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"http://edamontology.org/data_2603", "lbl": "Microarray data", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "Gene product profile" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "Gene product quantification data" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "Gene transcription profile" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "Gene transcription quantification data" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "Microarray data" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "Non-coding RNA profile" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "Non-coding RNA quantification data" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "RNA profile" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "RNA quantification data" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "RNA-seq data" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "Transcriptome profile" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "Transcriptome quantification data" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "mRNA profile" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "mRNA quantification data" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000412", "val": "http://edamontology.org/EDAM.owl" } ], "definition": { "val": "Image, hybridisation or some other data arising from a study of gene expression, typically profiling or quantification." } }, "type": "CLASS" }, { "id": "http://edamontology.org/data_2968", "lbl": "Image", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "Image data" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000412", "val": "http://edamontology.org/EDAM.owl" } ], "definition": { "val": "Biological or biomedical data has been rendered into an image, typically for display on screen." } }, "type": "CLASS" }, { "id": "http://edamontology.org/data_3768", "lbl": "Clustered gene expression profiles", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000412", "val": "http://edamontology.org/EDAM.owl" } ], "definition": { "val": "Groupings of gene expression profiles according to a clustering algorithm." } }, "type": "CLASS" }, { "id": "http://edamontology.org/format_1665", "lbl": "Taverna workflow format", "meta": { "definition": { "val": "Format of Taverna workflows." } }, "type": "CLASS" }, { "id": "http://edamontology.org/format_1936", "lbl": "GenBank format", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "GenBank" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000412", "val": "http://edamontology.org/EDAM.owl" } ], "definition": { "val": "Genbank entry format." } }, "type": "CLASS" }, { "id": "http://edamontology.org/format_2331", "lbl": "HTML", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://www.w3.org/TR/html401/" }, { "pred": "http://purl.org/dc/terms/creator", "val": "James Malone" } ], "definition": { "val": "html, or HyperText Markup Language in full, is a data format specification is a markup language for web pages and is the publishing language of the World Wide Web." } }, "type": "CLASS" }, { "id": "http://edamontology.org/format_2332", "lbl": "XML", "meta": { "basicPropertyValues": [ { "pred": "http://purl.org/dc/terms/creator", "val": "James Malone" } ], "definition": { "val": "Extensible Markup Language (XML) is a standard set of rules for encoding documents in a machine-readable form defined by the W3C." } }, "type": "CLASS" }, { "id": "http://edamontology.org/format_2549", "lbl": "OBO Flat File Format", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "OBO flat file format" } ], "definition": { "val": "OBO format is the text file format used by OBO-Edit, the open source, platform-independent application for viewing and editing ontologies. " } }, "type": "CLASS" }, { "id": "http://edamontology.org/format_2585", "lbl": "SBML", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "Systems Biology Markup Language" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://sbml.org" } ], "definition": { "val": "Systems Biology Markup Language (SBML) is a machine-readable format for representing models. It's oriented towards describing systems where biological entities are involved in, and modified by, processes that occur over time." } }, "type": "CLASS" }, { "id": "http://edamontology.org/format_3162", "lbl": "MAGE-TAB", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://www.mged.org/mage-tab/" } ], "comments": [ "A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB." ], "definition": { "val": "MAGE-TAB is a tab delimited data format comprimising of ADF file for array design, IDFfor experimental design, SDRF for sample data relationships and associated data files." } }, "type": "CLASS" }, { "id": "http://edamontology.org/format_3239", "lbl": "CopasiML", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000412", "val": "http://edamontology.org/EDAM.owl" } ], "definition": { "val": "CopasiML, the native format of COPASI." } }, "type": "CLASS" }, { "id": "http://edamontology.org/operation_0224", "lbl": "Query and retrieval", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "Database retrieval" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "Query" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000412", "val": "http://edamontology.org/EDAM.owl" } ], "definition": { "val": "Search or query a data resource and retrieve entries and / or annotation." } }, "type": "CLASS" }, { "id": "http://edamontology.org/operation_0362", "lbl": "Genome annotation", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "Metagenome annotation" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000412", "val": "http://edamontology.org/EDAM.owl" } ], "definition": { "val": "Annotate a genome sequence with terms from a controlled vocabulary." } }, "type": "CLASS" }, { "id": "http://edamontology.org/operation_2426", "lbl": "Modelling and simulation", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "Mathematical modelling" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000412", "val": "http://edamontology.org/EDAM.owl" } ], "definition": { "val": "Model or simulate some biological entity or system, typically using mathematical techniques including dynamical systems, statistical models, differential equations, and game theoretic models." } }, "type": "CLASS" }, { "id": "http://kt.ijs.si/panovp/OntoDM#OntoDM-KDD_778151", "lbl": "data processing task", "meta": { "comments": [ "A data processing task is an information processing objective that specifies the objective that a data processing algorithm execution process needs to achieve when executed on a dataset to produce as output a new dataset." ] }, "type": "CLASS" }, { "id": "http://kt.ijs.si/panovp/OntoDM#OntoDM_000034", "lbl": "generalization specification", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "OntoDM" } ], "definition": { "val": "Generalization specification of a directive informational entity class that specifies the type of generalization. It includes information about the types of data used to produced the generalization and the language in which the generalization is expressed." } }, "type": "CLASS" }, { "id": "http://kt.ijs.si/panovp/OntoDM#OntoDM_361570", "lbl": "data processing algorithm", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "Allyson Lister" } ], "comments": [ "A data processing algorithm is an algorithm that has as its objective a data processing task and has data items both as input and output." ] }, "type": "CLASS" }, { "id": "http://kt.ijs.si/panovp/OntoDM#OntoDM_953101", "lbl": "data visualization task", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0100001", "val": "http://purl.obolibrary.org/obo/OBI_0200111" }, { "pred": "http://www.ebi.ac.uk/efo/obsoleted_in_version", "val": "1.7" } ], "comments": [ "AL 25.9.19: Already obsoleted in originating ontology (OntoDM) so added here so people could see the history of the term.", "data visualization task is information processing objective achieved by a data visualization algorithm execution process." ], "deprecated": true }, "type": "CLASS" }, { "id": "http://purl.obofoundry.org/obo/IAO_0000136", "lbl": "is about", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "IAO" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "James Malone" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Alan Ruttenberg" } ], "definition": { "val": "'is about' relates an information entity to other entities in which the information entity holds some information which dscribes some facet of the other entity, such as the arrow direction on a sign." } }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/APOLLO_SV_00000008", "lbl": "software development", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "Mathias Brochhausen" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "William R. Hogan" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://en.wikipedia.org/wiki/Software_development" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000600", "val": "A planned process resulting in a software product involving the creation of source code." } ], "definition": { "val": "A planned process that has specified output a software product and that involves the creation of source code." } }, "type": "CLASS" }, { "id": "http://purl.obolibrary.org/obo/APOLLO_SV_00000796", "lbl": "dataset creating", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "creating a data set" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "William R. Hogan" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "data set creation" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "dataset creation" } ], "definition": { "val": "A planned process that has a data set as its specified output." } }, "type": "CLASS" }, { "id": "http://purl.obolibrary.org/obo/BFO_0000001", "lbl": "entity", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/BFO_0000179", "val": "entity" }, { "pred": "http://purl.obolibrary.org/obo/BFO_0000180", "val": "Entity" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "Julius Caesar" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "Verdi’s Requiem" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "the Second World War" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "your body mass index" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000116", "val": "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" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000116", "val": "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" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000600", "val": "An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])" }, { "pred": "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val": "http://purl.obolibrary.org/obo/bfo.owl" } ] }, "type": "CLASS" }, { "id": "http://purl.obolibrary.org/obo/BFO_0000002", "lbl": "continuant", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/BFO_0000179", "val": "continuant" }, { "pred": "http://purl.obolibrary.org/obo/BFO_0000180", "val": "Continuant" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "continuant" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000116", "val": "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" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000116", "val": "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" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000412", "val": "http://purl.obolibrary.org/obo/pato.owl" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000600", "val": "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])" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000601", "val": "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])" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000601", "val": "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])" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000601", "val": "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])" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000602", "val": "(forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] " }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000602", "val": "(forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] " }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000602", "val": "(forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] " }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000602", "val": "(forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] " }, { "pred": "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val": "http://purl.obolibrary.org/obo/bfo.owl" } ], "definition": { "val": "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." } }, "type": "CLASS" }, { "id": "http://purl.obolibrary.org/obo/BFO_0000003", "lbl": "occurrent", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/BFO_0000179", "val": "occurrent" }, { "pred": "http://purl.obolibrary.org/obo/BFO_0000180", "val": "Occurrent" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000116", "val": "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" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000116", "val": "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." }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000116", "val": "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." }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000116", "val": "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." }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000600", "val": "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])" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000601", "val": "Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000601", "val": "b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000602", "val": "(forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] " }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000602", "val": "(forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] " }, { "pred": "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val": "http://purl.obolibrary.org/obo/bfo.owl" } ], "definition": { "val": "An entity that has temporal parts and that happens, unfolds or develops through time." } }, "type": "CLASS" }, { "id": "http://purl.obolibrary.org/obo/BFO_0000004", "lbl": "independent continuant", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/BFO_0000179", "val": "ic" }, { "pred": "http://purl.obolibrary.org/obo/BFO_0000180", "val": "IndependentContinuant" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "a chair" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "a heart" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "a leg" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "a molecule" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "a spatial region" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "an atom" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "an orchestra." }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "an organism" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "the bottom right portion of a human torso" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "the interior of your mouth" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000601", "val": "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])" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000601", "val": "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])" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000602", "val": "(forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] " }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000602", "val": "(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] " }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000602", "val": "(iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] " }, { "pred": "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val": "http://purl.obolibrary.org/obo/bfo.owl" } ], "definition": { "val": "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])" } }, "type": "CLASS" }, { "id": "http://purl.obolibrary.org/obo/BFO_0000015", "lbl": "process", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/BFO_0000179", "val": "process" }, { "pred": "http://purl.obolibrary.org/obo/BFO_0000180", "val": "Process" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "a process of cell-division, \\ a beating of the heart" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "a process of meiosis" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "a process of sleeping" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "the course of a disease" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "the flight of a bird" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "the life of an organism" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "your process of aging." }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000116", "val": "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)" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000602", "val": "(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] " }, { "pred": "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val": "http://purl.obolibrary.org/obo/bfo.owl" } ], "definition": { "val": "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])" } }, "type": "CLASS" }, { "id": "http://purl.obolibrary.org/obo/BFO_0000016", "lbl": "disposition", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/BFO_0000179", "val": "disposition" }, { "pred": "http://purl.obolibrary.org/obo/BFO_0000180", "val": "Disposition" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "an atom of element X has the disposition to decay to an atom of element Y" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "certain people have a predisposition to colon cancer" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "children are innately disposed to categorize objects in certain ways." }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "the cell wall is disposed to filter chemicals in endocytosis and exocytosis" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000116", "val": "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." }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000600", "val": "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])" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000601", "val": "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])" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000602", "val": "(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] " }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000602", "val": "(forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] " }, { "pred": "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val": "http://purl.obolibrary.org/obo/bfo.owl" } ] }, "type": "CLASS" }, { "id": "http://purl.obolibrary.org/obo/BFO_0000017", "lbl": "realizable entity", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/BFO_0000179", "val": "realizable" }, { "pred": "http://purl.obolibrary.org/obo/BFO_0000180", "val": "RealizableEntity" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "the disposition of this piece of metal to conduct electricity." }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "the disposition of your blood to coagulate" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "the function of your reproductive organs" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "the role of being a doctor" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "the role of this boundary to delineate where Utah and Colorado meet" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000600", "val": "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])" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000601", "val": "All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000602", "val": "(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] " }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000602", "val": "(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] " }, { "pred": "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val": "http://purl.obolibrary.org/obo/bfo.owl" } ], "definition": { "val": "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." } }, "type": "CLASS" }, { "id": "http://purl.obolibrary.org/obo/BFO_0000019", "lbl": "quality", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/BFO_0000179", "val": "quality" }, { "pred": "http://purl.obolibrary.org/obo/BFO_0000180", "val": "Quality" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "the ambient temperature of this portion of air" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "the color of a tomato" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "the length of the circumference of your waist" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "the mass of this piece of gold." }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "the shape of your nose" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "the shape of your nostril" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000600", "val": "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])" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000601", "val": "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])" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000602", "val": "(forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] " }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000602", "val": "(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] " }, { "pred": "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val": "http://purl.obolibrary.org/obo/bfo.owl" } ] }, "type": "CLASS" }, { "id": "http://purl.obolibrary.org/obo/BFO_0000020", "lbl": "specifically dependent continuant", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/BFO_0000179", "val": "sdc" }, { "pred": "http://purl.obolibrary.org/obo/BFO_0000180", "val": "SpecificallyDependentContinuant" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "specifically dependent continuant" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "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" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "of one-sided specifically dependent continuants: the mass of this tomato" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "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." }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "the disposition of this fish to decay" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "the function of this heart: to pump blood" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "the mutual dependence of proton donors and acceptors in chemical reactions [79" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "the pink color of a medium rare piece of grilled filet mignon at its center" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "the role of being a doctor" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "the shape of this hole." }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "the smell of this portion of mozzarella" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000116", "val": "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." }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000412", "val": "http://purl.obolibrary.org/obo/pato.owl" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000602", "val": "(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] " }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000602", "val": "(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] " }, { "pred": "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val": "http://purl.obolibrary.org/obo/bfo.owl" } ], "definition": { "val": "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])" } }, "type": "CLASS" }, { "id": "http://purl.obolibrary.org/obo/BFO_0000023", "lbl": "role", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/BFO_0000179", "val": "role" }, { "pred": "http://purl.obolibrary.org/obo/BFO_0000180", "val": "Role" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "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." }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "the priest role" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "the role of a boundary to demarcate two neighboring administrative territories" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "the role of a building in serving as a military target" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "the role of a stone in marking a property boundary" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "the role of subject in a clinical trial" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "the student role" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000116", "val": "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." }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000600", "val": "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])" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000602", "val": "(forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] " }, { "pred": "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val": "http://purl.obolibrary.org/obo/bfo.owl" } ], "definition": { "val": "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." } }, "type": "CLASS" }, { "id": "http://purl.obolibrary.org/obo/BFO_0000031", "lbl": "generically dependent continuant", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/BFO_0000179", "val": "gdc" }, { "pred": "http://purl.obolibrary.org/obo/BFO_0000180", "val": "GenericallyDependentContinuant" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "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." }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "the pdf file on your laptop, the pdf file that is a copy thereof on my laptop" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule." }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000602", "val": "(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] " }, { "pred": "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val": "http://purl.obolibrary.org/obo/bfo.owl" } ], "definition": { "val": "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])" } }, "type": "CLASS" }, { "id": "http://purl.obolibrary.org/obo/BFO_0000034", "lbl": "function", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/BFO_0000179", "val": "function" }, { "pred": "http://purl.obolibrary.org/obo/BFO_0000180", "val": "Function" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "the function of a hammer to drive in nails" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "the function of a heart pacemaker to regulate the beating of a heart through electricity" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "the function of amylase in saliva to break down starch into sugar" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000116", "val": "BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc." }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000600", "val": "A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001])" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000602", "val": "(forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] " }, { "pred": "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val": "http://purl.obolibrary.org/obo/bfo.owl" } ] }, "type": "CLASS" }, { "id": "http://purl.obolibrary.org/obo/BFO_0000040", "lbl": "material entity", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/BFO_0000179", "val": "material" }, { "pred": "http://purl.obolibrary.org/obo/BFO_0000180", "val": "MaterialEntity" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "material entity" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "material entity" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "Collection of random bacteria, a chair, dorsal surface of the body." }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "a flame" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "a forest fire" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "a human being" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "a hurricane" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "a photon" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "a puff of smoke" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "a sea wave" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "a tornado" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "an aggregate of human beings." }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "an energy wave" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "an epidemic" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "the undetached arm of a human being" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000116", "val": "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" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000116", "val": "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." }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000116", "val": "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." }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "BFO" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000412", "val": "http://purl.obolibrary.org/obo/cl.owl" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000412", "val": "http://purl.obolibrary.org/obo/ido.owl" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000412", "val": "http://purl.obolibrary.org/obo/uberon.owl" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000600", "val": "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])" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000601", "val": "Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000601", "val": "every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000602", "val": "(forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] " }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000602", "val": "(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] " }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000602", "val": "(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] " }, { "pred": "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val": "http://purl.obolibrary.org/obo/bfo.owl" } ], "definition": { "val": "An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time." } }, "type": "CLASS" }, { "id": "http://purl.obolibrary.org/obo/BFO_0000050", "lbl": "part of", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "is part of" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "my brain is part of my body (continuant parthood, two material entities)" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "this day is part of this year (occurrent parthood)" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000116", "val": "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." }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000116", "val": "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 http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000116", "val": "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" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000116", "val": "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.)\n\nA 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'." }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "part_of" }, { "pred": "http://purl.obolibrary.org/obo/RO_0001900", "val": "http://purl.obolibrary.org/obo/RO_0001901" }, { "pred": "http://purl.obolibrary.org/obo/RO_0040042", "val": "http://purl.obolibrary.org/obo/BFO_0000002" }, { "pred": "http://purl.obolibrary.org/obo/RO_0040042", "val": "http://purl.obolibrary.org/obo/BFO_0000003" }, { "pred": "http://purl.obolibrary.org/obo/RO_0040042", "val": "http://purl.obolibrary.org/obo/BFO_0000004" }, { "pred": "http://purl.obolibrary.org/obo/RO_0040042", "val": "http://purl.obolibrary.org/obo/BFO_0000017" }, { "pred": "http://purl.obolibrary.org/obo/RO_0040042", "val": "http://purl.obolibrary.org/obo/BFO_0000019" }, { "pred": "http://purl.obolibrary.org/obo/RO_0040042", "val": "http://purl.obolibrary.org/obo/BFO_0000020" }, { "pred": "http://purl.obolibrary.org/obo/RO_0040042", "val": "http://purl.obolibrary.org/obo/BFO_0000031" }, { "pred": "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val": "http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections" }, { "pred": "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val": "http://ontologydesignpatterns.org/wiki/Submissions:PartOf" }, { "pred": "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val": "http://www.obofoundry.org/ro/#OBO_REL:part_of" } ], "definition": { "val": "a core relation that holds between a part and its whole" }, "subsets": [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_gp2term", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ] }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/BFO_0000051", "lbl": "has part", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "has part" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "my body has part my brain (continuant parthood, two material entities)" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "this year has part this day (occurrent parthood)" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000116", "val": "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." }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000116", "val": "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 http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000116", "val": "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" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000116", "val": "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.)\n\nA 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'." }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "has_part" }, { "pred": "http://purl.obolibrary.org/obo/RO_0001900", "val": "http://purl.obolibrary.org/obo/RO_0001901" } ], "definition": { "val": "a core relation that holds between a whole and its part" }, "subsets": [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ] }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/BFO_0000054", "lbl": "realized in", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "realized in" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "this disease is realized in this disease course" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "this fragility is realized in this shattering" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "this investigator role is realized in this investigation" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "is realized by" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "realized_in" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000600", "val": "[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])" }, { "pred": "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val": "http://purl.obolibrary.org/obo/bfo.owl" } ], "comments": [ "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" ] }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/BFO_0000055", "lbl": "realizes", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "realizes" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "this disease course realizes this disease" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "this investigation realizes this investigator role" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "this shattering realizes this fragility" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000600", "val": "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])" }, { "pred": "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val": "http://purl.obolibrary.org/obo/iao.owl" } ], "comments": [ "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" ] }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/BFO_0000062", "lbl": "preceded by", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "preceded by" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000116", "val": "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "is preceded by" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "preceded_by" }, { "pred": "http://purl.org/dc/elements/1.1/source", "val": "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" } ], "definition": { "val": "x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." }, "subsets": [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/BFO_0000063", "lbl": "precedes", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "precedes" } ], "definition": { "val": "x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." }, "subsets": [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/GO_0003674", "lbl": "molecular_function", "meta": { "comments": [ "Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex." ], "definition": { "val": "A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. These actions are described from two distinct but related perspectives: (1) biochemical activity, and (2) role as a component in a larger system/process.", "xrefs": [ "GOC:pdt" ] }, "synonyms": [ { "pred": "hasExactSynonym", "val": "molecular function" } ] }, "type": "CLASS" }, { "id": "http://purl.obolibrary.org/obo/GO_0008150", "lbl": "biological_process", "meta": { "basicPropertyValues": [ { "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", "val": "jl" }, { "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", "val": "2012-09-19T15:05:24Z" } ], "comments": [ "Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this." ], "definition": { "val": "A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.", "xrefs": [ "GOC:pdt" ] }, "synonyms": [ { "pred": "hasExactSynonym", "val": "biological process" }, { "pred": "hasExactSynonym", "val": "physiological process" }, { "pred": "hasRelatedSynonym", "val": "single organism process" }, { "pred": "hasRelatedSynonym", "val": "single-organism process" } ], "xrefs": [ { "val": "Wikipedia:Biological_process" } ] }, "type": "CLASS" }, { "id": "http://purl.obolibrary.org/obo/GO_0016301", "lbl": "kinase activity", "meta": { "comments": [ "Note that this term encompasses all activities that transfer a single phosphate group; although ATP is by far the most common phosphate donor, reactions using other phosphate donors are included in this term." ], "definition": { "val": "Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.", "xrefs": [ "ISBN:0198506732" ] }, "synonyms": [ { "pred": "hasExactSynonym", "val": "phosphokinase activity" } ], "xrefs": [ { "val": "Reactome:R-HSA-6788855" }, { "val": "Reactome:R-HSA-6788867" } ] }, "type": "CLASS" }, { "id": "http://purl.obolibrary.org/obo/IAO_0000002", "lbl": "example to be eventually removed", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "example to be eventually removed" } ] }, "type": "INDIVIDUAL" }, { "id": "http://purl.obolibrary.org/obo/IAO_0000003", "lbl": "measurement unit label", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "measurement unit label" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "Examples of measurement unit labels are liters, inches, weight per volume." }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000114", "val": "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000116", "val": "2009-03-16: provenance: a term measurement unit was\nproposed for OBI (OBI_0000176) , edited by Chris Stoeckert and\nCristian Cocos, and subsequently moved to IAO where the objective for\nwhich the original term was defined was satisfied with the definition\nof this, different, term." }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000116", "val": "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." }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "PERSON: Alan Ruttenberg" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "PERSON: Melanie Courtot" } ], "definition": { "val": "A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure." } }, "type": "CLASS" }, { "id": "http://purl.obolibrary.org/obo/IAO_0000005", "lbl": "objective specification", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "objective specification" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction." }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000114", "val": "http://purl.obolibrary.org/obo/IAO_0000122" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000116", "val": "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.\"" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000116", "val": "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." }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000116", "val": "Answers the question, why did you do this experiment?" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "PERSON: Alan Ruttenberg" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "PERSON: Barry Smith" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "PERSON: Bjoern Peters" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "PERSON: Jennifer Fostel" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "goal specification" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "OBI Plan and Planned Process/Roles Branch" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "OBI_0000217" } ], "definition": { "val": "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." } }, "type": "CLASS" }, { "id": "http://purl.obolibrary.org/obo/IAO_0000007", "lbl": "action specification", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "Pour the contents of flask 1 into flask 2" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000114", "val": "http://purl.obolibrary.org/obo/IAO_0000122" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "Alan Ruttenberg" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "OBI Plan and Planned Process branch" } ], "definition": { "val": "A directive information entity that describes an action the bearer will take." } }, "type": "CLASS" }, { "id": "http://purl.obolibrary.org/obo/IAO_0000009", "lbl": "datum label", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "datum label" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000114", "val": "http://purl.obolibrary.org/obo/IAO_0000123" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000116", "val": "http://www.golovchenko.org/cgi-bin/wnsearch?q=label#4n" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "GROUP: IAO" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000232", "val": "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. \n" } ], "definition": { "val": "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" } }, "type": "CLASS" }, { "id": "http://purl.obolibrary.org/obo/IAO_0000010", "lbl": "software", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "software" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000114", "val": "http://purl.obolibrary.org/obo/IAO_0000120" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000116", "val": "see sourceforge tracker discussion at http://sourceforge.net/tracker/index.php?func=detail&aid=1958818&group_id=177891&atid=886178" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "PERSON: Alan Ruttenberg" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "PERSON: Bjoern Peters" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "PERSON: Chris Stoeckert" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "PERSON: Melanie Courtot" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "GROUP: OBI" }, { "pred": "http://www.w3.org/2004/02/skos/core#exactMatch", "val": "http://www.ebi.ac.uk/swo/SWO_0000001" } ], "definition": { "val": "Software is a plan specification composed of a series of instructions that can be \ninterpreted by or directly executed by a processing unit." } }, "type": "CLASS" }, { "id": "http://purl.obolibrary.org/obo/IAO_0000025", "lbl": "programming language", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "programming language" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "R, Perl, Java" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000114", "val": "http://purl.obolibrary.org/obo/IAO_0000120" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "person:Alan Ruttenberg" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "person:Chris Stoeckert" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "IAO" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "OBI_0000058" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "group:OBI" } ], "definition": { "val": "A language in which source code is written, intended to executed/run by a software interpreter. Programming languages are ways to write instructions that specify what to do, and sometimes, how to do it." } }, "type": "CLASS" }, { "id": "http://purl.obolibrary.org/obo/IAO_0000027", "lbl": "data item", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "data item" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "Data items include counts of things, analyte concentrations, and statistical summaries." }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000114", "val": "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000116", "val": "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." }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000116", "val": "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." }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000116", "val": "2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym." }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000116", "val": "2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000116", "val": "JAR: datum -- well, this will be very tricky to define, but maybe some \ninformation-like stuff that might be put into a computer and that is \nmeant, by someone, to denote and/or to be interpreted by some \nprocess... I would include lists, tables, sentences... I think I might \ndefer to Barry, or to Brian Cantwell Smith\n\nJAR: A data item is an approximately justified approximately true approximate belief" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "PERSON: Alan Ruttenberg" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "PERSON: Chris Stoeckert" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "PERSON: Jonathan Rees" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "data" }, { "pred": "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val": "http://www.ontobee.org/browser/rdf.php?o=IAO&iri=http://purl.obolibrary.org/obo/IAO_0000027" } ], "definition": { "val": "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." } }, "type": "CLASS" }, { "id": "http://purl.obolibrary.org/obo/IAO_0000028", "lbl": "symbol", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "symbol" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "a serial number such as \"12324X\"" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "a stop sign" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "a written proper name such as \"OBI\"" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000114", "val": "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000116", "val": "20091104, MC: this needs work and will most probably change" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000116", "val": "2014-03-31: We would like to have a deeper analysis of 'mark' and 'sign' in the future (see https://github.com/information-artifact-ontology/IAO/issues/154)." }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "PERSON: James A. Overton" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "PERSON: Jonathan Rees" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "based on Oxford English Dictionary" } ], "definition": { "val": "An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity." } }, "type": "CLASS" }, { "id": "http://purl.obolibrary.org/obo/IAO_0000030", "lbl": "information content entity", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "information content entity" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "Examples of information content entites include journal articles, data, graphical layouts, and graphs." }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "Examples of information content entites include journal articles, data, graphical layouts, and graphs." }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000114", "val": "http://purl.obolibrary.org/obo/IAO_0000122" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000116", "val": "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)." }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000116", "val": "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).\n\nPrevious. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity." }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "PERSON: Chris Stoeckert" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "IAO" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "OBI_0000142" } ], "definition": { "val": "An information content entity is an entity that is generically dependent on some artifact and stands in relation of aboutness to some entity." } }, "type": "CLASS" }, { "id": "http://purl.obolibrary.org/obo/IAO_0000033", "lbl": "directive information entity", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000114", "val": "http://purl.obolibrary.org/obo/IAO_0000122" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000116", "val": "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." }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000116", "val": "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." }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000116", "val": "8/6/2009 Alan Ruttenberg: Changed label from \"information entity about a realizable\" after discussions at ICBO" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000116", "val": "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" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "PERSON: Alan Ruttenberg" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "PERSON: Bjoern Peters" } ], "definition": { "val": "An information content entity whose concretizations indicate to their bearer how to realize them in a process." } }, "type": "CLASS" }, { "id": "http://purl.obolibrary.org/obo/IAO_0000037", "lbl": "dot plot", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "dot plot" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "Dot plot of SSC-H and FSC-H." }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000114", "val": "http://purl.obolibrary.org/obo/IAO_0000002" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "person:Allyson Lister" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "person:Chris Stoeckert" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "OBI_0000123" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "group:OBI" } ], "definition": { "val": "A dot plot is a report graph which is a graphical representation of data where each data point is represented by a single dot placed on coordinates corresponding to data point values in particular dimensions." } }, "type": "CLASS" }, { "id": "http://purl.obolibrary.org/obo/IAO_0000038", "lbl": "graph", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "graph" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000114", "val": "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "PERSON: Lawrence Hunter" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "person:Alan Ruttenberg" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "person:Allyson Lister" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "OBI_0000240" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "group:OBI" } ], "definition": { "val": "A diagram that presents one or more tuples of information by mapping those tuples in to a two dimensional space in a non arbitrary way." } }, "type": "CLASS" }, { "id": "http://purl.obolibrary.org/obo/IAO_0000064", "lbl": "algorithm", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "algorithm" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "PMID: 18378114.Genomics. 2008 Mar 28. LINKGEN: A new algorithm to process data in genetic linkage studies." }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000114", "val": "http://purl.obolibrary.org/obo/IAO_0000120" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "Philippe Rocca-Serra" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "PlanAndPlannedProcess Branch" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "IAO" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "OBI_0000270" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg)" } ], "definition": { "val": "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." } }, "type": "CLASS" }, { "id": "http://purl.obolibrary.org/obo/IAO_0000078", "lbl": "curation status specification", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "curation status specification" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000114", "val": "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000116", "val": "Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "PERSON:Bill Bug" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "GROUP:OBI:" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "OBI_0000266" } ], "definition": { "val": "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." } }, "type": "CLASS" }, { "id": "http://purl.obolibrary.org/obo/IAO_0000096", "lbl": "source code module", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "source code module" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "The written source code that implements part of an algorithm. Test - if you know that it was written in a specific language, then it can be source code module. We mean here, roughly, the wording of a document such as a perl script." }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000114", "val": "http://purl.obolibrary.org/obo/IAO_0000123" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "person:Alan Ruttenberg" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "person:Chris Stoeckert" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "OBI_0000039" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "group:OBI" } ], "definition": { "val": "A source code module is a directive information entity that specifies, using a programming language, some algorithm." } }, "type": "CLASS" }, { "id": "http://purl.obolibrary.org/obo/IAO_0000098", "lbl": "data format specification", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "data format specification" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000114", "val": "http://purl.obolibrary.org/obo/IAO_0000123" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000116", "val": "2009-03-16: provenance: term imported from OBI_0000187, which had original definition \"A data format specification is a plan which organizes\ninformation. Example: The ISO document specifying what encompasses an\nXML document; The instructions in a XSD file\"" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "PERSON: Alan Ruttenberg" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "PlanAndPlannedProcess Branch" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "OBI branch derived" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "OBI_0000187" } ], "definition": { "val": "A data format specification is the information content borne by the document published defining the specification.\nExample: The ISO document specifying what encompasses an XML document; The instructions in a XSD file" } }, "type": "CLASS" }, { "id": "http://purl.obolibrary.org/obo/IAO_0000100", "lbl": "data set", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "data set" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves)." }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000114", "val": "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000116", "val": "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" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000116", "val": "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." }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "person:Allyson Lister" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "person:Chris Stoeckert" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "OBI_0000042" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "group:OBI" } ], "definition": { "val": "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." } }, "type": "CLASS" }, { "id": "http://purl.obolibrary.org/obo/IAO_0000101", "lbl": "image", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "image" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000114", "val": "http://purl.obolibrary.org/obo/IAO_0000122" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "person:Alan Ruttenberg" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "person:Allyson" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "person:Chris Stoeckert" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "OBI_0000030" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "group:OBI" } ], "definition": { "val": "An image is an affine projection to a two dimensional surface, of measurements of some quality of an entity or entities repeated at regular intervals across a spatial range, where the measurements are represented as color and luminosity on the projected on surface." } }, "type": "CLASS" }, { "id": "http://purl.obolibrary.org/obo/IAO_0000102", "lbl": "data about an ontology part", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "data about an ontology part" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "Person:Alan Ruttenberg" } ], "definition": { "val": "Data about an ontology part is a data item about a part of an ontology, for example a term" } }, "type": "CLASS" }, { "id": "http://purl.obolibrary.org/obo/IAO_0000103", "lbl": "failed exploratory term", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "failed exploratory term" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "Person:Alan Ruttenberg" } ], "definition": { "val": "The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job" } }, "type": "INDIVIDUAL" }, { "id": "http://purl.obolibrary.org/obo/IAO_0000104", "lbl": "plan specification", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "plan specification" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice." }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000114", "val": "http://purl.obolibrary.org/obo/IAO_0000122" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000116", "val": "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." }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000116", "val": "2014-03-31: A plan specification can have other parts, such as conditional specifications." }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000116", "val": "2022-01-16 Updated definition to that proposed by Clint Dowloand, IAO Issue 231." }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000116", "val": "Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "Alan Ruttenberg" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "Clint Dowland" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "OBI Plan and Planned Process branch" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "OBI_0000344" }, { "pred": "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val": "https://github.com/information-artifact-ontology/IAO/issues/231#issuecomment-1010455131" } ], "comments": [ "2/3/2009 Comment from OBI review.\n\nAction specification not well enough specified.\nConditional specification not well enough specified.\nQuestion whether all plan specifications have objective specifications.\n\nRequest that IAO either clarify these or change definitions not to use them" ], "definition": { "val": "A directive information entity with action specifications and objective specifications as parts, and that may be concretized as a realizable entity that, if realized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified." } }, "type": "CLASS" }, { "id": "http://purl.obolibrary.org/obo/IAO_0000111", "lbl": "editor preferred term~editor preferred label", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "editor preferred label" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "editor preferred label" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "editor preferred term" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "editor preferred term" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "editor preferred term~editor preferred label" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000114", "val": "http://purl.obolibrary.org/obo/IAO_0000122" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "PERSON:Daniel Schober" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "GROUP:OBI:" }, { "pred": "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val": "http://purl.obolibrary.org/obo/iao.owl" } ], "definition": { "val": "The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)" } }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/IAO_0000112", "lbl": "example of usage", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "example of usage" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000114", "val": "http://purl.obolibrary.org/obo/IAO_0000122" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "PERSON:Daniel Schober" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "GROUP:OBI:" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "IAO" }, { "pred": "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val": "http://purl.obolibrary.org/obo/iao.owl" } ], "definition": { "val": "A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold." } }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/IAO_0000115", "lbl": "textual definition", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "definition" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "definition" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "textual definition" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000114", "val": "http://purl.obolibrary.org/obo/IAO_0000122" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000116", "val": "2012-04-05: \nBarry Smith\n\nThe 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.\n\nCan you fix to something like:\n\nA statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property.\n\nAlan Ruttenberg\n\nYour 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. \n\nOn the specifics of the proposed definition:\n\nWe 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. \n\nPersonally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. \n\nWe 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. " }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "PERSON:Daniel Schober" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "GROUP:OBI:" }, { "pred": "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val": "http://purl.obolibrary.org/obo/iao.owl" } ], "definition": { "val": "The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions." } }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/IAO_0000117", "lbl": "term editor", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "term editor" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000114", "val": "http://purl.obolibrary.org/obo/IAO_0000122" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000116", "val": "20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115." }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "PERSON:Daniel Schober" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "GROUP:OBI:" }, { "pred": "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val": "http://purl.obolibrary.org/obo/iao.owl" } ], "definition": { "val": "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" } }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/IAO_0000118", "lbl": "alternative term", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "alternative label" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "alternative term" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000114", "val": "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "OBO Operations committee" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "PERSON:Daniel Schober" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "GROUP:OBI:" }, { "pred": "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val": "http://purl.obolibrary.org/obo/iao.owl" } ], "comments": [ "Consider re-defing to: An alternative name for a class or property which can mean the same thing as the preferred name (semantically equivalent, narrow, broad or related)." ], "definition": { "val": "An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent)" } }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/IAO_0000119", "lbl": "definition source", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "definition source" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000114", "val": "http://purl.obolibrary.org/obo/IAO_0000122" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "PERSON:Daniel Schober" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "GROUP:OBI:" }, { "pred": "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val": "http://purl.obolibrary.org/obo/iao.owl" } ], "definition": { "val": "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" } }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/IAO_0000120", "lbl": "metadata complete", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "metadata complete" } ], "definition": { "val": "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." } }, "type": "INDIVIDUAL" }, { "id": "http://purl.obolibrary.org/obo/IAO_0000121", "lbl": "organizational term", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "organizational term" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "PERSON:Alan Ruttenberg" } ], "definition": { "val": "Term created to ease viewing/sort terms for development purpose, and will not be included in a release" } }, "type": "INDIVIDUAL" }, { "id": "http://purl.obolibrary.org/obo/IAO_0000122", "lbl": "ready for release", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "ready for release" } ], "definition": { "val": "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.\"" } }, "type": "INDIVIDUAL" }, { "id": "http://purl.obolibrary.org/obo/IAO_0000123", "lbl": "metadata incomplete", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "metadata incomplete" } ], "definition": { "val": "Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors." } }, "type": "INDIVIDUAL" }, { "id": "http://purl.obolibrary.org/obo/IAO_0000124", "lbl": "uncurated", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "uncurated" } ], "definition": { "val": "Nothing done yet beyond assigning a unique class ID and proposing a preferred term." } }, "type": "INDIVIDUAL" }, { "id": "http://purl.obolibrary.org/obo/IAO_0000125", "lbl": "pending final vetting", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "pending final vetting" } ], "definition": { "val": "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." } }, "type": "INDIVIDUAL" }, { "id": "http://purl.obolibrary.org/obo/IAO_0000129", "lbl": "version number", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "version number" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000114", "val": "http://purl.obolibrary.org/obo/IAO_0000123" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000116", "val": "Note: we feel that at the moment we are happy with a general version number, and that we will subclass as needed in the future. For example, see 7. genome sequence version" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "GROUP: IAO" } ], "definition": { "val": "A version number is an information content entity which is a sequence of characters borne by part of each of a class of manufactured products or its packaging and indicates its order within a set of other products having the same name." } }, "type": "CLASS" }, { "id": "http://purl.obolibrary.org/obo/IAO_0000136", "lbl": "is about", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "This document is about information artifacts and their representations" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000114", "val": "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000116", "val": "7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of \"mentions\" relation. Weaken the is_about relationship to be primitive. \n\nWe will try to build it back up by elaborating the various subproperties that are more precisely defined.\n\nSome 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." }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "person:Alan Ruttenberg" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "Smith, Ceusters, Ruttenberg, 2000 years of philosophy" } ], "definition": { "val": "A (currently) primitive relation that relates an information artifact to an entity." } }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/IAO_0000178", "lbl": "material information bearer", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "material information bearer" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "A page of a paperback novel with writing on it. The paper itself is a material information bearer, the pattern of ink is the information carrier." }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "a brain" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "a hard drive" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000114", "val": "http://purl.obolibrary.org/obo/IAO_0000122" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "GROUP: IAO" } ], "definition": { "val": "A material entity in which a concretization of an information content entity inheres." } }, "type": "CLASS" }, { "id": "http://purl.obolibrary.org/obo/IAO_0000179", "lbl": "histogram", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "histogram" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000114", "val": "http://purl.obolibrary.org/obo/IAO_0000122" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "PERSON:Chris Stoeckert" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "PERSON:James Malone" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "PERSON:Melanie Courtot" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "GROUP:OBI" } ], "definition": { "val": "A histogram is a report graph which is a statistical description of a\ndistribution in terms of occurrence frequencies of different event classes." } }, "type": "CLASS" }, { "id": "http://purl.obolibrary.org/obo/IAO_0000180", "lbl": "heatmap", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "heatmap" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000114", "val": "http://purl.obolibrary.org/obo/IAO_0000122" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "PERSON:Chris Stoeckert" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "PERSON:James Malone" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "PERSON:Melanie Courtot" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "GROUP:OBI" } ], "definition": { "val": "A heatmap is a report graph which is a graphical representation of data\nwhere the values taken by a variable(s) are shown as colors in a\ntwo-dimensional map." } }, "type": "CLASS" }, { "id": "http://purl.obolibrary.org/obo/IAO_0000183", "lbl": "dendrogram", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "dendrogram" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "Dendrograms are often used in computational biology to\nillustrate the clustering of genes." }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000114", "val": "http://purl.obolibrary.org/obo/IAO_0000122" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "PERSON:Chris Stoeckert" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "PERSON:James Malone" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "PERSON:Melanie Courtot" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "WEB: http://en.wikipedia.org/wiki/Dendrogram" } ], "definition": { "val": "A dendrogram is a report graph which is a tree diagram\nfrequently used to illustrate the arrangement of the clusters produced by a\nclustering algorithm." } }, "type": "CLASS" }, { "id": "http://purl.obolibrary.org/obo/IAO_0000184", "lbl": "scatter plot", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "scatter plot" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "Comparison of gene expression values in two samples can be displayed in a scatter plot" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000114", "val": "http://purl.obolibrary.org/obo/IAO_0000122" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "PERSON:Chris Stoeckert" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "PERSON:James Malone" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "PERSON:Melanie Courtot" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "scattergraph" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "WEB: http://en.wikipedia.org/wiki/Scatterplot" } ], "definition": { "val": "A scatterplot is a graph which uses Cartesian coordinates to display values for two variables for a set of data. The data is displayed as a collection of points, each having the value of one variable determining the position on the horizontal axis and the value of the other variable determining the position on the vertical axis." } }, "type": "CLASS" }, { "id": "http://purl.obolibrary.org/obo/IAO_0000225", "lbl": "obsolescence reason specification", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "obsolescence reason specification" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000114", "val": "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000116", "val": "The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology." }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "PERSON: Alan Ruttenberg" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "PERSON: Melanie Courtot" } ], "definition": { "val": "The reason for which a term has been deprecated. 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." } }, "type": "CLASS" }, { "id": "http://purl.obolibrary.org/obo/IAO_0000226", "lbl": "placeholder removed", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "placeholder removed" } ] }, "type": "INDIVIDUAL" }, { "id": "http://purl.obolibrary.org/obo/IAO_0000227", "lbl": "terms merged", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "terms merged" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000116", "val": "An editor note should explain what were the merged terms and the reason for the merge." } ] }, "type": "INDIVIDUAL" }, { "id": "http://purl.obolibrary.org/obo/IAO_0000228", "lbl": "term imported", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "term imported" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000116", "val": "This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use." } ] }, "type": "INDIVIDUAL" }, { "id": "http://purl.obolibrary.org/obo/IAO_0000229", "lbl": "term split", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "term split" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000116", "val": "This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created." } ] }, "type": "INDIVIDUAL" }, { "id": "http://purl.obolibrary.org/obo/IAO_0000233", "lbl": "term tracker item", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "term tracker item" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000114", "val": "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg" } ], "comments": [ "The 'tracker item' can associate a tracker with a specific ontology term." ], "definition": { "val": "An IRI or similar locator for a request or discussion of an ontology term." } }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/IAO_0000308", "lbl": "figure", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "figure" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "Any picture, diagram or table" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000114", "val": "http://purl.obolibrary.org/obo/IAO_0000120" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "PERSON: Lawrence Hunter" } ], "definition": { "val": "An information content entity consisting of a two dimensional arrangement of information content entities such that the arrangement itself is about something." } }, "type": "CLASS" }, { "id": "http://purl.obolibrary.org/obo/IAO_0000309", "lbl": "diagram", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "diagram" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "A molecular structure ribbon cartoon showing helices, turns and sheets and their relations to each other in space." }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000114", "val": "http://purl.obolibrary.org/obo/IAO_0000120" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "PERSON: Lawrence Hunter" } ], "definition": { "val": "A figure that expresses one or more propositions" } }, "type": "CLASS" }, { "id": "http://purl.obolibrary.org/obo/IAO_0000310", "lbl": "document", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "document" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "A journal article, patent application, laboratory notebook, or a book" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000114", "val": "http://purl.obolibrary.org/obo/IAO_0000120" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "PERSON: Lawrence Hunter" } ], "definition": { "val": "A collection of information content entities intended to be understood together as a whole" } }, "type": "CLASS" }, { "id": "http://purl.obolibrary.org/obo/IAO_0000409", "lbl": "denotator type", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "denotator type" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are \"natural kinds\" and the latter arbitrary collections of entities." }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "Alan Ruttenberg" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "Barry Smith, Werner Ceusters" } ], "definition": { "val": "A denotator type indicates how a term should be interpreted from an ontological perspective." } }, "type": "CLASS" }, { "id": "http://purl.obolibrary.org/obo/IAO_0000410", "lbl": "universal", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "universal" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000116", "val": "Hard to give a definition for. Intuitively a \"natural kind\" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents." }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "Alan Ruttenberg" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf" } ] }, "type": "INDIVIDUAL" }, { "id": "http://purl.obolibrary.org/obo/IAO_0000412", "lbl": "imported from", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "imported from" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000114", "val": "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "PERSON:Alan Ruttenberg" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "PERSON:Melanie Courtot" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "GROUP:OBI:" }, { "pred": "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val": "http://purl.obolibrary.org/obo/iao.owl" } ], "definition": { "val": "For external terms/classes, the ontology from which the term was imported" } }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/IAO_0000420", "lbl": "defined class", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "defined class" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000116", "val": "\"definitions\", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal." }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "Alan Ruttenberg" } ], "definition": { "val": "A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal" } }, "type": "INDIVIDUAL" }, { "id": "http://purl.obolibrary.org/obo/IAO_0000421", "lbl": "named class expression", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "named class expression" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000116", "val": "named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "Alan Ruttenberg" } ], "definition": { "val": "A named class expression is a logical expression that is given a name. The name can be used in place of the expression." } }, "type": "INDIVIDUAL" }, { "id": "http://purl.obolibrary.org/obo/IAO_0000423", "lbl": "to be replaced with external ontology term", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "to be replaced with external ontology term" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "Alan Ruttenberg" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "group:OBI" } ], "definition": { "val": "Terms with this status should eventually replaced with a term from another ontology." } }, "type": "INDIVIDUAL" }, { "id": "http://purl.obolibrary.org/obo/IAO_0000428", "lbl": "requires discussion", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "requires discussion" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "Alan Ruttenberg" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "group:OBI" } ], "definition": { "val": "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." } }, "type": "INDIVIDUAL" }, { "id": "http://purl.obolibrary.org/obo/IAO_0100001", "lbl": "term replaced by", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "term replaced by" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000114", "val": "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "Person:Alan Ruttenberg" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "Person:Alan Ruttenberg" } ], "comments": [ "Add as annotation triples in the granting ontology" ], "definition": { "val": "Use on obsolete terms, relating the term to another term that can be used as a substitute" } }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/NCBITaxon_10239", "lbl": "Viruses", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "Viruses" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000412", "val": "http://purl.obolibrary.org/obo/ncbitaxon.owl" } ] }, "type": "CLASS" }, { "id": "http://purl.obolibrary.org/obo/NCBITaxon_117571", "lbl": "Euteleostomi", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "Euteleostomi" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "bony vertebrates" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000412", "val": "http://purl.obolibrary.org/obo/ncbitaxon.owl" } ] }, "type": "CLASS" }, { "id": "http://purl.obolibrary.org/obo/NCBITaxon_2", "lbl": "Bacteria", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "Bacteria" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "eubacteria" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000412", "val": "http://purl.obolibrary.org/obo/ncbitaxon.owl" } ] }, "type": "CLASS" }, { "id": "http://purl.obolibrary.org/obo/NCBITaxon_2157", "lbl": "Archaea", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "Archaea" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000412", "val": "http://purl.obolibrary.org/obo/ncbitaxon.owl" } ] }, "type": "CLASS" }, { "id": "http://purl.obolibrary.org/obo/NCBITaxon_2759", "lbl": "Eukaryota", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "Eukaryota" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "eucaryotes" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "eukaryotes" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000412", "val": "http://purl.obolibrary.org/obo/ncbitaxon.owl" } ] }, "type": "CLASS" }, { "id": "http://purl.obolibrary.org/obo/NCBITaxon_314146", "lbl": "Euarchontoglires", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "Euarchontoglires" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000412", "val": "http://purl.obolibrary.org/obo/ncbitaxon.owl" } ] }, "type": "CLASS" }, { "id": "http://purl.obolibrary.org/obo/NCBITaxon_32523", "lbl": "Tetrapoda", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "Tetrapoda" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "tetrapods" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000412", "val": "http://purl.obolibrary.org/obo/ncbitaxon.owl" } ] }, "type": "CLASS" }, { "id": "http://purl.obolibrary.org/obo/NCBITaxon_32524", "lbl": "Amniota", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "Amniota" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "amniotes" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000412", "val": "http://purl.obolibrary.org/obo/ncbitaxon.owl" } ] }, "type": "CLASS" }, { "id": "http://purl.obolibrary.org/obo/NCBITaxon_33154", "lbl": "Opisthokonta", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "Opisthokonta" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000412", "val": "http://purl.obolibrary.org/obo/ncbitaxon.owl" } ] }, "type": "CLASS" }, { "id": "http://purl.obolibrary.org/obo/NCBITaxon_33208", "lbl": "Metazoa", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "Metazoa" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "metazoans" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "multicellular animals" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000412", "val": "http://purl.obolibrary.org/obo/ncbitaxon.owl" } ] }, "type": "CLASS" }, { "id": "http://purl.obolibrary.org/obo/NCBITaxon_33213", "lbl": "Bilateria", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "Bilateria" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000412", "val": "http://purl.obolibrary.org/obo/ncbitaxon.owl" } ] }, "type": "CLASS" }, { "id": "http://purl.obolibrary.org/obo/NCBITaxon_40674", "lbl": "Mammalia", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "Mammalia" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "mammals" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000412", "val": "http://purl.obolibrary.org/obo/ncbitaxon.owl" } ] }, "type": "CLASS" }, { "id": "http://purl.obolibrary.org/obo/NCBITaxon_7742", "lbl": "Vertebrata ", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "Vertebrata " }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "Vertebrata" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "vertebrates" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000412", "val": "http://purl.obolibrary.org/obo/ncbitaxon.owl" } ] }, "type": "CLASS" }, { "id": "http://purl.obolibrary.org/obo/NCBITaxon_9606", "lbl": "Homo sapiens", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "Homo sapiens" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "human" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "human being" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000412", "val": "http://purl.obolibrary.org/obo/ncbitaxon.owl" } ] }, "type": "CLASS" }, { "id": "http://purl.obolibrary.org/obo/OBI_0000011", "lbl": "planned process", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "planned process" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "planned process" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "Injecting mice with a vaccine in order to test its efficacy" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000114", "val": "http://purl.obolibrary.org/obo/IAO_0000122" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000116", "val": "'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.)" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000116", "val": "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 \nobjectives is a planned process." }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "Bjoern Peters" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "branch derived" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000232", "val": "6/11/9: Edited at workshop. Used to include: is initiated by an agent" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000232", "val": "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)" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000412", "val": "http://purl.obolibrary.org/obo/obi.owl" } ], "definition": { "val": "A process that realizes a plan which is the concretization of a plan specification." } }, "type": "CLASS" }, { "id": "http://purl.obolibrary.org/obo/OBI_0000014", "lbl": "regulator role", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "regulator role" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "Fact sheet - Regulating the companies The role of the regulator. Ofwat is the economic regulator of the water and sewerage industry in England and Wales. http://www.ofwat.gov.uk/aptrix/ofwat/publish.nsf/Content/roleofregulator_factsheet170805" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000114", "val": "http://purl.obolibrary.org/obo/IAO_0000120" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "Person:Jennifer Fostel" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "regulator" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "OBI" } ], "definition": { "val": "a regulatory role involved with making and/or enforcing relevant legislation and governmental orders" } }, "type": "CLASS" }, { "id": "http://purl.obolibrary.org/obo/OBI_0000017", "lbl": "regulatory role", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "regulatory role" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "Regulatory agency, Ethics committee, Approval letter; example: Browse these EPA Regulatory Role subtopics http://www.epa.gov/ebtpages/enviregulatoryrole.html Feb 29, 2008" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000114", "val": "http://purl.obolibrary.org/obo/IAO_0000120" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "GROUP: Role branch" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "OBI, CDISC" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000232", "val": "govt agents responsible for creating regulations; proxies for enforcing regulations. CDISC definition: regulatory authorities. Bodies having the power to regulate. NOTE: In the ICH GCP guideline the term includes the authorities that review submitted clinical data and those that conduct inspections. These bodies are sometimes referred to as competent" } ], "definition": { "val": "a role which inheres in material entities and is realized in the processes of making, enforcing or being defined by legislation or orders issued by a governmental body." } }, "type": "CLASS" }, { "id": "http://purl.obolibrary.org/obo/OBI_0000018", "lbl": "material supplier role", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "material supplier role" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "Jackson Labs is an organization which provide mice as experimental material" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000114", "val": "http://purl.obolibrary.org/obo/IAO_0000120" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000116", "val": "Supplier role is a special kind of service, e.g. biobank" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "PERSON:Jennifer Fostel" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "material provider role" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "supplier" } ], "definition": { "val": "a role realized through the process of supplying materials such as animal subjects, reagents or other materials used in an investigation." } }, "type": "CLASS" }, { "id": "http://purl.obolibrary.org/obo/OBI_0000023", "lbl": "classified data set", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "classified data set" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000114", "val": "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "PERSON: James Malone" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "PERSON: Monnie McGee" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "data set with assigned class labels" } ], "definition": { "val": "A data set that is produced as the output of a class prediction data transformation and consists of a data set with assigned class labels." } }, "type": "CLASS" }, { "id": "http://purl.obolibrary.org/obo/OBI_0000047", "lbl": "processed material", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "processed material" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000114", "val": "http://purl.obolibrary.org/obo/IAO_0000122" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "PERSON: Alan Ruttenberg" } ], "definition": { "val": "Is a material entity that is created or changed during material processing." } }, "type": "CLASS" }, { "id": "http://purl.obolibrary.org/obo/OBI_0000094", "lbl": "material processing", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "material processing" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "A cell lysis, production of a cloning vector, creating a buffer." }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000114", "val": "http://purl.obolibrary.org/obo/IAO_0000122" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "PERSON: Bjoern Peters" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "PERSON: Frank Gibson" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "PERSON: Jennifer Fostel" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "PERSON: Melanie Courtot" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "PERSON: Philippe Rocca Serra" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "material transformation" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "OBI branch derived" } ], "definition": { "val": "A planned process which results in physical changes in a specified input material" } }, "type": "CLASS" }, { "id": "http://purl.obolibrary.org/obo/OBI_0000112", "lbl": "specimen role", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "specimen role" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "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." }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000114", "val": "http://purl.obolibrary.org/obo/IAO_0000122" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000116", "val": "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." }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000116", "val": "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." }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000116", "val": "blood taken from animal: animal continues in study, whereas blood has role specimen.\nsomething taken from study subject, leaves the study and becomes the specimen." }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000116", "val": "parasite example\n- when parasite in people we study people, people are subjects and parasites are specimen\n- when parasite extracted, they become subject in the following study\nspecimen can later be subject." }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "GROUP: Role Branch" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "OBI" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000233", "val": "https://github.com/obi-ontology/obi/issues/1013" } ], "definition": { "val": "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" } }, "type": "CLASS" }, { "id": "http://purl.obolibrary.org/obo/OBI_0000245", "lbl": "organization", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "organization" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "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." }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000114", "val": "http://purl.obolibrary.org/obo/IAO_0000122" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000116", "val": "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:\n\n1) there are organization_member_roles (president, treasurer, branch\neditor), with individual persons as bearers\n\n2) there are organization_roles (employer, owner, vendor, patent holder)\n\n3) an organization has a charter / rules / bylaws, which specify what roles\nthere are, how they should be realized, and how to modify the\ncharter/rules/bylaws themselves.\n\nIt is debatable what the organization itself is (some kind of dependent\ncontinuant or an aggregate of people). This also determines who/what the\nbearer of organization_roles' are. My personal favorite is still to define\norganization as a kind of 'legal entity', but thinking it through leads to\nall kinds of questions that are clearly outside the scope of OBI.\n\nInterestingly enough, it does not seem to matter much where we place\norganization itself, as long as we can subclass it (University, Corporation,\nGovernment Agency, Hospital), instantiate it (Affymetrix, NCBI, NIH, ISO,\nW3C, University of Oklahoma), and have it play roles.\n\nThis leads to my proposal: We define organization through the statements 1 -\n3 above, but without an 'is a' statement for now. We can leave it in its\ncurrent place in the is_a hierarchy (material entity) or move it up to\n'continuant'. We leave further clarifications to BFO, and close this issue\nfor now." }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "PERSON: Alan Ruttenberg" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "PERSON: Bjoern Peters" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "PERSON: Philippe Rocca-Serra" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "PERSON: Susanna Sansone" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "GROUP: OBI" } ], "definition": { "val": "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." } }, "type": "CLASS" }, { "id": "http://purl.obolibrary.org/obo/OBI_0000293", "lbl": "has_specified_input", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "has_specified_input" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "has_specified_input" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "see is_input_of example_of_usage" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000114", "val": "http://purl.obolibrary.org/obo/IAO_0000122" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000116", "val": "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." }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "PERSON: Alan Ruttenberg" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "PERSON: Bjoern Peters" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "PERSON: Larry Hunter" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "PERSON: Melanie Coutot" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000412", "val": "http://purl.obolibrary.org/obo/obi.owl" } ], "definition": { "val": "The inverse property of is_specified_input_of" } }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/OBI_0000295", "lbl": "is_specified_input_of", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "is_specified_input_of" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "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" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000114", "val": "http://purl.obolibrary.org/obo/IAO_0000122" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "Alan Ruttenberg" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "PERSON:Bjoern Peters" } ], "definition": { "val": "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." } }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/OBI_0000299", "lbl": "has_specified_output", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "has_specified_output" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "has_specified_output" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000114", "val": "http://purl.obolibrary.org/obo/IAO_0000122" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "PERSON: Alan Ruttenberg" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "PERSON: Bjoern Peters" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "PERSON: Larry Hunter" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "PERSON: Melanie Courtot" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000412", "val": "http://purl.obolibrary.org/obo/obi.owl" } ], "definition": { "val": "The inverse property of is_specified_output_of" } }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/OBI_0000304", "lbl": "is_manufactured_by", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "is_manufactured_by" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "http://www.affymetrix.com/products/arrays/specific/hgu133.affx is_manufactered_by http://www.affymetrix.com/ (if we decide to use these URIs for the actual entities)" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000114", "val": "http://purl.obolibrary.org/obo/IAO_0000123" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "Alan Ruttenberg" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "Liju Fan" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "has_make" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "has_manufacturer" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "OBI" } ], "definition": { "val": "c is_manufactured_by o means that there was a process p in which c was built in which a person, or set of people or machines did the work(bore the \"Manufacturer Role\", and those people/and or machines were members or of directed by the organization to do this." } }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/OBI_0000312", "lbl": "is_specified_output_of", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "is_specified_output_of" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "is_specified_output_of" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000114", "val": "http://purl.obolibrary.org/obo/IAO_0000122" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "Alan Ruttenberg" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "PERSON:Bjoern Peters" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000412", "val": "http://purl.obolibrary.org/obo/obi.owl" } ], "definition": { "val": "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." } }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/OBI_0000317", "lbl": "Transformation-ML", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "Transformation-ML" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "Transformation-ML file describing parameter transformations used in a GvHD experiment." }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000114", "val": "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "person:Jennifer Fostel" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "web-page:http://wiki.ficcs.org/ficcs/Transformation-ML?action=AttachFile&do=get&target=Transformation-ML_v1.0.26.pdf" } ], "definition": { "val": "Transformation-ML is a format standard of a digital entity that is conformant with the Transformation-ML standard.(http://wiki.ficcs.org/ficcs/Transformation-ML?action=AttachFile&do=get&target=Transformation-ML_v1.0.26.pdf)" } }, "type": "INDIVIDUAL" }, { "id": "http://purl.obolibrary.org/obo/OBI_0000321", "lbl": "ACS", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "ACS" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "d06.acs, ACS1.0 data file of well D06 of plate 2 of part 1 of a GvHD experiment." }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000114", "val": "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "person:Jennifer Fostel" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "web-page:http://www.isac-net.org/content/view/607/150/" } ], "definition": { "val": "ACS is a format standard of a digital entity that is conformant with the Analytical Cytometry Standard. (http://www.isac-net.org/content/view/607/150/)" } }, "type": "INDIVIDUAL" }, { "id": "http://purl.obolibrary.org/obo/OBI_0000322", "lbl": "XML", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "XML" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "RDF/XML file, OWL file, Compensation-ML file, WSDL document, SVG document" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000114", "val": "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "person:Jennifer Fostel" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "web-page:http://www.w3.org/XML/" } ], "definition": { "val": "XML is a format standard of a digital entity that is conformant with the W3C Extensible Markup Language Recommendation.(http://www.w3.org/XML/)" } }, "type": "INDIVIDUAL" }, { "id": "http://purl.obolibrary.org/obo/OBI_0000324", "lbl": "RDF", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "RDF" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "A FOAF file, a SKOS file, an OWL file." }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000114", "val": "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "person:Jennifer Fostel" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "web-page:http://www.w3.org/RDF/" } ], "definition": { "val": "RDF is a format standard of a digital entity that is conformant with the W3C Resource Description Framework RDF/XML Syntax specification.(http://www.w3.org/RDF/)" } }, "type": "INDIVIDUAL" }, { "id": "http://purl.obolibrary.org/obo/OBI_0000325", "lbl": "zip", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "zip" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "MagicDraw MDZIP archive, Java JAR file." }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000114", "val": "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "person:Jennifer Fostel" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "web-page:http://www.pkware.com/index.php?option=com_content&task=view&id=59&Itemid=103/" } ], "definition": { "val": "zip is a format standard of a digital entity that is conformant with the PKWARE .ZIP file format specification (http://www.pkware.com/index.php?option=com_content&task=view&id=59&Itemid=103/)" } }, "type": "INDIVIDUAL" }, { "id": "http://purl.obolibrary.org/obo/OBI_0000326", "lbl": "tar", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "tar" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "Example.tar file." }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000114", "val": "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "person:Jennifer Fostel" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "web-page:http://www.gnu.org/software/tar/manual/" } ], "definition": { "val": "tar is a format standard of a digital entity that is conformant with the tape archive file format as standardized by POSIX.1-1998, POSIX.1-2001, or any other tar format compliant with the GNU tar specification. (http://www.gnu.org/software/tar/manual/)" } }, "type": "INDIVIDUAL" }, { "id": "http://purl.obolibrary.org/obo/OBI_0000327", "lbl": "FCS", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "FCS" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "d01.fcs, FCS3 data file of well D06 of plate 2 of part 1 of a GvHD experiment." }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000114", "val": "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "person:Jennifer Fostel" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "web-page:http://www.fcspress.com/" } ], "definition": { "val": "FCS is a format standard of a digital entity that is conformant with the Flow Cytometry Data File Standard.(http://www.fcspress.com/)" } }, "type": "INDIVIDUAL" }, { "id": "http://purl.obolibrary.org/obo/OBI_0000329", "lbl": "Compensation-ML", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "Compensation-ML" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "compfoo.xml, Compensation-ML file describing compensation used in a GvHD experiment" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000114", "val": "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "person:Jennifer Fostel" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "web-page:http://wiki.ficcs.org/ficcs/Compensation-ML?action=AttachFile&do=get&target=Compensation-ML_v1.0.24.pdf" } ], "definition": { "val": "Compensation-ML is a format standard of a digital entity that is conformant with the Compensation-ML standard. (http://wiki.ficcs.org/ficcs/Compensation-ML?action=AttachFile&do=get&target=Compensation-ML_v1.0.24.pdf)" } }, "type": "INDIVIDUAL" }, { "id": "http://purl.obolibrary.org/obo/OBI_0000330", "lbl": "Gating-ML", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "Gating-ML" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "foogate.xml, Gating-ML file describing gates used in a GvHD experiment." }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000114", "val": "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "person:Jennifer Fostel" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "web-page:http://www.flowcyt.org/gating/" } ], "definition": { "val": "Gating-ML is a format standard of a digital entity that is conformant with the Gating-ML standard. (http://www.flowcyt.org/gating/)" } }, "type": "INDIVIDUAL" }, { "id": "http://purl.obolibrary.org/obo/OBI_0000332", "lbl": "OWL", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "OWL" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "OBI ontology file, Basic Formal Ontology file, BIRNLex file, BioPAX file." }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000114", "val": "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "person:Jennifer Fostel" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "web-page:http://www.w3.org/2004/OWL/" } ], "definition": { "val": "OWL is a format standard of a digital entity that is conformant with the W3C Web Ontology Language specification.(http://www.w3.org/2004/OWL/)" } }, "type": "INDIVIDUAL" }, { "id": "http://purl.obolibrary.org/obo/OBI_0000417", "lbl": "achieves_planned_objective", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "achieves_planned_objective" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "A cell sorting process achieves the objective specification 'material separation objective'" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000114", "val": "http://purl.obolibrary.org/obo/IAO_0000120" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "BP, AR, PPPB branch" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "PPPB branch derived" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000232", "val": "modified according to email thread from 1/23/09 in accordince with DT and PPPB branch" } ], "definition": { "val": "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." } }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/OBI_0000450", "lbl": "regulatory agency", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "regulatory agency" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "The US Environmental Protection Agency" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000114", "val": "http://purl.obolibrary.org/obo/IAO_0000122" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "GROUP: OBI Biomaterial Branch" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "WEB: en.wikipedia.org/wiki/Regulator" } ], "definition": { "val": "A regulatory agency is a organization that has responsibility over or for the legislation (acts and regulations) for a given sector of the government." } }, "type": "CLASS" }, { "id": "http://purl.obolibrary.org/obo/OBI_0000456", "lbl": "material transformation objective", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "material transformation objective" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "The objective to create a mouse infected with LCM virus. The objective to create a defined solution of PBS." }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000114", "val": "http://purl.obolibrary.org/obo/IAO_0000122" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "PERSON: Bjoern Peters" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "PERSON: Frank Gibson" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "PERSON: Jennifer Fostel" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "PERSON: Melanie Courtot" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "PERSON: Philippe Rocca-Serra" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "artifact creation objective" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "GROUP: OBI PlanAndPlannedProcess Branch" } ], "definition": { "val": "an objective specifiction that creates an specific output object from input materials." } }, "type": "CLASS" }, { "id": "http://purl.obolibrary.org/obo/OBI_0000457", "lbl": "manufacturing", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "manufacturing" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000114", "val": "http://purl.obolibrary.org/obo/IAO_0000122" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000116", "val": "Manufacturing implies reproducibility and responsibility AR" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000116", "val": "This includes a single scientist making a processed material for personal use." }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "PERSON: Bjoern Peters" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "PERSON: Frank Gibson" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "PERSON: Jennifer Fostel" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "PERSON: Melanie Courtot" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "PERSON: Philippe Rocca-Serra" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "GROUP: OBI PlanAndPlannedProcess Branch" } ], "definition": { "val": "Manufacturing is a process with the intent to produce a processed material which will have a function for future use. A person or organization (having manufacturer role) is a participant in this process" } }, "type": "CLASS" }, { "id": "http://purl.obolibrary.org/obo/OBI_0000458", "lbl": "manufacturing objective", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "manufacturing objective" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000114", "val": "http://purl.obolibrary.org/obo/IAO_0000122" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "PERSON: Bjoern Peters" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "PERSON: Frank Gibson" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "PERSON: Jennifer Fostel" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "PERSON: Melanie Courtot" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "PERSON: Philippe Rocca-Serra" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "GROUP: OBI PlanAndPlannedProcess Branch" } ], "definition": { "val": "is the objective to manufacture a material of a certain function (device)" } }, "type": "CLASS" }, { "id": "http://purl.obolibrary.org/obo/OBI_0000462", "lbl": "Affymetrix", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "Affymetrix" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "Affymetrix supplied microarray" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000114", "val": "http://purl.obolibrary.org/obo/IAO_0000123" } ], "definition": { "val": "An organization which supplies technology, tools and protocols for use in high throughput applications" } }, "type": "INDIVIDUAL" }, { "id": "http://purl.obolibrary.org/obo/OBI_0000571", "lbl": "manufacturer role", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "manufacturer role" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "With respect to The Accuri C6 Flow Cytometer System, the organization Accuri bears the role manufacturer role. With respect to a transformed line of tissue culture cells derived by a specific lab, the lab whose personnel isolated the cll line bears the role manufacturer role. 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"id": "http://purl.obolibrary.org/obo/OBI_0200172", "lbl": "partitioning objective", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "partitioning objective" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "A k-means clustering which has partitioning objective is a data transformation in which the input data is partitioned into k output sets." }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000114", "val": "http://purl.obolibrary.org/obo/IAO_0000122" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "Elisabetta Manduchi" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "James Malone" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "PERSON: Elisabetta Manduchi" } ], "definition": { "val": "A partitioning objective is a data transformation objective where the aim is to generate a collection of disjoint non-empty subsets whose union equals a non-empty input set." } }, "type": "CLASS" }, { "id": "http://purl.obolibrary.org/obo/OBI_0200175", "lbl": "class discovery data transformation", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "class discovery data transformation" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000114", "val": "http://purl.obolibrary.org/obo/IAO_0000122" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "James Malone" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "clustering data transformation" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "unsupervised classification data transformation" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "PERSON: James Malone" } ], "definition": { "val": "A class discovery data transformation (sometimes called unsupervised classification) is a data transformation that has objective class discovery." } }, "type": "CLASS" }, { "id": "http://purl.obolibrary.org/obo/OBI_0200178", "lbl": "class discovery objective", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "class discovery objective" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000114", "val": "http://purl.obolibrary.org/obo/IAO_0000122" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "James Malone" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "clustering objective" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "discriminant analysis objective" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "unsupervised classification objective" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "PERSON: Elisabetta Manduchi" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "PERSON: James Malone" } ], "definition": { "val": "A class discovery objective (sometimes called unsupervised classification) is a data transformation objective where the aim is to organize input data (typically vectors of attributes) into classes, where the number of classes and their specifications are not known a priori. Depending on usage, the class assignment can be definite or probabilistic." } }, "type": "CLASS" }, { "id": "http://purl.obolibrary.org/obo/OBI_0200179", "lbl": "class prediction objective", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "class prediction objective" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000114", "val": "http://purl.obolibrary.org/obo/IAO_0000122" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "James Malone" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "classification objective" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "supervised classification objective" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "PERSON: Elisabetta Manduchi" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "PERSON: James Malone" } ], "definition": { "val": "A class prediction objective (sometimes called supervised classification) is a data transformation objective where the aim is to create a predictor from training data through a machine learning technique. The training data consist of pairs of objects (typically vectors of attributes) and\nclass labels for these objects. The resulting predictor can be used to attach class labels to any valid novel input object. Depending on usage, the prediction can be definite or probabilistic. A classification is learned from the training data and can then be tested on test data." } }, "type": "CLASS" }, { "id": "http://purl.obolibrary.org/obo/OBI_0200188", "lbl": "cross validation objective", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "cross validation objective" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000114", "val": "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "James Malone" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "rotation estimation objective" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "WEB: http://en.wikipedia.org/wiki/Cross_validation" } ], "definition": { "val": "A cross validation objective is a data transformation objective in which the aim is to partition a sample of data into subsets such that the analysis is initially performed on a single subset, while the other subset(s) are retained for subsequent use in confirming and validating the initial analysis." } }, "type": "CLASS" }, { "id": "http://purl.obolibrary.org/obo/OBI_0200190", "lbl": "clustered data visualization", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "clustered data visualization" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000114", "val": "http://purl.obolibrary.org/obo/IAO_0000123" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "James Malone" } ], "definition": { "val": "A data visualization which has input of a clustered data set and produces an output of a report graph which is capable of rendering data of this type." } }, "type": "CLASS" }, { "id": "http://purl.obolibrary.org/obo/OMO_0001000", "lbl": "out of scope", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000116", "val": "This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease." }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "http://orcid.org/0000-0001-5208-3432" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000233", "val": "https://github.com/information-artifact-ontology/ontology-metadata/issues/77" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000234", "val": "https://orcid.org/0000-0001-5208-3432" } ], "definition": { "val": "The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not." } }, "type": "INDIVIDUAL" }, { "id": "http://purl.obolibrary.org/obo/PATO_0000001", "lbl": "quality", "meta": { "definition": { "val": "A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities", "xrefs": [ "PATOC:GVG" ] } }, "type": "CLASS" }, { "id": "http://purl.obolibrary.org/obo/RO_0000052", "lbl": "inheres in", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "inheres in" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "this fragility inheres in this vase" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "this fragility is a characteristic of this vase" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "this red color inheres in this apple" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "this red color is a characteristic of this apple" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000116", "val": "A dependent inheres in its bearer at all times for which the dependent exists." }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "inheres_in" }, { "pred": "http://purl.obolibrary.org/obo/RO_0001900", "val": "http://purl.obolibrary.org/obo/RO_0001901" } ], "comments": [ "Note that this relation was previously called \"inheres in\", but was changed to be called \"characteristic of\" because BFO2 uses \"inheres in\" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing." ], "definition": { "val": "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" } }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/RO_0000053", "lbl": "has characteristic", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "bearer of" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "this apple is bearer of this red color" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "this vase is bearer of this fragility" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000116", "val": "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." }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "bearer_of" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "is bearer of" }, { "pred": "http://purl.obolibrary.org/obo/RO_0001900", "val": "http://purl.obolibrary.org/obo/RO_0001901" } ], "definition": { "val": "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" } }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/RO_0000056", "lbl": "participates in", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "participates in" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "this blood clot participates in this blood coagulation" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "this input material (or this output material) participates in this process" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "this investigator participates in this investigation" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "participates_in" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Andy Brown" } ], "comments": [ "Please see the official RO definition for the inverse of this property, 'has participant.'" ], "definition": { "val": "a relation between a continuant and a process, in which the continuant is somehow involved in the process" } }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/RO_0000057", "lbl": "has participant", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "has participant" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "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." }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "this blood coagulation has participant this blood clot" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "this investigation has participant this investigator" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "this process has participant this input material (or this output material)" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000116", "val": "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." }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "has_participant" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://obo-relations.googlecode.com/svn/trunk/src/ontology/core.owl" }, { "pred": "http://purl.org/dc/elements/1.1/source", "val": "http://www.obofoundry.org/ro/#OBO_REL:has_participant" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Andy Brown" } ], "definition": { "val": "a relation between a process and a continuant, in which the continuant is somehow involved in the process" } }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/RO_0000058", "lbl": "is concretized as", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "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 journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant)." }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "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)." } ], "definition": { "val": "A relationship between a generically dependent continuant and a specifically 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. A generically dependent continuant may be concretized as multiple specifically dependent continuants." } }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/RO_0000059", "lbl": "concretizes", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "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)." }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "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)." } ], "definition": { "val": "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." } }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/RO_0000079", "lbl": "function of", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "this catalysis function is a function of this enzyme" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000116", "val": "A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists." }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "function_of" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "is function of" } ], "comments": [ "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020." ], "definition": { "val": "a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence" } }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/RO_0000080", "lbl": "quality of", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "this red color is a quality of this apple" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000116", "val": "A quality inheres in its bearer at all times for which the quality exists." }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "is quality of" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "quality_of" } ], "comments": [ "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020." ], "definition": { "val": "a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence" } }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/RO_0000081", "lbl": "role of", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "this investigator role is a role of this person" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000116", "val": "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." }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "is role of" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "role_of" } ], "comments": [ "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020." ], "definition": { "val": "a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence" } }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/RO_0000085", "lbl": "has function", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000116", "val": "A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists." }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "has_function" } ], "definition": { "val": "a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence" } }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/RO_0000086", "lbl": "has quality", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "this apple has quality this red color" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000116", "val": "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist." }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "has_quality" } ], "definition": { "val": "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence" } }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/RO_0000087", "lbl": "has_role", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "this person has role this investigator role (more colloquially: this person has this role of investigator)" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000116", "val": "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." }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "has_role" } ], "definition": { "val": "a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence" } }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/RO_0000091", "lbl": "has disposition", "meta": { "definition": { "val": "a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence" } }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/RO_0000092", "lbl": "disposition of", "meta": { "comments": [ "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020." ], "definition": { "val": "inverse of has disposition" }, "subsets": [ "http://purl.obolibrary.org/obo/RO_0002259" ] }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/RO_0002013", "lbl": "has regulatory component activity", "meta": { "basicPropertyValues": [ { "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", "val": "dos" }, { "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", "val": "2017-05-24T09:30:46Z" } ], "definition": { "val": "A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B." } }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/RO_0002014", "lbl": "has negative regulatory component activity", "meta": { "basicPropertyValues": [ { "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", "val": "dos" }, { "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", "val": "2017-05-24T09:31:01Z" } ], "comments": [ "By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'." ], "definition": { "val": "A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B." } }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/RO_0002015", "lbl": "has positive regulatory component activity", "meta": { "basicPropertyValues": [ { "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", "val": "dos" }, { "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", "val": "2017-05-24T09:31:17Z" } ], "comments": [ "By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'." ], "definition": { "val": "A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B." } }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/RO_0002017", "lbl": "has component activity", "meta": { "basicPropertyValues": [ { "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", "val": "dos" }, { "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", "val": "2017-05-24T09:44:33Z" } ], "comments": [ "A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B." ] }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/RO_0002018", "lbl": "has component process", "meta": { "basicPropertyValues": [ { "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", "val": "dos" }, { "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", "val": "2017-05-24T09:49:21Z" } ], "definition": { "val": "w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." } }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/RO_0002022", "lbl": "directly regulated by", "meta": { "basicPropertyValues": [ { "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", "val": "dos" }, { "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", "val": "2017-09-17T13:52:24Z" } ], "comments": [ "Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2." ] }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/RO_0002023", "lbl": "directly negatively regulated by", "meta": { "basicPropertyValues": [ { "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", "val": "dos" }, { "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", "val": "2017-09-17T13:52:38Z" } ], "definition": { "val": "Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1.", "xrefs": [ "GOC:dos" ] } }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/RO_0002024", "lbl": "directly positively regulated by", "meta": { "basicPropertyValues": [ { "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", "val": "dos" }, { "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", "val": "2017-09-17T13:52:47Z" } ], "definition": { "val": "Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1.", "xrefs": [ "GOC:dos" ] } }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/RO_0002025", "lbl": "has effector activity", "meta": { "basicPropertyValues": [ { "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", "val": "dos" }, { "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", "val": "2017-09-22T14:14:36Z" } ], "comments": [ "This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations." ], "definition": { "val": "A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity.", "xrefs": [ "GOC:dos" ] } }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/RO_0002086", "lbl": "ends after", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "David Osumi-Sutherland" } ], "comments": [ "X ends_after Y iff: end(Y) before_or_simultaneous_with end(X)" ], "subsets": [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/RO_0002087", "lbl": "immediately preceded by", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "David Osumi-Sutherland" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "starts_at_end_of" } ], "comments": [ "X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)" ] }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/RO_0002090", "lbl": "immediately precedes", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "David Osumi-Sutherland" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "https://orcid.org/0000-0002-7073-9172" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "ends_at_start_of" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "meets" }, { "pred": "http://purl.obolibrary.org/obo/RO_0002575", "val": "http://purl.obolibrary.org/obo/BFO_0000063" } ], "comments": [ "X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)" ], "subsets": [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/RO_0002131", "lbl": "overlaps", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000114", "val": "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000424", "val": "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)" }, { "pred": "http://purl.obolibrary.org/obo/RO_0001900", "val": "http://purl.obolibrary.org/obo/RO_0001901" } ], "definition": { "val": "x overlaps y if and only if there exists some z such that x has part z and z part of y" }, "subsets": [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco", "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ] }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/RO_0002180", "lbl": "has component", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000114", "val": "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000116", "val": "The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity." }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000232", "val": "For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit." }, { "pred": "http://purl.obolibrary.org/obo/RO_0001900", "val": "http://purl.obolibrary.org/obo/RO_0001901" }, { "pred": "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val": "http://ontologydesignpatterns.org/wiki/Submissions:Componency" } ], "definition": { "val": "w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." }, "subsets": [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/RO_0002211", "lbl": "regulates", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "https://orcid.org/0000-0001-7476-6306" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "https://orcid.org/0000-0002-3837-8864" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "https://orcid.org/0000-0002-6601-2165" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "GO" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://purl.obolibrary.org/obo/ro/docs/causal-relations" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000232", "val": "Regulation precludes parthood; the regulatory process may not be within the regulated process." }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000589", "val": "regulates (processual)" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000600", "val": "false" } ], "definition": { "val": "p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q." }, "subsets": [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ] }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/RO_0002212", "lbl": "negatively regulates", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "https://orcid.org/0000-0002-6601-2165" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://purl.obolibrary.org/obo/ro/docs/causal-relations" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000589", "val": "negatively regulates (process to process)" }, { "pred": "http://purl.obolibrary.org/obo/RO_0004050", "val": "http://purl.obolibrary.org/obo/RO_0002211" } ], "definition": { "val": "p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q." }, "subsets": [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ] }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/RO_0002213", "lbl": "positively regulates", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "https://orcid.org/0000-0002-6601-2165" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://purl.obolibrary.org/obo/ro/docs/causal-relations" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000589", "val": "positively regulates (process to process)" }, { "pred": "http://purl.obolibrary.org/obo/RO_0004049", "val": "http://purl.obolibrary.org/obo/RO_0002211" } ], "definition": { "val": "p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q." }, "subsets": [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ] }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/RO_0002215", "lbl": "capable of", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "osteoclast SubClassOf 'capable of' some 'bone resorption'" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "https://orcid.org/0000-0002-6601-2165" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "has function realized in" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://www.ncbi.nlm.nih.gov/pubmed/20123131" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://www.ncbi.nlm.nih.gov/pubmed/21208450" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000232", "val": "For compatibility with BFO, this relation has a shortcut definition in which the expression \"capable of some P\" expands to \"bearer_of (some realized_by only P)\"." } ], "definition": { "val": "A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. " }, "subsets": [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/RO_0002216", "lbl": "capable of part of", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "https://orcid.org/0000-0002-6601-2165" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "has function in" }, { "pred": "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val": "http://purl.obolibrary.org/obo/ro/docs/reflexivity/" } ], "definition": { "val": "c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p." } }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/RO_0002222", "lbl": "temporally related to", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000114", "val": "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "https://orcid.org/0000-0002-6601-2165" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "https://en.wikipedia.org/wiki/Allen%27s_interval_algebra" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000232", "val": "Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends." }, { "pred": "http://purl.org/dc/terms/source", "val": "https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1" } ], "comments": [ "A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations." ], "subsets": [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/RO_0002233", "lbl": "has input", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000114", "val": "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "https://orcid.org/0000-0002-6601-2165" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "consumes" } ], "definition": { "val": "p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p." }, "subsets": [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco", "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ] }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/RO_0002234", "lbl": "has output", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000114", "val": "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "https://orcid.org/0000-0002-6601-2165" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "produces" } ], "definition": { "val": "p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p." }, "subsets": [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco", "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ] }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/RO_0002263", "lbl": "acts upstream of", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision." }, { "pred": "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val": "http://wiki.geneontology.org/index.php/Acts_upstream_of" } ], "definition": { "val": "c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes." }, "subsets": [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ] }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/RO_0002264", "lbl": "acts upstream of or within", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway." }, { "pred": "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val": "http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within" } ], "definition": { "val": "c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process." }, "subsets": [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], "synonyms": [ { "pred": "hasRelatedSynonym", "val": "affects" } ] }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/RO_0002304", "lbl": "causally upstream of, positive effect", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/RO_0004049", "val": "http://purl.obolibrary.org/obo/RO_0002411" }, { "pred": "http://purl.org/dc/terms/creator", "val": "https://orcid.org/0000-0002-6601-2165" } ], "comments": [ "holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y" ], "definition": { "val": "p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q." }, "subsets": [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ] }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/RO_0002305", "lbl": "causally upstream of, negative effect", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/RO_0004050", "val": "http://purl.obolibrary.org/obo/RO_0002411" }, { "pred": "http://purl.org/dc/terms/creator", "val": "https://orcid.org/0000-0002-6601-2165" } ], "definition": { "val": "p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q." }, "subsets": [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ] }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/RO_0002314", "lbl": "characteristic of part of", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000116", "val": "Because part_of is transitive, inheres in is a sub-relation of characteristic of part of" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "https://orcid.org/0000-0002-6601-2165" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "inheres in part of" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://www.ncbi.nlm.nih.gov/pubmed/20064205" }, { "pred": "http://purl.obolibrary.org/obo/RO_0001900", "val": "http://purl.obolibrary.org/obo/RO_0001901" }, { "pred": "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val": "http://purl.obolibrary.org/obo/ro/docs/reflexivity/" } ], "definition": { "val": "q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w." } }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/RO_0002323", "lbl": "mereotopologically related to", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "https://orcid.org/0000-0002-6601-2165" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000232", "val": "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships" }, { "pred": "http://purl.obolibrary.org/obo/RO_0001900", "val": "http://purl.obolibrary.org/obo/RO_0001901" } ], "definition": { "val": "A mereological relationship or a topological relationship" } }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/RO_0002327", "lbl": "enables", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "a particular instances of akt-2 enables some instance of protein kinase activity" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "https://orcid.org/0000-0002-6601-2165" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "catalyzes" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "executes" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "has" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "is catalyzing" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "is executing" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000232", "val": "This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized." } ], "definition": { "val": "c enables p iff c is capable of p and c acts to execute p." }, "subsets": [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ] }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/RO_0002328", "lbl": "functionally related to", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "https://orcid.org/0000-0002-6601-2165" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000232", "val": "This is a grouping relation that collects relations used for the purpose of connecting structure and function" } ], "definition": { "val": "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities." } }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/RO_0002329", "lbl": "part of structure that is capable of", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "https://orcid.org/0000-0002-6601-2165" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "false" } ], "definition": { "val": "this relation holds between c and p when c is part of some c', and c' is capable of p." } }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/RO_0002331", "lbl": "involved in", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "https://orcid.org/0000-0002-6601-2165" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "actively involved in" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "enables part of" }, { "pred": "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val": "http://wiki.geneontology.org/index.php/Involved_in" } ], "definition": { "val": "c involved_in p if and only if c enables some process p', and p' is part of p" } }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/RO_0002333", "lbl": "enabled by", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "https://orcid.org/0000-0002-6601-2165" } ], "definition": { "val": "inverse of enables" }, "subsets": [ "http://purl.obolibrary.org/obo/valid_for_gocam" ] }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/RO_0002334", "lbl": "regulated by", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "https://orcid.org/0000-0002-6601-2165" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000589", "val": "regulated by (processual)" } ], "definition": { "val": "inverse of regulates" }, "subsets": [ "http://purl.obolibrary.org/obo/RO_0002259" ] }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/RO_0002335", "lbl": "negatively regulated by", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "https://orcid.org/0000-0002-6601-2165" } ], "definition": { "val": "inverse of negatively regulates" }, "subsets": [ "http://purl.obolibrary.org/obo/RO_0002259" ] }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/RO_0002336", "lbl": "positively regulated by", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "https://orcid.org/0000-0002-6601-2165" } ], "definition": { "val": "inverse of positively regulates" }, "subsets": [ "http://purl.obolibrary.org/obo/RO_0002259" ] }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/RO_0002350", "lbl": "member of", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "An organism that is a member of a population of organisms" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "is member of" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "member part of" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "SIO" }, { "pred": "http://purl.obolibrary.org/obo/RO_0001900", "val": "http://purl.obolibrary.org/obo/RO_0001901" } ], "definition": { "val": "is member of is a mereological relation between a item and a collection." } }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/RO_0002351", "lbl": "has member", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "SIO" }, { "pred": "http://purl.obolibrary.org/obo/RO_0001900", "val": "http://purl.obolibrary.org/obo/RO_0001901" } ], "definition": { "val": "has member is a mereological relation between a collection and an item." } }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/RO_0002352", "lbl": "input of", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "https://orcid.org/0000-0002-6601-2165" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "Allyson Lister" } ], "definition": { "val": "inverse of has input" }, "subsets": [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/RO_0002353", "lbl": "output of", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "A piece of software can be the output of a particular software company via a software publishing process; data might be the output of a particular piece of data-producing software." }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "https://orcid.org/0000-0002-6601-2165" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "Allyson Lister" } ], "definition": { "val": "inverse of has output" }, "subsets": [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/RO_0002404", "lbl": "causally downstream of", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000114", "val": "http://purl.obolibrary.org/obo/IAO_0000428" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "https://orcid.org/0000-0002-6601-2165" } ], "definition": { "val": "inverse of upstream of" } }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/RO_0002405", "lbl": "immediately causally downstream of", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000114", "val": "http://purl.obolibrary.org/obo/IAO_0000428" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "https://orcid.org/0000-0002-6601-2165" } ] }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/RO_0002407", "lbl": "indirectly positively regulates", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "https://orcid.org/0000-0002-6601-2165" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "indirectly activates" }, { "pred": "http://purl.obolibrary.org/obo/RO_0002579", "val": "http://purl.obolibrary.org/obo/RO_0002213" } ], "definition": { "val": "p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q." } }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/RO_0002409", "lbl": "indirectly negatively regulates", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "https://orcid.org/0000-0002-6601-2165" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "indirectly inhibits" }, { "pred": "http://purl.obolibrary.org/obo/RO_0002579", "val": "http://purl.obolibrary.org/obo/RO_0002212" } ], "definition": { "val": "p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q." } }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/RO_0002410", "lbl": "causally related to", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000116", "val": "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative?\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "https://orcid.org/0000-0002-6601-2165" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000232", "val": "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." } ], "definition": { "val": "relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause.", "xrefs": [ "https://en.wikipedia.org/wiki/Causality" ] } }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/RO_0002411", "lbl": "causally upstream of", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "https://orcid.org/0000-0002-6601-2165" } ], "definition": { "val": "p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q." }, "subsets": [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ] }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/RO_0002412", "lbl": "immediately causally upstream of", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "https://orcid.org/0000-0002-6601-2165" }, { "pred": "http://purl.obolibrary.org/obo/RO_0002575", "val": "http://purl.obolibrary.org/obo/RO_0002411" } ], "definition": { "val": "p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q." } }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/RO_0002418", "lbl": "causally upstream of or within", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000116", "val": "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "https://orcid.org/0000-0002-6601-2165" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "influences (processual)" } ], "definition": { "val": "p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q." }, "synonyms": [ { "pred": "hasRelatedSynonym", "val": "affects" } ] }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/RO_0002427", "lbl": "causally downstream of or within", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "https://orcid.org/0000-0002-6601-2165" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://purl.obolibrary.org/obo/ro/docs/causal-relations" } ], "definition": { "val": "inverse of causally upstream of or within" }, "subsets": [ "http://purl.obolibrary.org/obo/RO_0002259" ] }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/RO_0002428", "lbl": "involved in regulation of", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "https://orcid.org/0000-0002-6601-2165" } ], "definition": { "val": "c involved in regulation of p if c is involved in some p' and p' regulates some p" } }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/RO_0002429", "lbl": "involved in positive regulation of", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "https://orcid.org/0000-0002-6601-2165" }, { "pred": "http://purl.obolibrary.org/obo/RO_0004049", "val": "http://purl.obolibrary.org/obo/RO_0002428" } ], "definition": { "val": "c involved in regulation of p if c is involved in some p' and p' positively regulates some p" } }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/RO_0002430", "lbl": "involved in negative regulation of", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "https://orcid.org/0000-0002-6601-2165" }, { "pred": "http://purl.obolibrary.org/obo/RO_0004050", "val": "http://purl.obolibrary.org/obo/RO_0002428" } ], "definition": { "val": "c involved in regulation of p if c is involved in some p' and p' negatively regulates some p" } }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/RO_0002431", "lbl": "involved in or involved in regulation of", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000116", "val": "OWL does not allow defining object properties via a Union" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "https://orcid.org/0000-0002-6601-2165" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "involved in or reguates" } ], "definition": { "val": "c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p" } }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/RO_0002434", "lbl": "interacts with", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000116", "val": "Considering relabeling as 'pairwise interacts with'" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000116", "val": "This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact." }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "https://orcid.org/0000-0002-6601-2165" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000232", "val": "Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules." }, { "pred": "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val": "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" }, { "pred": "http://www.w3.org/2004/02/skos/core#closeMatch", "val": "http://purl.obolibrary.org/obo/MI_0914" } ], "definition": { "val": "A relationship that holds between two entities in which the processes executed by the two entities are causally connected." }, "subsets": [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "synonyms": [ { "pred": "hasExactSynonym", "val": "in pairwise interaction with" } ] }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/RO_0002436", "lbl": "molecularly interacts with", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "https://orcid.org/0000-0002-6601-2165" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "binds" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "molecularly binds with" }, { "pred": "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val": "http://purl.obolibrary.org/obo/ECO_0000353" }, { "pred": "http://www.w3.org/2004/02/skos/core#closeMatch", "val": "http://purl.obolibrary.org/obo/MI_0915" } ], "definition": { "val": "An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other." } }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/RO_0002447", "lbl": "phosphorylates", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000116", "val": "Axiomatization to GO to be added later" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "https://orcid.org/0000-0002-6601-2165" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y." } ] }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/RO_0002448", "lbl": "directly regulates activity of", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "https://orcid.org/0000-0002-6601-2165" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "https://orcid.org/0000-0003-4639-4431" } ], "definition": { "val": "The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B.\n\nA and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B." }, "synonyms": [ { "pred": "hasExactSynonym", "val": "molecularly controls" } ] }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/RO_0002449", "lbl": "directly negatively regulates activity of", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "https://orcid.org/0000-0002-6601-2165" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "https://orcid.org/0000-0003-4639-4431" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "directly inhibits" } ], "definition": { "val": "The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B." }, "synonyms": [ { "pred": "hasExactSynonym", "val": "molecularly decreases activity of" } ] }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/RO_0002450", "lbl": "directly positively regulates activity of", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "https://orcid.org/0000-0002-6601-2165" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "https://orcid.org/0000-0003-4639-4431" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "directly activates" } ], "definition": { "val": "The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B." }, "synonyms": [ { "pred": "hasExactSynonym", "val": "molecularly increases activity of" } ] }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/RO_0002464", "lbl": "helper property (not for use in curation)", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "https://orcid.org/0000-0002-6601-2165" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000232", "val": "This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning." } ] }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/RO_0002481", "lbl": "is kinase activity", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "https://orcid.org/0000-0002-6601-2165" } ] }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/RO_0002500", "lbl": "causal agent in process", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://purl.obolibrary.org/obo/ro/docs/causal-relations" } ], "definition": { "val": "A relationship between a material entity and a process where the material entity has some causal role that influences the process" } }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/RO_0002501", "lbl": "causal relation between processes", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "https://orcid.org/0000-0002-6601-2165" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://purl.obolibrary.org/obo/ro/docs/causal-relations" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000232", "val": "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." } ], "definition": { "val": "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q." } }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/RO_0002502", "lbl": "depends on", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "https://orcid.org/0000-0002-6601-2165" }, { "pred": "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val": "http://purl.obolibrary.org/obo/BFO_0000169" } ] }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/RO_0002506", "lbl": "causal relation between entities", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000116", "val": "The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "https://orcid.org/0000-0002-6601-2165" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://purl.obolibrary.org/obo/ro/docs/causal-relations" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000232", "val": "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." } ] }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/RO_0002559", "lbl": "causally influenced by", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "https://orcid.org/0000-0002-6601-2165" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://purl.obolibrary.org/obo/ro/docs/causal-relations" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000589", "val": "causally influenced by (entity-centric)" } ] }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/RO_0002563", "lbl": "interaction relation helper property", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "https://orcid.org/0000-0002-6601-2165" }, { "pred": "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val": "http://ontologydesignpatterns.org/wiki/Submissions:N-Ary_Relation_Pattern_%28OWL_2%29" }, { "pred": "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val": "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" } ] }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/RO_0002564", "lbl": "molecular interaction relation helper property", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "https://orcid.org/0000-0002-6601-2165" } ] }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/RO_0002566", "lbl": "causally influences", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "https://orcid.org/0000-0002-6601-2165" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "https://orcid.org/0000-0003-4639-4431" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://purl.obolibrary.org/obo/ro/docs/causal-relations" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000589", "val": "causally influences (entity-centric)" } ], "definition": { "val": "The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size)." } }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/RO_0002578", "lbl": "directly regulates", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "https://orcid.org/0000-0002-6601-2165" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://purl.obolibrary.org/obo/ro/docs/causal-relations" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000589", "val": "directly regulates (processual)" }, { "pred": "http://purl.obolibrary.org/obo/RO_0002575", "val": "http://purl.obolibrary.org/obo/RO_0002211" } ], "definition": { "val": "p directly regulates q iff p is immediately causally upstream of q and p regulates q." }, "subsets": [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ] }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/RO_0002581", "lbl": "is a defining property chain axiom", "meta": { "definition": { "val": "If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL" } }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/RO_0002582", "lbl": "is a defining property chain axiom where second argument is reflexive", "meta": { "definition": { "val": "If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R." } }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/RO_0002584", "lbl": "has part structure that is capable of", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "https://orcid.org/0000-0002-6601-2165" } ], "definition": { "val": "s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p" } }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/RO_0002595", "lbl": "causal relation between material entity and a process", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000116", "val": "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "https://orcid.org/0000-0002-6601-2165" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://purl.obolibrary.org/obo/ro/docs/causal-relations" } ], "definition": { "val": "A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity." } }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/RO_0002596", "lbl": "capable of regulating", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "pyrethroid -> growth" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://purl.obolibrary.org/obo/ro/docs/causal-relations" } ], "definition": { "val": "Holds between c and p if and only if c is capable of some activity a, and a regulates p." } }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/RO_0002597", "lbl": "capable of negatively regulating", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://purl.obolibrary.org/obo/ro/docs/causal-relations" } ], "definition": { "val": "Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p." } }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/RO_0002598", "lbl": "capable of positively regulating", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "renin -> arteriolar smooth muscle contraction" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://purl.obolibrary.org/obo/ro/docs/causal-relations" } ], "definition": { "val": "Holds between c and p if and only if c is capable of some activity a, and a positively regulates p." } }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/RO_0002608", "lbl": "process has causal agent", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://purl.obolibrary.org/obo/ro/docs/causal-relations" } ], "definition": { "val": "Inverse of 'causal agent in process'" } }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/RO_0002629", "lbl": "directly positively regulates", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://purl.obolibrary.org/obo/ro/docs/causal-relations" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000589", "val": "directly positively regulates (process to process)" }, { "pred": "http://purl.obolibrary.org/obo/RO_0004049", "val": "http://purl.obolibrary.org/obo/RO_0002578" } ], "definition": { "val": "p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q." }, "subsets": [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ] }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/RO_0002630", "lbl": "directly negatively regulates", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://purl.obolibrary.org/obo/ro/docs/causal-relations" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000589", "val": "directly negatively regulates (process to process)" }, { "pred": "http://purl.obolibrary.org/obo/RO_0004050", "val": "http://purl.obolibrary.org/obo/RO_0002578" } ], "definition": { "val": "p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q." }, "subsets": [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ] }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/RO_0004031", "lbl": "enables subfunction", "meta": { "basicPropertyValues": [ { "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", "val": "https://orcid.org/0000-0002-6601-2165" }, { "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", "val": "2018-01-25T23:20:13Z" } ], "definition": { "val": "Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P." } }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/RO_0004032", "lbl": "acts upstream of or within, positive effect", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/RO_0004049", "val": "http://purl.obolibrary.org/obo/RO_0002264" }, { "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", "val": "https://orcid.org/0000-0002-6601-2165" }, { "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", "val": "2018-01-26T23:49:30Z" }, { "pred": "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val": "http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within,_positive_effect" } ], "subsets": [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ] }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/RO_0004033", "lbl": "acts upstream of or within, negative effect", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/RO_0004050", "val": "http://purl.obolibrary.org/obo/RO_0002264" }, { "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", "val": "https://orcid.org/0000-0002-6601-2165" }, { "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", "val": "2018-01-26T23:49:51Z" } ], "subsets": [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ] }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/RO_0004034", "lbl": "acts upstream of, positive effect", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/RO_0004049", "val": "http://purl.obolibrary.org/obo/RO_0002263" }, { "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", "val": "https://orcid.org/0000-0002-6601-2165" }, { "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", "val": "2018-01-26T23:53:14Z" }, { "pred": "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val": "http://wiki.geneontology.org/index.php/Acts_upstream_of,_positive_effect" } ], "definition": { "val": "c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive" }, "subsets": [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ] }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/RO_0004035", "lbl": "acts upstream of, negative effect", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/RO_0004050", "val": "http://purl.obolibrary.org/obo/RO_0002263" }, { "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", "val": "https://orcid.org/0000-0002-6601-2165" }, { "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", "val": "2018-01-26T23:53:22Z" }, { "pred": "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val": "http://wiki.geneontology.org/index.php/Acts_upstream_of,_negative_effect" } ], "definition": { "val": "c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative" }, "subsets": [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ] }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/RO_0004046", "lbl": "causally upstream of or within, negative effect", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/RO_0004050", "val": "http://purl.obolibrary.org/obo/RO_0002418" }, { "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", "val": "https://orcid.org/0000-0002-6601-2165" }, { "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", "val": "2018-03-13T23:55:05Z" } ] }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/RO_0004047", "lbl": "causally upstream of or within, positive effect", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/RO_0004049", "val": "http://purl.obolibrary.org/obo/RO_0002418" }, { "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", "val": "https://orcid.org/0000-0002-6601-2165" }, { "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", "val": "2018-03-13T23:55:19Z" } ] }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/RO_0011002", "lbl": "regulates activity of", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "https://orcid.org/0000-0003-4639-4431" } ], "definition": { "val": "The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B." } }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/RO_0012011", "lbl": "indirectly causally upstream of", "meta": { "basicPropertyValues": [ { "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", "val": "pg" }, { "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", "val": "2022-09-26T06:07:17Z" } ], "definition": { "val": "p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q." } }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/RO_0012012", "lbl": "indirectly regulates", "meta": { "basicPropertyValues": [ { "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", "val": "pg" }, { "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", "val": "2022-09-26T06:08:01Z" } ], "definition": { "val": "p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q." } }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/RO_0017001", "lbl": "device utilizes material", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "A diagnostic testing device utilizes a specimen." }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "https://orcid.org/0000-0001-9625-1899" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "https://orcid.org/0000-0003-2620-0345" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000232", "val": "A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input." }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000232", "val": "See github ticket https://github.com/oborel/obo-relations/issues/497" }, { "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", "val": "2021-11-08T12:00:00Z" } ], "definition": { "val": "X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y." }, "synonyms": [ { "pred": "hasBroadSynonym", "val": "utilizes" } ] }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/RO_0019000", "lbl": "regulates characteristic", "meta": { "basicPropertyValues": [ { "pred": "http://purl.org/dc/terms/contributor", "val": "https://orcid.org/0000-0002-8688-6599" } ], "definition": { "val": "A relationship that holds between a process and a characteristic in which process (P) regulates characteristic (C) iff: P results in the existence of C OR affects the intensity or magnitude of C." } }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/RO_0019001", "lbl": "positively regulates characteristic", "meta": { "basicPropertyValues": [ { "pred": "http://purl.org/dc/terms/contributor", "val": "https://orcid.org/0000-0002-8688-6599" } ], "definition": { "val": "A relationship that holds between a process and a characteristic in which process (P) positively regulates characteristic (C) iff: P results in an increase in the intensity or magnitude of C." } }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/RO_0019002", "lbl": "negatively regulates characteristic", "meta": { "basicPropertyValues": [ { "pred": "http://purl.org/dc/terms/contributor", "val": "https://orcid.org/0000-0002-8688-6599" } ], "definition": { "val": "A relationship that holds between a process and a characteristic in which process (P) negatively regulates characteristic (C) iff: P results in a decrease in the intensity or magnitude of C." } }, "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/UO_0000001", "lbl": "length unit", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "length unit" }, { "pred": 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measure of the dimension in which events occur in sequence." } }, "type": "CLASS" }, { "id": "http://purl.obolibrary.org/obo/UO_0000005", "lbl": "temperature unit", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "temperature unit" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000412", "val": "http://purl.obolibrary.org/obo/uo.owl" } ] }, "type": "CLASS" }, { "id": "http://purl.obolibrary.org/obo/UO_0000006", "lbl": "substance unit", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "substance unit" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000412", "val": "http://purl.obolibrary.org/obo/uo.owl" } ] }, "type": "CLASS" }, { "id": "http://purl.obolibrary.org/obo/UO_0000008", "lbl": "meter", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "meter" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "m" }, { "pred": 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"http://purl.obolibrary.org/obo/UO_0000016", "lbl": "millimeter", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "millimeter" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "mm" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000412", "val": "http://purl.obolibrary.org/obo/uo.owl" } ], "definition": { "val": "A length unit which is equal to one thousandth of a meter or 10^[-3] m." } }, "type": "INDIVIDUAL" }, { "id": "http://purl.obolibrary.org/obo/UO_0000017", "lbl": "micrometer", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "micrometer" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "um" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000412", "val": "http://purl.obolibrary.org/obo/uo.owl" } ], "definition": { "val": "A length unit which is equal to one millionth of a meter or 10^[-6] m." } }, "type": "INDIVIDUAL" }, { "id": "http://purl.obolibrary.org/obo/UO_0000018", "lbl": "nanometer", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "nanometer" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "nm" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000412", "val": "http://purl.obolibrary.org/obo/uo.owl" } ], "definition": { "val": "A length unit which is equal to one thousandth of one millionth of a meter or 10^[-9] m." } }, "type": "INDIVIDUAL" }, { "id": "http://purl.obolibrary.org/obo/UO_0000019", "lbl": "angstrom", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "angstrom" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000412", "val": "http://purl.obolibrary.org/obo/uo.owl" } ], "definition": { "val": "A length unit which is equal to 10 [-10] m." } }, "type": "INDIVIDUAL" }, { "id": "http://purl.obolibrary.org/obo/UO_0000021", "lbl": "gram", "meta": { "basicPropertyValues": [ { 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The centigrade scale has its zero at 273.15 K." } }, "type": "INDIVIDUAL" }, { "id": "http://purl.obolibrary.org/obo/UO_0000031", "lbl": "minute", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "minute" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "min" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000412", "val": "http://purl.obolibrary.org/obo/uo.owl" } ], "definition": { "val": "A time unit which is equal to 60 seconds." } }, "type": "INDIVIDUAL" }, { "id": "http://purl.obolibrary.org/obo/UO_0000032", "lbl": "hour", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "hour" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "h" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "hr" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000412", "val": "http://purl.obolibrary.org/obo/uo.owl" } ], "definition": { "val": "A time unit which 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"type": "INDIVIDUAL" }, { "id": "http://purl.obolibrary.org/obo/UO_0000095", "lbl": "volume unit", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "volume unit" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000412", "val": "http://purl.obolibrary.org/obo/uo.owl" } ] }, "type": "CLASS" }, { "id": "http://purl.obolibrary.org/obo/UO_0000097", "lbl": "cubic centimeter", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000111", "val": "cubic centimeter" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "cc" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000412", "val": "http://purl.obolibrary.org/obo/uo.owl" } ], "definition": { "val": "A volume unit which is equal to one millionth of a cubic meter or 10^[-9] m^[3], or to 1 ml." } }, "type": "INDIVIDUAL" }, { "id": "http://purl.obolibrary.org/obo/UO_0000098", "lbl": "milliliter", "meta": { "basicPropertyValues": [ { "pred": 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Please see https://github.com/allysonlister/swo/issues/10 for more information." ], "deprecated": true }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/efo/swo/SWO_0000379", "lbl": "obsolete_SBML file", "meta": { "basicPropertyValues": [ { "pred": "http://purl.org/dc/elements/1.1/contributor", "val": "Marked as obsolete by Allyson Lister" }, { "pred": "http://www.ebi.ac.uk/efo/obsoleted_in_version", "val": "0.4" } ], "comments": [ "Identical to http://www.ebi.ac.uk/swo/data/SWO_3000037" ], "deprecated": true }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/efo/swo/SWO_0000380", "lbl": "obsolete_SBML model", "meta": { "basicPropertyValues": [ { "pred": "http://purl.org/dc/elements/1.1/contributor", "val": "Marked as obsolete by Allyson Lister." }, { "pred": "http://www.ebi.ac.uk/efo/obsoleted_in_version", "val": "0.5" } ], "comments": [ "'SBML model' was classed as a child of algorithm, when this clearly isn't the case. As SWO already contained 'SBML file' (to cover the data format itself), there was no need for this class at all. The one class (SBMLR) which referenced this class had the relevant axiom deleted. For referencing the SBML format, please use the class 'SBML file'." ], "deprecated": true }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/efo/swo/SWO_0000381", "lbl": "obsolete SDF format", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0100001", "val": "http://www.ebi.ac.uk/swo/SWO_0000381" }, { "pred": "http://www.ebi.ac.uk/efo/obsoleted_in_version", "val": "1.7" } ], "comments": [ "AL 1.10.2019: Improperly formatted IRI replaced with correct one. 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Please see https://github.com/allysonlister/swo/issues/10 for more information." ], "deprecated": true }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/efo/swo/SWO_0000393", "lbl": "obsolete_Information processing", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "James Malone" }, { "pred": "http://purl.org/dc/elements/1.1/contributor", "val": "Marked as obsolete by Allyson Lister." }, { "pred": "http://www.ebi.ac.uk/efo/obsoleted_in_version", "val": "0.4" } ], "comments": [ "Present both in the original file (SWO_0000393) and in the core file (SWO_0000003), and each have different identifiers. SWO_0000393 was initially created within the originalsoftwareontology.owl and later moved to swo_core.owl. SWO_0000003 was retained and SWO_0000393 deemed obsolete. Please use SWO_0000003 instead." ], "definition": { "val": "Information processing is a process in which input information is analysed or transformed in order to produce information as output." }, "deprecated": true }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/efo/swo/SWO_0000394", "lbl": "obsolete is developed by", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000233", "val": "https://github.com/allysonlister/swo/issues/59" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0100001", "val": "http://www.ebi.ac.uk/swo/SWO_0000394" } ], "comments": [ "AL 2023-03-05: Improperly created IRI (with 'efo' in the IRI) replaced by the correct form for SWO IRIs." ], "deprecated": true }, "type": "PROPERTY" }, { "id": "http://www.ebi.ac.uk/efo/swo/SWO_0000395", "lbl": "obsolete_is_published_by", "meta": { "basicPropertyValues": [ { "pred": "http://purl.org/dc/elements/1.1/contributor", "val": "Marked as obsolete by Allyson Lister." }, { "pred": "http://www.ebi.ac.uk/efo/obsoleted_in_version", "val": "0.5" } ], "comments": [ "This class can be entirely replaced with 'is published by', SWO_0004004. Please use SWO_0004004 instead." ], "definition": { "val": "The relationship between software and a software publisher." }, "deprecated": true }, "type": "PROPERTY" }, { "id": "http://www.ebi.ac.uk/efo/swo/SWO_0000396", "lbl": "obsolete software developer organization", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0100001", "val": "http://www.ebi.ac.uk/swo/SWO_0000396" }, { "pred": "http://www.ebi.ac.uk/efo/obsoleted_in_version", "val": "1.7" } ], "comments": [ "AL 1.10.2019: Improperly formatted IRI replaced with correct one. 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Please see https://github.com/allysonlister/swo/issues/10 for more information." ], "deprecated": true }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/efo/swo/SWO_0000398", "lbl": "obsolete 50-50 MANOVA algorithm", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0100001", "val": "http://www.ebi.ac.uk/swo/SWO_0000398" }, { "pred": "http://www.ebi.ac.uk/efo/obsoleted_in_version", "val": "1.7" } ], "comments": [ "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information." ], "deprecated": true }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/efo/swo/SWO_0000399", "lbl": "obsolete_html", "meta": { "basicPropertyValues": [ { "pred": "http://purl.org/dc/elements/1.1/contributor", "val": "Marked as obsolete by Allyson Lister." }, { "pred": "http://www.ebi.ac.uk/efo/obsoleted_in_version", "val": "0.4" } ], "comments": [ "There is one EDAM html class (EDAM_format:2331) and one SWO class (SWO_0000399) within swo_data.owl. EDAM_format:2331 was retained and SWO_0000399 deemed obsolete, as EDAM_format:2331 has a better location in the hierarchy and is an imported term. All axioms belonging to SWO_0000399 were transferred to EDAM_format:2331. Please use EDAM_format:2331 (in this ontology via its full URI http://edamontology.org/format_2331) instead." ], "deprecated": true }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/efo/swo/SWO_0000405", "lbl": "obsolete ArrayExpress Bioconductor", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0100001", "val": "http://www.ebi.ac.uk/swo/SWO_0000405" }, { "pred": "http://www.ebi.ac.uk/efo/obsoleted_in_version", "val": "1.7" } ], "comments": [ "AL 1.10.2019: Improperly formatted IRI replaced with correct one. 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Please see https://github.com/allysonlister/swo/issues/10 for more information." ], "deprecated": true }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/efo/swo/SWO_0000425", "lbl": "obsolete Similarity score", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0100001", "val": "http://www.ebi.ac.uk/swo/SWO_0000425" }, { "pred": "http://www.ebi.ac.uk/efo/obsoleted_in_version", "val": "1.7" } ], "comments": [ "AL 1.10.2019: Improperly formatted IRI replaced with correct one. 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Please see https://github.com/allysonlister/swo/issues/10 for more information." ], "deprecated": true }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/efo/swo/SWO_0000728", "lbl": "obsolete widgetTools", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0100001", "val": "http://www.ebi.ac.uk/swo/SWO_0000728" }, { "pred": "http://www.ebi.ac.uk/efo/obsoleted_in_version", "val": "1.7" } ], "comments": [ "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information." ], "deprecated": true }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/efo/swo/SWO_0000729", "lbl": "obsolete xcms", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0100001", "val": "http://www.ebi.ac.uk/swo/SWO_0000729" }, { "pred": "http://www.ebi.ac.uk/efo/obsoleted_in_version", "val": "1.7" } ], "comments": [ "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information." ], "deprecated": true }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/efo/swo/SWO_0000730", "lbl": "obsolete xps", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0100001", "val": "http://www.ebi.ac.uk/swo/SWO_0000730" }, { "pred": "http://www.ebi.ac.uk/efo/obsoleted_in_version", "val": "1.7" } ], "comments": [ "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information." ], "deprecated": true }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/efo/swo/SWO_0000731", "lbl": "obsolete yaqcaffy", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0100001", "val": "http://www.ebi.ac.uk/swo/SWO_0000731" }, { "pred": "http://www.ebi.ac.uk/efo/obsoleted_in_version", "val": "1.7" } ], "comments": [ "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information." ], "deprecated": true }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/efo/swo/SWO_0000739", "lbl": "has legal status", "meta": { "basicPropertyValues": [ { "pred": "http://purl.org/dc/elements/1.1/contributor", "val": "Marked as obsolete by Allyson Lister." }, { "pred": "http://www.ebi.ac.uk/efo/obsoleted_in_version", "val": "1.4" } ], "comments": [ "This property was not in use anywhere in the ontology. Further, it had no definition and therefore its intended usage was unclear. Until a time when this property is required and an official definition created, this property is obsolete so as not to introduce inconsistent usage." ], "deprecated": true }, "type": "PROPERTY" }, { "id": "http://www.ebi.ac.uk/efo/swo/SWO_0000740", "lbl": "obsolete implements", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000233", "val": "https://github.com/allysonlister/swo/issues/59" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0100001", "val": "http://www.ebi.ac.uk/swo/SWO_0000740" } ], "comments": [ "AL 2023-03-05: Improperly created IRI (with 'efo' in the IRI) replaced by the correct form for SWO IRIs." ], "deprecated": true }, "type": "PROPERTY" }, { "id": "http://www.ebi.ac.uk/efo/swo/SWO_0000741", "lbl": "obsolete is encoded in", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000233", "val": "https://github.com/allysonlister/swo/issues/59" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0100001", "val": "http://www.ebi.ac.uk/swo/SWO_0000741" } ], "comments": [ "AL 2023-03-05: Improperly created IRI (with 'efo' in the IRI) replaced by the correct form for SWO IRIs." ], "deprecated": true }, "type": "PROPERTY" }, { "id": "http://www.ebi.ac.uk/efo/swo/SWO_0000743", "lbl": "obsolete Strand Life Sciences", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000233", "val": "https://github.com/allysonlister/swo/issues/59" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0100001", "val": "http://www.ebi.ac.uk/swo/SWO_0000743" } ], "comments": [ "AL 2023-03-05: Improperly created IRI (with 'efo' in the IRI) replaced by the correct form for SWO IRIs." ], "deprecated": true }, "type": "INDIVIDUAL" }, { "id": "http://www.ebi.ac.uk/swo/SWO_0000001", "lbl": "software", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "James Malone" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "Modified in parts from https://en.wikipedia.org/wiki/Software" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "Robert Stevens" }, { "pred": "http://www.w3.org/2004/02/skos/core#exactMatch", "val": "http://purl.obolibrary.org/obo/IAO_0000010" } ], "comments": [ "AL 7.9.22: There are some reasoning oddities associated with marking IAO and SWO software as equivalent; once these are sorted out, the equivalence statement will take the place of this current parent-child relationship." ], "definition": { "val": "Computer software, or generally just software, is any set of machine-readable instructions (most often in the form of a computer program) that conform to a given syntax (sometimes referred to as a language) that is interpretable by a given processor and that directs a computer's processor to perform specific operations." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_0000002", "lbl": "software license", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "Modified from http://en.wikipedia.org/wiki/Software_license" }, { "pred": "http://purl.org/dc/terms/creator", "val": "James Malone" } ], "definition": { "val": "A licence is a legal instrument (usually by way of contract law, with or without printed material) governing the use or redistribution of the resource containing the licence." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_0000003", "lbl": "obsolete information processing", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "James Malone" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0100001", "val": "http://purl.obolibrary.org/obo/OBI_0200000" }, { "pred": "http://www.ebi.ac.uk/efo/obsoleted_in_version", "val": "1.7" } ], "comments": [ "AL 18.9.2019: This class is identical (based on its definition) with OBI 'data transformation' and is no longer required." ], "definition": { "val": "Information processing is a process in which input information is analysed or transformed in order to produce information as output." }, "deprecated": true }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_0000004", "lbl": "Microsoft Excel 2007", "meta": { "definition": { "val": "Microsoft Excel 2007 is a spreadsheet editing and viewing tool." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_0000005", "lbl": "MATLAB", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://www.mathworks.com/products/matlab/?s_cid=SA_trafrefpai_MLipspot_Doc_bioinfo_MATLAB" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Nandini Badarinarayan" } ], "definition": { "val": "MATLAB® is a high-level language and interactive environment that enables you to perform computationally intensive tasks faster than with traditional programming languages such as C, C++, and Fortran" } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_0000007", "lbl": "OmniOutliner", "meta": { "definition": { "val": "OmniOutliner is commercial outlining software for Mac OS X produced by The Omni Group" } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_0000008", "lbl": "Racket", "meta": { "definition": { "val": "Racket is a Scheme-based language interpreter and programming environment" } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_0000011", "lbl": "IntelliJ IDEA", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "IntelliJ" } ], "definition": { "val": "IntelliJ IDEA is a commercial Java IDE for developing software." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_0000013", "lbl": "COPASI", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://sbml.org/SBML_Software_Guide/SBML_Software_Summary, accessed 24 March 2015." } ], "definition": { "val": "COPASI is a software application for simulation and analysis of biochemical networks and their dynamics. COPASI is a stand-alone program that supports models in the SBML standard and can simulate their behavior using ODEs or Gillespie's stochastic simulation algorithm; arbitrary discrete events can be included in such simulations. COPASI provides an C++ API with language bindings for Perl, python, R, Java, and Octave and is able to communicate with the Systems Biology Workbench COPASI carries out several analyses of the network and its dynamics and has extensive support for parameter estimation and optimization. COPASI provides means to visualize data in customizable plots, histograms and animations of network diagrams. " } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_0000014", "lbl": "Microsoft Excel 2003", "meta": { "definition": { "val": "Microsoft Excel 2003 is a spreadsheet editing and viewing tool." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_0000021", "lbl": "operating system", "meta": { "definition": { "val": "An operating system is a piece of software which is responsible for managing software that runs on a computer and the interactions of that software with the hardware and system resources." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_0000024", "lbl": "Adobe Illustrator 10", "meta": { "basicPropertyValues": [ { "pred": "http://purl.org/dc/terms/creator", "val": "James Malone" } ], "definition": { "val": "Adobe Illustrator is a graphics editor for creating and editing vector graphics." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_0000027", "lbl": "OBO-Edit", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "OBO edit" } ], "definition": { "val": "OBO-Edit is an open source ontology editor optimized for the OBO biological ontology file format. It features an easy to use editing interface, a simple but fast reasoner, and powerful search capabilities." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_0000032", "lbl": "Agilent Scan Control", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "Scan Control Application software" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://www.chem.agilent.com/" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Nandini Badarinarayan" } ], "definition": { "val": "Scan Control Software is the user interface software that controls the Agilent scanner. This software is usable only with the Agilent high-resolution scanner (G2565CA) or high-resolution scanner upgrade. It will not function with earlier scanner versions" } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_0000034", "lbl": "Agilent Technologies Software", "meta": { "basicPropertyValues": [ { "pred": "http://purl.org/dc/terms/creator", "val": "Nandini Badarinarayan" } ] }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_0000035", "lbl": "'AnnotationDbi'", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://bioconductor.org/packages/2.4/bioc/html/AnnotationDbi.html" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Nandini Badarinarayan" } ], "definition": { "val": "This package provides user interface and database connection code for annotation data packages using SQLite data storage." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_0000037", "lbl": "Applied Biosystems 1700 Expression Array System Software", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://www.geneservice.co.uk/services/geneexpression/overview_1700.jsp" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Nandini Badarinarayan" } ], "definition": { "val": "Microarrays are powerful tools for discovering levels of gene expression. Geneservice have invested in the latest gene expression microarray system from Applied Biosystems so that the widest choice of platform is available to our customers. The key features of this system are:\nSensitivity: a detection threshold of as little as a femtomole of expresseed mRNA and requiring as little as 500ng of starting total RNA.\nContent: each probe is associated with a gene sequence buiult on unique Celera data and validated by public RefSeqs all of which have been curated.\nPipeline: complete integrated solutions for gene expression research including Applied Biosystems Bioinformatic tools and ready-to-go gene expression TaqMan assays for validation of results." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_0000039", "lbl": "ArrayGauge", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "ArrayGauge [FUJIFILM]" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://www.fujifilm.com/products/life_science_systems/science_imaging/arraygauge/" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Nandini Badarinarayan" } ], "definition": { "val": "Fujifilm ArrayGauge™ software is specifically designed for Macroarray and Microarray samples, with all the practical functions necessary for the most powerful array analysis.\nIts ultra-friendly navigation and functions can handle any kind of array (CLONTECH, Genome Systems, Research Genetics - even hand-made arrays). It already includes virtually every contemporary cDNA membrane template on the market, with the flexibility to handle others as they develop." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_0000040", "lbl": "ArrayNorm", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://bin.tugraz.at/Tools/ArrayNorm.html" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Nandini Badarinarayan" } ], "definition": { "val": "ArrayNorm is an platform-independent Java tool for normalization and statistical analysis for microarray-experiment data. It provides modules for visualization (scatterplot, histogram, boxplot, etc.), normalization and analysis." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_0000041", "lbl": "'ArrayTools'", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://bioconductor.org/packages/2.4/bioc/html/ArrayTools.html" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Nandini Badarinarayan" } ], "definition": { "val": "This package is designed to provide solutions for quality assessment and to detect differentially expressed genes for the Affymetrix GeneChips, including both 3' -arrays and gene 1.0-ST arrays." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_0000042", "lbl": "ArrayVision", "meta": { "basicPropertyValues": [ { "pred": "http://purl.org/dc/terms/creator", "val": "Nandini Badarinarayan" } ], "comments": [ "" ], "definition": { "val": "This software implements a robust algorithm for spot finding and quantitation, quality metrics, and use of pre-made protocols ensure accuracy and reproducibility. Choices for background correction, normalization, and ratio calculation between arrays provides flexibility.Wizard guides simplify operation.Automatic batch processing increases throughput and saves time.Data easily exported to Microsoft™ Excel or database programs for flexibility in reporting." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_0000043", "lbl": "has documentation", "meta": { "basicPropertyValues": [ { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "definition": { "val": "Should be used to link a particular class (e.g. a piece of software or an algorithm) with a publication(s) which act as the primary reference(s) for that class." } }, "type": "PROPERTY" }, { "id": "http://www.ebi.ac.uk/swo/SWO_0000044", "lbl": "BLAST+ 2.2.26", "meta": { "basicPropertyValues": [ { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "definition": { "val": "The C++ version of the command line BLAST+ tool made by the NCBI. (See also http://www.ncbi.nlm.nih.gov/books/NBK1763)" } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_0000045", "lbl": "Array_vision_(Interfocus)", "meta": { "basicPropertyValues": [ { "pred": "http://purl.org/dc/terms/creator", "val": "Nandini Badarinarayan" } ] }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_0000046", "lbl": "has download location", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "Allyson Lister" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "definition": { "val": "The location from where the software can be downloaded." } }, "type": "PROPERTY" }, { "id": "http://www.ebi.ac.uk/swo/SWO_0000047", "lbl": "Axon GenePix Pro 3", "meta": { "basicPropertyValues": [ { "pred": "http://purl.org/dc/terms/creator", "val": "Nandini Badarinarayan" } ] }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_0000048", "lbl": "BAC", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://bioconductor.org/packages/2.4/bioc/html/BAC.html" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Nandini Badarinarayan" } ], "definition": { "val": "This package uses a Bayesian hierarchical model to detect enriched regions from ChIP-chip experiments" } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_0000049", "lbl": "Binning clustering method", "meta": { "definition": { "val": "binning clustering method- The algorithm uses single-linkage clustering to join compounds into similarity groups, where every member in a cluster shares with at least one other member a similarity value above a user-specified threshold. The algorithm is optimized for speed and memory\neciency by avoiding the calculation of an all-against-all distance matrix." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_0000051", "lbl": "Clustal", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://www.clustal.org/, Accessed 13 June 2012." }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "definition": { "val": "Multiple alignment program for nucleic acid or protein sequences." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_0000052", "lbl": "Clustal Omega", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://www.clustal.org/omega/, Accessed 13 June 2012" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "definition": { "val": "Clustal Omega provides improved scalability over previous Clustal versions, allowing hundreds of thousands of sequences to be aligned in a few hours. It will also make use of multiple processors, where present. In addition, the quality of alignments is superior to previous versions, as measured by a range of popular benchmarks. " } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_0000053", "lbl": "ClustalW", "meta": { "basicPropertyValues": [ { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ] }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_0000054", "lbl": "ClustalX", "meta": { "basicPropertyValues": [ { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ] }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_0000055", "lbl": "Clustal Omega 1.1", "meta": { "basicPropertyValues": [ { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ] }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_0000056", "lbl": "ClustalW 2.1", "meta": { "basicPropertyValues": [ { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ] }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_0000057", "lbl": "ClustalX 2.1", "meta": { "basicPropertyValues": [ { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ] }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_0000058", "lbl": "EBI Clustal W2 Web Tool", "meta": { "basicPropertyValues": [ { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ] }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_0000059", "lbl": "EBI Clustal Omega Web Tool", "meta": { "basicPropertyValues": [ { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ] }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_0000060", "lbl": "MUSCLE", "meta": { "basicPropertyValues": [ { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ] }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_0000061", "lbl": "EBI Muscle Web Tool", "meta": { "basicPropertyValues": [ { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ] }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_0000062", "lbl": "MUSCLE 3.8.31", "meta": { "basicPropertyValues": [ { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ] }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_0000063", "lbl": "Drive5 MUSCLE", "meta": { "basicPropertyValues": [ { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ] }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_0000064", "lbl": "TCoffee", "meta": { "basicPropertyValues": [ { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ] }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_0000065", "lbl": "CRG TCoffee", "meta": { "basicPropertyValues": [ { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "definition": { "val": "TCoffee is a multiple sequence alignment program with a number of different modes. " } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_0000066", "lbl": "EBI TCoffee Web Tool", "meta": { "basicPropertyValues": [ { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "definition": { "val": "Performs an alignment of DNA, RNA or Proteins with the standard TCoffee mode. This Web tool provides both interactive access via a Web browser and programmatic SOAP Web service access. 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Its design philosophy emphasizes code readability, and its syntax allows programmers to express concepts in fewer lines of code than would be possible in languages such as C. The language provides constructs intended to enable clear programs on both a small and large scale.Python supports multiple programming paradigms, including object-oriented, imperative and functional programming or procedural styles." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_0000119", "lbl": "REXX", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://dbpedia.org/resource/REXX" } ] }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_0000120", "lbl": "Ruby", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://dbpedia.org/resource/Ruby_(programming_language)" } ] }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_0000122", "lbl": "Scala", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://dbpedia.org/resource/Scala_(programming_language)" } ] }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_0000123", "lbl": "Scheme", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://dbpedia.org/resource/Scheme_(programming_language)" } ] }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_0000125", "lbl": "Smalltalk", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://dbpedia.org/resource/Smalltalk" } ] }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_0000126", "lbl": "SQL", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://dbpedia.org/resource/SQL" } ] }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_0000127", "lbl": "Turing", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://dbpedia.org/resource/Turing_(programming_language)" } ] }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_0000128", "lbl": "Verilog", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://dbpedia.org/resource/Verilog" } ] }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_0000129", "lbl": "VHDL", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://dbpedia.org/resource/VHDL" } ] }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_0000130", "lbl": "Visual Basic", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://dbpedia.org/resource/Visual_Basic" } ] }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_0000131", "lbl": "directly preceded by", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "Microsoft version 2007 is directly preceded by Microsoft version 2003." }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "Allyson Lister" }, { "pred": "http://purl.org/dc/terms/creator", "val": "OBO Foundry" } ], "definition": { "val": "Entity A is 'directly preceded by' entity B if there are no intermediate entities temporally between the two entities. WIthin SWO this property is mainly used to describe versions of entities such as software." } }, "type": "PROPERTY" }, { "id": "http://www.ebi.ac.uk/swo/SWO_0000132", "lbl": "directly followed by", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "Allyson Lister" } ], "definition": { "val": "'directly followed by' is an object property which further specializes the parent 'followed by' property. In the assertion 'C directly followed by C1', says that Cs generally are immediately followed by C1s." } }, "type": "PROPERTY" }, { "id": "http://www.ebi.ac.uk/swo/SWO_0000133", "lbl": "DAVID", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "DAVID Bioinformatics resource" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "Database for Annotation, Visualization and Integrated Discovery" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://david.abcc.ncifcrf.gov/" }, { "pred": "http://purl.org/dc/terms/creator", "val": "James Malone" } ], "definition": { "val": "DAVID (the Database for Annotation, Visualization and Integrated Discovery) is a free online bioinformatics resource developed by the Laboratory of Immunopathogenesis and Bioinformatics (LIB). All tools in the DAVID Bioinformatics Resources aim to provide functional interpretation of large lists of genes derived from genomic studies, e.g. microarray and proteomics studies." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_0000135", "lbl": "PSI-BLAST", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "Position-Specific Iterative" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "NIH BLAST homepage" } ], "definition": { "val": "Position-Specific Iterated (PSI)-BLAST is the most sensitive BLAST program, making it useful for finding very distantly related proteins or new members of a protein family. Use PSI-BLAST when your standard protein-protein BLAST search either failed to find significant hits, or returned hits with descriptions such as \"hypothetical protein\" or \"similar to...\". " } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_0000138", "lbl": "Entrez", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "Entrez Global Query Cross-Database Search System" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "Ncbi Resource, C. (2012). \"Database resources of the National Center for Biotechnology Information\". Nucleic Acids Research 41 (Database issue): D8–D20. doi:10.1093/nar/gks1189. PMC 3531099." } ], "definition": { "val": "The Entrez Global Query Cross-Database Search System is a powerful federated search engine, or web portal that allows users to search many discrete health sciences databases at the National Center for Biotechnology Information (NCBI) website." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_0000139", "lbl": "web content search", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "website content search" } ], "definition": { "val": "Web content search is the searching for information on the World Wide Web." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_0000140", "lbl": "search engine", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "web search engine" } ], "definition": { "val": "A search engine is a software system that is designed to search for information on the World Wide Web." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_0000141", "lbl": "Weka", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "Waikato Environment for Knowledge Analysis" } ], "definition": { "val": "Weka (Waikato Environment for Knowledge Analysis) is a suite of machine learning software, originally intended for data mining tasks, written in Java and developed at the University of Waikato, New Zealand." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_0000142", "lbl": "PostgreSQL", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "Postgres" } ], "definition": { "val": "PostgreSQL, often simply Postgres, is an open source object-relational database management system (ORDBMS) with an emphasis on extensibility and standards compliance." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_0000143", "lbl": "data storage", "meta": { "definition": { "val": "The storing of digital information. Often this is done for archiving and retrieval purposes." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_0000145", "lbl": "Segway 1.2", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://pmgenomics.ca/hoffmanlab/proj/segway/, accessed 27 November 2014." } ], "definition": { "val": "The free Segway software package contains a novel method for analyzing multiple tracks of functional genomics data. Our method uses a dynamic Bayesian network (DBN) model, which enables it to analyze the entire genome at 1-bp resolution even in the face of heterogeneous patterns of missing data. This method is the first application of DBN techniques to genome-scale data and the first genomic segmentation method designed for use with the maximum resolution data available from ChIP-seq experiments without downsampling." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_0000146", "lbl": "Python 2.6", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "Allyson Lister" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "definition": { "val": "Version 2.6 of the Python programming language." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_0000147", "lbl": "Python 2.7", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "Allyson Lister" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "definition": { "val": "Version 2.7 of the Python programming language." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_0000149", "lbl": "Mac OS", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://en.wikipedia.org/wiki/History_of_Mac_OS, accessed 25 March 2015." }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "definition": { "val": "Mac OS is software which is used as the operating system for the Macintosh personal computer created by Apple Inc." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_0000150", "lbl": "uses platform", "meta": { "basicPropertyValues": [ { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "comments": [ "This property, together with 'uses software', is probably best modelled as a child of has_part. Its current position in the property hierarchy is based on simplicity of use. 'uses platform' was deemed an appropriate addition (rather than making use of already extant has_part or 'uses software') due to the already present definitions of those classes which restrict their use to particular situations." ], "definition": { "val": "'uses platform' should be used to link a particular piece of software to one or more operating systems which that software can run on. This is in contrast to both 'uses software' (which describes one piece of software directly executing another), and has_part, which can be used to describe related but independent software in a package, for example." } }, "type": "PROPERTY" }, { "id": "http://www.ebi.ac.uk/swo/SWO_0000151", "lbl": "OS X", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://en.wikipedia.org/wiki/History_of_Mac_OS#OS_X, accessed 25 March 2015." }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "definition": { "val": "OS X is a Mac OS operating system which succeeds the original Mac OS, which had been Apple's primary operating system since 1984. Unlike the earlier Macintosh operating system, OS X is a Unix-based operating system." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_0000152", "lbl": "iBioSim", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://www.async.ece.utah.edu/iBioSim/, accessed 25 March 2015." }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "definition": { "val": "iBioSim has been developed for the modeling, analysis, and design of genetic circuits. While iBioSim primarily targets models of genetic circuits, models representing metabolic networks, cell-signaling pathways, and other biological and chemical systems can also be analyzed. iBioSim also includes modeling and visualization support for multi-cellular and spatial models as well. " } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_0000153", "lbl": "VCell", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "Virtual Cell" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://sbml.org/SBML_Software_Guide/SBML_Software_Summary, accessed 26 March 2015. " }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "comments": [ "The licensing issue is not clear. On the VCell wikipedia page, the source is described as having an MIT license (see http://en.wikipedia.org/wiki/Virtual_Cell, accessed 26 March 2015). However, the exact type of license is not mentioned on the VCell homepage (http://www.vcell.org), therefore I have not added the statement that the MIT license is the *only* license for VCell." ], "definition": { "val": "VCell is a complete model building, editing and simulation environment. Includes spatial modeling capabilites, deterministic, stochastic, and hybrid algorithms. Parameter sensitivity analysis and parameter optimization. Desktop application and web-based environment. Bio- and math-based interfaces. Database and model sharing/publishing." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_0000154", "lbl": "COBRA", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "COnstraints Based Reconstruction and Analysis" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "definition": { "val": "COBRA (COnstraint-Based Reconstruction and Analysis Toolbox) includes implementations of many of the commonly used forms of constraint-based analysis such as FBA, gene deletions, flux variability analysis, sampling, and batch simulations together with tools to read in and manipulate constraint-based models." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_0000155", "lbl": "COBRApy", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "COnstraints Based Reconstruction and Analysis for Python" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "definition": { "val": "COBRA Toolbox is the version of the COBRA software for Python." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_0000156", "lbl": "COBRA Toolbox", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "COnstraints Based Reconstruction and Analysis Toolbox for MATLAB" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "definition": { "val": "COBRA Toolbox is the version of the COBRA software for Matlab." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_0000158", "lbl": "libSBML", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://sbml.org/SBML_Software_Guide/SBML_Software_Summary, accessed 27 March 2015." }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "definition": { "val": "LibSBML is a free, open-source programming library to help you read, write, manipulate, translate, and validate SBML files and data streams. It provides interfaces for C, C++, C#(.NET), Java, MATLAB, Octave, Perl, Python R and Ruby. LibSBML is available for free under LGPL terms in both source-code form and precompiled binaries for Windows, Mac OS X, and Linux." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_0000159", "lbl": "GNU Octave", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "https://www.gnu.org/software/octave/, accessed 27 March 2015." }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "definition": { "val": "GNU Octave is a high-level interpreted language, primarily intended for numerical computations. It provides capabilities for the numerical solution of linear and nonlinear problems, and for performing other numerical experiments. It also provides extensive graphics capabilities for data visualization and manipulation. Octave is normally used through its interactive command line interface, but it can also be used to write non-interactive programs. The Octave language is quite similar to Matlab so that most programs are easily portable. " } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_0000163", "lbl": "GGtools", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://bioconductor.org/packages/2.4/bioc/html/GGtools.html" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Nandini Badarinarayan" } ], "definition": { "val": "This package deals with hapmap SNP reports, GWAS, etc." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_0000164", "lbl": "GLAD", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://bioconductor.org/packages/2.4/bioc/html/GLAD.html" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Nandini Badarinarayan" } ], "definition": { "val": "Analysis of array CGH data : detection of breakpoints in genomic profiles and assignment of a status (gain, normal or lost) to each chromosomal regions identified." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_0000166", "lbl": "GLEAMS software", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://hmg.oxfordjournals.org/cgi/reprint/12/17/2145.pdf" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Nandini Badarinarayan" } ], "definition": { "val": "Microarray image quantification is performed using GLEAMS software" } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_0000167", "lbl": "GMS", "meta": { "basicPropertyValues": [ { "pred": "http://purl.org/dc/terms/creator", "val": "Nandini Badarinarayan" } ] }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_0000168", "lbl": "GOstats", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://bioconductor.org/packages/2.4/bioc/html/GOstats.html" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Nandini Badarinarayan" } ], "definition": { "val": "A set of tools for interacting with GO and microarray data. A variety of basic manipulation tools for graphs, hypothesis testing and other simple calculations" } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_0000170", "lbl": "GSEABase", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://bioconductor.org/packages/2.4/bioc/html/GSEABase.html" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Nandini Badarinarayan" } ], "definition": { "val": "This package provides classes and methods to support Gene Set Enrichment Analysis (GSEA)." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_0000171", "lbl": "GSEAlm", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://bioconductor.org/packages/2.4/bioc/html/GSEAlm.html" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Nandini Badarinarayan" } ], "definition": { "val": "Models and methods for fitting linear models to gene expression data, together with tools for computing and using various regression diagnostics." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_0000175", "lbl": "GeneData Expressionist Analyst v4.0.5", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://www.genedata.com/products/expressionist/overview.html" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Nandini Badarinarayan" } ], "definition": { "val": "Genedata Expressionist® is an enterprise solution that integrates, stores and analyzes transcriptomics, proteomics and metabolomics data as well as a wide variety of phenotypic data." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_0000176", "lbl": "Gene Pix", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "Gene Pix" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "Genepix" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://www.moleculardevices.com/pages/software/gn_genepix_pro.html" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Nandini Badarinarayan" } ], "definition": { "val": "GenePix is the industry standard microarray image analysis software because of its unique combination of imaging and analysis tools, visualizations, automation capabilities, performance and ease of use." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_0000177", "lbl": "GenePix 3.0.6", "meta": { "basicPropertyValues": [ { "pred": "http://purl.org/dc/terms/creator", "val": "Nandini Badarinarayan" } ] }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_0000178", "lbl": "GenePix 4.1", "meta": { "basicPropertyValues": [ { "pred": "http://purl.org/dc/terms/creator", "val": "Nandini Badarinarayan" } ] }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_0000179", "lbl": "GenePix 4100A", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": 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This combined with template adjustment features drives excellence in analysis performance." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_0000419", "lbl": "ScanArray v3.1 software", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "ScanArray version 3.1" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Nandini Badarinarayan" } ] }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_0000420", "lbl": "scanning software", "meta": { "basicPropertyValues": [ { "pred": "http://purl.org/dc/terms/creator", "val": "Nandini Badarinarayan" } ] }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_0000421", "lbl": "Scanning software G2565AA version A6.3.1", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://www.chem.agilent.com/en-us/products/instruments/dnamicroarrays/dnamicroarrayscanner/pages/default.aspx" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Nandini Badarinarayan" } ], "definition": { "val": "High resolution scanning with pixel sizes of 2, 3, 5, and 10 microns enables users to scan a range of array types from ultra-high density commercial arrays as well as low-density home-brew arrays.Low level detection resulting from optimized precision optics, broad dynamic range, minimal spectral cross talk allowing users to detect weak features, achieve rapid, accurate and dependable results" } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_0000422", "lbl": "ShortRead", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://bioconductor.org/packages/2.4/bioc/html/ShortRead.html" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Nandini Badarinarayan" } ], "definition": { "val": "Base classes, functions, and methods for representation of high-throughput, short-read sequencing data." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_0000424", "lbl": "Silicon Genetics Genespring", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "SiliconGenetics GeneSpring" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://www.silicongenetics.com/cgi/SiG.cgi/Support/gs_r_int.smf" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Nandini Badarinarayan" } ], "definition": { "val": "The GeneSpring-R integration package will allow you to expand the capability of GeneSpring by integrating R programs seamlessly into GeneSpring. 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SWO_9000003 was retained, while SWO_0000431 became an instance of obsolete class. 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It analysis tools for quality, visualizations for discovery and Data Management for Security." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_0000452", "lbl": "affxparser", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://bioconductor.org/packages/2.4/bioc/html/affxparser.html" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Nandini Badarinarayan" } ], "definition": { "val": "affxparser is a package for parsing Affymetrix files (CDF, CEL, CHP, BPMAP, BAR). 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In essence, it creates structured corruption within CEL data to demonstrate QA effectiveness." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_0000454", "lbl": "affyImGUI", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://bioconductor.org/packages/2.4/bioc/html/affylmGUI.html" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Nandini Badarinarayan" } ], "comments": [ "Removed the links to specified data inputs, as this software is a GUI wrapper for another package, and it is this package which takes the inputs. 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A hierarchical Bayesian approach is used, and the hyperparameters are estimated using empirical Bayes." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_0000593", "lbl": "limma", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://bioconductor.org/packages/2.4/bioc/html/limma.html" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Nandini Badarinarayan" } ], "definition": { "val": "Data analysis, linear models and differential expression for microarray data." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_0000594", "lbl": "limmaGUI", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://bioconductor.org/packages/2.4/bioc/html/limmaGUI.html" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Nandini Badarinarayan" } ], "definition": { "val": "A Graphical User Interface for the limma Microarray package" } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_0000599", "lbl": "logicFS", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://bioconductor.org/packages/2.4/bioc/html/logicFS.html" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Nandini Badarinarayan" } ], "definition": { "val": "Identification of interactions between binary variables using Logic Regression. Can, e.g., be used to find interesting SNP interactions. 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It includes functions of Illumina BeadStudio data input, quality control, BeadArray-specific variance stabilization, normalization and gene annotation at the probe level." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_0000604", "lbl": "maCorrPlot", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://bioconductor.org/packages/2.4/bioc/html/maCorrPlot.html" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Nandini Badarinarayan" } ], "definition": { "val": "Graphically displays correlation in microarray data that is due to insufficient normalization" } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_0000605", "lbl": "maDB", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://bioconductor.org/packages/2.4/bioc/html/maDB.html" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Nandini Badarinarayan" } ], "definition": { "val": "maDB allows to create a simple microarray database to store microarray experiments and annotation data into it. Affymetrix GeneChip expression values as well as values from two color microarrays can be stored into the database. Whole experiments or subsets from a experiment (or also values for a subset of genes in a subset of microarrays) can be fetched back to R. Additionally maDB provides different utility functions for the microarray data analysis like functions to draw MA plots or volcano plots with the data points color coded according to the local point density or functions that allow a replicate handling of miroarrays." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_0000606", "lbl": "maSigPro", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://bioconductor.org/packages/2.4/bioc/html/maSigPro.html" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Nandini Badarinarayan" } ], "definition": { "val": "maSigPro is a regression based approach to find genes for which there are significant gene expression profile differences between experimental groups in time course microarray experiments." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_0000607", "lbl": "maanova", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://bioconductor.org/packages/2.4/bioc/html/maanova.html" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Nandini Badarinarayan" } ], "definition": { "val": "Analysis of N-dye Micro Array experiment using mixed model effect. 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The functions have been tested on a publicly available data set about acute lymphoblastic leukemia (Yeoh et al.Cancer Cell 2002), which is provided in the library 'stjudem'." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_0000609", "lbl": "made4", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://bioconductor.org/packages/2.4/bioc/html/made4.html" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Nandini Badarinarayan" } ], "definition": { "val": "Multivariate data analysis and graphical display of microarray data. Functions include between group analysis and coinertia analysis. 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One reads a Affymetrix chip description file (CDF) and creates a hash table environment containing the location/probe set membership mapping. The other creates a package that automatically loads that environment." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_0000613", "lbl": "marray", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://bioconductor.org/packages/2.4/bioc/html/marray.html" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Nandini Badarinarayan" } ], "definition": { "val": "Class definitions for two-color spotted microarray data. 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Specifically, the set of methods handles the many-to-many relationship between miRNAs and the multiple genes they are predicted to target (and thus affect.) It also handles the gene-to-pathway relationships separately. 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The interface must be from the 'software interface' hierarchy." } }, "type": "PROPERTY" }, { "id": "http://www.ebi.ac.uk/swo/SWO_0004002", "lbl": "has format specification", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "Allyson Lister" } ], "definition": { "val": "Has format specification is a type of \"is encoded in\" relationship which specifically describes the relationship between data and a data format specification." } }, "type": "PROPERTY" }, { "id": "http://www.ebi.ac.uk/swo/SWO_0004003", "lbl": "obsolete_is developed by", "meta": { "basicPropertyValues": [ { "pred": "http://purl.org/dc/elements/1.1/contributor", "val": "Marked as obsolete by Allyson Lister." }, { "pred": "http://purl.org/dc/terms/creator", "val": "James Malone" }, { "pred": "http://www.ebi.ac.uk/efo/obsoleted_in_version", "val": "0.3" } ], "comments": [ "is developed by and is_developed_by. 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It contains functions for atom descriptor calculation, structure similarity searching, clustering of compound libraries and various utilities for managing complex compound data. It also offers a wide range of visualization functions for compound clusters and chemical structures. The package is integrated with the online ChemMine environment and allows bidirectional communications between the two services." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_1100064", "lbl": "ChipReader 3.1", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "VersArray ChipReader" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://www.bio-medicine.org/" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Nandini Badarinarayan" } ], "definition": { "val": "Versarray ChipReader systems are highly sensitive laser confocal systems designed for rapid imaging of microarrays. These are advanced scanners that meet your expectations, differentiating between a spot response and background level, and optimizing the signal on the bottom as well as the top end of the range for increased sensitivity. Results with versarray chipreader systems have a low background, enhanced weak signal detection, and virtually no photobleaching for a long dye lifetime." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_1100065", "lbl": "ChipSkipper", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "ChipSkipper Microarray Data Evaluation Software" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "ChipSkipper [EMBL]" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://angiogenesis.dkfz.de/software/chipskipper/index.htm" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Nandini Badarinarayan" } ], "definition": { "val": "ChipSkipper - an integrated tool for analysis, evaluation and quantitation of DNA micro-array data" } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_1100066", "lbl": "ChipSkipper V0.99", "meta": { "basicPropertyValues": [ { "pred": "http://purl.org/dc/terms/creator", "val": "Nandini Badarinarayan" } ] }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_1100067", "lbl": "multiscan", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://bioconductor.org/packages/2.4/bioc/html/multiscan.html" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Nandini Badarinarayan" } ], "definition": { "val": "A multiscan is an R package for combining multiple scans" } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_1100068", "lbl": "affy", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://bioconductor.org/packages/2.4/bioc/html/affy.html" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Nandini Badarinarayan" } ], "definition": { "val": "The affy package contains functions for exploratory oligonucleotide array analysis. The dependance to tkWidgets only concerns few convenience functions. 'affy' is fully functional without it." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_1100069", "lbl": "affycomp", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://bioconductor.org/packages/2.4/bioc/html/affycomp.html" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Nandini Badarinarayan" } ], "definition": { "val": "The affycomp package contains functions that can be used to compare expression measures for Affymetrix Oligonucleotide Arrays." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_1100070", "lbl": "PCMG", "meta": { "definition": { "val": "PCMG- a bipartite graph in which one set of nodes represents proteins, the other set represents complexes, and an edge from a protein node to a complex node represents membership of the protein in that complex." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_1100071", "lbl": "Feature Extraction Software", "meta": { "basicPropertyValues": [ { "pred": "http://purl.org/dc/terms/creator", "val": "Nandini Badarinarayan" } ] }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_1100073", "lbl": "Annotation-Driven Clustering", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://bioconductor.org/packages/2.4/bioc/html/adSplit.html" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Nandini Badarinarayan" } ], "definition": { "val": "adSplit implements clustering of microarray gene expression profiles according to functional annotations. For each term genes are annotated to, splits into two subclasses are computed and a significance of the supporting gene set is determined." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_1100075", "lbl": "R software", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://www.stat.berkeley.edu/users/terry/zarray/Software/smacode.html" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Nandini Badarinarayan" } ], "definition": { "val": "Statistical methods for identifying differentially expressed genes in replicated cDNA microarray experiments." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_1100076", "lbl": "BCRANK", "meta": { "definition": { "val": "BCRANK is a method that takes a ranked list of genomic regions as input and outputs short DNA sequences that are overrepresented in some part of the list." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_1100077", "lbl": "Cosmo", "meta": { "definition": { "val": "cosmo allows the user to target the motif search by specifying a set of constraints that the unknown position weight matrix must satisfy. The algorithm is based on a probabilistic model that describes the DNA sequences of interest through a two- component multinomial mixture model with estimates of the position weight matrix entries obtained by maximizing the observed data likelihood over the smaller parameter space corresponding to the imposed constraints. 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Together, these tools help optimize performance in an expression profiling study." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_1100085", "lbl": "CodeLink Expression Scanning Software", "meta": { "basicPropertyValues": [ { "pred": "http://purl.org/dc/terms/creator", "val": "Nandini Badarinarayan" } ], "definition": { "val": "Slides are scanned using CodeLink Expression Scanning Software" } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_1100087", "lbl": "Cyber-T", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://dmaf.biochem.uci.edu/affymetrix_analysis_software.html" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Nandini Badarinarayan" } ], "definition": { "val": "Cyber-T may be used to statistically determine what the probability is that a specific gene is differentially expressed by determining an associated p-value statistic." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_1100088", "lbl": "'DEDS'", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://bioconductor.org/packages/2.4/bioc/html/DEDS.html" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Nandini Badarinarayan" } ], "definition": { "val": "This library contains functions that calculate various statistics of differential expression for microarray data, including t statistics, fold change, F statistics, SAM, moderated t and F statistics and B statistics. It also implements a new methodology called DEDS (Differential Expression via Distance Summary), which selects differentially expressed genes by integrating and summarizing a set of statistics using a weighted distance approach." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_1100089", "lbl": "'DFP'", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://bioconductor.org/packages/2.4/bioc/html/DFP.html" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Nandini Badarinarayan" } ], "definition": { "val": "This package provides a supervised technique able to identify differentially expressed genes. The Fuzzy Patterns are built by means of applying 3 Membership Functions to discretized gene expression values." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_1100090", "lbl": "Discriminant Fuzzy Pattern Algorithm", "meta": { "definition": { "val": "A DFP version of a FP (fuzzy pattern) only includes those genes that can serve to differentiate it from the rest of the patterns.This algorithm is based on the discretization of float values (gene expression values) stored in an ExpressionSet object into labels combining 'Low', 'Medium' and 'High'" } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_1100093", "lbl": "'DNAcopy'", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://bioconductor.org/packages/2.4/bioc/html/DNAcopy.html" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Nandini Badarinarayan" } ], "definition": { "val": "Segments DNA copy number data using circular binary segmentation to detect regions with abnormal copy number" } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_1100094", "lbl": "'EBImage'", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://bioconductor.org/packages/2.4/bioc/html/EBImage.html" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Nandini Badarinarayan" } ], "definition": { "val": "EBImage is an R package which provides general purpose functionality for the reading, writing, processing and analysis of images. Furthermore, in the context of microscopy based cellular assays, EBImage offers tools to transform the images, segment cells and extract quantitative cellular descriptors." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_1100095", "lbl": "'EBarrays'", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://bioconductor.org/packages/2.4/bioc/html/EBarrays.html" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Nandini Badarinarayan" } ], "definition": { "val": "EBarrays provides tools for the analysis of replicated/unreplicated microarray data." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_1100098", "lbl": "Expert 2100", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://www.chem.agilent.com/en-US/products/instruments/lab-on-a-chip/2100expertsoftware/pages/default.aspx" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Nandini Badarinarayan" } ], "definition": { "val": "Exper 2100 offers powerful data evaluation tools for all available assays, automatic and manual integration, smear analysis and many assay-specific tools." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_1100099", "lbl": "FACS data", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://www.bioconductor.org/packages/2.12/bioc/vignettes/prada/inst/doc/fcs3.html, accessed 29 May 2013." }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "definition": { "val": "FACS data is data which describes flow cytometry data sets." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_1100104", "lbl": "Agilent Feature Extraction Software", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "Feature Extraction Software" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "Feature Extraction Software [Agilent Technologies]" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "Feature Extraction software" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://www.chem.agilent.com/en-us/products/instruments/dnamicroarrays/featureextractionsoftware/pages/default.aspx" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Nandini Badarinarayan" } ], "definition": { "val": "The software automatically finds and places microarray grids, rejects outlier pixels, accurately determines feature intensities and ratios, flags outlier pixels, and calculates statistical confidences. Application-specific QC reports summarize results and provide an at-a-glance quality assessment" } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_1100106", "lbl": "GACK", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://falkow.stanford.edu/whatwedo/software/software.html" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Nandini Badarinarayan" } ], "definition": { "val": "Dynamically chooses cutoffs for grouping into present/divergent genes based on the shape of the distribution. More resistant to variation in hybridization data than CCACK." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_1100108", "lbl": "GC-RMA Quantification", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "GC-RMA Quantification (Stratagene ArrayAssist Expression Software)" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://www.biocompare.com/ProductDetails/475470/ArrayAssist-Expression-Software-(1-year-academic-license).html" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Nandini Badarinarayan" } ], "definition": { "val": "Single-user desktop software package for analyzing microarray data from multiple microarray platforms." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_1100109", "lbl": "GEMTools 2.4", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://www.baymedia.com/gemtools/" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Nandini Badarinarayan" } ], "definition": { "val": "Incyte GEMTools software is an enterprise solution for managing gene expression data using the SQL Server and Oracle relational databases. It was one of the first integrated software packages designed with an easy-to-use interface to help scientist track and analyze the vast amounts of gene expression data generated from microarray experiments. GEMTools can be used quantify and graphically display your gene expression data. Incyte Genomics relied on the GEMTools for internal operations and to track each well, probe, cDNA target, and other components of GEM arrays through ordering, fabrication, image analysis, and final data delivery." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_1100111", "lbl": "GEOmetadb", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://bioconductor.org/packages/2.4/bioc/html/GEOmetadb.html" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Nandini Badarinarayan" } ], "definition": { "val": "The NCBI Gene Expression Omnibus (GEO) represents the largest public repository of microarray data. However, finding data of interest can be challenging using current tools. GEOmetadb is an attempt to make access to the metadata associated with samples, platforms, and datasets much more feasible. This is accomplished by parsing all the NCBI GEO metadata into a SQLite database that can be stored and queried locally. GEOmetadb is simply a thin wrapper around the SQLite database along with associated documentation. Finally, the SQLite database is updated regularly as new data is added to GEO and can be downloaded at will for the most up-to-date metadata." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_1100112", "lbl": "GEOquery", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://bioconductor.org/packages/2.4/bioc/html/GEOquery.html" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Nandini Badarinarayan" } ], "definition": { "val": "The NCBI Gene Expression Omnibus (GEO) is a public repository of microarray data. Given the rich and varied nature of these data, it is only natural to want to apply BioConductor tools to these data." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_1100113", "lbl": "GGBase", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://bioconductor.org/packages/2.4/bioc/html/GGBase.html" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Nandini Badarinarayan" } ], "definition": { "val": "This package is an infrastructure for dealing with hapmap SNP reports, GWAS, etc." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_1100116", "lbl": "AtlasImage", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://www.clontech.com/images/pacs/634650-PA27475.pdf" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Nandini Badarinarayan" } ], "definition": { "val": "Computer software for the analysis and comparison of Atlas™ nylon and plastic arrays." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_1100117", "lbl": "CBS", "meta": { "definition": { "val": "The circular binary segmentation (CBS) algorithm divides the genome into regions of equal copy number . The algorithm tests for change-points using a maximal t-statistic with a permutation reference distribution to obtain the corresponding p-value. The number of computations required for the maximal test statistic is O(N^2),where N is the number of markers. 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Visualization of profiles is also provided." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_1100121", "lbl": "'CGHregions'", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://bioconductor.org/packages/2.4/bioc/html/CGHregions.html" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Nandini Badarinarayan" } ], "definition": { "val": "Dimension Reduction for Array CGH Data with Minimal Information Loss" } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_1100122", "lbl": "CHP binary format", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://www.affymetrix.com/support/developer/powertools/changelog/gcos-agcc/chp.html, http://www.affymetrix.com/support/developer/powertools/changelog/gcos-agcc/chp-xda.html, accessed 22 May 2013." }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "comments": [ "As this is a child of Binary format, it is assumed that this class is intended to represent the binary form of this format. As described in the definition sources, there are other formats for CHP available." ], "definition": { "val": "CHP binary format is a binary data format specification created by Affymetrix, stored in little-endian format and used to store expression, resequencing and genotyping results from algorithms implemented in the GCOS 1.2, 1.3 and 1.4 and BRLMM Analysis Tool software applications." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_1100124", "lbl": "'DynDoc'", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://bioconductor.org/packages/2.4/bioc/html/DynDoc.html" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Nandini Badarinarayan" } ], "definition": { "val": "A set of functions to create and interact with dynamic documents and vignettes." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_1100128", "lbl": "bcbio", "meta": { "basicPropertyValues": [ { "pred": "http://purl.org/dc/elements/1.1/contributor", "val": "https://github.com/drmarkreuter" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "comments": [ "AL 8.10.2019: Added in reference to https://github.com/allysonlister/swo/issues/15" ], "definition": { "val": "bcbio provides a shared community resource that handles the data processing component of sequencing analysis, providing researchers with more time to focus on the downstream biology." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_1100129", "lbl": "shinyNGS", "meta": { "basicPropertyValues": [ { "pred": "http://purl.org/dc/elements/1.1/contributor", "val": "https://github.com/drmarkreuter" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "comments": [ "AL 8.10.2019: Added in reference to https://github.com/allysonlister/swo/issues/12" ], "definition": { "val": "Shinyngs is an R package designed to facilitate downstream analysis of RNA-seq and similar expression data with various exploratory plots and data mining tools." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_1100130", "lbl": "Seurat", "meta": { "basicPropertyValues": [ { "pred": "http://purl.org/dc/elements/1.1/contributor", "val": "https://github.com/drmarkreuter" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "comments": [ "AL 8.10.2019: Added in reference to https://github.com/allysonlister/swo/issues/13" ], "definition": { "val": "Seurat is an R package designed for QC, analysis, and exploration of single-cell RNA-seq data. Seurat aims to enable users to identify and interpret sources of heterogeneity from single-cell transcriptomic measurements, and to integrate diverse types of single-cell data." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_1100131", "lbl": "Graphpad Prism", "meta": { "basicPropertyValues": [ { "pred": "http://purl.org/dc/elements/1.1/contributor", "val": "https://github.com/drmarkreuter" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "comments": [ "AL 8.10.2019: Added in reference to https://github.com/allysonlister/swo/issues/14" ], "definition": { "val": "GraphPad Prism is a commercial scientific 2D graphing and statistics software available for both Windows and Macintosh computers." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_1100132", "lbl": "Salmon", "meta": { "basicPropertyValues": [ { "pred": "http://purl.org/dc/elements/1.1/contributor", "val": "https://github.com/drmarkreuter" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "comments": [ "AL 8.10.2019: Added in reference to https://github.com/allysonlister/swo/issues/15" ], "definition": { "val": "Salmon is a tool for quantifying the expression of transcripts using RNA-seq data. Salmon uses new algorithms (specifically, coupling the concept of quasi-mapping with a two-phase inference procedure) to provide accurate expression estimates very quickly (i.e. wicked-fast) and while using little memory. 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This comprehensive post-processing utility provides optimized workflows for sample-to-sample comparison, target component analysis, quantitation and library searching for data generated from any LC-MS and GC-MS platform" } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_1100137", "lbl": "SWATH Software", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "Allyson Lister" }, { "pred": "http://purl.org/dc/elements/1.1/contributor", "val": "Allyson Lister" }, { "pred": "http://purl.org/dc/elements/1.1/contributor", "val": "Mark Reuter" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Mark Reuter" } ], "comments": [ "AL 21.10.2019: Added in reference to https://github.com/allysonlister/swo/issues/30" ], "definition": { "val": "SWATH is the only data independent acquisition (DIA) technique that allows comprehensive detection and quantitation of virtually every detectable compound in a sample (MS/MSALL). This provides confidence in your quantitative results and virtually eliminates the risk of missing a critical component. SWATH Acquisition strategy can only be achieved through the power and speed of SCIEX TripleTOF® and QTOF technology." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_1100138", "lbl": "Supernovo", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "Allyson Lister" }, { "pred": "http://purl.org/dc/elements/1.1/contributor", "val": "Allyson Lister" }, { "pred": "http://purl.org/dc/elements/1.1/contributor", "val": "Mark Reuter" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Mark Reuter" } ], "comments": [ "AL 21.10.2019: Added in reference to https://github.com/allysonlister/swo/issues/29" ], "definition": { "val": "SupernovoTM is a unique, hands-free solution for end-to-end de novo sequencing of monoclonal antibodies (mAbs), enabling high throughput protein discovery." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_1100139", "lbl": "PEAKS DB", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "Allyson Lister" }, { "pred": "http://purl.org/dc/elements/1.1/contributor", "val": "Allyson Lister" }, { "pred": "http://purl.org/dc/elements/1.1/contributor", "val": "Mark Reuter" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Mark Reuter" } ], "comments": [ "AL 21.10.2019: Added in reference to https://github.com/allysonlister/swo/issues/28" ], "definition": { "val": "Protein Identification Software including an LC-MS/MS search engine, modification search and PTM profiling, sequence variant search, integration with de novo sequencing, and support for all types of fragment ions." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_1100140", "lbl": "HTSeq", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "Allyson Lister" }, { "pred": "http://purl.org/dc/elements/1.1/contributor", "val": "Allyson Lister" }, { "pred": "http://purl.org/dc/elements/1.1/contributor", "val": "Mark Reuter" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Mark Reuter" } ], "comments": [ "AL 21.10.2019: Added in reference to https://github.com/allysonlister/swo/issues/27" ], "definition": { "val": "HTSeq is a Python package that provides infrastructure to process data from high-throughput sequencing assays." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_1100141", "lbl": "RNA-SeQC", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "Allyson Lister" }, { "pred": "http://purl.org/dc/elements/1.1/contributor", "val": "Allyson Lister" }, { "pred": "http://purl.org/dc/elements/1.1/contributor", "val": "Mark Reuter" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Mark Reuter" } ], "comments": [ "AL 21.10.2019: Added in reference to https://github.com/allysonlister/swo/issues/26" ], "definition": { "val": "RNA-SeQC is a java program which computes a series of quality control metrics for RNA-seq data. The input can be one or more BAM files. The output consists of HTML reports and tab delimited files of metrics data. This program can be valuable for comparing sequencing quality across different samples or experiments to evaluate different experimental parameters. It can also be run on individual samples as a means of quality control before continuing with downstream analysis." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_1100142", "lbl": "RSeQC", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "Allyson Lister" }, { "pred": "http://purl.org/dc/elements/1.1/contributor", "val": "Allyson Lister" }, { "pred": "http://purl.org/dc/elements/1.1/contributor", "val": "Mark Reuter" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Mark Reuter" } ], "comments": [ "AL 21.10.2019: Added in reference to https://github.com/allysonlister/swo/issues/25" ], "definition": { "val": "RSeQC package provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. Some basic modules quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while RNA-seq specific modules evaluate sequencing saturation, mapped reads distribution, coverage uniformity, strand specificity, transcript level RNA integrity etc." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_1100143", "lbl": "SAMtools", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "Allyson Lister" }, { "pred": "http://purl.org/dc/elements/1.1/contributor", "val": "Allyson Lister" }, { "pred": "http://purl.org/dc/elements/1.1/contributor", "val": "Mark Reuter" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Mark Reuter" } ], "comments": [ "AL 21.10.2019: Added in reference to https://github.com/allysonlister/swo/issues/24" ], "definition": { "val": "SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_1100144", "lbl": "FastQC", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "Allyson Lister" }, { "pred": "http://purl.org/dc/elements/1.1/contributor", "val": "Allyson Lister" }, { "pred": "http://purl.org/dc/elements/1.1/contributor", "val": "Mark Reuter" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Mark Reuter" } ], "comments": [ "AL 21.10.2019: Added in reference to https://github.com/allysonlister/swo/issues/23" ], "definition": { "val": "FastQC aims to provide a simple way to do some quality control checks on raw sequence data coming from high throughput sequencing pipelines. It provides a modular set of analyses which you can use to give a quick impression of whether your data has any problems of which you should be aware before doing any further analysis." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_1100145", "lbl": "CutAdapt", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000117", "val": "Allyson Lister" }, { "pred": "http://purl.org/dc/elements/1.1/contributor", "val": "Allyson Lister" }, { "pred": "http://purl.org/dc/elements/1.1/contributor", "val": "Mark Reuter" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Mark Reuter" } ], "comments": [ "AL 21.10.2019: Added in reference to https://github.com/allysonlister/swo/issues/22" ], "definition": { "val": "Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_1200005", "lbl": "Biometric Research Branch", "meta": { "comments": [ "" ] }, "type": "INDIVIDUAL" }, { "id": "http://www.ebi.ac.uk/swo/SWO_1200009", "lbl": "EMBL", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "European Molecular Biology Laboratory" } ] }, "type": "INDIVIDUAL" }, { "id": "http://www.ebi.ac.uk/swo/SWO_9000005", "lbl": "licence clause", "meta": { "basicPropertyValues": [ { "pred": "http://purl.org/dc/terms/creator", "val": "James Malone" } ], "definition": { "val": "A licence clause is a component of a licence which defines some aspect of a restriction or conversely permission in how something corresponding to a licence may be legally redistributed, partially redistrubed, extended, modified or otherwise used in some way." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_9000006", "lbl": "Attribution clause", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "Modified by Allyson Lister from http://creativecommons.org/tag/attribution" } ], "definition": { "val": "An Attribution clause is a license clause intended to provide a specified level of recognition of the licensor as the copyright holder of the work. This can take many forms, including the requirement to preserve any copyright notice, attribution statements and the URL (link) to the original work. The attribution requirement thus serves the dual purpose of ensuring that the publisher receives appropriate credit, and that provenance information is kept intact. There are varying strengths of these clauses, from licensors requesting not to be attributed at all to requiring attribution for all uses of the resource." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_9000007", "lbl": "Derivatives clause", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "Allyson Lister" } ], "definition": { "val": "Derivatives clauses are license clauses which state what requirements on derivative resource, if any, are attached to a license. The license for a resource may or may not allow the creation of new resources derived from it. If it is allowed, such usage may be restricted in a variety of ways." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_9000008", "lbl": "Source code clause", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "Allyson Lister" } ], "definition": { "val": "A source code clause is a license clause which states the restrictions placed on the source code for the licensed software, if any. The license for a piece of software may or may not allow access to the source code. If such access is allowed, usage may be restricted in a variety of ways." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_9000009", "lbl": "Platform clause", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "Allyson Lister" } ], "definition": { "val": "A Platform clause is a license clause which states the platform restrictions for the licensed resource, if any. The license for a resource may or may not allow the use of any platform. If it is allowed, such usage may be restricted in a variety of ways." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_9000010", "lbl": "Number of installations clause", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "Allyson Lister" } ], "definition": { "val": "A Number of installations clause is a license clause which may limit the number of installations a particular licensee may peform." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_9000011", "lbl": "Number of users clause", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "Allyson Lister" } ], "definition": { "val": "A Number of users clause is a license clause which may limit the number of users a particular licensee may allow to use the resource." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_9000012", "lbl": "Time clause", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "Allyson Lister" } ], "definition": { "val": "A time clause is a license clause which states the restrictions placed on the length of time the licensed resource may be used, if any. The license for a resource may or may not allow access to the resource for an unlimited time. If such access is allowed, usage may be restricted in a variety of ways." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_9000013", "lbl": "Usage clause", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "Allyson Lister" } ], "definition": { "val": "A usage clause is a license clause which states the restrictions placed on how the licensed resource may be used. The license for a resource may restrict how the licensee may use the software. If such access is allowed, usage may be restricted in a variety of ways." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_9000016", "lbl": "No restrictions on derivatives", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "Allyson Lister" } ], "definition": { "val": "No restrictions on derivatives is a derivatives clause which places no rules or restrictions on how derivative software is created." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_9000017", "lbl": "Restrictions on derivative software", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "Allyson Lister" } ], "definition": { "val": "Restrictions on derivative software is a derivatives clause which allows the creation of derivatives but which also places some kind of restriction on how derivative software may be created." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_9000018", "lbl": "Derivatives not allowed", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "Allyson Lister" } ], "definition": { "val": "Derivatives not allowed clauses are derivatives clauses which state that derivative resources are never allowed using the licensed resource." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_9000019", "lbl": "derivative code same license", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "Allyson Lister" } ], "definition": { "val": "Derivative code same license is a restrictive derivatives clause where derivative software must be released under the same license." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_9000020", "lbl": "Source code available", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "Allyson Lister" } ], "definition": { "val": "A source code available clause is a source code clause which states that the source code for the licensed software is available to the licensee. However, usage of the source code may or may not be restricted in a variety of ways." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_9000021", "lbl": "Source code unavailable", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "Allyson Lister" } ], "definition": { "val": "A source code unavailable clause is a source code clause which states that the source code for the licensed software is not available to the licensee." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_9000022", "lbl": "Platform restricted", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "Allyson Lister" } ], "definition": { "val": "Platform restricted is a platform clause which places restrictions on which platform the licensed resource may be installed on." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_9000023", "lbl": "Platform unrestricted", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "Allyson Lister" } ], "definition": { "val": "Platform unrestrictred is a platform clause which does not place any restrictions on which type of platform the resource may be licensed for." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_9000024", "lbl": "Number of installations restricted", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "Allyson Lister" } ], "definition": { "val": "A Number of installations restricted clause is a number of installations clause which restricts the number of times the resource may be installed by any given licensee." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_9000025", "lbl": "Number of installations unrestricted", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "Allyson Lister" } ], "definition": { "val": "A Number of installations unrestricted clause is a number of installations clause which does not restrict the number of times the resource may be installed by any given licensee." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_9000026", "lbl": "Number of users restricted", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "Allyson Lister" } ], "definition": { "val": "A Number of users restricted clause is a number of users clause which restricts the number of users the resource may have for a particular licensee. This may be number of total users, or number of concurrent users." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_9000027", "lbl": "Number of users unrestricted", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "Allyson Lister" } ], "definition": { "val": "A Number of users unrestricted clause is a number of users clause which does not restrict the number of users of the licensed resource." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_9000028", "lbl": "Time for use restricted", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "Allyson Lister" } ], "definition": { "val": "Time for use restricted is a time clause which places restrictions on the length of time the licensed resource may be used." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_9000029", "lbl": "Time for use unrestricted", "meta": { "definition": { "val": "Time for use unrestrictred is a time clause which does not place any restrictions on the length of time the resource may be licensed for." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_9000030", "lbl": "Usage unrestricted", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "Allyson Lister" } ], "definition": { "val": "Usage unrestricted is a usage clause which places no restrictions on how the licensed resource may be used." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_9000031", "lbl": "Usage restricted", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "Allyson Lister" } ], "definition": { "val": "Usage restricted is a usage clause which places restrictions on how the licensed resource may be used. These restrictions will vary according to the individual license." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_9000032", "lbl": "Non-commercial use only", "meta": { "definition": { "val": "Non-commercial use only is a usage restricted clause which restricts the use of the licensed resource only to licensees who are not commercial entites." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_9000033", "lbl": "Academic use only", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "Allyson Lister" } ], "definition": { "val": "Academic use only is a usage restricted clause which restricts the use of the licensed resource to academic licensees only." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_9000034", "lbl": "derivative code linked same license", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "Allyson Lister" } ], "definition": { "val": "Derivative code linked same license is a restrictive derivatives clause where code may only be linked to in derivative software that is released under the same license." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_9000050", "lbl": "software interface", "meta": { "definition": { "val": "The mode of interaction with a piece of software." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_9000058", "lbl": "obsolete_is specified output of", "meta": { "basicPropertyValues": [ { "pred": "http://purl.org/dc/elements/1.1/contributor", "val": "Marked as obsolete by Allyson Lister." }, { "pred": "http://www.ebi.ac.uk/efo/obsoleted_in_version", "val": "0.3" } ], "comments": [ "There is an object property duplication for is specified output of, where one is from OBI (OBI_0000312) and one is from SWO (SWO_9000058); additionally, the reasoner infers these two object properties as equivalent. Both are the inverse properties for has specified output. It makes sense to retain the OBI object property. The SWO class URI was renamed to the OBI term URI (to make the moving of the axioms across to the OBI term simple), and then an SWO class with the original URI was marked as obsolete. Please use OBI_0000312 instead." ], "deprecated": true }, "type": "PROPERTY" }, { "id": "http://www.ebi.ac.uk/swo/SWO_9000072", "lbl": "Microsoft Windows", "meta": { "comments": [ "The Windows Operating System" ] }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_9000077", "lbl": "Adobe Acrobat Reader", "meta": { "basicPropertyValues": [ { "pred": "http://purl.org/dc/elements/1.1/contributor", "val": "Andy Brown" } ] }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_9000078", "lbl": "Annotare", "meta": { "basicPropertyValues": [ { "pred": "http://purl.org/dc/elements/1.1/contributor", "val": "Andy Brown" } ] }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_9000081", "lbl": "BioPerl", "meta": { "basicPropertyValues": [ { "pred": "http://purl.org/dc/elements/1.1/contributor", "val": "Andy Brown" } ] }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_9000083", "lbl": "DNDC", "meta": { "basicPropertyValues": [ { "pred": "http://purl.org/dc/elements/1.1/contributor", "val": "Andy Brown" } ], "comments": [ "Soil Chemistry Model" ] }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_9000089", "lbl": "DROID", "meta": { "comments": [ "Digital Record Object Identification" ] }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_9000091", "lbl": "Eclipse", "meta": { "basicPropertyValues": [ { "pred": "http://purl.org/dc/elements/1.1/contributor", "val": "Andy Brown" } ], "comments": [ "The Eclipse IDE" ] }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_9000093", "lbl": "Endnote", "meta": { "basicPropertyValues": [ { "pred": "http://purl.org/dc/elements/1.1/contributor", "val": "Andy Brown" } ], "comments": [ "Citation management software" ] }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_9000094", "lbl": "Grimoires", "meta": { "basicPropertyValues": [ { "pred": "http://purl.org/dc/elements/1.1/contributor", "val": "Andy Brown" } ] }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/SWO_9001002", "lbl": "has clause", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "Allyson Lister" } ], "definition": { "val": "Axioms using the 'has clause' property, e.g. C 'has clause' C1, provide links from the left hand class to the instances within the 'license clause' hierarchy. This provides a way to more precisely assert the constraints of the licensing applied." } }, "type": "PROPERTY" }, { "id": "http://www.ebi.ac.uk/swo/algorithm/SWO_4000004", "lbl": "SAEM", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://www.math.u-bordeaux1.fr/MAS10/DOC/PDF-PRES/Lavielle.pdf" } ], "definition": { "val": "A stochastic algorithm for population pharmacology modeling" } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/algorithm/SWO_4000005", "lbl": "dynamic Bayesian network model", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://en.wikipedia.org/wiki/Dynamic_Bayesian_network, accessed 27 November 2014." } ], "definition": { "val": "A Dynamic Bayesian Network model is a Bayesian Network which relates variables to each other over adjacent time steps." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/algorithm/SWO_4000006", "lbl": "ODE Algorithm", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "Ordinary Differential Equation Algorithm" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://en.wikipedia.org/wiki/Ordinary_differential_equation, accessed 25 March 2015." }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "definition": { "val": "In mathematics, an ordinary differential equation or ODE is an equation containing a function of one independent variable and its derivatives. The term \"ordinary\" is used in contrast with the term partial differential equation which may be with respect to more than one independent variable." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/algorithm/SWO_4000007", "lbl": "Gillespie's Stochastic Simulation Algorithm", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://en.wikipedia.org/wiki/Gillespie_algorithm, accessed 25 March 2015." }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "definition": { "val": "Gillespie's Stochastic Simulation Algorithm is an algorithm which generates a statistically correct trajectory (possible solution) of a stochastic equation. It can be used to simulate chemical or biochemical systems of reactions efficiently and accurately using limited computational power. The algorithm is particularly useful for simulating reactions within cells where the number of reagents typically number in the tens of molecules (or less). Mathematically, it is a variety of a dynamic Monte Carlo method and similar to the kinetic Monte Carlo methods. It is used heavily in computational systems biology" } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/algorithm/SWO_4000008", "lbl": "Monte Carlo", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://en.wikipedia.org/wiki/Stochastic_simulation#Monte_Carlo_simulation, accessed 25 March 2015, and http://www.async.ece.utah.edu/iBioSim/docs/iBioSim.html, accessed 25 March 2015." }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "definition": { "val": "Monte Carlo is a discrete stochastic simulation algorithm and an estimation procedure algorithm. If it is necessary to know the average value of some random variable and its distribution can not be stated, and if it is possible to take samples from the distribution, we can estimate it by taking the samples, independently, and averaging them. If there are sufficiently enough samples, then the law of large numbers says the average must be close to the true value. The central limit theorem says that the average has a Gaussian distribution around the true value." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/algorithm/SWO_4000009", "lbl": "DAE Algorithm", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "Differential Algebraic Equation Algorithm" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://en.wikipedia.org/wiki/Differential_algebraic_equation, accessed 26 March 2015." }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "definition": { "val": "Differential Algebraic equations (DAEs) are a general form of (systems of) differential equations for vector–valued functions in one independent variable. In practical terms, the distinction between DAEs and ODEs is often that the solution of a DAE system depends on the derivatives of the input signal and not just the signal itself as in the case of ODEs." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/algorithm/SWO_4000010", "lbl": "PDE Algorithm", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "Partial Differential Equation Algorithm" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://en.wikipedia.org/wiki/Partial_differential_equation, accessed 26 March 2015." }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "definition": { "val": "A partial differential equation (PDE) is a differential equation that contains unknown multivariable functions and their partial derivatives. This is in contrast to ordinary differential equations, which deal with functions of a single variable and their derivatives." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/data/SWO_3000001", "lbl": "spreadsheet format", "meta": { "basicPropertyValues": [ { "pred": "http://purl.org/dc/terms/creator", "val": "James Malone" } ], "definition": { "val": "A spreadsheet data format is one in which data is organised into a matrix (or matrices) of columns and rows to form cells in which values are entered." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/data/SWO_3000002", "lbl": "XLS spreadsheet", "meta": { "basicPropertyValues": [ { "pred": "http://purl.org/dc/terms/creator", "val": "James Malone" } ], "definition": { "val": "A spreadsheet data format designed for Microsoft Excel." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/data/SWO_3000003", "lbl": "XML spreadsheet", "meta": { "basicPropertyValues": [ { "pred": "http://purl.org/dc/terms/creator", "val": "James Malone" } ], "definition": { "val": "A spreadsheet data format in which the structure of the data is described using XML, such as column and row headers and cell identity." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/data/SWO_3000004", "lbl": "Matlab .m file", "meta": { "basicPropertyValues": [ { "pred": "http://purl.org/dc/terms/creator", "val": "James Malone" } ] }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/data/SWO_3000005", "lbl": "obsolete_XML", "meta": { "basicPropertyValues": [ { "pred": "http://purl.org/dc/elements/1.1/contributor", "val": "Marked as obsolete by Allyson Lister." }, { "pred": "http://www.ebi.ac.uk/efo/obsoleted_in_version", "val": "1.5" } ], "comments": [ "Equivalence with EDAM http://edamontology.org/format_2332, please use that instead." ], "deprecated": true }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/data/SWO_3000006", "lbl": "RDF", "meta": { "basicPropertyValues": [ { "pred": "http://edamontology.org#def", "val": "\"Resource Description Framework (RDF) format.\" [http://edamontology.org]" }, { "pred": "http://edamontology.org#namespace", "val": "format" }, { "pred": "http://edamontology.org#subset", "val": "bioinformatics" }, { "pred": "http://edamontology.org#subset", "val": "edam" }, { "pred": "http://edamontology.org#subset", "val": "formats" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://www.w3.org/TR/REC-rdf-syntax/" }, { "pred": "http://purl.org/dc/terms/creator", "val": "James Malone" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Jon Ison" } ], "comments": [ "Data in RDF format can be serialised into XML, textual, or binary format.", "Merged with now-obsolete EDAM class 'RDF' http://edamontology.org/format_2376 by Allyson Lister." ], "definition": { "val": "The Resource Description Framework (RDF) is a general-purpose language for representing information in the Web." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/data/SWO_3000007", "lbl": "RDF-XML", "meta": { "basicPropertyValues": [ { "pred": "http://purl.org/dc/terms/creator", "val": "James Malone" } ], "definition": { "val": "A serialisation of RDF into an XML format." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/data/SWO_3000009", "lbl": "DWG", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://en.wikipedia.org/wiki/.dwg" }, { "pred": "http://purl.org/dc/terms/creator", "val": "James Malone" } ], "definition": { "val": "DWG (\"drawing\") is a binary file format used for storing two and three dimensional design data and metadata" } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/data/SWO_3000010", "lbl": "DXF", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://en.wikipedia.org/wiki/AutoCAD_DXF" }, { "pred": "http://purl.org/dc/terms/creator", "val": "James Malone" } ], "definition": { "val": "DXF (Drawing Interchange Format, or Drawing Exchange Format) is a CAD data file format developed by Autodesk for enabling data interoperability between AutoCAD and other programs." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/data/SWO_3000011", "lbl": "BMP", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://www.fileformat.info/format/bmp/egff.htm" }, { "pred": "http://purl.org/dc/terms/creator", "val": "James Malone" } ], "definition": { "val": "The BMP File Format is a Raster graphics image file format used to store bitmap digital images, independently of the display device (such as a graphics adapter)." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/data/SWO_3000012", "lbl": "CGM", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://en.wikipedia.org/wiki/Computer_Graphics_Metafile" }, { "pred": "http://purl.org/dc/terms/creator", "val": "James Malone" } ], "definition": { "val": "Computer Graphics Metafile (CGM) is a free and open international standard file format for 2D vector graphics, raster graphics, and text, and is defined by ISO/IEC 8632." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/data/SWO_3000015", "lbl": "pdf", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "Portable Document Format" } ], "definition": { "val": "PDF is an open standard for document exchange. " } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/data/SWO_3000016", "lbl": "TIFF", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "Tagged Image File Format" } ], "definition": { "val": "TIFF is a flexible, adaptable file format for handling images and data within a single file, by including the header tags (size, definition, image-data arrangement, applied image compression) defining the image's geometry." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/data/SWO_3000017", "lbl": "JPEG", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "JPG" } ], "definition": { "val": "JPEG is a lossy file format for storing images" } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/data/SWO_3000018", "lbl": "PNG", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "Portable Network Graphics" } ], "definition": { "val": "PNG is a bitmapped image format and video codec that employs lossless data compression." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/data/SWO_3000019", "lbl": "GIF", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "Graphics Interchange Format" } ], "definition": { "val": "The Graphics Interchange Format (GIF) is a bitmap image format. The format supports up to 8 bits per pixel thus allowing a single image to reference a palette of up to 256 distinct colors. The colors are chosen from the 24-bit RGB color space. It also supports animations and allows a separate palette of 256 colors for each frame. The color limitation makes the GIF format unsuitable for reproducing color photographs and other images with continuous color, but it is well-suited for simpler images such as graphics or logos with solid areas of color. [wikipedia]" } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/data/SWO_3000020", "lbl": "raster image format", "meta": { "definition": { "val": "A raster image is a format for representing a rectangular grid of dots (pixels) which contains information on the specific colour of each pixel." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/data/SWO_3000021", "lbl": "vector image format", "meta": { "definition": { "val": "A vector image is a collection of connected lines and curves that produce objects. This geometric description enables the image to be displayed without loss at any size rendering." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/data/SWO_3000022", "lbl": "SVG", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "Scalable Vector Graphics" } ] }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/data/SWO_3000023", "lbl": "AI", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "Adobe Illustrator format" } ] }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/data/SWO_3000024", "lbl": "PostScript", "meta": { "definition": { "val": "PostScript is a format used for describing documents." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/data/SWO_3000025", "lbl": "tex", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "LaTeX format" } ], "definition": { "val": "tex is a format for documents written in the document markup language and document preparation system LaTeX." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/data/SWO_3000026", "lbl": "outline document format", "meta": { "definition": { "val": "A format specification for data used or produced by outliner software" } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/data/SWO_3000027", "lbl": "OmniOutline format", "meta": { "definition": { "val": "A proprietary format for documents created and edited using OmniOutliner outliner software," } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/data/SWO_3000028", "lbl": "OPML", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "Outline Processor Markup Language" } ], "definition": { "val": "OPML (Outline Processor Markup Language) is an XML format for outlines" } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/data/SWO_3000029", "lbl": "JPEG 2000", "meta": { "definition": { "val": "JPEG 2000 is a compression standard enabling both lossless and lossy storage. The compression methods used are different from the ones in standard JFIF/JPEG; they improve quality and compression ratios, but also require more computational power to process. [wikipedia]" } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/data/SWO_3000032", "lbl": "Microsoft Word doc", "meta": { "definition": { "val": "A file format for word processing documents for Microsoft Word. " } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/data/SWO_3000034", "lbl": ".java file", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "James Malone" } ], "definition": { "val": "A source code file format which is specified to be used with the Java programming language." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/data/SWO_3000035", "lbl": ".class file", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "James Malone" } ], "definition": { "val": "A format in which a .java file has been compiled into bytecode using a Java compiler and which is specified to be executed using the Java virtual machine." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/data/SWO_3000036", "lbl": "obsolete CopasiML", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": ".cps" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0100001", "val": "http://edamontology.org/format_3239" }, { "pred": "http://www.ebi.ac.uk/efo/obsoleted_in_version", "val": "1.7" } ], "comments": [ "AL 17.9.2019: The EDAM CopasiML (format_3239) was used elsewhere in SWO and therefore this class was no longer required." ], "definition": { "val": "An XML-based file format for use with the COPASI software." }, "deprecated": true }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/data/SWO_3000037", "lbl": "obsolete_SBML", "meta": { "basicPropertyValues": [ { "pred": "http://purl.org/dc/elements/1.1/contributor", "val": "Marked as obsolete by Allyson Lister." }, { "pred": "http://www.ebi.ac.uk/efo/obsoleted_in_version", "val": "Obsoleted after the 0.4 release." } ], "comments": [ "Equivalence with the EDAM SBML class format_2585." ], "deprecated": true }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/data/SWO_3000038", "lbl": "OWL-XML", "meta": { "definition": { "val": "The Web Ontology Language (OWL) in XML serialization" } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/data/SWO_3000039", "lbl": "OWL2-XML", "meta": { "definition": { "val": "Web Ontology Language version 2 in XML Serialization" } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/data/SWO_3000040", "lbl": "obsolete_OBO flat file format", "meta": { "basicPropertyValues": [ { "pred": "http://purl.org/dc/elements/1.1/contributor", "val": "Marked as obsolete by Allyson Lister." }, { "pred": "http://www.ebi.ac.uk/efo/obsoleted_in_version", "val": "Obsoleted after the 0.4 release." } ], "comments": [ "Equivalence with EDAM term format_2549." ], "deprecated": true }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/data/SWO_3000041", "lbl": "obsolete_text file format", "meta": { "basicPropertyValues": [ { "pred": "http://purl.org/dc/elements/1.1/contributor", "val": "Marked as obsolete by Allyson Lister." }, { "pred": "http://www.ebi.ac.uk/efo/obsoleted_in_version", "val": "1.5" } ], "comments": [ "Equivalence with EDAM http://edamontology.org/format_2330, please use that class instead." ], "deprecated": true }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/data/SWO_3000045", "lbl": "obsolete_MAGE tab format", "meta": { "basicPropertyValues": [ { "pred": "http://purl.org/dc/elements/1.1/contributor", "val": "Marked as obsolete by Allyson Lister." }, { "pred": "http://www.ebi.ac.uk/efo/obsoleted_in_version", "val": "Obsoleted after release 0.4" } ], "comments": [ "Equivalent with EDAM format_3162." ], "deprecated": true }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/data/SWO_3000046", "lbl": "tab delimited file format", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://en.wikipedia.org/wiki/Tab-separated_values, accessed 6 June 2013." }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "definition": { "val": "Tab delimited file format is a plain text file format where each field value of a record is separated from the next by a tab stop character." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/data/SWO_3000048", "lbl": "obsolete_PSI-MI format", "meta": { "basicPropertyValues": [ { "pred": "http://purl.org/dc/elements/1.1/contributor", "val": "Marked as obsolete by Allyson Lister." }, { "pred": "http://www.ebi.ac.uk/efo/obsoleted_in_version", "val": "Obsoleted after the version 0.4 release." } ], "comments": [ "Equivalence with EDAM format_3158." ], "deprecated": true }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/data/SWO_3000049", "lbl": "SIF", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://wiki.cytoscape.org/GettingStarted and http://wiki.cytoscape.org/Cytoscape_User_Manual/Network_Formats, accessed 20 June 2012" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "definition": { "val": "SIF stands for Simple Interaction Format, and is a text format invented for Cytoscape. If the file contains any tab characters, then tabs are used to delimit the fields and spaces are considered part of the name. If the file contains no tabs, then any spaces are delimiters that separate names (and names cannot contain spaces). " } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/data/SWO_3000050", "lbl": "GML", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://wiki.cytoscape.org/GettingStarted, accessed 20 June 2012" } ], "definition": { "val": "GML stands for Graph Markup Language, and is a standard network file format; supported by multiple generic network software packages " } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/data/SWO_3000051", "lbl": "XGMML", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://wiki.cytoscape.org/GettingStarted, accessed 20 June 2012" } ], "definition": { "val": "XGMML stands for eXtensible Graph Markup and Modelling Language, and it is a XML standard; similar to but preferred over GML." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/data/SWO_3000052", "lbl": "Interaction data", "meta": { "basicPropertyValues": [ { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "definition": { "val": "A type of data which defines interactions between items in the file. This can be simple pairwise interactions or more complex ones. Used to provide a class of data for software requiring specific types of interaction data as input." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/data/SWO_3000053", "lbl": "Knowledge representation", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "Modified from http://en.wikipedia.org/wiki/Knowledge_representation, accessed 10 February 2014" } ], "comments": [ "AL 6.9.22: This has been moved from 'role' and used to be called 'knowledge representation role'. The issue in its former placement is to do with the domain and range of role. Bcause this class is intended as a role for a data format, it means that we use it for various children of IAO data format specification (http://purl.obolibrary.org/obo/IAO_0000098). has_role is an RO property with a domain of independent continuant, and data format specification is an ICE (a generically dependent continuant). This means we cannot use has_role for this class. Therefore, we have moved the class out of role and updated the label, and are now using 'characteristic of'/'has characteristic' instead. We may wish to refine the placement of this class in future." ], "definition": { "val": "A knowledge representation role is a role borne by a data format which utilizes formalisms to make complex systems easier to design and build. Knowledge representation is the field of artificial intelligence devoted to representing information about the world in a form that a computer system can utilize to solve complex tasks." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/data/SWO_3000054", "lbl": "is alternative format of", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "The format for BioPAX Manchester OWL syntax is an alternative format of the BioPAX RDF/XML format." }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "Allyson Lister" } ], "definition": { "val": "With both a domain and range of 'data format specification', this property provides a means of stating that two different data format specifications are valid specifications for the same type of data." } }, "type": "PROPERTY" }, { "id": "http://www.ebi.ac.uk/swo/data/SWO_3000055", "lbl": "BioPAX RDF/XML format", "meta": { "comments": [ "AL 6.9.22: I would prefer to use the updated RO label 'has characteristic', but for some reason Protege only allows the use of the label RO deems older, 'bearer of'" ] }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/data/SWO_3000057", "lbl": "CDF ASCII format", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://www.affymetrix.com/support/developer/powertools/changelog/gcos-agcc/cdf.html, accessed 22 May 2013" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "definition": { "val": "The CDF ASCII format is an ASCII data format specification created by Affymetrix similar to the Windows INI format. This format describes the layout for an Affymetrix GeneChip array. An array may contain Expression, Genotyping, CustomSeq, Copy Number and/or Tag probe sets. All probe set names within an array are unique. Multiple copies of a probe set may exist on a single array as long as each copy has a unique name." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/data/SWO_3000058", "lbl": "BAR", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://www.affymetrix.com/support/developer/powertools/changelog/gcos-agcc/bar.html, accessed 22 May 2013." }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "definition": { "val": "BAR is a binary data format specification created by Affymetrix where the data is stored in big-endian format. The format of the file is a header section followed by sequences sections (one section per sequence defined). The BAR file contains one and two sample analysis results (signal and p-values) from the tiling array software." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/data/SWO_3000059", "lbl": "CEL ASCII format", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://www.affymetrix.com/support/developer/powertools/changelog/gcos-agcc/cel.html, accessed 22 May 2013." }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "definition": { "val": "CEL ASCII format is ASCII data format specification created by Affymetrix similar to the Windows INI format. The CEL format stores the results of the intensity calculations on the pixel values of the DAT file. This includes an intensity value, standard deviation of the intensity, the number of pixels used to calculate the intensity value, a flag to indicate an outlier as calculated by the algorithm and a user defined flag indicating the feature should be excluded from future analysis. The file stores the previously stated data for each feature on the probe array." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/data/SWO_3000060", "lbl": "Affymetrix-compliant data", "meta": { "basicPropertyValues": [ { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "definition": { "val": "Affymetrix-compliant data is data produced in a format compatible with Affymetrix software. This is a defined class where other data classes will be inferred to be members if they have a data format specification which has been published by Affymetrix." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/data/SWO_3000061", "lbl": "Data File Standard for Flow Cytometry", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "FCS" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://www.bioconductor.org/packages/2.12/bioc/vignettes/prada/inst/doc/fcs3.html, accessed May 29. 2013." }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "definition": { "val": "The flow cytometry data file standard provides the specifications needed to completely describe flow cytometry data sets within the confines of the file containing the experimental data. The principal goal of the Standard is to provide a uniform file format allowing files created by one type of acquisition hardware and software to be analyzed by another type." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/data/SWO_3000062", "lbl": "FCS3.0", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://www.bioconductor.org/packages/2.12/bioc/vignettes/prada/inst/doc/fcs3.html, accessed May 29. 2013." }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "definition": { "val": "FCS3.0 is version 3.0 of the Data File Standard for Flow Cytometry. It contains a mechanism for handling data sets of 100 megabytes and larger, support for UNICODE text for keyword values, support for cyclic redundancy check (CRC) validation for each data set, a requirement for the inclusion of information describing the method of signal amplification and increased support for the inclusion of time as a measurement parameter." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/data/SWO_3000065", "lbl": "DNA nucleotide sequence", "meta": { "definition": { "val": "A nucleic acid sequence that indicate the order of nucleotides within some DNA." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/data/SWO_3000066", "lbl": "biological sequence data", "meta": { "definition": { "val": "Data about primary biological sequence information, such as DNA neucleotide sequences." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/data/SWO_3000067", "lbl": "amino acid protein sequence data", "meta": { "definition": { "val": "Data which contains information about amino acid sequences of proteins." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/data/SWO_3000068", "lbl": "BLASTN", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "Nucleotide-nucleotide BLAST" } ], "definition": { "val": "Nucleotide-nucleotide BLAST (blastn) is a type of BLAST software that takes a given DNA query and returns the most similar DNA sequences from the DNA database that the user specifies." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/data/SWO_3000070", "lbl": "tabix file format", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://samtools.sourceforge.net/tabix.shtml" } ], "definition": { "val": "Tabix indexes a TAB-delimited genome position file and creates an index file when region is absent from the command-line. The input data file must be position sorted and compressed by bgzip which has a gzip like interface. After indexing, tabix is able to quickly retrieve data lines overlapping regions specified in the format \"chr:beginPos-endPos\". Fast data retrieval also works over network if URI is given as a file name and in this case the index file will be downloaded if it is not present locally." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/data/SWO_3000071", "lbl": "genomedata format", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://pmgenomics.ca/hoffmanlab/proj/genomedata/doc/1.3.5/genomedata.html and http://www.hdfgroup.org/why_hdf/, accessed 27 November 2014." }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "definition": { "val": "Genomedata provides a way to store and access large-scale functional genomics data in a format which is both space-efficient and allows efficient random-access. Genomedata archives are implemented as one or more HDF5 files, either as single files or as directory archives. HDF5 archives are self describing, like XML, but may also contain more complex structures such contain binary data." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/data/SWO_3000072", "lbl": "BedGraph", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://genome.ucsc.edu/goldenpath/help/bedgraph.html, accessed December 3, 2014." }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "definition": { "val": "The bedGraph format is a line-oriented text file format. Bedgraph data are preceeded by a track definition line, which adds a number of options for controlling the default display of this track. Following the track definition line are the track data in four column BED format. The bedGraph format allows display of continuous-valued data in track format. This display type is useful for probability scores and transcriptome data. This track type is similar to the wiggle (WIG) format, but unlike the wiggle format, data exported in the bedGraph format are preserved in their original state." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/data/SWO_3000073", "lbl": "GMTK parameter data", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "Graphical Models Toolkit parameter data" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "Allyson Lister" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://noble.gs.washington.edu/proj/philius/README, accessed 3 December 2014." }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "definition": { "val": "GMTK parameter data is a type of data which contains the various parameter files required by GMTK to define a dynamic Bayesian network." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/data/SWO_3000074", "lbl": "MathML 2.0", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://www.w3.org/Math/" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" }, { "pred": "http://purl.org/dc/terms/creator", "val": "James Malone" } ], "definition": { "val": "MathML 2.0 is an XML format which is a low-level specification for describing mathematics as a basis for machine to machine communication. It is a W3C Recommendation and was released on 21 Feb 2001. A product of the W3C Math working group, it provides a much needed foundation for the inclusion of mathematical expressions in Web pages." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/data/SWO_3000075", "lbl": "FieldML", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://www.physiomeproject.org/xml_languages/fieldml" }, { "pred": "http://purl.org/dc/terms/creator", "val": "James Malone" } ], "definition": { "val": "FieldML is an XML-based language for describing time-varying and\nspatially-varying fields. The aims of the language design process are to\nkeep the language concise, consistent, intuitive and flexible." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/data/SWO_3000076", "lbl": "WKn", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://support.sas.com/documentation/cdl/en/acpcref/63184/HTML/default/viewer.htm#a003103772.htm and http://en.wikipedia.org/wiki/Lotus_1-2-3, accessed 3 December 2014." }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "comments": [ "Please note that this is a collective class for all versions of the WKn format, and the specific version required should be created as necessary and placed as a child of this class." ], "definition": { "val": "WKn is a collective name for a spreadsheet format created for Lotus 1-2-3." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/data/SWO_3000077", "lbl": ".gz", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "GZipped format" } ] }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/data/SWO_3000078", "lbl": ".zip", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "Zipped format" } ] }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/data/SWO_3000080", "lbl": "RIFF", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "Resource Interchange File Format" } ] }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/data/SWO_3000081", "lbl": ".bw", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "BigWig format" } ] }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/data/SWO_3000082", "lbl": ".csv", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "Comma-separated value format" } ] }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/data/SWO_3000083", "lbl": ".mgf", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "MASCOT generic format" } ] }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/data/SWO_3000084", "lbl": ".mysql", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "MySQL format" } ] }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/data/SWO_3000085", "lbl": ".sql", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "SQL format" } ] }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/has_license", "lbl": "has license", "meta": { "definition": { "val": "The relationship between an entity and the set of legal restrictions, i.e. license, which are applied in using or otherwise interacting with that entity. Eg. relationship between software and a software license." } }, "type": "PROPERTY" }, { "id": "http://www.ebi.ac.uk/swo/interface/SWO_5000002", "lbl": "web user interface", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "WUI" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "Web UI" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "definition": { "val": "A Web User interface is a Graphical User Interface which is loaded and run via a Web browser rather than within the user's operating system." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/interface/SWO_5000003", "lbl": "desktop graphical user interface", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "Desktop GUI" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "definition": { "val": "A Desktop Graphical User interface is a Graphical User Interface which is loaded and run within the user's operating system rather than via a Web browser." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/interface/SWO_5000004", "lbl": "SOAP service", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "SOAP Service" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "Modified from http://en.wikipedia.org/wiki/SOAP, accessed 6 June 2013; modified from http://www.w3.org/TR/ws-arch, accessed 6 June 2013." }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "definition": { "val": "A SOAP service is a Web service which provides a standard, extensible, composable framework for packaging and exchanging XML messages. The service may expose an arbitrary, application-specific set of operations." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/interface/SWO_5000005", "lbl": "REST service", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "REST Service" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "Modified from http://www.w3.org/TR/ws-arch, accessed 6 June 2013, Modified from http://en.wikipedia.org/wiki/Web_service, accessed 6 June 2013." }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "definition": { "val": "A REST service is a Web service in which the primary purpose of the service is to manipulate XML representations of Web resources using a uniform set of \"stateless\" operations. RESTful APIs do not require XML-based web service protocols (SOAP and WSDL) to support their light-weight interfaces." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/interface/SWO_5000006", "lbl": "JSON web service", "meta": { "definition": { "val": "A web service in which calls invoked return JSON." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/interface/SWO_9000051", "lbl": "web service", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "Web Service" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "Modified from http://www.w3.org/TR/ws-arch/, accessed 6 June 2013; Modified from http://en.wikipedia.org/wiki/Web_service, accessed 6 June 2013." }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "definition": { "val": "A web service is a software interface which works as a method of communication between two electronic devices over the World Wide Web and which is provided at a particular network address. There are two major classes of Web services: REST-compliant Web services, and arbitrary (or application-specific) Web services." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/interface/SWO_9000052", "lbl": "graphical user interface", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "GUI" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "definition": { "val": "https://en.wikipedia.org/wiki/Graphical_user_interface, accessed 6 June 2013." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/interface/SWO_9000053", "lbl": "command-line interface", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "Command line" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "Command line interface" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "Command-line" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://en.wikipedia.org/wiki/Command-line_interface, accessed 25 November 2014." } ], "definition": { "val": "A command-line interface is a means of interacting with a computer program where the user (or client) issues commands to the program in the form of successive lines of text (command lines)." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/interface/SWO_9000054", "lbl": "application programming interface", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "API" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://en.wikipedia.org/wiki/Application_programming_interface, accessed 25 November 2014." } ], "definition": { "val": "An application programming interface is a set of routines, protocols, and tools for building software applications. An API expresses a software component in terms of its operations, inputs, outputs, and underlying types. An API defines functionalities that are independent of their respective implementations, which allows definitions and implementations to vary without compromising each other. The API specifies how software components should interact." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/is_license_for", "lbl": "is license for", "meta": { "definition": { "val": "The relationship between an entity and the set of legal restrictions, i.e. license, which are applied in using or otherwise interacting with that entity. Eg. relationship between a software license and the software which implements it." } }, "type": "PROPERTY" }, { "id": "http://www.ebi.ac.uk/swo/license/SWO_1000001", "lbl": "Creative Commons", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "CC" } ] }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/license/SWO_1000003", "lbl": "MPL v1.1", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "Mozilla Public License Version 1.1" } ] }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/license/SWO_10000035", "lbl": "Distribution clause", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "Allyson Lister" } ], "definition": { "val": "Distribution clauses are license clauses which state the requirements on how the licensed resource is redistributed. The license for a resource may or may not allow the redistribution of that resource. If it is allowed, such usage may be restricted in a variety of ways." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/license/SWO_10000036", "lbl": "Distribution restricted", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "Allyson Lister" } ], "definition": { "val": "Distribution restricted is a distribution clause which places restrictions on how the licensed resource may be distributed by third parties. These restrictions may be complete, e.g. no further redistribution, or partial." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/license/SWO_10000037", "lbl": "Distribution unrestricted", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "Allyson Lister" } ], "definition": { "val": "Distribution unrestricted is a distribution clause which states that the licensed resource can be redistributed by a third party in whatever manner that party wishes." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/license/SWO_10000038", "lbl": "Derivatives allowed", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "Allyson Lister" } ], "definition": { "val": "Derivatives allowed clauses are derivatives clauses which state that derivative resources are allowed using the licensed resource. Even when allowed, such a clause may or may not restrict the usage of the licensed resource in a variety of ways." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/license/SWO_1000004", "lbl": "GNU GPL", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "GNU General Public License" } ] }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/license/SWO_1000005", "lbl": "Apache License Version 2.0", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://www.gnu.org/licenses/license-list.html, accessed 12 June 2013." }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "definition": { "val": "This is a free software license under the definition of \"free\" by the GNU Project, and is compatible with version 3 of the GNU GPL." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/license/SWO_1000006", "lbl": "Academic Free License version 3", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "AFL" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://directory.fsf.org/wiki/License:AFLv3, accessed 12 June 2013; http://www.gnu.org/licenses/license-list.html, accessed 12 June 2013" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Andy Brown" } ], "definition": { "val": "The Academic Free License is a free software license under the definition of \"free\" by the GNU Project, is not copyleft, and is incompatible with the GNU GPL." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/license/SWO_1000007", "lbl": "FreeBSD", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "2-clause BSD License" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://www.gnu.org/licenses/license-list.html, accessed 12 June 2013." }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Andy Brown" } ], "definition": { "val": "This is the original BSD license with the advertising clause and another clause removed. (It is also sometimes called the “2-clause BSD license”.) It is a lax, permissive non-copyleft free software license, compatible with the GNU GPL." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/license/SWO_1000043", "lbl": "GNU Project Free License Type", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://www.gnu.org/philosophy/free-sw.html, accessed 12 June 2013." }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "comments": [ "Allyson Lister: This class defines those licenses which are free licenses, but which may or may not be compatible with any version of the GNU GPL." ], "definition": { "val": "A licensed is a free license according to GNU if the users have the four essential freedoms:\n\n The freedom to run the program, for any purpose (freedom 0).\n The freedom to study how the program works, and change it so it does your computing as you wish (freedom 1). Access to the source code is a precondition for this.\n The freedom to redistribute copies so you can help your neighbor (freedom 2).\n The freedom to distribute copies of your modified versions to others (freedom 3). By doing this you can give the whole community a chance to benefit from your changes. Access to the source code is a precondition for this.\n\nA program is free software if users have all of these freedoms. Thus, you should be free to redistribute copies, either with or without modifications, either gratis or charging a fee for distribution, to anyone anywhere. Being free to do these things means (among other things) that you do not have to ask or pay for permission to do so.\n\n“Free software” does not mean “noncommercial”. A free program must be available for commercial use, commercial development, and commercial distribution. Commercial development of free software is no longer unusual; such free commercial software is very important. You may have paid money to get copies of free software, or you may have obtained copies at no charge. But regardless of how you got your copies, you always have the freedom to copy and change the software, even to sell copies. " } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/license/SWO_1000044", "lbl": "GNU GPL Compatible License Type", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "Modified from http://www.gnu.org/copyleft/copyleft.html, accessed 12 June 2013." }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "definition": { "val": "GNU GPL Compatible License Type is a GNU Project Free License Type which is also compatible with one or more versions of the GNU GPL" } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/license/SWO_1000045", "lbl": "Copyleft", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "Modified from http://www.gnu.org/copyleft/copyleft.html, accessed 12 June 2013." }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "definition": { "val": "Copyleft is a derivative code same license clause which says that anyone who redistributes the software, with or without changes, must pass along the freedom to further copy and change it. In other words, it requires that all derivative code uses the same license, but further limits the type of license to one which gives everyone the rights to use, modify, and redistribute the program's code, or any program derived from it, but only if the distribution terms are unchanged. To copyleft a program, you first state that it is copyrighted; then the distribution terms described above are added. This makes copyleft a legal instrument ensuring that the code and the freedoms become legally inseparable." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/license/SWO_1000046", "lbl": "GNU GPL v3", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "GNU General Public License Version 3" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "https://www.gnu.org/licenses/license-list.html, accessed on 23 June 2016." }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "definition": { "val": "The GNU GPL v3 is the latest version of the GNU GPL: a free software license, and a copyleft license. Please note that GPLv3 is not compatible with GPLv2 by itself. However, most software released under GPLv2 allows you to use the terms of later versions of the GPL as well. When this is the case, you can use the code under GPLv3 to make the desired combination." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/license/SWO_1000047", "lbl": "GNU GPL v2", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "GNU General Public License Version 2" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "https://www.gnu.org/licenses/license-list.html, accessed 23 June 2016." } ], "definition": { "val": "The GNU GPL v2 is an earlier version of the GNU GPL: a free software license, and a copyleft license. Please note that GPLv2 is, by itself, not compatible with GPLv3. However, most software released under GPLv2 allows you to use the terms of later versions of the GPL as well. When this is the case, you can use the code under GPLv3 to make the desired combination." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/license/SWO_1000048", "lbl": "is compatible license of", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://www.gnu.org/licenses/gpl-faq.html#WhatDoesCompatMean, accessed 12 June 2013." }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "definition": { "val": "'is compatible license of' provides a method of marking two software licenses as compatible and without conflicts, e.g. that the Apache License version 2 is compatible with GNU GPL version 3. If two licenses are connected with this property, it means code released under one license can be released with code from the other license in a larger program." } }, "type": "PROPERTY" }, { "id": "http://www.ebi.ac.uk/swo/license/SWO_1000049", "lbl": "CC0 1.0", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "CC0 1.0 Universal (CC0 1.0) Public Domain Dedication" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://www.gnu.org/licenses/license-list.html, accessed 12 June 2013." }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "definition": { "val": "CC0 is a public domain dedication from Creative Commons. A work released under CC0 is dedicated to the public domain to the fullest extent permitted by law. If that is not possible for any reason, CC0 also provides a lax, permissive license as a fallback. Both public domain works and the lax license provided by CC0 are compatible with the GNU GPL." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/license/SWO_1000050", "lbl": "CC BY 2.0", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "Creative Commons Attribution 2.0 Generic (CC BY 2.0)" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "Modified from http://www.gnu.org/licenses/license-list.html, accessed 12 June 2013 and 28 June 2016; Modified from http://creativecommons.org/licenses/, accessed 12 June 2013." }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "definition": { "val": "CC BY 2.0 is a non-copyleft free (free by the definition of the GNU Project) license which lets others distribute, remix, tweak, and build upon your work, even commercially, as long as they credit you for the original creation. This is the most accommodating of Creative Commons licenses offered. Recommended for maximum dissemination and use of licensed materials. The GNU Project recommend it for art, entertainment works, and educational works. It is compatible with all versions of the GNU GPL; however, like all CC licenses, it should not be used on software." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/license/SWO_1000051", "lbl": "Attribution required", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "Allyson Lister" } ], "definition": { "val": "Attribution required is an attribution clause which states that attribution of the type specified in the license must be provided whenever the resource is used." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/license/SWO_1000052", "lbl": "CC BY-SA 2.0", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "Creative Commons Attribution-Sharealike 2.0 Generic" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "Modified from http://www.gnu.org/licenses/license-list.html, accessed 12 June 2013; Modified from http://creativecommons.org/licenses/, accessed 12 June 2013." }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "definition": { "val": "CC BY-SA 2.0 is a copyleft free (free by the definition of the GNU Project) license which lets others remix, tweak, and build upon your work even for commercial purposes, as long as they credit you and license their new creations under the identical terms. The GNU Project recommend this license for art, entertainment and educational works, but also recommend that it is not used for software or documentation, since it is tricky as to how exactly this license is compatible with the GNU GPL." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/license/SWO_1000053", "lbl": "LPPL v1.3c", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "Latex Project Public License v1.3c" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "Modified from http://en.wikipedia.org/wiki/LaTeX_Project_Public_License, accessed 12 June 2013; modified from http://www.gnu.org/licenses/license-list.html, accessed 12 June 2013." } ], "definition": { "val": "LPPL v1.3 is a free software license (by the defintion of the GNU Project), with less stringent requirements on distribution than LPPL 1.2. It is still incompatible with the GPL because some modified versions must include a copy of or pointer to an unmodified version.Software projects other than LaTeX rarely use it." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/license/SWO_1000054", "lbl": "LPPL v1.2", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "Latex Project Public License v1.2" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "Modified from http://en.wikipedia.org/wiki/LaTeX_Project_Public_License, accessed 12 June 2013; modified from http://www.gnu.org/licenses/license-list.html, accessed 12 June 2013." } ], "definition": { "val": "LPPL v1.2 is a free software license (by the defintion of the GNU Project), This license is an incomplete statement of the distribution terms for LaTeX. While it is a free software license, it is incompatible with the GPL because it has many requirements that are not in the GPL. Software projects other than LaTeX rarely use it." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/license/SWO_1000055", "lbl": "Mozilla Public License Version 2.0", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://www.gnu.org/licenses/license-list.html, accessed 12 June 2013; http://en.wikipedia.org/wiki/Mozilla_Public_License, accessed 12 June 2013." } ], "definition": { "val": "MPL v2.0 a free software license as defined by the GNU Project. Section 3.3 provides indirect compatibility between this license and the GNU GPL version 2.0, the GNU LGPL version 2.1, the GNU AGPL version 3.0, and all later versions of those licenses. The MPL allows covered source code to be mixed with other files under a different, even proprietary license. However, code files licensed under the MPL must remain under the MPL and freely available in source form." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/license/SWO_1000056", "lbl": "Artistic License", "meta": { "basicPropertyValues": [ { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ] }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/license/SWO_1000057", "lbl": "Artistic License 2.0", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://www.gnu.org/licenses/license-list.html, accessed 12 June 2013." }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "definition": { "val": "The Artistic License v 2.0 is a free software license by the definition of the GNU Project and compatible with the GPL thanks to the relicensing option in section 4(c)(ii) (as compared with the Artistic License 1.0)." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/license/SWO_1000058", "lbl": "Purchase cost", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "Allyson Lister" } ], "comments": [ "Allyson Lister", "In some ways, purchase cost is similar to the already-extant usage clause hierarchy, which includes restricted and unrestricted usage. However, a usage limitation is not necessarily due to whether or not something costs money: even if the usage is academic only, it could still be either free or non-free. A license could have multiple usage clauses, e.g. academic only when free, and unrestricted if a fee is paid. Purchase cost was created which, together with a usage clause, defines both limitations and cost." ], "definition": { "val": "Purchase cost is a license clause which states whether there is a cost involved with a particular usage or licensing of a resource." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/license/SWO_1000059", "lbl": "Free", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "Allyson Lister" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "comments": [ "This class refers only to the cost of the resource, not to the definition of \"free software\" as provided by the GNU Project and which is commonly used to describe software that respects users' freedom and community (http://www.gnu.org/philosophy/free-sw.html)." ], "definition": { "val": "Free is a type of purchase cost clause which, when applied, means that there is no cost for the users of the resource to which the license is attached. This clause can be combined with other clauses (such as usage clauses) to specify that only certain usages are free." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/license/SWO_1000060", "lbl": "Not Free", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "Allyson Lister" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "comments": [ "This class refers only to the cost of the resource, not to the definition of \"free software\" as provided by the GNU Project and which is commonly used to describe software that respects users' freedom and community (http://www.gnu.org/philosophy/free-sw.html)." ], "definition": { "val": "Not Free is a type of purchase cost clause which, when applied, means that there is a cost for the users of the resource to which the license is attached. This clause can be combined with other clauses (such as usage clauses) to specify that only certain usages incur a purchase cost." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/license/SWO_1000061", "lbl": "free to use license", "meta": { "definition": { "val": "A license which allows any form of usage of the artifact." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/license/SWO_1000065", "lbl": "CC BY 4.0", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "Creative Commons Attribution 4.0 International (CC BY 4.0)" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://creativecommons.org/licenses/by/4.0/ accessed June 22, 2016; https://www.gnu.org/licenses/license-list.html, accessed on June 28, 2016." }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "comments": [ "Allyson Lister: The only restriction on derivatives is that of the attribution requirement. " ], "definition": { "val": "The CC BY 4.0 license is a Creative Commons license. This is a non-copyleft free license that is good for art and entertainment works, and educational works. It is compatible with all versions of the GNU GPL; however, like all CC licenses, it should not be used on software. People are free to:\nShare — copy and redistribute the material in any medium or format;\nAdapt — remix, transform, and build upon the material for any purpose, even commercially.\nThe licensor cannot revoke these freedoms as long as you follow the license terms.\nBut they must conform to the following terms:\nAttribution — You must give appropriate credit, provide a link to the license, and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use.\nNo additional restrictions — You may not apply legal terms or technological measures that legally restrict others from doing anything the license permits." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/license/SWO_1000066", "lbl": "Attribution not required", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "Allyson Lister" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "definition": { "val": "Attribution not required is an attribution clause which states that no attribution need be provided whenever the resource is used." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/license/SWO_1000067", "lbl": "CC BY 2.0 UK", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "Creative Commons Attribution 2.0 UK: England & Wales (CC BY 2.0 UK)" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "Modified from the definition of http://www.ebi.ac.uk/swo/license/SWO_1000050." }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "definition": { "val": "CC BY 2.0 UK is a UK-specific non-copyleft free (free by the definition of the GNU Project) license which lets others distribute, remix, tweak, and build upon your work, even commercially, as long as they credit you for the original creation. This is the most accommodating of Creative Commons licenses offered. Recommended for maximum dissemination and use of licensed materials. The GNU Project recommend it for art, entertainment works, and educational works. It is compatible with all versions of the GNU GPL; however, like all CC licenses, it should not be used on software." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/license/SWO_1000068", "lbl": "GNU LGPL v3", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "GNU Lesser General Public License (LGPL) version 3 " }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "https://www.gnu.org/licenses/license-list.html, accessed 23 June 2016." } ], "definition": { "val": "This is the latest version of the LGPL: a free software license, but not a strong copyleft license, because it permits linking with nonfree modules. It is compatible with GPLv3. It is therefore recommend for special circumstances only.\n\nPlease note that LGPLv3 is not compatible with GPLv2 by itself. However, most software released under GPLv2 allows you to use the terms of later versions of the GPL as well. When this is the case, you can use the code under GPLv3 to make the desired combination." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/license/SWO_1000070", "lbl": "GNU AGPL v3", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "GNU Affero General Public License (AGPL) version 3" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "https://www.gnu.org/licenses/license-list.html, accessed on 23 June 2016." }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "definition": { "val": "This is a free software, copyleft license. Its terms effectively consist of the terms of GPLv3, with an additional paragraph in section 13 to allow users who interact with the licensed software over a network to receive the source for that program. It is recommended that developers consider using the GNU AGPL for any software which will commonly be run over a network." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/license/SWO_1000071", "lbl": "GNU LGPL v2.1", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "GNU Lesser General Public License (LGPL) version 2.1" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "https://www.gnu.org/licenses/license-list.html, accessed 28 June 2016." } ], "definition": { "val": "This is the previous version of the LGPL: a free software license, but not a strong copyleft license, because it permits linking with nonfree modules. It is compatible with GPLv2 and GPLv3. We generally recommend the latest version of the LGPL, for special circumstances only." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/license/SWO_1000072", "lbl": "CC BY 2.1 JP", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "Creative Commons Attribution 2.1 Japan (CC BY 2.1 JP)" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "Modified from the definition of http://www.ebi.ac.uk/swo/license/SWO_1000050." }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "definition": { "val": "CC BY 2.1 JP is a Japan-specific non-copyleft free (free by the definition of the GNU Project) license which lets others distribute, remix, tweak, and build upon your work, even commercially, as long as they credit you for the original creation. This is the most accommodating of Creative Commons licenses offered. Recommended for maximum dissemination and use of licensed materials. The GNU Project recommend it for art, entertainment works, and educational works. It is compatible with all versions of the GNU GPL; however, like all CC licenses, it should not be used on software." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/license/SWO_1000073", "lbl": "CC BY 2.5", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "Creative Commons Attribution 2.5 Generic (CC BY 2.5)" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "Modified from the definition of http://www.ebi.ac.uk/swo/license/SWO_1000050." }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "definition": { "val": "CC BY 2.5 is a non-copyleft free (free by the definition of the GNU Project) license which lets others distribute, remix, tweak, and build upon your work, even commercially, as long as they credit you for the original creation. This is the most accommodating of Creative Commons licenses offered. Recommended for maximum dissemination and use of licensed materials. The GNU Project recommend it for art, entertainment works, and educational works. It is compatible with all versions of the GNU GPL; however, like all CC licenses, it should not be used on software." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/license/SWO_1000074", "lbl": "CC BY 3.0 AU", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "Creative Commons Attribution 3.0 Australia (CC BY 3.0 AU)" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "Modified from the definition of http://www.ebi.ac.uk/swo/license/SWO_1000050." }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "definition": { "val": "CC BY 3.0 AU is an Australia-specific non-copyleft free (free by the definition of the GNU Project) license which lets others distribute, remix, tweak, and build upon your work, even commercially, as long as they credit you for the original creation. This is the most accommodating of Creative Commons licenses offered. Recommended for maximum dissemination and use of licensed materials. The GNU Project recommend it for art, entertainment works, and educational works. It is compatible with all versions of the GNU GPL; however, like all CC licenses, it should not be used on software." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/license/SWO_1000075", "lbl": "CC BY 3.0", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "Creative Commons Attribution 3.0 Unported (CC BY 3.0)" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "Modified from the definition of http://www.ebi.ac.uk/swo/license/SWO_1000050." }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "definition": { "val": "CC BY 3.0 is a non-copyleft free (free by the definition of the GNU Project) license which lets others distribute, remix, tweak, and build upon your work, even commercially, as long as they credit you for the original creation. This is the most accommodating of Creative Commons licenses offered. Recommended for maximum dissemination and use of licensed materials. The GNU Project recommend it for art, entertainment works, and educational works. It is compatible with all versions of the GNU GPL; however, like all CC licenses, it should not be used on software." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/license/SWO_1000076", "lbl": "CC BY 3.0 US", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "Creative Commons Attribution 3.0 United States (CC BY 3.0 US)" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "Modified from the definition of http://www.ebi.ac.uk/swo/license/SWO_1000050." }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "definition": { "val": "CC BY 3.0 US is a US-specific non-copyleft free (free by the definition of the GNU Project) license which lets others distribute, remix, tweak, and build upon your work, even commercially, as long as they credit you for the original creation. This is the most accommodating of Creative Commons licenses offered. Recommended for maximum dissemination and use of licensed materials. The GNU Project recommend it for art, entertainment works, and educational works. It is compatible with all versions of the GNU GPL; however, like all CC licenses, it should not be used on software." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/license/SWO_1000077", "lbl": "CC BY-ND 3.0", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "Creative Commons Attribution-NoDerivs 3.0 Unported (CC BY-ND 3.0)" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "https://www.gnu.org/licenses/license-list.html accessed 29 June 2016; https://creativecommons.org/licenses/by-nd/3.0/ accessed 29 June 2016." }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "definition": { "val": "CC BY-ND 3.0 is a nonfree license, as there are restrictions on distributing modified versions. You must give appropriate credit, provide a link to the license, and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use. If you remix, transform, or build upon the material, you may not distribute the modified material. This license is generally used for documentation." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/license/SWO_1000078", "lbl": "CC BY-ND 4.0", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "https://www.gnu.org/licenses/license-list.html accessed 29 June 2016; https://creativecommons.org/licenses/by-nd/3.0/ accessed 29 June 2016." }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "definition": { "val": "CC BY-ND 4.0 is a nonfree license, as there are restrictions on distributing modified versions. You must give appropriate credit, provide a link to the license, and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use. If you remix, transform, or build upon the material, you may not distribute the modified material. This license is generally used for documentation." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/license/SWO_1000079", "lbl": "CC BY-NC 3.0", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "Creative Commons Attribution-NonCommercial 3.0 Unported (CC BY-NC 3.0)" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "https://www.gnu.org/licenses/license-list.html accessed 29 June 2016." }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "definition": { "val": "CC BY-NC 3.0 is a nonfree license, as there are restrictions on charging money for copies. You must give appropriate credit, provide a link to the license, use the work for non-commercial purposes, and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use. The GNU Project does not recommend that you use this license for documentation. In addition, it has a drawback for any sort of work: when a modified version has many authors, in practice getting permission for commercial use from all of them would become infeasible.\n\n" } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/license/SWO_1000080", "lbl": "CC BY-NC 4.0", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "https://www.gnu.org/licenses/license-list.html accessed 29 June 2016." }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "definition": { "val": "CC BY-NC 4.0 is a nonfree license, as there are restrictions on charging money for copies. You must give appropriate credit, provide a link to the license, use the work for non-commercial purposes, and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use. The GNU Project does not recommend that you use this license for documentation. In addition, it has a drawback for any sort of work: when a modified version has many authors, in practice getting permission for commercial use from all of them would become infeasible.\n\n" } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/license/SWO_1000081", "lbl": "CC BY-NC-ND 3.0", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "Creative Commons Attribution-NonCommercial-NoDerivs 3.0 Unported (CC BY-NC-ND 3.0)" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "https://www.gnu.org/licenses/license-list.html accessed 29 June 2016." }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "definition": { "val": "CC BY-NC-ND 3.0 is a nonfree license, as there are restrictions on distributing modified versions and on charging money for copies. You must give appropriate credit, provide a link to the license, and use the work for non-commercial purposes. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use. If you remix, transform, or build upon the material, you may not distribute the modified material. " } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/license/SWO_1000083", "lbl": "CC BY-NC-ND 2.5", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "Creative Commons Attribution-NonCommercial-NoDerivs 2.5 Generic (CC BY-NC-ND 2.5)" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "https://www.gnu.org/licenses/license-list.html accessed 29 June 2016." }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "definition": { "val": "CC BY-NC-ND 2.5 is a nonfree license, as there are restrictions on distributing modified versions and on charging money for copies. You must give appropriate credit, provide a link to the license, and use the work for non-commercial purposes. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use. If you remix, transform, or build upon the material, you may not distribute the modified material. " } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/license/SWO_1000084", "lbl": "CC BY-NC-ND 2.5 CH", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "Creative Commons Attribution-NonCommercial-NoDerivs 2.5 Switzerland (CC BY-NC-ND 2.5 CH)" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "https://www.gnu.org/licenses/license-list.html accessed 29 June 2016." }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "definition": { "val": "CC BY-NC-ND 2.5 CH is a nonfree license, as there are restrictions on distributing modified versions and on charging money for copies. You must give appropriate credit, provide a link to the license, and use the work for non-commercial purposes. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use. If you remix, transform, or build upon the material, you may not distribute the modified material. " } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/license/SWO_1000085", "lbl": "CC BY-NC-ND 4.0", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "Creative Commons Attribution-NonCommercial-NoDerivs 4.0 International (CC BY-NC-ND 4.0)" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "https://www.gnu.org/licenses/license-list.html accessed 29 June 2016." }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "definition": { "val": "CC BY-NC-ND 4.0 is a nonfree license, as there are restrictions on distributing modified versions and on charging money for copies. You must give appropriate credit, provide a link to the license, and use the work for non-commercial purposes. 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You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use. This license also lets others build upon the original work for non-commercial purposes, as long as they credit you and license their new creations under the identical terms. The GNU Project does not recommend that you use this license for documentation. In addition, it has a drawback for any sort of work: when a modified version has many authors, in practice getting permission for commercial use from all of them would become infeasible.\n\n" } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/license/SWO_1000087", "lbl": "CC BY-NC-SA 3.0", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported (CC BY-NC-SA 3.0)" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "https://www.gnu.org/licenses/license-list.html accessed 29 June 2016." }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "definition": { "val": "CC BY-NC-SA 3.0 is a nonfree license, as there are restrictions on charging money for copies. You must give appropriate credit, provide a link to the license, and indicate if changes were made. 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You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use. This license also lets others build upon the original work for non-commercial purposes, as long as they credit you and license their new creations under the identical terms. The GNU Project does not recommend that you use this license for documentation. 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You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use. This license also lets others build upon the original work for non-commercial purposes, as long as they credit you and license their new creations under the identical terms. The GNU Project does not recommend that you use this license for documentation. In addition, it has a drawback for any sort of work: when a modified version has many authors, in practice getting permission for commercial use from all of them would become infeasible.\n\n" } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/license/SWO_1000091", "lbl": "CC BY-SA 2.1 JP", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "Creative Commons Attribution-Sharealike 2.1 Japan" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "Modified from http://www.gnu.org/licenses/license-list.html, accessed 12 June 2013; Modified from http://creativecommons.org/licenses/, accessed 12 June 2013." }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "definition": { "val": "CC BY-SA 2.1 JP is a copyleft free (free by the definition of the GNU Project) license which lets others remix, tweak, and build upon your work even for commercial purposes, as long as they credit you and license their new creations under the identical terms. 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The GNU Project recommend this license for art, entertainment and educational works, but also recommend that it is not used for software or documentation, since it is tricky as to how exactly this license is compatible with the GNU GPL." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/license/SWO_1000094", "lbl": "CC BY-SA 4.0", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "Creative Commons Attribution-Sharealike 4.0 International" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "Modified from http://www.gnu.org/licenses/license-list.html, accessed 12 June 2013; Modified from http://creativecommons.org/licenses/, accessed 12 June 2013." }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "definition": { "val": "CC BY-SA 4.0 is a copyleft free (free by the definition of the GNU Project) license which lets others remix, tweak, and build upon your work even for commercial purposes, as long as they credit you and license their new creations under the identical terms. The GNU Project recommend this license for art, entertainment and educational works, but also recommend that it is not used for software or documentation, since it is tricky as to how exactly this license is compatible with the GNU GPL." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/license/SWO_1000096", "lbl": "ODbL v1.0", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "Open Database License (ODbL) v1.0" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://opendatacommons.org/licenses/odbl/summary/, accessed 5 July 2016." }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "definition": { "val": "The ODbL v1.0 allows a user of the databases to share, create and adapt the database. You must attribute any public use of the database, or works produced from the database. For redistribution of the database or derivative works, you must make the use of this license clear to others, and you must keep intact any notices on the original database. If you publicly use any adapted version of this database, or works produced from an adapted database, you must also offer that adapted database under the ODbL. If you redistribute the database, or an adapted version of it, then you may use technological measures that restrict the work (such as DRM) as long as you also redistribute a version without such measures." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/license/SWO_1000097", "lbl": "DbCL v1.0", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "ODC Database Contents License (DbCL) v1.0" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://opendatacommons.org/licenses/odbl/summary/, accessed 5 July 2016; http://opendatacommons.org/licenses/dbcl/1.0/, accessed 5 July 2016." }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "definition": { "val": "The DbCL v1.0 allows a user of the database contents to share, create and adapt the contents. You must attribute any public use of the contents, or works produced from them. For redistribution or derivative works, you must make the use of this license clear to others, and you must keep intact any notices on the original. If you publicly use any adapted version, or works produced from an adapted version, you must also offer it under the DbCL. If you redistribute the contents, or an adapted version of them, then you may use technological measures that restrict the work (such as DRM) as long as you also redistribute a version without such measures. 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The software can only be used for academic research projects. This explicitly excludes projects which charge a fee, or projects that are done in\ncollaboration with a third party that is funding the research in whole or in part in exchange for commercial rights on the results and/or possible delay in publication of any relevant results to the academic community. The user and any research assistants, co-workers or other workers who may use the Software agree to not grant licenses on any software that includes the Licensed Software, alone or integrated into other software, to third parties. Modification of the Licensed Software code is prohibited without the prior written consent of EMBLEM." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/license/SWO_1000099", "lbl": "FlowRepository Open Access Terms of Use", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://flowrepository.org/terms_of_service, accessed 6 July 2016." }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "definition": { "val": "The FlowRepository Open Access Terms of Use license allows any individual to access the licensed product (originally the Flow Cytometry Data Repository) for any purpose. There are no restrictions on the use or redistribution of the data associated with this license, though it makes the statement that some data covered may also be included under more restrictive licensing." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/license/SWO_1000100", "lbl": "ODC-By v1.0", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "Open Data Commons Attribution License (ODC-By) v1.0" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://opendatacommons.org/licenses/by/summary/, accessed 6 July 2016." }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "definition": { "val": "The ODbL v1.0 allows a user of the databases to share, create and adapt the database. You must attribute any public use of the database, or works produced from the database. For redistribution of the database or derivative works, you must make the use of this license clear to others, and you must keep intact any notices on the original database. If you redistribute the database, or an adapted version of it, then you may use technological measures that restrict the work (such as DRM) as long as you also redistribute a version without such measures." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/license/SWO_1000101", "lbl": "PDDL v1.0", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "ODC Public Domain Dedication and Licence" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://opendatacommons.org/licenses/pddl/1.0/, accessed 7 July 2016." }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "definition": { "val": "The ODC Public Domain Dedication and Licence is a document intended to allow you to freely share, modify, and use this work for any purpose and without any restrictions. This licence is intended for use on databases or their contents (“data”), either together or individually. The goal is to eliminate restrictions held by the original creator of the data and database on the use of it by others. Rightsholders will not be able to “dual license” their work by releasing the same work under different licences. This is because they have allowed anyone to use the work in whatever way they choose. Rightsholders therefore can’t re-license it under copyright or database rights on different terms because they have nothing left to license. " } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/license/SWO_1000102", "lbl": "obsolete_Modified BSD License", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "obsolete_3-clause BSD License" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://www.gnu.org/licenses/license-list.html, accessed 12 June 2013." }, { "pred": "http://purl.org/dc/elements/1.1/contributor", "val": "Marked as obsolete by Allyson Lister" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Andy Brown" }, { "pred": "http://www.ebi.ac.uk/efo/obsoleted_in_version", "val": "1.6 (expected version number, after 1.5)" } ], "comments": [ "This class is a duplicate of http://www.ebi.ac.uk/swo/license/SWO_9000085." ], "definition": { "val": "This is the original BSD license, modified by removal of the advertising clause. It is a lax, permissive non-copyleft free software license, compatible with the GNU GPL.\n\nThis license is sometimes referred to as the 3-clause BSD license.\n\nAccording to the GNU Project, the modified BSD license is not bad, as lax permissive licenses go, though the Apache 2.0 license is preferable. However, it is risky to recommend use of “the BSD license”, even for special cases such as small programs, because confusion could easily occur and lead to use of the flawed original BSD license. To avoid this risk, you can suggest the X11 license instead. The X11 license and the modified BSD license are more or less equivalent.\n\nAccording to the GNU project, the Apache 2.0 license is better for substantial programs, since it prevents patent treachery." }, "deprecated": true }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/license/SWO_1000103", "lbl": "Vendor-specific License", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "Allyson Lister" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "definition": { "val": "A vendor-specific license is a license which was, at least originally, created by a specific organization to be used just on the resources created within that organization. This is a hierarchy of convenience rather than of shared philosophy. Many of the licenses have since been taken up by other groups whose licensing requirements matched those of the originating organization." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/license/SWO_1000104", "lbl": "NIDA NIH Data Access Policy", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "Allyson Lister" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "definition": { "val": "The NIDA NIH Data Access Policy specifies under what legal requirements NIDA NIH data may be accessed. Researchers may gain access to clinical data, genetic analysis data, and DNA by obtaining formal approval from the NIDA Genetic Data Access Request Committee. " } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/license/SWO_1000105", "lbl": "Addgene Terms of Use", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "https://www.addgene.org/terms-of-use/, accessed 7 July 2016" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "definition": { "val": "The Addgene Terms of Use specifies under what legal requirements Addgene data may be accessed. Data is available for use for non-commercial purposes, but users must get express written consent of Addgene to exploit the data for commercial purposes. All copyright, trademark and other proprietary notices must be retained on the data. As consent must be aquired for commercial use, this license only allows non-commercial use (a separate agreement must be entered into for commercial use)." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/license/SWO_1000106", "lbl": "CAS Information Use Policy", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://www.cas.org/legal/infopolicy accessed 7 July 2016." }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "definition": { "val": "The CAS Information Use Policy specifies under what legal requirements CAS Information may be accessed. Attribution to ACS must be included whenever creating derivatives or redistributing data covered under this license.Each User is permitted to download and retain a maximum of 5,000 Records and a maximum of 5,000 Molfiles at any given time for personal use or to share within a Project team for the life of the Project. There are also limits on how long records may be stored with the licensee, and how records may be linked." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/license/SWO_1000107", "lbl": "CellFinder Copyright", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://cellfinder.de/contact/disclaimer/, accessed 7 July 2016." }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "definition": { "val": "The created contents and works provided under this license by CellFinder are subject to the German copyright law. Third-party contributions are marked as such. Reproduction, adaptation, dissemination and any kind of exploitation outside the limits of the copyright require the written consent of the author or creator. Downloads and copies of these pages are only permitted for private, non-commercial use. The operators of these pages aim to observe the copyright of others or will refer to their own or license-free works." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/license/SWO_1000108", "lbl": "LINCS Data Policy", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://www.lincsproject.org/data/data-release-policy/, accessed 7 July 2016." }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "definition": { "val": "The LINCS Data Policy is a license which allows redistribution and derivative works as long as the original data is attributed correctly. All investigators are encouraged, to publish results based on LINCS data. These results may include, but would not be limited to, integrating LINCS data with data from other sources. LINCS data are released with the sole restriction that they must be correctly cited so that others can establish provenance and access the original data; the correct citation will be released with each data set and will comprise either a PMID/PMCID reference or a unique LINCS identifier. " } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/license/SWO_1000109", "lbl": "GeneNetwork Conditions of Use", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://www.genenetwork.org/conditionsofUse.html, accessed 7 July 2016." }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "definition": { "val": "The GeneNetwork Conditions of Use describes the data licensing for the resource covered. Commercial and non-commercial use is allowed, though attribution is requested via either acknowledgement or co-authorship. Further restrictions on the bulk download of as-yet unpublished data is also described. (While mentioned in the document, software licensing is not the focus of this conditions of use and therefore is not modelled here.)" } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/license/SWO_1000110", "lbl": "GMD Academic License", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "Golm Metabolome Database Academic License" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://gmd.mpimp-golm.mpg.de/termsconditions.aspx, accessed 7 July 2016." } ], "definition": { "val": "The GMD Academic License is a vendor-specific license which allows the access and use of the licensed data for non-commercial purposes, as long as the appropriate attribution is used and copyright notices retained. A separate license agreement is required for commercial users and as such, they are not covered by this license. Without written consent by the GMD, no part of the GMD - in its original or in any way processed or reformatted form - may be re-distributed in any way." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/license/SWO_1000111", "lbl": "GeneProf Academic License", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://www.geneprof.org/GeneProf/terms_and_conditions.jsp, accessed 7 July 2016." } ], "definition": { "val": "The GeneProf Academic License is a vendor-specific license which allows the access and use of the licensed resource for non-commercial purposes." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/license/SWO_1000112", "lbl": "European Medicines Agency Copyright", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://www.ema.europa.eu/ema/index.jsp?curl=pages/regulation/general/general_content_000178.jsp, accessed 12 July 2016." }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "definition": { "val": "The European Medicines Agency Copyright states that the Agency is the owner of copyright and other intellectual property rights for documents and other content published on their website.\n\nInformation and documents made available on the Agency's webpages are public and may be reproduced and/or distributed, totally or in part, irrespective of the means and/or the formats used, for non-commercial and commercial purposes, provided that the Agency is always acknowledged as the source of the material. Such acknowledgement must be included in each copy of the material.\n\nCitations may be made from such material without prior permission, provided the source is always acknowledged.\n\nThe above-mentioned permissions do not apply to content supplied by third parties. Therefore, for documents where the copyright vests in a third party, permission for reproduction must be obtained from this copyright holder." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/license/SWO_1000113", "lbl": "miRTaBase Data License", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://mirtarbase.mbc.nctu.edu.tw/cache/download/LICENSE, accessed 12 July 2016" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "definition": { "val": "miRTaBase Data License is a simple vendor license which allows academic users to make use of the data for free." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/license/SWO_1000114", "lbl": "GBIF Data Sharing Agreement", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://www.gbif.org/terms/licences/data-sharing, accessed 12 July 2016" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "definition": { "val": "GBIF Data Sharing Agreement is a simple vendor license which allows all users to make use of the data for free, as long as the source of the data is properly attributed." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/license/SWO_1000115", "lbl": "IUPAC/InChI-Trust InChI Licence No. 1.0", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "IUPAC/InChI-Trust Licence for the International Chemical Identifier (InChI)\nSoftware version 1.04" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://www.inchi-trust.org/wp/wp-content/uploads/2014/06/LICENCE.pdf, accessed 12 July 2016" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "definition": { "val": "IUPAC/InChI-Trust InChI Licence No. 1.0 is a vendor license which allows all users to make use of the resource, including the source code, for free, as long as its source is properly attributed. It is broadly compatible with the GNU GPL v3 and v2 in that it states in the license that you can change the license from this one to the GNU GPL if you wish." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/license/SWO_1000116", "lbl": "Labome Copyright", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://www.labome.com/about/copyright.html, accessed 12 July 2016." }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "definition": { "val": "The Labome copyright makes the contents of their resource freely available for browsing. Any redistribution or reproduction of part or all of the contents in any form is prohibited other than the following: you may print or download to a local hard disk extracts for your use only, with a daily limit of 50 webpages; and you may copy the content to individual third parties for their use, but only if you acknowledge the website as the source of the material.\nYou may not, except with our express written permission, distribute or commercially exploit the content." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/license/SWO_1000117", "lbl": "CTD Legal Notice and Terms of Data Use", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "Comparative Toxicogenomics Database Legal Notice and Terms of Use" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://ctdbase.org/about/legal.jsp, accessed 12 July 2016" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "definition": { "val": "The CTD Legal Notice and Terms of Data Use specifies under what legal requirements the CTD data may be accessed. Data is available for use for non-commercial purposes as long as the data is properly attributed, but users must get express written consent of CTD to exploit the data for commercial purposes. As consent must be aquired for commercial use, this license only allows non-commercial use (a separate agreement must be entered into for commercial use). Additionally,You must notify CTD and describe your use of their data. For quality control purposes, you must provide CTD with periodic access to your publication of their data." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/license/SWO_1000118", "lbl": "LOINC RELMA Terms of Use", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "https://loinc.org/terms-of-use/, accessed 12 July 2016" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "definition": { "val": "LOINC RELMA Terms of Use is a vendor license which allows all users to make use of the data for free, as long as the source of the data is properly attributed. An unlimited number of copies of the licensed material may be used. " } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/license/SWO_1000119", "lbl": "MIACA Full Copyright", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://miaca.sourceforge.net/copyrightNotice.txt, accessed 12 July 2016" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "definition": { "val": "MIACA Full Copyright is a vendor-specific license which allows the document it references to be copied and furnished to others, and derivative works that comment on or otherwise explain it or assist in its implementation may be prepared, copied, published and distributed, in whole or in part, without restriction of any kind, provided that the above copyright notice and this paragraph are included on all such copies and derivative works. However, this document itself may not be modified in any way, such as by removing the copyright notice or references to the MIACA Standards Initiative or other organizations, except as needed for the purpose of developing MIACA Standards Initiative Recommendations in which case the procedures for copyrights defined in the MIACA Document process must be followed, or as required to translate it into languages other than English." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/license/SWO_1000120", "lbl": "ORCID MIT-Style License (MIT)", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "https://github.com/ORCID/ORCID-Source/blob/master/LICENSE.md, accessed 12 July 2016; https://www.gnu.org/licenses/license-list.html, accessed 28 June 2016." } ], "definition": { "val": "The ORCID MIT-style license is identical to the MIT License, except for the addition of the following two clauses: 1. \"The above license does not apply to the branding or the \"look and feel\" of the websites located at the orcid.org URL even if elements thereof are contained in the Software.\"; 2. \"Except to provide the copyright notice required above or as allowed under ORCID Inc.'s Trademark Use Policy (available at http://orcid.org, under \"Policies\"), you may not use the name of ORCID, Inc., ORCID, its marks and logo, to advertise, promote or suggest any affiliation with or endorsement by ORCID, Inc. in connection with your use of the Software.\". The MIT License is is a lax, permissive non-copyleft free software license, compatible with the GNU GPL. " } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/license/SWO_1000121", "lbl": "NIH Genomic Data Sharing Policy", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "https://gds.nih.gov/PDF/NIH_GDS_Policy.pdf" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "definition": { "val": "The NIH Genomic Data Sharing Policy specifies under what legal requirements NIH genomic data may be accessed. Access to human data is through a tiered model involving unrestricted- and controlled-data\naccess mechanisms. Requests for controlled-access data are reviewed by NIH Data Access Committees (DACs)." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/license/SWO_1000122", "lbl": "Facebase Data Access Policy", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "https://www.facebase.org/methods/policies/, accessed 12 July 2016" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "definition": { "val": "The Facebase Data Access Policy specifies under what legal requirements Facebase data may be accessed. Non-sensitive data is available for use for all purposes and usages. As consent must be aquired for sensitive (or closed) data, this license only covers the use of the open data (a separate agreement must be entered into for restricted access data)." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/license/SWO_1000123", "lbl": "ORCID Terms of Use", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://orcid.org/content/orcid-terms-use, accessed 12 July 2016" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "definition": { "val": "The ORCID Terms of Use is a vendor-specific license for describing how the data in the ORCID resource may be used. ORCID data can be sublicensed, reproduced, stored, transmitted, distributed, publicly performed and publicly displayed for non-commercial and commercial uses." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/license/SWO_1000124", "lbl": "PPDB Academic License", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "Plant Promoter Database Academic License" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://ppdb.agr.gifu-u.ac.jp/ppdb/cgi-bin/license.cgi, accessed 12 July 2016" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "definition": { "val": "The PPDB Academic Licens specifies under what legal requirements PPDB data may be accessed. Data is available for use for non-commercial purposes, but users must get express written consent of PPDB to exploit the data for commercial purposes. The resource will be used for teaching or not-for-profit research purposes only. The resource will not be further distributed to others. The recipient agrees to acknowledge the source of the material in any publication reporting its use. As consent must be aquired for commercial use, this license only allows non-commercial use (a separate agreement must be entered into for commercial use)." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/license/SWO_1000125", "lbl": "SciCrunch Terms and Conditions", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "https://neuinfo.org/page/terms, accessed 12 July 2016." }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "definition": { "val": "The SciCrunch Terms and Conditions specifies under what legal requirements SciCrunch data may be accessed. Broadly speaking, the site conforms, both for data and for the site documents themselves, to the CC BY 3.0 license. However, particular details for this resource (other than attribution requirements) are unclear." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/license/SWO_1000126", "lbl": "ProDom Commercial License", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://prodom.prabi.fr/prodom/current/html/downcom.php, accessed 12 July 2016." } ], "definition": { "val": "The ProDom Commercial License is a vendor-specific license which allows the access and use of the licensed data for commercial purposes for a fee. Non-commercial use does not require licensing or a fee, and is covered by a separate license." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/license/SWO_1000127", "lbl": "SBGN Open License with Attribution", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "Systems Biology Graphical Notation Open License with Attribution" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://www.sbgn.org/About, accessed 12July 2016." }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "definition": { "val": "The SBGN Open License with Attribution is a very simple statement of openness for the SBGN standard and related resources available on its website. No one—not the principal investigators, nor the SBGN Editors, nor the members of the SBGN Scientific Committee, nor the funding agencies or anyone else—owns SBGN; it is a free and open community effort that extends beyond any single group, and they view themselves only as organizers and fellow developers." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/license/SWO_1000128", "lbl": "NLM Open License with Attribution", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "National Library of Medicine Open License with Attribution" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "https://www.nlm.nih.gov/copyright.html, accessed 12 July 2016." }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "definition": { "val": "The NLM Open License with Attribution is a vendor-specific license which is similar to public domain, but which requests attribution. Government information at NLM Web sites is in the public domain. Public domain information may be freely distributed and copied, but it is requested that in any subsequent use the National Library of Medicine (NLM) be given appropriate acknowledgement. When using NLM Web sites, you may encounter documents, illustrations, photographs, or other information resources contributed or licensed by private individuals, companies, or organizations that may be protected by U.S. and foreign copyright laws. Transmission or reproduction of protected items beyond that allowed by fair use as defined in the copyright laws requires the written permission of the copyright owners. Specific NLM Web sites containing protected information provide additional notification of conditions associated with its use." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/license/SWO_1000129", "lbl": "RegenBase Terms of Use", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://regenbase.org/terms-of-use.html, accessed 12 July 2016" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "definition": { "val": "The RegenBase Terms of Use is a vendor-specific license which requires attribution and which does not meet the requirements for open source code, as there is a statement saying that the user will NOT translate, reverse engineer, decompile or disassemble the SYSTEM, or disclose the SYSTEM or any underlying information or technology to any third party." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/license/SWO_1000130", "lbl": "SABIO-RK Non-Commercial Purpose License", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://sabiork.h-its.org/layouts/content/termscondition.gsp, accessed 13 July 2016" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "definition": { "val": "The SABIO-RK Non-Commercial Purpose License covers use of the Database for Non-Commercial Purpose only, and appropriate attribution must be given. Non-Commercial Purpose means the use of the Database solely for internal non-commercial research and academic purposes. As consent must be aquired for commercial use, a separate agreement must be entered into for commercial use and is not covered here." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/license/SWO_1000131", "lbl": "Terms of Use for EMBL-EBI Services", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://www.ebi.ac.uk/about/terms-of-use, accessed 13 July 2016." }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "definition": { "val": "The Terms of Use for EMBL-EBI Services reflect EMBL-EBI’s commitment to OpenScience through its mission to provide freely available online services, databases and software relating to data contributed from life science experiments to the largest possible community. They impose no additional constraints on the use of the contributed data than those provided by the data owner.
EMBL-EBI expects attribution (e.g. in publications, services or products) for any of its online services, databases or software in accordance with good scientific practice. The expected attribution will be indicated on the appropriate web page. " } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/license/SWO_1000132", "lbl": "UCUM Terms of Use", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "The Unified Code for Units of Measure Terms of Use" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://unitsofmeasure.org/trac/wiki/TermsOfUse, accessed 13 July 2016" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "definition": { "val": "The UCUM Terms of Use is a vendor-specific license which allows the resource it references to be used for commercial or non-commercial purposes without restriction of any kind, provided that appropriate attribution is given. However, the resource itself may not be modified in any way. Users may make and distribute an unlimited number of copies of the Licensed Materials. Each copy thereof must include the Copyright Notice and License." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/license/SWO_1000133", "lbl": "UMLS Metathesaurus License", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "https://uts.nlm.nih.gov/license.html, accessed 13 July 2016." }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "definition": { "val": "The UMLS Metathesaurus License is a vendor-specific license which allows redistribution (as part of a larger computer application) as long as the original data is attributed correctly and a summary of data use provided each year. There is no cost to use the service, and may be used both commercially and non-commercially. Users must inform the resource if it is redistributed within a computer application." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/license/SWO_1000134", "lbl": "MHAS Data Policy", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://www.mhasweb.org/Data.aspx, accessed 13 July 2016." }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "definition": { "val": "The MHAS Data Policy is a vendor-specific license which requires that users attribute the data properly. The data is accessible free of charge to all commercial and non-commercial users. " } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/license/SWO_1000135", "lbl": "ALFRED Copyright", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "The ALlele FREquency Database Copyright" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "https://alfred.med.yale.edu/alfred/fullcopyrightpage.asp, accessed 13 July 2016." }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "definition": { "val": "The ALFRED Copyright is a vendor-specific license which states that the resource is freely available to the scientific community for statistical analysis, the only condition being that attribution is required." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/license/SWO_1000136", "lbl": "Commercial use only", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "Allyson Lister" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "comments": [ "Allyson Lister: Some licenses are expressly written for their commercial users. In such cases, a vendor will normally have multiple licenses, one for non-commercial use and one for commercial use." ], "definition": { "val": "Commercial use only is a usage restricted clause which restricts the use of the licensed resource only to licensees who are commercial entites." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/license/SWO_1000137", "lbl": "Fee-Based Commercial License", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "Allyson Lister" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "comments": [ "Allyson Lister: This is a convenience class which combines multiple license clauses to create a defined class, such that any license type which meets the requirements will be inferred to fall into this category." ], "definition": { "val": "Fee-Based Commercial License is a license which, among its license clauses, states that commercial entities may use the resource for a fee." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/license/SWO_1000138", "lbl": "BRENDA License", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://www.brenda-enzymes.org/copy.php, accessed 13 July 2016." }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "definition": { "val": "The BRENDA License is a vendor-specific license which allows access to the official website and its data free of charge. Any inclusion of BRENDA components into other data bases, or redistribution of BRENDA requires a license. To obtain commercial in-house versions please contact our distributor Biobase GmbH ( http://www.biobase-international.com). In-house versions for academic users are available from Enzymeta GmbH (http://www.enzymeta.de). The copyright of the printed version is held by Springer publishers. Users of the website may retrieve a copy of the data but must not alter the BRENDA data or charge money for a copy of it, and must not distribute any BRENDA data without prior permission of the copyright holder. As there are separate licenses for in-house versions of BRENDA, please note that this license only describes the website-accessible version of BRENDA." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/license/SWO_1000139", "lbl": "TCGA Data Use Certification", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "The Cancer Genome Atlas Data Use Certification" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://cancergenome.nih.gov/pdfs/Data_Use_Certv082014, accessed 13 July 2016" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "definition": { "val": "The TCGA Data Use Certification is a vendor-specific license which specifies the certification which must be officially agreed to before data may be accessed. There are a number of requirements in this license including attribution, non-transferability, annual progress updates, and a number of security measures." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/license/SWO_1000140", "lbl": "Non-Commercial No-Fee License", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "Allyson Lister" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "comments": [ "Allyson Lister: This is a convenience class which combines multiple license clauses to create a defined class, such that any license type which meets the requirements will be inferred to fall into this category." ], "definition": { "val": "Non-Commercial No-Fee License is a license which, among its license clauses, states that non-commercial entities may use the resource without a purchase or usage cost." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/license/SWO_1000141", "lbl": "DrugBank Academic License", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://www.drugbank.ca/about, accessed 13 July 2016" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "definition": { "val": "DrugBank is offered to the public as a freely available resource. Use and re-distribution of the data, in whole or in part, for commercial purposes (including internal use) requires a license. We ask that users who download significant portions of the database cite the DrugBank paper in any resulting publications. As consent must be aquired for commercial use, this license only describes the non-commercial aspects of data usage (a separate agreement must be entered into for commercial use)." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/license/SWO_1000142", "lbl": "UCSC Genome Browser Commercial Software License", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://genome.cse.ucsc.edu/license/gblicense.pdf, accessed 13 July 2016." } ], "definition": { "val": "The UCSC Genome Browser Commercial Software License is a vendor-specific license which allows the access and use of the licensed data for commercial purposes under specific restrictions for a fee. The licensee shall not have the right to create Derivative Works of the Licensed Products, and the Licensee shall not have the right to sublicense, sell, transfer, or assign the Licensed Products. Non-commercial use does not require licensing or a fee, and is covered by a separate license." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/license/SWO_1000143", "lbl": "Permission required for commercial use", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "Allyson Lister" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "comments": [ "Allyson Lister: Some licenses are expressly written for their commercial users. In such cases, a vendor will normally have multiple licenses, one for non-commercial use and one for commercial use." ], "definition": { "val": "Permission required for commercial use is a clause which restricts the use of the licensed resource only to licensees who are commercial entites which have received explicit permission in the manner stipulated by the resource." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/license/SWO_1000144", "lbl": "Permission required for derivative work", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "Allyson Lister" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "definition": { "val": "Permission required for derivative work is a clause which restricts the production of derivative work based on the licensed resource only to licensees who have received explicit permission in the manner stipulated by the resource." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/license/SWO_1000145", "lbl": "Xenbase Academic Conditions of Use", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://www.xenbase.org/other/static/aboutXenbase.jsp, accessed 13 July 2016" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "definition": { "val": "Data are to be used only for purposes of research and education. Commercial use is prohibited without written permission from Xenbase.\nThe contributor(s) of unpublished data should be explicitly acknowledged in any publication that incorporates, or is based in part or entirely on these data. Xenbase should be explicitly acknowledged when data used in any publication, has been in part or solely derived from analysis of data from this website. As consent must be aquired for commercial use, this license only describes the non-commercial aspects of data usage (a separate agreement must be entered into for commercial use)." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/license/SWO_1000146", "lbl": "RIKEN Copyright", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://www.riken.jp/en/terms/, accessed 14 July 2016" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "definition": { "val": "The RIKEN copyright is a vendor-specific license which states that all text, photographs, diagrams, and other materials on their website are copyrighted by RIKEN unless explicitly specified otherwise on the website. It is prohibited to use, reproduce, or modify any of the material without RIKEN's permission." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/license/SWO_1000147", "lbl": "Design Science License", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "https://www.gnu.org/licenses/dsl.html, accessed 13 July 2016; https://www.gnu.org/licenses/license-list.html, accessed 13 July 2016; https://en.wikipedia.org/wiki/Design_science_license, accessed 13 July 2016." }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "definition": { "val": "The Design Science License is a license intended to be a general \"copyleft\" that can be applied to any kind of work that has protection under copyright. This license states those certain conditions under which a work published under its terms may be copied, distributed, and modified. Unlike other open source licenses, the DSL was intended to be used on any type of copyrightable work, including documentation and source code. It was the first \"generalized copyleft\" license. This is a free and copyleft license meant for general data. THe GNU Project does not recommend it for software or documentation, since it is incompatible with the GNU GPL and with the GNU FDL; however, they consider it appropriate for other kinds of data. The DSL was written by Michael Stutz. The DSL came out in the 1990s, before the formation of the Creative Commons. According to Wikipedia, once the Creative Commons arrived, Stutz considered the DSL experiment \"over\" and no longer recommended its use." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/license/SWO_1000148", "lbl": "University of Concordia Terms of Use", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://www.concordia.ca/web/terms.html, accessed 14 July 2016" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "definition": { "val": "The University of Concordia Terms of Use is a vendor-specific license which states that no document appearing on this website or any other website owned, operated or controlled by Concordia may be copied, sold, reproduced, republished, downloaded, posted, transmitted or distributed by any means with the exception of downloading or printing the contents of the site for personal, non-commercial use. This use must bear in mind that Concordia reserves its copyright and its rights to exclusivity over the material." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/license/SWO_1000149", "lbl": "OME Software Conditons of Use", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://www.openmicroscopy.org/site/about/licensing-attribution/licensing, accessed on 23 June 2016." }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "definition": { "val": "All OME formats and software are freely available, and all OMERO and Bio-Formats source code is available under GNU public \"copyleft\" licenses or through commercial license from Glencoe Software. FLIMfit is also now available under a GNU public \"copyleft\" license.\n\nFor questions about the GNU license refer to the Frequently Asked Questions about the GNU Licenses page.\n\nBio-Formats - under the terms of the GNU public \"copyleft\" license, any software package linking to Bio-Formats, either directly or indirectly, cannot be distributed unless its source code is also made available under the terms of the GPL. Some components which provide reader and writer implementations for open file formats, are released under a more permissive BSD-2 license which enables non-GPL third party software. For a complete list of which file formats are included in the BSD license, see the BSD column of the supported formats table. Developers of non-GPL software wishing to leverage Bio-Formats components not covered by the BSD license may purchase a commercial license from Glencoe Software; please contact them at bioformats@glencoesoftware.com to discuss your requirements.\n\nThe core OME Model Schema files (.XSD) use the Creative Commons Attribution 4.0 International License, and as such you are free to share or adapt them as long as you attribute the OME consortium as follows; \"This work is derived in part from the OME specification. Copyright (C) 2002-2016 Open Microscopy Environment\". See further information about using OME-XML in your work.\n\nThis website is also covered by the Creative Commons Attribution 4.0 International License - you are free to share or adapt content as long as you credit the Open Microscopy Environment. The exception to this is the screenshots and videos which can only be used for non-commercial purposes, see Attributions below.\n\n" } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/license/SWO_1000150", "lbl": "ImmPort Conditions of Use", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "https://aspera-immport.niaid.nih.gov:9443/displayAgreement, accessed 14 July 2016" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "definition": { "val": "The ImmPort Conditions of Use is a vendor-specific license which allows the use of ImmPort data for any legal purpose except for those prohibited elsewhere in this agreement. There are very few prohibitions, and no requirement for attribution." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/license/SWO_9000059", "lbl": "Distribution with notices", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "Andy Brown" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Andy Brown" } ], "definition": { "val": "Distribution with notices is a distribution clause in which distribution is unrestricted, except that all distributions must retain certain licence information (e.g., copyright notices)." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/license/SWO_9000074", "lbl": "MIT License", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "Expat License" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "https://www.gnu.org/licenses/license-list.html, accessed 28 June 2016." } ], "definition": { "val": "This is a lax, permissive non-copyleft free software license, compatible with the GNU GPL. It is sometimes ambiguously referred to as the MIT License.\n\nFor substantial programs it is better to use the Apache 2.0 license since it blocks patent treachery." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/license/SWO_9000080", "lbl": "GNU LGPL", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "GNU Lesser General Public License" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://en.wikipedia.org/wiki/GNU_Lesser_General_Public_License, accessed 27 March 2015." }, { "pred": "http://purl.org/dc/elements/1.1/contributor", "val": "Allyson Lister" } ], "definition": { "val": "The GNU Lesser General Public License (LGPL) is a free software license published by the Free Software Foundation (FSF). The license allows developers and companies to use and integrate LGPL software into their own (even proprietary) software without being required by the terms of a strong copyleft license to release the source code of their own software-parts. The license requires that only the LGPL software-parts be modifiable by end-users via source code availability. " } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/license/SWO_9000082", "lbl": "Artistic License 1.0", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://www.gnu.org/licenses/license-list.html, accessed 13 June 2013." }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Andy Brown" } ], "definition": { "val": "The Artistic License v1.0 is not considered a free software license by the definition of the GNU Project because it is too vague; some passages are "too clever for their own good", and their meaning is not clear. The GNU Project recommends that it is not used except as part of the disjunctive license of Perl." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/license/SWO_9000084", "lbl": "EPL v1", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "Eclipse Public License Version 1.0" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "https://www.gnu.org/licenses/license-list.html, accessed 28 June 2016." } ], "definition": { "val": "The Eclipse Public License is similar to the Common Public License. This is a free software license. Unfortunately, its weak copyleft and choice of law clause make it incompatible with the GNU GPL. The only change is that the EPL removes the broader patent retaliation language regarding patent infringement suits specifically against Contributors to the EPL'd program." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/license/SWO_9000085", "lbl": "Modified BSD", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "3 clause BSD License" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://www.gnu.org/licenses/license-list.html, accessed June 12, 2013." }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Andy Jones" } ], "definition": { "val": "The Modified BSD is a software license based on he original FreeBSD license, modified by removal of the advertising clause. It is a lax, permissive non-copyleft free software license, compatible with the GNU GPL.\n\nThis license is sometimes referred to as the 3-clause BSD license.\n\nAccording to the GNU Project, the modified BSD license is not bad, as lax permissive licenses go, though the Apache 2.0 license is preferable. However, it is risky to recommend use of “the BSD license”, even for special cases such as small programs, because confusion could easily occur and lead to use of the flawed original BSD license. To avoid this risk, you can suggest the X11 license instead. The X11 license and the modified BSD license are more or less equivalent.\n\nAccording to the GNU project, the Apache 2.0 license is better for substantial programs, since it prevents patent treachery." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/license/SWO_9000086", "lbl": "LPPL", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "Latex Project Public License" } ] }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/license/SWO_9000087", "lbl": "OPL v1.0", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "Open Public License Version 1.0" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://www.gnu.org/licenses/license-list.html, accessed 12 June 2013." } ], "definition": { "val": "OPL v1.0 is not a free software license according to the definition of the GNU Project because it requires sending every published modified version to a specific initial developer. " } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/license/SWO_9000088", "lbl": "MPL", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "Mozilla Public License" } ] }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/maturity/SWO_9000061", "lbl": "Development status", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "Allyson Lister" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Andy Brown" } ], "definition": { "val": "Development status is an information content entity which indicates the maturity of a software entity within the context of the software life cycle." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/maturity/SWO_9000062", "lbl": "alpha", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "Modified from http://en.wikipedia.org/wiki/Software_release_life_cycle, accessed 11 June 2013." }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "definition": { "val": "Alpha is a development status which is applied to software by the developer/publisher during initial development and testing. Software designated alpha is commonly unstable and prone to crashing. It may or may not be released publicly." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/maturity/SWO_9000063", "lbl": "beta", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "Modified from http://en.wikipedia.org/wiki/Software_release_life_cycle, accessed 11 June 2013." }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "definition": { "val": "Beta is a development status which is generally applied to software by the developer/publisher once the majority of features have been implemented, but when the software may still contain bugs or cause crashes or data loss. Software designated beta is often released publicly, either on a general release or to a specific subset of users called beta testers. " } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/maturity/SWO_9000064", "lbl": "Release candidate", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "http://en.wikipedia.org/wiki/Software_release_life_cycle#Release_candidate, accessed 22 October 2014." } ], "definition": { "val": "A release candidate (RC) is a beta version with potential to be a final product, which is ready to release unless significant bugs emerge." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/maturity/SWO_9000065", "lbl": "Live", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "Production" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "Allyson Lister, Jon Ison, and Modified from http://en.wikipedia.org/wiki/Software_release_life_cycle, accessed 11 June 2013." }, { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ], "definition": { "val": "Live is a development status which is applied to software that has been designated as suitable for production environments by the developer/publisher. If a non-free product, software at this stage is available for purchase" } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/maturity/SWO_9000066", "lbl": "Obsolete", "meta": { "definition": { "val": "Sofware is no longer being supplied by the developers/publishers" } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/maturity/SWO_9000067", "lbl": "has declared status", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "Allyson Lister" } ], "definition": { "val": "'has declared status' provides a way to assert the developmental status of a class, such as whether it is stable or under development. Is especially useful for software that might not be complete or stable yet, and when combined with version information." } }, "type": "PROPERTY" }, { "id": "http://www.ebi.ac.uk/swo/maturity/SWO_9000068", "lbl": "has release date", "meta": { "basicPropertyValues": [ { "pred": "http://purl.org/dc/terms/creator", "val": "Andy Brown" } ], "comments": [ "The official date of release of software" ] }, "type": "PROPERTY" }, { "id": "http://www.ebi.ac.uk/swo/maturity/SWO_9000069", "lbl": "Superseded", "meta": { "basicPropertyValues": [ { "pred": "http://purl.org/dc/terms/creator", "val": "Andy Brown" } ], "definition": { "val": "An updated version of the software is available." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/maturity/SWO_9000070", "lbl": "has support URL", "meta": { "basicPropertyValues": [ { "pred": "http://purl.org/dc/terms/creator", "val": "Andy Brown" } ], "comments": [ "A URL for a source of support information about software" ] }, "type": "PROPERTY" }, { "id": "http://www.ebi.ac.uk/swo/maturity/SWO_9000071", "lbl": "First release", "meta": { "basicPropertyValues": [ { "pred": "http://purl.org/dc/terms/creator", "val": "James Malone" } ], "definition": { "val": "The first release of a piece of software. A first release does not imply any particular levels of maturity other than is this is the first instance of this software to be considered released." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/maturity/SWO_9000072", "lbl": "Latest release", "meta": { "basicPropertyValues": [ { "pred": "http://purl.org/dc/terms/creator", "val": "James Malone" } ], "definition": { "val": "The latest release of a piece of software. This does not imply any levels of maturity other than indicating this is the most recent release." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/maturity/SWO_9000073", "lbl": "Maintained", "meta": { "basicPropertyValues": [ { "pred": "http://purl.org/dc/terms/creator", "val": "Andy Brown" } ], "definition": { "val": "Software has developers actively maintaining it (fixing bugs)" } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/objective/SWO_4000007", "lbl": "obsolete software development", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0100001", "val": "http://www.ebi.ac.uk/swo/organization/SWO_9000056" }, { "pred": "http://www.ebi.ac.uk/efo/obsoleted_in_version", "val": "1.7" } ], "comments": [ "AL 24.9.2019: Duplicate of http://www.ebi.ac.uk/swo/organization/SWO_9000056" ], "deprecated": true }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/objective/SWO_4000009", "lbl": "laboratory information management", "meta": { "definition": { "val": "Manage Laboratory information such is commonly performed by LIMS software." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/objective/SWO_4000010", "lbl": "manage computer operations", "meta": { "definition": { "val": "the objective of performing the actions of an operation system such as managing the software running a computer and the interactions with the system resources and hardware." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/objective/SWO_4000011", "lbl": "text editing", "meta": { "definition": { "val": "Text editing is the objective of editing plain text files." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/objective/SWO_4000012", "lbl": "file rendering", "meta": { "comments": [ "Renders a file in such a way that its contents can be understood by users." ] }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/objective/SWO_4000015", "lbl": "obsolete modelling", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0100001", "val": "http://edamontology.org/operation_2426" }, { "pred": "http://www.ebi.ac.uk/efo/obsoleted_in_version", "val": "1.7" } ], "comments": [ "AL 18.9.2019: Redundant with EDAM 'Modelling and simulation'." ], "deprecated": true }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/objective/SWO_4000017", "lbl": "citation management", "meta": { "basicPropertyValues": [ { "pred": "http://purl.org/dc/elements/1.1/contributor", "val": "Andy Brown" } ] }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/objective/SWO_7000002", "lbl": "sequence alignment", "meta": { "basicPropertyValues": [ { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ] }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/objective/SWO_7000003", "lbl": "multiple sequence alignment", "meta": { "basicPropertyValues": [ { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ] }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/objective/SWO_7000004", "lbl": "pairwise sequence alignment", "meta": { "basicPropertyValues": [ { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ] }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/objective/SWO_7000005", "lbl": "averaging", "meta": { "basicPropertyValues": [ { "pred": "http://purl.org/dc/terms/creator", "val": "James Malone" } ], "definition": { "val": "An averaging objective is a data transformation objective where the aim is to perform mean calculations on the input of the data transformation." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/objective/SWO_7000006", "lbl": "center calculation", "meta": { "basicPropertyValues": [ { "pred": "http://purl.org/dc/terms/creator", "val": "James Malone" } ], "definition": { "val": "A center calculation objective is a data transformation objective where the aim is to calculate the center of an input data set." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/objective/SWO_7000007", "lbl": "class discovery", "meta": { "basicPropertyValues": [ { "pred": "http://purl.org/dc/terms/creator", "val": "James Malone" } ], "definition": { "val": "A class discovery objective (sometimes called unsupervised classification) is a data transformation objective where the aim is to organize input data (typically vectors of attributes) into classes, where the number of classes and their specifications are not known a priori. Depending on usage, the class assignment can be definite or probabilistic." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/objective/SWO_7000008", "lbl": "class prediction", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "PERSON: Elisabetta Manduchi" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "PERSON: James Malone" } ], "definition": { "val": "A class prediction objective (sometimes called supervised classification) is a data transformation objective where the aim is to create a predictor from training data through a machine learning technique. The training data consist of pairs of objects (typically vectors of attributes) and class labels for these objects. The resulting predictor can be used to attach class labels to any valid novel input object. Depending on usage, the prediction can be definite or probabilistic. A classification is learned from the training data and can then be tested on test data." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/objective/SWO_7000010", "lbl": "correction", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "PERSON: James Malone" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "PERSON: Melanie Courtot" } ], "definition": { "val": "A correction is where the aim is to correct for error, noise or other impairments to the input of the data transformation or derived from the data transformation itself." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/objective/SWO_7000011", "lbl": "background correction", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "PERSON: Elisabetta Manduchi" }, { "pred": "http://purl.org/dc/terms/creator", "val": "James Malone" } ], "definition": { "val": "A background correction is where the aim is to remove irrelevant contributions from the measured signal, e.g. those due to instrument noise or sample preparation." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/objective/SWO_7000012", "lbl": "error correction", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "PERSON: James Malone" }, { "pred": "http://purl.org/dc/terms/creator", "val": "James Malone" } ], "definition": { "val": "An error correction is a data transformation objective where the aim is to remove (correct for) erroneous contributions arising from the input data, or the transformation itself." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/objective/SWO_7000014", "lbl": "curve fitting", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "PERSON: Elisabetta Manduchi" }, { "pred": "http://purl.org/dc/terms/creator", "val": "Elisabetta Manduchi" }, { "pred": "http://purl.org/dc/terms/creator", "val": "James Malone" } ], "definition": { "val": "curve fitting is a data transformation in which the aim is to find a curve which matches a series of data points and possibly other constraints." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/objective/SWO_7000015", "lbl": "data normalization", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "PERSON: Elisabetta Manduchi" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "PERSON: Helen Parkinson" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "PERSON: James Malone" }, { "pred": "http://purl.org/dc/terms/creator", "val": "James Malone" } ], "definition": { "val": "A normalization is a data transformation objective where the aim is to remove systematic sources of variation to put the data on equal footing in order to create a common base for comparisons." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/objective/SWO_7000016", "lbl": "decision tree induction", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "PERSON: James Malone" }, { "pred": "http://purl.org/dc/terms/creator", "val": "James Malone" } ], "definition": { "val": "A decision tree induction objective is a data transformation objective in which a tree-like graph of edges and nodes is created and from which the selection of each branch requires that some type of logical decision is made." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/objective/SWO_7000017", "lbl": "descriptive statistical calculation", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "mean calculation" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "PERSON: Elisabetta Manduchi" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "PERSON: James Malone" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "PERSON: Melanie Courtot" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "PERSON: Monnie McGee" } ], "definition": { "val": "James Malone" } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/objective/SWO_7000019", "lbl": "feature extraction", "meta": { "definition": { "val": "A feature extraction objective is a data transformation objective where the aim of the data transformation is to generate quantified values from a scanned image." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/ontology", "lbl": "obsolete_ontology", "meta": { "basicPropertyValues": [ { "pred": "http://purl.org/dc/elements/1.1/contributor", "val": "Marked as obsolete by Allyson Lister." }, { "pred": "http://www.ebi.ac.uk/efo/obsoleted_in_version", "val": "Obsoleted after the 0.4 release." } ], "comments": [ "Equivalence with EDAM data_0582." ], "deprecated": true }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/organization/SWO_9000010", "lbl": "The Community", "meta": { "basicPropertyValues": [ { "pred": "http://purl.org/dc/elements/1.1/contributor", "val": "Andy Brown" } ], "comments": [ "An undefined, or ill-defined, group of people. May be used, for example, to denote software development as being done by 'the community', with contributions by many individuals, but no over-arching organisation." ] }, "type": "INDIVIDUAL" }, { "id": "http://www.ebi.ac.uk/swo/organization/SWO_9000055", "lbl": "software publishing process", "meta": { "basicPropertyValues": [ { "pred": "http://purl.org/dc/terms/creator", "val": "Andy Brown" } ], "definition": { "val": "The process of publishing software. Typically this process involves a software publisher performing acts such as licensing, marketing, publicising and/or providing support for a product." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/organization/SWO_9000056", "lbl": "software development", "meta": { "basicPropertyValues": [ { "pred": "http://purl.org/dc/terms/creator", "val": "Andy Brown" } ], "comments": [ "AL 24.9.19: Merged the now-obsolete http://www.ebi.ac.uk/swo/objective/SWO_4000007 into this class as they were describing the same concept. See also https://github.com/allysonlister/swo/issues/2" ], "definition": { "val": "The process of developing software, typically involving the design, implementation and testing of software." } }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/organization/SWO_9000059", "lbl": "obsolete_has_participant", "meta": { "basicPropertyValues": [ { "pred": "http://www.ebi.ac.uk/efo/obsoleted_in_version", "val": "1.4" } ], "comments": [ "Exact equivalence with RO class http://purl.obolibrary.org/obo/RO_0000057, to the extent that the inverse of RO_0000057 was already present in this ontology as the inverse of this SWO class." ], "deprecated": true }, "type": "PROPERTY" }, { "id": "http://www.ebi.ac.uk/swo/organization/SWO_9000064", "lbl": "Uppsala Molekylmekaniska HB", "meta": { "basicPropertyValues": [ { "pred": "http://purl.org/dc/elements/1.1/contributor", "val": "Allyson Lister" } ], "comments": [ "AL 8.10.2019: References https://github.com/allysonlister/swo/issues/19" ] }, "type": "INDIVIDUAL" }, { "id": "http://www.ebi.ac.uk/swo/software_before_Microsoft_2007", "lbl": "obsolete software before Microsoft 2007", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0100001", "val": "http://www.ebi.ac.uk/swo/SWO_1100127" }, { "pred": "http://www.ebi.ac.uk/efo/obsoleted_in_version", "val": "1.7" } ], "comments": [ "AL 2.10.2019: Incorrectly-formatted IRI. See also https://github.com/allysonlister/swo/issues/18" ], "deprecated": true }, "type": "CLASS" }, { "id": "http://www.ebi.ac.uk/swo/version/SWO_2000027", "lbl": "BLAST+ version 2.2.26", "meta": { "basicPropertyValues": [ { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ] }, "type": "INDIVIDUAL" }, { "id": "http://www.ebi.ac.uk/swo/version/SWO_2000028", "lbl": "ClustalW version 2.1", "meta": { "basicPropertyValues": [ { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ] }, "type": "INDIVIDUAL" }, { "id": "http://www.ebi.ac.uk/swo/version/SWO_2000029", "lbl": "ClustalX version 2.1", "meta": { "basicPropertyValues": [ { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ] }, "type": "INDIVIDUAL" }, { "id": "http://www.ebi.ac.uk/swo/version/SWO_2000030", "lbl": "Clustal Omega version 1.1", "meta": { "basicPropertyValues": [ { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ] }, "type": "INDIVIDUAL" }, { "id": "http://www.ebi.ac.uk/swo/version/SWO_2000031", "lbl": "MUSCLE version 3.8.31", "meta": { "basicPropertyValues": [ { "pred": "http://purl.org/dc/terms/creator", "val": "Allyson Lister" } ] }, "type": "INDIVIDUAL" }, { "id": "http://www.obofoundry.org/ro/ro.owl#has_part", "lbl": "has_part", "meta": { "comments": [ "The inverse property. 'part of', contains the full official RO definition." ] }, "type": "PROPERTY" }, { "id": "http://www.obofoundry.org/ro/ro.owl#part_of", "lbl": "part of", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "Cytoscape plugins would be linked to the Cytoscape application via uses software, while Microsoft Excel is linked to Microsoft Office via has_part." }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "OBO Foundry RO" } ], "definition": { "val": "This property can be used to describe related but independent members of a larger software package. In other cases, where parts of a larger software package are independent of one another in development but one piece of software executes another directly, please use \"uses software\"." } }, "type": "PROPERTY" }, { "id": "http://www.ontodm.com/OntoDM-core/OntoDM_000037", "lbl": "ensemble specification", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "OntoDM" } ], "definition": { "val": "A ensemble of generalizations specification is a generalization specification and denotes a type of generalization that is produced by a ensemble algorithm. This algorithm produces a set of generalizations at its output." } }, "type": "CLASS" }, { "id": "http://www.ontodm.com/OntoDM-core/OntoDM_000038", "lbl": "data mining algorithm", "meta": { "comments": [ "A data mining algorithm is an algorithm that has as its objective a data mining task and outputs as a result a generalization specified by a generalization specification." ] }, "type": "CLASS" }, { "id": "http://www.ontodm.com/OntoDM-core/OntoDM_000072", "lbl": "clustering algorithm", "meta": { "definition": { "val": "Clustering algorithm is a data mining algorithm that solves a clustering task and as a result produces a clustering." } }, "type": "CLASS" }, { "id": "http://www.ontodm.com/OntoDM-core/OntoDM_000078", "lbl": "pattern specification", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "OntoDM" } ], "definition": { "val": "A patten specification is a single generalization specification and denotes a pattern P on type T which is a boolean funtion on objects of type T." } }, "type": "CLASS" }, { "id": "http://www.ontodm.com/OntoDM-core/OntoDM_000087", "lbl": "probability distribution estimation task", "meta": { "comments": [ "Estimating the (Joint) Probability Distribution. A set of data (of type\nT) is often assumed to be a sample taken from a population according to a\nprobability distribution. A probability distribution/density function assigns a\nnon-negative probability/density to each object of type T. Probably the most\ngeneral data mining task (Hand et al. 2001) is the task of estimating the (joint)\nprobability distribution D over type T from a set of data items or a sample\ndrawn from that distribution.\nAs mentioned above, in the most typical case we would have T = Tuple(T1,\n. . ., Tk), where each of T1, . . ., Tk is Boolean, Discrete(S) or Real. We talk about\nthe joint probability distribution to emphasize the difference to the marginal\ndistributions of each of the variables of type T1, . . ., Tk: the joint distribution\ncaptures the interactions among the variables.\nRepresenting multi-variate distributions is a non-trivial task. Two approaches\nare commonly used in data mining. In the density-based clustering paradigm,\nmixtures of multi-variate Gaussian distributions are typically considered (Hand\net al. 2001). Probabilistic graphical models, most notably Bayesian networks,\nrepresent graphically the (in)dependencies between the variables: Learning their\nstructure and parameters is an important approach to the problem of estimating\nthe joint probability distribution." ] }, "type": "CLASS" }, { "id": "http://www.ontodm.com/OntoDM-core/OntoDM_000092", "lbl": "pattern discovery task", "meta": { "comments": [ "the task of pattern discovery is to find all local patterns from a given\npattern language that satisfy the required conditions. A prototypical instantiation\nof this task is the task of finding frequent itemsets (sets of items, such as\n{bread, butter}), which are often found together in a transaction (e.g., a market\nbasket) (Aggrawal et al 1993). The condition that a pattern (itemset) has to\nsatisfy in this case is to appear in (hold true for) a sufficiently high proportion\n(called support and denoted by s) of the transactions in the input dataset.\nWith the increasing interest in mining complex data, mining frequent patterns\nis also considered for structured data. We can thus talk about mining frequent\nsubsequences or mining frequent subgraphs in sequence or graph data. We can\nconsider as frequency the multiple occurrences of a pattern in a single data\nstructure (e.g., sequence or graph) or the single occurrences of a pattern in\nmultiple data structures." ] }, "type": "CLASS" }, { "id": "http://www.ontodm.com/OntoDM-core/OntoDM_000098", "lbl": "data mining task", "meta": { "comments": [ "A data mining task is an objective specification that specifies the objective that a data mining algorithm needs to achieve when executed on a dataset to produce as output a generalization." ] }, "type": "CLASS" }, { "id": "http://www.ontodm.com/OntoDM-core/OntoDM_000112", "lbl": "clustering specification", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "OntoDM" } ], "definition": { "val": "Clustering specification is a single generalization specification is a generalization specification and denotes a type of generalization that models the mapping of a set of objects S of type T from S to a set of natural numbers {1,...K}. This generalization is obtained by appliing a clustering algorithm on a set of data." } }, "type": "CLASS" }, { "id": "http://www.ontodm.com/OntoDM-core/OntoDM_000160", "lbl": "predictive modeling algorithm", "meta": { "definition": { "val": "Predictive modeling algorithm is a data mining algorithm that solves a predictive modeling task and as a result produces a predictive model." } }, "type": "CLASS" }, { "id": "http://www.ontodm.com/OntoDM-core/OntoDM_000192", "lbl": "pattern discovery algorithm", "meta": { "definition": { "val": "Pattern discovery algorithm is a data mining algorithm that solves a pattern discovery task and as a result produces a set of patterns." } }, "type": "CLASS" }, { "id": "http://www.ontodm.com/OntoDM-core/OntoDM_000228", "lbl": "predictive model specification", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", "val": "OntoDM" } ], "definition": { "val": "Predictive model specification is a single generalization specification and denotes a type of generalization that represents a mapping taking objects of type Td and returns objects of type To." } }, "type": "CLASS" }, { "id": "http://www.ontodm.com/OntoDM-core/OntoDM_000235", "lbl": "predictive modeling task", "meta": { "comments": [ "Learning a (Probabilistic) Predictive Model. In this task, we are given\na dataset that consists of examples of the form (d, c), where each d is of type\nTd and each c is of type Tc. We will refer to d as the description and c as the\nclass or target. To learn a predictive model means to find a mapping from the\ndescription to the target, m :: Td → Tc, that fits the data closely. This means\nthat the observed target values and the target values predicted by the model,\ni.e., c and ˆc = m(d), have to match closely." ] }, "type": "CLASS" }, { "id": "http://www.ontodm.com/OntoDM-core/OntoDM_000264", "lbl": "clustering task", "meta": { "comments": [ "Clustering. Clustering in general is concerned with grouping objects into classes\nof similar objects (Kaufman and Rousseeuw 1990). Given a set of examples (object\ndescriptions), the task of clustering is to partition these examples into subsets,\ncalled clusters." ] }, "type": "CLASS" }, { "id": "http://www.ontodm.com/OntoDM-core/OntoDM_000285", "lbl": "probability distribution specification", "meta": { "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000119", "val": "OntoDM" } ], "definition": { "val": "A probability distribution specification is a single generalization specification and denotes a type of generalization that is a mapping from objects of type T to non-negative reals. 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