The Human Disease Ontology (DO) is a comprehensive classification of human disease represented in the semantic Web Ontology Language (OWL) that captures the relations between diseases (etiological, anatomical, etc.), incorporates descriptive disease features or factors, and cross maps to other disease vocabularies.

The Disease Ontology is the semantic data that describes diseases, while the DO-KB is an integrated data system, built upon the DO's semantic disease knowledge backbone, with resources that expose the DO's semantic knowledge and connects disease-related data across Open Linked Data resources on the web. The DO-KB comprises the DO web browser, a SPARQL service, and a faceted search.

The editor's version of the Disease Ontology (src/ontology/doid-edit.owl in the DO's GitHub repository) is updated continuously, while formal data releases occur monthly.

The DO files are documented in DO's GitHub in README_DO_Files.

The most up to date DO files can be downloaded from DO's GitHub repository, in the src/ontology directory.

Sadly, there is no one size fits all solution. However, the data are accessible in numerous ways so you can choose the one that works best for you.

• The full data are released on GitHub in multiple, standard ontology formats (refer to FAQs above).
• Some data are also released as tab-delimited files to enhance data accessibility. These are updated with each monthly release and available in the DOreports directory of the GitHub repository.
• The data are also accessible directly via a SPARQL endpoint (see the FAQ: "What can I do with DO-KB SPARQL service?").

Requests for new or revised data (terms, names/synonyms, definitions, mappings, etc.), suggestions and questions regarding the Disease Ontology can be submitted to the DO's Issue Tracker on GitHub.

The Disease Ontology browser (https://disease-ontology.org/do) is a web application that supports exploration of individual terms and the Disease Ontology as a whole. It includes two text-based tree/hierarchy views, individual term pages, search capabilities, and an expandable relationship visualizer. The text-based trees include an "OBO" tree, focused strictly on disease terms, and an "OWL" tree, that additionally includes imported disease-related terms used to describe diseases. Note that individual term page content may differ when opened depending on which tree is currently selected. Search capabilities include a default full text search over the whole ontology and an advanced search by disease name, synonym, definition, subset, DOID, alternative ID, Xrefs (disease vocabulary cross references), and logical relations, or some combination of these.

To search for DO metadata via our API, use the URL https://www.disease-ontology.org/api/metadata/. Note that this data is not as complete as the data in the production files.
Example:https://www.disease-ontology.org/api/metadata/DOID:4

Add an 'id' query with a DO identifier (DOID) to the website URL or use the term's persistent URL (PURL).
Examples:https://www.disease-ontology.org/?id=DOID:9256 http://purl.obolibrary.org/obo/DOID_9256

In the Advanced Search box, you can include multiple search terms to create a complex query, by clicking on "Add New Field" and specifying your Boolean query (AND, OR, NOT) from the Advanced Search menu.

The DO-KB SPARQL service is a server that implements the SPARQL Protocol and RDF Query Language specification. It includes the website-embedded SPARQL Sandbox, that can be used to edit and execute SPARQL queries against the DO and/or other disease-centric SPARQL endpoints across the internet, and a programmatic endpoint (https://sparql.disease-ontology.org/) that can be used in federated SPARQL queries submitted to other SPARQL servers that access the internet.

The DO-KB Faceted Search can be used to identify similar diseases by selecting values from one or more facets, with each facet including the disease-related terms imported from a specific ontology that are used to semantically define diseases (e.g. anatomy, phenotypes, taxonomy, etc.).

The Disease Ontology is designed around clinical terminology. The DO team has prepared a glossary of clinical terms to clarify difficult concepts.

When BFO was developed the biomedical ontology community discussed how to connect the DO and other ontologies that pre-date BFO, e.g. Gene Ontology (GO), with it. It was determined that single domain ontologies (DO being the OBO Foundry domain ontology for diseases) are interoperable with BFO and that diseases would be treated as BFO dispositions. Thus, DO's 'disease' class (DOID:4) should be considered a subclass of BFO's 'disposition' class (BFO:0000016).

When OGMS was created, they utilized the DO's 'disease' (DOID:4) to make an equivalent OGMS 'Disease' term (OGMS:0000031).