Biositemap is a way for a biomedical research institution of
organisation to show how biological information is distributed
Information Technology systems and networks. This
information may be shared with other organisations and researchers.
Biositemap enables web browsers, crawlers and robots to easily
access and process the information to use in other systems, media and
computational formats. Biositemaps protocols provide clues for the
Biositemap web harvesters, allowing them to find resources and content
across the whole interlink of the
Biositemap system. This means that
human or machine users can access any relevant information on any
topic across all organisations throughout the
Biositemap system and
bring it to their own systems for assimilation or analysis.
1.1 Data formats
Biositemap Information Model
2 See also
4 External links
iTools representation of a biositemap
The information is normally stored in a biositemap.rdf or
biositemap.xml file which contains lists of information about the
data, software, tools material and services provided or held by that
organisation. Information is presented in metafields and can be
created online through sites such as the biositemaps online editor.
The information is a blend of sitemaps and
RSS feeds and is created
using the Information Model (IM) and Biomedical Resource Ontology
(BRO). The IM is responsible for defining the data held in the
metafields and the BRO controls the terminology of the data held in
the resource_type field. The BRO is critical in aiding the
interactivity of both the other organisations and third parties to
search and refine those searches.
The Biositemaps Protocol allows scientists, engineers, centers and
institutions engaged in modeling, software tool development and
analysis of biomedical and informatics data to broadcast and
disseminate to the world the information about their latest
computational biology resources (data, software tools and web
services). The biositemap concept is based on ideas from Efficient,
Automated Web Resource Harvesting and Crawler-friendly Web
Servers, and it integrates the features of sitemaps and
into a decentralized mechanism for computational biologists and
bio-informaticians to openly broadcast and retrieve meta-data about
These site, institution, or investigator specific biositemap
descriptions are published in RDF format online and are searched,
parsed, monitored and interpreted by web search engines, web
applications specific to biositemaps and ontologies, and other
applications interested in discovering updated or novel resources for
bioinformatics and biomedical research investigations. The biositemap
mechanism separates the providers of biomedical resources
(investigators or institutions) from the consumers of resource content
(researchers, clinicians, news media, funding agencies, educational
and research initiatives).
Biositemap is an RDF file that lists the biomedical and
bioinformatics resources for a specific research group or consortium.
It allows developers of biomedical resources to describe the
functionality and usability of each of their software tools, databases
Biositemaps supplement and do not replace the existing frameworks for
dissemination of data, tools and services. Using a biositemap does not
guarantee that resources will be included in search indexes nor does
it influence the way that tools are ranked or perceived by the
community. What the Biositemaps protocol will do is provide clues,
information and directives to all
Biositemap web harvesters that point
to the existence and content of biomedical resources at different
Biositemap Information Model
Biositemap protocol relies on an extensible information model that
includes specific properties that are commonly used and necessary
for characterizing biomedical resources:
Stage of development
Resource Ontology Label
Up-to-date documentation on the information model is available at the
^ Biositemaps online editor Archived July 30, 2010, at the Wayback
^ a b Dinov ID, Rubin D, Lorensen W, et al. (2008). "iTools: A
Framework for Classification, Categorization and Integration of
Computational Biology Resources". PLoS ONE. 3 (5): e2265.
doi:10.1371/journal.pone.0002265. PMC 2386255 .
^ M.L. Nelson; J.A. Smith; del Campo; H. Van de Sompel; X. Liu (2006).
"Efficient, Automated Web Resource Harvesting" (PDF). WIDM'06.
^ Brandman O, Cho J, Garcia-Molina H, Shivakumar N (2000).
"Crawler-friendly Web Servers". ACM SIGMETRICS Performance Evaluation
Review. 28 (2). doi:10.1145/362883.362894.
^ Cannata N, Merelli E, Altman RB (December 2005). "Time to organize
the bioinformatics resourceome". PLoS Comput. Biol. 1 (7): e76.
doi:10.1371/journal.pcbi.0010076. PMC 1323464 .
^ Chen YB, Chattopadhyay A, Bergen P, Gadd C, Tannery N (January
2007). "The Online Bioinformatics Resources Collection at the
University of Pittsburgh Health Sciences Library System—a one-stop
gateway to online bioinformatics databases and software tools".
Nucleic Acids Res. 35 (Database issue): D780–5.
doi:10.1093/nar/gkl781. PMC 1669712 . PMID 17108360.
Biomedical Resource Ontology