మూస:Infobox biodatabase/doc

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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[మార్చు]

Content[మార్చు]

  • 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[మార్చు]

  • 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[మార్చు]

  • 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[మార్చు]

  • webapp: Web application(s)
  • standalone: Standalone tool(s)

Misc.[మార్చు]

  • 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[మార్చు]

{{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[మార్చు]

GenBank
Content
వివరణGenBank, the NIH genetic sequence database
సేకరించే
డేటా రకాలు
Nucleotide Sequence, Protein sequence
జీవులుall
Contact
పరిశోధనా కేంద్రంNCBI
ప్రాథమిక ఉల్లేఖనPMID 21071399
Access
ఫైలు ఆకృతిXML
ASN.1
Genbank format
వెబ్‌సైటుNCBI
దింపుకునే URLncbi ftp
వెబ్ సర్వీసు URLeutils
soap
Tools
వెబ్ అప్లికేషనుBLAST
కంప్యూటరు సాఫ్టువేరుBLAST
Miscellaneous
LicensePublic domain-US Government
బుక్‌మార్కబుల్
ఎంటిటీలు
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[మార్చు]

The following XSLT stylesheet https://gist.github.com/768553 can be used to generate a stub from a PubMed article.

Example with xsltproc[మార్చు]

$ 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[మార్చు]

See also[మార్చు]