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Critical Assessment of Information Extraction in Biology - data sets are available from Resources/Corpora and require registration.

BioCreative II.5

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Workshop [2009-08-05]

The workshop on BioCreative II.5 will be held in Madrid at the CNIO during October 7th and 9th, 2009, sponsored by the ENFIN Network and the EMBRACE Grid Network. It will focus on the tasks created for the challenge, especially the extraction of protein-protein interactions (PPIs), with the background of creating structured annotations for full-text papers. These PPIs were generated by the paper authors themselves and MINT database curators (a PPI DB). There will be invited speakers discussing various topics relevant to Information Extraction in Text Mining and the topic of digital annotations, meta-services and applications in Bioinformatics.

Given the topic of the SDAs and online digital annotations, we are organizing a special session on the first day (Wed, Oct 7th). This "round table" should generally cover the topic of electronic/structured annotations on publications from the viewpoints of the most important stakeholders: the academic world, (pharma) industry, the publishers, and the databases.

We will have at least one prominent speaker from each of these areas followed by a discourse about how all stakeholders can cooperate to overcome issues in the evening and achieve the necessary requirements for creating and maintaining such structured descriptors. Speakers will be:

  • Judith Blake (JAX)
  • Alan Bridge (SIB)
  • Udo Hahn (Uni Jena)
  • Ian Harrow (Pfizer UK)
  • Adriaan Klinkenberg (Elsevier)

Additionally, there will be a session dedicated to applied systems in text mining related to the issue of digital annotations that will be held in the afternoon of the second day (Thu, Oct 8th). Speakers during this session will be:

  • Stefano Bocconi (Elsevier, OKKAM/Word plugin for SDAs)
  • Se├ín O'Donoghue (EMBL, Reflect)
  • Robert Hoffmann (MIT, WikiGenes)
  • Florian Leitner (CNIO, BCMS)

The workshop will cover presentations from several participant systems of the challenge, the result evaluation, an inter-annotator- and curator to author-agreement study, the SDAs and the FEBS Letters Experiments, and a talk about the BioCreative Meta-Server, as well as some plans on the future of BioCreative (BC III). This also means we will continue in the tradition of former BioCreative challenges and - much like the CASP challenges in Structural Biology - present the final results of all the participants during the workshop. In addition, there will be three keynote speakers:

  • Larry Hunter (UCHSC)
  • Dietrich Rebholz-Schuhmann (EBI)
  • Anna Tramontano (Uni Roma)


To register for the workshop, please visit the CNIO event page. Please note that the abstract submission is only for the poster sessions, challenge participant system talk entries (and papers) should be made via EasyChair as explained to each of them via mail.

Final Schedule

Wed, 7th of Oct., 8:30-18:30

Registration (08:30-09:00)

  • 09:00-09:20 - Workshop Opening (Alfonso Valencia, CNIO)
  • 09:20-10:00 - Digital annotations: the publishers (Adriaan Klinkenberg, Elsevier)
  • 10:00-10:40 - Digital annotations: the academic world/text miners (Udo Hahn, Uni Jena)
  • 10:40-11:20 - Digital annotations: the databases (Judith Blake, JAX)

Coffee Break

  • 11:40-12:20 - Digital Annotations: the databases (Alan Bridge, SIB)
  • 12:20-13:00 - Digital Annotations: the industry (Ian Harrow, Pfizer UK)


  • 14:30-15:10 - The FEBS Letters experiment (Gianni Cesareni, MINT & FEBS)
  • 15:10-15:50 - The BioCreative II.5 challenge (Martin Krallinger, CNIO)
  • 15:50-16:30 - Author- and systems-agreement studies (Lynette Hirschman, MITRE)

Coffe Break

  • 17:00-17:40 - BC II.5 Evaluation results (Florian Leitner, CNIO & Lynette Hirschman, MITRE)
  • 17:40-18:30 - Discussion on BC II.5 and digital annotations

Thu, 8th of Oct., 09:00-18:30

  • 09:00-09:50 - Keynote (Larry Hunter, UCHSC)
  • 09:50-10:40 - Particiapnt systems 1

Coffee Break

  • 11:10-13:00 - Participant systems 2

Lunch & Posters

  • 14:30-15:20 - Keynote (Anna Tramontano)
  • 15:20-15:50 - Applied systems: WikiGenes (Robert Hoffmann)
  • 15:50-16:20 - Applied systems: Reflect (Sean O'Donoghue)

Coffee Break & Posters

  • 16:50-17:20 - Applied systems: OKKAM/Word (Stefano Bocconi)
  • 17:20-17:50 - Applied systems: BCMS (Florian Leitner)
  • 17:50-18:30 - Discussion on applied systems

Workshop Dinner (20:00 - 22:30)

Fri, 9th of Oct., 09:30-13:00

  • 09:30-10:20 - Keynote (Dietrich Rebholz-Schuhmann, EBI)
  • 10:20-10:45 - Participant systems 3

Coffee Break

  • 11:15-12:05 - Participant systems 4
  • 12:05-12:45 - Retrospective & future: BioCreative III (Alfonso Valencia)
  • 12:45-13:00 - Workshop closing (Alfonso Valencia)