Integration of biomedical data and electronic publications
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Integration of biomedical dataand electronic publications
Lars Juhl JensenEMBL Heidelberg
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printed publications
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dead wood
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electronic publications
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virtual dead wood
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de Lichtenberg et al., Science, 2005
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small font sizes
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“no”
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Jensen et al., Nature Reviews Genetics, 2006
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small font sizes
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hyperlinks
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“no”
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“hell no”
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why?
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archival
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reanalysis
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data mining
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reader interaction
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what?
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raw data
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processed data
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final data
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“facts”
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where?
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part of the document
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too much data
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too coarse grained
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escalates the problem
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institutional repositories
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too many types of data
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lack of standardization
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difficult to download all data
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public databases
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specialization
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standardization
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mandatory deposition
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easy to download all data
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cross references
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examples from biomedicine
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GenBank
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17.9 million sequences
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80 billion nucleotides
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UniProt
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4.7 million sequences
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Ensembl
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35 complete genomes
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PDB
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44000 protein structures
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GEO
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5800 data sets
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152000 samples
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ArrayExpress
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1800 data sets
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BioGRID
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186000 interactions
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129000 proteins
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MINT
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103000 interactions
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28000 proteins
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PubChem
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7.5 million compounds
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PubMed Central
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330 open access journals
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12000 open access papers
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downloadable
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standardized formats
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cross-referenced
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archival
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reanalysis
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data mining
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reader interaction
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thank you!