1. disgenet2r
The DisGeNET R package
Núria Queralt Rosinach
Integrative Biomedical Informatics Group (IBI)
Research Programme on Biomedical Informatics (GRIB)
Hospital del Mar Research Institute (IMIM)
Pompeu Fabra University (UPF)
Barcelona
3. 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
4. DisGeNET – 2016 release (v4.0)
New sources
Updated ontology
New annotation
New indexes
New mappings
New RDF and nanopublications distributions
17. 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)
18. 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
19. 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, laura.furlong@upf.edu
BioHackathon contact: Nuria Queralt (speaker),
nqueralt.r@gmail.com
20. 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
21. 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
22. 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
23. disgenet2r – Functions and Visualization
Query Gene-Disease Associations
By Gene(s) or by Disease(s)
Filters: database and score
Visualization: network and heatmap
24. disgenet2r – Functions and Visualization
Query Gene-Disease Associations
Visualization: grouping by class
MeSH disease class PANTHER protein class
26. disgenet2r – Functions and Visualization
Query Disease-Disease Associations
By disease(s)
Disease-Disease Network Comorbidity Network
27. disgenet2r – Functions and Visualization
Query Disease-Disease Associations
By disease(s)
Disease-Disease Network
28. disgenet2r – Functions and Visualization
Query Disease-Disease Associations
By disease(s)
Comorbidity Network
29. disgenet2r – Functions and Visualization
Query Disease-Disease Associations
By disease(s)
Comorbidity Network
30. 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
31. ANALYSISANALYSIS
KNOWLEDGE
DISCOVERY
ACTIONABLE
INFORMATION
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
33. Acknowledgments
IBI Group
Alba Gutiérrez-Sacristán
Àlex Bravo
Angela Leis
Emilio Centeno
Janet Piñero
Núria Queralt Rosinach
Santiago de la Pena
Alexia Giannoula
Miguel A. Mayer
Laura I. Furlong
Ferran Sanz
Special thanks
Michel Dumontier
Simon Jupp
Nick Juty
Tobias Kuhn
and
DisGeNET users!!!