Format:Infocaseta Biodatabase

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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

Format:Infobox biodatabase

{{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

See also

Format:Sandbox other

Format de bază

Codul formatului, schematic, punând în evidență cei mai utilizați parametri.

Parametri

Descrierea completă a tuturor parametrilor, în cazul în care formatul are parametri.

Mod de folosire

Dacă trebuie urmați anumiți pași pentru a utiliza formatul, explicați procedura.

Exemple

Dați câteva exemple ale modului de folosire, folosind cod și exemple.

Codul exemplului 1

Format:Formatul care demonstrează exemplul 1

Codul exemplului 2

Format:Formatul care demonstrează exemplul 2

Detalii tehnice

Dacă formatul este mai complex, puteți da detalii despre modul în care este construit. Acestea pot fi utile utilizatorilor care vor să îmbunătățească formatul.

Vezi și

  • legături
  • spre alte
  • formate
  • sau pagini