Science of Collaboratories logo - link
An alliance to advance the understanding of collaboratories
Science of Collaboratories

Return to the list of Collaboratory Projects


Name of Collaboratory :


Biosemantics Group


URL :  

Collaboratory Status :

Completed   Start Date : End Date : Info Last Updated : Thu, Dec 9 2010 4:01pm PST

Primary Collaboratory Function :

  Community Infrastructure Development  

Secondary Collaboratory Functions :


Domain(s) :

  MATHEMATICS/COMPUTER SCIENCES >Computer Science >Information Science and Systems
BIOLOGICAL/AGRICULTURAL SCIENCES >Biological Sciences >Molecular Biology

Brief Description of the Collaboratory :


With the explosion of information in the biomolecular field, there is a dire need for tools that assist biologists in retrieving, extracting, and relating information and knowledge in the literature and in molecular databases. The Biosemantics Association develops and evaluates such tools, focussing on the elucidation of hidden or implicit knowledge by the massive meta-analysis of textual documents.
The groups currently address three areas of research:

Concept identification and disambiguation algorithms.
Proper recognition of concepts that characterize a document and disambiguation of terms that can have more than one meaning, is the basis for all subsequent steps in text analysis. We make extensive use of thesauri that contain the concepts relevant for a particular field.
Meta-analysis and visualization techniques.
For meta-analysis, we are studying different approaches that relate the information in many (possibly hundreds of thousands) documents from the literature. Visualization deals with reducing the often multi-dimensional output of the meta-analysis tools to two dimensions that can easily be interpreted.
Evaluation of applications in the biological field.
In several studies we are investigating the potential of the developed technology to interconnect genes and proteins and discover knowledge that is hidden in the literature, while the technology is also being evaluated for semi-automated annotation of protein function. Development and evaluation is done in close cooperation with domain experts, both in national and international collaborations.


Access to Instruments :

  All of their developed software is available freely on their Website.  

Access to Information Resources :


Access to People as Resources :

  They had a "First Biosemantics User Day" back in 2007 but it does not seem like they have ever had another one.  

Funding Agency or Sponsor :


Notes on Funding Agencies/Sponsors:
I couldn't find anything about their funding situation.

Organizations with Funded Participants:
Organization name:
Approx # of participants:
Description of organization's role(s):
Leiden University
   Leiden University Medical Center (LUMC)
      Center for Human and Clinical Genetics (Leiden University Medical Center)
Erasmus Medical Center
   Department of Medical Informatics (Erasmus)

Notes on Participants/Organizations:
They are involved with the following collaboratories: EU-ADR,
CALBC, Infobiomed, BioRange, epiGeniusHD, BBMRI-NL, CMSB


Communications Technology Used :

  They have three modes of communication:

1. Leiden BioSemantics Users Group on myExperiment that people can request to join

2. A BioSemantics' users mailing list that interested parties can use to ask any question about their tools or research. All biosemanticians and special users are on this list. People who would like to become an active member of their user community can request to join the list through their Website.

3. Members can send an e-mail to the mailing list for internal discussions of biosemantics researchers, developers, and some users. This list is mostly use for internal discussions.


Technical Capabilities :

  Key Articles :    

Project-reported performance data :

  Home | About SOC | Workshops | Resources | News & Events  

University of California, Irvine Logo

University of California, Irvine

School of Information Logo

School of Information University of Michigan