applications of text and data mining of biomedical databases
TRANSCRIPT
Applications of Text and
Data Mining of biomedical
databases
Miguel Andrade Computational Biology & Data Mining group Max Delbrück Center for Molecular Medicine
Gene structures
Gene expression
Protein sequences
Protein databases
Literature databases
Biological predictions
Human disease
001001001000100101011110110110
AGCTGGTACGAAGATGTCTCGCA
MLVPIEKAEVPRYILKTEFRKAILTS
In a phosphorylation dependent ma
Protein and nucleotide sequences (UniProt, Entrez),
Protein domains (PFAM, SMART), Structures (PDB), Diseases (OMIM),
Gene expression (GEO),
Bibliography (records, MEDLINE)
(full text, PubMed Central)
Molecular Biology databases
Compressed PubMed in XML: 17GB 23M items (exhaustive back to 1966, oldest from 1809) PubMed Central open access subset 26GB of raw XML files (text only), compressed 8GB. 2.6M items
Bibliography (records, MEDLINE)
(full text, PubMed Central)
Molecular Biology databases
Compressed PubMed in XML: 17GB 23M items (exhaustive back to 1966, oldest from 1809) PubMed Central open access subset 26GB of raw XML files (text only), compressed 8GB. 2.6M items 1 Human Genome 320GB
Bibliography (records, MEDLINE)
(full text, PubMed Central)
Molecular Biology databases
K2
Mapping systems
K1
ENTRY
Mapping systems
Trans membrane
PROTEIN
GPCR Receptor
GO
KW
SwissProt
ENTRY
Mapping systems
K2
K1 ENTRY
PAPER
Mapping systems
K2
K1 PROTEIN
GO
MeSH SwissProt MEDLINE
PAPER
Mapping systems
K2
K1 PROTEIN STRUCTURE
SCOP
MeSH PDB MEDLINE
TIM barrel
Enzyme
PAPER
Iterate!
GENE K2
K1 PROTEIN
KW
MeSH SwissProt MEDLINE
EntrezGene
MEDLINE
Entrez Gene
UniProt
KW
authors words MeSH
GO
GO
NetAffx
GO UniGene
ProDom
PDB
GO
fold OMIM words
GEO
PubMed
PubMed
PubMed
Rank MEDLINE according to a topic
Fontaine et al. (2009) Nucleic Acids Research
Jean-Fred Fontaine
http://cbdm.mdc-berlin.de/tools/medlineranker/
MedlineRanker
Jean-Fred Fontaine
http://cbdm.mdc-berlin.de/tools/medlineranker/
MedlineRanker
Génie
http://cbdm.mdc-berlin.de/tools/genie/
Ranks a set of genes from a whole genome according to a topic
Fontaine et al. (2011) Nucleic Acids Research
Human
Génie
http://cbdm.mdc-berlin.de/tools/genie/
PESCADOR
http://cbdm.mdc-berlin.de/tools/pescador/
Extract interactions and filter by concepts
Barbosa-Silva et al. (2010) BMC Bioinformatics
Adriano Barbosa
Barbosa-Silva et al. (2011) BMC Bioinformatics
PESCADOR
Co-occurrences types PESCADOR
co-occurrence in abstract
Type 4
Type 3
Term + Term
Type 2
[Biointeraction] +Term + Term + [Biointeraction]
Type 1
Term + [Biointeraction] + Term
Country-specific variations of English
Netzel et al. (2003)
EMBO Reports
Country-specific variations of English
Netzel et al. (2003)
EMBO Reports
Worldwide scientific publishing activity
Perez-Iratxeta and Andrade
(2002) Science
Approximate amount of publications for the years 1996–2001 per million
inhabitants by country:
10,000 100
1,000 10 1
Ratio publications for 1996–2001 / 1989–95
Worldwide scientific publishing activity
+++ -
++ = --
+ ---
Perez-Iratxeta and Andrade
(2002) Science
Find referees
peer2ref
Andrade-Navarro et al (2012) BioData Mining
Carolina Perez-Iratxeta
(OHRI-Ottawa)
http://www.ogic.ca/peer2ref/
Andrade-Navarro et al (2012) BioData Mining
Find referees
peer2ref
Carolina Perez-Iratxeta
(OHRI-Ottawa)
http://www.ogic.ca/peer2ref/
Gareth Palidwor (OHRI-Ottawa)
http://www.ogic.ca/mltrends/
Graph historical term usage in MEDLINE
MLTrends
Palidwor and Andrade-Navarro (2010) Journal of Biomedical Discovery and Collaboration
Graph historical term usage in MEDLINE
MLTrends
Gareth Palidwor (OHRI-Ottawa)
http://www.ogic.ca/mltrends/
Palidwor and Andrade-Navarro (2010) Journal of Biomedical Discovery and Collaboration
http://cbdm.mdc-berlin.de/
Enrique Muro
Martin Schaefer
Arvind Mer
David Fournier
Nancy Mah
Marie Gebhardt
Jean-Fred Fontaine
Computational Biology and Data Mining group