Difference between revisions of "FlyBase:Reference Manual F. Links to and from FlyBase"

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FlyBase provides stable links to FlyBase for use by other databases, and links to other databases from FlyBase. Links to FlyBase data items, and links between data items in FlyBase and other databases are described in the sections that follow. Drosophila Resources includes a linked list of additional databases likely to be of interest to users of FlyBase.
 
FlyBase provides stable links to FlyBase for use by other databases, and links to other databases from FlyBase. Links to FlyBase data items, and links between data items in FlyBase and other databases are described in the sections that follow. Drosophila Resources includes a linked list of additional databases likely to be of interest to users of FlyBase.
  
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=F.1. FlyBase Identifier Numbers=
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'''FlyBase-curated links'''
  
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FlyBase assigns unique identifier numbers to several classes of object within the database. One reason for this is to allow unambiguous cross-references both within FlyBase and between FlyBase and other databases.
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These are accession numbers that are incorporated into the FlyBase database, for sequence and certain other molecular data, and for reference data.
  
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FlyBase identifier numbers have the general form FBxxnnnnnnn where xx is an alphabetical code for the identifier class and nnnnnnn is a 7 digit number, padded with leading zeros.
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'''Linkouts'''
  
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The following classes of object are now publicly available in FlyBase data:
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These links derive from linking tables that are maintained and provided to FlyBase by the external database. Linkouts are combined with FlyBase data for reporting on FlyBase web pages.
  
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FBab - aberration
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==F.2.1. FlyBase-curated links==
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FBal - allele
 
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FBba - balancer/genotype variant
 
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FBcl - clone
 
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FBgn - gene
 
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FBim - image
 
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FBmc - molecular construct
 
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FBms - molecular segment
 
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FBpp - polypeptide
 
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FBrf - reference
 
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FBst - stock
 
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FBti - transposable element insertion
 
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FBtp - transgenic construct or natural transposon
 
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FBtr - transcript
 
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Each object has a single Primary identifier number that is used to uniquely identify it in the database.
 
  
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An object may also have any number of Secondary identifier numbers. If an object has a secondary identifier number, it generally indicates that at some point an entry has been merged with or split from other entries in the database. This may have occured due to more data becoming available in the literature or due to correction of previous errors in the database.
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==FlyBase-curated links==
  
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The rules for when primary identifier numbers become secondary are complex. Some examples are included below:
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Accession numbers from the following databases are currently incorporated into FlyBase records as FlyBase-curated links:
  
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A merge:
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[http://www.ddbj.nig.ac.jp/ DDBJ]/[http://www.ebi.ac.uk/embl/ EMBL]/[http://www.ncbi.nlm.nih.gov/Genbank/ GenBank] - the nucleic acid sequence databases of Japan, the U.S., and Europe
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If two entries A and B are found to refer to the same object, then a new primary identifier number will be given to the merged entry, and the old identifier numbers of entries A and B will be listed under this merged entry as secondary identifier numbers.
 
  
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A split (case 1):
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[http://www.epd.isb-sib.ch/ EPD] - Eukaryotic Promoter Database (Bucher)
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If one entry is found to correspond to two (or more) objects, e.g., entry A does, in fact, refer to objects X and Y, then X and Y, as new objects, each get new primary identifier numbers and the old primary identifier number of the suppressed entry A is listed as a secondary identifier number under both X and Y.
 
  
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A split (case 2):
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[http://www.gpcr.org/7tm/ GPCRDB] - The G protein-coupled receptor database
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If one entry is found to correspond to two (or more) objects, e.g. entry A refers to objects A and X, then the existing entry for A and the new entry for X each get a new primary identifier number and the old primary identifier number of A is listed as a secondary identifier number under both A and X.
 
  
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If an object is simply renamed, i.e. its valid symbol in FlyBase is changed without there being a merge or a split, its primary identifier number does not change.
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[http://www.ebi.ac.uk/interpro/ InterPro] - a database of protein families, domains and functional sites
  
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The following classes of identifier were previously used in FlyBase, but are no longer in current use as identifier numbers in the database.
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[http://merops.sanger.ac.uk/ MEROPS] - Protease database
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[http://merops.sanger.ac.uk/ MEROPS] - Protease database
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[http://microrna.sanger.ac.uk/sequences/index.shtml miRBase] - microRNA data
  
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FBan - annotation
 
  
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=F.2. Links to Drosophila data outside of FlyBase=
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[http://mitodrome.ba.itb.cnr.it/ MitoDrome] - MitoDrome
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FlyBase includes "pointers" to data kept by other databases in two different ways.
 
  
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FlyBase-curated links
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[http://www.rcsb.org/pdb/home/home.do PDB] - Protein Data Bank (Brookhaven)
  
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These are accession numbers that are incorporated into the FlyBase database, for sequence and certain other molecular data, and for reference data.
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[http://www.ncbi.nlm.nih.gov/pubmed PubMed] - biomedical literature citations and abstracts
  
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Linkouts
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Rfam - RNA families database of alignments and CMs
  
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These links derive from linking tables that are maintained and provided to FlyBase by the external database. Linkouts are combined with FlyBase data for reporting on FlyBase web pages.
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TRANSFAC - A database of transcription factors and their binding sites
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==F.2.1. FlyBase-curated links==
 
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Accession numbers from the following databases are currently incorporated into FlyBase records as FlyBase-curated links:
 
  
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DDBJ/EMBL/GenBank - the nucleic acid sequence databases of Japan, the U.S., and Europe
 
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EPD - Eukaryotic Promoter Database (Bucher)
 
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GPCRDB - The G protein-coupled receptor database
 
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InterPro - a database of protein families, domains and functional sites
 
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MEROPS - Protease database
 
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miRBase - microRNA data
 
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MitoDrome - A database of annotated Dmel nuclear genes encoding mitochondrial proteins.
 
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PDB - Protein Data Bank (Brookhaven)
 
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PubMed - biomedical literature citations and abstracts
 
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Rfam - RNA families database of alignments and CMs
 
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TRANSFAC - A database of transcription factors and their binding sites
 
 
UniProtKB/Swiss-Prot - UniProt Knowledgebase, Swiss-Prot section
 
UniProtKB/Swiss-Prot - UniProt Knowledgebase, Swiss-Prot section
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UniProtKB/TrEMBL - UniProt Knowledgebase, TrEMBL section
 
UniProtKB/TrEMBL - UniProt Knowledgebase, TrEMBL section
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==F.2.2. FlyBase linkouts==
 
==F.2.2. FlyBase linkouts==

Latest revision as of 18:40, 10 February 2014

FlyBase provides stable links to FlyBase for use by other databases, and links to other databases from FlyBase. Links to FlyBase data items, and links between data items in FlyBase and other databases are described in the sections that follow. Drosophila Resources includes a linked list of additional databases likely to be of interest to users of FlyBase.

FlyBase-curated links

These are accession numbers that are incorporated into the FlyBase database, for sequence and certain other molecular data, and for reference data.

Linkouts

These links derive from linking tables that are maintained and provided to FlyBase by the external database. Linkouts are combined with FlyBase data for reporting on FlyBase web pages.

F.2.1. FlyBase-curated links

FlyBase-curated links

Accession numbers from the following databases are currently incorporated into FlyBase records as FlyBase-curated links:

DDBJ/EMBL/GenBank - the nucleic acid sequence databases of Japan, the U.S., and Europe

EPD - Eukaryotic Promoter Database (Bucher)

GPCRDB - The G protein-coupled receptor database

InterPro - a database of protein families, domains and functional sites

MEROPS - Protease database MEROPS - Protease database miRBase - microRNA data


MitoDrome - MitoDrome

PDB - Protein Data Bank (Brookhaven)

PubMed - biomedical literature citations and abstracts

Rfam - RNA families database of alignments and CMs

TRANSFAC - A database of transcription factors and their binding sites

UniProtKB/Swiss-Prot - UniProt Knowledgebase, Swiss-Prot section

UniProtKB/TrEMBL - UniProt Knowledgebase, TrEMBL section

F.2.2. FlyBase linkouts

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