Template:Infobox biodatabase/doc

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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

Script error: No such module "If empty".
File:US-NLM-NCBI-Logo.svg
Content
DescriptionGenBank, the NIH genetic sequence database
Data types
captured
Nucleotide Sequence, Protein sequence
Organismsall
Contact
Research centerNCBI
Primary citationScript error: No such module "If empty".
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

<syntaxhighlight lang="moin" style="overflow:auto">

Script error: No such module "If empty".
File:US-NLM-NCBI-Logo.svg
Content
DescriptionGenBank, the NIH genetic sequence database
Data types
captured
Nucleotide Sequence, Protein sequence
Organismsall
Contact
Research centerNCBI
Primary citationScript error: No such module "If empty".
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

</syntaxhighlight>

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

<syntaxhighlight lang="console"> $ 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 (...) </syntaxhighlight>

Tracking categories

See also



Infobox for biological databases

Template parameters

This template prefers block formatting of parameters.

ParameterDescriptionTypeStatus
box_widthbox_width

no description

Unknownoptional
Nametitle name

no description

Unknownoptional
logologo

no description

Unknownoptional
logo_sizelogo_size

no description

Unknownoptional
Logo upright scaling factorlogo_upright

See MOS:UPRIGHT

Unknownoptional
logo_altlogo_alt

no description

Unknownoptional
logo_captionlogo_caption

no description

Unknownoptional
screenshotscreenshot

no description

Unknownoptional
collapsiblecollapsible

no description

Unknownoptional
image_sizeimage_size imagesize

no description

Unknownoptional
altalt

no description

Unknownoptional
captioncaption

no description

Unknownoptional
Descriptiondescription

no description

Example
A short description
Unknownoptional
Scopescope

no description

Unknownoptional
organismorganism

no description

Unknownoptional
centercenter

no description

Unknownoptional
laboratorylaboratory

no description

Unknownoptional
authorauthor

no description

Unknownoptional
citationcitation

no description

Unknownoptional
pmidpmid

no description

Unknownoptional
centrecentre

no description

Unknownoptional
releasedreleased

no description

Unknownoptional
standardstandard

no description

Unknownoptional
formatformat

no description

Unknownoptional
urlurl

no description

Unknownoptional
downloaddownload

no description

Unknownoptional
webservicewebservice

no description

Unknownoptional
sqlsql

no description

Unknownoptional
sparqlsparql

no description

Unknownoptional
webappwebapp

no description

Unknownoptional
standalonestandalone

no description

Unknownoptional
licenselicense

no description

Unknownoptional
versioningversioning

no description

Unknownoptional
frequencyfrequency

no description

Unknownoptional
versionversion

no description

Unknownoptional
curationcuration

no description

Unknownoptional
bookmarkbookmark

no description

Unknownoptional