DO Ontology files in the DiseaseOntology/HumanDiseaseOntology/src/ontology directory

DO production work, conducted by the University of Maryland team, is done on the

doid-edit.owl file.

The DO team will update the other files in this directly on a bi-weekly basis

as part of our DO release. This creates several OWL and OBO version of DO.

The DO project produces BOTH our traditional single parentage ontology (based on disease etiology) as well as a

logically defined multiple parentage ontology (since 2015), which builds on DO's disease etiology classification providing multiple parentage

defined by the anatomical location of the disease and cell type of origin through extensive logical definitions based on OBO Foundry

ontologies.

DO Single Parentage ontology.

The DO's disease classification is represented as both a single is_a hierarchy (doid-non-classified.obo).

This file is equivalent to DO's HumanDO.obo file. We will continue to produce both files as the HumanDO naming

schema was utilized and published for the first decade of the project.

Multi-parent Disease Classification in DO

DO's logically inferred multiple parentage classification is produced as our doid.owl file.

This file integrates logical definitions defining the anatomical location or cell or origin of a disease.

This README is to document and describe what is found in each file/set of files.

The DO production file was previously named: HumanDO.obo.

Previous versions of this are archived in DO's SVN directory.

In the current DO production environment, the HumanDO.obo and HumanDO.owl files are equivalent to the

doid-non-classified.obo and doid-non-classified.owl files produced in this GitHub repository.

DO Production Ontology Files:

doid-edit.owl : DO team editing environment

-- this file is ONLY edited by the DO team.

-- this file includes logical definitions to ontology files in the IMPORTS directory.

-- DO includes logical definition to:

Anatomy: UBERON; Cell type of origin: Cell Ontology (CL); Taxonomy: NCBITaxon;

Symptoms: Symptom Ontology: SYMP; Phenotype: Human Phenotype Ontology (HPO);

Transmission Process: Pathogen Transmission Methods (TRANS);

Sequence features: Sequence Ontology (SO); RO (Relations Ontology)

And are next adding:

FoodON: allergic triggers; CHEBI: chemical triggers/environmental triggers/drivers;

BRENDA tissue/ enzyme source (BTO): allergic triggers

DO data releases in GitHub: produces a suite of files.

(contain inferred links)

doid.obo : --Disease Ontology, OBO format. This file omits the equivalent axioms

doid.owl : --Disease Ontology, OWL format. This reasoned OWL file contains DO's is_a asserted hierarchy plus

equivalent axioms to other OBO Foundry ontologies.

<u>DO merged files</u>: created for the Alliance of Genome Resources (AGR) that includes OMIM to DO associations as xrefs plus defined relationships between OMIM susceptibility IDs and DO terms.

doid-merged.obo : includes the inferred branches, includes ontology imported.

doid-merged.owl : includes the inferred brances, includes ontology imported 'susceptibility to' OMIM terms.

(contain ONLY asserted links)

doid-non-classified.obo : DO's single asserted is_a hierarchy (HumanDO.obo), this file does not contain logical definitions

doid-non-classified.owl : DO's OWL version, of single asserted is_a hierarchy, this file does not contain logical definitions

DO files in the OBO Foundry:

OBO Foundry products:

- doid.owl: https://raw.githubusercontent.com/DiseaseOntology/HumanDiseaseOntology/master/src/ontology/doid.owl

- doid.obo: https://raw.githubusercontent.com/DiseaseOntology/HumanDiseaseOntology/master/src/ontology/doid.obo

DO Production Non-Ontology Files

- doid-idranges.owl

- ext.owl