Template:Infobox biodatabase

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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

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 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

  • 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)

Model

{{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

GenBank
US-NLM-NCBI-Logo.svg
Content
DescriptionGenBank, the NIH genetic sequence database
Data types
captured
Nucleotide Sequence, Protein sequence
Organismsall
Contact
Research centerNCBI
Primary citationPMID 21071399
Access
Data formatXML
ASN.1
Genbank format
WebsiteNCBI
Download URLncbi ftp
Web service URLeutils
soap
Tools
WebBLAST
StandaloneBLAST
Miscellaneous
LicensePublic domain-US Government
Bookmarkable
entities
yes
{{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 = [https://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

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 = 19846593
(...)

Tracking categories

See also