Template:Infobox biodatabase

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

Template documentation[view] [edit] [history] [purge]

This template uses Lua:

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

{{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

Template parameters[Edit template data]
This template prefers block formatting of parameters.
Parameter		Description	Type	Status
box_width	`box_width`	no description	Unknown	optional
Name	`title` `name`	no description	Unknown	optional
logo	`logo`	no description	Unknown	optional
logo_size	`logo_size`	no description	Unknown	optional
Logo upright scaling factor	`logo_upright`	See MOS:UPRIGHT	Unknown	optional
logo_alt	`logo_alt`	no description	Unknown	optional
logo_caption	`logo_caption`	no description	Unknown	optional
screenshot	`screenshot`	no description	Unknown	optional
collapsible	`collapsible`	no description	Unknown	optional
image_size	`image_size` `imagesize`	no description	Unknown	optional
alt	`alt`	no description	Unknown	optional
caption	`caption`	no description	Unknown	optional
Description	`description`	no description Example A short description	Unknown	optional
Scope	`scope`	no description	Unknown	optional
organism	`organism`	no description	Unknown	optional
center	`center`	no description	Unknown	optional
laboratory	`laboratory`	no description	Unknown	optional
author	`author`	no description	Unknown	optional
citation	`citation`	no description	Unknown	optional
pmid	`pmid`	no description	Unknown	optional
centre	`centre`	no description	Unknown	optional
released	`released`	no description	Unknown	optional
standard	`standard`	no description	Unknown	optional
format	`format`	no description	Unknown	optional
url	`url`	no description	Unknown	optional
download	`download`	no description	Unknown	optional
webservice	`webservice`	no description	Unknown	optional
sql	`sql`	no description	Unknown	optional
sparql	`sparql`	no description	Unknown	optional
webapp	`webapp`	no description	Unknown	optional
standalone	`standalone`	no description	Unknown	optional
license	`license`	no description	Unknown	optional
versioning	`versioning`	no description	Unknown	optional
frequency	`frequency`	no description	Unknown	optional
version	`version`	no description	Unknown	optional
curation	`curation`	no description	Unknown	optional
bookmark	`bookmark`	no description	Unknown	optional

The above documentation is transcluded from Template:Infobox biodatabase/doc.
Editors can experiment in this template's sandbox and testcases pages.
Add categories to the /doc subpage. Subpages of this template.