 | 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
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. 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
- 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 =
|citation =
|released =
|standard =
|format =
|url =
|download =
|webservice =
|sql =
|sparql =
|webapp =
|standalone =
|license =
|versioning =
|frequency =
|curation =
|bookmark =
|version =
))
Example
 | |
| 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
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 = 19846593
(...)
Tracking categories
- Category:Pages using infobox biodatabase with a malformed pmid (1)
- Category:Pages using infobox biodatabase with unknown parameters (0)
See also
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 |