Empowering disease knowledge representation with the Disease Ontology Knowledgebase (DO-KB) J. Allen Baron, Mike Schor, Claudia Sanchez-Beato Johnson, Lynn Schriml Institute for Genome Sciences, University of Maryland School of Medicine. Let’s talk: allenbaron@som.umaryland.edu ... or msg me on the conf app! A Global Core Biodata Resource As a recognized Global Core Biodata Resource (GCBR) the Human Disease Ontology Knowledgebase is: “[O]f fundamental importance to the wider biological and life sciences community and the long term preservation of biological data.” The DO-KB and ~ 400 biomedical resources & databases are powered by the disease data and relationships in the Human Disease Ontology (DO), including many of the genomic databases at TAGC. The Disease Ontology Knowledgebase: Tools powered by data from the Human Disease See how the Alliance of Genome Resources uses the DO to organize links from alleles, genes, and models to diseases. Example: DOID:0050117 disease by infectious agent Other biomedical and genomic resources that use the DO include Reactome, CIViC and the Common Fund Data Ecosystem, along with a number of the Common Fund programs it collects data from. The DO is used for research in a variety of fields. The number publications citing a DO publication by field are shown. Courtesy lens.org. doi:10.6084/m9.figshare.25320946 TAGC disease presentations -- What could have been... Want to find all the presentations at TAGC 2024 related to neurodegenerative disease without searching for each individually? Tagging presentations with diseases from the Disease Ontology could have made that possible, as this figure shows. A larger version of this figure with presentation program numbers colored by type (poster, talk, etc.) is available on figshare to make it easier to find TAGC24 presentations by disease. Dashed lines represent simplified relationships (intermediate diseases removed). 567T - Homology and Disease curation at Saccharomyces Genome Database: Budding yeast as a model for eukaryotic biology - Stacia R Engel, et al 594F - Xenbase: latest support for genomics and disease models - Malcolm Fisher, et al Alliance presentations with the DO NIH/NHGRI U24-HG012557 NIH/NHGRI U41-HG008735 Funded by FAIR & TRUST For a detailed look at how the DO makes data FAIR-er and is managed to ensure TRUST, check out our recent poster from Rare Disease Day at NIH. doi: 10.6084/m9.figshare.25292731 Using the SPARQL query language and the DO Sandbox or endpoint it’s possible to query diffuse data across the web. Data can be pulled to or from the DO. For example, add synonyms from MeSH to the DO, hierarchically organize the disease- linked proteins in UniProt, and more. disease-ontology.org OBO & OWL Tree Browsers with (Advanced) Search DO-KB SPARQL Sandbox & Endpoint DO-KB Faceted Search Interface DO-KB SPARQL sandbox: https://disease-ontology.org/do-kb/sparql DO-KB SPARQL endpoint: https://sparql.disease-ontology.org/ SPARQL info: https://www.w3.org/TR/sparql11-query/ The browser and basic or advanced searches can be used to look up information. The OBO tree is limited to diseases, while the OWL tree includes semantically-linked terms from other ontologies. The tree selected affects basic search results. The Human Disease Ontology (DO) is an expertly curated, etiological disease classification written in OWL/RDF (Web Ontology Language). The DO has 37,000 vocabulary mappings to authoritative biomedical resources (OMIM, Orphanet, etc.) and semantically integrates disease features like inheritance, phenotypes, chemical and environmental drivers, anatomy, and infectious agents. The Human Disease Ontology Knowledgebase (DO-KB) comprises the data in the DO and the tools at disease-ontology.org that make that data easier to search or expand interoperability. Think simple! All eye diseases that involve inflammation... yep! This is just one more possible application of the DO. Enjoy the conference!