Bản mẫu:Infobox biodatabase/doc

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 = [[Trung tâm Thông tin Công nghệ sinh học quốc gia Hoa Kỳ|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
}}

GenBank

Nội dung
Mô tả	GenBank, the NIH genetic sequence database
Dạng dữ liệu thu thập	Nucleotide Sequence, Protein sequence
Sinh vật	all
Liên hệ
Trung tâm nghiên cứu	NCBI
Chú thích gốc	PMID 21071399
Truy cập
Data format	XML ASN.1 Genbank format
Website	NCBI
URL tải về	ncbi ftp
URL Dịch vụ web	eutils soap
Công cụ
Ứng dụng Web	BLAST
Phần mềm máy tính	BLAST
Linh tinh
Bản quyền phần mềm	Public domain-US Government
Các thực thể đánh dấu	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
(...)

See also

• Template talk:Infobox biodatabase talk page
• first proposal