A Biositemap is a way for a

biomedical research Medical research (or biomedical research), also known as experimental medicine, encompasses a wide array of research, extending from "basic research" (also called ''bench science'' or ''bench research''), – involving fundamental scientif ...

institution of organisation to show how biological information is distributed throughout their

Information Technology Information technology (IT) is the use of computers to create, process, store, retrieve, and exchange all kinds of data . and information. IT forms part of information and communications technology (ICT). An information technology system (I ...

systems and networks. This information may be shared with other organisations and researchers. The Biositemap enables

web browser A web browser is application software for accessing websites. When a user requests a web page from a particular website, the browser retrieves its files from a web server and then displays the page on the user's screen. Browsers are used on ...

s, crawlers and

robots "\n\n\n\n\nThe robots exclusion standard, also known as the robots exclusion protocol or simply robots.txt, is a standard used by websites to indicate to visiting web crawlers and other web robots which portions of the site they are allowed to visi ...

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.

File framework

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 The Sitemaps protocol allows a webmaster to inform search engines about URLs on a website that are available for crawling. A Sitemap is an XML file that lists the URLs for a site. It allows webmasters to include additional information about ea ...

and RSS feeds and is created using the

Information Model An information model in software engineering is a representation of concepts and the relationships, constraints, rules, and operations to specify data semantics for a chosen domain of discourse. Typically it specifies relations between kinds of t ...

(IM) and Biomedical Resource

Ontology In metaphysics, ontology is the philosophical study of being, as well as related concepts such as existence, becoming, and reality. Ontology addresses questions like how entities are grouped into categories and which of these entities exis ...

(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.

Data formats

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 Computational biology refers to the use of data analysis, mathematical modeling and computational simulations to understand biological systems and relationships. An intersection of computer science, biology, and big data, the field also has fo ...

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

and

RSS RSS ( RDF Site Summary or Really Simple Syndication) is a web feed that allows users and applications to access updates to websites in a standardized, computer-readable format. Subscribing to RSS feeds can allow a user to keep track of many di ...

feeds into a decentralized mechanism for computational biologists and bio-informaticians to openly broadcast and retrieve meta-data about biomedical resources. 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). A 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 or web-services. 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 sites.

Biositemap Information Model

The Biositemap protocol relies on an extensible information model that includes specific properties that are commonly used and necessary for characterizing biomedical resources: * Name * Description * URL * Stage of development * Organization * Resource Ontology Label * Keywords * License Up-to-date documentation on the information model is available at the Biositemaps website.

References

External links

* {{Official website, http://www.biositemaps.org/
Biomedical Resource Ontology

Biositemaps online editor
Domain-specific knowledge representation languages Biological techniques and tools Bioinformatics

File framework

Data formats

Biositemap Information Model

See also

References

External links