imported>AntiCompositeNumber: Reverted edits by 185.65.253.122 (talk) to last version by Elli

2022-01-23T03:53:45Z

Reverted edits by 185.65.253.122 (talk) to last version by Elli

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{{documentation subpage}}
{{Lua|Module:Infobox|Module:InfoboxImage|Module:Check for unknown parameters}}

[[Help:Infobox|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. [[National Center for Biotechnology Information|NCBI]]
* '''laboratory''': the laboratory
* '''author''': the author(s) of this database
* '''citation''': the primary citation for an article describing the database (alternatively use <code>pmid=</code> for the PubMed ID, but don't use both)
* '''pmid''': [[PMID]] for an article describing the database (alternatively use <code>citation=</code>, 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==
<pre>
{{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 =
}}
</pre>

==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 = [https://www.ncbi.nlm.nih.gov/ NCBI]
| download = [ftp://ftp.ncbi.nih.gov/ ncbi ftp]
| webservice = [http://eutils.ncbi.nlm.nih.gov/ eutils] [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]] [[ASN.1]] Genbank format
| bookmark= yes
}}
<syntaxhighlight lang="moin" style="overflow:auto">{{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] 
[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]] [[ASN.1]] Genbank format
| bookmark=yes
}}</syntaxhighlight>
{{Clear}}

==Quick generation with XSLT==
The following [[XSLT]] stylesheet https://gist.github.com/768553 can be used to generate a [[Wikipedia:stub|stub]] from a [[PubMed]] article.

===Example with [[xsltproc]]===
<syntaxhighlight lang="console">
$ 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
(...)
</syntaxhighlight>

== Tracking categories ==
* {{clc|Pages using infobox biodatabase with a malformed pmid}}
* {{clc|Pages using infobox biodatabase with unknown parameters}}

== See also ==
* [[Wikipedia:WikiProject Molecular and Cell Biology/Proposals#Infobox_biodatabase|The initial template proposal]]

<includeonly>{{sandbox other||

[[Category:Biology infobox templates]]
[[Category:Templates that add a tracking category]]
}}</includeonly>

Template:Infobox biodatabase/doc - Revision history

imported>AntiCompositeNumber: Reverted edits by 185.65.253.122 (talk) to last version by Elli