模板: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

Screenshot
Content
Description	GenBank, the NIH genetic sequence database
Data types captured	Nucleotide Sequence, Protein sequence
Organisms	all
Contact
Research center	NCBI
Primary citation	模板:Ifnumber
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

模板参数

此模板首选参数换行的代码块格式。

参数		描述	类型	状态
box_width	box_width	无描述	未知	可选
Name	titlename	无描述	未知	可选
logo	logo	无描述	未知	可选
logo_size	logo_size	无描述	未知	可选
Logo upright scaling factor	logo_upright	See MOS:UPRIGHT	未知	可选
logo_alt	logo_alt	无描述	未知	可选
logo_caption	logo_caption	无描述	未知	可选
screenshot	screenshot	无描述	未知	可选
collapsible	collapsible	无描述	未知	可选
image_size	image_sizeimagesize	无描述	未知	可选
alt	alt	无描述	未知	可选
caption	caption	无描述	未知	可选
Description	description	无描述 示例值 A short description	未知	可选
Scope	scope	无描述	未知	可选
organism	organism	无描述	未知	可选
center	center	无描述	未知	可选
laboratory	laboratory	无描述	未知	可选
author	author	无描述	未知	可选
citation	citation	无描述	未知	可选
pmid	pmid	无描述	未知	可选
centre	centre	无描述	未知	可选
released	released	无描述	未知	可选
standard	standard	无描述	未知	可选
format	format	无描述	未知	可选
url	url	无描述	未知	可选
download	download	无描述	未知	可选
webservice	webservice	无描述	未知	可选
sql	sql	无描述	未知	可选
sparql	sparql	无描述	未知	可选
webapp	webapp	无描述	未知	可选
standalone	standalone	无描述	未知	可选
license	license	无描述	未知	可选
versioning	versioning	无描述	未知	可选
frequency	frequency	无描述	未知	可选
version	version	无描述	未知	可选
curation	curation	无描述	未知	可选
bookmark	bookmark	无描述	未知	可选