 |
Semantic Enrichment of the Scientific Literature 2009 (SESL 2009)
March 30th to March 31st, 2009
|
Date of main workshop: | March 31st, 2009 |
| Location: | Wellcome Trust Conference Center, Hinxton, Cambridge |
| Conference fees: | None |
| Registration: | Closed |
Motivation
Over the last 10 years, innovation has changed the ways in which scientific publications are gathered and delivered to the public. Since the start of the electronic era:
publishers have moved from paper presentation of their content to electronic delivery;
the US National Library of Medicine (NLM) has opened up its archives and delivered Medline abstracts to the public in electronic form;
open access publishers have been making their content freely available;
curation teams are increasingly working with the publishers to gather ever more data and provide it to the public and
proposals have been made that authors should contribute more details to their manuscript (FEBS letter experiment).
These changes require novel ways to capture and deliver the content to the public and to exchange the content and the annotations between different sites. This has led to increased activities to capture more information from the authors, to align it with the bioinformatics data resources, to deliver the content as part of the scientific literature and to improve the interoperability between existing automatic systems for text processing and exploitation.
This workshop will focus on semantic enrichment of the scientific literature. To this end, workshop participants will have the opportunity to hear about and discuss solutions that capture information from the authors directly and that deliver documents with their annotations. Furthermore, we will discuss the needs of different user groups for the benefits from the scientific literature of the future, e.g. librarians, researchers, automatic text processing and data mining research community, ontologists, others.
Participants
The participants in this workshop are all users who profit from better information retrieval (e.g., librarians in pharmaceutical companies) and information provision (e.g., bioinformatics research community). In addition, members of the text mining research community, members of publishing companies and industrial users of scientific information, curation teams and teams working on ontological or terminological resources.
Intended Outcomes
The intended outcomes of the workshop are:
to exchange views on the reuse of literature in all possible ways and to the benefit of all involved parties;
to have a better understanding for the infrastructure requirements coming from the automatic gathering and distribution of semantically enriched text (open standards and connectivity);
to exchange views on what contributions could come from the publishers with regards to better exploitation of the publicly available literature and
to assess current solutions for the gathering of semantic details from the authors while writing their scientific manuscripts.
Pre-workshop Meeting: 30 March 2009, 9h00 – 17h00
Title: Reliable factual data from the literature based on ontological resources
Presentations and discussions on advanced solutions to model ontological resources for gathering facts from the literature and for integration into a fact database: gene regulatory events as a working example.
Agenda
|
09.00
|
Registration Open (tea/coffee)
|
|
10.00
|
Welcome and Introductions (Dietrich Rebholz-Schuhmann&)
|
|
10.30
|
Session 1: Semantic representation of Gene Regulatory Events (GREs)
Confirmed Speakers (exact times and titles to be agreed)
[10.30] Keynote: "Refine and PathText, which combines text Mining with Pathways" (Junichi Tsujii, NaCTeM, Manchester, UK and University of Tokyo, Tokyo, Japan) [11.00] "Gene regulation ontology: design and exploitation for information extraction" (Jung-Jae Kim, EBI, Hinxton, Cambridge, UK) [11.30] "OregAnnO: curated gene regulatory events" (Stephen Montgomery, Sanger, Wellcome Trust Genome Campus, UK) [12.00] "Ontology development for information extraction (ODIE) from clinical text" (Wendy Chapman, University of Pittsburgh)
|
|
12.30
|
Lunch
|
|
13.45
|
Session 2: Identification of Gene Regulation Events in the scientific literature (BootStrep)
Confirmed Speakers (exact times and titles to be agreed)
[13.45] "BioLexicon"
(Simonetta Montemagni, CNR, Pisa) [14.15] "Identification of gene regulatory events from the literature" (Udo Hahn, Friedrich-Schiller University, Jena, Germany) [14.45] "Language Resource Assessment for Information Access" (Su Jian, InfoComm Research, Singapore)
|
|
15.30
|
Tea/Coffee
|
|
16.00
|
Session 3: Clinical data and Novel publishing solutions
Confirmed Speakers (exact times and titles to be agreed)
[16.00] "Exploiting semantic technologies to build an application ontology" (James Malone, EBI, Hinxton, Cambridge, UK) [16.30] "Embedding semantic data during manuscript authoring" (Lynn Fink, University of California San Diego) [17.00] "PaperMaker: consistency analysis of published manuscripts" (Piotr Pezik, EBI, Hinxton, Cambridge, UK)
Discussion and closing remark (Dietrich Rebholz-Schuhmann, Udo Hahn)
|
|
18.15
|
Pre-dinner drinks and networking
|
|
19.30
|
Workshop Dinner (Hinxton Hall restaurant)
|
Main workshop: 31 March 2009, 9h00 – 17h00
Title: Semantic Enrichment of the literature for the benefit of all users
Existing solutions for the processing and standardization of annotations in the scientific literature: authoring solutions, access to data through publishers, requirements from curators and "information scientists" in pharmaceutical companies.
Agenda
|
08.30
|
Registration Open (tea/coffee)
|
|
09.15
|
Welcome
and Introductions (Dietrich Rebholz-Schuhmann&
Dominic Clark)
|
|
09.30
|
Session 1: User's and publishers perspective of future publishing
Confirmed Speakers (exact times and titles to be agreed)
[09.30] Keynote: "Completing the Circuit: Publishing with Linked Data" (Eric Neumann, Clinical Semantics Group) [10.00] "The needs of information scientists in Pharma companies" (Jasen Chooramun, AstraZeneca) [10.30] "The needs of bioinformaticians in Pharma companies" (Ian Harrow, Phoebe Roberts,
Pfizer)
|
|
11.00
|
Tea/Coffee
|
|
11.30
|
Session 1 cont:
Confirmed Speakers (exact times and titles to be agreed)
- [11.30] "Elixir: European Infrastructure to support Interoperability between
Text Repositories and Biological Databases" (Alfonso Valencia, CNIO, Madrid, Spain)
[12.00] "CALBC + UKPMC: Producing a large scale annotated corpus for
standardized literature" (Dietrich Rebholz-Schuhmann, EBI, UK) "[12.30] “Funding opportunities in Europe" (Stefano Bertolo, European Commission, Luxembourg)
|
|
12.45
|
Lunch
|
|
14.00
|
Session 2: Semantic enrichment
Confirmed Speakers (exact times and titles to be agreed)
[14.00] Keynote: "Reconciling annotations made to different
terminologies: The role of terminology integration services" (Olivier Bodenreider, NLM) [14.30] "From Text to Knowledge and Back. Semantic enrichment for
knowledge discovery" (Sophia Ananiadou, NaCTeM, Manchester) [15.00] "On the Semantics of Semantic Enrichment - Conceptual Resources for Text Mining Analytics and Information Access" (Udo Hahn, Friedrich-Schiller University, Jena, Germany)
|
|
15.30
|
Tea/Coffee
|
|
16.00
|
Session 3: Use of ontologies in applications and novel publishing solutions
Confirmed Speakers (exact times and titles to be agreed)
[16.00] Keynote: "Semantic Enrichment of Elsevier's literature" (Anita de Waard, Elsevier, Amsterdam, Nl) [16.30] "WikiGene: Novel ways to publish information on the Web" (Robert Hoffmann, MIT) [17.00] "Use of electronic healthcare records and biomedical literature/databases for the early detection of adverse drugs events (EU-ADR)" (Erik van Mulligen, Erasmus Medical Center, Rotterdam, Nl)
|
|
17.30 - 18.00
|
Closing remark and Discussion (Dietrich Rebholz-Schuhmann)
|
|
19.00
|
Workshop Dinner (location to be
advised for industry programme members and speakers/contributors)
|
Post-workshop meeting: 1 April 2009, 9h00 – 17h00
Industry program (by invitation only)
Acknowledgements
This workshop is sponsored by the EC STREP project "BOOTStrep" (FP6-028099, web page) and by the industry program at the EBI.
|