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.

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