Template:Infobox biodatabase/doc

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

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

{{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

• Category:Pages using infobox biodatabase with a malformed pmid (0)
• Category:Pages using infobox biodatabase with unknown parameters (0)

See also

• The initial template proposal

Infobox for biological databases

Template parameters

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