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Name of Collaboratory :

 

A Cross-Species Anatomy Network (XSPAN)

 
 

URL :

  http://www.xspan.org/  
 

Collaboratory Status :

 
Completed   Start Date : 2002 End Date : 2005 Info Last Updated : Mon, Oct 31 2011 8:01pm PDT
 
 

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 >Anatomy
Databases and ontologies, bioinformatics, bio-ontologies, anatomy/trends, animals, biology/methods, biology/trends, humans, mice, genomics, anatomics, gene expression database, human
anatomy, mereology, mouse anatomy, systems biology
 
 

Brief Description of the Collaboratory :

 

XSPAN aims to develop a distributed, XML-based software system which facilitates a core level of interoperability across different anatomy databases. A set of tools allows easy integration of existing anatomy databases into the new system and provides query facilities across them.

This system will provide interoperability between databases of key model embryos which will, in turn, facilitate access to gene expression and other tissue-based data across species, and to other genomics and proteomics resources.

The XSPAN project aims to provide seamless access to existing ontologies of developmental anatomy of some key model organisms: mouse, drosophila, C. elegans, zebrafish and human.

Access and query software use rules and translation tables to support inter-operability between anatomy ontologies while a prototype of a formal ontology for cross-species anatomy links into the species-specific anatomy ontologies to provide support for identifying and hypothesizing cross-species tissue equivalents.

The overall objective of XSPAN is to support access to cross-species tissue-based genetic information through the development of an internet-based cross-species anatomy network, i.e. a cross-species anatomy ontology integration system.

XSPAN is a joint project between the School of Mathematical and Computer Sciences at Heriot-Watt University, and the Schools of Biomedical Sciences and Informatics at the University of Edinburgh.

XSPAN is funded by the UK's Biotechnology and Biological Sciences Research Council (BBSRC)

 
 

Access to Instruments :

  The XSPAN database is accessible to the public via the Web.  
 

Access to Information Resources :

  The XSPAN project aims to provide seamless access to existing ontologies of developmental anatomy of some key model organisms: mouse, drosophila, C. elegans, zebrafish and human.

Access and query software use rules and translation tables to support inter-operability between anatomy ontologies while a prototype of a formal ontology for cross-species anatomy links into the species-specific anatomy ontologies to provide support for identifying and hypothesizing cross-species tissue equivalents
 
 

Access to People as Resources :

   
 

Funding Agency or Sponsor :

 
Biotechnology and Biological Sciences Research Council (BBSRC)
 
 
 

Notes on Funding Agencies/Sponsors:

 
 
 
Organizations with Funded Participants:
 
Organization name:
Approx # of participants:
Description of organization's role(s):
Melbourne University
   Research Centre for High Energy Physics
University of Edinburgh
   School of Informatics - University of Edinburgh
4
1 principal investigator, 2 researchers, 1 previous Masters student
   School of Biomedical Sciences - University of Edinburgh
1
1 principal investigator
Heriot-Watt University
   School of Mathematical and Computer Sciences - Heriot-Watt University (MACS)
9
1 principal investigator, 2 co-investigators, 2 researchers, 1 doctoral student, 3 previous Masters students
 
TOTAL PARTICIPANTS:
14
 

Notes on Participants/Organizations:
XSPAN has an advisory board with the following members:
Dr. J. Douglas Armstrong, Edinburgh University
Dr. Duncan Davidson, Human Genetics Unit, MRC, Edinburgh
Dr. Shona Kerr, Wellcome Trust Clinical Research Facility, Edinburgh
Dr. Andy Law, Roslin Institute, Edinburgh
Dr. Mary Porteous, Consultant Clinical Geneticist
Mr. David White, IBM Life Sciences - Academia

XSPAN works with the following existing anatomy and gene expression databases:
The Mouse Atlas and Gene Expression Database Project (Mouse)
Atlas and Database of Human Developmental Anatomy (Human)
FlyBase (Drosophila)
MGH / CVRC Zebrafish Server (Zebrafish)
WormBase (C. elegans)

The XSPAN Website lists the following as "Other Institutions" (but does not specify the nature of the collaboration):
Bioinformatics at the Roslin Institute (http://www.roslin.ac.uk/research/genomics.html)
The Jackson Laboratory (http://www.jax.org/)

   
     
 
 

Communications Technology Used :

   
 

Technical Capabilities :

   
  Key Articles :  

Aitken, J.S., Korf, R., Webber, B.L. and Bard, J.B.L. (2004). COBrA: a bio-ontology editor Bioinformatics, 21 (6), 825-826.

 
 

Project-reported performance data :

   
  Images of the Collaboratory:  
XSPAN Applet GUI
 
 
         
    
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