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A discovery platform for the
dynamical exploration of human
diseases and their genes
Núria QueraltRosinach
IntegrativeBiom...
Big Questions 4 Big Data
Genotype Phenotype
Environment (life-style, chemicals, radiation,
infections, clinical care
inter...
Translational Research
Genotype Phenotype
Environment
Molecular Patient
Understanding
Human
Diseases -EMR, EHR, IoT
-Imagi...
OMIM:300123; OMIM:312000
ORPHA393; ORPHA90695; ORPHA3157; ORPHA79495; ORPHA67045
MentalRetardation;Panhypopituitarism;46,X...
Large volume
Data Silos
Knowledgepockets
Different
Standards
BioHackathon 2015
Access to Gene-Disease Associations
http://www.disgenet.org/
•Piñero et al. DisGeNET:a discovery platformfor the dynamical exploration of human diseases andth...
DisGeNET Implementation
Bio-Entity Finder and Relation Extraction
Gene-disease associationsGene-disease associations
Biome...
CURATED PREDICTED LITERATURE
GAD
LHGDN
DisGeNET Sources
BioHackathon 2015
DisGeNETv3.0
Source Genes Diseases Associations
Curated 7,878 6,761 26,522
Predicted 2,557 2,003 9,536
Literature 16,298 11,374 408,175...
Text Mining
BioHackathon 2015
Need
of
biocuration pipelines
Little overlap between text mined GDAs and curated GDAs in DBs...
DisGeNET Standardization
disgenet:DGN1
gene:ncbigene_6658disease:UMLS_C0342376
BioHackathon 2015
http://semanticscience.or...

x
Data Integration

x
x
Edge=EVIDENCE
(Source, PMID,
type of relation)
Panhypopituitarism
SOX3
Score
SNP
BioHackathon 2...
•Metadata description (W3C HCLS)
•Interlinking
•Bio2RDF
•Linked Life Data
•Access
•Download Data Dump
•SPARQL Endpoint
•Fa...
Disease Annotation in DisGeNET
• X-ref to other disease terminologies:
– MeSH
– OMIM
– DO (Human Disease Ontology)
– Orpha...
Tools for exploration
BioHackathon 2015
Usage stats (May2014-May 2015):
• 7 695 users, 15539 sessions (4:39 min/session)
•...
Genotype Phenotype
Environment
Biomedical
Research
Health
Care
PPI
DDI
Comorbidities
Key in
Translational
Research
Underst...
Acknowledgments
IBI Group
AlbaGutiérrez-Sacristán
ÀlexBravo
JanetPiñero
Núria Queralt Rosinach
Alexia Giannoula
MiguelA. M...
Especially
Organizers
BioHackathon 2015
ToshiakiKatayama
ShinKawano
ShuichiKawashima
Jin-DongKim
YujiKohara
MariMinowa
Hir...
Thanks for your attention!
Questions are welcome!
BioHackathon 2015
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DisGeNET: A discovery platform for the dynamical exploration of human diseases and their genes

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Presentation of DisGeNET at the Symposium day of the BioHackathon 2015

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DisGeNET: A discovery platform for the dynamical exploration of human diseases and their genes

  1. 1. A discovery platform for the dynamical exploration of human diseases and their genes Núria QueraltRosinach IntegrativeBiomedical InformaticsGroup(IBI) Research Programmeon Biomedical Informatics(GRIB) Hospital del Mar Research Institute(IMIM) Pompeu FabraUniversity (UPF) Barcelona
  2. 2. Big Questions 4 Big Data Genotype Phenotype Environment (life-style, chemicals, radiation, infections, clinical care intervention,…) Human Biology Medical Sciences Understanding Human Diseases PPI DDI Comorbidities -EMR, EHR, IoT -Imaging -Patient registries -Clinical trials -Epidemiologic studies -… -Data Bases -Literature -OMICS -Animal models -… BioHackathon 2015
  3. 3. Translational Research Genotype Phenotype Environment Molecular Patient Understanding Human Diseases -EMR, EHR, IoT -Imaging -Patient registries -Clinical trials -Epidemiologic studies -… -Data Bases -Literature -OMICS -Animal models -… Key in Translational Research •Decision-making •Prevention •Diagnosis •Therapies •ResearchDiscoveryBioHackathon 2015
  4. 4. OMIM:300123; OMIM:312000 ORPHA393; ORPHA90695; ORPHA3157; ORPHA79495; ORPHA67045 MentalRetardation;Panhypopituitarism;46,XX sex reversal 3 MESH:C538613; MESH:C538613 No Data Mental retardation -?- SOX3 Access to Gene-Disease Associations BioHackathon 2015 SOX3
  5. 5. Large volume Data Silos Knowledgepockets Different Standards BioHackathon 2015 Access to Gene-Disease Associations
  6. 6. http://www.disgenet.org/ •Piñero et al. DisGeNET:a discovery platformfor the dynamical exploration of human diseases andtheir genes. Database(2015) Vol. 2015: articleID bav028, (2015) • Knowledge platform on human gene-disease associations(GDAs) • Integrates informationfrom expert-curated databases and from the literature(text mining) • All disease areas • Supporting evidence BioHackathon 2015
  7. 7. DisGeNET Implementation Bio-Entity Finder and Relation Extraction Gene-disease associationsGene-disease associations Biomedicaldatabases BioHackathon 2015 Text mining http://ibi.imim.es/befree/
  8. 8. CURATED PREDICTED LITERATURE GAD LHGDN DisGeNET Sources BioHackathon 2015 DisGeNETv3.0
  9. 9. Source Genes Diseases Associations Curated 7,878 6,761 26,522 Predicted 2,557 2,003 9,536 Literature 16,298 11,374 408,175 All 17,181 14,619 429,111 DisGeNET Statistics (May 15th, 2015) 82 % BioHackathon 2015 Large volume of information unlocked by text mining the literature DisGeNETv3.0
  10. 10. Text Mining BioHackathon 2015 Need of biocuration pipelines Little overlap between text mined GDAs and curated GDAs in DBs DisGeNETv3.0
  11. 11. DisGeNET Standardization disgenet:DGN1 gene:ncbigene_6658disease:UMLS_C0342376 BioHackathon 2015 http://semanticscience.org/ontology/sio.owl • DisGeNET ontology (type of relation) • Normalization ofID • Controlledvocabularies UMLS STY PANTHER class Reactome Pathway MeSH class
  12. 12.  x Data Integration  x x Edge=EVIDENCE (Source, PMID, type of relation) Panhypopituitarism SOX3 Score SNP BioHackathon 2015 Panhypopituitarism UMLS:C0342376 SOX3 NCBI:6658
  13. 13. •Metadata description (W3C HCLS) •Interlinking •Bio2RDF •Linked Life Data •Access •Download Data Dump •SPARQL Endpoint •Faceted Browser •Open PHACTS • Open license •DataHub •Software DisGeNET as Linked Data • RDF and trusty nanopublications – URIs: RDF providers or – SIO – Use of standards (11 ontologies in NCBO) BioHackathon 2015 http://lod-cloud.net/; Aug 2014
  14. 14. Disease Annotation in DisGeNET • X-ref to other disease terminologies: – MeSH – OMIM – DO (Human Disease Ontology) – Orphanet – NCI – ICD9CM – HPO (Human Phenotype Ontology) • Phenotype annotation from HPO BioHackathon 2015 Interoperability
  15. 15. Tools for exploration BioHackathon 2015 Usage stats (May2014-May 2015): • 7 695 users, 15539 sessions (4:39 min/session) • 16 130 downloads (database, Cytoscape plugin, RDF/Nanopubs) • DisGeNETused in 20+ publications, cited in +60 articles
  16. 16. Genotype Phenotype Environment Biomedical Research Health Care PPI DDI Comorbidities Key in Translational Research Understanding Human Diseases BioHackathon 2015 •Decision-making •Prevention •Diagnosis •Therapies •ResearchDiscovery
  17. 17. Acknowledgments IBI Group AlbaGutiérrez-Sacristán ÀlexBravo JanetPiñero Núria Queralt Rosinach Alexia Giannoula MiguelA. Mayer LauraI. Furlong FerranSanz BioHackathon 2015 Special thanks ChristineChichester MichelDumontier TobiasKuhn Mark Thompson Jesse Van Dam Open PHACTS collaborators and DisGeNETusers!!!
  18. 18. Especially Organizers BioHackathon 2015 ToshiakiKatayama ShinKawano ShuichiKawashima Jin-DongKim YujiKohara MariMinowa HiroyukiMishima YukiMoriya Toshihisa Takagi Toshiaki Tokimatsu HongyanWu Atsuko Yamaguchi YasunoriYamamoto
  19. 19. Thanks for your attention! Questions are welcome! BioHackathon 2015

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