Mining the biomedical literature: Dictionary-based identification of proteins in text

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Lars Juhl Jensen Mining the biomedical literature Dictionary-based identification of proteins in text

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Mining the biomedical literature: Dictionary-based identification of proteins in text

Transcript of Mining the biomedical literature: Dictionary-based identification of proteins in text

Page 1: Mining the biomedical literature: Dictionary-based identification of proteins in text

Lars Juhl Jensen

Mining the biomedical literature

Dictionary-based identification of proteins in text

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>10 km

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too much to read

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computer

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as smart as a dog

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teach it specific tricks

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named entity recognition

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text corpus

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~2 million full-text articles

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PubMed Central OA

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freely available from journals

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~22 million abstracts

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Medline

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comprehensive lexicon

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genes and proteins

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CDC2

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cyclin dependent kinase 1

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expansion rules

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prefixes and suffixes

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hCdc2

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CDC2

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flexible matching

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spaces and hyphens

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cyclin-dependent kinase 1

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cyclin dependent kinase 1

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“black list”

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SDS

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fast efficient software

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publication count

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reviews and ‘omics studies

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document weight

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occurrences of protein Xoccurrences of any protein

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Median MeanTclin 295 864.8Tchem 190 393.5Tmacro

39 154.2

Tdark 0 11.1

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cooccurrences

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diseases

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tissues

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cellular compartments

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