![]() | This is a documentation subpage for Template:Infobox biodatabase. It may contain usage information, categories and other content that is not part of the original template page. |
![]() | This template uses Lua: |
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
editContent
edit- 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
edit- 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
edit- 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
edit- webapp: Web application(s)
- standalone: Standalone tool(s)
Misc.
edit- 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
edit{{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
edit![]() | |
Content | |
---|---|
Description | GenBank, the NIH genetic sequence database |
Data types captured | Nucleotide Sequence, Protein sequence |
Organisms | all |
Contact | |
Research center | NCBI |
Primary citation | PMID 21071399 |
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
editThe following XSLT stylesheet https://gist.github.com/768553 can be used to generate a stub from a PubMed article.
$ 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
edit- Category:Pages using infobox biodatabase with a malformed pmid (0)
- Category:Pages using infobox biodatabase with unknown parameters (0)
See also
edit
Infobox for biological databases
Parameter | Description | Type | Status | |
---|---|---|---|---|
box_width | box_width | no description | Unknown | optional |
Name | title name | no description | Unknown | optional |
logo | logo | no description | Unknown | optional |
logo_size | logo_size | no description | Unknown | optional |
Logo upright scaling factor | logo_upright | See MOS:UPRIGHT | Unknown | optional |
logo_alt | logo_alt | no description | Unknown | optional |
logo_caption | logo_caption | no description | Unknown | optional |
screenshot | screenshot | no description | Unknown | optional |
collapsible | collapsible | no description | Unknown | optional |
image_size | image_size imagesize | no description | Unknown | optional |
alt | alt | no description | Unknown | optional |
caption | caption | no description | Unknown | optional |
Description | description | no description
| Unknown | optional |
Scope | scope | no description | Unknown | optional |
organism | organism | no description | Unknown | optional |
center | center | no description | Unknown | optional |
laboratory | laboratory | no description | Unknown | optional |
author | author | no description | Unknown | optional |
citation | citation | no description | Unknown | optional |
pmid | pmid | no description | Unknown | optional |
centre | centre | no description | Unknown | optional |
released | released | no description | Unknown | optional |
standard | standard | no description | Unknown | optional |
format | format | no description | Unknown | optional |
url | url | no description | Unknown | optional |
download | download | no description | Unknown | optional |
webservice | webservice | no description | Unknown | optional |
sql | sql | no description | Unknown | optional |
sparql | sparql | no description | Unknown | optional |
webapp | webapp | no description | Unknown | optional |
standalone | standalone | no description | Unknown | optional |
license | license | no description | Unknown | optional |
versioning | versioning | no description | Unknown | optional |
frequency | frequency | no description | Unknown | optional |
version | version | no description | Unknown | optional |
curation | curation | no description | Unknown | optional |
bookmark | bookmark | no description | Unknown | optional |