Template:Infobox biodatabase/doc

The Template:infobox biodatabase
Infobox used to describe a Biological database. For each database we want to know if the database is still in use, if a web service or a sql access is available, if it is specific to a given organism, etc...

Please, don't forget to add w:Category:Biological databases at the bottom of the article.

Content

 * title: title e.g. FusariumDB
 * description: short description e.g.: Cyber infrastructure for Fusarium
 * scope: Could be one of : Nucleotide Sequence, RNA sequence, Protein sequence, Structure, Genomics (non-vertebrate), Metabolic and Signaling Pathways, Human and other Vertebrate Genomes, Human Genes and Diseases, Microarray Data and other Gene Expression, Proteomics Resources, Other Molecular Biology, Organelle, Plant, Immunological...
 * organism: one or more organisms specific to this database

Contact

 * center: the research center. e.g. NCBI
 * laboratory: the laboratory
 * author: the author(s) of this database
 * pmid: PMID for an article describing the database
 * released: release date

Access

 * standard: MIs, Data formats, Terminologies
 * format: Data formats
 * sql: if the database is available as a public SQL server (could be a URL pointing to the documentation )
 * webservice: if there is a web service for this database (could be a URL pointing to a WSDL file.
 * sparql: sparql endpoint(s) if any
 * download: download area, FTP site...

Tools

 * webapp: Web application(s)
 * standalone: Standalone tool(s)

Misc.

 * versioning: Versioning policy/ access to historical files
 * license: license for the data.
 * frequency: Data release frequency
 * curation: Curation policy
 * version: release version
 * bookmark: Can you bookmark the entity in this database (http GET method)

Quick generation with XSLT
The following XSLT stylesheet https://gist.github.com/768553 can be used to generate a stub from a Pubmed article.

Example with xsltproc
xsltproc --novalid \ pubmed4biodb.xsl \ "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=19846593&retmode=xml"

{{infobox_biodatabase (...)
 * title = REBASE--a database for DNA restriction and modification: enzymes, genes and genomes.
 * logo =[[File:Database.png]]
 * description = REBASE--a database for DNA restriction and modification: enzymes, genes and genomes.
 * scope =
 * organism =
 * center =
 * laboratory = New England Biolabs, Inc, 240 County Road, Ipswich, MA 01938, USA.
 * author = Richard J Roberts
 * pmid = PMID 19846593