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 Ontology for Immune Epitopes

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Showing 100 results starting at 0. Download as TSV.

IRIlabelobsoletereplacement
http://purl.obolibrary.org/obo/BFO_0000015process
http://purl.obolibrary.org/obo/GO_0008150biological process
http://purl.obolibrary.org/obo/IAO_0000030information content entity
http://purl.obolibrary.org/obo/IAO_0000112example of usage
http://purl.obolibrary.org/obo/IAO_0000115definition
http://purl.obolibrary.org/obo/IAO_0000118alternative term
http://purl.obolibrary.org/obo/IAO_0000232curator note
http://purl.obolibrary.org/obo/IAO_0100001replacement
http://purl.obolibrary.org/obo/NCBITaxon_10009Tamiasciurus hudsonicus
http://purl.obolibrary.org/obo/NCBITaxon_10036Mesocricetus auratus
http://purl.obolibrary.org/obo/NCBITaxon_1006061Duck hepatitis A virus 1
http://purl.obolibrary.org/obo/NCBITaxon_1006063Duck hepatitis A virus 3
http://purl.obolibrary.org/obo/NCBITaxon_10090Mus musculus
http://purl.obolibrary.org/obo/NCBITaxon_10116Rattus norvegicus
http://purl.obolibrary.org/obo/NCBITaxon_10141Cavia porcellus
http://purl.obolibrary.org/obo/NCBITaxon_10239Viruses
http://purl.obolibrary.org/obo/NCBITaxon_10243Cowpox virus
http://purl.obolibrary.org/obo/NCBITaxon_10244Monkeypox virus
http://purl.obolibrary.org/obo/NCBITaxon_10245Vaccinia virus
http://purl.obolibrary.org/obo/NCBITaxon_10255Variola virus
http://purl.obolibrary.org/obo/NCBITaxon_102793H5N1 subtype
http://purl.obolibrary.org/obo/NCBITaxon_102796H9N2 subtype
http://purl.obolibrary.org/obo/NCBITaxon_102801H10N7 subtype
http://purl.obolibrary.org/obo/NCBITaxon_102862Proteus penneri
http://purl.obolibrary.org/obo/NCBITaxon_10298Human alphaherpesvirus 1
http://purl.obolibrary.org/obo/NCBITaxon_10306Human herpesvirus 1 strain KOS
http://purl.obolibrary.org/obo/NCBITaxon_10310Human alphaherpesvirus 2
http://purl.obolibrary.org/obo/NCBITaxon_10320Bovine alphaherpesvirus 1
http://purl.obolibrary.org/obo/NCBITaxon_10326Equid alphaherpesvirus 1
http://purl.obolibrary.org/obo/NCBITaxon_10331Equid alphaherpesvirus 4
http://purl.obolibrary.org/obo/NCBITaxon_10335Human alphaherpesvirus 3
http://purl.obolibrary.org/obo/NCBITaxon_10345Suid alphaherpesvirus 1
http://purl.obolibrary.org/obo/NCBITaxon_10359Human betaherpesvirus 5
http://purl.obolibrary.org/obo/NCBITaxon_10366Murid betaherpesvirus 1
http://purl.obolibrary.org/obo/NCBITaxon_10367Murine cytomegalovirus (strain Smith)
http://purl.obolibrary.org/obo/NCBITaxon_10372Human betaherpesvirus 7
http://purl.obolibrary.org/obo/NCBITaxon_10376Human gammaherpesvirus 4
http://purl.obolibrary.org/obo/NCBITaxon_10407Hepatitis B virus
http://purl.obolibrary.org/obo/NCBITaxon_10432Woodchuck hepatitis virus 7
http://purl.obolibrary.org/obo/NCBITaxon_104388Anatid herpesvirus 1
http://purl.obolibrary.org/obo/NCBITaxon_10497African swine fever virus
http://purl.obolibrary.org/obo/NCBITaxon_10515Human adenovirus 2
http://purl.obolibrary.org/obo/NCBITaxon_10566Human papillomavirus
http://purl.obolibrary.org/obo/NCBITaxon_10586Human papillomavirus type 33
http://purl.obolibrary.org/obo/NCBITaxon_10600Human papillomavirus type 6b
http://purl.obolibrary.org/obo/NCBITaxon_10623Kappapapillomavirus 2
http://purl.obolibrary.org/obo/NCBITaxon_10632JC polyomavirus
http://purl.obolibrary.org/obo/NCBITaxon_10788Canine parvovirus
http://purl.obolibrary.org/obo/NCBITaxon_10796Porcine parvovirus
http://purl.obolibrary.org/obo/NCBITaxon_10798Human parvovirus B19
http://purl.obolibrary.org/obo/NCBITaxon_108098Human mastadenovirus B
http://purl.obolibrary.org/obo/NCBITaxon_10941Human rotavirus A
http://purl.obolibrary.org/obo/NCBITaxon_10969Rhesus rotavirus
http://purl.obolibrary.org/obo/NCBITaxon_10995Infectious bursal disease virus
http://purl.obolibrary.org/obo/NCBITaxon_110195Foot-and-mouth disease virus - type Asia 1
http://purl.obolibrary.org/obo/NCBITaxon_11021Eastern equine encephalitis virus
http://purl.obolibrary.org/obo/NCBITaxon_11033Semliki Forest virus
http://purl.obolibrary.org/obo/NCBITaxon_11034Sindbis virus
http://purl.obolibrary.org/obo/NCBITaxon_11036Venezuelan equine encephalitis virus
http://purl.obolibrary.org/obo/NCBITaxon_11039Western equine encephalitis virus
http://purl.obolibrary.org/obo/NCBITaxon_11041Rubella virus
http://purl.obolibrary.org/obo/NCBITaxon_11048Lactate dehydrogenase-elevating virus
http://purl.obolibrary.org/obo/NCBITaxon_11049Lelystad virus
http://purl.obolibrary.org/obo/NCBITaxon_11053Dengue virus 1
http://purl.obolibrary.org/obo/NCBITaxon_11060Dengue virus 2
http://purl.obolibrary.org/obo/NCBITaxon_11069Dengue virus 3
http://purl.obolibrary.org/obo/NCBITaxon_11070Dengue virus 4
http://purl.obolibrary.org/obo/NCBITaxon_11072Japanese encephalitis virus
http://purl.obolibrary.org/obo/NCBITaxon_11073Japanese encephalitis virus strain SA-14
http://purl.obolibrary.org/obo/NCBITaxon_11077Kunjin virus
http://purl.obolibrary.org/obo/NCBITaxon_11080St. Louis encephalitis virus
http://purl.obolibrary.org/obo/NCBITaxon_11082West Nile virus
http://purl.obolibrary.org/obo/NCBITaxon_11084Tick-borne encephalitis virus
http://purl.obolibrary.org/obo/NCBITaxon_11088Tick-borne encephalitis virus (WESTERN SUBTYPE)
http://purl.obolibrary.org/obo/NCBITaxon_11089Yellow fever virus
http://purl.obolibrary.org/obo/NCBITaxon_11096Classical swine fever virus
http://purl.obolibrary.org/obo/NCBITaxon_11099Bovine viral diarrhea virus 1
http://purl.obolibrary.org/obo/NCBITaxon_11103Hepatitis C virus
http://purl.obolibrary.org/obo/NCBITaxon_11120Infectious bronchitis virus
http://purl.obolibrary.org/obo/NCBITaxon_11128Bovine coronavirus
http://purl.obolibrary.org/obo/NCBITaxon_11135Feline infectious peritonitis virus
http://purl.obolibrary.org/obo/NCBITaxon_11138Murine hepatitis virus
http://purl.obolibrary.org/obo/NCBITaxon_11149Transmissible gastroenteritis virus
http://purl.obolibrary.org/obo/NCBITaxon_11151Porcine transmissible gastroenteritis coronavirus strain Purdue
http://purl.obolibrary.org/obo/NCBITaxon_11176Newcastle disease virus
http://purl.obolibrary.org/obo/NCBITaxon_11191Sendai virus
http://purl.obolibrary.org/obo/NCBITaxon_11232Canine distemper virus
http://purl.obolibrary.org/obo/NCBITaxon_11234Measles virus
http://purl.obolibrary.org/obo/NCBITaxon_11240Phocine distemper virus
http://purl.obolibrary.org/obo/NCBITaxon_11241Rinderpest virus
http://purl.obolibrary.org/obo/NCBITaxon_11250Human respiratory syncytial virus
http://purl.obolibrary.org/obo/NCBITaxon_11292Rabies lyssavirus
http://purl.obolibrary.org/obo/NCBITaxon_11303Bovine ephemeral fever virus
http://purl.obolibrary.org/obo/NCBITaxon_11320Influenza A virus
http://purl.obolibrary.org/obo/NCBITaxon_114727H1N1 subtype
http://purl.obolibrary.org/obo/NCBITaxon_114728H1N2 subtype
http://purl.obolibrary.org/obo/NCBITaxon_114732H2N8 subtype
http://purl.obolibrary.org/obo/NCBITaxon_114742Pythium insidiosum
http://purl.obolibrary.org/obo/NCBITaxon_11520Influenza B virus
http://purl.obolibrary.org/obo/NCBITaxon_11588Rift Valley fever virus