How to cite this record FAIRsharing.org: DOID; Disease Ontology; DOI: https://doi.org/10.25504/FAIRsharing.8b6wfq; Last edited: Aug. 5, 2019, 1:31 p.m.; Last accessed: Jan 26 2021 3:15 a.m.
Publication for citation Disease Ontology 2015 update: an expanded and updated database of human diseases for linking biomedical knowledge through disease data. Kibbe WA,Arze C,Felix V,Mitraka E,Bolton E,Fu G,Mungall CJ,Binder JX,Malone J,Vasant D,Parkinson H,Schriml LM; Nucleic Acids Res ; 2014; 10.1093/nar/gku1011;
Record updated: July 13, 2019, 10:03 p.m. by The FAIRsharing Team.
Edits to 'https://fairsharing.org/FAIRsharing.8b6wfq' by 'The FAIRsharing Team' at 22:03, 13 Jul 2019 (approved): 'organizations' has been modified: Before: ELIXIR Italy|http://elixir-italy.org|Funds Northwestern University, Chicago, IL, USA|http://www.northwestern.edu/|Funds Institute for Genome Sciences, University of Maryland, Baltimore, MD, USA|http://www.igs.umaryland.edu/|Maintains After: ELIXIR Italy|http://elixir-italy.org|Funds Northwestern University, Chicago, IL, USA|http://www.northwestern.edu/|Funds Institute for Genome Sciences, University of Maryland, Baltimore, MD, USA|http://www.igs.umaryland.edu/|Maintains WT HIPSCI (EMBL)|https://www.embl.org/|Funds National Center for Research Resources, National Institutes of Health, Bethesda, MD, USA|http://www.nih.gov/about/almanac/organization/NCRR.htm|Funds National Institutes of Health (NIH), Bethesda, MD, USA|http://www.nih.gov|Funds Added: WT HIPSCI (EMBL)|https://www.embl.org/|Funds National Center for Research Resources, National Institutes of Health, Bethesda, MD, USA|http://www.nih.gov/about/almanac/organization/NCRR.htm|Funds National Institutes of Health (NIH), Bethesda, MD, USA|http://www.nih.gov|Funds Removed: 'grants' has been modified: Before: R01RR025341 After: 098503/D/12/Z R01RR025341 R01RR025342 R24OD011883 U54-HG004028 Added: 098503/D/12/Z R01RR025342 R24OD011883 U54-HG004028 Removed: 'onto_disciplines' has been modified: Before: Biomedical Science Life Sciences After: Biomedical Science Life Sciences Ontology and Terminology Added: Ontology and Terminology Removed: 'contactORCID' has been modified: Before: After: 0000-0001-8910-9851 'onto_domains' has been modified: Before: Classification disease disease process modeling objective After: Classification disease disease phenotype disease process modeling objective genetic disorder infection process mental health Added: disease phenotype genetic disorder infection process mental health Removed:
Edits to 'https://fairsharing.org/FAIRsharing.8b6wfq' by 'The FAIRsharing Team' at 14:30, 14 Mar 2019 (approved): 'supportLinks' has been modified: Before: FAQ|http://www.disease-ontology.org/faq/ contact form|http://www.disease-ontology.org/contact/ forum|https://lists.sourceforge.net/lists/listinfo/diseaseontology-discussion online documentation|https://sourceforge.net/p/diseaseontology/code/HEAD/tree/trunk/DO_info_files/DO_Style_Guide_v2015.pdf twitter|@diseaseontology After: FAQ|http://www.disease-ontology.org/faq/ contact form|http://www.disease-ontology.org/contact/ forum|https://github.com/DiseaseOntology/HumanDiseaseOntology/issues mailing list|https://lists.sourceforge.net/lists/listinfo/diseaseontology-discussion online documentation|http://www.disease-ontology.org/resources/ online documentation|http://www.disease-ontology.org/about/ online documentation|https://github.com/DiseaseOntology/HumanDiseaseOntology online documentation|https://sourceforge.net/p/diseaseontology/code/HEAD/tree/trunk/DO_info_files/DO_Style_Guide_v2015.pdf training|http://www.disease-ontology.org/tutorial/ twitter|@diseaseontology Added: forum|https://github.com/DiseaseOntology/HumanDiseaseOntology/issues mailing list|https://lists.sourceforge.net/lists/listinfo/diseaseontology-discussion online documentation|http://www.disease-ontology.org/resources/ online documentation|http://www.disease-ontology.org/about/ online documentation|https://github.com/DiseaseOntology/HumanDiseaseOntology training|http://www.disease-ontology.org/tutorial/ Removed: forum|https://lists.sourceforge.net/lists/listinfo/diseaseontology-discussion 'description' has been modified: Before: The Disease Ontology focusing on Human Disease. The Disease Ontology is a community driven, open source ontology that is designed to link disparate datasets through disease concepts. They provide a computable structure of inheritable, environmental and infectious origins of human disease to facilitate the connection of genetic data, clinical data, and symptoms through the lens of human disease. After: The Disease Ontology has been developed as a standardized ontology for human disease with the purpose of providing the biomedical community with consistent, reusable and sustainable descriptions of human disease terms, phenotype characteristics and related medical vocabulary disease concepts. 'related_standards' has been modified: Before: OBO Format Syntax and Semantics Molecular Connections Cell Line Ontology After: OBO Format Syntax and Semantics Molecular Connections Cell Line Ontology Medical Subject Headings NCI Thesaurus Systematized Nomenclature of Medicine-Clinical Terms Online Mendelian Inheritance in Man Ontology Added: Medical Subject Headings NCI Thesaurus Systematized Nomenclature of Medicine-Clinical Terms Online Mendelian Inheritance in Man Ontology Removed: 'dataProcesses' has been modified: Before: Browse Download Submit After: Download Submit Added: Removed: Browse 'contactEmail' has been modified: Before: After: firstname.lastname@example.org 'contact' has been modified: Before: After: Lynn Schriml 'miriam_id' has been modified: Before: None After:
|contact form||DOID Contact Form|
|forum||GitHub Issue Tracker|
|Mailing List||Sourceforge Mailing List|
|online documentation||Style Guide (PDF)|
|online documentation||Further Resources|
|online documentation||About DOID|
|online documentation||GitHub Project|
|Contact||Lynn Schriml ORCID|
No XSD schemas defined
Conditions of UseApplies to: Data use
Disease Ontology: a backbone for disease semantic integration.
Schriml LM,Arze C,Nadendla S,Chang YW,Mazaitis M,Felix V,Feng G,Kibbe WA
Nucleic Acids Res 2011
From disease ontology to disease-ontology lite: statistical methods to adapt a general-purpose ontology for the test of gene-ontology associations.
Du P,Feng G,Flatow J,Song J,Holko M,Kibbe WA,Lin SM
Disease Ontology 2015 update: an expanded and updated database of human diseases for linking biomedical knowledge through disease data.
Kibbe WA,Arze C,Felix V,Mitraka E,Bolton E,Fu G,Mungall CJ,Binder JX,Malone J,Vasant D,Parkinson H,Schriml LM
Nucleic Acids Res 2014
Models and Formats
No identifier schema standards defined
No metrics standards defined
Genetic, genomic and molecular information pertaining to the model organism Drosophila melanogaster and related sequences. This database also contains information relating to human disease models in Drosophila, the use of transgenic constructs containing sequence from other organisms in Drosophila, and information on where to buy Drosophila strains and constructs.
GWASdb comprises of collections of traits/diseases associated SNP (TASs) from current GWAS and their comprehensive functional annotations, as well as disease classifications.
Stem Cell Discovery Engine
Comparison system for cancer stem cell analysis
WormBase is an international consortium of biologists and computer scientists dedicated to providing the research community with accurate, current, accessible information concerning the genetics, genomics and biology of C. elegans and related nematodes.
Comparative Toxicogenomics Database
The Comparative Toxicogenomics Database (CTD) advances understanding of the effects of environmental chemicals on human health. Biocurators manually curate chemical-gene, chemical-disease, and gene-disease relationships from the scientific literature. This core data is then internally integrated to generate inferred chemical-gene-disease networks. Additionally, the core data is integrated with external data sets (such as Gene Ontology and pathway annotations) to predict many novel associations between different data types. A unique and powerful feature of CTD is the inferred relationships generated by data integration that helps turn knowledge into discoveries by identifying novel connections between chemicals, genes, diseases, pathways, and GO annotations that might not otherwise be apparent using other biological resources.
European Mouse Mutant Archive
The European Mouse Mutant Archive (EMMA) is a non-profit repository for the collection, archiving (via cryopreservation) and distribution of relevant mutant strains essential for basic biomedical research. The laboratory mouse is the most important mammalian model for studying genetic and multi-factorial diseases in man. Thus the work of EMMA will play a crucial role in exploiting the tremendous potential benefits to human health presented by the current research in mammalian genetics.
Mouse Genome Database - a Mouse Genome Informatics (MGI) Resource
MGI is the international database resource for the laboratory mouse, providing integrated genetic, genomic, and biological data to facilitate the study of human health and disease. Data includes gene characterization, nomenclature, mapping, gene homologies among mammals, sequence links, phenotypes, allelic variants and mutants, and strain data.
Xenopus laevis and tropicalis biology and genomics resource
Xenbase is the model organism database for Xenopus laevis and X. (Silurana) tropicalis. It contains genomic, development data and community information for Xenopus research. It includes gene expression patterns that incorporate image data from the literature, large scale screens and community submissions.
GWAS Central stores genome-wide association study data. The database content comprises direct submissions received from GWAS authors and consortia in addition to actively gathered data sets from various public sources. GWAS data are discoverable from the perspective of genetic markers, genes, genome regions or phenotypes, via graphical visualizations and detailed downloadable data reports.
DisGeNET: a knowledge base for disease genomics
DisGeNET is a discovery platform containing one of the largest collections available of genes and variants involved in human diseases. DisGeNET integrates data from expert curated repositories, GWAS catalogues, animal models, and the scientific literature, and covers the whole landscape of human diseases. The current version of DisGeNET (v7.0) contains 1,134,942 gene-disease associations (GDAs), between 21,671 genes and 30,170 diseases, disorders, traits, and clinical or abnormal human phenotypes, and 369,554 variant-disease associations (VDAs), between 194,515 variants and 14,155 diseases, traits, and phenotypes. The data are homogeneously annotated with controlled vocabularies and community-driven ontologies. Additionally, several original metrics are provided to assist the prioritization of genotype-phenotype relationships. The information is accessible through a web interface, a Cytoscape App, an RDF SPARQL endpoint, a REST API, and an R package.
MouseMine @ MGI
A database of integrated mouse data from MGI, powered by InterMine. MouseMine is member of InterMOD, a consortium of model organism databases dedicated to making cross-species data analysis easier through ongoing coordination and collaborative system development.
UniCarbKB is an initiative that aims to promote the creation of an online information storage and search platform for glycomics and glycobiology research. The knowledgebase will offer a freely accessible and information-rich resource supported by querying interfaces, annotation technologies and the adoption of common standards to integrate structural, experimental and functional data.
The Jackson Laboratory Clinical Knowledgebase (CKB) is a semi-automated/manually curated database of gene/variant annotations, therapy knowledge, diagnostic/prognostic information, and clinical trials related to oncology. CKB not only contains current information on the protein effect of somatic gene variants, but also connects the variant to targeted therapies through an efficacy evidence annotation. In addition, CKB captures clinical trial patient eligibility criteria that include genomic alterations (genotype-specific). The public access version of CKB encompasses 82 commonly known driver genes. Users can search CKB via gene, gene variants, drug, drug class, indication, and clinical trials. The web-based version of CKB is designed to interrogate the knowledgebase for specific data attributes while also enabling a robust browse like feature when the desired content is unknown.
DrugCentral is online drug information that provides information on active ingredients, chemical entities, pharmaceutical products, drug mode of action, indications, and pharmacologic mode of action. DrugCentral monitors FDA, EMA, and PMDA for new drug approval on regular basis to ensure currency of the resource. This resource was created and is maintained by the Division of Translational Informatics at the University of New Mexico School of Medicine.
Target Central Resource Database
TCRD is the central resource behind the Illuminating the Druggable Genome Knowledge Management Center (IDG-KMC). TCRD contains information about human targets, with special emphasis on four families of targets that are central to the NIH IDG initiative: GPCRs, kinases, ion channels and nuclear receptors. Olfactory GPCRs (oGPCRs) are treated as a separate family. A key aim of the KMC is to classify the development/druggability level of targets. The official public portal for TCRD is Pharos (pharos.nih.gov). Based on modern web design principles the Pharos interface provides facile access to all data types collected by the KMC. Given the complexity of the data surrounding any target, efficient and intuitive visualization has been a high priority, to enable users to quickly navigate & summarize search results and rapidly identify patterns. A critical feature of the interface is the ability to perform flexible search and subsequent drill down of search results. Underlying the interface is a RESTful API that provides programmatic access to all KMC data, allowing for easy consumption in user applications.
Alliance of Genome Resources
The primary mission of the Alliance of Genome Resources (the Alliance) is to develop and maintain sustainable genome information resources that facilitate the use of diverse model organisms in understanding the genetic and genomic basis of human biology, health and disease.
The Open Biological and Biomedical Ontology (OBO) Foundry is a collective of ontology developers that are committed to collaboration and adherence to shared principles. The mission of the OBO Foundry is to develop a family of interoperable ontologies that are both logically well-formed and scientifically accurate. To achieve this, OBO Foundry participants voluntarily adhere to and contribute to the development of an evolving set of principles including open use, collaborative development, non-overlapping and strictly-scoped content, and common syntax and relations, based on ontology models that work well, such as the Gene Ontology (GO). The OBO Foundry is overseen by an Operations Committee with Editorial, Technical and Outreach working groups.
TargetMine integrates many types of data for human, rat and mouse. Flexible queries, export of results and data analysis are available.
DISNOR is a resource that uses a comprehensive collection of disease associated genes, as annotated in DisGeNET, to interrogate SIGNOR (https://signor.uniroma2.it) in order to assemble disease-specific logic networks linking disease associated genes by causal relationships. DISNOR is an open resource where more than 4000 disease-networks, linking ~ 2800 disease genes, can be explored. For each disease curated in DisGeNET, DISNOR links disease genes through manually annotated causal relationships and the inferred 'patho-pathways' can be visualised at different level of complexity.
Heart Diseases related Noncoding RNA Database
The Heart Disease-related Non-coding RNAs Database (HDncRNA) provides information about common heart diseases and their related noncoding RNAs. The HDncRNA database contains manually annotated associations of ncRNAs with heart disease. Sources of data in this database are published articles, ncRNA databases and public RNA-seq datasets.
MetaSRA is a database of normalized SRA human sample-specific metadata following a schema inspired by the metadata organization of the ENCODE project. This schema involves mapping samples to terms in biomedical ontologies, labeling each sample with a sample-type category, and extracting real-valued properties.
Domain-centric GO provides associations between ontological terms and protein domains at the superfamily and family levels. Some functional units consist of more than one domain acting together or acting at an interface between domains; therefore, ontological terms associated with pairs of domains, triplets and longer supra-domains are also provided.
GlyGen: Computational and Informatics Resources for Glycoscience
GlyGen is a data integration and dissemination project for carbohydrate and glycoconjugate related data. GlyGen retrieves information from multiple international data sources and integrates and harmonizes this data. This web portal allows exploring this data and performing unique searches that cannot be executed in any of the integrated databases alone.
Editome Disease Knowledgebase
The Editome Disease Knowledgebase (EDK) is an integrated knowledgebase of RNA editome-disease associations manually curated from published literature. It stores information on RNA editing events in mRNA, miRNA, lncRNA, viruses and RNA editing enzymes associated with different human diseases.
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This record is maintained by lschriml
ELIXIR Italy (Government body)
Northwestern University, Chicago, IL, USA (University)
National Institutes of Health (NIH), Bethesda, MD, USA (Government body)
Institute for Genome Sciences, University of Maryland, Baltimore, MD, USA (Research institute)
098503/D/12/Z (WT HIPSCI (EMBL))
R01RR025341 (National Center for Research Resources, National Institutes of Health, Bethesda, MD, USA)
R01RR025342 (National Center for Research Resources, National Institutes of Health, Bethesda, MD, USA)
R24OD011883 (National Institutes of Health (NIH), Bethesda, MD, USA)
U54-HG004028 (National Institutes of Health (NIH), Bethesda, MD, USA)