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

From FlyBase Wiki
Jump to: navigation, search
Line 8: Line 8:
  
 
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.
 
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==
 
==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:
 
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
+
[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
EPD - Eukaryotic Promoter Database (Bucher)
+
 
GPCRDB - The G protein-coupled receptor database
+
[http://www.epd.isb-sib.ch/ EPD] - Eukaryotic Promoter Database (Bucher)
InterPro - a database of protein families, domains and functional sites
+
 
MEROPS - Protease database
+
[http://www.gpcr.org/7tm/ GPCRDB] - The G protein-coupled receptor database
miRBase - microRNA data
+
 
 +
[http://www.ebi.ac.uk/interpro/ InterPro] - a database of protein families, domains and functional sites
 +
 
 +
[http://merops.sanger.ac.uk/ MEROPS] - Protease database
 +
 
 +
[http://microrna.sanger.ac.uk/sequences/index.shtml miRBase] - microRNA data
 +
 
 
MitoDrome - A database of annotated Dmel nuclear genes encoding mitochondrial proteins.
 
MitoDrome - A database of annotated Dmel nuclear genes encoding mitochondrial proteins.
 +
 
PDB - Protein Data Bank (Brookhaven)
 
PDB - Protein Data Bank (Brookhaven)
 +
 
PubMed - biomedical literature citations and abstracts
 
PubMed - biomedical literature citations and abstracts
 +
 
Rfam - RNA families database of alignments and CMs
 
Rfam - RNA families database of alignments and CMs
 +
 
TRANSFAC - A database of transcription factors and their binding sites
 
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
 +
 
UniProtKB/TrEMBL - UniProt Knowledgebase, TrEMBL section
 
UniProtKB/TrEMBL - UniProt Knowledgebase, TrEMBL section
 +
 
==F.2.2. FlyBase linkouts==
 
==F.2.2. FlyBase linkouts==
 
[http://flybase.org FlyBase]
 
[http://flybase.org FlyBase]
 

Revision as of 17:07, 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/[ http://www.ncbi.nlm.nih.gov/Genbank/ 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

miRBase - microRNA data

MitoDrome - A database of annotated Dmel nuclear genes encoding mitochondrial proteins.

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