BioCreative II.5 Workshop 2009 Special Session on Digital Annotations The purified IRF-4 was also The main role of BRCA2 shown to be capable of binding appears to involve regulating the DNA in a PU.1-dependent manner function of RAD51 in the repair by by electrophoretic mobility shift homologous recombination . analysis. brca2 irf4 We found that cells ex- Moreover, expression of pressing Olig2, Nkx2.2, and NG2 Carma1 induces phosphorylation were enriched among virus- of Bcl10 and activation of the infected, GFP-positive (GFP+) transcription factor NF-kappaB. cells. carma1 BB I O olig2 The region of VHL medi- The Rab5 effector ating interaction with HIF-1 alpha Rabaptin-5 and its isoform C R E A T I V E overlapped with a putative Rabaptin-5delta differ in their macromolecular binding site within ability to interact with the rsmallab5 the crystal structure. GTPase Rab4. vhl Translocation RCC, bearing We show that ERBB2-dependenterbb2 atf1 TFE3 or TFEB gene fusions, are Both ATF-1 homodimers and tfe3 medulloblastoma cell invasion and ATF-1/CREB heterodimers bind to recently recognized entities for prometastatic gene expression can the CRE but not to the related which risk factors have not been be blocked using the ERBB tyrosine phorbol ester response element. identified. kinase inhibitor OSI-774. C r i t i c a l A s s e s s m e n t o f I n f o r m a t i o n E x t r a c t i o n i n B i o l o g y October 7th - 9th, 2009 www.BioCreative.org BioCreative II.5 Workshop 2009 special session | Digital Annotations Auditorium of the Spanish National Cancer Research Centre (CNIO) Madrid, Spain, October 7th - 9th 2009 Organizers ‣ Belén Bañeres Spanish National Cancer Research Centre (CNIO), Spain ‣ Gianni Cesareni Department of Biology, University of Rome Tor Vergata, Italy ‣ Lynette Hirschman Biomedical Informatics for the Information Technology Center (MITRE), USA ‣ Martin Krallinger Spanish National Cancer Research Centre (CNIO), Spain ‣ Florian Leitner Spanish National Cancer Research Centre (CNIO), Spain ‣ Alfonso Valencia Spanish National Cancer Research Centre (CNIO), Spain Sponsors BioCreative is supported by the Spanish National Bioinformatics Institute (www.inab.org) - a platform of Genoma España, and the Spanish National Cancer Research Centre (CNIO). The BioCreative II.5 workshop is supported by the European Commission FP6 NoEs ENFIN LSHG- CT-2005-518254 and EMBRACE LSG-CT-2004-512092. 1 table | Contents workshop | Programme 7 wednesday | Oct 7 7 thursday | Oct 8 8 friday | Oct 9 9 digital annotations | The Proponents 11 Digital Annotations: the publishers 11 Adriaan Klinkenberg Active Learning for More Efficient Corpus Annotation 12 Udo Hahn Digital Annotation for Production Bioinformatics Systems 13 Judith A. Blake UniProt KnowledgeBase (UniProtKB) annotation and text mining 14 Alan Bridge Text Mining needs of bioinformaticians in the Pharmaceutical Industry 15 Ian Harrow digital annotations | FEBS & BioCreative 17 The curation process in the context of the FEBS letters SDA experiment 17 Gianni Cesareni Analysis of Author, Expert and System Curation Results for the INT (Interacting Proteins) Task 18 Lynette Hirschman The BioCreative II.5 challenge overview 19 Martin Krallinger BioCreative II.5: Evaluation and ensemble system performance 20 Florian Leitner and Lynette Hirschman 3 Proceedings of the BioCreative II.5 Workshop 2009 on Digital Annotations keynotes | Workshop 21 Rethinking the goals of BioNLP research: What are we trying to accomplish? 21 Larry Hunter Predicting the future of prediction 22 Anna Tramontano CALBC: Producing a large-scale biomedical corpus is a challenge 23 Dietrich Rebholz-Schuhmann systems | Applied 25 WikiGenes - Collaborative scientific publishing on the Web 25 Robert Hoffmann Reflect: An Augmented Browsing Tool for Scientists 26 Seán I. O’Donoghue The OKKAM authoring platform for entity annotation: the SDA case 27 Stefano Bocconi The BioCreative Meta-Server in the challenge and as a collaborative text-mining platform 28 Florian Leitner systems | Participants 29 Normalizing Interactor Proteins and Extracting Interaction Protein Pairs using Support Vector Machines 29 Yifei Chen Online protein interaction extraction and normalization at Arizona State University 30 Jörg Hakenberg IASL-IISR interactor normalization system using a multi-stage cross-species gene normalization algorithm and SVM-based ranking 31 Hong-Jie Dai OntoGene in BioCreative II.5 32 Fabio Rinaldi AkaneRE Relation Extraction: Protein Normalization (INT) and Interaction (IPT) in the BioCreAtIvE II.5 Challenge 33 Rune Sætre Classification of protein-protein interaction documents using text and citation network features 34 Luis M. Rocha 4 Proceedings of the BioCreative II.5 Workshop 2009 on Digital Annotations Combining regular expressions and lexical frequency for online extraction of protein-protein interactions 35 Frederic Ehrler A Probabilistic Dimensional Data Model for Protein Identification, Disambiguation, and Interaction Discovery 36 Jay Urbain Information Extraction of Normalized Protein Interaction Pairs Utilizing Linguistic and Semantic Cues 37 Karin Verspoor Empirical investigations into full-text protein interaction article categorization task (ACT) in the BioCreative II.5 Challenge 38 Man Lan Applying Lazy Local Learning in BC II.5 Article Categorization Task 39 Cheng-Ju Kuo abstracts | Posters 41 BioAlvis II, NLP-based semantic mining of literature on molecular biology of bacteria 41 Using Full Text from Scientific Articles in Portable Document Format 42 portfolios | Speakers 43 Judith Blake 43 Stefano Bocconi 43 Alan Bridge 44 Gianni Cesareni 44 Udo Hahn 44 Ian Harrow 45 Lynette Hirschman 46 Robert Hoffmann 46 Larry Hunter 47 Adriaan Klinkenberg 47 Martin Krallinger 48 Florian Leitner 48 Seán I. O’Donoghue 49 5 Proceedings of the BioCreative II.5 Workshop 2009 on Digital Annotations Dietrich Rebholz-Schuhmann 49 Anna Tramontano 50 Alfonso Valencia 51 overview | Participants 53 proccedings | Notes 55 6 workshop | Programme wednesday | Oct 7 digital 08:30 09:00 Registration annotations the 09:00 09:20 Workshop opening and welcome proponents Alfonso Valencia, CNIO 09:20 10:00 Digital Annotations: the publishers Adriaan Klinkenberg, Elsevier 10:00 10:40 Active Learning for More Efficient Corpus Annotation Udo Hahn, Friedrich-Schiller-Universität Jena 10:40 11:20 Digital Annotation for Production Bioinformatics Systems Judith Blake, The Jackson Laboratory coffee | Break digital 11:40 12:20 UniProt KnowledgeBase (UniProtKB) annotation and text mining annotations the Alan Bridge, Swiss Institute of Bioinformatics proponents 12:20 13:00 Text Mining needs of bioinformaticians in the Pharmaceutical Industry Ian Harrow, Pfitzer Global Research and Development lunch | Break digital 14:30 15:10 The curation process in the context of the FEBS letters SDA annotations febs & experiment biocreative Gianni Cesareni, University of Rome Tor Vergata 15:10 15:50 The BioCreative II.5 challenge overview Martin Krallinger, CNIO 15:50 16:30 Analysis of Author, Expert and System Curation Results for the INT (Interacting Proteins) Task Lynette Hirschman, MITRE coffee | Break digital 17:00 17:40 BioCreative II.5: Evaluation and Ensemble System Performance annotations febs & Florian Leitner, CNIO & Lynette Hirschman, MITRE biocreative 17:40 18:30 Discussion | Digital annotations, the FEBS experiment, and the BioCreative challenge 7 Proceedings of the BioCreative II.5 Workshop 2009 on Digital Annotations thursday | Oct 8 participant 09:00 09:50 Keynote | Rethinking the goals of BioNLP research: What are we trying to systems accomplish? Larry Hunter, University of Colorado Denver School of Medicine 09:50 10:15 Normalizing Interactor Proteins and Extracting Interaction Protein Pairs using Support Vector Machines Yifei Chen, Vrije Universiteit Brussel 10:15 10:40 Online protein interaction extraction and normalization at Arizona State University Jörg Hakenberg, Arizona State University coffee | Break & Poster Session participant 11:20 11:45 IASL-IISR interactor normalization system using a multi-stage cross-species gene systems normalization algorithm and SVM-based ranking Hong-Jie Dai, Institute of Information Science 11:45 12:10 OntoGene in BioCreative II.5 Fabio Rinaldi, University of Zurich 12:10 12:35 AkaneRE Relation Extraction: Protein Normalization (INT) and Interaction (IPT) in the BioCreAtIvE II.5 Challenge Rune Sætre, University of Tokyo 12:35 13:00 Classification of protein-protein interaction documents using text and citation network features Luis M. Rocha, Indiana University and Instituto Gulbenkian de Ciência lunch | Break applied 14:30 15:20 Keynote | Predicting the future of prediction systems Anna Tramontano, Sapienza University of Rome 15:20 15:50 WikiGenes - Collaborative scientific publishing on the Web Robert Hoffmann, Memorial Sloan-Kettering Cancer Center 15:50 16:20 Reflect: An Augmented Browsing Tool for Scientist Seán I. O’Donoghue, EMBL coffee | Break & Photo Session applied 16:50 17:20 The OKKAM authoring platform for entity annotation: the SDA case systems Stefano Bocconi, Elsevier Labs and University of Trento 17:20 17:50 The BioCreative Meta-Server in the challenge and as a collaborative text-mining platform Florian Leitner, CNIO 17:50 18:30 Discussion | Applied systems in text mining - now and where we need to go dinner | Workshop 8 Proceedings of the BioCreative II.5 Workshop 2009 on Digital Annotations friday | Oct 9 participant 09:30 10:20 Keynote | CALBC: Producing a large-scale biomedical corpus is a systems challenge Dietrich