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

Kibbe, Warren A.; Arze, Cesar; Felix, Victor; Mitraka, Elvira; Bolton, Evan; Fu, Gang; Mungall, Christopher J.; Binder, Janos X.; Malone, James; Vasant, Drashtti; Parkinson, Helen; Schriml, Lynn M.

doi:10.1093/nar/gku1011

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

Abstract

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. In conclusion, 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.

Authors:

Kibbe, Warren A. ^[1]; Arze, Cesar ^[2]; Felix, Victor ^[2]; Mitraka, Elvira ^[2]; Bolton, Evan ^[3]; Fu, Gang ^[3]; Mungall, Christopher J. ^[4]; Binder, Janos X. ^[5]; Malone, James ^[6]; Vasant, Drashtti ^[7]; Parkinson, Helen ^[7]; Schriml, Lynn M. ^[2]

National Cancer Inst., Rockville, MD (United States)
Univ. of Maryland School of Medicine, Baltimore, MD (United States)
PubChem, National Center for Biotechnology Information, Bethesda, MD (United States). National Library of Medicine National Institutes of Health Department of Health and Human Services
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
European Molecular Biology Laboratory (EMBL), Heidelberg (Germany); Univ. of Luxembourg (Luxembourg)
European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge (United Kingdom)
European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge (United Kingdom)

Publication Date:: Mon Oct 27 00:00:00 EDT 2014

Research Org.:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Org.:: USDOE Office of Science (SC), Basic Energy Sciences (BES)

OSTI Identifier:: 1256071

Grant/Contract Number:: AC02-05CH11231

Resource Type:: Accepted Manuscript

Journal Name:: Nucleic Acids Research

Additional Journal Information:: Journal Volume: 43; Journal Issue: D1; Journal ID: ISSN 0305-1048

Publisher:: Oxford University Press

Country of Publication:: United States

Language:: English

Subject:: 59 BASIC BIOLOGICAL SCIENCES

Citation Formats


                    Kibbe, Warren A., Arze, Cesar, Felix, Victor, Mitraka, Elvira, Bolton, Evan, Fu, Gang, Mungall, Christopher J., Binder, Janos X., Malone, James, Vasant, Drashtti, Parkinson, Helen, and Schriml, Lynn M. Disease Ontology 2015 update: An expanded and updated database of human diseases for linking biomedical knowledge through disease data.  United States: N. p., 2014. 
Web.  doi:10.1093/nar/gku1011.

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                    Kibbe, Warren A., Arze, Cesar, Felix, Victor, Mitraka, Elvira, Bolton, Evan, Fu, Gang, Mungall, Christopher J., Binder, Janos X., Malone, James, Vasant, Drashtti, Parkinson, Helen, & Schriml, Lynn M. Disease Ontology 2015 update: An expanded and updated database of human diseases for linking biomedical knowledge through disease data.  United States.  https://doi.org/10.1093/nar/gku1011

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                    Kibbe, Warren A., Arze, Cesar, Felix, Victor, Mitraka, Elvira, Bolton, Evan, Fu, Gang, Mungall, Christopher J., Binder, Janos X., Malone, James, Vasant, Drashtti, Parkinson, Helen, and Schriml, Lynn M. Mon .  
"Disease Ontology 2015 update: An expanded and updated database of human diseases for linking biomedical knowledge through disease data".  United States.  https://doi.org/10.1093/nar/gku1011.  https://www.osti.gov/servlets/purl/1256071.

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@article{osti_1256071,

  title        = {Disease Ontology 2015 update: An expanded and updated database of human diseases for linking biomedical knowledge through disease data},

  author       = {Kibbe, Warren A. and Arze, Cesar and Felix, Victor and Mitraka, Elvira and Bolton, Evan and Fu, Gang and Mungall, Christopher J. and Binder, Janos X. and Malone, James and Vasant, Drashtti and Parkinson, Helen and Schriml, Lynn M.},

  abstractNote = {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. In conclusion, 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.},

  doi          = {10.1093/nar/gku1011},

  journal      = {Nucleic Acids Research},

  number       = D1,

  volume       = 43,

  place        = {United States},

  year         = {Mon Oct 27 00:00:00 EDT 2014},

  month        = {Mon Oct 27 00:00:00 EDT 2014}

}

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Pengelly, Reuben J.; Alom, Thahmina; Zhang, Zijian
Scientific Reports, Vol. 7, Issue 1
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ChemDIS-Mixture: an online tool for analyzing potential interaction effects of chemical mixtures
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Tung, Chun-Wei; Wang, Chia-Chi; Wang, Shan-Shan
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DES-Mutation: System for Exploring Links of Mutations and Diseases
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Kordopati, Vasiliki; Salhi, Adil; Razali, Rozaimi
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MeinteR: A framework to prioritize DNA methylation aberrations based on conformational and cis-regulatory element enrichment
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Malousi, Andigoni; Kouidou, Sofia; Tsagiopoulou, Maria
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Ontology-driven integrative analysis of omics data through Onassis
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Galeota, Eugenia; Kishore, Kamal; Pelizzola, Mattia
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Utility of the JAX Clinical Knowledgebase in capture and assessment of complex genomic cancer data
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Caufield, J. Harry; Zhou, Yijiang; Garlid, Anders O.
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Gkoutos, Georgios V.; Schofield, Paul N.; Hoehndorf, Robert
Briefings in Bioinformatics, Vol. 19, Issue 5
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OVA: integrating molecular and physical phenotype data from multiple biomedical domain ontologies with variant filtering for enhanced variant prioritization
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Antanaviciute, Agne; Watson, Christopher M.; Harrison, Sally M.
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Jumping across biomedical contexts using compressive data fusion
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Zitnik, Marinka; Zupan, Blaz
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Predicting drug-induced transcriptome responses of a wide range of human cell lines by a novel tensor-train decomposition algorithm
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CoCoScore: context-aware co-occurrence scoring for text mining applications using distant supervision
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Junge, Alexander; Jensen, Lars Juhl
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EXTRACT: interactive extraction of environment metadata and term suggestion for metagenomic sample annotation
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Pafilis, Evangelos; Buttigieg, Pier Luigi; Ferrell, Barbra
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Better living through ontologies at the Immune Epitope Database
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Vita, Randi; Overton, James A.; Sette, Alessandro
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FAIR principles and the IEDB: short-term improvements and a long-term vision of OBO-foundry mediated machine-actionable interoperability
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Vita, Randi; Overton, James A.; Mungall, Christopher J.
Database, Vol. 2018
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BioDataome: a collection of uniformly preprocessed and automatically annotated datasets for data-driven biology
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Lakiotaki, Kleanthi; Vorniotakis, Nikolaos; Tsagris, Michail
Database, Vol. 2018
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ChemDIS 2: an update of chemical-disease inference system
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Tung, Chun-Wei; Wang, Shan-Shan
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ResMarkerDB: a database of biomarkers of response to antibody therapy in breast and colorectal cancer
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Pérez-Granado, Judith; Piñero, Janet; Furlong, Laura I.
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The Sickle Cell Disease Ontology: enabling universal sickle cell-based knowledge representation
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Klinefelter syndrome comorbidities linked to increased X chromosome gene dosage and altered protein interactome activity
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Belling, Kirstine; Russo, Francesco; Jensen, Anders B.
Human Molecular Genetics, Vol. 26, Issue 7
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GWASdb v2: an update database for human genetic variants identified by genome-wide association studies
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Li, Mulin Jun; Liu, Zipeng; Wang, Panwen
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IMP 2.0: a multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks
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Wong, Aaron K.; Krishnan, Arjun; Yao, Victoria
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The Comparative Toxicogenomics Database: update 2017
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Davis, Allan Peter; Grondin, Cynthia J.; Johnson, Robin J.
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COEXPEDIA: exploring biomedical hypotheses via co-expressions associated with medical subject headings (MeSH)
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eRAM: encyclopedia of rare disease annotations for precision medicine
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mTCTScan: a comprehensive platform for annotation and prioritization of mutations affecting drug sensitivity in cancers
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BO-LSTM: classifying relations via long short-term memory networks along biomedical ontologies
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Abstract

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Enabling enrichment analysis with the Human Disease Ontology
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Evaluation of research in biomedical ontologies
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The National Center for Biomedical Ontology
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Disease Ontology: a backbone for disease semantic integration
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NCI Thesaurus: A semantic model integrating cancer-related clinical and molecular information
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The Unified Medical Language System (UMLS): integrating biomedical terminology
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A new face and new challenges for Online Mendelian Inheritance in Man (OMIM®)
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Orphanet et son réseau : où trouver une information validée sur les maladies rares
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A collection of bioconductor methods to visualize gene-list annotations
journal, January 2010

The Comparative Toxicogenomics Database: update 2013
journal, October 2012

Data, information, knowledge and principle: back to metabolism in KEGG
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Annotating the human genome with Disease Ontology
journal, January 2009

The SPECIES and ORGANISMS Resources for Fast and Accurate Identification of Taxonomic Names in Text
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Gene Wiki Reviews: Marrying crowdsourcing with traditional peer review
journal, December 2013

A framework for organizing cancer-related variations from existing databases, publications and NGS data using a High-performance Integrated Virtual Environment (HIVE)
journal, January 2014

ArrayExpress update—trends in database growth and links to data analysis tools
journal, November 2012

Development and use of Ontologies Inside the Neuroscience Information Framework: A Practical Approach
journal, January 2012

Neurocarta: aggregating and sharing disease-gene relations for the neurosciences
journal, January 2013

The NeuroDevNet Autism Spectrum Disorders Demonstration Project
journal, March 2011

Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications
journal, May 2011

Metadata Standard and Data Exchange Specifications to Describe, Model, and Integrate Complex and Diverse High-Throughput Screening Data from the Library of Integrated Network-based Cellular Signatures (LINCS)
journal, January 2014

SemFunSim: A New Method for Measuring Disease Similarity by Integrating Semantic and Gene Functional Association
journal, June 2014

dcGO: database of domain-centric ontologies on functions, phenotypes, diseases and more
journal, November 2012

The disease and gene annotations (DGA): an annotation resource for human disease
journal, November 2012

Uberon, an integrative multi-species anatomy ontology
journal, January 2012

The Reactome Pathway Knowledgebase
journal, November 2017

Neurocarta: aggregating and sharing disease-gene relations for the neurosciences
text, January 2013

The reactome pathway knowledgebase
journal, November 2019

A new face and new challenges for Online Mendelian Inheritance in Man (OMIM®)
journal, April 2011

NCI Thesaurus: A semantic model integrating cancer-related clinical and molecular information
journal, February 2007

Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications
journal, May 2011

The Unified Medical Language System (UMLS): integrating biomedical terminology
journal, January 2004

Disease Ontology: a backbone for disease semantic integration
journal, November 2011

dcGO: database of domain-centric ontologies on functions, phenotypes, diseases and more
journal, November 2012

ArrayExpress update—trends in database growth and links to data analysis tools
journal, November 2012

The disease and gene annotations (DGA): an annotation resource for human disease
journal, November 2012

The Comparative Toxicogenomics Database: update 2013
journal, October 2012

The reactome pathway knowledgebase
journal, November 2019

Metadata Standard and Data Exchange Specifications to Describe, Model, and Integrate Complex and Diverse High-Throughput Screening Data from the Library of Integrated Network-based Cellular Signatures (LINCS)
journal, January 2014

Chapter 9: Analyses Using Disease Ontologies
journal, December 2012

The SPECIES and ORGANISMS Resources for Fast and Accurate Identification of Taxonomic Names in Text
journal, June 2013

Neurocarta: aggregating and sharing disease-gene relations for the neurosciences
text, January 2013

Moving toward System Genetics through Multiple Trait Analysis in Genome-Wide Association Studies
journal, January 2012

Genome sequencing uncovers phenocopies in primary progressive multiple sclerosis: MS Phenocopies in PPMS
journal, July 2018

Identification of prognostic miRNA biomarkers for predicting overall survival of colon adenocarcinoma and bioinformatics analysis: A study based on The Cancer Genome Atlas database
journal, December 2018

Formatting biological big data for modern machine learning in drug discovery
journal, December 2018

Primer on Ontologies
book, November 2016

MicroRNA epigenetic signatures in human disease
journal, August 2016

Extraction and analysis of signatures from the Gene Expression Omnibus by the crowd
journal, September 2016

CIViC is a community knowledgebase for expert crowdsourcing the clinical interpretation of variants in cancer
journal, January 2017

Global hotspots and correlates of emerging zoonotic diseases
journal, October 2017

Integrating biomedical research and electronic health records to create knowledge-based biologically meaningful machine-readable embeddings
journal, July 2019

Pan-cancer whole-genome analyses of metastatic solid tumours
journal, October 2019

A genetics-led approach defines the drug target landscape of 30 immune-related traits
journal, June 2019

CancerMine: a literature-mined resource for drivers, oncogenes and tumor suppressors in cancer
journal, May 2019

PathoPhenoDB, linking human pathogens to their phenotypes in support of infectious disease research
journal, June 2019

DES-Mutation: System for Exploring Links of Mutations and Diseases
journal, September 2018

Quantitative evaluation of ontology design patterns for combining pathology and anatomy ontologies
journal, March 2019

Precision annotation of digital samples in NCBI’s gene expression omnibus
journal, September 2017

Sustainable data and metadata management at the BD2K-LINCS Data Coordination and Integration Center
journal, June 2018

A reference set of curated biomedical data and metadata from clinical case reports
journal, November 2018

Analysis of the human diseasome using phenotype similarity between common, genetic and infectious diseases
journal, June 2015

Computer-aided biomarker discovery for precision medicine: data resources, models and applications
journal, November 2017

Network embedding in biomedical data science
journal, December 2018

Biomedical data and computational models for drug repositioning: a comprehensive review
journal, February 2020

MetaSRA: normalized human sample-specific metadata for the Sequence Read Archive
journal, May 2017

DincRNA: a comprehensive web-based bioinformatics toolkit for exploring disease associations and ncRNA function
journal, January 2018

ResMarkerDB: a database of biomarkers of response to antibody therapy in breast and colorectal cancer
journal, January 2019

Integrating ontologies of human diseases, phenotypes, and radiological diagnosis
journal, January 2019

COEXPEDIA: exploring biomedical hypotheses via co-expressions associated with medical subject headings (MeSH)
journal, September 2016

Function-driven discovery of disease genes in zebrafish using an integrated genomics big data resource
journal, October 2016

DisGeNET: a comprehensive platform integrating information on human disease-associated genes and variants
journal, October 2016

AAgAtlas 1.0: a human autoantigen database
journal, October 2016

The Reactome Pathway Knowledgebase
journal, November 2017

Human Disease Ontology 2018 update: classification, content and workflow expansion
journal, November 2018

ECO, the Evidence & Conclusion Ontology: community standard for evidence information
journal, November 2018

LncRNADisease 2.0: an updated database of long non-coding RNA-associated diseases
journal, October 2018