Semantic Map for Structural Bioinformatics.
Project
definition:
This project aims at building a Semantic Map of resources for
Structural Bioinformatics applied to proteins, i.e., various methods to
predict and analyze protein structures in silico. The map would depict
resources on two levels: a logical level that provides a
high-level description of the scientific concepts using a domain
ontology; a physical level, that describes the actual resources
implementing these connections. Scientists could use the system to
express a query that captures their scientific aim, and are guided to
identify the resources best meeting their needs. It is intended to
provide scientists a tool to register and share knowledge about the
available services in this field. Such approach addresses the problem
of semantic interoperability of scientific resources publicly available
on the web.
Publications:
- P. Tuffery, Z. Lacroix, and H. Ménager "Semantic Map of Services for Structural Bioinformatics", 18th International Conference on Scientific and Statistical Database Management (SSDBM), Vienna, Austria, July 3-5, 2006 - published by IEEE Press - paper also presented at the 6th Journées Ouvertes de Biologie, Informatique et Mathématiques (JOBIM), Bordeaux, France, July 2006.
- paper
acceptedtoCSB 2006
- H. Ménager, Z. Lacroix and P. Tufféry
"Bioinformatics Services Discovery Using Ontology Classification". First IEEE International Workshop on Service Oriented Technologies for Biological Databases and Tools, In conjunction with ICWS/SCC, Salt Lake City, Utah, July 13 2007 - published by IEEE Press (DOI 10.1109/SERVICES.2007.20), pp 106-113.
More information:
Arizona State University SemanticMap project Web Page.
Who is presently involved in this project:
Candidate
Ontology:
A candidate ontology has been proposed following an initial seminar at
RPBS (Nowember 2005), followed by a round of interviews with different
teams at RPBS (LMCP-J. Chomilier, ABI-J. Pothier, GBS-B. Villoutreix,
J.-F. Zagury) during November-December 2005.
A complete
picture of the ontology (generated with Protege).
Sub-images (molecular
entities, protein
entities, structure
entities)
Since then, several updates have been performed, and the ontology is directly
propagated to the online service.
Under
progress:
- Travel though the ontology. We are currently implementing a tool
to
navigate through the ontology. The overall size and complexity of the
ontology poses several problems of display. We are using the ZVTM API
to implement an improved interface. The current implementation is accessible here .
- CGI for service registration given the ontology. This will allow
to describe a service of the field of structural bioinformatics using
some concept(s) of the ontology. At the same time, the registration
will provide a low level descritpion of the service (nam, purpose,
datatypes, input/output).
- This interface will be coupled to the search engine of
BioNavigation to allow the identification of paths linking concepts,
i.e. identifying series of services that combined, can, given input
data of the first task, be chained to produce output relevant of the
output concept.
- Ontology evolution: Users can subtmit enhancements to a comittee
that will validate it. This is to ensure the consistence of the
ontology and its links with the declared services is maintained. Interested in being a member of the
comittee : please contact
References:
- ZVTM: Emmanuel Pietriga. "A toolkit
for addressing hci issues in visual language environments." In
IEEE Symposium on Visual Languages and Human-Centric Computing, pages
145--152, September 2005.
- BioNavigation: Zoé Lacroix, Kaushal Parekh, Maria-Esther
Vidal, Marelis Cardenas, and Natalia Marquez. "BioNavigation: Selecting Optimum Paths
Through Biological Resources to Evaluate Ontological Navigational
Queries." In Bertram Ludäscher and Louiqa Raschid, editors,
DILS, volume 3615 of
Lecture Notes in Computer Science, pages 275--283. Springer, 2005.