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

Warren A. Kibbe, Cesar Arze, Victor Felix, Elvira Mitraka, Evan Bolton, Gang Fu, Christopher J. Mungall, Janos X. Binder, James Malone, Drashtti Vasant, Helen Parkinson, Lynn M. Schriml
2014 Nucleic Acids Research  
protein, drug and epitope data through the lens of human disease.  ...  The current version of the Human Disease Ontology (DO) ( database expands the utility of the ontology for the examination and comparison of genetic variation, phenotype,  ...  We appreciate and thank everyone who has used the DO website and the Disease Ontology, provided suggestions, corrections and improvements for DO over the years.  ... 
doi:10.1093/nar/gku1011 pmid:25348409 pmcid:PMC4383880 fatcat:b2dpphbncbdi5bv6paspxcveoy

Integrating ontologies of rare diseases and radiological diagnosis

C. E. Kahn
2015 JAMIA Journal of the American Medical Informatics Association  
manifestations of disorders specified by OMIM. 27, 28 The 2287 ORDO disease names mapped to RGO expanded the set of terms and the scope of knowledge available through RGO.  ...  To manage and apply evolving biomedical knowledge, scientists have turned to ontologies-formal knowledge models that comprise a set of concepts and their relationships to one another. 7 Biomedical ontologies  ...  CONTRIBUTORS The author is solely responsible for this work.  ... 
doi:10.1093/jamia/ocv020 pmid:25833393 fatcat:wg5e6dsvgjdwxcd6kg26lgrkei

The Human Disease Ontology 2022 update

Lynn M Schriml, James B Munro, Mike Schor, Dustin Olley, Carrie McCracken, Victor Felix, J Allen Baron, Rebecca Jackson, Susan M Bello, Cynthia Bearer, Richard Lichenstein, Katharine Bisordi (+3 others)
2021 Nucleic Acids Research  
The Human Disease Ontology (DO) ( database, has significantly expanded the disease content and enhanced our userbase and website since the DO's 2018 Nucleic Acids Research DATABASE  ...  The DO, funded as a NHGRI Genomic Resource, plays a key role in disease knowledge organization, representation, and standardization, serving as a reference framework for multiscale biomedical data integration  ...  Radoslav Davidovic at the Center for Multidisciplinary Research, Institute of Nuclear Sciences VINA, Belgrade, Serbia for his team's contributions for completing the sarcoma branch review and revision.  ... 
doi:10.1093/nar/gkab1063 pmid:34755882 pmcid:PMC8728220 fatcat:hpj2qrshtbdzdki5rdzciv36pe

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

Lynn M Schriml, Elvira Mitraka, James Munro, Becky Tauber, Mike Schor, Lance Nickle, Victor Felix, Linda Jeng, Cynthia Bearer, Richard Lichenstein, Katharine Bisordi, Nicole Campion (+8 others)
2018 Nucleic Acids Research  
data across biomedical databases, bioinformatics tools, genomic and cancer resources and demonstrated by a 6.6× growth in DO's user community since 2015.  ...  new disease terms, a 30% increase of textual definitions, and an expanding suite of disease classification hierarchies constructed through defined logical axioms.  ...  ACKNOWLEDGEMENTS The authors acknowledge and thank all of the DO's contributors and collaborators.  ... 
doi:10.1093/nar/gky1032 pmid:30407550 fatcat:q3u7vqejlbechc25orcqbgawzi

PDON: Parkinson's disease ontology for representation and modeling of the Parkinson's disease knowledge domain

Erfan Younesi, Ashutosh Malhotra, Michaela Gündel, Phil Scordis, Alpha Tom Kodamullil, Matt Page, Bernd Müller, Stephan Springstubbe, Ullrich Wüllner, Dieter Scheller, Martin Hofmann-Apitius
2015 Theoretical Biology and Medical Modelling  
for knowledge exchange or systems modeling of disease mechanism.  ...  Disease ontologies provide a novel means for organizing, integrating, and standardizing the knowledge domains specific to disease in a compact, formalized and computer-readable form and serve as a reference  ...  ontology.  ... 
doi:10.1186/s12976-015-0017-y pmid:26395080 pmcid:PMC4580356 fatcat:ueseobwo4rga7bdggm3uicgg7e

Describing the Breakbone Fever: IDODEN, an Ontology for Dengue Fever

Elvira Mitraka, Pantelis Topalis, Vicky Dritsou, Emmanuel Dialynas, Christos Louis, Rebekah Crockett Kading
2015 PLoS Neglected Tropical Diseases  
Conclusions/Significance The availability of the dengue ontology will enable databases hosting dengue-associated data and decision-support systems for that disease to perform most efficiently and to link  ...  To address the need to expand the toolbox available for the control and prevention of vector-borne diseases we embarked on the construction of specific ontologies.  ...  It represents a focused way to access data and knowledge.  ... 
doi:10.1371/journal.pntd.0003479 pmid:25646954 pmcid:PMC4315569 fatcat:42z6fksjibhknpwz6wwgh5wbim

The Comparative Toxicogenomics Database: update 2017

Allan Peter Davis, Cynthia J. Grondin, Robin J. Johnson, Daniela Sciaky, Benjamin L. King, Roy McMorran, Jolene Wiegers, Thomas C. Wiegers, Carolyn J. Mattingly
2016 Nucleic Acids Research  
In this update, we report a 33% increase in our core data content since 2015, describe our new exposure module (that harmonizes exposure science information with core toxicogenomic data) and introduce  ...  a novel dataset of GO-disease inferences (that identify common molecular underpinnings for seemingly unrelated pathologies).  ...  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  ... 
doi:10.1093/nar/gkw838 pmid:27651457 pmcid:PMC5210612 fatcat:povogyqyofcebnljc3jnl4fnoq

The BioGRID interaction database: 2013 update

Andrew Chatr-aryamontri, Bobby-Joe Breitkreutz, Sven Heinicke, Lorrie Boucher, Andrew Winter, Chris Stark, Julie Nixon, Lindsay Ramage, Nadine Kolas, Lara O'Donnell, Teresa Reguly, Ashton Breitkreutz (+8 others)
2012 Nucleic Acids Research  
BioGRID data are directly downloadable without restriction in a variety of standardized formats and are freely distributed through partner model organism databases and meta-databases.  ...  Bi-oGRID curates the biomedical literature for major model organism species, including humans, with a recent emphasis on central biological processes and specific human diseases.  ...  ACKNOWLEDGEMENTS The authors thank Chris Grove, Paul Sternberg and Anastasia Baryshnikova for ongoing collaborative development of the Genetic Interaction Structured Terminology.  ... 
doi:10.1093/nar/gks1158 pmid:23203989 pmcid:PMC3531226 fatcat:nmn2ijk3qje6jfpsgpzgk2p2nm

Generating a focused view of disease ontology cancer terms for pan-cancer data integration and analysis

T.-J. Wu, L. M. Schriml, Q.-R. Chen, M. Colbert, D. J. Crichton, R. Finney, Y. Hu, W. A. Kibbe, H. Kincaid, D. Meerzaman, E. Mitraka, Y. Pan (+5 others)
2015 Database: The Journal of Biological Databases and Curation  
The disease ontology (DO) was developed over the past decade to address data integration, standardization and annotation issues for human disease data.  ...  A major issue of biomedical data integration is the development of overlapping terms, ambiguous classifications and inconsistencies represented across databases and publications.  ...  Acknowledgements The authors thank COSMIC, TCGA, ICGC, TARGET, IntOGen and EDRN for providing the data and Naila Gulzar, Pascale Gaudet and Yu Hu for their suggestions and comments.  ... 
doi:10.1093/database/bav032 pmid:25841438 pmcid:PMC4385274 fatcat:uifubwm7qjbzxcittpu3xxg4ba

VectorBase: an updated bioinformatics resource for invertebrate vectors and other organisms related with human diseases

Gloria I. Giraldo-Calderón, Scott J. Emrich, Robert M. MacCallum, Gareth Maslen, Emmanuel Dialynas, Pantelis Topalis, Nicholas Ho, Sandra Gesing, Gregory Madey, Frank H. Collins, Daniel Lawson
2014 Nucleic Acids Research  
VectorBase is a National Institute of Allergy and Infectious Diseases supported Bioinformatics Resource Center (BRC) for invertebrate vectors of human pathogens.  ...  Here we describe improvements to our resource and the set of tools available for interrogating and accessing BRC data including the integration of Web Apollo to facilitate community annotation and providing  ...  ACKNOWLEDGEMENTS We would like to acknowledge the many scientists that have provided data to VectorBase including gene manual annotations, microarrays, SNPs, insecticide assays, RNAseq and proteomics data  ... 
doi:10.1093/nar/gku1117 pmid:25510499 pmcid:PMC4383932 fatcat:nbcsiqnxzbc5fpxzdyofyrtyuu

Gene-Disease Interaction Retrieval from Multiple Sources: A Network Based Method

Lan Huang, Ye Wang, Yan Wang, Tian Bai
2016 BioMed Research International  
Those databases are filled with various gene functions, pathways, interactions, and so forth, while much biomedical knowledge about human diseases is stored as text in all kinds of literatures.  ...  This paper combines both efforts and biomedical ontologies to build an interaction network of multiple biomedical ontologies, which guarantees its robustness as well as its wide coverage of biomedical  ...  Some gene features extracted from those databases are not related to human or human diseases; thus, there are a lot of noises from gene databases while extracting gene features for biomedical research  ... 
doi:10.1155/2016/3594517 pmid:27478829 pmcid:PMC4961833 fatcat:f5vrkhbdazebtnzsxvdfljcxg4

Wikidata as a FAIR knowledge graph for the life sciences [article]

Andra Waagmeester, Gregory Stupp, Sebastian Burgstaller-Muehlbacher, Benjamin M Good, Malachi Griffith, Obi Griffith, Kristina Hanspers, Henning Hermjakob, Kevin Hybiske, Sarah M. Keating, Magnus Manske, Michael Mayers (+12 others)
2019 bioRxiv   pre-print
Wikidata is a well-suited infrastructure for creating, editing, integrating, and accessing biomedical knowledge.  ...  Finally, we demonstrate how the continuously updated, crowd-contributed knowledge in Wikidata can be used to improve the representation, integration, and analysis of biomedical information.  ...  For phenotype-based disease diagnosis, BOQA takes 32 as input a list of phenotypes (using the Human Phenotype Ontology (HPO) [63]) and an association file 33 between phenotypes and diseases.  ... 
doi:10.1101/799684 fatcat:inurqfmvv5cbxhoucg5grj6srm

Recent advances in predicting gene–disease associations

Kenneth Opap, Nicola Mulder
2017 F1000Research  
Kibbe WA, Arze C, Felix V, et al.: Disease Ontology 2015 update: an expanded and updated database of human diseases for linking biomedical knowledge through disease data.  ...  .: DisGeNET: a discovery platform for the dynamical exploration of human diseases and their genes. Database (Oxford). 2015; 2015: bav028.  ...  Many tools make use of ontologies such as the disease 35, 44 and phenotype ontologies 45 for data standardisation.  ... 
doi:10.12688/f1000research.10788.1 pmid:28529714 pmcid:PMC5414807 fatcat:hzph7zrm55ecje7fsp2yfk66uq

An Ebola virus-centered knowledge base

Maulik R. Kamdar, Michel Dumontier
2015 Database: The Journal of Biological Databases and Curation  
We retrieve and aggregate knowledge from several open data sources, web services and biomedical ontologies.  ...  In this article, we present our approach for the development of an Ebola virus-centered Knowledge Base (Ebola-KB) using Linked Data and Semantic Web Technologies.  ...  They have exposed the associated data sources through SPARQL query endpoints, and have also agreed on a concise set of ontologies and standards for exchanging experimental data and biomedical information  ... 
doi:10.1093/database/bav049 pmid:26055098 pmcid:PMC4460400 fatcat:dqaksgbqnndxfh4ugsn3n6kwyu

PolySearch2: a significantly improved text-mining system for discovering associations between human diseases, genes, drugs, metabolites, toxins and more

Yifeng Liu, Yongjie Liang, David Wishart
2015 Nucleic Acids Research  
PolySearch2 ( is an online textmining system for identifying relationships between biomedical entities such as human diseases, genes, SNPs, proteins, drugs, metabolites, toxins, metabolic  ...  An example query might be: 'Find all diseases associated with Bisphenol A'. To find its answers,  ...  custom thesauri and term collections; an expanded number of text collections and databases (by >80%); along with significantly improved support for caching and automated updating.  ... 
doi:10.1093/nar/gkv383 pmid:25925572 pmcid:PMC4489268 fatcat:sbl3ac4cxzfzfeucjpel5kwqo4
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