Biositemaps

The Biositemaps Working Group of the NIH Roadmap National Centers of Biomedical Computing (NCBC) (www.ncbcs.org) has developed technologies to address (i) locating, (ii) querying, (iii) composing or combining, and (iv) mining biomedical resources. Each site which intends to contribute to the inventory instantiates a file on its Internet site ‘'biositemap.rdf' which conforms to a defined RDF schema and uses concepts from the Biomedical Resource Ontology to describe the resources.

What is a Biositemap? Biositemaps represent a mechanism for computational biologists and bio-informaticians to openly broadcast and retrieve meta-data about biomedical resources. All institutions with an interest in biomedical research can publish a biositemap.rdf file on their Internet site. Each biositemap.rdf file is simply a list of controlled metadata about resources (data, software, tools, material, and services) that your organization uses or believes are important to biomedical research. The key enabling technologies are the Information Model (IM) which is the list of metadata fields about each resource (resource_name, description, contact_person, resource_type,...) and the Biomedical Resource Ontology (BRO) which is a controlled terminology for the 'resource_type', 'area of research', and 'activity' and which are used to improve the sensitivity and specificity of web searches. [more...]

What is the Biomedical Resource Ontology (BRO)? A key enabling technology for Biositemaps is the Biomedical Resource Ontology (BRO) which is a controlled terminology for the 'resource_type', 'area of research', and 'activity' and which are used to improve the sensitivity and specificity of web searches. This is under development by a number of NIH-funded researchers who have a combined interest in classification of biomedical resources. The publication site for BRO is the BioPortal.

QuickStart for Biositemaps

  1. Use the Biositemaps Editor to fill in the information about the resources on your site and generate a biositemap.rdf file. There are also customized editors for CTSA and NCBC. Important: Internet Explorer users must first configure their browser. [help...]
  2. Your biositemap.rdf file will need to be deployed to your local web server prior to being published [help...]
  3. Use the Biositemap Registration to publish your biositemap after it has been deployed [help...]
    Biositemaps need only be published once, and may be freely updated after their initial publication.
  4. You can query information about resources that you or others have published using the biositemaps search tool.

How can researchers author and consume Biositemaps and the BRO?

  • The Biositemaps Editor provides an authoring web interface to fill in the information about the resources on your site and generate a biositemap.rdf file. There are also customized editors for CTSA and NCBC. Important: Internet Explorer users must first configure their browser.
  • The Resource Discovery System leverages biositemaps to provide a searchable inventory of research resources of the CTSA consortium.
  • The BioPortal supports queries based on the Biomedical Resource Ontology (BRO).
  • The iTools application and iTools services provide the functions of (i) authoring, (ii) locating and (iii) querying biositemaps.

How can developers author and consume Biositemaps and the BRO?

  • The Biositemap API reference documents Java APIs to author (create/update) and consume (read/query) biositemaps, as well services for querying the BRO ontology.
  • The Biositemap RDF technical reference documents the RDF implementation of the information model, as well as how to extend the information model for institution-specific metadata.

Where can I find more information?