disgenet2r: the disgenet r package
TRANSCRIPT
disgenet2rThe DisGeNET R package
Núria Queralt RosinachIntegrative Biomedical Informatics Group (IBI)
Research Programme on Biomedical Informatics (GRIB)Hospital del Mar Research Institute (IMIM)
Pompeu Fabra University (UPF) Barcelona
DisGeNET
http://www.disgenet.org/
• Piñero et al. DisGeNET: a discovery platform for the dynamical exploration of human diseases and their genes. Database (2015) Vol. 2015: article ID bav028, (2015)
• Knowledge platform on human gene-disease associations (GDAs)
Integrates information from the literature (text mining) and expert-curated
databases
• All disease areas
• Supporting evidence
• Analysis tools
DisGeNET – 2016 release (v4.0)
New sources
Updated ontology
New annotation
New indexes
New mappings
New RDF and nanopublications distributions
New Sources
* diseases, disease groups and phenotypes
New Sources
* diseases, disease groups and phenotypes
BeFree is the major source
All sources updated
Data Model
Gene-DiseaseAssociation
Disease Gene
Gene-DiseaseAssociation
Ontology-based integration ID normalization Use of standards
Data Model
Gene-DiseaseAssociation
Disease Gene
EvidenceScore
Gene-DiseaseAssociation
SourcePubMed Sentence SNP
Ontology-based integration ID normalization Use of standards
DisGeNET ontology
Gene Association Disease
PO SP O
http://semanticscience.org/ontology/sio.owl
DisGeNET Association Type Ontology
rdf:type
DisGeNET ontologyhttp://semanticscience.org/ontology/sio.owl
DisGeNET Association Type Ontology
New Annotation
Gene-DiseaseAssociation
Disease Gene
Gene-DiseaseAssociation
MeSH ClassUMLS STY DO Class HPO Class
Disease Ontology (DO) Human Phenotype Ontology (HPO)
New Indexes
Gene-DiseaseAssociation
Disease Gene
Gene-DiseaseAssociation
Protein PathwayPANTHER
ClassDisease
SpecificityPleiotropy
DisGeNET Disease Specificity DisGeNET Pleiotropy
New Mappings
COVERAGE
Experimental Factor Ontoloty (EFO) <= BioHackathon 2015
Disease
New RDF and Nanopublications datasets• RDF
Metadata description (W3C HCLS) Interlinking
• Trusty Nanopublications
• Access• Download Data Dump • SPARQL Endpoint• Faceted Browser• Open PHACTS
• Nanopublication Network
• FAIR (ELIXIR and NIH)
http://lod-cloud.net/; Aug 2014DisGeNET - Tutorial
Tools for exploration
disgenet2r
disgenet2r
What is it? R package To query and expand DisGeNET data To analyze and visualize the results within the
powerful R framework To engage with the R/Bioconductor community Launched within the release of DisGeNET v4.0
(April, 2016)
disgenet2r
How is it implemented? R programming language S4 Object System Free open source To be added to the Bioconductor software project Data
Query: DisGeNET Expand: DisGeNET-RDF
disgenet2r
Who is developing it? DisGeNET project
The IBI Lab, GRIB-IMIM-UPF; Barcelona http://ibi.imim.es/
Developers Alba Gutierrez-Sacristan, PhD student Janet Pinero, PhD Nuria Queralt-Rosinach, PhD Emilio Centeno, Bioinformatician Laura I. Furlong, PhD (PI)
Maintainer: Alba Gutierrez-Sacristan Contact: Laura Furlong, [email protected] BioHackathon contact: Nuria Queralt (speaker),
disgenet2r
Why is it developed? New tool on Bioconductor to analyze high-
throughput genomics data Interaction with other R/Bioconductor packages
AtlasRDF, RpathVisio, DOSE,... Integration in workflows
KNIME
disgenet2r
Where to find it? https://bitbucket.org/ibi_group/disgenet2r Bitbucket repository used for package distribution
and testing until it is ready to be published in Bioconductor
Please test it! Feedback will be very welcome
disgenet2r - Functions
Query Gene-Disease Associations Query Variant-Disease Associations Query Disease-Phenotype Associations Query Disease-Disease Associations Query DisGeNET in the Linked Open Data
Query federation with WikiPathways and ChEMBL More to be added… + Visualization funcionalities
disgenet2r – Functions and Visualization
Query Gene-Disease Associations By Gene(s) or by Disease(s) Filters: database and score Visualization: network and heatmap
disgenet2r – Functions and Visualization
Query Gene-Disease Associations Visualization: grouping by class
MeSH disease class PANTHER protein class
disgenet2r - Functions and Visualization
Query Variant-Disease Associations
disgenet2r – Functions and Visualization
Query Disease-Disease Associations By disease(s)
Disease-Disease Network Comorbidity Network
disgenet2r – Functions and Visualization
Query Disease-Disease Associations By disease(s)
Disease-Disease Network
disgenet2r – Functions and Visualization
Query Disease-Disease Associations By disease(s)
Comorbidity Network
disgenet2r – Functions and Visualization
Query Disease-Disease Associations By disease(s)
Comorbidity Network
disgenet2r - Functions from RDF
IDs and URIs Query Disease-Phenotype Associations
disease2phenotype or phenotype2disease
Query DisGeNET in the Linked Open Data Query federation with WikiPathways and ChEMBL
disease2pathway or pathway2disase disease2compound or compound2disease
Disease Mappings UMLS to other ontologies and viceversa
Ontologies: MeSH, OMIM, ORPHANET, DO, ICD9, EFO, NCIT, DECIPHER, HPO
ANALYSISANALYSIS
KNOWLEDGE DISCOVERY
ACTIONABLEINFORMATION
Evidence
• Which genes are associated to Marfan syndrome?
• Which disease genes have approved drugs annotated?
• Which disease genes have differential expression?
• Which disease genes share a pathway?
• Is there genetic variation related to the MECP2 and Rett Syndrome association?
• What evidence supports the association between APP gene and Alzheimer Disease?
• Which genes and evidence support the comorbidity between Chronic Kidney disease and Diabetes Mellitus, Type 2?
Research Questions
Availability
● DisGeNET
http://www.disgenet.org
● disgenet2r
https://bitbucket.org/ibi_group/disgenet2r
● Open PHACTS, OpenLifeData, Pubannotation, FAIR data port (ELIXIR)
AcknowledgmentsIBI Group
Alba Gutiérrez-SacristánÀlex BravoAngela LeisEmilio CentenoJanet PiñeroNúria Queralt RosinachSantiago de la PenaAlexia GiannoulaMiguel A. MayerLaura I. FurlongFerran Sanz
Special thanksMichel DumontierSimon JuppNick JutyTobias KuhnandDisGeNET users!!!
Especially
OrganizersToshiaki KatayamaShin KawanoShuichi KawashimaJin-Dong KimYuji KoharaMari MinowaHiroyuki Mishima
Yuki MoriyaToshihisa TakagiToshiaki TokimatsuHongyan WuAtsuko YamaguchiYasunori Yamamoto
Thanks for your attention!Questions are welcome!