Internationalized Resource Identifiers (IRIs), Ontologies, and External Links
The IEDB uses Internationalized Resource Identifiers (IRIs), ontologies and external links as a way to be machine-readable, interoperable, and integrated into other overlapping public resources.
Internationalized Resource Identifiers (IRIs)
The results of website queries can be exported with or without IRIs, which are stable links to the formal identifiers for data elements. Most IRIs used by the IEDB are for ontology terms. Descriptions of the ontologies used are described below.
Internal IEDB specific IRIs can be found throughout the details pages and in the exports. They are stable and can be used for IEDB LinkOuts.
Epitope - IEDB IRI links directly to a single epitope structure and all of its data derived from all references having experiments specific to that epitope.
Assay ID - IEDB IRI links directly to a single assay.
Reference - IEDB IRI links directly to a single publication or submission with links to all of its epitopes and assays.
Ontologies
We link the terms used to annotate experimental data to Open Biological and Biomedical Ontology (OBO) Foundry ontologies.
Ontologies exist in different domains to provide formal representation, terminologies, definitions, synonyms and relationships between terms.
Chemical Entities of Biological Interest (ChEBI)
ChEBI is a manually curated database and ontology of chemical entities which is used to describe nonpeptidic epitopes and epitope related objects, and the link to these terms will appear on the epitope details pages and in the exports as the Epitope IRI and Related Object IRI.ChEBI is also used for non-peptidic immunogens and antigens in the assay details pages and in assay exports.
The National Center for Biotechnology Information (NCBI) Taxonomy includes organism names and classifications that are determined to be nomenclaturally correct. NCBI taxonmy is used to identify organisms throughout IEDB data and will be seen on epitope and assay details pages, as well as in the exports. The links to these terms is shown as the Epitope Source Organism IRI and Host IRI. Immunogen and antigen organisms in assays will also use NCBI taxonomy.
Gazetteer (Gaz) is a large, ontologically-oriented resource listing place names which can be treated as instances of environments. The IEDB uses Gaz for the location of hosts at the time of their immune exposures and can be seen on the assay details pages and in the assay exports. These identifiers appear as the Host Geolocation IRI.
Disease Ontology (DO) is an open-source ontology that serves as a genomic resource for the integration of biomedical data associated with human disease, disease features and mechanisms. DO is used in the assay details pages and in the exports to depict diseases relevant to the adaptive immune reponse. DO links are shown as the Disease IRI.
Cells are captured using either the Cell Ontology (CL) or the Cell Line Ontology (CLO). CL is an OBO Foundry ontology covering the domain of canonical, natural biological cell types. CLO is an ontology used to standardize and integrate cell line information and to support computer-assisted reasoning. The IRIs for these terms can be found on the assay deatils pages and in the exports as the in vitro Responder Cell IRI, in vitro Stimulator Cell IRI, Effector Cell IRI, or Antigen Presenting Cell IRI. Additionally, when cells are used as immunogens or antigens in assays, these same identifiers are used.
Ontology for Biomedical Investigations (OBI) covers scientific investigations by defining more than 2500 terms for assays, devices, objectives, and more. The IEDB links all assay types to OBI terms via their Assay IRI.
Uberon multi-species anatomy ontology (Uberon), an integrated cross-species anatomy ontology covering animals and bridging multiple species-specific ontologies is used to describe tissue types. The IRIs for these terms and are found on the asasy details pages and in the exports as the Effector Cell Source Tissue IRI, Antigen Presenting Cell Source Tissue IRI, and also as the IRIs for tissues when they are used as immunogens or antigens.
MHC Restriction Ontology (MRO), an ontology for Major Histocompatibility Complex (MHC) restriction in experiments, is used for MHC terms in T cell and MHC assay details and their exports, linked via the MHC Restriction IRI.
Evidence and Conclusion Ontology (ECO) is an ontology for experimental and other evidence statements. ECO is used as evidence for MHC restriction in T cell assays and for MHC identity in MHC elution assays, with their IRIs displayed as the MHC Restriction Evidence IRI.
External Links
We seek out overlapping public resources in order to link shared data or add external value to both projects.
When applicable, non-peptidic epitopes will have link outs to GlyTouCan and/or PubChem at the bottom of the epitope details page in the EXTERNAL RESOURCES table.
GlyTouCan is the international glycan structure repository.
PubChem® is the world’s largest collection of freely accessible chemical information.
Proteins in the IEDB are described using UniProt, GenPept, or PDB entries. Through these links, we gain synonyms, amino acid sequences, and organism links. These accessions are found on the assay details pages and in the assay exports as the Epitope Source Molecule IRI. Additionally, we use UniProt reference proteomes to group protein isoforms. These entries appear in the Epitope Source Antigen query Finder, on the result tables, and as the Soure Molecule Parent IRIs in the exports. The UniProt entries serve as the basis for the Antigen pages, provide synonyms, and links to the Protein Ontology (PRO) and to iPTMnet. These links also enable IEDB annotations to be propogated to UniProt entries.
iPTMnet is a bioinformatics resource for integrated understanding of protein post-translational modifications (PTMs) in systems biology context.
PRO provides an ontological representation of protein-related entities by explicitly defining them and showing the relationships between them.
When applicable, links to PRO and/or iPTMnet can be found at the bottom of the Antigen summary page in the EXTERNAL RESOURCES table.
When the data in an IEDB record is present in another resource, we provide alternate IRIs that link to the ther projects housing the data. Examples are datasets submitted in the PRIDE database.
The PRIDE PRoteomics IDEntifications (PRIDE) Archive database is a centralized, standards compliant, public data repository for mass spectrometry proteomics data, including protein and peptide identifications and the corresponding expression values, post-translational modifications and supporting mass spectra evidence (both as raw data and peak list files).
Alternate IRIs are located on the Reference details pages and in the data export of the References tab.