DisGeNET: Difference between revisions

Revision as of 06:05, 16 August 2015

Revision as of 06:42, 16 August 2015

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{{infobox biodatabase

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|description = [[Gene Disease Database]]

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'''DisGeNET''' is a discovery platform designed to address a variety of questions concerning the genetic underpinning of human diseases. DisGeNET is one of the largest and comprehensive repositories of human gene-disease associations (GDAs) currently available .<ref name=Pinero>{{cite journal|last1=Piñero|first1=J.|last2=Queralt-Rosinach|first2=N.|last3=Bravo|first3=A.|last4=Deu-Pons|first4=J.|last5=Bauer-Mehren|first5=A.|last6=Baron|first6=M.|last7=Sanz|first7=F.|last8=Furlong|first8=L. I.|title=DisGeNET: a discovery platform for the dynamical exploration of human diseases and their genes|journal=Database|date=15 April 2015|volume=2015|issue=0|pages=bav028–bav028|doi=10.1093/database/bav028|accessdate=15 August 2015}}</ref>. It also offers a set of bioinformatic tools to facilitate the analysis of these data by different user profiles. It is maintained by the [http://ibi.imim.es/ Integrative Biomedical Informatics (IBI) Group], of the (GRIB)-IMIM/UPF, based at the [[Barcelona Biomedical Research Park]] (PRBB), Barcelona, Catalonia, Spain.

==Scope and access==

In the pursuit to gather different aspects of the current knowledge on the genetic basis of human diseases, DisGeNET covers information on all disease areas (Mendelian, complex and environmental diseases). With more than 400 000 genotype-phenotype relationships from different origins integrated and annotated with explicit provenance and evidence information, DisGeNET is a valuable knowledge and evidence-based discovery resource for [[Translational Research]].

DisGeNET is an open access resource that makes available a comprehensive knowledge base on disease genes and different tools for their exploitation and analysis. DisGeNET is available through a [http://www.disgenet.org/ Web interface], a [[Cytoscape]] plugin,<ref name="Bauer">{{cite journal|last1=Bauer-Mehren|first1=A|last2=Rautschka|first2=M|last3=Sanz|first3=F|last4=Furlong|first4=LI|title=DisGeNET: a Cytoscape plugin to visualize, integrate, search and analyze gene-disease networks.|journal=Bioinformatics (Oxford, England)|date=15 November 2010|volume=26|issue=22|pages=2924-62924–6|doi=10.1093/bioinformatics/btq538|pmid=20861032}}</ref>, as [[linked data]] for the Semantic Web, and supports programmatic access to its data. These valuable set of tools allows investigating the molecular mechanisms underlying diseases of genetic origin, and are designed to support the data exploitation from different perspectives and to fulfil the needs of different types of users, including bioinformaticians, biologists and healthcare practitioners.

==Integrated data==

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==The DisGeNET Association Type Ontology==

For a seamless integration of gene-disease association data, we developed the DisGeNET association type ontology. All association types as found in the original source databases are formally structured from a parent GeneDiseaseAssociation class if there is a relationship between the gene/protein and the disease, and represented as ontological classes. It is an OWL ontology that is integrated into the [http://code.google.com/p/semanticscience/wiki/SIO Sematicscience Integrated Ontology (SIO)], which provides essential types and relations for the rich description of objects, processes and their attributes.<ref>{{cite journal|last1=Dumontier|first1=Michel|last2=Baker|first2=Christopher JO|last3=Baran|first3=Joachim|last4=Callahan|first4=Alison|last5=Chepelev|first5=Leonid|last6=Cruz-Toledo|first6=José|last7=Del Rio|first7=Nicholas R|last8=Duck|first8=Geraint|last9=Furlong|first9=Laura I|last10=Keath|first10=Nichealla|last11=Klassen|first11=Dana|last12=McCusker|first12=James P|last13=Queralt-Rosinach|first13=Núria|last14=Samwald|first14=Matthias|last15=Villanueva-Rosales|first15=Natalia|last16=Wilkinson|first16=Mark D|last17=Hoehndorf|first17=Robert|title=The Semanticscience Integrated Ontology (SIO) for biomedical research and knowledge discovery|journal=Journal of Biomedical Semantics|date=2014|volume=5|issue=1|pages=14|doi=10.1186/2041-1480-5-14}}</ref>. You can check SIO gene-disease association classes from this [http://semanticscience.org/resource/SIO_000983 URL].

==Cytoscape plugin==

The DisGeNET Cytoscape plugin<ref name="Bauer" /> offers a network representation of the gene-disease associations. It represents gene-disease associations in terms of bipartite graphs and additionally provides gene centric and disease centric views of the data. It assists the user in the interpretation and exploration of human complex diseases with respect to their genetic origin by a variety of built-in functions. Using the DisGeNET Cytoscape plugin you can perform queries restricted to (i) the original data source, (ii) the association type, (iii) the disorder class of interest and (iv) specific diseases or genes.

==Linked Data==

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[[:Category:Biological databases| ]]

[[:Category:Bioinformatics| ]]

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