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Curation Tools and Documentation

SPARQL

The "SPARQL Protocol and RDF Query Language" (SPARQL) enables semantic queries of the Disease Ontology database and data retrieval of customized datasets (upon request of DO Users) and reports utilized for Quality Control assessment, identification of targeted curation datasets and reporting of DO release statistics.

• DO SPARQL queries

Documentation

• Semantic Web
• SPARQL 1.1 Query Language
• The Cheatsheet

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

Websites for Browsing Other Medical Vocabularies

• GARD: https://rarediseases.info.nih.gov/diseases?category=&page=1&letter=&search=
• ICD-9-CM: 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://ncit.nci.nih.gov/ncitbrowser/pages/home.jsf
• NORD: https://rarediseases.org/rare-diseases/
• OMIM: https://www.omim.org
• Orphanet: https://www.orpha.net/consor/cgi-bin/Disease_Search.php?lng=EN
• SNOMED CT: https://browser.ihtsdotools.org/?perspective=full&edition=MAIN&languages=en
• UMLS: https://uts.nlm.nih.gov/uts/umls/home (requires account)

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.