Semantic Enrichment of Scientific Literature

One-day Mini-Symposium Details
Title: “Semantic Enrichment of Scientific Literature”
Date: 20th February 2006
Venue: EBI, Hinxton, Cambridgeshire, UK

Dietrich Rebholz-Schuhmann, Group leader, EBI
Graham Cameron, Associate Director, EBI
Paul Matthews, Coordinator Industry Programme, EBI


Semantic enrichment is the integration of metadata into text. It allows facts within text to be annotated and linked to electronic resources such as the biological databases maintained by the EMBL-EBI and its collaborators. This makes free text better suited for automatic exploitation in text mining, information retrieval and presentation.

We cordially invite key players in the text-mining field, representatives from STM publishing, representatives from other industries who share an interest in making the most of semantic enrichment, researchers and curators to exchange their views on automatic annotation of scientific text and to better understand their requirements at a one-day mini-symposium at the EBI on February 20th as part of the Industry Programme allowing presentations from invited speakers and discussions.

The meeting will be used to exchange views on automatic annotation of scientific text and to help us understand the requirements of curators, researchers, authors, publishers and other interested fields.

Semantic Enrichment of Scientific Literature (SESL) Agenda

eProtein Printable ScheduleClick here to view a printable version of the schedule.

Time SESL Agenda
09.00 Registration and coffee
09.30 Welcome and Introductions -
Dietrich Rebholz-Schuhmann, EMBL-EBI, UK
09.45 The impact of biomedical terminologies on curation and publishing -
Prof. Michael Ashburner, Univ. of Cambridge, UK
10.15 TBD -
Henning Hermjakob, Evelyn Camon, EMBL-EBI, UK
10.40 Metadata in biomedical articles: UniProtKB curators' requirements -
Anne-Lise Veuthey, SIB, Ch
11.00 Coffee break
11.20 Concepts in Semantically Enriched Literature support Navigating the Knowledge Space -
Martin Romacker, Novartis, Ch
11.40 NLM resources for semantic enrichment -
Olivier Bodenreider, NLM, USA
12.00 Practical benefits of semantically-enriched articles for authors and readers -
Matt Cockerill, BioMed Central
12.20 Prof. Peter Murray-Rust, Univ. of Cambridge, UK
12.40 Linking database information and textual sources -
Alfonso Valencia, CNB-CSIC, Madrid, E
13.00 Lunch
13.30 Semantic Enrichment of the GENIA corpus -
Prof. Jun'ichi Tsujii, NaCTeM, Manchester, UK
13.50 Barend Mons, Erasmus Medical Center, NI
14.10 Jasmin Saric, EML, Heidelberg
14.30 Recognition of Chemical Entities in Scientific Literature -
Stefan Geissler, Temis S.A., Paris
15.00 Coffee break
15.20 Discussion forum
17.00 Close of symposium & drinks reception

Questions to be discussed during the meeting include:

  • What benefit results from annotations contained in scientific publications?
  • What are the types of data that should be marked up in scientific documents?  (protein/gene names, species, experimental methods, etc.)
  • What benefit do ontologies offer to the annotation of data in the literature?
  • How can we work together to enable semantic enrichment of published papers, and at which phase of the publishing process?
  • Can we envisage automatic delivery of facts from a publication into other knowledge resources?  What benefits will result from this process?

Call for contributions:

As a complement to presentations from invited speakers, we encourage short presentations (5-7 minutes) from participants to express their view on any of these questions.  To register your interest in giving such a presentation, please submit a short abstract (no more than 250 words) to

Please forward this information to colleagues that may be interested to contribute to this mini-symposium. 

Rebholz group is headed by Dietrich Rebholz-Schuhmann.