Biositemap

The Biositemaps [cite conference| author= Dinov ID, Rubin D, Lorensen W, Dugan J, Ma J, Murphy S, Kirschner B, Bug W, Sherman M, Floratos A, Kennedy D, Jagadish HV, Schmidt J, Athey B, Califano A, Musen M, Altman R, Kikinis R, Kohane I, Delp S, Parker DS, Toga AW | title=iTools: A Framework for Classification, Categorization and Integration of Computational Biology Resources | booktitle=PLoS ONE 3(5): e2265. doi:10.1371/journal.pone.0002265 | year=2008 |url=http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0002265] 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 [http://www.biositemap.org biositemap] concept is based on ideas from [cite conference | author= M.L. Nelson, J.A. Smith, del Campo, H. Van de Sompel, X. Liu| title=Efficient, Automated Web Resource Harvesting | booktitle=WIDM'06 | year=2006 |url=http://public.lanl.gov/herbertv/papers/f140-nelson.pdf] and [http://portal.acm.org/citation.cfm?id=362894&coll=portal&dl=ACM Crawler-friendly Web Servers] , [cite conference | title=Crawler-friendly web servers | booktitle = Proceedings of ACM SIGMETRICS Performance Evaluation Review, Volume 28, Issue 2 | year=2000 | url=http://portal.acm.org/citation.cfm?id=362894&coll=portal&dl=ACM, | author=O. Brandman, J. Cho, Hector Garcia-Molina, and Narayanan Shivakumar] and it integrates the features of Sitemaps and RSS feeds into a decentralized mechanism for announcing and communicating updates to existent and introduction of new biomedical data and computing resources. These site, institution or investigator specific "biositemap" descriptions are posted in XML format online and are searched, parsed, monitored and interpreted by web search engines, human and machine interfaces, custom-design web crawlers and other outlets 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 XML file that lists the biomedical and bioinformatics resources for a specific research group or consortium. It allows developers of biomedical resources to completely describe the functionality and usability and of each of their software tools, databases or web-services.

Biositemaps are particularly beneficial in situations
* when providers and consumers of bioinformatics and biomedical computing resources need to communicate in a scalable, efficient, agile and decentralized fashion. In these cases, a human (graphical) or a machine (computer) interface connects the descriptions of resources and facilities the search, comparison and utilization of most relevant resources for specific scientific studies. This infrastructure enables effective and timely matching of services and needs among biomedical investigators and the public in general.
* where meta-resources, computational or digital libraries need to update their contents to reflect the current states of newly developed biomedical materials and resources using AJAX, JSON or WSDL protocols.

Biositemaps supplement and do not replace the existing frameworks for dissemination of data, tools and services. By broadcasting a relevant and up-to-date Biositemap file on the web, investigators and institutions are only helping different engine's crawlers, machine interfaces and users dynamically acquire, interpret, process and utilize the most accurate information about the state of the resources disseminated by the developing group. Using this biositemap protocol does not guarantee that your resources will be included in search indexes nor does it influence the way that your tools are ranked or perceived by the community.

Computational biology resources

There are several types of computational biology resources [cite conference | author= Cannata N, Merelli E, Altman RB | title=Time to Organize the Bioinformatics Resourceome | booktitle=PLoS Computational Biology Vol. 1, No. 7, e76, 0531-0533 | year=2005 |url=http://dx.doi.org/10.1371/journal.pcbi.0010076] [cite conference| author= Dinov ID, Rubin D, Lorensen W, Dugan J, Ma J, Murphy S, Kirschner B, Bug W, Sherman M, Floratos A, Kennedy D, Jagadish HV, Schmidt J, Athey B, Califano A, Musen M, Altman R, Kikinis R, Kohane I, Delp S, Parker DS, Toga AW | title=iTools: A Framework for Classification, Categorization and Integration of Computational Biology Resources | booktitle=PLoS ONE 3(5): e2265. doi:10.1371/journal.pone.0002265 | year=2008 |url=http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0002265]

oftware Resources (Tools)

* Computational Algorithms (e.g., Level sets, Bioinformatics Algorithms)
* Software Suites (e.g., Vista, geWorkbench, FEATURE, ShapeViewer, Slicer3D, Pipeline)
* Downloadable libraries (e.g., Insight Segmentation and Registration Toolkit)
* Locally Executable programs (e.g., [http://www.loni.ucla.edu/Software/Software_Detail.jsp?software_id=11 Debabeler] )

(Downloadable) Data Resources

* Raw Data - acquired data, going in various SW tools (e.g., [https://www.loni.ucla.edu/ida/login.jsp CCB IDA] )
* Model Data - processed data coming out of SW tools (e.g., [http://www.loni.ucla.edu/Atlases/ CCB Atlases] )
* Textual Data - spread sheets, web-pages (e.g., Imaging Glossary)
* Data Types
** XML (e.g., Module Descriptions)
** JSON Objects - language independent, data transfer, data attributes (e.g., JSON output from the Yahoo! Web Services contain the same data as an XML object; the only difference is in the format, Get GeoNames PostalCodes within convert|10|mi|km of US 90095)
** Binary Data
** Comma-separated-values, .csv

ervices

* Web-services
* Collaborative Services
* Other Services

Required Resource Description Fields

The Biositemap protocol allows many optional fields, but it requires several specific descriptors that are commonly used and necessary for characterizing biomedical resources. There required fields [cite conference | author= Chen YB, Chattopadhyay A, Bergen P, Gadd C, Tannery N | title=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 | booktitle=Nucleic Acids Res. 2007 Jan;35(Database issue):D780-5 | year=2006 |url=http://nar.oxfordjournals.org/cgi/content/full/35/suppl_1/D780] are:
* Name, txt, single line
* Description, txt, multiline
* Type of Resource, typed list
* URL, txt
* Stage, typed list
* Organization
* Resource Ontology Label
* Keywords, txt, single line (May be related to NCBC Ontology)
* License, typed list, with otherSome very useful, but optional, resource descriptors include the type, specification and expectations of the inputs, as well as the characteristics of the outputs, of these resources.

ee also

* Information visualization
* ITools Resourceome
* Sitemaps

References

External links

* [http://www.ncbcs.org/biositemaps NCBC Biositemaps]
* [http://www.bisti.nih.gov/biositemaps/ NIH BISTI Initiative]
* [http://cms.loni.ucla.edu/iToolsNCBCschema.aspx NCBC Biositemap XSD schema definition]
* [http://www.loni.ucla.edu/BioSiteMap.xml CCB instance of a biositemap]
* [http://bioontology.org/projects/xml/NCBO_BioSiteMap.xml NCBO instance of a biositemap]
* [http://portal.ncibi.org/biositemap.xml NCIBI instance of a biositemap]