IEDB Source of Truth

SoT is a system for dynamically creating, maintaining, and sharing an application ontology that builds on multiple reference resources. A reference resource could be a reference ontology such as OBI, or a similar non-ontological resource such as UniProt. We intend for the SoT system to be general, but the primary goal is to serve projects at LJI, including IEDB, LabKey database for HIPC and DORAS, TopCat, and Bioinformatics Core.

The core of SoT is an application ontology (ONTIE) with its own terms and axioms. ONTIE builds on reference resources including NCBI Taxonomy, MRO, OBI, UniProt, and GenPept. We reuse terms from reference resources as much as possible, but when this is not possible we add terms to ONTIE. Examples include taxa not in NCBI Taxonomy, and proteins not in GenPept. New terms can be added to ONTIE immediately, and will be maintained indefinitely. However, if a better term is found in a reference ontology, the ONTIE term will be marked obsolete and mapped to the reference term.

Each reference resource is pulled in and validated using an importer module. Specific versions of reference resources are used, and updates to reference resources are carefully checked for terms that have been dropped, added, merged, or had their logic changed.

Users can search, browse, and query SoT (i.e. the union of ONTIE and the reference resources) using a uniform web-based interface and API.

SoT consumers such as IEDB will usually have their own internal identifiers for terms, but must keep track of the IRIs for the terms they use from SoT. They can then query SoT using IRIs, ask whether the IRIs have been mapped to new IRIs, and get tables of data for those terms. Consumers can send their users to SoT to find and request terms, but the consumer is responsible for maintaining and displaying terms, local versions of labels and synonyms, and tree structure.

SoT is public and does not contain secret or confidential information. Unauthenticated users can browse and search for terms. Authenticated users can request new terms by selecting a term template and filling in the required information. If SoT can validate that information, it immediately creates a new ONTIE term and provides the user with the new IRI.

A secondary goal of SoT is to demonstrate tight integration across OBO Foundry ontologies. We intend for ONTIE to have a single, integrated and logically-consistent hierarchy, with a unified set of OWL annotation properties and object properties. The term creation and management aspect of SoT may also serve as a good example of how term request can percolate up from specific use-cases to community reference ontologies, while keeping the originating application ontology and annotated datasets in sync.

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Subjects for All Resources

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IRIlabelobsoletereplacement
http://example.com/bfo-spec-label
http://iedb.org/has-sort-name
http://protege.stanford.edu/plugins/owl/protege#defaultLanguage
http://purl.obolibrary.org/obo/BFO_0000001entity
http://purl.obolibrary.org/obo/BFO_0000002continuant
http://purl.obolibrary.org/obo/BFO_0000003occurrent
http://purl.obolibrary.org/obo/BFO_0000004independent continuant
http://purl.obolibrary.org/obo/BFO_0000005obsolete dependent continuanttrue
http://purl.obolibrary.org/obo/BFO_0000006spatial region
http://purl.obolibrary.org/obo/BFO_0000008temporal region
http://purl.obolibrary.org/obo/BFO_0000009two-dimensional spatial region
http://purl.obolibrary.org/obo/BFO_0000011spatiotemporal region
http://purl.obolibrary.org/obo/BFO_0000015process
http://purl.obolibrary.org/obo/BFO_0000016disposition
http://purl.obolibrary.org/obo/BFO_0000017realizable entity
http://purl.obolibrary.org/obo/BFO_0000018zero-dimensional spatial region
http://purl.obolibrary.org/obo/BFO_0000019quality
http://purl.obolibrary.org/obo/BFO_0000020specifically dependent continuant
http://purl.obolibrary.org/obo/BFO_0000023role
http://purl.obolibrary.org/obo/BFO_0000024fiat object|fiat object part
http://purl.obolibrary.org/obo/BFO_0000026one-dimensional spatial region
http://purl.obolibrary.org/obo/BFO_0000027object aggregate
http://purl.obolibrary.org/obo/BFO_0000028three-dimensional spatial region
http://purl.obolibrary.org/obo/BFO_0000029site
http://purl.obolibrary.org/obo/BFO_0000030object
http://purl.obolibrary.org/obo/BFO_0000031generically dependent continuant
http://purl.obolibrary.org/obo/BFO_0000034function
http://purl.obolibrary.org/obo/BFO_0000035process boundary
http://purl.obolibrary.org/obo/BFO_0000038one-dimensional temporal region
http://purl.obolibrary.org/obo/BFO_0000040material entity
http://purl.obolibrary.org/obo/BFO_0000050part of
http://purl.obolibrary.org/obo/BFO_0000051has part
http://purl.obolibrary.org/obo/BFO_0000054realized in
http://purl.obolibrary.org/obo/BFO_0000055realizes
http://purl.obolibrary.org/obo/BFO_0000062preceded by
http://purl.obolibrary.org/obo/BFO_0000063precedes
http://purl.obolibrary.org/obo/BFO_0000066occurs in
http://purl.obolibrary.org/obo/BFO_0000067contains process
http://purl.obolibrary.org/obo/BFO_0000134
http://purl.obolibrary.org/obo/BFO_0000140continuant fiat boundary
http://purl.obolibrary.org/obo/BFO_0000141immaterial entity
http://purl.obolibrary.org/obo/BFO_0000142one-dimensional continuant fiat boundary
http://purl.obolibrary.org/obo/BFO_0000144process profile
http://purl.obolibrary.org/obo/BFO_0000145relational quality
http://purl.obolibrary.org/obo/BFO_0000146two-dimensional continuant fiat boundary
http://purl.obolibrary.org/obo/BFO_0000147zero-dimensional continuant fiat boundary
http://purl.obolibrary.org/obo/BFO_0000148zero-dimensional temporal region
http://purl.obolibrary.org/obo/BFO_0000179BFO OWL specification label
http://purl.obolibrary.org/obo/BFO_0000180BFO CLIF specification label
http://purl.obolibrary.org/obo/BFO_0000182history
http://purl.obolibrary.org/obo/CHEBI_1truehttp://purl.obolibrary.org/obo/CHEBI_18357
http://purl.obolibrary.org/obo/CHEBI_10(+)-Atherospermoline
http://purl.obolibrary.org/obo/CHEBI_100(-)-medicarpin
http://purl.obolibrary.org/obo/CHEBI_1000truehttp://purl.obolibrary.org/obo/CHEBI_16713
http://purl.obolibrary.org/obo/CHEBI_10000Vismione D
http://purl.obolibrary.org/obo/CHEBI_100000(2S,3S,4R)-3-[4-(3-cyclopentylprop-1-ynyl)phenyl]-4-(hydroxymethyl)-1-(2-methoxy-1-oxoethyl)-2-azetidinecarbonitrile
http://purl.obolibrary.org/obo/CHEBI_100001N-[(2R,3S,6R)-2-(hydroxymethyl)-6-[2-[[oxo-[4-(trifluoromethyl)anilino]methyl]amino]ethyl]-3-oxanyl]-3-pyridinecarboxamide
http://purl.obolibrary.org/obo/CHEBI_1000023-chloro-N-[(5S,6S,9S)-5-methoxy-3,6,9-trimethyl-2-oxo-11-oxa-3,8-diazabicyclo[10.4.0]hexadeca-1(12),13,15-trien-14-yl]benzenesulfonamide
http://purl.obolibrary.org/obo/CHEBI_100003(4R,7S,8R)-8-methoxy-4,7,10-trimethyl-11-oxo-14-(1-oxobutylamino)-N-propyl-2-oxa-5,10-diazabicyclo[10.4.0]hexadeca-1(12),13,15-triene-5-carboxamide
http://purl.obolibrary.org/obo/CHEBI_1000041-(2,5-difluorophenyl)-3-[(5S,6S,9S)-5-methoxy-3,6,9-trimethyl-2-oxo-8-[oxo(2-pyrazinyl)methyl]-11-oxa-3,8-diazabicyclo[10.4.0]hexadeca-1(12),13,15-trien-14-yl]urea
http://purl.obolibrary.org/obo/CHEBI_100005N-[(1S,3S,4aS,9aR)-1-(hydroxymethyl)-3-[2-oxo-2-(1-piperidinyl)ethyl]-3,4,4a,9a-tetrahydro-1H-pyrano[3,4-b]benzofuran-6-yl]-3-methoxybenzenesulfonamide
http://purl.obolibrary.org/obo/CHEBI_100006N-(1,3-benzodioxol-5-ylmethyl)-2-[(2R,3R,6S)-3-[[(2,5-difluoroanilino)-oxomethyl]amino]-2-(hydroxymethyl)-3,6-dihydro-2H-pyran-6-yl]acetamide
http://purl.obolibrary.org/obo/CHEBI_100007LSM-11386
http://purl.obolibrary.org/obo/CHEBI_100008(2R,3R,4R)-1-[1,3-benzodioxol-5-yl(oxo)methyl]-4-(hydroxymethyl)-3-phenyl-2-azetidinecarbonitrile
http://purl.obolibrary.org/obo/CHEBI_100009(2R,3S,4S)-1-(4-fluorophenyl)sulfonyl-4-(hydroxymethyl)-3-phenyl-2-azetidinecarbonitrile
http://purl.obolibrary.org/obo/CHEBI_10001Visnadin
http://purl.obolibrary.org/obo/CHEBI_100010N-[(5S,6S,9S)-5-methoxy-3,6,9-trimethyl-2-oxo-8-(2-phenylethyl)-11-oxa-3,8-diazabicyclo[10.4.0]hexadeca-1(12),13,15-trien-14-yl]propanamide
http://purl.obolibrary.org/obo/CHEBI_1000112-[(3R,6aR,8R,10aR)-1-[(4-fluorophenyl)-oxomethyl]-3-hydroxy-3,4,6,6a,8,9,10,10a-octahydro-2H-pyrano[2,3-c][1,5]oxazocin-8-yl]-1-(1-piperidinyl)ethanone
http://purl.obolibrary.org/obo/CHEBI_100012N-[(2R,4aR,12aR)-2-[2-(cyclohexylmethylamino)-2-oxoethyl]-5-methyl-6-oxo-2,3,4,4a,12,12a-hexahydropyrano[2,3-c][1,5]benzoxazocin-8-yl]-2-pyrazinecarboxamide
http://purl.obolibrary.org/obo/CHEBI_1000132-[(2S,4aR,12aS)-8-(ethylcarbamoylamino)-5-methyl-6-oxo-2,3,4,4a,12,12a-hexahydropyrano[2,3-c][1,5]benzoxazocin-2-yl]-N-[(1S)-1-phenylethyl]acetamide
http://purl.obolibrary.org/obo/CHEBI_100014N-[(4S,7R,8R)-8-methoxy-4,7,10-trimethyl-11-oxo-2-oxa-5,10-diazabicyclo[10.4.0]hexadeca-1(12),13,15-trien-14-yl]-3,5-dimethyl-4-isoxazolesulfonamide
http://purl.obolibrary.org/obo/CHEBI_100015N-[(4-chlorophenyl)methyl]-2-[(2S,3R,6R)-2-(hydroxymethyl)-3-[(2-methoxy-1-oxoethyl)amino]-3,6-dihydro-2H-pyran-6-yl]acetamide
http://purl.obolibrary.org/obo/CHEBI_1000162-[(3R,6aR,8S,10aR)-3-hydroxy-1-(pyridin-4-ylmethyl)-3,4,6,6a,8,9,10,10a-octahydro-2H-pyrano[2,3-c][1,5]oxazocin-8-yl]-N-ethylacetamide
http://purl.obolibrary.org/obo/CHEBI_1000172-[(1R,3S,4aR,9aS)-1-(hydroxymethyl)-6-[(1-oxo-2-pyridin-4-ylethyl)amino]-3,4,4a,9a-tetrahydro-1H-pyrano[3,4-b]benzofuran-3-yl]-N-(2-pyridinylmethyl)acetamide
http://purl.obolibrary.org/obo/CHEBI_100018(3S)-2-tert-butylsulfinyl-4-[3-(3-fluorophenyl)phenyl]-3-(2-hydroxyethyl)-N-[3-(4-morpholinyl)propyl]-1,3-dihydropyrrolo[3,4-c]pyridine-6-carboxamide
http://purl.obolibrary.org/obo/CHEBI_1000191-[(2S,3R,6R)-2-(hydroxymethyl)-6-[2-[4-(methoxymethyl)-1-triazolyl]ethyl]-3-oxanyl]-3-[4-(trifluoromethyl)phenyl]urea
http://purl.obolibrary.org/obo/CHEBI_10002visnagin
http://purl.obolibrary.org/obo/CHEBI_1000202-[(2R,3S,6S)-2-(hydroxymethyl)-3-[[1-oxo-2-(2-pyridinyl)ethyl]amino]-3,6-dihydro-2H-pyran-6-yl]-N-[(1S)-1-phenylethyl]acetamide
http://purl.obolibrary.org/obo/CHEBI_100021N-[(2R,4aR,12aS)-2-[2-(3,4-dihydro-1H-isoquinolin-2-yl)-2-oxoethyl]-5-methyl-6-oxo-2,3,4,4a,12,12a-hexahydropyrano[2,3-c][1,5]benzoxazocin-8-yl]-3-fluorobenzenesulfonamide
http://purl.obolibrary.org/obo/CHEBI_100022N-[(1S,3R,4aR,9aS)-1-(hydroxymethyl)-3-[2-oxo-2-(3-pyridinylmethylamino)ethyl]-3,4,4a,9a-tetrahydro-1H-pyrano[3,4-b]benzofuran-6-yl]-1,3-benzodioxole-5-carboxamide
http://purl.obolibrary.org/obo/CHEBI_100023N-[(5R,6S,9R)-5-methoxy-3,6,9-trimethyl-2-oxo-8-(2-phenylethyl)-11-oxa-3,8-diazabicyclo[10.4.0]hexadeca-1(12),13,15-trien-14-yl]propanamide
http://purl.obolibrary.org/obo/CHEBI_100024(2S,3S,4R)-2-cyano-3-[4-(2-cyclohexylethynyl)phenyl]-4-(hydroxymethyl)-N-propan-2-yl-1-azetidinecarboxamide
http://purl.obolibrary.org/obo/CHEBI_100025LSM-11404
http://purl.obolibrary.org/obo/CHEBI_1000262-[(1R,3R,4aR,9aS)-1-(hydroxymethyl)-6-[[(4-methoxyanilino)-oxomethyl]amino]-3,4,4a,9a-tetrahydro-1H-pyrano[3,4-b]benzofuran-3-yl]-N-cyclohexylacetamide
http://purl.obolibrary.org/obo/CHEBI_1000272-[(2R,4aS,12aS)-8-[[(3,5-dimethylanilino)-oxomethyl]amino]-5-methyl-6-oxo-2,3,4,4a,12,12a-hexahydropyrano[2,3-c][1,5]benzoxazocin-2-yl]acetic acid methyl ester
http://purl.obolibrary.org/obo/CHEBI_100028N-[(1R,3S,4aS,9aR)-1-(hydroxymethyl)-3-[2-oxo-2-[[(1R)-1-phenylethyl]amino]ethyl]-3,4,4a,9a-tetrahydro-1H-pyrano[3,4-b]benzofuran-6-yl]-1,3-benzodioxole-5-carboxamide
http://purl.obolibrary.org/obo/CHEBI_1000292-[(3S,6aR,8R,10aR)-3-hydroxy-1-[oxo(3-pyridinyl)methyl]-3,4,6,6a,8,9,10,10a-octahydro-2H-pyrano[2,3-c][1,5]oxazocin-8-yl]-N-(4-phenylphenyl)acetamide
http://purl.obolibrary.org/obo/CHEBI_10003ribostamycin sulfate
http://purl.obolibrary.org/obo/CHEBI_1000302-methoxy-N-[(4S,7R,8S)-8-methoxy-4,7,10-trimethyl-11-oxo-2-oxa-5,10-diazabicyclo[10.4.0]hexadeca-1(12),13,15-trien-14-yl]benzenesulfonamide
http://purl.obolibrary.org/obo/CHEBI_1000312-[(3S,6aS,8S,10aS)-1-[cyclopentyl(oxo)methyl]-3-hydroxy-3,4,6,6a,8,9,10,10a-octahydro-2H-pyrano[2,3-c][1,5]oxazocin-8-yl]-N,N-dimethylacetamide
http://purl.obolibrary.org/obo/CHEBI_100032(2S,3R,4R)-3-[4-[2-(3-fluorophenyl)ethynyl]phenyl]-4-(hydroxymethyl)-1-[4-oxanyl(oxo)methyl]-2-azetidinecarbonitrile
http://purl.obolibrary.org/obo/CHEBI_100033N-[(1R,3R,4aS,9aR)-1-(hydroxymethyl)-3-[2-oxo-2-[2-(1-piperidinyl)ethylamino]ethyl]-3,4,4a,9a-tetrahydro-1H-pyrano[3,4-b]benzofuran-6-yl]-3-pyridinecarboxamide
http://purl.obolibrary.org/obo/CHEBI_1000342-[(2S,5R,6R)-5-[(2-fluorophenyl)sulfonylamino]-6-(hydroxymethyl)-2-oxanyl]acetic acid methyl ester
http://purl.obolibrary.org/obo/CHEBI_100035LSM-11414
http://purl.obolibrary.org/obo/CHEBI_100036N-[(5R,6S,9R)-5-methoxy-8-(2-methoxy-1-oxoethyl)-3,6,9-trimethyl-2-oxo-11-oxa-3,8-diazabicyclo[10.4.0]hexadeca-1(12),13,15-trien-14-yl]-2-pyrazinecarboxamide
http://purl.obolibrary.org/obo/CHEBI_1000371-(3-fluorophenyl)-3-[(5S,6R,9R)-5-methoxy-3,6,9-trimethyl-2-oxo-11-oxa-3,8-diazabicyclo[10.4.0]hexadeca-1(12),13,15-trien-14-yl]urea
http://purl.obolibrary.org/obo/CHEBI_100038N-[(5R,6S,9R)-5-methoxy-3,6,9-trimethyl-2-oxo-11-oxa-3,8-diazabicyclo[10.4.0]hexadeca-1(12),13,15-trien-14-yl]-4-phenylbenzamide
http://purl.obolibrary.org/obo/CHEBI_1000392-[(2S,3R,6R)-2-(hydroxymethyl)-3-[[(3-methoxyanilino)-oxomethyl]amino]-3,6-dihydro-2H-pyran-6-yl]-N-(4-phenylphenyl)acetamide
http://purl.obolibrary.org/obo/CHEBI_10004truehttp://purl.obolibrary.org/obo/CHEBI_33229
http://purl.obolibrary.org/obo/CHEBI_100040LSM-11419