Biositemap
Encyclopedia
A Biositemap is a way for a biomedical research institution of organisation to show how biological information is distributed throughout their Information Technology
systems and networks. This information may be shared with other organisations and researchers.
The Biositemap enables web browser
s, 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.
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 metafield
s 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.
Crawler-friendly Web Servers, and it integrates the features of sitemaps and RSS
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.
Up-to-date documentation on the information model is available at the Biositemaps website.
Information technology
Information technology is the acquisition, processing, storage and dissemination of vocal, pictorial, textual and numerical information by a microelectronics-based combination of computing and telecommunications...
systems and networks. This information may be shared with other organisations and researchers.
The Biositemap enables web browser
Web browser
A web browser is a software application for retrieving, presenting, and traversing information resources on the World Wide Web. An information resource is identified by a Uniform Resource Identifier and may be a web page, image, video, or other piece of content...
s, crawlers and robots
Web Bot
Web Bot, or the Web Bot Project, refers to an Internet bot software program that is claimed to be able to predict future events by tracking keywords entered on the Internet. It was created in 1997, originally to predict stock market trends...
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
Meta element
Meta elements are the HTML or XHTML <meta … > element used to provide structured metadata about a Web page. Multiple elements are often used on the same page: the element is the same, but its attributes are different...
s and can be created online through sites such as the biositemaps online editor.
The information is a blend of sitemaps
Site map
A site map is a list of pages of a web site accessible to crawlers or users. It can be either a document in any form used as a planning tool for web design, or a web page that lists the pages on a web site, typically organized in hierarchical fashion...
and RSS feeds
RSS
-Mathematics:* Root-sum-square, the square root of the sum of the squares of the elements of a data set* Residual sum of squares in statistics-Technology:* RSS , "Really Simple Syndication" or "Rich Site Summary", a family of web feed formats...
and is created using the Information Model
Information model
An information model in software engineering is a representation of concepts, relationships, constraints, rules, and operations to specify data semantics for a chosen domain of discourse...
(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.
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 resources (data, software tools and web services). The biositemap concept is based on ideas from Efficient, Automated Web Resource Harvesting andCrawler-friendly Web Servers, and it integrates the features of sitemaps and RSS
RSS
-Mathematics:* Root-sum-square, the square root of the sum of the squares of the elements of a data set* Residual sum of squares in statistics-Technology:* RSS , "Really Simple Syndication" or "Rich Site Summary", a family of web feed formats...
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
Resource Description Framework
The Resource Description Framework is a family of World Wide Web Consortium specifications originally designed as a metadata data model...
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
Resource Description Framework
The Resource Description Framework is a family of World Wide Web Consortium specifications originally designed as a metadata data model...
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.