قالب:جدول قاعدة بيانات بيولوجية

GenBank
المحتوى
الوصف	GenBank, the NIH genetic sequence database
Data types captured	Nucleotide Sequence, Protein sequence
العضيات	all
الاتصال
مركز الأبحاث	NCBI
المرجع الأولي	PMID 21071399
الولوج
تنسيق البيانات	XML; ASN.1; Genbank format
الموقع الإلكتروني	NCBI
رابط التحميل	ncbi ftp
رابط خدمة الوب	eutils; soap
Tools
Web	BLAST
Standalone	BLAST
متفرقات
License	Public domain-US Government
Bookmarkable entities	yes

المحتوى
الوصف	{{{description}}}
Data types captured	{{{scope}}}
العضيات	{{{organism}}}
الاتصال
مركز الأبحاث	{{{center}}}
المعمل	{{{laboratory}}}
المؤلفون	{{{author}}}
المرجع الأولي	{{{pmid}}}
تاريخ النشر	{{{released}}}
الولوج
المعايير	{{{standard}}}
تنسيق البيانات	{{{format}}}
الموقع الإلكتروني	{{{url}}}
رابط التحميل	{{{download}}}
رابط خدمة الوب	{{{webservice}}}
public SQL access	{{{sql}}}
Sparql endpoint	{{{sparql}}}
Tools
Web	{{{webapp}}}
Standalone	{{{standalone}}}
متفرقات
License	{{{license}}}
Versioning	{{{versioning}}}
Data release frequency	{{{frequency}}}
الإصدار	{{{version}}}
Curation policy	{{{curation}}}
Bookmarkable entities	{{{bookmark}}}

Template documentation[view] [edit] [history] [purge]

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
(...)