallest air passages of the lungs. It is caused by viruses and bacteria. The disease has_symptom cough, has_symptom wheezing, has_symptom shortness of breath, has_symptom fever, has_symptom nasal flaring in infants and has_symptom bluish skin due to lack of oxygen. bronchiolitis gingivitis anus disease A bone disease that results_in inflammation of the located_in bone. bone inflammation disease periodontal disease A skin disease where there is a diffuse infection of connective tissue with severe inflammation of dermal and subcutaneous layers of the skin. Cellulitis can be caused by normal skin flora or by exogenous bacteria, and often occurs where the skin has previously been broken: cracks in the skin, cuts, blisters, burns, insect bites, surgical wounds, or sites of intravenous catheter insertion. cellulitis An integumentary system disease that is located_in skin. skin disease A disease is a disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism. disease A gastrointestinal system disease that is located_in the mouth. mouth disease Pyoderma is a skin infectious disease where the infection is pyogenic causing the formation of pus. pyoderma A dermatophytosis that results_in contagious fungal infection located_in scalp, located_in hair of head, located_in eyebrow or located_in eyelash, has_material_basis_in Ascomycota fungi that belong to a group called dermatophytes and has_symptom itching of the scalp, has_symptom pus filled lesions on the scalp, and has_symptom patches of hair loss, sometimes with a 'black dot' pattern. tinea capitis folliculitis A rhinitis that is an allergic inflammation and irritation of the nasal airways involving sneezing, runny nose, nasal congestion, itching and tearing of the eyes caused by exposure to an allergen such as pollen, dust, mold, animal dander and droppings of cockroaches or house dust mites. allergic rhinitis pancreatitis middle ear disease A gastrointestinal system disease that is located_in the intestine. intestinal disease dental pulp disease A lung disease that involves lung parenchyma or alveolar inflammation and abnormal alveolar filling with fluid (consolidation and exudation). It results from a variety of causes including infection with bacteria, viruses, fungi or parasites, and chemical or physical injury to the lungs. It is accompanied by fever, chills, cough, and difficulty in breathing. pneumonia An eye and adnexa disease that is located_in the eye. eye disease A conjunctival disease characterized by an inflammation of the conjunctiva, the outermost layer of the eye and the inner surface of the eyelids. conjunctivitis An arthritis that is an autoimmune disease which develops due to an infection located elsewhere in the body. reactive arthritis A musculoskeletal system disease that affects tissues such as skin, tendons, and cartilage. connective tissue disease A disease that manifests in a defined anatomical structure. disease of anatomical entity A disease of anatomical entity that has_material_basis_in hematopoietic cells. hematopoietic system disease peptic ulcer disease A disease of anatomical entity that is located_in the gastrointestinal tract. gastrointestinal system disease periodontitis A mite infestation that is a contagious ectoparasite skin infection caused by human itch mite Sarcoptes scabiei type hominis, which burrows into the upper layer of the skin but never below the stratum corneum causing severe itching and a rash found on the hands, folds of the wrist, elbow or knee, penis, breast, and shoulder blades. scabies A bone inflammation disease that involves a response to irritation or injury, characterized by joint pain, swelling, stiffness located_in joint and/or redness located_in skin over the joint. arthritis A lower respiratory tract disease in which the function of the lungs is adversely affected by narrowing or blockage of the airways resulting in poor air flow, a loss of elasticity in the lungs that produces a decrease in the total volume of air that the lungs are able to hold, and clotting, scarring, or inflammation of the blood vessels that affect the ability of the lungs to take up oxygen and to release carbon dioxide. lung disease A pyoderma consisting of three forms of skin lesions having either a thick, adherent, recurrent, dirty yellow crust with an erythematous margin (common or superficial impetigo) or lessions which are superficial, thin-walled, and bullous as found in bullous impetigo. The lesions in bullous (staphylococcal) impetigo, which are always caused by S aureus, are superficial, thin-walled, and bullous. impetigo An autoimmune disease of skin and connective tissue characterized by large blisters. bullous pemphigoid A viral infectious disease that results_in infection located_in nerve fiber, has_material_basis_in Human herpesvirus 3, which reactivates after appearing as chickenpox in childhood. The virus is transmitted_by direct contact with the rash, which can develop into chickenpox in newly-infected individuals. The infection has_symptom rash which is followed by blisters, has_symptom headache, has_symptom fever, has_symptom malaise, has_symptom itching, has_symptom burning pain, and has_symptom paresthesia. herpes zoster A viral infectious disease that results_in_formation_of lesions, located_in mouth, located_in face, located_in genitalia, or located_in hands, has_material_basis_in Human herpesvirus 1 or has_material_basis_in Human herpesvirus 2, which are transmitted_by direct contact with an active lesion or body fluid of an infected person. herpes simplex A viral infectious disease that results_in infection located_in skin, has_material_basis_in Measles virus, which is transmitted_by contact with oronasal secretions, or semen of an infected person. The infection has_symptom fever, has_symptom cough, has_symptom coryza, has_symptom conjunctivitis, and has_symptom maculopapular, erythematous rash. measles A disease of anatomical entity that is located_in the central nervous system or located_in the peripheral nervous system. nervous system disease A viral infectious disease that results_in infection located_in skin, has_material_basis_in Human herpesvirus 3, which is transmitted_by direct contact with secretions from the rash, or transmitted_by droplet spread of respiratory secretions. The infection has_symptom anorexia, has_symptom myalgia, has_symptom nausea, has_symptom fever, has_symptom headache, has_symptom sore throat, and has_symptom blisters. chickenpox viral exanthem pyomyositis A parasitic infectious disease that occurs when part of the body is infested with parasitic worms such as cestodes, nematodes and trematodes. parasitic helminthiasis infectious disease A parasitic protozoa infectious disease that involves infection caused by protozoan parasite of the genus Leishmania, which is transmitted by the bite of sand fly (subfamily Phlebotominae). leishmaniasis A leishmaniasis that involves skin infection caused by Leishmania species, resulting in one or more cutaneous lesions. cutaneous leishmaniasis A leishmaniasis that is the most severe form of the disease caused by protozoan parasites of the Leishmania genus, resulting in the infection of the internal organs such as liver, spleen and bone marrow. The symptoms include fever, weight loss, and an enlarged spleen and liver. visceral leishmaniasis A parasitic protozoa infectious disease that involves infection caused by the amoeba Entamoeba histolytica. Amebic invasion of the intestinal lining causes dysentery, colitis or diarrhea. The infection can also spread through the blood to the liver and, rarely, to the lungs, brain or other organs. amebiasis rectal prolapse A disease by infectious agent that results in infection, has material basis in Viruses. viral infectious disease keratoconjunctivitis An external ear disease that involves inflammation of the outer ear and ear canal. It can be caused by active bacterial or fungal infections. otitis externa A central nervous system disease that is characterized by an inflammation of the pia-arachnoid meninges. It can be caused by growth of bacteria, fungi, or parasites within the subarachnoid space or by the growth of bacteria or viruses within the meningeal or ependymal cells. meningitis A stomatitis characterized by the repeated formation of benign and non-contagious mouth ulcers. aphthous stomatitis A respiratory system disease which involves the upper respiratory tract. upper respiratory tract disease Hordeolum is a sequelae of infectious and parasitic disease consisting of an infection of the sebaceous glands at the base of the eyelashes. Styes are generally caused by a Staphylococcus aureus bacterial infection. hordeolum A glucose metabolism disease that is characterized by abnormally low levels of blood glucose. ICEMR protein array hypoglycemia the role of a material entity to prevent, diagnose, treat, or study disease and/or its effects clinical drug role a material entity (1) containing at least one scattered molecular aggregate as part that is the bearer of an active ingredient role and (2) that is itself the bearer of a clinical drug role drug product artemether lumefantrine A drug product in solution form for injection that has the chemical ingredient chloroquine and used in the treatment or prevention of malaria. chloroquine injection Chloroquine Injectable Solution A drug product in tablet form for oral administration that has the chemical ingredient chloroquine and used in the treatment or prevention of malaria. chloroquine tablets Chloroquine Oral Tablet geographic feature An anthropogenic geographic feature is a geographic feature resulting from the influence of human beings on nature. An anthropogenic geographic feature is a geographic feature'resulting from the influence of human beings on nature. anthropogenic geographic feature A geographical feature associated with water. hydrographic feature Artificial watercourse with no flow or a controlled flow used for navigation, drainage or irrigation. canal A large expanse of saline water usually connected with an ocean. sea A body of water or other liquid of considerable size contained in a depression on a landmass. lake A stream which, through permanent or seasonal flow processes, moves from elevated land towards lower elevations through a definite channel and empties either into a sea, lake, or another river or ends on land as bed seepage and evapotranspiration exceed water supply. river Linear body of water flowing on the Earth's surface. stream An artificial body of water, often contained by a dam, constructed for the purpose of water storage. reservoir A point where groundwater or steam flows out of the ground, and is thus where the aquifer surface meets the ground surface or where there is a fissure. spring A flowing body of water. watercourse A body of water, usually of smaller size than a lake. pond A wetland ecosystem which includes communities of grasses, rushes, reeds, typhas, sedges, and other herbaceous plants (possibly with low-growing woody plants). marsh A spring that is produced by the emergence of geothermally-heated groundwater from the Earth's crust. hot spring A pond or lake used for the artificial culture of fish. fishpond An accumulation of water of varying size. water body Naturally formed, subterranean open area or chamber. cave A feature that has been constructed by deliberate human effort. construction A permanent walled and roofed construction. building An area of land which is used for the cultivation of crops or grazing of livestock, including any agricultural constructions therein. farm A landform that extends above the surrounding terrain in a limited area. A mountain is generally steeper than a hill, but there is no universally accepted standard definition for the height of a mountain or a hill although a mountain usually has an identifiable summit and a local relief of more than 300m. mountain Area of dry or relatively dry land surrounded by water or low wetland. island An area with a high density of trees. A small forest may be called a wood. forested area A landform elevated above the surrounding area. elevation An elevated and comparatively level expanse of land. plateau A part of an astronomical body which is primarily composed of a continuous volume of solid material, shaped by one or more environmental processes. solid landform A wetland ecosystem in which land mass is permanently inundated by shallow bodies of water, generally with a substantial number of hummocks, or dry-land protrusions. swamp ecosystem A paddy field for the cultivation of rice. rice field A speleothem projecting vertically upwards from a cave floor and formed by precipitation from drips. stalagmite A lake purposefully constructed. artificial lake A biome is an ecosystem to which resident ecological communities have evolved adaptations. biome A reservoir constructed for the purpose of providing drinking water. drinking water reservoir The line of contact between a body of water and the land. shoreline The portion of the ground surface which lies below water. bed Incorporated populated place. city A rock is a naturally occurring solid aggregate of one or more minerals or mineraloids. rock Soil is an environmental material which is primarily composed of minerals, varying proportions of sand, silt, and clay, organic material such as humus, gases, liquids, and a broad range of resident micro- and macroorganisms. soil Water that has been adversely affected in quality by anthropogenic influence. waste water An excreta material which is composed primarily of feces, an excreta consisting of waste products expelled from an animal's digestive tract through the anus (or cloaca) during defecation. fecal material An environmental material primarily composed of dihydrogen oxide in its liquid form. water Sediment is an environmental substance comprised of any particulate matter that can be transported by fluid flow and which eventually is deposited as a layer of solid particles on the bedor bottom of a body of water or other liquid. sediment Minute solid particles with diameters less than 500 micrometers. Occurs in and may be deposited from, the atmosphere. dust Water which contains a significant concentration of dissolved salts. saline water Water which has a low concentration of dissolved solutes, particularly that of sodium chloride. fresh water Wastewater that is contaminated with feces or urine, sewage A complex aggregation of microorganisms marked by the excretion of a protective and adhesive matrix; usually adhering to a substratum. biofilm wood Water that is found on the surface of an astronomical object. surface water wastewater treatment plant The residual semi-solid material left from domestic or industrial processes, or wastewater treatment processes. sludge beach sand The aerobically decomposed remnants of organic materials. compost A hospital is a building in which health care services are provided by specialized staff and equipment. hospital pond water A portion of soil which is found in a forested area. forest soil A material which is not the desired output of a process and which is typically the input of a process which removes it from its producer (e.g. a disposal process). waste material A material entity which determines an environmental system. environmental feature Drinking water is water which may be consumed by humans with no adverse effects on their health. Water that is safe enough to be consumed by humans or used with low risk of immediate or long term harm. http://en.wikipedia.org/wiki/Drinking_water drinking water A material entity that has been processed by humans or their technology in any way, including intermediate products as well as final products. manufactured product tap water bore hole water A portion of soil which is part of a cropland or a rangeland biome. farm soil A portion of soil which is found in a grassland. grassland soil Soil in which trees from an orchard grow. orchard soil Soil which is found in a pasture and in which vegetation, such as the grass used for the grazing of ungulates, grows. pasture soil The narrow region of soil that is directly influenced by root secretions and associated soil microorganisms. rhizosphere environmental material A portion of environmental material is a fiat object part which forms the medium or part of the medium of an environmental system. A portion of environmental material is a fiat object which forms the medium or part of the medium of an environmental system. Material in or on which organisms may live. Environmental Material CS20 NIAID GSCID-BRC environmental material Airborne solid particles (also called dust or particulate matter (PM)) or liquid droplets. aerosol Anthropogenic material in or on which organisms may live. anthropogenic environmental material agricultural environmental material A liquid or semi-liquid mixture of water and some combination of soil, silt, and clay. mud water well A naturally occurring granular material composed of finely divided rock and mineral particles. sand Environmental material derived from living organisms. organic material A system which has the disposition to environ one or more material entities. environmental system A site which has its extent determined by the presence or influence of one or more components of an environmental system or the processes occurring therein. environmental zone Concrete is a composite material composed of an aggregate bonded together with a fluid cement which hardens over time. concrete A roof is the covering on the uppermost part of a building which provides protection from animals and weather, notably rain, but also heat, wind and sunlight. A roof is also the framing or structure which supports the covering roof building roof Thatch is material composed of dry vegetation such as straw, water reed, sedge (Cladium mariscus), rushes, or heather. thatch A brick is a masonry unit which is composed of kneaded clay-bearing soil, expanded clay aggregate, sand and lime, or concrete material, fire-hardened or air-dried. brick A tile is a manufactured piece of hard-wearing material such as ceramic, stone, metal, or even glass, generally used for covering roofs, floors, walls, showers, or other objects such as tabletops. Alternatively, tile can sometimes refer to similar units made from lightweight materials such as perlite, wood, and mineral wool, typically used for wall and ceiling applications. tile A fixture which is used primarily for the collection and, in some cases, disposal of human urine and feces. toilet fixture A pit latrine is a latrine which is constructed by digging a hole in the ground. pit latrine A toilet fixture which uses water to flush liquid and solid excreta into a sewage containment or processing facility through a drainpipe. flush toilet fixture A ventilated improved pit latrine is a pit latrine which includes a vent pipe fitted to the pit with a flyscreen covering the pipe's outlet. Air currents moving across the outlet of the vent pipe create a vaccum which draws odors out of the latrine's superstructure. ventilated improved pit latrine A covered pit latrine is a building which comprises a pit latrine sheltered by an outhouse. covered pit latrine A covered pit latrine with slab is a building which comprises a pit latrine with a slab floor sheltered by an outhouse. covered pit latrine with slab floor A composting toilet fixture is a dry toilet fixture in which managed, aerobic decomposition converts human excreta into organic matter suitable for the fertilisation or amendment of soils. composting toilet Charcoal is a light, black residue, consisting of carbon and any remaining ash, obtained by removing water and other volatile constituents from animal and vegetation substances. Charcoal is usually produced by slow pyrolysis, the heating of wood or other substances in the absence of oxygen. charcoal A flat-wick lamp is a simple type of paraffin lamp, which burns paraffin drawn up through a wick by capillary action. flat-wick lamp A paraffin lantern is a lantern which houses a parrafin lamp in a structure of soldered or crimped-together sheet metal stampings and glass or other translucent material. paraffin lantern An electric lamp is a lamp which produces light from electricity. electric lamp A battery-powered electric lamp is an electric lamp which draws its power from a device composed of two or more electrochemical cells that convert stored chemical energy into electrical energy. battery-powered electric lamp A candle is a lamp composed of a wax within which an ignitable wick is embedded. candle A device capable of receiving and/or transmitting information encoded in electromagnetic radiation through wave modulation. radio device A cassette deck is a device capable of playing and recording audio compact cassettes. cassette player A television set is a device that combines a tuner, display, and loudspeakers for the purpose of converting digital or analog information signals into moving images and sound. television set A telephone is a telecommunications device which converts sound into electronic signals suitable for transmission via cables or other transmission media, and reconverts such signals into sound waves. telephone A mobile phone is a telephone which transmits sound information to a mobile phone network via radio transmissions. mobile phone A landline telephone is a telephone which is connected to a telephone network with wires through which electronic signals are carried. landline telephone A refrigerator is a device which consists of a thermally insulated compartment and a mechanical, chemical, or electronic heat pump that transfers heat from the inside of the fridge to its external environment such that the inside of the fridge is cooled to a temperature below the ambient temperature of the room refrigerator A table is a form of furniture with a flat horizontal upper surface used to support objects, for storage, show, and/or manipulation. table A chair is a piece of furniture with a raised surface commonly used to seat a single person. chair A piece of furniture is a movable object intended to support various human activities such as seating (e.g., chairs, stools and sofas) and sleeping (e.g., beds). piece of furniture A sofa is a bench which is partially or entirely upholstered, and often fitted with springs and tailored cushions. sofa A cabinet is a roughly cuboidal piece of furniture which is used to store miscellaneous items in compartments accessible through doors or drawers. cabinet A cupboard is a cabinet which is used indoors to store household objects such as food, crockery, textiles and liquor, and to protect them from dust and dirt cupboard A clock is an instrument which may indicate, keep, and/or co-ordinate time. clock A pressure lamp is a portable paraffin or oil lamp in which fuel is forced up into the mantle or burner by air pressure in the reservoir, which can be increased by pumping with a plunger. pressure lamp A spring which emits fresh water. freshwater spring river water A motor vehicle is a vehicle which is propelled by an engine or motor and that does not operate on rails. motor vehicle A water truck is a truck which transports water. water truck A vehicle is a mobile machine which transports people or cargo. vehicle A bicycle is a human-powered, pedal-driven, single-track vehicle, having two wheels attached to a frame, one behind the other. bicycle A motorcycle is a two- or three-wheeled motor vehicle. motorcycle A lentic water body is a water body in which the accumulated water, in its totality, has very little to no directed flow. lentic water body A self-contained constructed feature used by one or more households as a home, such as a house, apartment, mobile home, houseboat or other 'substantial' structure. A dwelling typically includes nearby outbuildings, sheds etc. within the curtilage of the property, excluding any 'open fields beyond'. It has significance in relation to search and seizure, conveyancing of real property, burglary, trespass, and land use planning. human dwelling A material part of an astronomical body. astronomical body part An environmental material which is in a solid state. solid environmental material An environmental system which includes both living and non-living components. ecosystem An environmental zone which is bounded by material parts of a land mass or the atmosphere or space adjacent to it. terrestrial environmental zone A terrestrial ecosystem which is inundated or saturated by surface or ground water at a frequency and duration sufficient to support, and that under normal circumstances does support, a prevalence of vegetation typically adapted for life in saturated soil conditions. wetland ecosystem A bodily fluid material which is composed primarily of excreta, bodily fluids consisting of matter which contains the waste products of biological processes, including urine or feces, discharged from an organism's body. excreta material A relationship between persons related as members of a domestic group, or a number of domestic groups linked through descent from a common ancestor, marriage, or adoption family relationship A material entity used to build a dwelling or part of a dwelling. Person: Jie Zheng, Chris Stoeckert Penn Group PRISM building material A material entity for accommodation, such as a building, part of a building, caravan, houseboat or other mobile home. A tent is not normally considered to be substantial. false Person: Jie Zheng, Chris Stoeckert Penn Group http://en.wikipedia.org/wiki/Dwelling PRISM obsolete_dwelling true A building material used in the construction of a roof. Person: Jie Zheng, Chris Stoeckert Penn Group PRISM roof material deprecated in favor of ENVO_01000472 'building roof' obsolete_roof true A building material used in the construction of a floor Person: Jie Zheng, Chris Stoeckert Penn Group PRISM floor material A building material used in the construction of a wall. Person: Jie Zheng, Chris Stoeckert Penn Group PRISM wall material A processed material shaped a small rectangular block typically made of clay mixed with sand and fired in a kiln or baked by the sun, used in building wall construction. http://www.thefreedictionary.com/brick wall brick was ICEMR PRISM household, no longer used obsolete_traditional house true was ICEMR household, no longer used obsolete_modern house true A data item of a household's cumulative living standard represented in a numerical datum. The wealth index is calculated using easy-to-collect data on a household's ownership of selected assets, such as televisions and bicycles; materials used for housing construction; and types of water access and sanitation facilities. Person: Jie Zheng, Chris Stoeckert Penn Group http://dhsprogram.com/topics/Wealth-Index.cfm PRISM numerical household wealth index A processed material that is the bottom edge of a roof. The primary function of the eaves is to keep rain water off the walls and to prevent the ingress of water at the junction where the roof meets the wall. The secondary function is to control solar penetration; the eaves overhang can be designed to adjust the building's solar heat gain to suit the local climate, the latitude and orientation of the building, refer to passive solar building design. The eaves overhang may also shelter openings to ventilate the roof space. Person: Jie Zheng, Chris Stoeckert Penn Group http://en.wikipedia.org/wiki/Eaves PRISM eaves was ICEMR PRISM, no longer used obsolete_open eaves true was ICEMR PRISM household, no longer used obsolete_closed eaves true A brick with holes which is embedded in a wall to allow ventilation through it. Person: Jie Zheng, Chris Stoeckert Penn Group http://en.wiktionary.org/wiki/air_brick PRISM air brick A scalar measurements datum of resident in a dwelling. Person: Jie Zheng, Chris Stoeckert Penn Group PRISM number of residents in a dwelling An information content entity to indicate whether a household has electricity in a dwelling. Person: Jie Zheng, Chris Stoeckert Penn Group PRISM household having electricity information A material entity that consists of fuel mainly used for cooking. Person: Jie Zheng, Chris Stoeckert PRISM Penn Group PRISM cooking fuel material A material entity that consists of an energy source for lighting. Person: Jie Zheng, Chris Stoeckert PRISM Penn Group PRISM obsolete_lighting material true number of rooms in a dwelling that are used for sleeping. Person: Jie Zheng, Chris Stoeckert number of bedrooms in a dwelling PRISM Penn Group PRISM number of rooms for sleeping in a dwelling land area measured in acres: a scalar measurement datum of land measured in acres that may be of a particular type such as land owned by a household. Person: Jie Zheng, Chris Stoeckert Penn Group Person: Chris Stoeckert PRISM land area measured in acres A scalar measurement datum of meals per day in a household Person: Jie Zheng, Chris Stoeckert PRISM Penn Group PRISM number of meals per day A scalar measurement datum of days eating meat in a week in a household Person: Jie Zheng, Chris Stoeckert PRISM Penn Group PRISM number of days eating meat in a week how often problems satisfying food needs in a household Person: Jie Zheng, Chris Stoeckert PRISM Penn Group PRISM frequency of not satisfying food needs A length measurement datum of the distance in kilometers to from a dwelling to the nearest health facility. Person: Jie Zheng, Chris Stoeckert Penn Group Person: Chris Stoeckert PRISM distance to health facility in km replaced by EFO_0004950: date of birth ICEMR protein array obsolete_date of birth true A genotype information which is about the presence of certain genetic variants of glucose-6-phosphate dehydrogenase. Person: Jie Zheng, Chris Stoeckert Penn Group PRISM glucose 6 phosphate dehydrogenase genotype A genotype information which is about the presence and degree of alpha-thalassemia, a form of thalassemia involving the number of functional HBA1 and HBA2 genes. Person: Jie Zheng, Chris Stoeckert Penn Group PRISM alpha thalassemia genotype A genotype information which is about the presence of sickle-cell hemoglobin (HbS), an abnormal form of hemoglobin which is the oxygen-carrying protein within the red blood cells. Person: Jie Zheng, Chris Stoeckert Penn Group PRISM sickle hemoglobin genotype a diagnosis that is an assertion that a patient, who is the subject of a diagnostic process, has malaria Person: John Judkins diagnosis of malaria A phenotypic abnormality of the presence of bacteria in the blood. http://en.wikipedia.org/wiki/Bacteremia presence of bacteria in the blood A diagnosis of malaria without evidence of complicated malaria. Person: Jie Zheng, Chris Stoeckert, Grant Dorsey Grant Dorsey PRISM diagnosis of uncomplicated malaria A phenotypic abnormality of the presence of a virus in the blood. It is a medical condition where viruses enter the bloodstream and hence have access to the rest of the body. http://en.wikipedia.org/wiki/Viremia presence of virus in the blood A diagnosis of malaria with the presence of any danger signs including inability to sit up or stand, vomiting everything, unable to breastfeed or drink and lethargy or meeting criteria for severe malaria. Person: Jie Zheng, Chris Stoeckert, Grant Dorsey Grant Dorsey PRISM diagnosis of complicated malaria was ICEMR PRISM observation, no longer used obsolete_diagnosis of complicated malaria with high parasite density true A diagnosis of complicated malaria with signs and symptoms, such as inability to sit up or stand, vomiting everything, unable to breastfeed or drink, lethargy, which are not listed as WHO criteria used to diagnose severe malaria. Person: Jie Zheng, Chris Stoeckert, Grant Dorsey Grant Dorsey PRISM diagnoses of complicated malaria with danger signs A diagnosis of complicated malaria based on WHO criteria that include the presence of parasite infections, most commonly P.falciparum, and any one or more of symptoms/signs of serious organ failures or abnormalities, including cerebral malaria, severe anemia, generalized convulsions, hypoglycemia, respiratory distress, fluid and electrolyte disturbances, acute renal failure, ARDS, circulatory collapse, abnormal bleeding, and Jaundice. Person: Jie Zheng, Chris Stoeckert, Grant Dorsey Grant Dorsey PRISM diagnosis of severe malaria a malaria characterized by serious organ failures or abnormalities including cerebral malaria, severe anemia, generalized convulsions, hypoglycemia, respiratory distress, fluid and electrolyte disturbances, acute renal failure, ARDS, circulatory collapse, abnormal bleeding, and jaundice. Person: John Judkins severe malaria A symptom or sign that is used for the diagnosis of severe malaria based on World Health Organization (WHO) criteria. Person: Jie Zheng, Chris Stoeckert Penn Group PRISM severe malaria symptom or sign A scalar measurement datum about the level of hemoglobin in the blood with a value in units of g/dl. Person: Jie Zheng, Chris Stoeckert Penn Group PRISM ICEMR protein array hemoglobin level in g per dL A categorical measurement datum that indicates the presence of asexual parasites in blood cells by microscopy using a value of positive or negative. Person: Jie Zheng, Chris Stoeckert asexual parasites present by microscopy Penn Group PRISM ICEMR protein array blood smear reading as positive or negative A planned process in which a patient is seen by a medical practitioner. Person: Jie Zheng, Chris Stoeckert Penn Group PRISM clinical visit A clinical visit that is primarily for a regular examination. Person: Jie Zheng, Chris Stoeckert Penn Group PRISM routine clinical visit a human being who bears a participant under investigation role Person: John Judkins human study subject human participant under investigation A material entity whichis part of a dwelling for providing fresh air to the dwelling. Person: Jie Zheng, Chris Stoeckert Penn Group PRISM dwelling ventilation A geographical location which is part of Uganda. Person: Jie Zheng, Chris Stoeckert Penn Group PRISM subcounty in Uganda was ICEMR PRISM, no longer used obsolete_CDC light trap assay true A role borne by some material entity which can be delivered/administrated into some organisms and the role is realized during clinical treatment process aiming to treat symptoms, signs or diagnosed disease. Person: Jie Zheng, Chris Stoeckert Penn Group medication role quinine used in malaria medication blood used in transfusion for replacement blood lost during surgery or due to a serious injury. A material entity that is bearer of a medication role. replaced by OBIB_0000029:medication material Person: Jie Zheng, Chris Stoeckert Penn Group obsolete_medication material true A medication material intended to prevent or treat malaria. Person: Jie Zheng, Chris Stoeckert Penn Group malaria medication A medication material intended to prevent or treat a disease other than malaria. Person: Jie Zheng, Chris Stoeckert Penn Group non-malaria medication A drug product that has the chemical ingredient quinine and has antipyretic (fever-reducing), antimalarial, analgesic (painkilling), and anti-inflammatory properties. Person: Jie Zheng, Chris Stoeckert quinine PRISM http://en.wikipedia.org/wiki/Quinine quinine drug product A drug product that is the of combination artemether/lumefantrine (trade names Coartem and Riamet, Falcynate-LF). It is generally used for the treatment of acute uncomplicated Plasmodium falciparum malaria. Person: Jie Zheng, Chris Stoeckert artemether-lumefantrine coartem PRISM http://en.wikipedia.org/wiki/Artemether/lumefantrine artemether-lumefantrine drug product A dependent continuant which is either disease or phenotypic abnormality. clinical characteristics An information content entity is about household. Person: Jie Zheng, Chris Stoeckert Penn Group PRISM household information A diagnosis of uncomplicated malaria that occurs with the first trimester of pregnancy. Person: Jie Zheng, Chris Stoeckert Penn Group PRISM diagnosis of uncomplicated malaria in the 1st trimester of pregnancy A diagnosis based on presence of asexual parasites by microscopy in the absence of subjective fever or documented elevated temperature Person: Jie Zheng, Chris Stoeckert, Grant Dorsey Penn Group PRISM diagnosis of asymptomatic microscopic parasitemia A diagnosis of malaria based on positive blood smear with subjective fever or elevated temperature resulting in antimalarial treatment. Person: Jie Zheng, Chris Stoeckert, Grant Dorsey Penn Group PRISM diagnosis of symptomatic malaria A time measurement datum that specifies the date of a clinical visit. Person: Jie Zheng, Chris Stoeckert Penn Group PRISM clinical visit date A scalar measurement datum that is the number of asexual parasites per ul in a specimen using microscopy. Person: Jie Zheng, Chris Stoeckert Penn Group PRISM asexual parasite density in count per ul by microscope An information content entity about dwelling. Person: Jie Zheng, Chris Stoeckert Penn Group PRISM dwelling information A symbol that denotes a specific household. Person: Jie Zheng, Chris Stoeckert Penn Group PRISM household identifier A symbol that denotes a specific human participant under investigation. Person: Jie Zheng, Chris Stoeckert Penn Group PRISM ICEMR protein array human study subject identifier An information content entity which is about features of a human participant under investigation. Person: Jie Zheng, Chris Stoeckert Penn Group PRISM ICEMR protein array study participant information elevated temperature or subjective fever Person: Jie Zheng, Chris Stoeckert Penn Group PRISM ICEMR protein array febrile A function to provide fresh air to a closed space. ventilation function A material entity in a dwelling that is designed, built, installed, selected, etc., to serve a specific function affording a convenience or service to people who are living in the dwelling. Person: Jie Zheng, Chris Stoeckert Penn Group PRISM dwelling facility A phenotypic abnormality of a subjective fever as reported by the study participant or their parent/guardian Person: Jie Zheng, Chris Stoeckert, Grant Dorsey Grant Dorsey PRISM subjective fever a febrile quality of an abnormally high temperature Person: John Judkins elevated temperature A scalar measurement datum that is about temperature. temperature measurement datum was in ICEMR, no longer used A ventilation function to provide fresh air to a dwelling. obsolete_dwelling ventilation function true an organism that is the bearer of a partipant under investigation role Person: John Judkins study subject participant under investigation A role that inheres in a material entity that is realized in a building process in which the material entity will become part of a structure with a roof and walls standing more or less permanently in one place. Person: Jie Zheng, Chris Stoeckert Penn Group building material role A building material role that inheres in a material entity that is realized in a building process in which the material entity will become part of a roof. Person: Jie Zheng, Chris Stoeckert Penn Group roof material role A building material role that inheres in a material entity that is realized in a building process in which the material entity will become part of a wall. Person: Jie Zheng, Chris Stoeckert Penn Group wall material role A building material role that inheres in a material entity that is realized in a building process in which the material entity will become part of a floor. Person: Jie Zheng, Chris Stoeckert Penn Group floor material role A role that inheres in a material entity that is realized in a process that provides a convenience or service to people who are living in a dwelling. dwelling facility role A temperature measurement datum that is about an organism. Person: Jie Zheng, Chris Stoeckert Penn Group PRISM blood smear reading as positive or negative organismal body temperature measurement datum A processed material shaped a small rectangular block typically made of clay mixed with sand and fired in a kiln or baked by the sun, used in building floor construction. http://www.thefreedictionary.com/brick floor brick An age since birth measurement datum at the time of a clinical visit. Person: Jie Zheng, Chris Stoeckert, Shon cade, Grant Dorsey Penn Group PRISM ICEMR protein array age since birth at time of visit An average value of asexual parasites counted per microliter of blood (i.e. malaria parasite density) across mulitiple clinical visits of a participant who was diagnosed with asymptomatic microscopic parasitemia. Person: Jie Zheng, Chris Stoeckert, Shon cade, Grant Dorsey Penn Group PRISM average asexual parasite density of a participant with asymptomatic microscopic parasitemia An average value of asexual parasites counted per microliter of blood (i.e. malaria parasite density) across mulitiple clinical visits of a participant who was diagnosed with malaria. Person: Jie Zheng, Chris Stoeckert, Shon cade, Grant Dorsey Penn Group PRISM average asexual parasite density of a participant with malaria An average value of female Anopheles mosquitoes collected across multiple collections (e.g. from one or more households on a number of nights). Person: Jie Zheng, Chris Stoeckert, Shon cade, Grant Dorsey Penn Group PRISM average number of female Anopheles per night An average value of Anopheles mosquitoes tested for sporozoites across multiple collections (e.g. from a given household across CDC light trap collections) in a given period. Person: Jie Zheng, Chris Stoeckert, Shon cade, Grant Dorsey Penn Group PRISM average number of female Anopheles tested for sporozoite An average value of sporozoite positive female Anopheles mosquitoes across multiple collections (e.g. from a given household over a number of nights of collections). Person: Jie Zheng, Chris Stoeckert, Shon cade, Grant Dorsey Penn Group PRISM average number of sporozoite-positive female Anopheles An average precentage value of female Anopheles mosquitoes tested as sporozoites-positive in all female mosquitoes tested for sporozoites across multiple collections. Person: Jie Zheng, Chris Stoeckert, Shon cade, Grant Dorsey Penn Group PRISM average percent of female Anopheles with Plasmodium sporozoites An age since birth measurement datum at the time of subject enrollment. Person: Jie Zheng Penn Group PRISM age since birth at time of enrollment A data item of the total number of clinical visits by a participant in an investigation. Person: Jie Zheng, Chris Stoeckert, Shon cade, Grant Dorsey Penn Group PRISM number of clinical visits A data item of the number of clinical visits during which the participant was diagnosed with malaria Person: Jie Zheng, Chris Stoeckert, Shon cade, Grant Dorsey Penn Group PRISM number of clinical visits resulting in a malaria diagnosis A data item of the number of clinical visits during which the participant was diagnosed with asymptomatic microscopic parasitemia. Person: Jie Zheng, Chris Stoeckert, Shon cade, Grant Dorsey Penn Group PRISM number of clinical visits resulting in an asymptomatic microscopic parasitemia diagnosis A data item of the total number of clinical visits which were not sheduled routine visits. Person: Jie Zheng, Chris Stoeckert, Shon cade, Grant Dorsey Penn Group PRISM number of non-routine clinical visits A data item of the total number of clinical visits which were sheduled routine visits. Person: Jie Zheng, Chris Stoeckert, Shon cade, Grant Dorsey Penn Group PRISM number of routine clinical visits An information content entity that is about the type of sample/specimen collected during a clinical visit. Person: Jie Zheng, Chris Stoeckert PRISM sample available information A blood specimen that is located on a filter paper. Person: Jie Zheng, Chris Stoeckert Gruop: Penn group blood specimen on filter paper A processed specimen that is extracted from whole blood using gradient centrifugation that separates the blood into a layer of peripheral blood mononuclear cell under the top layer of plasma. It contains lymphocytes, monocytes or macrophages that are critical components in the immune system. Person: Jie Zheng, Chris Stoeckert PBMC specimen http://en.wikipedia.org/wiki/Peripheral_blood_mononuclear_cell peripheral blood mononuclear cell specimen A processed specimen consisting of red blood cells isolated from whole blood by centrifugation. Person: Jie Zheng, Chris Stoeckert RBC specimen erythrocyte specimen http://www.ruf.rice.edu/~bioslabs/studies/sds-page/gellab1.html red blood cell specimen An average value for female Anopheles mosquitoes tested positive for carrying Plasmodium parasites across multiple collections (e.g. from a given household across CDC light trap collections) in a given period. Person: Jie Zheng, Chris Stoeckert, Shon cade, Grant Dorsey Penn Group PRISM average number of Plasmodium parasite-positive female Anopheles An average value for female Anopheles mosquitoes tested for carrying Plasmodium parasites across multiple collections (e.g. from a given household across CDC light trap collections) in a given period. Person: Jie Zheng, Chris Stoeckert, Shon cade, Grant Dorsey Penn Group PRISM average number of female Anopheles tested for Plasmodium parasite An average percentage value for female Anopheles mosquitoes carrying Plasmodium parasites in all female mosquitoes tested for carrying Plasmodium parasites across multiple collections. Person: Jie Zheng, Chris Stoeckert, Shon cade, Grant Dorsey Penn Group PRISM average percent of Plasmodium parasite-positive female Anopheles A count of Anopheles mosquitoes collections performed (e.g. from a given household) in a given period. Person: Jie Zheng, Chris Stoeckert, Shon cade, Grant Dorsey Penn Group PRISM number of Anopheles collections A sum value for all species of female Anopheles mosquitoes in a given collections. Person: Jie Zheng, Chris Stoeckert, Shon cade, Grant Dorsey Penn Group PRISM sum number of female Anopheles in a collection A sum value for all female Anopheles funestus mosquitoes in a given collections. Person: Jie Zheng, Chris Stoeckert, Shon cade, Grant Dorsey Penn Group PRISM sum number of female Anopheles funestus in a collection A sum value for all female Anopheles gambiae mosquitoes in a given collections. Person: Jie Zheng, Chris Stoeckert, Shon cade, Grant Dorsey Penn Group PRISM sum number of female Anopheles gambiae in a collection A time datum for the duration of a patients participation in an investigation. Person: Jie Zheng, Chris Stoeckert, Shon cade, Grant Dorsey Penn Group PRISM participant observation duration time An average value for the number of clinical visits of a patient based on calendar years Person: Jie Zheng, Chris Stoeckert, Shon cade, Grant Dorsey Penn Group PRISM average number of clinical visits per year An average value for the number of clinical visits of a patient with asymptomatic microscopic parasitemia based on calendar years. Person: Jie Zheng, Chris Stoeckert, Shon cade, Grant Dorsey Penn Group PRISM average number of clinical visits with asymptomatic microscopic parasitemia diagnosis per year An average value for the number of clinical visits of a patient with malaria based on calendar years Person: Jie Zheng, Chris Stoeckert, Shon cade, Grant Dorsey Penn Group PRISM average number of clinical visits with malaria diagnosis per year A clinical visit date that specifies the date/time period of a routine clinical visit. Person: Jie Zheng Penn Group PRISM routine clinical visit date A data item about a household's cumulative living standard represented in a categorical datum. The wealth index is calculated using data on a household's ownership of selected assets, such as televisions and bicycles; materials used for housing construction; and types of water access and sanitation facilities. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey http://dhsprogram.com/topics/Wealth-Index.cfm PRISM categorical household wealth index An information content entity about items that a household owns such as a car, funiture, etc. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey Penn Group PRISM household asset information An information content entity indicating whether a person was given antimalarial therapy outside the study since last seen as part of the study. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey Penn Group PRISM antimalarial therapy given outside the study since last seen information An information content entity indicating the cause of death for a participant in the study. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey Penn Group PRISM cause of participant death A clinical visit occuring because of a sickness. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey Penn Group PRISM clinical visit when sick A covered pit latrine that does not have a latrine slab. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey Penn Group PRISM covered pit latrine without slab A time measurement datum specifying the date of death Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey Penn Group PRISM date of death A time measurement datum that specified the date of participant first enrolled in a study Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey Penn Group PRISM date of participant first enrolled in a study A time measurement datum that specified the date of participant last seen in a study Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey Penn Group PRISM date of participant last seen in a study A time measurement datum measuring the number of days since a clinical visit took place which resulted in a malaria diagnosis. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey Penn Group PRISM days since a clinical visit with a malaria diagnosis A time measurement datum that measures the duration of having abdominal pain. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey Penn Group PRISM duration of abdominal pain A time measurement datum that measures the duration of having anorexia. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey Penn Group PRISM duration of anorexia A time measurement datum that measures the duration of having a cough. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey Penn Group PRISM duration of cough A time measurement datum that measures the duration of having diarrhea. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey Penn Group PRISM duration of diarrhea A time measurement datum that measures the duration of having fatigue. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey Penn Group PRISM duration of fatigue A time measurement datum that measures the duration of having a headache. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey Penn Group PRISM duration of headache A time measurement datum that measures the duration of having jaundice. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey Penn Group PRISM duration of jaundice A time measurement datum that measures the duration of having joint pains. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey Penn Group PRISM duration of joint pains A time measurement datum that measures the duration of having muscle aches. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey Penn Group PRISM duration of muscle aches A time measurement datum that measures the duration of having seizures. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey Penn Group PRISM duration of seizures A time measurement datum that measures the duration of having subjective fever. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey Penn Group PRISM duration of subjective fever A time measurement datum that measures the duration of having vomiting. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey Penn Group PRISM duration of vomiting A household asset information indicating whether a member of a household has or owns an animal-drawn cart. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey Penn Group PRISM household animal-drawn cart asset A household asset information indicating whether a member of a household has a bank account. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey Penn Group PRISM household bank account asset A household asset information indicating whether a household has a bed. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey Penn Group PRISM household bed asset A household asset information indicating whether a member of a household has or owns a bicycle. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey Penn Group PRISM household bicycle asset A household asset information indicating whether a member of a household has or owns a boat without a motor. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey Penn Group PRISM household boat without a motor asset A household asset information indicating whether a member of a household has or owns a car or truck. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey Penn Group PRISM household car asset A household asset information indicating whether a household has a cassette player. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey Penn Group PRISM household cassette player asset A household asset information indicating whether a household has a chair. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey Penn Group PRISM household chair asset A household asset information indicating whether a household has a clock. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey Penn Group PRISM household clock asset A household asset information indicating whether a household has a cupboard. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey Penn Group PRISM household cupboard asset A household asset information indicating whether a household has electricity in their dwelling. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey Penn Group PRISM household electricity asset A household asset information indicating whether a household has a land line or fixed location phone. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey Penn Group PRISM household fixed phone asset A household asset information indicating whether a household has a mobile phone. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey Penn Group PRISM household mobile phone asset A household asset information indicating whether a member of a household has or owns a boat with a motor. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey Penn Group PRISM household motorboat asset A household asset information indicating whether a member of a household has or owns a motorcycle or motor scooter. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey Penn Group PRISM household motorcycle or scooter asset A household asset information indicating whether a household has a radio. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey Penn Group PRISM household radio asset A household asset information indicating whether a household has a refrigerator. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey Penn Group PRISM household refrigerator asset A household asset information indicating whether a household has a sofa. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey Penn Group PRISM household sofa asset A household asset information indicating whether a household has a table. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey Penn Group PRISM household table asset A household asset information indicating whether a household has a television. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey Penn Group PRISM household television asset A household asset information indicating whether a member of a household has or owns a watch. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey Penn Group PRISM household watch asset An information content entity indicating whether a malaria episode occurred Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey Penn Group PRISM incident of malaria episode information A material entity where a clinical visit took place. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey Penn Group PRISM location of clinical visit A material entity where a death occurred. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey Penn Group PRISM location of death An information content entity indicating whether medical care occurred outside the study clinic since last seen as part of the study. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey Penn Group PRISM medical care outside the study clinic since last seen information A time measurement datum of the days from the time of participant enrollment in a study until the current visit. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey Penn Group PRISM number of days from time of participant enrollment in a study until current visit A measurement datum of the number of female Anopheles funestus with a recent blood meal in a given collection Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey Penn Group PRISM number of fed female Anopheles funestus in a collection A measurement datum of the number of female Anopheles gambiae with a recent blood meal in a given collection Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey Penn Group PRISM number of fed female Anopheles gambiae in a collection A measurement datum of the number of female Anopheles dissected for parity in a given collection. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey Penn Group PRISM number of female Anopheles dissected for parity in a collection A measurement datum of the number of female Anopheles that have never layed eggs in a given collection. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey Penn Group PRISM number of female null parous Anopheles in a collection A measurement datum of the number of female Anopheles that have layed eggs before or are pregnant in a given collection. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey Penn Group PRISM number of female parous Anopheles in a collection A measurement datum of the number of gravid or semi-gravid female Anopheles funestus in a given collection Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey Penn Group PRISM number of gravid or semi-gravid Anopheles funestus in a collection A measurement datum of the number of gravid or semi-gravid female Anopheles gambiae in a given collection Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey Penn Group PRISM number of gravid or semi-gravid female Anopheles gambiae in a collection An average value for the number of insecticide treated mosquito net(s) per person. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey Penn Group PRISM number of insecticide treated mosquito net(s) per person A measurement datum of the number of female Anopheles that are not gambiae nor funestus in a given collection. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey Penn Group PRISM number of non-gambiae or funestus female Anopheles species in a collection A data item of the number of sleeping spaces in a dwelling. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey Penn Group PRISM number of sleeping places in dwelling with a household A measurement datum of the number of Anopheles funestus that could not be accessed in a given collection Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey Penn Group PRISM number of unassessable Anopheles funestus in a collection A measurement datum of the number of Anopheles gambiae that could not be assessed in a given collection Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey Penn Group PRISM number of unassessable Anopheles gambiae in a collection A measurement datum of the number of female Anopheles funestus without a recent blood meal in a given collection Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey Penn Group PRISM number of unfed female Anopheles funestus in a collection A measurement datum of the number of female Anopheles gambiae without a recent blood meal in a given collection Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey Penn Group PRISM number of unfed female Anopheles gambiae in a collection An information content entity that indicates whether a plasma sample is lost or not. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey Penn Group PRISM plasma sample lost information A categorical measurement datum that indicates whether Plasmodium gametocytes were present in a specimen using microscopy. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey Penn Group PRISM presence of Plasmodium gametocytes by microscopy An information content entity indicating the reason why a participant withdrew from a study. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey Penn Group PRISM reason for participant withdrawal An information content entity that indicates whether a redraw of a symptom occurred after a clinical visit. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey Penn Group PRISM redraw of a symptom after clinical visit information A routine clinical visit in which a blood specimen was collected for a T-cell study. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey Penn Group PRISM routine clinical visit for T-cell study A routine clinical visit in which a blood specimen was collected by finger prick and sent for lab testing (e.g., blood smear, hemoglobin level measurement). Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey Penn Group PRISM routine clinical visit with finger prick A routine clinical visit in which a blood specimen was collected using venipuncture and sent for lab testing (e.g., blood smear, hemoglobin level measurement). Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey Penn Group PRISM routine clinical visit with venipuncture A routine clinical visit in which no routine assessment was done during the visit. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey Penn Group PRISM routine clinical visit without any routine assessment done An air brick with a screen that can prevent some insects get in the dwelling. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey Penn Group PRISM screened air brick An anemia with hemoglobin levels less than 5 gm/dL. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey Penn Group PRISM ICEMR protein array severe anemia An information content entity indicating whether a person slept in an insecticide treated net the previous night. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey Penn Group PRISM slept in an insecticide treated net last night information A sum value for all female Anopheles examined for sporozoites in a given collection. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey Penn Group PRISM sum number of female Anopheles examined for sporozoites in a collection A sum value for all female Anopheles with Plasmodium sporozoites in a given collection. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey Penn Group PRISM sum number of female Anopheles with Plasmodium sporozoites in a collection A time measurement datum indicating when screening of a human study subject was perfomed. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey Penn Group PRISM time of screening A pit latrine that is not sheltered by an outhouse but has a latrine slab. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey Penn Group PRISM uncovered pit latrine with slab A pit latrine that is not sheltered by an outhouse and does not have a latrine slab. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey Penn Group PRISM uncovered pit latrine without slab An air brick without a screen to prevent insects from enetering the dwelling. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey Penn Group PRISM unscreened air brick Pain perceived to originate in the muscle. PRISM PRISM Muscle aches A light source that light is produced from solar energy. Person: Jie Zheng, Chris Stoeckert solar light source drinking water that is obtained from a publicly accessible water well without a constructed barrier built around it to limit movement of waste or runoff into it Person: John Judkins drinking water from open public well drinking water that is obtained from a water well with a constructed barrier built around it to limit movement of waste or runoff into the well and the well is located in the yard of a dwelling Person: John Judkins drinking water from open well in yard drinking water accessed through a plumbing fixture located inside a human dwelling Person: John Judkins drinking water from pipe into dwelling drinking water obtained through a plumbing fixture located in the yard of a human dwelling Person: John Judkins drinking water from pipe into yard was ClinEpi household, no longer used obsolete_drinking water from protected public well true from ClinEpi household, no longer used obsolete_drinking water from freshwater spring true ClinEpi household, no longer used obsolete_drinking water from protected well in yard true drinking water that is obtained from a freshwater spring without a constructed barrier built around it that would limit movement of waste or runoff into it Person: John Judkins drinking water from unprotected freshwater spring was ICEMR PRISM household, no longer used obsolete_drinking water from water truck true A centrally registered identifier symbol assigned by the American Type Culture Collection (ATCC). ATCC # ATCC number half life datum (t 1/2) for cleaning parasite clearance half life parasite clearance half life a rate measurement datum that represents the number of parasite organisms removed from the bearer of a host role by means of the biological processes of the bearer of the host role Person: John Judkins clearance rate parasite clearance rate a time measurement datum that is the result of measuring the time it takes for the biological processes of the bearer of a host role to remove parasite organisms within it, until such time as the organisms cannot be detected Person: John Judkins clearance time parasite clearance time was in ICEMR Amazonia, no longer used obsolete_symptomatic episode true was in EuPathDB/PlasmoDB, no longer used obsolete_chloroquine resistant true was in EuPathDB/PlasmoDB, no longer used obsolete_pyrimethamine and chloroquine resistant true was in EuPathDB/PlasmoDB, no longer used obsolete_pyrimethamine, mefloquine and chloroquine resistant true was in EuPathDB/PlasmoDB, no longer used obsolete_pyrimethamine resistant, chloroquine sensitive true was in ICEMR prism, no longer used obsolete_record of unknown information true same as EUPATH_0000282: pyrimethamine, mefloquine and chloroquine resistant obsolete_pyrimethamine,chloroquine, and mefloquine resistant true was in EuPathDB/PlasmoDB, no longer used not responsive to SAG therapy obsolete_sodium antimony gluconate resistant true was EuPathDB/PlasmoDB term, no longer used Sensitive to SAG obsolete_sodium antimony gluconate sensitive true was ICEMR PRISM observation, no longer used obsolete_no malaria parasite infection diagnosis true A population of people who share a common ancestor on the patrilineal or matrilineal line. haplogroup a time measurement datum that represents the beginning of the first process in which a parasitemia is realized Person: John Judkins parasitemia start parasitemia start time an information content entity that describes the success, failure, or indeterminacy of a treatment Person: John Judkins treatment outcome treatment outcome information was in EuPathDB/PlasmoDB, no longer used ETF obsolete_early treatment failure true was in EuPathDB/PlasmoDB, no longer used LCF obsolete_late clinical failure true Shannon Takala Harrison: Also not sure about LF, it could either be late failure or lost to follow-up. Term need for annotation NIH-10K experiment, treatment outcome was in EuPathDB/PlasmoDB, no longer used LF obsolete_late failure true Shannon Takala Harrison: LOSS probably also means the patient was lost to follow-up. Term need for annotation NIH-10K experiment, treatment outcome no longer used LOSS obsolete_lost to follow-up true was in EuPathDB/PlasmoDB, no longer used LPF obsolete_late parasitological failure true was in EuPathDB/PlasmoDB, no longer used LTF obsolete_Late Treatment Failure true Shannon Takala Harrison: Not sure what NULL means; it could also indicate lost to follow-up. Term need for annotation NIH-10K experiment, treatment outcome was EuPathDB/PlasmoDB term, no longer used NULL obsolete_unknown outcome true was ICEMR Amazonia, no longer used VIVAX obsolete_have a subsequent P. vivax infection true was in EuPathDB/PlasmoDB, no longer used WTH obsolete_withdrew from the study true was ICEMR, no longer used obsolete_summary information about a dwelling true an information content entity that is about a process in which a human being occupying a dwelling participates. It either specifies the bearer of the function that is realized in the process, or it specifies that the process does not occur in the dwelling or its yard. Person: John Judkins information on dwelling facilities a information content entity that is about a part of a dwelling Person: John Judkins information on dwelling physical characteristics an information content entity that is about a household and is an estimator of capabilities of household members to participate in processes that maintain their health, social status, and economic freedom Person: John Judkins socioeconomic factor a data item that is about an investigation and is the specified output of a data transformation that has only clinical visit data as input Person: John Judkins aggregated clinical visit information a genotype information that is about the genetic material of a human being Person: John Judkins human genotype information an information content entity that is about a part of a study design execution that is part of an investigation under which a human being is a participant Person: John Judkins information on participant study details an information content entity that is about a part of a health care encounter that occurs in a hospital facility Person: John Judkins ICEMR protein array hospitalization information an information content entity that is about a sign or symptom of a patient This should stay consistent w/OGMS's definitions, so this definition may need to be changed if OGMS changes their definitions of sign and symptom to information content entities. Person: John Judkins ICEMR protein array symptom or sign information an information content entity that is about a clinical visit Person: John Judkins information on observation details an information content entity that specifies whether a clinical visit is scheduled or unscheduled Person: John Judkins clinical visit type information an entomological data item that results from either (a) counting insect collections from multiple catches of live specimens or (b) an averaging data transformation that has single catch entomological measurement data as input Person: John Judkins aggregated entomological measurement data aggregated entomological data item an entomological data item that is the specified output of an assay that has a collection of insect specimens as specified input; this collection is the specified output of exactly one catch of live specimens Person: John Judkins individual entomological measurement data single catch entomological measurement datum a clinical visit that realizes the concretization of a protocol specifying the time of the visit Person: John Judkins scheduled clinical visit a clinical visit that occurs at a time that is not mentioned in a protocol that directs the time of the visit Person: John Judkins unscheduled clinical visit an information content entity that is about a malaria diagnosis and describes the severity of the disease or the basis for the diagnosis Person: John Judkins malaria severity and basis information a diagnosis that is an assertion that a patient, who is the subject of a diagnostic process, has a disease other than malaria Person: John Judkins diagnosis of disease other than malaria an information content entity that is about a participant under investigation and specifies the hospital admitting the participant Person: John Judkins hospital admission information a time measurement datum that is about a human being who bears a patient role and specifies the date of the patient's admission to a hospital Person: John Judkins date of hospital admission a time measurement datum that is about a human being who bears a patient role and specifies the date of the patient's discharge from a hospital Person: John Judkins date of hospital discharge A diagnosis given at time of discharge. ICEMR prism diagnosis at discharge an information content entity that is about a collection of Anopheles funestus Person: John Judkins Anopheles funestus related information an information content entity that is about a collection of Anopheles gambiae sensu lato Person: John Judkins Anopheles gambiae sensu lato related information an information content entity that is about a number of mosquitos that have given birth Person: John Judkins mosquito parity information an entomological data item that is the specified output of an analyte assay to determine whether a sporozoite is present in any insect in a collection of insects Person: John Judkins sporozoite testing information a data item that is the specified output of a data transformation that has only sporozoite testing information as input Person: John Judkins aggregated sporozoite testing information a data item that is about a collection of insects Person: John Judkins entomological measurement data entomological data item was ICEMR PRISM, no longer used obsolete_clinical visit information true One dimensional cartesian spatial coordinate datum refers to eastward-measured distance (or the x-coordinate). The terms easting and northing are geographic Cartesian coordinates for a point. Easting and northing coordinates are commonly measured in meters from a horizontal datum. easting coordinate measurement datum One dimensional cartesian spatial coordinate datum refers to the northward-measured distance (or the y-coordinate). The terms easting and northing are geographic Cartesian coordinates for a point. Easting and northing coordinates are commonly measured in meters from a horizontal datum. northing coordinate measurement datum A human waste disposal in a household. human waste disposal in a household A count of the total number of non-scheduled clinical visits in an investigation. number of non-scheduled visits A count of the total number of scheduled clinical visits in an investigation. number of scheduled visits An information content entity that is about malaria diagnosis and parasite status testing by blood smear or LAMP. Person: Jie Zheng, Grant Dorsey PRISM malaria diagnosis and parasite status information A dwelling information about animal living in a human dwelling. dwelling animal information An information content entity that is about human traveling. human traveling information An information content entity that is about vector control intervention towards interruption of transmission of infectious diseases. vector control intervention information An information content entity that is about employment. employment information An organism that raised by people and lives in a human dwelling. domesticated animal in a human dwelling An information content entity that is about when the bed net is last treated. information of when bed net last treated An information content entity that is about the highest level of schooling that a person has reached. educational level information A count of the total times of a person who infected with P. vivax in his lifetime. number of infections with P. vivax in lifetime A count of the total times of a person who infected with P. falciparum last year. number of infections with P. vivax in the last year A count of the total times of a person who infected with P. vivax in his lifetime. number of infections with P. falciparum in lifetime A count of the total times of a person who infected with P. falciparum last year. number of infections with P. falciparum in the last year A time measurement datum of days in a week at primary job. number of days per week at primary job A time measurement datum of days in a week at secondary job. number of days per week at secondary job "A human social role realized in a process that often performed in exchange for payment. Many people have multiple job roles, such as those of parent, homemaker, and employee." https://en.wikipedia.org/wiki/Job job role A planned process that a person participates in exchange for payment. The job role born by the person is realized in the process. economic activity An economic activity that a person is involved in primarily. primary economic activity An economic activity that a person is not involved in primarily. secondary economic activity A textual entity that describes a person's primary economic activity. primary economic activity description A textual entity that describes a person's secondary economic activity. secondary economic activity description An information content entity about secondary economic activity a person participates in the last month. secondary economic activity in last month an activity in which one engages An information content entity that is about something people are occupied with and you're not necessarily doing it to exchange for payment. occupation A time measurement datum about the pay period of primary economic activity. primary economic activity pay period A time measurement datum about the pay period of secondary economic activity. secondary economic activity pay period An information content entity about whether a person received payment from primary economic activity. information of received payment from primary economic activity An information content entity about whether a person received payment from secondary economic activity. information of received payment from secondary economic activity A data item of salary of primary job. salary of primary economic activity A data item of salary of other job. salary of secondary economic activity A time measurement datum about number of hours per day spend at primary economic activity. number of hours per day at primary economic activity A time measurement datum about number of hours per day spend at secondary economic activity. number of hours per day at secondary economic activity An environmental feature for disposing garbage. garbage disposal A textual entity about community where a person is living. community name A textual entity about community where a study taken place. study location name A malaria medication that is generally taken for initial treatment of malaria. first line malaria medication "A malaria medication that is given when first-line medication doesn't work, or stops working." second line malaria medication was in ICEMR Amazonia, no longer used obsolete_information of whether malaria medication is given true a categorical value specification that is about a human being and specifies whether that human being is joined to another human being in marriage Person: John Judkins marital status a categorical value specification that specifies whether a human being plans to change within two years the dwelling which that human being occupies Person: John Judkins information of whether a person plans to move an information content entity that specifies the relationship between a participant under investigation and the head of the participant's household Person: John Judkins relationship to head of Family a time measurement datum that represents the time a human being resides in a human dwelling Person: John Judkins years of living in the dwelling a time measurement datum that is about a human being, has years as its unit, and represents the time interval that the human being has lived in a geographic location where the inhabitants share a common trait Person: John Judkins years of living in the community a count of the number of instances of a site, within a human dwelling and its yard, to which any resident of the dwelling has access Person: John Judkins number of common areas in a dwelling a scalar measurement datum that has the square meter as its measurement label and is the result of a measurement of area that is covered by a roof Person: John Judkins covered area measured in square meter An information content entity about where the kitchen is located inside or outside of a dwelling. information of kitchen location a scalar measurement datum that is the result of a measurement of area and has the square meter as its measurement label Person: John Judkins total area measured in square meter a categorical value specification that is about a dwelling and specifies whether (a) it is owned by an occupant of the dwelling or (b) a rental agreement exists such that an occupant has an obligation to pay rent to someone who does not occupy the dwelling Person: John Judkins information on whether occupant owns or pays rent on dwelling was ICEMR Amazonia, no longer used obsolete_days of travel true was in ICEMR Amazonia, no longer used obsolete_information of whether ship is taken during a trip true an information content entity that is about a geographic location in which part of a journey occurs Person: John Judkins information of place visited during a trip An information content entity about travel to any place more than 10 km away from where a person live. information of travel in the last month an information content entity that is about a patient diagnosed with malaria and describes geographic locations the patient visited Person: John Judkins information about travel before malaria A material entity that is used to make bed net. bed net material a time measurement datum that is about a human dwelling and specifies the most recent date on which the dwelling was fumigated, i.e. filled with pesticide Person: John Judkins date of last fumigation an information content entity that specifies the organization that administers insecticide to a collection of bed nets Person: John Judkins information of organization responsible for treating bed nets an information content entity that specifies whether a human participant under investigation is a contact for malaria, based on the partipant's association with sites in which malaria infections are known to occur Person: John Judkins information of contact with malaria an information content entity that is about a human participant under investigation and specifies whether the person is present for a scheduled clinical visit Person: John Judkins information of participant status at visit was ICEMR Amazonia, no longer used obsolete_information of whether address has changed true a count of the number of instances of a domesticated animal that is raised in an agricultural setting to produce labor and commodities Person: John Judkins number of livestock a count of the number of instances of a domesticated animal that is kept for pleasure rather than utility Person: John Judkins number of pets was in ICEMR Amazonia, no longer used obsolete_bed net treatment information true a count of the number of instances of a bed net to which insecticide was applied in the past six months Person: John Judkins number of insecticide-treated bed nets treated less than 6 months ago a count of the number of instances of a bed net to which insecticide was applied before the previous six months Person: John Judkins number of insecticide-treated bed nets treated more than 6 months ago a count of the number of instances of bed net to which long last insecticide is administered Person: John Judkins number of long last insecticide-treated bed nets a count of the number of instances of a bed net to which insecticide has not been applied Person: John Judkins number of untreated bed net no longer used obsolete_blood pressure measurement datum true A categorical measurement datum about proximity to case dwelling. proximity to case dwelling datum no longer used obsolete_information of whether a census form filled at enrollment true an organization that administrates a medical care center that provides healthcare services on an outpatient basis Person: John Judkins obsolete_clinic organization true A geographic location where the clinic is located. clinic location a textual entity that denotes a political entity that is a division of a state or territory of India Person: John Judkins district of India name A textual entity about a 'division' or 'ward' being a sub-division of a city. division number a categorical value specification that specifies whether a patient complies with a dose specification that specifies the dose of malaria medication to self-administer Person: John Judkins information on whether antimalarial drugs taken as advised an information content entity that specifies whether a participant under investigation self-administered antimalarial drugs in the past 2 weeks Person: John Judkins information of whether took antimalarial drugs in last 2 weeks an information content entity that is about a human participant under investigation that has a disease and specifies the disease Person: John Judkins information of existing illness an information content entity that is about a human participant under investigation and specifies whether the participant has a disease Person: John Judkins information of whether having an existing illness a categorical value specification that is about a health care provider role that is realized in a treatment to alleviate symptoms of a fever. It either specifies whether this role is borne by a hospital or clinic, private practice, or the patient, or it specifies that this information is missing. Person: John Judkins treatment provider information A time measurement datum that measures the duration of having febrile. Person: Jie Zheng, Chris Stoeckert ICEMR protein array duration of being febrile was ICEMR Amazonia, no longer used obsolete_information of whether a person is family head true was ICEMR Amazonia, no longer used obsolete_hospital registration number true an information content entity that specifies whether a human being is manifesting a disease Person: John Judkins information of whether a person is sick now "An information content entity is about who are indoor residents, such as only human, or human and animals." indoor residents information a measurement datum that approximates the temporal interval between applications of larvicide at the same site Person: John Judkins frequency of larvicide in use an information content entity that specifies any locations in which a diagnostic process has occurred in the past twelve months that resulted in a diagnosis of malaria Person: John Judkins information of where malaria diagnosed in last 12 months a count of the number of instances of a parasite in a life cycle stage in which reproduction is asexual Person: John Judkins number of asexual parasite was ICEMR, no longer used obsolete_number of sexual parasite true A data item of which parasite species detected in a blood specimen. parasite species information A country name denote where a person was born. birth country name an information content entity that is part of a diagnosis of malaria, resulting from a diagnostic process that occurred within the past year, and specifies the species of the infectious agent causing the malaria Person: John Judkins information of malaria parasite infection diagnosis past year A count of malaria diagnosis past year. number of malaria diagnosis past year A time measurement datum of number of months since malaria diagnosis. number of months since malaria diagnosis An information content entity about whether antimalarial drug treated last year information of whether antimalarial drug treated last year A time measurement datum about when the antimalarial drug used last year antimalarial drug used date An information content entity about what antimalarial drug used last year information of antimalarial drug used last year An information about who treated malaria last year information of who treated malaria last year A specimen that is used for DNA extraction and following PCR assay. specimen used for DNA PCR An organism identification assay that identifies the species of parasites by PCR. parasite species identification by PCR assay A textual entity that denotes the public health clinic/hospital that the human subject normally uses (for non malaria illness). primary health center name A data item of income level issued annually by the Department of Health and Human Services. Federal poverty levels are used to determine your eligibility for certain programs and benefits. poverty line An information that specifies a person has no illness. no illness information A laboratory test that can quickly establishing the diagnosis of P. falciparum or P. vivax malaria infection by detecting the antigens in a person's blood. falcivax rapid diagnostic test "A laboratory test that is a rapid, sensitive malaria test that is able to differentiate between P. falciparum and other malaria parasites. " optimal-IT rapid diagnostic test A material entity that a person uses to deter mosquitoes from approaching or settling. personal mosquito repellent "An information content entity about a person's resident status, permanent or temporary." resident status information An information content entity about repellent sprayed in last 12 months in a dwelling. information of mosquito repellent sprayed in last 12 months A text entity denotes to a state where a person was born. state name of birth An information content entity that is about whether a person take fever suppressant. take fever suppressant information A text entity denotes to a taluk. taluk name A country name denote a geographic location that a person has visited. visited country name A text entity denotes to a district that a person has visited. visited district name A text entity denotes to a state that a person has visited. visited state name A taluk name denote a geographic location that a person has visited. visited taluk name A village name denote a geographic location that a person has visited. visited village name An information content entity about whether a person travelled in last 14 days. traveled information in last 14 days An information content entity about healthcare that is private or public. healthcare information A text entity denotes to a village. village name A text entity of a zone number denotes to a geographic location. location zone number deprecated in favor of GENEPIO_0000092 'read coverage' obsolete_average mapping coverage true a data item that is about a sequencing assay and is the ratio of the count of mapped reads to the total count of reads Person: John Judkins proportion mapped reads was in EuPathDB/PlasmoDB, no longer used obsolete_number mapped reads true was EuPathDB/PlasmoDB term, no longer used obsolete_average read length true was in EuPathDB/PlasmoDB, no longer used obsolete_unstranded unique average mapping coverage true was in EuPathDB/PlasmoDB, no longer used obsolete_unstranded unique proportion mapped reads true was EuPathDB/PlasmoDB term, no longer used obsolete_unstranded unique number mapped reads true was in EuPathDB/PlasmoDB, no longer used obsolete_unstranded unique average read length true was in EuPathDB/PlasmoDB, no longer used obsolete_unstranded non unique average mapping coverage true was in EuPathDB/PlasmoDB, no longer used obsolete_unstranded non unique proportion mapped reads true was in EuPathDB/PlasmoDB, no longer used obsolete_unstranded non unique number mapped reads true was in EuPathDB/PlasmoDB, no longer used obsolete_unstranded non unique average read length true was in EuPathDB/PlasmoDB, no longer used obsolete_first strand unique average mapping coverage true was in EuPathDB/PlasmoDB, no longer used obsolete_first strand unique proportion mapped reads true was in EuPathDB/PlasmoDB, no longer used obsolete_first strand unique number mapped reads true was in EuPathDB/PlasmoDB, no longer used obsolete_first strand unique average read length true was EuPathDB/PlasmoDB term, no longer used obsolete_first strand non unique unstranded unique average mapping coverage true was EuPathDB/PlasmoDB term, no longer used obsolete_first strand non unique unstranded unique proportion mapped reads true was EuPathDB/PlasmoDB term, no longer used obsolete_first strand non unique unstranded unique number mapped reads true was EuPathDB/PlasmoDB term, no longer used obsolete_first strand non unique unstranded unique average read length true was in EuPathDB/PlasmoDB, no longer used obsolete_second strand unique unstranded non unique average mapping coverage true was in EuPathDB/PlasmoDB, no longer used obsolete_second strand unique unstranded non unique proportion mapped reads true was in EuPathDB/PlasmoDB, no longer used obsolete_second strand unique unstranded non unique number mapped reads true was in EuPathDB/PlasmoDB, no longer used obsolete_second strand unique unstranded non unique average read length true was in EuPathDB/PlasmoDB, no longer used obsolete_second strand non unique first strand unique average mapping coverage true was in EuPathDB/PlasmoDB, no longer used obsolete_second strand non unique first strand unique proportion mapped reads true was in EuPathDB/PlasmoDB, no longer used obsolete_second strand non unique first strand unique number mapped reads true was in EuPathDB/PlasmoDB, no longer used obsolete_second strand non unique first strand unique average read length true was in EuPathDB/PlasmoDB, no longer used https://www.beiresources.org/Catalog/Fungi/NR-29444.aspx obsolete_Candida albicans strain 12C true was in EuPathDB/PlasmoDB, no longer used https://www.beiresources.org/Catalog/Fungi/NR-29445.aspx obsolete_Candida albicans strain L26 true A diagnosis based on parasites detected by microscopy (parasite density > 0) or LAMP assay (LAMP result is positive) in the absence of febrile (subjective fever and temperature>=38). diagnosis of asymptomatic parasitemia A diagnosis based on presence of parasites by LAMP assay when microscopy result was negative in the absence of subjective fever or documented elevated temperature. Person: Grant Dorsey, Jie Zheng diagnosis of submicroscopic parasitemia A data item of the number of clinical visits during which the participant was diagnosed with asymptomatic parasitemia. Person: Jie Zheng, Shon cade, Grant Dorsey PRISM number of clinical visits resulting in an asymptomatic parasitemia diagnosis a presence of parasite that indicates whether parasites too small to be seen under light microscopy are present in a specimen. It is the specified output of a loop-mediated isothermal amplification assay Person: Jie Zheng, Grant Dorsey, John Judkins presence of submicrosopic parasites by LAMP Penn group PRISM presence of submicrosopic parasites by loop-mediated isothermal amplification assay An information content entity is about blood smear not performed. Person: Jie Zheng, Grant Dorsey PRISM information of blood smear not performed A laboratory finding about parasite present which is negative in both blood smear and LAMP assay. Person: Jie Zheng, Grant Dorsey PRISM negative blood smear and negative LAMP An information content entity is about parasite status with negative blood smear and LAMP test is not performed. Person: Jie Zheng, Grant Dorsey PRISM information of negative blood smear and LAMP not done An average value for the number of clinical visits of a patient with asymptomatic parasitemia based on calendar years. Person: Jie Zheng, Shon cade, Grant Dorsey PRISM average number of clinical visits with asymptomatic parasitemia diagnosis per year A count of the number of courses of antibiotics received by the human or animal. Person: Daniel Beiting, Jie Zheng microbiome number of courses of antibiotics given A symbol that denotes a specific family, rather than the physical home in which they live. Person: Daniel Beiting, Jie Zheng microbiome family identifier A symbol denotes a physical structure/home/dwelling, rather than the human inhabitants. Person: Daniel Beiting, Jie Zheng microbiome dwelling identifier An information content entity that idicates whether the hive was treated with tetracyline to prevent infection with the bacterial pathogen Paenibacillus larvae. Person: Daniel Beiting, Jie Zheng microbiome information of hive treated with tetracyline An information indicates that samples from child or from the mother, or both. Person: Daniel Beiting, Jie Zheng microbiome information of specimen from mother or child A number of courses of antibiotics given to a mother during delivery. Person: Daniel Beiting, Jie Zheng microbiome number of courses of antibiotics received by mom prior to delivery A region of the 16S rRNA gene that was PCR amplified and sequenced. replaced by: SO_0001000: rRNA_16S Person: Daniel Beiting, Jie Zheng microbiome false obsolete_16S rRNA gene region for sequencing true An organism that realizes host role in laboratory. lab host was EuPathDB/PlasmoDB term, no longer used obsolete_bronchial wash specimen true was EuPathDB/PlasmoDB term, no longer used obsolete_bronchoalveolar lavage fluid specimen true was EuPathDB/PlasmoDB term, no longer used obsolete_lung aspirate specimen true was EuPathDB/PlasmoDB term, no longer used obsolete_lung lesion specimen true was in EuPathDB/PlasmoDB, no longer used obsolete_lung mold bronch specimen true was in EuPathDB/PlasmoDB, no longer used obsolete_lung nodule specimen true was in EuPathDB/PlasmoDB, no longer used obsolete_TGH specimen true was in EuPathDB/PlasmoDB, no longer used obsolete_TGH mold iso specimen true was in EuPathDB/PlasmoDB, no longer used obsolete_number of contigs true was EuPathDB/PlasmoDB term, no longer used obsolete_number of genes called true was in EuPathDB/PlasmoDB, no longer used obsolete_number of bases true was in EuPathDB/PlasmoDB, no longer used obsolete_lesion on arm specimen true A textual entity refers to a taxon or organism that is based on the normal language of everyday life; this kind of name is often contrasted with the scientific name for the same organism, which is Latinized. https://en.wikipedia.org/wiki/Common_name common name of organism An information content entity specify any molecular data associated with specimen source is available. Person: Jie Zheng, Chris Stoeckert ICEMR protein array information on availability of molecular data An information content entity indicates whether the specimen collection is original collection or follow up collection from same study subject. Person: Jie Zheng, Chris Stoeckert ICEMR protein array information on original or follow up specimen collection An information content entity specifies whether study subject signed informed consent for data collection and usage. Person: Jie Zheng, Chris Stoeckert ICEMR protein array information on informed consent for data collection and usage deprecated in favor of HP_0003111 'Abnormality of ion homeostasis' Person: Jie Zheng, Chris Stoeckert, John Judkins ICEMR protein array obsolete_electrolyte disturbances true was in EuPathDB/PlasmoDB, no longer used https://www.beiresources.org/Catalog/Fungi/NR-29447.aspx obsolete_Candida albicans strain P37005 true A categorical measurement datum that indicates whether Plasmodium falciparum were present in a specimen. Person: Jie Zheng, Chris Stoeckert ICEMR protein array presence of Plasmodium falciparum A categorical measurement datum that indicates whether gametocyte were present in a specimen. Person: Jie Zheng, Chris Stoeckert ICEMR protein array presence of gametocyte A categorical measurement datum that indicates whether Plasmodium knowlesi were present in a specimen. Person: Jie Zheng, Chris Stoeckert ICEMR protein array presence of Plasmodium knowlesi A categorical measurement datum that indicates whether Plasmodium malariae were present in a specimen. Person: Jie Zheng, Chris Stoeckert ICEMR protein array presence of Plasmodium malariae A categorical measurement datum that indicates whether Plasmodium ovale were present in a specimen. Person: Jie Zheng, Chris Stoeckert ICEMR protein array presence of Plasmodium ovale A categorical measurement datum that indicates whether parasite were present in a specimen. Person: Jie Zheng, Chris Stoeckert ICEMR protein array presence of parasite A categorical measurement datum that indicates whether Plasmodium vivax were present in a specimen. Person: Jie Zheng, Chris Stoeckert ICEMR protein array presence of Plasmodium vivax A time measurement datum measuring the number of days from the first specimen collection to current specimen collection from same study subject. Person: Jie Zheng, Chris Stoeckert ICEMR protein array days of follow up specimen collection A scalar measurement datum that is about gametocyte density measured using microscopy. Person: Jie Zheng, Chris Stoeckert ICEMR protein array gametocyte density by microscope A scalar measurement datum that is about gametocyte density measured by RT-PCR. Person: Jie Zheng, Chris Stoeckert ICEMR protein array gametocyte density by RT-PCR An assay that detects parasite gametocyte in a specimen. Person: Jie Zheng, Chris Stoeckert ICEMR protein array gametocyte detection assay A protocol that specifies how to measure the density of parasite gametocyte. Person: Jie Zheng, Chris Stoeckert ICEMR protein array gametocyte detection protocol a site in which a global positioning system receiver produces a data item specifying the location of the site Person: Jie Zheng, Chris Stoeckert ICEMR protein array location where GPS coordinates were taken An information content entity specify any host genetics data associated with specimen source is available. Person: Jie Zheng, Chris Stoeckert ICEMR protein array information on availabilty of host genetics data An information content entity specify any immune response data associated with specimen source is available. Person: Jie Zheng, Chris Stoeckert ICEMR protein array information on availability of immune response data An information content entity specify any parasite genetics data associated with specimen source is available. Person: Jie Zheng, Chris Stoeckert ICEMR protein array information on availability of parasite genetics data An information content entity specify any molecular data other than host genetics, parasite genetics, and immune response, associated with specimen source is available. Person: Jie Zheng, Chris Stoeckert ICEMR protein array information on availability of other molecular data A centrally registered identifier symbol assigned to a research project by Institutional Review Board (IRB). The IRB is a committee established to review and approve applications for research projects involving human subjects. The primary purpose of the IRB is to protect the rights and welfare of the human subjects. Person: Jie Zheng, Chris Stoeckert ICEMR protein array IRB number A scalar measurement datum that is about parasite density measured by PCR. Person: Jie Zheng, Chris Stoeckert ICEMR protein array parasite density by PCR A scalar measurement datum that is about parasite density measured by microscope. Person: Jie Zheng, Chris Stoeckert ICEMR protein array parasite density by microscope An assay that detects parasite in a specimen. Person: Jie Zheng, Chris Stoeckert ICEMR protein array parasite detection assay An assay that detects parasite in a specimen using PCR. Person: Jie Zheng, Chris Stoeckert ICEMR protein array parasite detection by PCR assay A categorical measurement datum that indicates whether asexual parasite were present in a specimen using PCR. Person: Jie Zheng, Chris Stoeckert ICEMR protein array presence of asexual parasite by PCR A categorical measurement datum that is the result of rapid diagnosis test using a value of positive or negative. Person: Jie Zheng, Chris Stoeckert ICEMR protein array rapid diagnosis test result as positive or negative The site where specimen collection taken place. Person: Jie Zheng, Chris Stoeckert ICEMR protein array location of specimen collection a research organization that is located in an area where malaria is endemic and is one of many centers established by the National institute of Allergy and Infectious Diseases with the following aims: to design and conduct multidisciplinary research on the epidemiology, transmission, and pathogenesis of malaria in its specific region, to design and conduct special projects to capitalize on new opportunities and emerging public health needs, and to build clinical research capacity and improve malaria control and prevention Person: Jie Zheng, Chris Stoeckert, John Judkins ICEMR protein array ICEMR organization An assay that detects body temperature of an organism. Person: Jie Zheng, Chris Stoeckert ICEMR protein array organismal body temperature measurement assay An assay that is quick and easy in the diagnosis of malaria by detecting evidence of malaria parasites (antigens) in human blood. Person: Jie Zheng, Chris Stoeckert ICEMR protein array malaria rapid diagnosis test gametocyte density by microscope that is the output of an assay that realizes an analyte role that inheres in Plasmodium falciparum Person: Jie Zheng, Chris Stoeckert, John Judkins ICEMR protein array Plasmodium falciparum gametocyte density by microscope gametocyte density by microscope that is the output of an assay that realizes an analyte role that inheres in Plasmodium vivax Person: Jie Zheng, Chris Stoeckert, John Judkins ICEMR protein array Plasmodium vivax gametocyte density by microscope A scalar measurement datum that is about gametocyte density measured by RT-PCR. Person: Jie Zheng, Chris Stoeckert ICEMR protein array Plasmodium vivax gametocyte density by RT-PCR parasite density by PCR that is the output of an assay that realizes an analyte role that inheres in Plasmodium vivax Person: Jie Zheng, Chris Stoeckert, John Judkins ICEMR protein array Plasmodium vivax parasite density by PCR parasite density by microscope that is the output of an assay that realizes an analyte role that inheres in Plasmodium falciparum Person: Jie Zheng, Chris Stoeckert, John Judkins ICEMR protein array Plasmodium falciparum parasite density by microscope parasite density by microscope that is the output of an assay that realizes an analyte role that inheres in Plasmodium vivax Person: Jie Zheng, Chris Stoeckert, John Judkins ICEMR protein array Plasmodium vivax parasite density by microscope parasite density by PCR that is the output of an assay that realizes an analyte role that inheres in Plasmodium falciparum Person: Jie Zheng, Chris Stoeckert, John Judkins ICEMR protein array Plasmodium falciparum parasite density by PCR An information content entity specifies whether study subject signed informed consent for future use of specimen. Person: Jie Zheng, Chris Stoeckert ICEMR protein array information on informed consent for future use of specimen was in EuPathDB/PlasmoDB, no longer used https://www.beiresources.org/Catalog/Fungi/NR-29449.aspx obsolete_Candida albicans strain 19F true was in EuPathDB/PlasmoDB, no longer used https://www.beiresources.org/Catalog/Fungi/NR-29434.aspx obsolete_Candida albicans strain P78048 true was in EuPathDB/PlasmoDB, no longer used https://www.beiresources.org/Catalog/Fungi/NR-29450.aspx obsolete_Candida albicans strain P37037 true was in EuPathDB/PlasmoDB, no longer used https://www.beiresources.org/Catalog/Fungi/NR-29451.aspx obsolete_Candida albicans strain P37039 true was in EuPathDB/PlasmoDB, no longer used obsolete_Candida albicans strain SC5314 true was in EuPathDB/PlasmoDB, no longer used https://www.beiresources.org/Catalog/Fungi/NR-29435.aspx obsolete_Candida albicans strain P57072 true was in EuPath/PlasmoDB, no longer used https://www.beiresources.org/Catalog/Fungi/NR-29441.aspx obsolete_Candida albicans strain P76055 true was EuPathDB/PlasmoDB term, no longer used https://www.beiresources.org/Catalog/Fungi/NR-29442.aspx obsolete_Candida albicans strain P76067 true was in EuPathDB/PlasmoDB, no longer used https://www.beiresources.org/Catalog/Fungi/NR-29439.aspx obsolete_Candida albicans strain P57055 true was in EuPathDB/PlasmoDB, no longer used https://www.beiresources.org/Catalog/Fungi/NR-29443.aspx obsolete_Candida albicans strain P78042 true was in EuPathDB/PlasmoDB, no longer used https://www.beiresources.org/Catalog/Fungi/NR-29436.aspx obsolete_Candida albicans strain P34048 true was in EuPathDB/PlasmoDB, no longer used https://www.beiresources.org/Catalog/Fungi/NR-29453.aspx obsolete_Candida albicans strain P87 true was in EuPathDB/PlasmoDB, no longer used https://www.beiresources.org/Catalog/Fungi/NR-29452.aspx obsolete_Candida albicans strain GC75 true was in EuPathDB/PlasmoDB, no longer used https://www.beiresources.org/Catalog/Fungi/NR-29438.aspx obsolete_Candida albicans strain P75016 true was in EuPathDB/PlasmoDB, no longer used https://www.beiresources.org/Catalog/Fungi/NR-29440.aspx obsolete_Candida albicans strain P75063 true was in EuPathDB/PlasmoDB, no longer used https://www.beiresources.org/Catalog/Fungi/NR-29446.aspx obsolete_Candida albicans strain P94015 true was in EuPathDB/PlasmoDB, no longer used https://www.beiresources.org/Catalog/Fungi/NR-29448.aspx obsolete_Candida albicans strain P60002 true was EuPathDB/PlasmoDB term, no longer used https://www.beiresources.org/Catalog/Fungi/NR-29437.aspx obsolete_Candida albicans strain P75010 true A genotype information of parasite organism. parasite organism genotype information deprecated in favor of APOLLO_SV_00000232 'clade name' obsolete_genetic clade of organism true NLST Clade of organism a data item that is about some virulence and is the count of infectious agents that kill half of a collection of human beings infected with the agents Person: John Judkins virulence score (LDt50) a data item that is about some virulence and is the proportion of the number of human beings with a disease (caused by the bearer of the virulence) that die of the disease Person: John Judkins virulence score (slope) A centrally registered identifier symbol assigned by the BEI Resources (https://www.beiresources.org/) to cultures and reagents for microbiology and infectious diseases research. BEI repository identifier A measurement datum of vertical distance below local surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectivly. vertical distance below a surface measurement datum An age since birth measurement datum measured in days. age in days age since birth in days An information content entity about whether child exposed to antibiotics. information of whether child exposed to antibiotics a health care encounter in which a health care provider assists a mother in the birth of a child Person: John Judkins baby's delivery mode of baby delivery A medication material that is used in the treatment and prevention of bacterial infections. It may either kill or inhibit the growth of bacteria. https://en.wikipedia.org/wiki/Antibiotics antibiotics An information content entity about whether bee colony treated with tetracycline. information of whether bee colony treated with tetracycline main source of nutrition for a child child's diet main source of nutrition for a child for each month child's diet by month An information content entity about any drug used by a participant under investigation and the frequency of usage. drug usage information An information content entity about environmental material, environmental feature, environmental system, etc. environment information household information that specifies whether the household relocated during its time under investigation Person: John Judkins information of whether a family move an information content entity that is about the bearer of a host role Person: John Judkins host information the diet of an animal that is the bearer of a host role Person: John Judkins type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types host's diet An organism that has host role host organism a categorical value specification that is about a collection of bee larvae and specifies whether tetracycline was administered to the larvae Person: John Judkins information of whether bee larvae treated with tetracycline mass measurement datum is about a host that measured at specimen collection process host mass measurement datum at specimen collection same as EUPATH_0000496 obsolete_information of specimen obtained from the mother or chid true a count that is about a dwelling and is also the result of counting the instances of a child that occupies the dwelling Person: John Judkins number of child occupants in a dwelling An environmental feature for disposing human waste. human waste disposal a ratio that is about a dwelling, is expressed as a percent, has a count of adult occupants of the dwelling as the numerator, and has a count of all occupants of the dwelling as the denominator Person: John Judkins percent adult occupants in a dwelling a ratio that is about a dwelling, is expressed as a percent, has a count of male occupants of the dwelling as the numerator, and has a count of all occupants of the dwelling as the denominator Person: John Judkins percent male occupants in a dwelling a categorical value specification that specifies whether a mother received an antimicrobial agent Person: John Judkins information of whether antibiotics given to mom an information content entity that is about an antimicrobial agent given to a mother and specifies the agent by chemical compound Person: John Judkins information of class of antibiotics given to mom an information content entity that specifies the trimester of a pregnancy for which a mother receives an antimicrobial agent Person: John Judkins information of trimester antibiotics given to mom An information content entity about presence of pets or farm animals in the environment of subject, if yes the animals should be specified; can include multiple animals present. environmental pets or farm animals information a protocol that, when concretized, is realized in an assay that uses chemical or biological means to infer the sequence of a biomaterial Person: John Judkins sequencing protocol An information content entity about In which batch were samples sequenced together. sequencing batch information an information content entity that is about an investigation and has as parts only the most significant information content entities that result from the investigation Person: John Judkins summary information of investigation a symbol that denotes the bearer of a participant under investigation role Person: John Judkins participant identifier an information content entity that is about weight loss occurring in a three-month period Person: John Judkins information of weight loss in last three months a protocol such that, if it is concretized and its concretization is realized, its concretization is realized in a planned process that has as its objective collecting a specimen Person: John Judkins specimen collection protocol an information content entity about the bearer of a specimen role Person: John Judkins specimen information symptom or sign information that results from an examination of either the skin of the patient or a process in which the skin participates Person: John Judkins skin symptom or sign information an information content entity that is about a specimen collection process Person: John Judkins specimen source information an information content entity that specifies whether an animal is also human Person: John Judkins information specifying human or animal a specimen collection time measurement datum that is the measure of a time when specimens are collected after an infection starts Person: John Judkins specimen collection time post infection skin symptom or sign information that is about the thickness of the ear of the patient Person: John Judkins ear thickness skin symptom or sign information that specifies the rate at which water passes through the epidermis of the patient into the air Person: John Judkins transepidermal water loss was microbiomeDB, no longer used obsolete_site of ear swabbed true a categorical measurement datum that is about the skin of a human being and specifies whether the skin is either dry, moist, or sebaceous Person: John Judkins skin type swabbed a categorical value specification that is about a portion of skin that has a disorder hypothesized to be clinically significant. It specifies the degree to which a portion of skin is clinically abnormal. Person: John Judkins skin pathology score a count of the number of instances of a treatment Person: John Judkins number of treatments skin symptom or sign information that is about increased thickness of the skin Person: John Judkins degree of skin thickening skin symptom or sign information that specifies the size of a disorder on the skin of a patient Person: John Judkins lesion size skin symptom or sign information that is about a lesion on the axilla of a patient and specifies the extent of damage to the tissue before a treatment to alleviate the lesion Person: John Judkins axillary lesion score before treatment skin symptom or sign information that is about a lesion on the axilla of a patient and specifies the extent of damage to the tissue during a treatment to alleviate the lesion Person: John Judkins axillary lesion score during treatment skin symptom or sign information that is about a lesion on the axilla of a patient and specifies the extent of damage to the tissue that remains after a treatment to alleviate the lesion Person: John Judkins axillary lesion score after treatment skin symptom or sign information that is about a lesion on the groin of a patient and specifies the extent of damage to the tissue before a treatment to alleviate the lesion Person: John Judkins groin lesion score before treatment skin symptom or sign information that is about a lesion on the groin of a patient and specifies the extent of damage to the tissue during a treatment to alleviate the lesion Person: John Judkins groin lesion score during treatment skin symptom or sign information that is about a lesion on the groin of a patient and specifies the extent of damage to the tissue that remains after a treatment to alleviate the lesion Person: John Judkins groin lesion score after treatment skin symptom or sign information that is about a lesion on a pinna of a patient and specifies the extent of damage to the tissue before a treatment to alleviate the lesion Person: John Judkins pinna lesion score before treatment skin symptom or sign information that is about a lesion on a pinna of a patient and specifies the extent of damage to the tissue during a treatment to alleviate the lesion Person: John Judkins pinna lesion score during treatment skin symptom or sign information that is about a lesion on a pinna of a patient and specifies the extent of damage to the tissue that remains after a treatment to alleviate the lesion Person: John Judkins pinna lesion score after treatment treatment outcome information that specifies whether the treatment of a skin lesion was successful Person: John Judkins information of whether skin lesion cured after treatment a time measurement datum that represents the time interval between the first appearance of a skin lesion and the time it is swabbed for specimen collection Person: John Judkins skin lesion duration a categorical value specification that specifies the degree of erythema Person: John Judkins degree of skin redness skin symptom or sign information that specifies the area of a part of a patient's skin that participates in an inflammation process Person: John Judkins degree of skin inflammation a measurement datum that is a measurement of the hydration of the outer epidermis Person: John Judkins Pubmed 2459872 & https://academic.oup.com/jn/article/134/8/2110S/4688890 corneometry an information content entity that specifies the degree to which alopecia has been realized in a patient Person: John Judkins degree of hairloss a skin symptom or sign information that specifies whether the patient has atopic dermatitis Person: John Judkins information of affected by atopic dermatitis A diagnosis given at time of hospitalization. ICEMR prism diagnosis at hospitalization a population that is the bearer of a study group role Person: John Judkins study group a symbol that denotes a cage that has the function to keep an animal that is the bearer of a participant under investigation role Person: John Judkins animal cage number for experiment a symbol that denotes a cage that has the function to keep a mouse that is the bearer of a participant under investigation role Person: John Judkins mouse cage number A human waste disposal that has the function of disposing of waste material produced by a human child Person: John Judkins human child waste disposal Assay that subjects a stool sample to a test for microorganisms. Person: Cristian Cocos, Jie Zheng, Chris Stoeckert Penn Group GEMS stool test for microorganisms A biological process that breeds a plant or animal by natural processes from the parent stock. Term added for annotation of a Crypto SNP dataset but the term is not used. Person: Jie Zheng propagation A genotype information which is about cluster of differentiation 36 (CD36) gene, which encodes an integral membrane protein in many cell types and a member of the scavenger receptor family that imports fatty acids into cells (Canton et al., 2013). CD36 is also an endothelial receptor for binding of erythrocytes infected with P. falciparum. Grant Dorsey: The human CD36 antigen is an integral membrane protein in many cell types and a member of the scavenger receptor family that imports fatty acids into cells (Canton et al., 2013). CD36 is also an endothelial receptor for binding of erythrocytes infected with P. falciparum; this cytoadhesion is believed to be an important feature of the virulence of falciparum malaria, due both to its prevention of clearance of infected erythrocytes by the spleen and to local effects of cytoadhering parasites (Newbold et al., 1999). Importantly, expression of CD36 is low in the brain, even in the setting of cerebral malaria (Silamut et al., 1999), suggesting that binding to CD36 is most relevant in non-cerebral forms of severe malaria. CD36 is also believed to be an important macrophage pattern recognition receptor that mediates innate recognition and clearance of infected erythrocytes (Cabrera et al., 2014). Considering our current understanding, CD36 expression might be seen to contribute to malaria severity, by mediating cytoadherence, or to help control malaria, via immune effects. Results with murine malaria models have been complex; mice with decreased CD36-mediated cytoadherence had decreased growth of P. berghei (Fonager et al., 2012), but CD36-deficient mice had increased risk of fatal P. chabaudi malaria (Patel et al., 2007). Considering human populations, many CD36 polymorphisms, including nonsense mutations that prevent production of the molecule, are common, particularly in African populations (Aitman et al., 2000). However, attempts to identify associations between common polymorphisms and malaria risk have led to inconsistent results, with evidence for enhancement of(Aitman et al., 2000; Omi et al., 2002), no effect (Fry et al., 2009), or protection from (Das et al., 2009; Omi et al., 2003; Pain et al., 2001; Sinha et al., 2008) severe malaria with different polymorphisms. CD3T188G is a polymophism on the human CD36 gene. cluster of differentiation 36 genotype An information content entity is about a process. information of process A planned process that an organism exposed to that are not one of the variables under study. MO_55 EnvironmentalHistory environmental history A treatment to alleviate the signs and symptoms associated with malaria. malaria treatment A time measurement datum of duration of an individual acquires, develops, or first experiences a condition or symptoms of a disease or disorder. time to onset A time measurement datum that specifies when the DNA was extracted DNA extraction date The measurement datum generated by Inverse polymerase chain reaction (Inverse PCR). iPCR datum A time measurement datum of duration of the observation at the end of an observation period. end of observation period A time measurement datum of a person first diagnosed as malaria time to first malaria diagnosis A time measurement datum of the duration for reinfection. time to reinfection A genotype information about 60 kDa glycoprotein (gp60) gene. gp60 genotype A specimen collection time measurement datum in year. specimen collection time in year An information content entity of multiple blood smear results during an observation period. information of blood smear result An organism that has pathogen role. pathogen organism A quality inheres in parasite organism. parasite phenotype A genotype information of fungus. fungal organism genotype information A Fungus that is bred to have some uniform behavioral, morphological, physiological, or genetic characteristics with similarly bred Fungus fungal strain A Candida albicans that is bred to have some uniform behavioral, morphological, physiological, or genetic characteristics with similarly bred Candida albicans Candida albicans strain A parasite that is bred to have some uniform behavioral, morphological, physiological, or genetic characteristics with similarly bred parasite organisms parasite strain Administering substance in vivo where an antibiotic substance is administered to a living organism. Person: Cristian Cocos, Jie Zheng, Chris Stoeckert Penn Group GEMS antibiotic administration process Treatment whose aim is to restore the normal hydration state of a living organism. Person: Cristian Cocos, Jie Zheng, Chris Stoeckert Penn Group GEMS rehydration treatment Environmental system used as dwelling by humans. Person: Cristian Cocos, Jie Zheng, Chris Stoeckert Penn Group GEMS environment associated with human dwelling Specimen collection process aimed at collecting a stool sample. Person: Cristian Cocos, Jie Zheng, Chris Stoeckert Penn Group GEMS stool collection process Organization that undertakes a clinical study at some point in time. Person: Cristian Cocos, Jie Zheng, Chris Stoeckert Penn Group GEMS study center Site where a human life process ended. Person: Cristian Cocos, Jie Zheng, Chris Stoeckert Penn Group GEMS place of death Container used by humans to drink water. Person: Cristian Cocos, Jie Zheng, Chris Stoeckert Penn Group GEMS water container Information Content entity that is a boolean-valued measurement datum, outcome of a chlorine testing assay that aims at testing a body of drinking water for a specified minimum concentration of Chlorine. Person: Cristian Cocos, Jie Zheng, Chris Stoeckert Penn Group GEMS chlorine test result Site where humans wash their hands. Person: Cristian Cocos, Jie Zheng, Chris Stoeckert Penn Group GEMS hand washing location Measurement datum resulted from the volume measurement process of an entire stool. Person: Cristian Cocos, Jie Zheng, Chris Stoeckert Penn Group GEMS stool volume in ml Process of feeding of babies and young children with milk from a woman's breast. Person: Cristian Cocos, Jie Zheng, Chris Stoeckert Penn Group GEMS breastfeeding process Child study subject identifier received upon enrolling into a healthcare study for the first time. Person: Cristian Cocos, Jie Zheng, Chris Stoeckert Penn Group GEMS child study subject identifier at first enrollment A passage history record is a data item recording in sequential order the hosts in which the strain has been previously subcultured in. passage history record A mushroom (or toadstool) is the fleshy, spore-bearing fruiting body of a fungus, typically produced above ground on soil or on its food source. mushroom (food source) infant formula liquid (food source) A solid product is a hard or soft product capable of retaining its own shape at room temperature (20 degrees C.). A soft product that is spreadable or formable is considered semisolid. food (solid) Coverage (read depth or depth) is the average number of reads representing a given nucleotide in the reconstructed sequence. average mapping coverage read coverage 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. biological_process The covalent alteration of one or more amino acid residues within a histone protein. histone modification A reduction in the level of performance of the kidneys in areas of function comprising the concentration of urine, removal of wastes, the maintenance of electrolyte balance, homeostasis of blood pressure, and calcium metabolism. ICEMR protein array Renal insufficiency A phenotypic abnormality. Phenotypic abnormality Epistaxis, or nosebleed, refers to a hemorrhage localized in the nose. Epistaxis Abnormal alignment, positioning, or spacing of the teeth, i.e., misaligned teeth. Misalignment of teeth Yellow pigmentation of the skin due to bilirubin, which in turn is the result of increased bilirubin concentration in the bloodstream. ICEMR protein array Jaundice Abnormal excessive perspiration (sweating) despite the lack of appropriate stimuli like hot and humid weather. Hyperhidrosis Abnormally pale skin. Pallor Pruritus is an itch or a sensation that makes a person want to scratch. This term refers to an abnormally increased disposition to experience pruritus. Pruritus Complete absence of wakefulness and content of conscience, which manifests itself as a lack of response to any kind of external stimuli. ICEMR protein array Coma Abnormal increased size of the spleen. Splenomegaly An abnormal susceptibility to bleeding, often referred to as a bleeding diathesis. A bleeding diathesis may be related to vascular, platelet and coagulation defects. ICEMR protein array Abnormal bleeding Dehydration Forceful ejection of the contents of the stomach through the mouth by means of a series of involuntary spasmic contractions. Vomiting A sensation of unease in the stomach together with an urge to vomit. Nausea An unpleasant sensation characterized by physical discomfort (such as pricking, throbbing, or aching) and perceived to originate in the abdomen. Abdominal pain Difficulty in breathing. The physical presentation of respiratory distress is generally referred to as labored breathing, while the sensation of respiratory distress is called shortness of breath or dyspnea. Respiratory distress Cephalgia, or pain sensed in various parts of the head, not confined to the area of distribution of any nerve. Headache Abnormality of the homeostasis (concentration) of a monoatomic ion. electrolyte disturbances Abnormality of ion homeostasis Genital ulcers An unpleasant sensation characterized by physical discomfort (such as pricking, throbbing, or aching) localized to the lower back. Low back pain Malnutrition Increased size of the parotid gland. Enlargement of parotid gland A type of abdominal pain that comes and goes in waves, most often starting and ending suddenly and being of severe intensity. Abdominal colic An unpleasant sensory and emotional experience associated with actual or potential tissue damage, or described in terms of such damage. Pain Fluid accumulation in the lungs. Pulmonary edema An unpleasant sensation characterized by physical discomfort (such as pricking, throbbing, or aching) localized to the chest. Chest pain An acute hypersensitivity reaction due to exposure to a previously encountered antigen. Anaphylactic shock A small elevation of the skin containing cloudy or purulent material usually consisting of necrotic inflammatory cells. Pustule Warts, benign growths on the skin or mucous membranes that cause cosmetic problems as well as pain and discomfort. Warts most often occur on the hands, feet, and genital areas. Verrucae measurement unit label Examples of measurement unit labels are liters, inches, weight per volume. A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure. 2009-03-16: provenance: a term measurement unit was proposed for OBI (OBI_0000176) , edited by Chris Stoeckert and Cristian Cocos, and subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definition of this, different, term. 2009-03-16: review of this term done during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI. PERSON: Alan Ruttenberg PERSON: Melanie Courtot measurement unit label objective specification In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction. a directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved. 2009-03-16: original definition when imported from OBI read: "objective is an non realizable information entity which can serve as that proper part of a plan towards which the realization of the plan is directed." 2014-03-31: In the example of usage ("In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction") there is a protocol which is the ChIP assay protocol. In addition to being concretized on paper, the protocol can be concretized as a realizable entity, such as a plan that inheres in a person. The objective specification is the part that says that some protein and DNA interactions are identified. This is a specification of a process endpoint: the boundary in the process before which they are not identified and after which they are. During the realization of the plan, the goal is to get to the point of having the interactions, and participants in the realization of the plan try to do that. Answers the question, why did you do this experiment? PERSON: Alan Ruttenberg PERSON: Barry Smith PERSON: Bjoern Peters PERSON: Jennifer Fostel goal specification OBI Plan and Planned Process/Roles Branch OBI_0000217 objective specification action specification Pour the contents of flask 1 into flask 2 a directive information entity that describes an action the bearer will take Alan Ruttenberg OBI Plan and Planned Process branch action specification datum label A label is a symbol that is part of some other datum and is used to either partially define the denotation of that datum or to provide a means for identifying the datum as a member of the set of data with the same label http://www.golovchenko.org/cgi-bin/wnsearch?q=label#4n GROUP: IAO 9/22/11 BP: changed the rdfs:label for this class from 'label' to 'datum label' to convey that this class is not intended to cover all kinds of labels (stickers, radiolabels, etc.), and not even all kind of textual labels, but rather the kind of labels occuring in a datum. datum label data item Data items include counts of things, analyte concentrations, and statistical summaries. a data item is an information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements. 2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers. 2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum. 2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym. 2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/ JAR: datum -- well, this will be very tricky to define, but maybe some information-like stuff that might be put into a computer and that is meant, by someone, to denote and/or to be interpreted by some process... I would include lists, tables, sentences... I think I might defer to Barry, or to Brian Cantwell Smith JAR: A data item is an approximately justified approximately true approximate belief PERSON: Alan Ruttenberg PERSON: Chris Stoeckert PERSON: Jonathan Rees data data item symbol a serial number such as "12324X" a stop sign a written proper name such as "OBI" An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity. 20091104, MC: this needs work and will most probably change 2014-03-31: We would like to have a deeper analysis of 'mark' and 'sign' in the future (see https://code.google.com/p/information-artifact-ontology/issues/detail?id=154). PERSON: James A. Overton PERSON: Jonathan Rees based on Oxford English Dictionary symbol information content entity Examples of information content entites include journal articles, data, graphical layouts, and graphs. A generically dependent continuant that is about some thing. 2014-03-10: The use of "thing" is intended to be general enough to include universals and configurations (see https://groups.google.com/d/msg/information-ontology/GBxvYZCk1oc/-L6B5fSBBTQJ). information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907). Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity. PERSON: Chris Stoeckert OBI_0000142 information content entity 1 1 scalar measurement datum 10 feet. 3 ml. a scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label. 2009-03-16: we decided to keep datum singular in scalar measurement datum, as in this case we explicitly refer to the singular form Would write this as: has_part some 'measurement unit label' and has_part some numeral and has_part exactly 2, except for the fact that this won't let us take advantage of OWL reasoning over the numbers. Instead use has measurment value property to represent the same. Use has measurement unit label (subproperty of has_part) so we can easily say that there is only one of them. PERSON: Alan Ruttenberg PERSON: Melanie Courtot scalar measurement datum directive information entity An information content entity whose concretizations indicate to their bearer how to realize them in a process. 2009-03-16: provenance: a term realizable information entity was proposed for OBI (OBI_0000337) , edited by the PlanAndPlannedProcess branch. Original definition was "is the specification of a process that can be concretized and realized by an actor" with alternative term "instruction".It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term. 2013-05-30 Alan Ruttenberg: What differentiates a directive information entity from an information concretization is that it can have concretizations that are either qualities or realizable entities. The concretizations that are realizable entities are created when an individual chooses to take up the direction, i.e. has the intention to (try to) realize it. 8/6/2009 Alan Ruttenberg: Changed label from "information entity about a realizable" after discussions at ICBO Werner pushed back on calling it realizable information entity as it isn't realizable. However this name isn't right either. An example would be a recipe. The realizable entity would be a plan, but the information entity isn't about the plan, it, once concretized, *is* the plan. -Alan PERSON: Alan Ruttenberg PERSON: Bjoern Peters directive information entity algorithm PMID: 18378114.Genomics. 2008 Mar 28. LINKGEN: A new algorithm to process data in genetic linkage studies. A plan specification which describes the inputs and output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata. Philippe Rocca-Serra PlanAndPlannedProcess Branch OBI_0000270 adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg) algorithm curation status specification The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting) PERSON:Bill Bug GROUP:OBI:<http://purl.obolibrary.org/obo/obi> OBI_0000266 curation status specification data set Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves). A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets. 2009/10/23 Alan Ruttenberg. The intention is that this term represent collections of like data. So this isn't for, e.g. the whole contents of a cel file, which includes parameters, metadata etc. This is more like java arrays of a certain rather specific type 2014-05-05: Data sets are aggregates and thus must include two or more data items. We have chosen not to add logical axioms to make this restriction. person:Allyson Lister person:Chris Stoeckert OBI_0000042 group:OBI data set data about an ontology part data about an ontology part is a data item about a part of an ontology, for example a term Person:Alan Ruttenberg data about an ontology part plan specification PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice. A directive information entity with action specifications and objective specifications as parts that, when concretized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified. 2009-03-16: provenance: a term a plan was proposed for OBI (OBI_0000344) , edited by the PlanAndPlannedProcess branch. Original definition was " a plan is a specification of a process that is realized by an actor to achieve the objective specified as part of the plan". It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term. 2014-03-31: A plan specification can have other parts, such as conditional specifications. Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved Alan Ruttenberg OBI Plan and Planned Process branch OBI_0000344 2/3/2009 Comment from OBI review. Action specification not well enough specified. Conditional specification not well enough specified. Question whether all plan specifications have objective specifications. Request that IAO either clarify these or change definitions not to use them plan specification measurement datum Examples of measurement data are the recoding of the weight of a mouse as {40,mass,"grams"}, the recording of an observation of the behavior of the mouse {,process,"agitated"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}. A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device. 2/2/2009 is_specified_output of some assay? person:Chris Stoeckert OBI_0000305 group:OBI measurement datum textual entity Words, sentences, paragraphs, and the written (non-figure) parts of publications are all textual entities A textual entity is a part of a manifestation (FRBR sense), a generically dependent continuant whose concretizations are patterns of glyphs intended to be interpreted as words, formulas, etc. AR, (IAO call 2009-09-01): a document as a whole is not typically a textual entity, because it has pictures in it - rather there are parts of it that are textual entities. Examples: The title, paragraph 2 sentence 7, etc. MC, 2009-09-14 (following IAO call 2009-09-01): textual entities live at the FRBR (http://en.wikipedia.org/wiki/Functional_Requirements_for_Bibliographic_Records) manifestation level. Everything is significant: line break, pdf and html versions of same document are different textual entities. PERSON: Lawrence Hunter text textual entity document A journal article, patent application, laboratory notebook, or a book A collection of information content entities intended to be understood together as a whole PERSON: Lawrence Hunter document publication A journal article or book A document that has been accepted by a publisher PERSON: Lawrence Hunter publication publication about an investigation Most scientific journal articles A publication that is about an investigation PERSON: Lawrence Hunter scientific publication publication about an investigation A cartesion spatial coordinate datum that uses one value to specify a position along a one dimensional spatial region one dimensional cartesian spatial coordinate datum A scalar measurement datum that is the result of measurement of length quality length measurement datum A scalar measurement datum that is the result of measurement of mass quality mass measurement datum time measurement datum A scalar measurement datum that is the result of measuring a temporal interval 2009/09/28 Alan Ruttenberg. Fucoidan-use-case Person:Alan Ruttenberg time measurement datum email address Alan Ruttenberg 1/3/2012 - Provisional id, see issue at http://code.google.com/p/information-artifact-ontology/issues/detail?id=130&thanks=130&ts=1325636583 Person:Alan Ruttenberg Person:Chris Stoeckart email address documenting Recording the current temperature in a laboratory notebook. Writing a journal article. Updating a patient record in a database. a planned process in which a document is created or added to by including the specified input in it. 6/11/9: Edited at OBI workshop. We need to be able identify a child form of information artifact which corresponds to something enduring (not brain like). This used to be restricted to physical document or digital entity as the output, but that excludes e.g. an audio cassette tape Bjoern Peters wikipedia http://en.wikipedia.org/wiki/Documenting documenting assigning a centrally registered identifier A new pubmed ID being created for a journal article, and the associated pubmed record containing information to the journal article. A license plate number registered at the DMV to be belonging to a specific vehicle and owner. Placing a barcode on a product and entering information in a database that this barcode is assigned. a planned process in which a new CRID is created, associated with an entity, and stored in the CRID registry thereby registering it as being associated with some entity 2014-05-05: It is the CRID registry that assigns CRIDs, not the users of the registry. Person:Alan Ruttenberg Person:Bjoern Peters Person:Melanie Courtot assigning a CRID assigning a centrally registered identifier centrally registered identifier symbol The sentence "The article has Pubmed ID 12345." contains a CRID that has two parts: one part is the CRID symbol, which is '12345'; the other part denotes the CRID registry, which is Pubmed. A symbol that is part of a CRID and that is sufficient to look up a record from the CRID's registry. PERSON: Alan Ruttenberg PERSON: Bill Hogan PERSON: Bjoern Peters PERSON: Melanie Courtot CRID symbol Original proposal from Bjoern, discussions at IAO calls centrally registered identifier symbol centrally registered identifier The sentence "The article has Pubmed ID 12345." contains a CRID that has two parts: one part is the CRID symbol, which is '12345'; the other part denotes the CRID registry, which is Pubmed. An information content entity that consists of a CRID symbol and additional information about the CRID registry to which it belongs. 2014-05-05: In defining this term we take no position on what the CRID denotes. In particular do not assume it denotes a *record* in the CRID registry (since the registry might not have 'records'). Alan, IAO call 20101124: potentially the CRID denotes the instance it was associated with during creation. Note, IAO call 20101124: URIs are not always CRID, as not centrally registered. We acknowledge that CRID is a subset of a larger identifier class, but this subset fulfills our current needs. OBI PURLs are CRID as they are registered with OCLC. UPCs (Universal Product Codes from AC Nielsen)are not CRID as they are not centrally registered. PERSON: Alan Ruttenberg PERSON: Bill Hogan PERSON: Bjoern Peters PERSON: Melanie Courtot CRID Original proposal from Bjoern, discussions at IAO calls centrally registered identifier centrally registered identifier registry PubMed is a CRID registry. It has a dataset of PubMed identifiers associated with journal articles. A CRID registry is a dataset of CRID records, each consisting of a CRID symbol and additional information which was recorded in the dataset through a assigning a centrally registered identifier process. PERSON: Alan Ruttenberg PERSON: Bill Hogan PERSON: Bjoern Peters PERSON: Melanie Courtot CRID registry Original proposal from Bjoern, discussions at IAO calls centrally registered identifier registry A proper name is an information content entity that is the outcome of a dubbing process and is used to refer to one instance of entity shared by a group of people to refer to that individual entity. identifier proper name A role borne by pathogen in virtue of the fact that it or one of its products is sufficiently close to an organism towards which it has the pathogenic disposition to allow realization of the pathogenic disposition. pathogen role An infection bearing the primary infection role. primary infection A part of an extended organism that itself has as part a population of one or more infectious agents and that (1) exists as a result of processes initiated by members of the infectious agent population and is (2) clinically abnormal in virtue of the presence of this infectious agent population, or (3) has a disposition to bring clinical abnormality to immunocompetent organisms of the same Species as the host (the organism corresponding to the extended organism) through transmission of a member or offspring of a member of the infectious agent population. infection human pathogenicity disposition A disposition to initiate processes that result in a disorder in a human organism. Human Pathogenicity of Suspected Organism(s) in Specimen CS19 NIAID GSCID-BRC human pathogenicity disposition Hymenolepis nana Viruses Viruses Adenoviridae Rotavirus Entamoeba coli Endolimax nana Euteleostomi bony vertebrates Euteleostomi Norovirus GI Norovirus GII Vibrio cholerae O1 Shigella flexneri 2b Norovirus Clostridioides difficile Shigella flexneri 4c Shigella flexneri X variant Campylobacter Campylobacter coli Campylobacter jejuni Bacteria eubacteria Bacteria Helicobacter pylori Archaea Archaea Eukaryota eucaryotes eukaryotes Eukaryota Euarchontoglires Euarchontoglires Tetrapoda tetrapods Tetrapoda Amniota amniotes Amniota Opisthokonta Opisthokonta Bilateria Bilateria Ancylostomatoidea Trichuris trichiura Shigella flexneri 1a Astroviridae Mammalia mammals Mammalia Shigella flexneri 1b Shigella flexneri 3a Shigella flexneri 5a Shigella flexneri Y Shigella flexneri 2a Shigella flexneri 3b Cyclospora Chilomastix mesnili Fungi Ancylostoma duodenale Enterobius vermicularis Necator americanus Candida albicans Escherichia coli Isospora Giardia Entamoeba histolytica Cryptosporidium Plasmodium Salmonella Schistosoma Shigella Taenia Shigella boydii Hymenolepis diminuta Shigella dysenteriae Shigella flexneri Shigella sonnei Strongyloides stercoralis Ascaris lumbricoides Yersinia enterocolitica Aeromonas Vibrio Vibrio cholerae Vibrio parahaemolyticus Plesiomonas shigelloides Balantioides coli Vertebrata <Metazoa> Vertebrata vertebrates Vertebrata <Metazoa> Bacteroides fragilis Sapovirus Homo sapiens human human being man Homo sapiens Canis lupus familiaris Shigella flexneri 4a A species of nonpathogenic parasitic amoeba. Transmission of I. butschlii is by a fecal-oral route and infection is usually asymptomatic. Iodamoeba butschlii A kingdom of eukaryotic, heterotrophic organisms that live as saprobes or parasites, including mushrooms, yeasts, smuts, molds, etc. They reproduce either sexually or asexually, and have life cycles that range from simple to complex. Filamentous fungi refer to those that grow as multicellular colonies (mushrooms and molds). Fungus A note acknowledging a source of information or quoting a passage. Reference A data transformation that add two or more numbers, magnitudes, quantities, or particulars as determined by or as if by the mathematical process of addition. tracker: https://github.com/obcs/obcs/issues/7 Person: Jie Zheng http://dictionary.reference.com/browse/summing PRISM summing data transformation A data item that is produced as the output of a summing data transformation and represents the total value of the input data. Tracker:https://github.com/obcs/obcs/issues/7 Person: Jie Zheng Jie Zheng sum value A material entity that is bearer of a medication role. medication material A processed specimen which is the output of a density gradient centrifugation of an anticoagulated blood specimen that contains most of the white blood cells and platelets. buffy coat specimen A scalar measurement datum that is the output of a volume measurement assay that has a blood specimen as evaluant. blood specimen volume planned process Injecting mice with a vaccine in order to test its efficacy A processual entity that realizes a plan which is the concretization of a plan specification. '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.) We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some objectives is a planned process. Bjoern Peters branch derived 6/11/9: Edited at workshop. Used to include: is initiated by an agent 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 biological feature identification objective Biological_feature_identification_objective is an objective role carried out by the proposition defining the aim of a study designed to examine or characterize a particular biological feature. Jennifer Fostel biological feature identification objective processed material Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples Is a material entity that is created or changed during material processing. PERSON: Alan Ruttenberg processed material investigation Lung cancer investigation using expression profiling, a stem cell transplant investigation, biobanking is not an investigation, though it may be part of an investigation a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s). Bjoern Peters OBI branch derived Could add specific objective specification Following OBI call November 2012,26th: it was decided there was no need for adding "achieves objective of drawing conclusion" as existing relations were providing equivalent ability. this note closes the issue and validates the class definition to be part of the OBI core editor = PRS study investigation evaluant role When a specimen of blood is assayed for glucose concentration, the blood has the evaluant role. When measuring the mass of a mouse, the evaluant is the mouse. When measuring the time of DNA replication, the evaluant is the DNA. When measuring the intensity of light on a surface, the evaluant is the light source. a role that inheres in a material entity that is realized in an assay in which data is generated about the bearer of the evaluant role Role call - 17nov-08: JF and MC think an evaluant role is always specified input of a process. Even in the case where we have an assay taking blood as evaluant and outputting blood, the blood is not the specified output at the end of the assay (the concentration of glucose in the blood is) examples of features that could be described in an evaluant: quality.... e.g. "contains 10 pg/ml IL2", or "no glucose detected") GROUP: Role Branch OBI Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term. evaluant role reporting party role Person who prepares microarray data in MAGE-TAB format and submits to a database, such as ArrayExpress. The first section has been pre-designated as the 'Reporting Party' section and should be filled with the Reporting Party's personal information. http://www.mercedsheriff.com/SelfReporting.htm a study personnel role played by a party who reports the outcome of a study component MO:submitter mapped to this term. So, alternative term 'submitter' was added. Jennifer Fostel reporting party submitter OBI reporting party role assay Assay the wavelength of light emitted by excited Neon atoms. Count of geese flying over a house. A planned process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies. 12/3/12: BP: the reference to the 'physical examination' is included to point out that a prediction is not an assay, as that does not require physical examiniation. PlanAndPlannedProcess Branch measuring scientific observation OBI branch derived study assay any method assay sample preparation for assay A sample_preparation_for_assay is a protocol_application including material_enrollments and biomaterial_transformations. definition_source: OBI. PlanAndPlannedProcess Branch study OBI branch derived sample preparation for assay culture medium A growth medium or culture medium is a substance in which microorganisms or cells can grow. Wikipedia, growth medium, Feb 29, 2008 a processed material that provides the needed nourishment for microorganisms or cells grown in vitro. changed from a role to a processed material based on on Aug 22, 2011 dev call. Details see the tracker item: http://sourceforge.net/tracker/?func=detail&aid=3325270&group_id=177891&atid=886178 Modification made by JZ. Person: Jennifer Fostel, Jie Zheng OBI culture medium material processing A cell lysis, production of a cloning vector, creating a buffer. A planned process which results in physical changes in a specified input material PERSON: Bjoern Peters PERSON: Frank Gibson PERSON: Jennifer Fostel PERSON: Melanie Courtot PERSON: Philippe Rocca Serra material transformation OBI branch derived material processing A role that is realized through the execution of a study design in which the bearer of the role participates and in which data about that bearer is collected. participant under investigation role responsible party role he THERAPIST has the ability to print a separate statement for the patient and each responsible party. http://www.beaverlog.com/therapist/ez_support/billing/responsible_party_statements.htm a study personnel role played by a party who is accountable for the execution of a study component and can make decisions about the conduct of the study Person: Jennifer Fostel responsible party OBI responsible party role principal investigator role a responsible party role played by a person responsible for the overall conduct of a study Person: Jennifer Fostel principal investigator CDISC definition: A person responsible for the conduct of the clinical trial at a trial site. If a trial is conducted by a team of individuals at a trial site, the investigator is the responsible leader of the team and may be called the principal investigator. 2. The individual principal investigator. 2. The individual under whose immediate direction the test article is administered or dispensed to, or used involving, a subject, or, in the event of an investigation conducted by a team of individuals, is See also sponsor-investigator.; Leiter der klinischen Prufung.Under the German Drug Law, the physician who is head of the clinical investigation (CDISC): coordinating investigator (CDISC) (also study coordinator, MUSC); sponsor-investigator. An individual who both initiates and conducts, alone or with others, a clinical trial, and under whose immediate direction the investigational product is administered to, dispensed to, or used by a subject.NOTE: The term does not include any person other than an individual, hence not a corporation, agency (CDISC) principal investigator role specimen role liver section; a portion of a culture of cells; a nemotode or other animal once no longer a subject (generally killed); portion of blood from a patient. a role borne by a material entity that is gained during a specimen collection process and that can be realized by use of the specimen in an investigation 22Jun09. The definition includes whole organisms, and can include a human. The link between specimen role and study subject role has been removed. A specimen taken as part of a case study is not considered to be a population representative, while a specimen taken as representing a population, e.g. person taken from a cohort, blood specimen taken from an animal) would be considered a population representative and would also bear material sample role. Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation. blood taken from animal: animal continues in study, whereas blood has role specimen. something taken from study subject, leaves the study and becomes the specimen. parasite example - when parasite in people we study people, people are subjects and parasites are specimen - when parasite extracted, they become subject in the following study specimen can later be subject. GROUP: Role Branch OBI specimen role a population is a collection of individuals from the same taxonomic class living, counted or sampled at a particular site or in a particular area population investigation agent role The person perform microarray experiments and submit microarray results (including raw data, processed data) with experiment description to ArrayExpress. A role borne by an entity and that is realized in a process that is part of an investigation in which an objective is achieved. These processes include, among others: planning, overseeing, funding, reviewing. Implementing a study means carrying out or performing the study and providing reagents or other materials used in the study and other tasks without which the study would not happen. Philly2013: Historically, this role would have been borne only by humans or organizations. However, we now also want to enable representing investigations run by robot scientists such as ADAM (King et al, Science, 2009) GROUP: Role Branch investigator OBI Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term. study person role Philly2013: Historically, this role would have been borne only by humans or organizations. However, we now also want to enable investigations run by robot scientists such as ADAM (King et al, Science, 2009) investigation agent role organization PMID: 16353909.AAPS J. 2005 Sep 22;7(2):E274-80. Review. The joint food and agriculture organization of the United Nations/World Health Organization Expert Committee on Food Additives and its role in the evaluation of the safety of veterinary drug residues in foods. An entity that can bear roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members. BP: The definition summarizes long email discussions on the OBI developer, roles, biomaterial and denrie branches. It leaves open if an organization is a material entity or a dependent continuant, as no consensus was reached on that. The current placement as material is therefore temporary, in order to move forward with development. Here is the entire email summary, on which the definition is based: 1) there are organization_member_roles (president, treasurer, branch editor), with individual persons as bearers 2) there are organization_roles (employer, owner, vendor, patent holder) 3) an organization has a charter / rules / bylaws, which specify what roles there are, how they should be realized, and how to modify the charter/rules/bylaws themselves. It is debatable what the organization itself is (some kind of dependent continuant or an aggregate of people). This also determines who/what the bearer of organization_roles' are. My personal favorite is still to define organization as a kind of 'legal entity', but thinking it through leads to all kinds of questions that are clearly outside the scope of OBI. Interestingly enough, it does not seem to matter much where we place organization itself, as long as we can subclass it (University, Corporation, Government Agency, Hospital), instantiate it (Affymetrix, NCBI, NIH, ISO, W3C, University of Oklahoma), and have it play roles. This leads to my proposal: We define organization through the statements 1 - 3 above, but without an 'is a' statement for now. We can leave it in its current place in the is_a hierarchy (material entity) or move it up to 'continuant'. We leave further clarifications to BFO, and close this issue for now. PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Philippe Rocca-Serra PERSON: Susanna Sansone GROUP: OBI organization protocol PCR protocol, has objective specification, amplify DNA fragment of interest, and has action specification describes the amounts of experimental reagents used (e..g. buffers, dNTPS, enzyme), and the temperature and cycle time settings for running the PCR. A plan specification which has sufficient level of detail and quantitative information to communicate it between investigation agents, so that different investigation agents will reliably be able to independently reproduce the process. PlanAndPlannedProcess Branch OBI branch derived + wikipedia (http://en.wikipedia.org/wiki/Protocol_%28natural_sciences%29) study protocol protocol drawing a conclusion based on data Concluding that a gene is upregulated in a tissue sample based on the band intensity in a western blot. Concluding that a patient has a infection based on measurement of an elevated body temperature and reported headache. Concluding that there were problems in an investigation because data from PCR and microarray are conflicting. Concluding that 'defects in gene XYZ cause cancer due to improper DNA repair' based on data from experiments in that study that gene XYZ is involved in DNA repair, and the conclusion of a previous study that cancer patients have an increased number of mutations in this gene. A planned process in which data gathered in an investigation is evaluated in the context of existing knowledge with the objective to generate more general conclusions or to conclude that the data does not allow one to draw general conclusion PERSON: Bjoern Peters PERSON: Jennifer Fostel Bjoern Peters drawing a conclusion based on data planning The process of a scientist thinking about and deciding what reagents to use as part of a protocol for an experiment. Note that the scientist could be human or a "robot scientist" executing software. a process of creating or modifying a plan specification 7/18/2011 BP: planning used to itself be a planned process. Barry Smith pointed out that this would lead to an infinite regression, as there would have to be a plan to conduct a planning process, which in itself would be the result of planning etc. Therefore, the restrictions on 'planning' were loosened to allow for informal processes that result in an 'ad hoc plan '. This required changing from 'has_specified_output some plan specifiction' to 'has_participant some plan specification'. Bjoern Peters Bjoern Peters Plans and Planned Processes Branch planning extract Up-regulation of inflammatory signalings by areca nut extract and role of cyclooxygenase-2 -1195G>a polymorphism reveal risk of oral cancer. Cancer Res. 2008 Oct 15;68(20):8489-98. PMID: 18922923 an extract is a material entity which results from an extraction process PERSON: Philippe Rocca-Serra extracted material GROUP: OBI Biomatrial Branch extract averaging objective A mean calculation which has averaging objective is a descriptive statistics calculation in which the mean is calculated by taking the sum of all of the observations in a data set divided by the total number of observations. It gives a measure of the 'center of gravity' for the data set. It is also known as the first moment. An averaging objective is a data transformation objective where the aim is to perform mean calculations on the input of the data transformation. Elisabetta Manduchi James Malone PERSON: Elisabetta Manduchi averaging objective assay objective the objective to determine the weight of a mouse. an objective specification to determine a specified type of information about an evaluated entity (the material entity bearing evaluant role) PPPB branch PPPB branch assay objective material transformation objective The objective to create a mouse infected with LCM virus. The objective to create a defined solution of PBS. an objective specifiction that creates an specific output object from input materials. PERSON: Bjoern Peters PERSON: Frank Gibson PERSON: Jennifer Fostel PERSON: Melanie Courtot PERSON: Philippe Rocca-Serra artifact creation objective GROUP: OBI PlanAndPlannedProcess Branch material transformation objective study design execution injecting a mouse with PBS solution, weighing it, and recording the weight according to a study design. a planned process that realizes the concretization of a study design removed axiom has_part some (assay or 'data transformation') per discussion on protocol application mailing list to improve reasoner performance. The axiom is still desired. branch derived 6/11/9: edited at workshop. Used to be: study design execution is a process with the objective to generate data according to a concretized study design. The execution of a study design is part of an investigation, and minimally consists of an assay or data transformation. study design execution A sequencing assay which determines information on the sequence of a DNA molecule. DNA sequencing assay material separation objective The objective to obtain multiple aliquots of an enzyme preparation. The objective to obtain cells contained in a sample of blood. is an objective to transform a material entity into spatially separated components. PPPB branch PPPB branch material separation objective a portion of urine collected from an organism urine specimen a material entity derived from a portion of blood collected from an organism blood specimen specimen collection process drawing blood from a patient for analysis, collecting a piece of a plant for depositing in a herbarium, buying meat from a butcher in order to measure its protein content in an investigation A planned process with the objective of collecting a specimen. Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation. Philly2013: A specimen collection can have as part a material entity acquisition, such as ordering from a bank. The distinction is that specimen collection necessarily involves the creation of a specimen role. However ordering cell lines cells from ATCC for use in an investigation is NOT a specimen collection, because the cell lines already have a specimen role. Philly2013: The specimen_role for the specimen is created during the specimen collection process. label changed to 'specimen collection process' on 10/27/2014, details see tracker: http://sourceforge.net/p/obi/obi-terms/716/ Bjoern Peters specimen collection 5/31/2012: This process is not necessarily an acquisition, as specimens may be collected from materials already in posession 6/9/09: used at workshop ICEMR protein array specimen collection process sample from organism a material obtained from an organism in order to be a representative of the whole 5/29: This is a helper class for now we need to work on this: Is taking a urine sample a material separation process? If not, we will need to specify what 'taking a sample from organism' entails. We can argue that the objective to obtain a urine sample from a patient is enough to call it a material separation process, but it could dilute what material separation was supposed to be about. sample from organism portioning objective The objective to obtain multiple aliquots of an enzyme preparation. A material separation objective aiming to separate material into multiple portions, each of which contains a similar composition of the input material. portioning objective average value A data item that is produced as the output of an averaging data transformation and represents the average value of the input data. PERSON: James Malone PERSON: Monnie McGee arithmetic mean average value separation into different composition objective The objective to obtain cells contained in a sample of blood. A material separation objective aiming to separate a material entity that has parts of different types, and end with at least one output that is a material with parts of fewer types (modulo impurities). We should be using has the grain relations or concentrations to distinguish the portioning and other sub-objectives separation into different composition objective specimen collection objective The objective to collect bits of excrement in the rainforest. The objective to obtain a blood sample from a patient. A objective specification to obtain a material entity for potential use as an input during an investigation. Bjoern Peters Bjoern Peters specimen collection objective host role is a role played by an organism and realized by providing nourishment, shelter or a means of reproduction to another organism within the organism playing the host role host role material sample role a role borne by a portion of blood taken to represent all the blood in an organism; the role borne by a population of humans with HIV enrolled in a study taken to represent patients with HIV in general. A material sample role is a specimen role borne by a material entity that is the output of a material sampling process. 7/13/09: Note that this is a relational role: between the sample taken and the 'sampled' material of which the sample is thought to be representative off. material sample role material sample blood drawn from patient to measure his systemic glucose level. A population of humans with HIV enrolled in a study taken to represent patients with HIV in general. A material entity that has the material sample role OBI: workshop sample population sample material sample material maintenance objective An objective specification maintains some or all of the qualities of a material over time. PERSON: Bjoern Peters PERSON: Bjoern Peters material maintenance objective A planned process in which a person or their legal representative is informed about key facts about potential risks and benefits of a process and makes a documented decision as to whether the person in question will participate. ICEMR protein array informed consent process material maintenance a process with that achieves the objective to maintain some or all of the characteristics of an input material over time material maintenance A medical organization at which sick or injured people are given clinical care hospital a information content entity created to indicate that information about something is not available to the person recording it. record of missing knowledge sequence feature annotation Information about a sequence region Bjoern Peters Bjoern Peters place holder for sequence ontology term sequence feature annotation infectious agent is a material entity bearing the disposition to infect an organism IEDB IEDB Suspected Organism(s) in Specimen CS17, CS18 NIAID GSCID-BRC infectious agent A measurement datum that is reported on a categorical scale categorical measurement datum service consumer role A biologist who uses a sequencing services fulfills the role of a service consumer a role which inheres in a person who uses a service Person:Helen Parkinson OBI service consumer role service provider role Jackson Lab provides experimental animals, EBI provides training on databases, a core facility provides access to a DNA sequencer. is a role which inheres in a person or organization and is realized in in a planned process which provides access to training, materials or execution of protocols for an organization or person PERSON:Helen Parkinson service provider role A specimen that has been intentionally physically modified. processed specimen A device that can be used to restrict the location of material entities over time container A material entity that is designed to perform a function in a scientific investigation, but is not a reagent. device sequence data example of usage: the representation of a nucleotide sequence in FASTA format used for a sequence similarity search. A measurement datum that representing the primary structure of a macromolecule(it's sequence) sometimes associated with an indicator of confidence of that measurement. Person:Chris Stoeckert GROUP: OBI sequence data The directed combination of a material entity with a specimen. administration of material to specimen individual organism identifier a CRID symbol used to distinguish one individual organism from another. PERSON: Chris Stoeckert, Jie Zheng MO_169 Individual Specimen Source ID CS1 NIAID GSCID-BRC individual organism identifier age measurement assay An assay that measures the duration of temporal interval of a process that is part of the life of the bearer, where the initial time point of the measured process is the beginning of some transitional state of the bearer such as birth or when planted. This assay measures time not developmental stage. we recognize that development takes different time periods under different conditions such as media / temperature. For example, age measurement assay of fly age, the output likes 28 days but not mid-life of age at room temperature. PERSON: Alan Ruttenberg OBI group age measurement assay age measurement datum A time measurement datum that is the result of measurement of age of an organism note that we are currently defining subtypes of age measurement datum that specify when the age is relative to, e.g. planting, as we don't have adequate temporal predicates yet. life of bearer doesn't imply organism this assay measures time not developmental stage. we recognize that development can take different time periods under different conditions such as media / temperature age as a quality is dubious; we plan to revisit stages in development are currently handled with controlled vocabulary, such as 2-somite stage PERSON: Alan Ruttenberg, Chris Stoeckert, Jie Zheng MO_178 Age In MageTab file, we use initialTimePoint (a process) + age (a number expected) + TimeUnit (definied in UO, such as year, hour, day, etc.) Now we use the term label indicating the start time point of measuring the age, (number + TimeUnit) are expected instances of the class discussed on Nov 15, dev call All subtype will be defined by textual definition now. Specimen Source Age - Value CS6 NIAID GSCID-BRC age measurement datum An age measurement datum that is the result of the measurement of the age of an organism since birth, the process of emergence and separation of offspring from the mother. age since birth measurement datum The time it takes for 50% of a class of stochastic processes to occur. half life datum (t 1/2) service providing a training course for UCSD employees how to run a DNA sequencer; sequencing a DNA sample provided by a service consumer restricted to non-human samples; giving access to tissue samples in a biobank within OHSU; JAX shipping mice from their colony A planned process in which a service provider performs a task (i.e. a planned process) for a service consumer. Carlo; Matt OBI workshop San Diego 2011 service An organism that is bred to have some uniform behavioral, morphological, physiological, or genetic characteristics with similarly bred organisms selectively maintained organism a genetic characteristics information that is about the genetic material of an organism and minimally includes information about the genetic background and can in addition contain information about specific alleles, genetic modifications, etc. genotype information a data item that is about genetic material including polymorphisms, disease alleles, and haplotypes. genetic characteristics information tissue specimen A specimen that derives from an anatomical part or substance arising from an organism. Examples of tissue specimen include tissue, organ, physiological system, blood, or body location (arm). PERSON: Chris Stoeckert, Jie Zheng MO_954 organism_part Specimen Type CS16 NIAID GSCID-BRC tissue specimen material maintenance service model organism colony maintanance A material processing service in which a service provider makes physical modifications to a specified input material, such that at least one of the specified outputs of this process is a modified version of a specified input material. PERSON: Carlo Torniai PERSON: Matthew Brush PERSON: Matthew Brush Here we need to go back to the defintoin of storage process. It has object specification which is material maintenance. Not necessareley a material maintenance is needed in a storage process. material maintenance service sequence assembly algorithm An algorithm used to assemble individual sequence reads into larger contiguous sequences (contigs). Assembly details include but are not limited to assembler type (overlap-layout-consensus, deBruijn), assembler version, and any relevant quality control information such as per cent known genes/ESTs captured. Person: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Assembly Method SA6 NIAID GSCID-BRC NIAID GSCID-BRC sequence assembly algorithm material service A service performing DNA sequencing, a service preforming cell analysis. A service performing cell line immortalization A service which has a material entity as specified input and/or specified output. PERSON: Carlo Torniai PERSON: Matthew Brush PERSON: Carlo Torniai material service material analysis service Services performing DNA sequencing or Cell Analysis A service in which a service consumer provides some input material and a service provider performs some analysis of this material to generate data that is returned to the service consumer. PERSON: Carlo Torniai PERSON: Matthew Brush PERSON: Matthew Brush material analysis service A scalar measurement datum that represents the number of events occuring over a time interval rate measurement datum material storage service A service that offers liquid nitrogen stroage. A storage service in which a service consumer provides some material as input which a service provider stores and returns as output. PERSON: Carlo Torniai PERSON: Matthew Brush PERSON: Matthew Brush material storage service GenBank ID A CRID symbol uniquely indentifies the submitted GeneBank sequence record. Person: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group GenBank Record ID SA10 NIAID GSCID-BRC NIAID GSCID-BRC GenBank ID investigation description A textual entity that describes an investigation. Person: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group study description Project Description CP3 NIAID GSCID-BRC NIAID GSCID-BRC investigation description specimen identifier A CRID symbol denotes a specimen and used to distinguish one specimen from another in an investigation. Person: Chris Stoeckert, Jie Zheng specimen ID NIAID GSCID-BRC metadata working group Specimen ID CS15 NIAID GSCID-BRC ICEMR protein array NIAID GSCID-BRC specimen identifier PubMed ID A CRID symbol that is sufficient to look up a citation from the PubMed, a literature database of life sciences and biomedical information. Person: Chris Stoeckert, Jie Zheng PMID PubMed Identifier Website: http://en.wikipedia.org/wiki/Wikipedia:PMID Publication Citation CP12 NIAID GSCID-BRC NIAID GSCID-BRC PubMed ID average depth of sequence coverage An average value of the depth of sequence coverage based both on external (e.g. Cot-based size estimates) and internal (average coverage in the assembly) measures of genome size. Person: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Genome Coverage SA7 NIAID GSCID-BRC NIAID GSCID-BRC average depth of sequence coverage specimen collection time measurement datum A time measurement datum that is the measure of the time when the specimens are collected. Person: Chris Stoeckert, Jie Zheng collection date NIAID GSCID-BRC metadata working group Specimen Collection Date CS10 NIAID GSCID-BRC ICEMR protein array NIAID GSCID-BRC specimen collection time measurement datum latitude coordinate measurement datum A measurement datum that is the measure of the latitude coordinate of a site. Person: Chris Stoeckert, Jie Zheng latitude NIAID GSCID-BRC metadata working group Specimen Collection Location - Latitude CS11 NIAID GSCID-BRC ICEMR protein array NIAID GSCID-BRC latitude coordinate measurement datum longitude coordinate measurement datum A measurement datum that is the measure of the longitude coordinate of a site. Person: Chris Stoeckert, Jie Zheng longitude NIAID GSCID-BRC metadata working group Specimen Collection Location - Longitude CS12 NIAID GSCID-BRC ICEMR protein array NIAID GSCID-BRC longitude coordinate measurement datum investigation title A textual entity that denotes an investigation. Person:Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group study title Project Title CP1 NIAID GSCID-BRC NIAID GSCID-BRC investigation title organism identification objective A biological feature identification objective to identify the organism species in a specimen. Person: Chris Stoeckert, Jie Zheng Penn Group organism identification objective organism identification assay An assay that identifies the organism species in a specimen. Person: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Organism Detection Method CS21 NIAID GSCID-BRC NIAID GSCID-BRC organism identification assay sequence annotation algorithm An algorithm used to identify sequence features (e.g. protein coding regions) in the assembled contig sequence. This may also include a description of any manual curation that may have generated or validated the annotation. Person: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group NIAID GSCID-BRC sequence annotation algorithm Bioinformatics Resource Center An organization that is one of the Internet-based research centers established and funded by NIAID (the National Institute of Allergy and Infectious Diseases). The Bioinformatics Resource Centers (BRCs) were formed in response to the threats posed by emerging and re-emerging pathogens, particularly CDC Category A, B, and C pathogens, and their potential use in bioterrorism. The intention of NIAID in funding these bioinformatics centers is to assist researchers involved in the experimental characterization of such pathogens and the formation of drugs, vaccines, or diagnostic tools to combat them. Person: Chris Stoeckert, Jie Zheng BRC Website: http://en.wikipedia.org/wiki/Bioinformatics_Resource_Centers Bioinformatics Resource Center CP20 NIAID GSCID-BRC NIAID GSCID-BRC Bioinformatics Resource Center country name A textual entity that denotes a geographic location that is a site or part of a site that is identified as a country in the political geography. Person: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Website: http://en.wikipedia.org/wiki/Country Specimen Collection Location - Country CS14 NIAID GSCID-BRC ICEMR protein array NIAID GSCID-BRC country name investigation identifier A CRID symbol used to identify an investigation. Person: Chris Stoeckert, Jie Zhneg NIAID GSCID-BRC metadata working group Project ID CP2 NIAID GSCID-BRC NIAID GSCID-BRC investigation identifier grant identifier A CRID symbol used to identify a grant. Person: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Supporting Grants/Contract ID CP11 NIAID GSCID-BRC NIAID GSCID-BRC grant identifier grant A plan specification of organization A to give money to organization B so that B conducts investigations. Organization A has funder role and Organization B has research organization role. Discussed on Feb 13, 2012 dev call. Details see the tracker: https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891&atid=886178 Group: OBI OBI AR: Grant isn't a plan specification, it has a part which is a plan specification. See tracker: https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891&atid=886178 grant contact representative role A role inhering in a person who represents an institution, organization, or service provider and realized when communication is directed at them about the entity they represent. Discussed on May 7, 2012 dev call propose:contact role, type of organization role, and create shortcut relation between 'organization role' and 'organization' ? Whether it works for communicating author in manuscript or not? Tracker: https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891&atid=886178 Person: Chris Stoeckert NIAID GSCID-BRC contact representative role specimen collector role An Investigation agent role borne by a person or organization which is realized in a specimen collection process. Person: Jie Zheng, Chris Stoeckert Penn Group NIAID GSCID-BRC specimen collector role A material entity comprised of cultured cells and the media in which they are being propagated or stored. cell culture organization of specimen provider principal investigator An organization that is the affiliation of the principal investigator providing the specimens for the investigation PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Sample Provider PI's Institution CP14 NIAID GSCID-BRC NIAID GSCID-BRC organization of specimen provider principal investigator organization of Bioinformatics Resource Center contact person An organization that is the affiliation of the person who is contact representative of a Bioinformatics Resource Center PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Bioinformatics Resource Center Contact's Institution CP22 NIAID GSCID-BRC NIAID GSCID-BRC organization of Bioinformatics Resource Center contact person target material in specimen specification Some examples of target material are Genome, Purified chromosome, Transcriptome, Phenotype, Proteome. A plan specification which specifies the type of material that will be assayed in an investigation. PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Target Material CP6 NIAID GSCID-BRC NIAID GSCID-BRC target material in specimen specification Bioinformatics Resource Center contact person A person who is the contact representative of a Bioinformatics Resource Center PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Bioinformatics Resource Center Contact Name CP21 NIAID GSCID-BRC NIAID GSCID-BRC Bioinformatics Resource Center contact person specimen-based scope of investigation specification Some examples of specimen scope are Monoisolate, Multiisolate, Multi-species, Environment, or Synthetic. A plan specification which specifies the scope of an investigation based on the heterogeneity of organisms or type of material that are the specified input of specimen collection. PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Sample Scope CP5 NIAID GSCID-BRC NIAID GSCID-BRC specimen-based scope of investigation specification specimen repository organization An organization that provides a service to store and distribute specimens PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Specimen Repository CS22 NIAID GSCID-BRC NIAID GSCID-BRC specimen repository organization email address of Bioinformatics Resource Center contact person An email address of the person who is contact representative of a Bioinformatics Resource Center PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Bioinformatics Resource Center Contact's email CP23 NIAID GSCID-BRC NIAID GSCID-BRC email address of Bioinformatics Resource Center contact person sequencing facility contact person A person who is the contact representative at the sequencing facility PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Sequencing Facility Contact Name CP17 NIAID GSCID-BRC NIAID GSCID-BRC sequencing facility contact person specimen provider principal investigator A person who is a principal investigator and provides the specimen PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Sample Provider Principal Investigator (PI) Name CP13 NIAID GSCID-BRC NIAID GSCID-BRC specimen provider principal investigator email address of specimen collector An email address of the person collecting the specimen PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Specimen Collector's email CS27 NIAID GSCID-BRC NIAID GSCID-BRC email address of specimen collector sequencing facility organization An organization that provides sequence determination service PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Sequencing Facility CP16 NIAID GSCID-BRC NIAID GSCID-BRC sequencing facility organization specification of data to be generated in an investigation Some examples of Project Objectives are Raw sequence reads, Sequence, Analysis, Assembly, Annotation, Variation, Epigenetic markers, expression, maps, phenotype An objective specification which indicates the type of data that will be generated and submitted to a database. PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Project Objectives CP9 NIAID GSCID-BRC NIAID GSCID-BRC specification of data to be generated in an investigation organization of specimen collector An organization that is the affiliation of the person collecting the specimen PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Specimen Collector's Institution CS26 NIAID GSCID-BRC NIAID GSCID-BRC organization of specimen collector email address of sequencing facility contact person An email address of the contact representative at the sequencing facility PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Sequencing Facility Contact's email CP19 NIAID GSCID-BRC NIAID GSCID-BRC email address of sequencing facility contact person specimen collector A person who collects the specimen PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Specimen Collector Name CS25 NIAID GSCID-BRC NIAID GSCID-BRC specimen collector investigation assay specification Some examples of Project Method are Sequence, Array, Mass Spectrometry A plan specification which indicates the assay type used to obtain data. PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Project Method CP8 NIAID GSCID-BRC NIAID GSCID-BRC investigation assay specification organization of sequencing facility contact person An organization that is the affiliation of the contact representative at the sequencing facility PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Sequencing Facility Contact's Institution CP18 NIAID GSCID-BRC NIAID GSCID-BRC organization of sequencing facility contact person comment on investigation A textual entity that is about any of the aspects of an investigation worth noting PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Comments CS24 NIAID GSCID-BRC ICEMR protein array NIAID GSCID-BRC comment on investigation target capture specification Some examples of target capture are Whole, CloneEnds, Exome, TargetedLocusLoci, RandomSurvey A plan specification which specifies how the material enrichment procedure will influence the scale, or type of material that will be assayed in the specimen. PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Target Capture CP7 NIAID GSCID-BRC NIAID GSCID-BRC target capture specification specimen identifier assigned by specimen repository A specimen identifier which is assigned by a specimen repository PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Specimen Repository Sample ID CS23 NIAID GSCID-BRC NIAID GSCID-BRC specimen identifier assigned by specimen repository specimen identifier assigned by sequencing facility A specimen identifier which is assigned by a sequencing facility PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Sample ID - Sequencing Facility SA1 NIAID GSCID-BRC NIAID GSCID-BRC specimen identifier assigned by sequencing facility sample preparation for sequencing assay A sample preparation for assay that preparation of nucleic acids for a sequencing assay PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Nucleic Acid Preparation Method SA3 NIAID GSCID-BRC NIAID GSCID-BRC sample preparation for sequencing assay email address of specimen provider principal investigator An email address of the principal investigator providing the specimens for the investigation PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Sample Provider PI's email CP15 NIAID GSCID-BRC NIAID GSCID-BRC email address of specimen provider principal investigator sequencing service A service provides sequencing service which is the realization of some sequencing such as RNA and DNA sequencing in which the service provider role is realized. Person: Jie Zheng Adpated from 'DNA sequencing service' NIAID GSCID-BRC sequencing service conclusion based on data The conclusion that a gene is upregulated in a tissue sample based on the band intensity in a western blot. The conclusion that a patient has a infection based on measurement of an elevated body temperature and reported headache. The conclusion that there were problems in an investigation because data from PCR and microarray are conflicting. The following are NOT conclusions based on data: data themselves; results from pure mathematics, e.g. "13 is prime". An information content entity that is inferred from data. In the Philly 2013 workshop, we recognized the limitations of "conclusion textual entity", and we introduced this as more general. The need for the 'textual entity' term going forward is up for future debate. Group:2013 Philly Workshop group Group:2013 Philly Workshop group conclusion based on data cell freezing medium A processed material that serves as a liquid vehicle for freezing cells for long term quiescent stroage, which contains chemicls needed to sustain cell viability across freeze-thaw cycles. PERSON: Matthew Brush cell freezing medium 1 1 scalar value specification A value specification that consists of two parts: a numeral and a unit label PERSON:Bjoern Peters scalar value specification value specification The value of 'positive' in a classification scheme of "positive or negative"; the value of '20g' on the quantitative scale of mass. An information content entity that specifies a value within a classification scheme or on a quantitative scale. This term is currently a descendant of 'information content entity', which requires that it 'is about' something. A value specification of '20g' for a measurement data item of the mass of a particular mouse 'is about' the mass of that mouse. However there are cases where a value specification is not clearly about any particular. In the future we may change 'value specification' to remove the 'is about' requirement. PERSON:Bjoern Peters value specification grant agency An organization that provides funding support for projects such as investigations. PERSON: Jie Zheng, Chris Stoeckert funding organization NIAID GSCID-BRC metadata working group Grant Agency CP10 NIAID GSCID-BRC NIAID GSCID-BRC grant agency 'funding organization' http://vivoweb.org/ontology/core#FundingOrganization sequence annotation A planned process that identifies and reports sequence features (e.g. protein coding regions) in sequence data. PERSON: Jie Zheng, Chris Stoeckert NIAID GSCID-BRC metadata working group Annotation Method SA9 NIAID GSCID-BRC NIAID GSCID-BRC sequence annotation sequence annotation provider A person or organization reporting the feature annotation results from the analysis of a macromolecular sequence. PERSON: Jie Zheng, Chris Stoeckert NIAID GSCID-BRC metadata working group Annotation Provider SA8 NIAID GSCID-BRC NIAID GSCID-BRC sequence annotation provider sequence assembly name A textual entity that is used to denote a sequence assembly. PERSON: Jie Zheng, Chris Stoeckert NIAID GSCID-BRC metadata working group Assembly Name SA5 NIAID GSCID-BRC NIAID GSCID-BRC sequence assembly name sequence annotation reporting role A reporting party role that is realized by a person or organization who reports the feature annotation results from the analysis of a macromolecular sequence. PERSON: Jie Zheng, Chris Stoeckert NIAID GSCID-BRC metadata working group NIAID GSCID-BRC sequence annotation reporting role A specimen that is derived from cerbrospinal fluid. cerebrospinal fluid specimen A specimen that is derived from feces. feces specimen A specimen that is derived from sputum. sputum specimen A specimen that is derived from bone marrow. bone marrow specimen A specimen that is derived from pleural fluid. pleural fluid specimen A specimen that is derived from lung. lung specimen a material entity which corresponds to the liquid component of blood, in which the blood cells are suspended. blood plasma specimen organism animal fungus plant virus A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs. 10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms') 13-02-2009: OBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus. This issue is outside the scope of OBI. GROUP: OBI Biomaterial Branch WEB: http://en.wikipedia.org/wiki/Organism Specimen Source Species CS3, CS4 NIAID GSCID-BRC organism specimen Biobanking of blood taken and stored in a freezer for potential future investigations stores specimen. A material entity that has the specimen role. Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation. PERSON: James Malone PERSON: Philippe Rocca-Serra GROUP: OBI Biomaterial Branch Specimen Category CS2 NIAID GSCID-BRC specimen cultured cell population A cultured cell population applied in an experiment: "293 cells expressing TrkA were serum-starved for 18 hours and then neurotrophins were added for 10 min before cell harvest." (Lee, Ramee, et al. "Regulation of cell survival by secreted proneurotrophins." Science 294.5548 (2001): 1945-1948). A cultured cell population maintained in vitro: "Rat cortical neurons from 15 day embryos are grown in dissociated cell culture and maintained in vitro for 8–12 weeks" (Dichter, Marc A. "Rat cortical neurons in cell culture: culture methods, cell morphology, electrophysiology, and synapse formation." Brain Research 149.2 (1978): 279-293). A processed material comprised of a collection of cultured cells that has been continuously maintained together in culture and shares a common propagation history. 2013-6-5 MHB: This OBI class was formerly called 'cell culture', but label changed and definition updated following CLO alignment efforts in spring 2013, during which the intent of this class was clarified to refer to portions of a culture or line rather than a complete cell culture or line. PERSON:Matthew Brush cell culture sample PERSON:Matthew Brush The extent of a 'cultured cell population' is restricted only in that all cell members must share a propagation history (ie be derived through a common lineage of passages from an initial culture). In being defined in this way, this class can be used to refer to the populations that researchers actually use in the practice of science - ie are the inputs to culturing, experimentation, and sharing. The cells in such populations will be a relatively uniform population as they have experienced similar selective pressures due to their continuous co-propagation. And this population will also have a single passage number, again owing to their common passaging history. Cultured cell populations represent only a collection of cells (ie do not include media, culture dishes, etc), and include populations of cultured unicellular organisms or cultured multicellular organism cells. They can exist under active culture, stored in a quiescent state for future use, or applied experimentally. cultured cell population data transformation The application of a clustering protocol to microarray data or the application of a statistical testing method on a primary data set to determine a p-value. A planned process that produces output data from input data. Elisabetta Manduchi Helen Parkinson James Malone Melanie Courtot Philippe Rocca-Serra Richard Scheuermann Ryan Brinkman Tina Hernandez-Boussard data analysis data processing Branch editors data transformation data transformation objective normalize objective An objective specification to transformation input data into output data Modified definition in 2013 Philly OBI workshop James Malone PERSON: James Malone data transformation objective averaging data transformation An averaging data transformation is a data transformation that has objective averaging. James Malone PERSON: James Malone averaging data transformation extraction nucleic acid extraction using phenol chloroform A material separation in which a desired component of an input material is separated from the remainder Current the output of material processing defined as the molecular entity, main component in the output material entity, rather than the material entity that have grain molecular entity. 'nucleic acid extract' is the output of 'nucleic acid extraction' and has grain 'nucleic acid'. However, the output of 'nucleic acid extraction' is 'nucleic acid' rather than 'nucleic acid extract'. We are aware of this issue and will work it out in the future. Person:Bjoern Peters Philippe Rocca-Serra extraction storage PMID: 18550121.Total Prostate Specific Antigen Stability Confirmed After Long-Term Storage of Serum at -80C. J Urol. 2008 Jun 10. A maintenance process by which material entities that are not actively metabolizing are placed in well identified location and possibly under controlled environment in ad-hoc devices/structures in order to preserve and protect them from decay/alteration and maintain availability Philippe Rocca-Serra OBI-Branch storage A light source is an optical subsystem that provides light for use in a distant area using a delivery system (e.g., fiber optics). Light sources may include one of a variety of lamps (e.g., xenon, halogen, mercury). Most light sources are operated from line power, but some may be powered from batteries. They are mostly used in endoscopic, microscopic, and other examination and/or in surgical procedures. The light source is part of the optical subsystem. In a flow cytometer the light source directs high intensity light at particles at the interrogation point. The light source in a flow cytometer is usually a laser. light source study design a matched pairs study design describes criteria by which subjects are identified as pairs which then undergo the same protocols, and the data generated is analyzed by comparing the differences between the paired subjects, which constitute the results of the executed study design. A plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of an investigation and is realized during a study design execution. Editor note: there is at least an implicit restriction on the kind of data transformations that can be done based on the measured data available. PERSON: Chris Stoeckert experimental design rediscussed at length (MC/JF/BP). 12/9/08). The definition was clarified to differentiate it from protocol. Project Relevance CP4 ICEMR protein array NIAID GSCID-BRC study design A planned process with the objective to obtain a population of human subjects to participate in an investigation by determining eligibility of subjects and obtaining informed consent. human subject enrollment collecting specimen from organism taking a sputum sample from a cancer patient, taking the spleen from a killed mouse, collecting a urine sample from a patient a process with the objective to obtain a material entity that was part of an organism for potential future use in an investigation PERSON:Bjoern Peters IEDB collecting specimen from organism A process by which a substance is intentionally given to an organism resulting in exposure of the organism to that substance. administering substance in vivo material component separation Using a cell sorter to separate a mixture of T cells into two fractions; one with surface receptor CD8 and the other lacking the receptor, or purification a material processing in which components of an input material become segregated in space Bjoern Peters IEDB material component separation maintaining cell culture When harvesting blood from a human, isolating T cells, and then limited dilution cloning of the cells, the maintaining_cell_culture step comprises all steps after the initial dilution and plating of the cells into culture, e.g. placing the culture into an incubator, changing or adding media, and splitting a cell culture a protocol application in which cells are kept alive in a defined environment outside of an organism. part of cell_culturing PlanAndPlannedProcess Branch OBI branch derived maintaining cell culture establishing cell culture a process through which a new type of cell culture or cell line is created, either through the isolation and culture of one or more cells from a fresh source, or the deliberate experimental modification of an existing cell culture (e.g passaging a primary culture to become a secondary culture or line, or the immortalization or stable genetic modification of an existing culture or line). PERSON:Matthew Brush PERSON:Matthew Brush A 'cell culture' as used here referes to a new lineage of cells in culture deriving from a single biological source.. New cultures are established through the initial isolation and culturing of cells from an organismal source, or through changes in an existing cell culture or line that result in a new culture with unique characteristics. This can occur through the passaging/selection of a primary culture into a secondary culture or line, or experimental modifications of an existing cell culture or line such as an immortalization process or other stable genetic modification. This class covers establishment of cultures of either multicellular organism cells or unicellular organisms. establishing cell culture sequencing assay The use of the Sanger method of DNA sequencing to determine the order of the nucleotides in a DNA template An assay the uses chemical or biochemical means to infer the sequence of a biomaterial the use of a chemical or biochemical means to infer the sequence of a biomaterial has_output should be sequence of input; we don't have sequence well defined yet PlanAndPlannedProcess Branch OBI branch derived Sequencing Technology SA4 NIAID GSCID-BRC sequencing assay sequencing assay nucleic acid extraction Phenol / chlorophorm extraction disolvation of protein content folllowed by ethanol precipitation of the nucleic acid fraction over night in the fridge followed by centrifugation to obtain a nucleic acid pellet. a material separation to recover the nucleic acid fraction of an input material PlanAndPlannedProcess Branch OBI branch derived requested by Helen Parkinson for MO. Could be defined class Nucleic Acid Extraction Method SA2 NIAID GSCID-BRC nucleic acid extraction infection the detrimental process in which an infectious agent colonizes or replicates in a host environment IEDB IEDB infection A cell specimen comprised of a mixed population of cells obtained by processing whole lymph node into individual cells, typically performed using a sieve. This population includes T cells, B cells, macrophages, and other cell types. lymph node cell specimen disposition to infect an organism Is a role borne by an agent, and realized when in contact with or inside another organism in which it is capable of replicating and causing disease IEDB IEDB disposition to infect an organism pathologic process abnormal, harmful processes caused by or associated with a disease IEDB IEDB pathologic process A representation that is either the output of a clinical history taking or a physical examination or an image finding, or some combination thereof. ICEMR protein array clinical finding A series of statements representing health-relevant qualities of a patient and of a patient's family. clinical history A representation of a quality of a specimen that is the output of a laboratory test and that can support an inference to an assertion about some quality of the patient. ICEMR protein array laboratory finding A clinically abnormal phenotype. clinical phenotype disease A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism. Specimen Source Disease CS9 NIAID GSCID-BRC disease A measurement assay that has as input a patient-derived specimen, and as output a result that represents a quality of the specimen. laboratory test The representation of a conclusion of a diagnostic process. ICEMR protein array diagnosis TODO: Define. physical examination finding A processual entity whose completion is hypothesized (by a healthcare provider) to alleviate the signs and symptoms associated with a disorder treatment A microbial phenotype related to the resistance or sensitivity of a microbe to antimicrobial agents that kill (microbiocidal) or inhibit growth (microbiostatic) of a microbe. antimicrobial agent resistance phenotype A social role inhering in a human being. human social role Life cycle stage of a parasite. parasite lifecycle stage An organism living in, with, or on another organism in parasitism. Individual members of parasite species, such as Leishmania, Plasmodium, Trypanosoma, etc. are members of this class. parasite organism age A time quality inhering in a bearer by virtue of how long the bearer has existed. age biological sex An organismal quality inhering in a bearer by virtue of the bearer's ability to undergo sexual reproduction in order to differentiate the individuals or types involved. Specimen Source Gender CS5 ICEMR protein array NIAID GSCID-BRC biological sex A biological sex quality inhering in an individual or a population that only produces gametes that can be fertilised by male gametes. female A biological sex quality inhering in an individual or a population whose sex organs contain only male gametes. male quality of a single physical entity A physical object quality which inheres in a single-bearer. quality of a single physical entity A quality inhering in a population by virtue of the proportion of its members that are ill at a given time. morbidity A biological sex quality inhering in an individual or a population that undergo sexual reproduction. mating type organismal quality A quality that inheres in an entire organism or part of an organism. Specimen Source Health Status CS8 NIAID GSCID-BRC organismal quality A material entity that consists of one or more people who live in the same dwelling and also share at meals or living accommodation, and may consist of a single family or some other grouping of people. household A multi-tissue plant structure (PO:0025496) that develops from a gynoecium (PO:0009062), or a single carpel (PO:0009030), and at maturity may have as parts one or more seeds (PO:0009010). fruit A determinate reproductive shoot system (PO:0025082) that has as part at least one carpel (PO:0009030) or at least one stamen (PO:0009029) and does not contain any other determinate shoot system (PO:0009006) as a part. flower An anatomical entity that is or was part of a plant. plant anatomical entity protein antithrombin III is a protein An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA. protein social role region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. primary structure of sequence macromolecule sequence region sequence_assembly A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences. sequence_assembly A large polynucleotide in Bacteria and Archaea, which functions as the small subunit of the ribosome. rRNA_16S assembly A region of the genome of known length that is composed by ordering and aligning two or more different regions. assembly a count is a data item denoted by an integer and represented the number of instances or occurences of an entity count A general symptom that is characterized as an act, instance, or result of being bled or the process by which something is bled: as a the escape of blood from vessels. bleeding joint pain A sensation perception where there is an unpleasant sensation that usually indicates the body is threatened or damaged. The sensation may be sharp or dull, short-lived or chronic, intermittent or continual, confined to one area or spread over the entire body. pain seizure Wasting is a nutrition, metabolism, and development symptom characterized by the unintended loss of weight and lean body tissue characteristic of many diseases (as cancer, tuberculosis, and AIDS). wasting underweight Anorexia is a nutrition, metabolism, and development symptom characterized by a loss of appetite especially when prolonged. anorexia ICEMR protein array convulsion Dizziness is a neurological and physiological symptom characterized by a sensation of unsteadiness accompanied by a feeling of movement within the head. dizziness Cough is a respiratory system and chest symptom characterized by an explosive expulsion of air from the lungs acting as a protective mechanism to clear the air passages or as a symptom of pulmonary disturbance. cough ICEMR protein array respiratory distress abscess septicemia chills Fatigue is a neurological and physiological symptom characterized by a weariness or exhaustion from labor, exertion, or stress. fatigue An organ that is capable of transducing sensory stimulus to the nervous system. sense organ Any of the rounded masses of lymphoid tissue that are surrounded by a capsule of connective tissue, are distributed along the lymphatic vessels, and contain numerous lymphocytes which filter the flow of lymph. lymph node The head is the anterior-most division of the body [GO]. head Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome. anatomical structure Anatomical structure that performs a specific function or group of functions [WP]. organ A multicellular structure that is a part of an organ. organ part An anatomical structure that develops from the endoderm and the mesoderm. mixed endoderm/mesoderm-derived structure A spatiotemporal region encompassing some part of the life cycle of an organism. life cycle stage 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. intestine Anatomical cavity at the start of the digestive tract that that is enclosed by the mouth. The boundaries and contents vary depending on the species. In vertebrates, the boundaries are the oral opening, the cheeks, the palate and (if present) the palatoglossal arch - if this is not present then the mouth and pharynx form the oropharyngeal cavity. The buccal cavity contains the teeth, tongue and palate (when present) oral cavity 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 excreta A fluid that is composed of blood plasma and erythrocytes. blood 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] mucosa 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. organism substance Anatomical entity that has mass. material anatomical entity Anatomical entity that has no mass. immaterial anatomical entity Anatomical structure that is an individual member of a species and consists of more than one cell. multicellular organism 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. tissue 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]. epithelium Unilaminar epithelium, which consists of a single layer of columnar cells. Examples: ciliated columnar epithelium, gastric epithelium, microvillus columnar epithelium.[FMA] simple columnar epithelium Compound organ that contains one or more macroscopic anatomical spaces. cavitated compound organ 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. stomach A myogenic muscular circulatory organ found in the vertebrate cardiovascular system composed of chambers of cardiac muscle. It is the primary circulatory organ. heart 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]. brain the transparent anterior portion of the fibrous coat of the eye that serves as the chief refractory structure cornea An organ that detects light. eye Blood analogue used by all arthropods and most mollusks that have an open circulatory system. In these animals there is no distinction between blood and interstitial fluid. The liquid fills all of the interior (the hemocoel) of the body and surrounds all cells. hemolymph saliva-secreting exocrine glands of the oral cavity[GO] saliva-secreting gland 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]. midgut The caudalmost subdivision of a digestive tract. hindgut 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. anatomical entity Transudate contained in the pleural cavity. pleural fluid Excretion that is the output of a kidney urine A thin musculomebranous barrier that separates the abdominal and thoracic cavities. Often used for breathing control diaphragm Muscle tissue that consists primarily of skeletal muscle fibers. skeletal muscle tissue 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. caecum Anatomical cavity bounded by visceral and parietal peritoneum peritoneal cavity Mucosal layer that lines the intestine. intestinal mucosa A clear, colorless, bodily fluid, that occupies the subarachnoid space and the ventricular system around and inside the brain and spinal cord. cerebrospinal fluid 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]. muscle organ A muscular organ in the floor of the mouth. tongue the smooth stratified squamous epithelium that covers the outer surface of the cornea corneal epithelium A skeletal muscle organ that is part of the trunk region. skeletal muscle of trunk A thick watery refractive medium that fills the space between the lens and the cornea[WP]. aqueous humor of eyeball A fluid produced in the oral cavity by salivary glands, typically used in predigestion, but also in other functions. saliva 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]. medulla oblongata Organism substance that is composed of sperm cells suspended in seminal fluid. semen organ of metabolic interchange between fetus and mother, partly of embryonic origin and partly of maternal origin[GO]. The fetal portion of the placenta is known as the villous chorion. The maternal portion is known as the decidua basalis. The two portions are held together by anchoring villi that are anchored to the decidua basalis by the cytotrophoblastic shell. placenta Portion of semisolid bodily waste discharged through the anus[MW,modified] feces Respiration organ that develops as an oupocketing of the esophagus. lung the organ that functions to filter blood and to store red corpuscles and platelets spleen 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]. liver An organ that aids digestion and stores bile produced by the liver[WP]. gall bladder A paired organ of the urinary tract which has the production of urine as its primary function. kidney the middle layer of the heart, comprised mainly of striated cardiac muscle fibers myocardium 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 exocrine gland Endocrine glands are glands of the endocrine system that secrete their products directly into the circulatory system rather than through a duct.[WP, modified]. endocrine gland Anatomical structure of largely lymphoid tissue that functions in cell-mediated immunity by being the site where T cells develop. thymus the soft tissue that fills the cavities of bones bone marrow Muscle tissue is a contractile tissue made up of actin and myosin fibers[GO]. muscle tissue An external caudal extension of the body. In chordates, the tail is post-anal, in other animals the anus ends in the tail tail an organ that functions as a secretory or excretory organ gland Anatomical surface structure found in many aquatic organisms. It is a respiration organ whose function is the extraction of oxygen from water and the excretion of carbon dioxide. The microscopic structure of a gill is such that it presents a very large surface area to the external environment. Gills usually consist of thin filaments of tissue, branches, or slender tufted processes which have a highly folded surface to increase surface area. A high surface area is crucial to the gas exchange of aquatic organisms as water contains only 1/20 parts dissolved Oxygen compared to air. With the exception of some aquatic insects, the filaments and lamellae (folds) contain blood or coelomic fluid, from which gases are exchanged through the thin walls. Oxygen is carried by the blood to other parts of the body. Carbon dioxide passes from the blood through the thin gill tissue into the water. Gills or gill-like organs, located in different parts of the body, are found in various groups of aquatic animals, including mollusks, crustaceans, insects, fish, and amphibians. gill A distinct juvenile form many animals undergo before metamorphosis into adults. Animals with indirect development such as insects, amphibians, or cnidarians typically have a larval phase of their life cycle. larva 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. anatomical cavity Anatomical structure that overlaps the outer epithelial layer and is adjacent to the space surrounding the organism. surface structure 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. compound organ A gland that is part of a digestive tract [Automatically generated definition]. gland of digestive tract Any muscle organ that is part of a thorax [Automatically generated definition]. thoracic segment muscle An anatomical structure that develops (entirely or partially) from the endoderm. endoderm-derived structure An anatomical structure that develops (entirely or partially) from the mesoderm. mesoderm-derived structure An anatomical structure that develops (entirely or partially) from the ectoderm. ectoderm-derived structure Organ that is part of the hematopoietic system. hemopoietic organ 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 respiratory tract epithelium A proximal-distal subdivision of the digestive tract. subdivision of digestive tract A part of a wall of an organ that forms a layer. organ component layer An organ that is part of a immune system [Automatically generated definition]. immune organ Muscle structures are contractile cells, tissues or organs that are found in multicellular organisms[GO]. muscle structure The avian beak is an external anatomical structure, in the head region, that is adapted for feeding self and young, catching prey, probing, etc. It encompasses, but is not restricted to, the maxilla, mandible, maxillary ramaphotheca, mandibular ramaphotheca, nostril, nasal fossa, nasal bones, egg tooth and rictus[GO]. The beak, bill or rostrum is an external anatomical structure of birds which is used for eating and for grooming, manipulating objects, killing prey, probing for food, courtship and feeding young. . beak An organ or element that is in the abdomen. Examples: spleen, intestine, kidney, abdominal mammary gland. abdomen 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. trunk region element An organ that part of the thoracic segment region. This region can be further subdividied chest and thoracic cavity regions. thoracic segment organ An epithelium that lines the nasal cavity. nasal cavity epithelium Epithelium that derives from the endoderm. Examples: urothelium, transitional epithelium of ureter, epithelium of prostatic gland.[FMA] endo-epithelium The laminar structure of the heart heart layer Liquid components of living organisms. includes fluids that are excreted or secreted from the body as well as body water that normally is not. bodily fluid Any gland that is part of the digestive system. digestive system gland A pouched enlargement of the gullet of many birds that serves as a receptacle for food and for its preliminary maceration. crop Simple columnar epithelium in which the luminal side of the cells bears cilia. Examples: epithelium of trachea, epithelium of uterine tube.[FMA] ciliated columnar epithelium Any bodily fluid that has passed through a membrane such as the capillary wall, as a result of unbalanced hydrostatic and osmotic forces transudate An organism containing a developing embryo, fetus, or unborn offspring within the body. ICEMR protein array gravid organism Branch or outpocketing of the digestive tract. digestive tract diverticulum sac An anatomical structure that has more than one cell as a part. multicellular anatomical structure Gland of the epithelium lining the oral cavity. The most common are the salivary glands. oral gland An anatomical structure that develops from the neural crest. neural crest-derived structure An anatomical structure that has some part that develops from the neural crest. structure with developmental contribution from neural crest Epithelium composed of cells that develops from the ectoderm[FMA,modified]. ecto-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. pseudostratified ciliated columnar epithelium 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. subdivision of organism along main body axis Any of the organs or elements that are part of the digestive system. Examples: tongue, esophagus, spleen, crop, lunge feeding organ, tooth elements. digestive system element Any structure that is placed on one side of the left-right axis of a bilaterian. lateral structure A epithelium that is part of a camera-type eye. eye epithelium A viscus that is part of a abdomen. abdominal viscera A membranous sac in animals that serves as the receptacle of a liquid or contains gas. bladder organ Any region of epithelium that is part of a skin region. skin epithelium sensory organ epithelium nose epithelium time unit A unit which is a standard measure of the dimension in which events occur in sequence. Specimen Source Age - Unit CS7 NIAID GSCID-BRC time unit A time unit which is equal to 24 hours. day A time unit which is approximately equal to the length of time of one of cycle of the moon's phases which in science is taken to be equal to 30 days. month A time unit which is equal to 12 months which in science is taken to be equal to 365.25 days. year A unit which represents a standard measurement of how much of a given substance there is mixed with another substance. concentration unit A dimensionless concentration notation which denotes the acidity of a solution in terms of activity of hydrogen ions (H+). pH An antibody function (or antigen binding function) is an infection-fighting protein molecule in blood or secretory fluids that tags, neutralizes, and helps destroy pathogenic microorganisms such as bacteria, viruses and toxins. antibody Damage inflicted on the body as the direct or indirect result of an external force, with or without disruption of structural continuity. injury A role played by a a biological sample in the context of an experiment where the intent is that biological or technical variation is measured. replicate Regular course of eating and drinking adopted by a person or animal. This does not include DIET THERAPY, a specific diet prescribed in the treatment of a disease. The customary allowance of food and drink taken by a person or an animal from day to day, particularly one especially planned to meet specific requirements of the individual, including or excluding certain items of food; a prescribed course of eating and drinking in which the amount and kind of food, as well as the times at which it is to be taken, are regulated for therapeutic purposes or selected with reference to a particular state of health. diet The number of PLATELETS per unit volume in a sample of venous BLOOD. platelet count The number of times the HEART VENTRICLES contract per unit of time, usually per minute. heart rate The volume of packed RED BLOOD CELLS in a blood specimen. The volume is measured by centrifugation in a tube with graduated markings, or with automated blood cell counters. It is an indicator of erythrocyte status in disease. For example, ANEMIA shows a low value; POLYCYTHEMIA, a high value. hematocrit The point in time at which an individual was born. ICEMR protein array date of birth The age at which death occurs. age at death A categorical household wealth index representing the bottom third of values for the numerical household wealth index. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey Penn Group PRISM bottom household wealth index A categorical household wealth index representing the middle third of values for the numerical household wealth index. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey Penn Group PRISM middle household wealth index A categorical household wealth index representing the top third of values for the numerical household wealth index. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey Penn Group PRISM top household wealth index A information content entity created to indicate the lack of air bricks in the dwelling. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey Penn Group PRISM no airbrick A information content entity indicating that the household eats in restaurants. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey Penn Group PRISM record of eating in restaurants A information content entity indicating that the household does not cook in the dwelling. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey Penn Group PRISM record of no cooking at home An information content entity indicates no toilet facility in the dwelling. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey Penn Group PRISM record of no toilet facility An information content entity indicating that a household uses a neighbours' toilet facility. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey Penn Group PRISM record of using neighbours' toilet A time of screening occurring during the initial human subject enrollment period. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey Penn Group PRISM time of screening during initial enrollment A time of screening occuring after the initial enrollment period had ended and the study had begun. Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey Penn Group PRISM time of screenng after initial enrollment PRISM unknown withdrawal reason PRISM withdrew due to death PRISM inability to comply with protocol PRISM moved out of area PRISM reached 11 years of age PRISM unable to be located for over 120 days PRISM withdrawal of all children under care PRISM withdrawal of informed consent PRISM unknown cause of death PRISM complications of HIV PRISM diarrheal illness PRISM suicide PRISM Bwindi Hospital PRISM Jinja Hospital PRISM Kauka Health Centre PRISM Kihihi Health Centre IV PRISM Nagongera Health Centre IV PRISM Tororo District Hospital PRISM record of unknown death location A landlocked country in East Africa, bordered on the east by Kenya, the north by Sudan, on the west by the Democratic Republic of the Congo, on the southwest by Rwanda, and on the south by Tanzania. The southern part of the country includes a substantial portion of Lake Victoria, within which it shares borders with Kenya and Tanzania. Uganda is divided into 80 districts, spread across four administrative regions: Northern, Eastern, Central and Western. The districts are subdivided into counties. Uganda example to be eventually removed example to be eventually removed metadata complete Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete. metadata complete organizational term term created to ease viewing/sort terms for development purpose, and will not be included in a release PERSON:Alan Ruttenberg organizational term ready for release Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release." ready for release metadata incomplete Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors. metadata incomplete uncurated Nothing done yet beyond assigning a unique class ID and proposing a preferred term. uncurated pending final vetting All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor. pending final vetting to be replaced with external ontology term Terms with this status should eventually replaced with a term from another ontology. Alan Ruttenberg group:OBI to be replaced with external ontology term requires discussion A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues. Alan Ruttenberg group:OBI requires discussion axiom holds for all times ## Elucidation This is used when the statement/axiom is assumed to hold true 'eternally' ## How to interpret (informal) First the "atemporal" FOL is derived from the OWL using the standard interpretation. This axiom is temporalized by embedding the axiom within a for-all-times quantified sentence. The t argument is added to all instantiation predicates and predicates that use this relation. ## Example Class: nucleus SubClassOf: part_of some cell forall t : forall n : instance_of(n,Nucleus,t) implies exists c : instance_of(c,Cell,t) part_of(n,c,t) ## Notes This interpretation is *not* the same as an at-all-times relation axiom holds for all times Specimen Collection Location - Location A reference to a place on the Earth, by its name or by its geographical location. geographic location NIAID GSCID-BRC geographic location CS13