قالب:جدول قاعدة بيانات بيولوجية/doc
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The Template:infobox biodatabase
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 w: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: the research center. e.g. NCBI
- laboratory: the laboratory
- author: the author(s) of this database
- pmid: PMID for an article describing the database
- 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 =
|pmid =
|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 = [http://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 = 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 = PMID 19846593
(...)