BioPortal

NCBO BioPortal

An instance of the NCBO BioPortal software to be hosted by GBIF was one of the recommendations from the GBIF KOS Task Group report (Catapano et al 2011). The BioPortal platform supports the sharing of ontologies in a collaborative manner within a wide and open community. The BioPortal ontology repository does not provide a tool for actual collaborative development of ontologies, but does support the mapping of concepts between different ontologies uploaded to the platform.

The BioPortal software is developed and provided from Stanford University as open source software. The source code is freely and easily available from the Stanford code repository as a Subversion (SVN) resource. The BioPortal platform includes a suite of different Java software projects that can be run using eg a Tomcat application server. Content loaded into the BioPortal is stored using a MySQL database server. The basic Java software projects (Bioportal core) provide a machine accessible REST interface (API). The graphical user interface that can be seen in a web browser is implemented using Ruby On Rails code. The resource index is developed as a PHP software application. The BioPortal is also using a Virtuoso RDF triplestore.

The NCBO BioPortal software is also made available as a complete package (virtual machine) developed for the VMware platform. Starting with version 0.4 the BioPortal virtual appliance is distributed as an Open Virtualization Format (OVF) file and can be readily applied using the open source Virtual Box virtualization software.

Links

• NCBO BioPortal: http://bioportal.bioontology.org/
• CGIAR BioPortal "slice": http://cgiar.bioportal.bioontology.org/
• Source Code: https://bmir-gforge.stanford.edu/gf/project/bioportal_core/
• Virtual Appliance: http://www.bioontology.org/wiki/index.php/Category:NCBO_Virtual_Appliance

References

• Whetzel PL, Noy NF, Shah NH, Alexander PR, Nyulas C, Tudorache T, and Musen MA (2011). BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications. Nucleic Acids Res. 2011 July 1; 39(Web Server issue): W541–W545. DOI:10.1093/nar/gkr469. Available at http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125807/

• Noy NF, Shah NH, Whetzel PL, Dai B, Dorf M, Griffith N, Jonquet C, Rubin DL, Storey M-A, Chute CG, and Musen MA (2009). BioPortal: ontologies and integrated data resources at the click of a mouse. Nucleic Acids Res. 2009 July 1; 37(Web Server issue): W170–W173. DOI:10.1093/nar/gkp440 PMCID: PMC2703982. Available at http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2703982/