Template:Infobox biodatabase/doc

GenBank
Content
Description	GenBank, the NIH genetic sequence database
Data types; captured	Nucleotide Sequence, Protein sequence
Organisms	all
Contact
Research center	NCBI
Primary citation	PMID 21071399
Access
Data format	XML; ASN.1; Genbank format
Website	NCBI
Download URL	ncbi ftp
Web service URL	eutils; soap
Tools
Web	BLAST
Standalone	BLAST
Miscellaneous
License	Public domain-US Government
Bookmarkable; entities	yes

This is a documentation subpage for Template:Terminate sentence
It may contain usage information, categories and other content that is not part of the original template page.

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 Category:Biological databases at the bottom of the article.

Fields[edit]

Content[edit]

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[edit]

center or centre: the research center. e.g. NCBI
laboratory: the laboratory
author: the author(s) of this database
citation: the primary citation for an article describing the database (alternatively use pmid= for the PubMed ID, but don't use both)
pmid: PMID for an article describing the database (alternatively use citation=, but don't use both)
released: release date

Access[edit]

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[edit]

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

Misc.[edit]

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)

Model[edit]

{{Infobox biodatabase
|title =
|logo =
|description = 
|scope = 
|organism = 
|center = 
|laboratory = 
|author = 
|citation = 
|released = 
|standard = 
|format = 
|url = 
|download = 
|webservice = 
|sql = 
|sparql = 
|webapp = 
|standalone = 
|license = 
|versioning = 
|frequency = 
|curation = 
|bookmark =
|version =
}}

Example[edit]

{{Infobox biodatabase
| title = [[GenBank]]
| author =
| center = [[National Center for Biotechnology Information|NCBI]]
| organism = all
| description = GenBank, the NIH genetic sequence database
| scope = Nucleotide Sequence, Protein sequence
| url = [http://www.ncbi.nlm.nih.gov/ NCBI]
| download = [ftp://ftp.ncbi.nih.gov/ ncbi ftp]
| webservice = [http://eutils.ncbi.nlm.nih.gov/ eutils]<br/>
               [http://eutils.ncbi.nlm.nih.gov/soap/v2.0/eutils.wsdl soap]
| license = Public domain-US Government
| pmid = 21071399
| logo = [[File:US-NLM-NCBI-Logo.svg|60px]]
| standalone=[[BLAST]]
| webapp=[[BLAST]]
| format= [[XML]]<br/>[[ASN.1]]<br/>Genbank format
| bookmark=yes
}}

Quick generation with XSLT[edit]

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

Example with xsltproc[edit]

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 = 19846593
(...)