TM Workshop: theory and hands-on

Overview of the workshop• Short introduction: D. Rebholz-Schuhmann• Features from text (IR, NER): Piotr Pezik• Natural Language Processing: Ian Lewin• H<strong>and</strong>s-On Solutions (EBI ... ): D. Rebholz-Schuhmann• H<strong>and</strong>s-On Solutions (NaCTEM ...): S. Ananiadou• Discussion at the end of the day• Biomedical Semantics Solutions: J.-j. Kim• Computational Methods: A Jimeno-Yepes, D. Rebholz-Schuhmann206.10.2009Literature Web <strong>and</strong> DAS services from <strong>TM</strong> research

ResearchUse conceptsnot terms(Semantics)Questions <strong>and</strong> AnswersDeliver reliableFacts(Integration)406.10.2009Literature Web <strong>and</strong> DAS services from <strong>TM</strong> research

Behavioral patterns in information seekingDifferentiating <strong>and</strong> Chaining are difficult to get.Jung-JaeKim506.10.2009Literature Web <strong>and</strong> DAS services from <strong>TM</strong> research

UKPMC: Joining Literature <strong>and</strong> DataLiterature Web <strong>and</strong> DAS services from <strong>TM</strong> research

Exploitation of literature for biomedical data resourcesGenes / ProteinsFunctions, PathwaysGenes to Diseases(MeSH, GO)Chemical EntitiesDrugs – Drug targetsProtein residues706.10.2009Literature Web <strong>and</strong> DAS services from <strong>TM</strong> research

DocumentEntitiesTokensConceptsFacts806.10.2009Literature Web <strong>and</strong> DAS services from <strong>TM</strong> research

“The function of OmpR appears to bethe enhancement of a basal level of ompC expression”OmpRompC… the of appear …basal levelof ompCexpressionOmpR increases ompC expression906.10.2009Literature Web <strong>and</strong> DAS services from <strong>TM</strong> research

Science, Nature, Elsevier,PLoS, BMC, PNAS …UniProtKbPubChemUMLS, …… BNC…OBOfoundryIntACT, OMIM, BioModels, …1006.10.2009Literature Web <strong>and</strong> DAS services from <strong>TM</strong> research

SwissProtBiolexicon,humanChemicalsentitiesDiseaseNEREntities + conceptsBest performance=> 100% Precision=> 100% RecallMeSH termsGo terms(@ Rank 1)All solutions arestate of the artJimeno et al., BMC Bioinformatics, 20081106.10.2009Literature Web <strong>and</strong> DAS services from <strong>TM</strong> research

Text Mining Research: Challenges• Normalisation of annotations of semantic types in thescientific literature (chemical entities, diseases)• Quality control (e.g., BioCreAtIve, others)• Integration of <strong>TM</strong> solutions into bioinformatics solutions(e.g., integration with bioinformatics data resources)=> DAS services• Validation of paper content=> authoring tools=> have the author adding additional information (FEBSLetter)• Full papers: OUP (NAR), NPG, MolSysBio, (Elsevier)• Use <strong>and</strong> design of ontological resources for informationextraction (Example GRO, EU FP6 BootStrep project)1206.10.2009Literature Web <strong>and</strong> DAS services from <strong>TM</strong> research

Objectives of Tm <strong>Workshop</strong>• Short introduction: D. Rebholz-Schuhmann=> Get an overview on biomedical text mining?• Features from text (IR, NER): Piotr Pezik=> How to decompose text <strong>and</strong> use its features?• Natural Language Processing: Ian Lewin=> How sentence structure works <strong>and</strong> how to exploit it?• H<strong>and</strong>s-On Solutions (EBI ... ): D. Rebholz-SchuhmannH<strong>and</strong>s-On Solutions (NaCTEM ...): S. Ananiadou=> What do existing IR tools deliver to you?• Biomedical Semantics Solutions: J.-j. Kim=> How do we integrate semantics for better results?• Computational Methods: A Jimeno-Yepes=> How do you exploit our solutions <strong>and</strong> what you get?1306.10.2009Literature Web <strong>and</strong> DAS services from <strong>TM</strong> research

DietrichRebholz-SchuhmannPiotrPezikAnnikaOellrichKevinAu-yeungJung-JaeKimJee-HyubKimVivian LeeAntonioJimenoYepesChristophGrabmuellerNicolasRodriguezAdamBernardIan LewinSpecial thankstoHarald KirschMiguel ArreguiSylvain GaudanMenakaNarayasamySilvestrasKavilauskas1406.10.2009Literature Web <strong>and</strong> DAS services from <strong>TM</strong> research