The Joint BioLINK and Bio-Ontologies SIG Meeting, August 4-5, 2006 In association with ISMB 2006, Fortaleza, Brazil, 2006


The two long-standing ISMB SIGS, Bio-ontologies and BioLINK, will hold a single joint two-day workshop this year. The meeting will consist of sessions that focus on the intersection of bio-ontologies and text mining, as well as individual sessions on ontologies in the life sciences (organized by the BioOntologies committee (, and on biomedical text mining, linking text data to biology, (organized by the BioLINK committee:

Registration and participation will be for a single two-day workshop.

Key Information

Program chairs:

Bio-Ontologies Section: Robert Stevens (1), Phillip Lord (2), Robin McEntire (3), James.A.Butler(3)

  1. School of Computer Science, University of Manchester, United Kingdom
  2. School of Computing Science, University of Newcastle, United Kingdom
  3. GlaxoSmithKline, USA

BioLINK Section:

Hagit Shatkay (1), Lynette Hirschman (2), Christian Blaschke (3), Alfonso Valencia (4)

  1. School of Computing, Queen's University, Canada
  3. Bioalma, Spain
  4. Centro Nacional de Biotecnologia, Universidad Autonoma, Spain


Main Conference:

About the Workshop

Our goals in organizing the workshop are:

  1. To allow researchers in the two communities to participate in the activities of both SIGs;
  2. To encourage exchange of ideas and presentation cross-cutting research.

The joint sessions will encourage discussion on topics such as ontology-based curation from the biomedical literature, (semi-)automated creation of ontologies, use of ontologies to improve text mining, and evaluation of ontologies, especially in terms of ability to consistently capture biologically significant concepts from the literature.

The ontology session will continue the important topics from previous workshops. Ontologies provide a mechanism for organising, sharing and reconciling data. Within recent years, there has been a great deal of interest in the use of ontologies within bioinformatics, particularly in providing computationally accessible annotation, or standard data models for complex data for microarray or pathway information. With the increase in scope and use of ontologies within bioinformatics, issues of scalability, expressiveness and best practices for modeling are becoming more important. On the ontologies side, we are therefore particularly interested in work involving multiple source ontologies, and which cut across the different levels of granularity implicit within biological systems.

The BioLink session will explore resources and tools for biomedical text-mining. As biomedical literature and text in biology continue their exponential growth, text-mining, information retrieval, and natural language processing (NLP) are all becoming main-stream practices in bioinformatics. This field is interdisciplinary in nature and brings researchers applying NLP, text mining, information extraction and retrieval in the biomedical domain, together with scientists from bioinformatics and biology. We solicit submissions from researchers working on all aspects of text mining as they apply to bioinformatics and bio-medicine.

The workshop will offer an informal environment for presentation and discussion of current research in biomedical ontologies and text-mining. The program will include presentations of short papers, invited talks and posters. Papers and poster-abstracts will be reviewed by the program committee. All accepted submissions will be included in the SIG notes.


We are inviting two types of submissions:

  1. Short papers (up to 4 pages)
  2. Poster abstracts (up to 1/2 page).

Authors should clearly indicate whether they would like their work to be considered as related to Bio-Ontologies, Biomedical Text Mining (BioLINK) or to the joint session.

Full submission details are at

Listed below are suggested topics for each section. However, we particularly encourage submissions that integrate aspects of both text-mining and ontologies, for instance discussing the role of ontologies and knowledge bases in text mining, use of ontologies to improve biomedical text analysis, automated text categorization based on ontology structure etc.

Suggested topics for Bio-Ontologies include but are not restricted to:

Suggested topics for BioLINK include but are not restricted to:

Deadline Extension May 5: Papers (up to 4 pages) and poster-abstracts (up to 1 page) due. June 10: Notification to authors June 20: Final version due

Call for Papers