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Curation Tools and Documentation

Curation Guidelines

• DO Style Guide: Guidelines for defining new disease terms in the DO, cleaning up term format, creating and tracking provenance of definitions, and creating database cross-references (dbxrefs: one-to-one references to external clinical vocabulary resources).
• Design Patterns for Method of Inheritance: Outline of logical axioms for defining EquivalentTo and SubClassOf statements for DO genetic diseases, to define the mode of inheritance.
• DO merges FAQ: Guidelines for combining two disease terms.
• DO Cancer Nomenclature Definitions: A resource guide for devising cancer definitions including ontology browsers, authoritative sources for definitions, formatting examples and NCI cell type cancer definitions.
• DO Ticket Review Steps: Guidelines for creating new DO disease terms.
• Common Logical Axioms: Generic patterns for the most common equivalent class and subclass of logical axioms.

Websites for Browsing Other Medical Vocabularies

Disease Vocabularies

• GARD: https://rarediseases.info.nih.gov/diseases?category=&page=1&letter=&search=
• ICD-9-CM: https://www.aapc.com/codes/icd9-codes-range/ or http://icd9.chrisendres.com/index.php or http://www.icd9data.com
• ICD-10: https://icd.who.int/browse10/
• ICD-10-CM: https://icd10cmtool.cdc.gov or http://www.icd10data.com
• ICD-O: https://apps.who.int/iris/bitstream/handle/10665/96612/9789241548496_eng.pdf
• MeSH: https://meshb.nlm.nih.gov
• NCI Dictionary of Cancer Terms: https://www.cancer.gov/publications/dictionaries/cancer-terms
• NCI Thesaurus: https://evsexplore.semantics.cancer.gov/evsexplore/welcome?terminology=ncit
  • https://ncit.nci.nih.gov/ncitbrowser/pages/home.jsf prior to 2025
• NORD: https://rarediseases.org/rare-diseases/
• OMIM: https://www.omim.org
• Orphanet: https://www.orpha.net/consor/cgi-bin/Disease_Search.php?lng=EN
• SNOMEDCT US: https://browser.ihtsdotools.org/?perspective=full&edition=MAIN/SNOMEDCT-US&languages=en
• UMLS: https://uts.nlm.nih.gov/uts/umls/home (requires account)

Other Vocabularies

• ICTV: https://ictv.global/
• NCBI Taxonomy: https://www.ncbi.nlm.nih.gov/taxonomy

ROBOT

ROBOT is a powerful, command-line tool designed for Open Biomedical Ontologies. It was developed in collaboration with the DO team and designed to improve quality control, automated updates, reproducibility and interoperability.

• ROBOT homepage
• ROBOT in the DO project

SPARQL

The "SPARQL Protocol and RDF Query Language" (SPARQL) enables semantic queries of the Disease Ontology for retrieval of customized datasets (upon request of DO Users), quality control assessment, targeted curation datasets, and reporting of DO release statistics.

The DO team has created a library of SPARQL queries that can be found in the following GitHub repositories:

• Human Disease Ontology (in the src/sparql directory), to support creation and management of the ontology
• SPARQLqueries, provided as examples for the SPARQL Sandbox

SPARQL is a product of the World Wide Web Consortium (W3C). See the following sources for documentation:

• Semantic Web
• SPARQL 1.1 Query Language
• The Cheatsheet