Program

BioLINK SIG 2013 @ ISMB 2013

Saturday, July 20, 2013

Room: Salon Koch 11/12, ICC Berlin

Please note that the USB Flash Drive distributed at ISMB/ECCB 2013 has inadvertently left off the full proceedings volume, with page numbers for each paper below. The full proceedings is available here: Proceedings BioLINK SIG 2013. You can also find the page numbers in the proceedings in the Proceedings BioLINK SIG 2013 Front Matter.

Also, you can now find a BioLINK SIG 2013 BibTeX file attached below including the citation for each paper and poster.

We are pleased to confirm our Keynote Speaker will be Lars Juhl Jensen, Professor, Group Leader, The Novo Nordisk Foundation Center for Protein Research, Disease Systems Biology.

The title of Lars' talk will be, "The pragmatic text miner: From literature to electronic health records".

Our schedule for the day will be:

  • 08:45-09:00 Arrival and Welcome

Short Papers (* ahead of the title indicates presentations that will also be presented as posters)

  • 09:00-09:12 [Pages 28-31]

    • David Campos, Sérgio Matos and José Luís Oliveira.

* Neji: a tool for heterogeneous biomedical concept identification (presentation) (poster)

  • 09:15-09:27 [Pages 32-38]

    • Jin-Dong Kim and K. Bretonnel Cohen.

Natural language query processing for SPARQL generation: A prototype system for SNOMED-CT. (presentation)

  • 09:30-09:42 [Pages 39-43]

    • Antonio Jimeno Yepes and Karin Verspoor.

* Towards automatic large-scale curation of genomic variation: improving coverage based on supplementary material. (presentation) (poster)

  • 09:45-09:57 [Pages 44-47]

    • Maria Kissa, Michael Schroeder and George Tsatsaronis.

* Towards an Integrated Compound to Compound Relatedness Measure.

  • 10:00-10:12 [Pages 48-51]

    • Paea Le Pendu, Anna Bauer-Mehren, Kenneth Jung, Tyler Cole, Jonathan Mortensen, Srinivasan Iyer and Nigam Shah.

Case studies in making sense of clinical text.

  • 10:15-10:45 Coffee Break

Keynote

  • 10:45-11:45 Keynote: Lars Juhl Jensen The pragmatic text miner: From literature to electronic health records

Short Papers (continued)

  • 11:45-11:57 [Pages 52-55]

    • Philippe Thomas and Ulf Leser.

HistoNer: Histone modification extraction from text.

Shared Tasks and Discussion

  • 12:00-12:15 Shared Task update: BioCreative, BioNLP Shared Task, BioASQ

  • 12:15-12:30 Discussion

  • 12:30-13:30 LUNCH

Long Papers

    • 13:30-13:55 [Pages 5-12]

      • Florian Leitner, Martin Krallinger, Sushil Tripathi, Martin Kuiper, Astrid Laegreid and Alfonso Valencia.

Mining cis-Regulatory Transcription Networks from Literature (presentation)

  • 14:00-14:25 [Pages 13-19]

    • Michael Bada, Dmitry Sitnikov, Judith Blake and Lawrence Hunter.

Occurrence of Gene Ontology, Protein Ontology, and NCBI Taxonomy Concepts in Text toward Automatic Gene Ontology Annotation.

  • 14:30-14:55 [Pages 20-26]

    • Christoph Jacob, Philippe Thomas and Ulf Leser.

Comprehensive Benchmark of Gene Ontology Concept Recognition tools.

Posters

  • 15:00-15:15 Poster Boasters

  • 15:15-15:30 Discussion

  • 15:30-16:00 Coffee Break

  • 16:00-17:00 Poster Session

    • A quantitative analysis of causal and associative events involving genes and proteins. Phoebe Roberts. [Page 57]

      • Automatic Generation of BEL Statements from Text-mined Biological Events. Haibin Liu, William Baumgartner Jr., Natalie Catlett, Andrea Matthews, Phoebe Roberts, Christophe Roeder, Aaron Hooser, Daniel Ziemek, Lawrence Hunter and Kevin Bretonnel Cohen. [Page 58] (poster PDF)

      • Biotea. Alexander Garcia, Casey McLaughlin and Leyla Jael García Castro. [Page 59]

      • Explaining genome-wide association study results using concept profile analysis and the Kyoto Encyclopedia of Genes and Genomes pathway database. Kristina M. Hettne, Harish Dharuri, Reinout van Schouwen, Peter A.C. 'T Hoen, Barend Mons and Marco Roos. [Page 60] (poster PDF)

      • In the Pursuit of Open Science. Alexander Garcia, Leyla Jael García Castro and Olga Giraldo. [Page 61]

      • PubAnnotation - a storage system for sharing of literature annotation. Jin-Dong Kim. [Page 62] (poster PDF)

      • PDFJailbreak - a communal architecture for making biomedical PDFs semantic. Alexander Garcia, Peter Murray-Rust, Gully APC Burns, Robert Stevens, Dominika Tkaczyk, Casey McLaughlin, Amaury Belin, Angelo Di Iorio, Leyla García, Célya Gruson-Daniel, Ross Mounce, Andrea Giovanni Nuzzolese, Silvio Peroni Jeremy Spinks, Boris Villazon-Terrazas, Oscar Corcho, Olga Giraldo, Mike Wabiszewski. [Page 63]

      • Text mining for characterizing cells and tissues. Mariana Neves, Alexander Damaschun, Nancy Mah, Fritz Lekschas, Stefanie Seltmann, Harald Stachelscheid, Jean-Fred Fontaine, Andreas Kurtz and Ulf Leser. [Page 64] (poster PDF)