Disease Ontology 2015 update: an expanded and updated database of human diseases for linking biomedical knowledge through disease data

By Warren A. Kibbe, Cesar Arze, V. Felix, Elvira Mitraka, Evan E. Bolton, Gang Fu, C. Mungall, Janos X. Binder, J. Malone, Drashtti Vasant and 2 more. Nucleic Acids Res., 2014

568 citations recorded by the source corpus.

The current version of the Human Disease Ontology (DO) (http://www.disease-ontology.org) database expands the utility of the ontology for the examination and comparison of genetic variation, phenotype, protein, drug and epitope data through the lens of human disease. DO is a biomedical resource of standardized common and rare disease concepts with stable identifiers organized by disease etiology. The content of DO has had 192 revisions since 2012, including the addition of 760 terms. Thirty-two percent of all terms now include definitions. DO has expanded the number and diversity of research communities and community members by 50+ during the past two years. These community members actively submit term requests, coordinate biomedical resource disease representation and provide expert curation guidance. Since the DO 2012 NAR paper, there have been hundreds of term requests and a steady increase in the number of DO listserv members, twitter followers and DO website usage. DO is moving to a multi-editor model utilizing Protégé to curate DO in web ontology language. This will enable closer collaboration with the Human Phenotype Ontology, EBI's Ontology Working Group, Mouse Genome Informatics and the Monarch Initiative among others, and enhance DO's current asserted view and multiple inferred views through reasoning.

Subfields: Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/d71926c313b8810af60fd632946202f462e1c9da

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Citations in the corpus

The Comparative Toxicogenomics Database: update 2017 (2016, methodology): “In 2015, CTD began analyzing and comparing the disease terms and hierarchical structure used in MEDIC against the newly established Disease Ontology (DO) (35), in an effort to coordinate MEDIC with this new resource.”
Open Targets: a platform for therapeutic target identification and validation (2016, methodology): “To enable this we have started mapping several existing ontologies like ORDO (Orphanet Rare Disease Ontology (24)), DO (disease ontology, (25)) and HPO (Human Phenotype Ontology,(26)) or widely-used terminologies like MeSH (http://www.”
MalaCards: an amalgamated human disease compendium with diverse clinical and genetic annotation and structured search (2016, background): “This is in contrast to the concept of ontology, an organizational system basically designed to portray the relationships between various concepts, as exemplified by GO, (25) DO (12) and HPO (11).”
Human Disease Ontology 2018 update: classification, content and workflow expansion (2018, background): “org), established in 2003, includes the breadth of common and rare diseases, organized as a directed acyclic graph (DAG) representing disease etiology classes, both an axiomatized OWL and an OBO formatted ontology (5).”
The IUPHAR/BPS Guide to PHARMACOLOGY in 2016: towards curated quantitative interactions between 1300 protein targets and 6000 ligands (2015, methodology): “Disease Ontology terms are linked to the Ontobee browser (27) which provides contextual visualisation.”
The Reactome Pathway Knowledgebase (2017, methodology): “These tallies include 1334 mutant variants and their post-translationally modified forms derived from 285 gene products, used to annotate 906 disease-specific reactions, tagged with 294 Disease Ontology terms (6).”
The Reactome Pathway Knowledgebase 2024 (2023, background): “Genetic disease annotations cover 4919 variant proteins and post-translationally modified forms of them, derived from 354 human gene products, and anno-tate 1544 disease-specific reactions tagged with 623 Disease Ontology terms ( 6 ).”
The Reactome pathway Knowledgebase (2015, methodology): “These tallies include 1155 mutant variants and their post-translationally modified forms derived from 249 gene products, used to annotate 787 disease-specific reactions, tagged with 262 Disease Ontology terms (2).”
Global hotspots and correlates of emerging zoonotic diseases (2017, methodology): “We selected articles matching terms from the Human Disease Ontology 59 and exported extracted toponyms.”
LncRNADisease 2.0: an updated database of long non-coding RNA-associated diseases (2018, background): “0 offers several distinct advantages from its first release: (i) integration from experimentally and/or computationally supported data, exceeding an over 40-fold lncRNA-disease associations enhancement over the previous version; (ii) providing the transcriptional regulatory relationships among lncRN”
WormBase 2016: expanding to enable helminth genomic research (2015, background): “We annotate C. elegans genes that have relevance to the study of human disease (42), curating descriptions of the association and forming connections to terms from the Disease Ontology (34) and to disease and gene records in the Online Mendelian Inheritance in Man (OMIM) (43).”
HMDD v3.0: a database for experimentally supported human microRNA–disease associations (2018, methodology): “For each miRNA–disease association entry, we also standardized miRNA names on the basis of the miRBase (http://www.mirbase.org/) (3) and the disease names mainly according to Disease Ontology (http: //www.disease-ontology.org) (15) and MeSH Terms (https: //www.ncbi.nlm.nih.gov/mesh).”