Transcript Open access
Open access – making the most of biomedical literature mining Lars Juhl Jensen EMBL Heidelberg why open access? why biomedicine? why literature mining? MEDLINE Mitotic cyclin (Clb2)-bound Cdc28 (Cdk1 homolog) directly phosphorylated Swe1 and this modification served as a priming step to promote subsequent Cdc5-dependent Swe1 hyperphosphorylation and degradation information retrieval finding the papers if you can’t find them … … they don’t exist! ad hoc retrieval users-specified query “yeast AND cell cycle” Mitotic cyclin (Clb2)-bound Cdc28 (Cdk1 homolog) directly phosphorylated Swe1 and this modification served as a priming step to promote subsequent Cdc5-dependent Swe1 hyperphosphorylation and degradation MEDLINE abstracts complete papers tricks stemming yeast / yeasts synonyms yeast / S. cerevisiae dynamic query expansion next logical step ontologies annotation Cdc28 yeast gene Cdc28 cell cycle Mitotic cyclin (Clb2)-bound Cdc28 (Cdk1 homolog) directly phosphorylated Swe1 and this modification served as a priming step to promote subsequent Cdc5-dependent Swe1 hyperphosphorylation and degradation “yeast AND cell cycle” entity recognition identifying the substance(s) Mitotic cyclin (Clb2)-bound Cdc28 (Cdk1 homolog) directly phosphorylated Swe1 and this modification served as a priming step to promote subsequent Cdc5-dependent Swe1 hyperphosphorylation and degradation if you can’t find them … … they don’t exist! abstracts MEDLINE tricks good synonyms list manual curation orthographic variation CDC28 Cdc28p disambiguation hairy SDS Cdc2 information extraction formalizing the facts co-mentioning Mitotic cyclin (Clb2)-bound Cdc28 (Cdk1 homolog) directly phosphorylated Swe1 and this modification served as a priming step to promote subsequent Cdc5-dependent Swe1 hyperphosphorylation and degradation NLP Natural Language Processing Mitotic cyclin (Clb2)-bound Cdc28 (Cdk1 homolog) directly phosphorylated Swe1 and this modification served as a priming step to promote subsequent Cdc5-dependent Swe1 hyperphosphorylation and degradation Gene and protein names Cue words for entity recognition Verbs for relation extraction [nxexpr The expression of [nxgene the cytochrome genes [nxpg CYC1 and CYC7]]] is controlled by [nxpg HAP1] new discoveries text mining temporal trends buzzwords grant applications global correlations 3592 79 32 Regulates 83 Regulated P < 910-9 transcriptional networks 3704 27 11 Phosphorylates 44 Phosphorylated P < 210-7 signal cascades 3625 107 8 Expression 47 Phosphorylation P < 510-4 integration of text and data network mining linking genes to diseases multifactorial diseases genotype to phenotype where are we now? abstracts complete papers restricted access open access the tools are there now we need the text! Acknowledgments Jasmin Saric Rossitza Ouzounova Michael Kuhn Isabel Rojas Miguel Andrade Peer Bork