PaperMaker, BeyondThePdf, RebholzSchuhmann, 19Jan2011

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Presentation on Whatizit, LexEBI, IeXML, CALBC, SESL, PaperMaker

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PaperMaker: Validation of biomedical scientificpublicationsJanuary 19th, 2011Workshop: BeyondThePdfDietrich Rebholz-Schuhmann, MD, PhDGroup Leader Rebholz GroupEuropean Bioinformatics Institute Publishing is about ... Agreeing / disagreeing about current science Only peer review can judge current science ... Bringing new results Conceptual results are more difficult than new data ... Gaining new knowledge New data and new results can imply new knowledge where even the author is still unaware of ... Rewarding the scientist Count whatever you can count that could have an impact. Validating the scientists claim is the key reward. Any scientist can fool any system, but (hopefully) only short-term2 20.01.2011 Literature and Text Mining BioCreative III, Rebholz Future of biomedical text mining Working towards ... ... Literature integration to have it full fledged as part of bioinformatics data resources ... Cross-domain support to deliver the content to different scientific communities. ... Provenance to carry credit of findings into analytical biomedical research ... Inference & Reasoning to make use of the full semantic support in the scientific literature3 20.01.2011 Literature and Text Mining BioCreative III, Rebholz Literature content in the Semantic Web4 20.01.2011 Literature and Text Mining Terminologies vs. Ontologies Ontological resources Database type Resource building Explicit semantics Terminologies, collection of terms Manual generation Automatic generation Consistency, inference, reasoning Exploitation of terminological features Interoperability with all semantic Standardisation of TM solutions resources Interoperability with database Working towards a reasoning resources infrastructure5 Literature and Text Mining Efforts in the Rebholz group towards interoperability of literature with bioinformatics Whatizit infrastructure Biomedical NER as a public, large-scale service LexEBI / BioLexicon (collab. w. NaCTeM, Pisa-U) Biomedical terminological resource, standardisation of semantics IeXML (BioLink SIG 2006, Brasil) Put the annotations into the document (inline annotations) CALBC project Collaborative annotation of a large-scale biomedical corpus UKPMC: U.K. Pubmed Central (collab. w. NaCTeM, BL) Use of Whatizit, BioLexicon, IeXML, CALBC alignments for the delivery of quality annotation services to the public SESL project Joint project with pharma & publishers, literature content in a triple store PaperMaker Validation of the scientific literature against the above6 20.01.2011 Literature and Text Mining BioCreative III, Rebholz 1 Whatizit7 20.01.2011 Literature and Text Mining BioCreative III, Rebholz Integrating biomedical literature and data Rebholz-Schuhmann, D., et al. Text Processing through Web Services: Calling Whatizit. Bioinformatics 24, no. 2 (2008): 296-98.8 20.01.2011 Literature and Text Mining 2 BioLexicon LexEBI9 20.01.2011 Literature and Text Mining BioCreative III, Rebholz LexEBI: content # Labels # Variants Total Total / # Unique Uniq. T. / Labels terms Labels Prot. Gene GP 7.0 516,113 4,005,040 4,521,153 8.76 1,726,853 3.35 / GP 6.0 488,577 3,389,316 3,877,893 7.94 1,564,436 3.20 Jochem 278,578 1,691,980 1,970,558 7.07 1,527,752 5.48 Chemi- cals ChEBI 19,645 94,748 114,393 5.82 101,307 5.16 ChEBI (all) 549,838 1,187,322 1,737,160 3.16 Enzymes 4,905 8,082 12,987 2.65 12,377 2.52 Other Species 643,280 199,130 842,410 1.31 838,135 1.30 Interpro 20,671 0 20,671 1.00 20,671 1.00 Antineuro., 4,718 6,488 11,206 2.38 Neo Bio. Act. 54,148 87,209 141,357 2.61 UMLS Enzymes 26,065 56,332 82,397 3.16 Lipid, Carb. 11,518 9,770 21,288 1.85 Pharm. Act. 104,201 123,840 228,041 2.19 Vit., Horm. 6,877 10,258 17,135 2.4910 20.01.2011 Literature and Text Mining 3 IeXML11 20.01.2011 Literature and Text Mining BioCreative III, Rebholz IeXML: Annotating entities in text Inline annotations to any part of the document with the annotations No hassle with character or byte counts or layout modifications to the document Alignment of annotated documtents to Compare annotations Validate annotations Harmonise annotations (SESL project)12 20.01.2011 Literature and Text Mining BioCreative III, Rebholz 4 CALBC13 20.01.2011 Literature and Text Mining BioCreative III, Rebholz The challenge 150,000 documents or more ... Test set for all systems Assessment, benchmarking14 20.01.2011 Literature and Text Mining BioCreative III, Rebholz CALBC Challenge II(1) 75,000 documents training data(2) 175,000 testing data(3) Additional 700,000 testing data September 13th 2010: Second harmonized corpus available for CALBC Challenge II December 15th, 2010: Challenge II closes March 2011: CALBC Workshop II June 30th, 2011: Final harmonized corpus available Literature and Text Mining BioCreative III, Rebholz 5 Ukpmc/Elixir16 20.01.2011 Literature and Text Mining BioCreative III, Rebholz 17 20.01.2011 Literature and Text Mining BioCreative III, Rebholz UKPMC ~ 10 % the size of PubMed18 20.01.2011 Literature and Text Mining BioCreative III, Rebholz 6 sesl19 20.01.2011 Literature and Text Mining BioCreative III, Rebholz SESL Project: from publisher to pharma Multiple Consumers Disease Knowledge Dossier Applications Service Layer (RDF, Web 2.0) Std PublicOpen Common Assertions, SPARQL, Triple Store VocabulariesStan- Service Integration, Inference, Reasoning Businessdards Broker Sharing of data Rules Content Suppliers20 20.01.2011 Literature20 and Text Mining Literature content in the Semantic Web21 20.01.2011 Literature and Text Mining 7 Papermaker22 20.01.2011 Literature and Text Mining BioCreative III, Rebholz PaperMaker - Overview Inte PaperMaker - a tool to support authors writing biomedical papers: Interactive feedback on the contents of papers (related work and concept annotations) Formal consistency criteria checking (spelling, terminology, acronyms, references)30.03.2009 Literature and Text Mining BioCreative III, Rebholz Consistency parametersDomain-independent General spelling and grammar General readability Appropriate use of references Finding and acknowledging related work30.03.2009 Literature and Text Mining BioCreative III, Rebholz Consistence parametersDomain-specific The use of terminology: Should be consistent with naming domain-specific guidelines Should not be ambiguous Should conform to the conventional usage (possible clashes between naming guidelines and common-sense convention) Useful to resolve terminology to reference databases (e. g. UniProt for protein names, ChEBI chemical entities, etc.) The special case of acronyms30.03.2009 Literature and Text Mining BioCreative III, Rebholz Content feedback Resolving the contents to literature repositories Finding related work (document retrieval) Finding related ideas (passage retrieval) Resolving the contents to ontological reference databases MeSH descriptors have been demonstrated to improve biomedical information retrieval. Can we suggest MeSH terms directly to the authors? Gene Ontology (GO) terms are increasingly used in information extraction systems.30.03.2009 Literature and Text Mining BioCreative III, Rebholz PaperMaker workflow30.03.2009 Literature and Text Mining BioCreative III, Rebholz Literature and Text Mining Literature and Text Mining Literature and Text Mining Literature and Text Mining Conclusions PaperMaker can help the author conform to the formal requirements of paper writing with special emphasis on the domain It also provides feedback on the contents by relating it to reference resources and literature repositories It may improve the indexing of a paper in literature repositories (less ambiguous terminology) http://www.ebi.ac.uk/Rebholz-srv/PaperMaker Work in progress 30.03.2009 Literature and Text Mining BioCreative III, Rebholz 8 Summary33 20.01.2011 Literature and Text Mining BioCreative III, Rebholz Efforts in the Rebholz group towards interoperability of literature with bioinformatics Whatizit infrastructure Biomedical NER as a public, large-scale service LexEBI / BioLexicon (collab. w. NaCTeM, Pisa-U) Biomedical terminological resource, standardisation of semantics IeXML (BioLink SIG 2006, Brasil) Put the annotations into the document (inline annotations) CALBC project Collaborative annotation of a large-scale biomedical corpus UKPMC: U.K. Pubmed Central (collab. w. NaCTeM, BL) Use of Whatizit, BioLexicon, IeXML, CALBC alignments for the delivery of quality annotation services to the public SESL project Joint project with pharma & publishers, literature content in a triple store PaperMaker Validation of the scientific literature against the above34 20.01.2011 Literature and Text Mining BioCreative III, Rebholz Literature and Text MiningBioCreative III, Rebholz