xref_config.ini 181 KB
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# $Id$

########################################################################
# SOURCES                                                              #
#                                                                      #
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# Keys:                                                                #
#   name        - name of this source (required)                       #
#   download    - must be downloaded (Y or N, required)                #
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#   order       - parsing order for this source                        #
#   priority    - priority of these data files when more files belong  #
#                 to the same source 'name'                            #
#   prio_descr  - label for the 'priority'                             #
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#   parser      - the parser to be used (required)                     #
#   release_uri - URI pointing to release information (optional)       #
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#   data_uri    - URI pointing to the data files (multiple, required)  #
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#   dependent   - These must be loaded first                           #
#                 Note is sepecies does not have this source then test #
#                 ignores these                                        #
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#                                                                      #
########################################################################

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[source EC_NUMBER::saccharomyces_cerevisiae]
# Used by S.cerevisiae
name            = EC_NUMBER
download        = N
order           = 50
priority        = 70
prio_descr      =
parser          = 
release_uri     =
data_uri        = 

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[source MEROPS::drosophila_melanogaster]
# Used by the 12 drosophila genomes
name            = MEROPS
download        = N
order           = 50
priority        = 1
prio_descr      =
parser          = FlybaseParser
release_uri     =
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data_uri        = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r5.39_FB2011_07/gff/dmel-all-*.gff.gz
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[source MEROPS::drosophila_grimshawi]
# Used by the 12 drosophila genomes
name            = MEROPS
download        = N
order           = 50
priority        = 1
prio_descr      =
parser          = FlybaseParser
release_uri     =
data_uri        = ftp://ftp.flybase.net/genomes/Drosophila_grimshawi/current/gff/dgri-all-*.gff.gz

[source MEROPS::drosophila_erecta]
# Used by the 12 drosophila genomes
name            = MEROPS
download        = N
order           = 50
priority        = 1
prio_descr      =
parser          = FlybaseParser
release_uri     =
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data_uri        = ftp://ftp.flybase.org/releases/current/dere_1.3/gff/dere-all-r1.3.gff.gz
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[source MEROPS::drosophila_virilis]
# Used by the 12 drosophila genomes
name            = MEROPS
download        = N
order           = 50
priority        = 1
prio_descr      =
parser          = FlybaseParser
release_uri     =
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data_uri        = ftp://ftp.flybase.org/releases/current/dvir_1.2/gff/dvir-all-r1.2.gff.gz
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[source miRBase::drosophila_melanogaster]
# Used by the 12 drosophila genomes
name            = miRBase
download        = N
order           = 50
priority        = 1
prio_descr      =
parser          = FlybaseParser
release_uri     =
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data_uri        = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r5.39_FB2011_07/gff/dmel-all-*.gff.gz
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[source miRBase::drosophila_pseudoobscura]
# Used by the 12 drosophila genomes
name            = miRBase
download        = N
order           = 50
priority        = 1
prio_descr      =
parser          = FlybaseParser
release_uri     =
data_uri        = ftp://ftp.flybase.net/genomes/Drosophila_pseudoobscura/current/gff/dpse-all-*.gff.gz

[source TransFac::drosophila_melanogaster]
# Used by the 12 drosophila genomes
name            = TransFac
download        = N
order           = 50
priority        = 1
prio_descr      =
parser          = FlybaseParser
release_uri     =
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data_uri        = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r5.39_FB2011_07/gff/dmel-all-*.gff.gz
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[source TransFac::drosophila_pseudoobscura]
# Used by the 12 drosophila genomes
name            = TransFac
download        = N
order           = 50
priority        = 1
prio_descr      =
parser          = FlybaseParser
release_uri     =
data_uri        = ftp://ftp.flybase.net/genomes/Drosophila_pseudoobscura/current/gff/dpse-all-*.gff.gz

[source EPD::drosophila_melanogaster]
# Used by the 12 drosophila genomes
name            = EPD
download        = N
order           = 50
priority        = 1
prio_descr      =
parser          = FlybaseParser
release_uri     =
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data_uri        = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r5.39_FB2011_07/gff/dmel-all-*.gff.gz
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[source EPD::drosophila_pseudoobscura]
# Used by the 12 drosophila genomes
name            = EPD
download        = N
order           = 50
priority        = 1
prio_descr      =
parser          = FlybaseParser
release_uri     =
data_uri        = ftp://ftp.flybase.net/genomes/Drosophila_pseudoobscura/current/gff/dpse-all-*.gff.gz

[source EPD::drosophila_simulans]
# Used by the 12 drosophila genomes
name            = EPD
download        = N
order           = 50
priority        = 1
prio_descr      =
parser          = FlybaseParser
release_uri     =
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data_uri        = ftp://ftp.flybase.org/releases/current/dsim_r1.3/gff/dsim-all-r1.3.gff.gz
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[source EPD::drosophila_sechellia]
# Used by the 12 drosophila genomes
name            = EPD
download        = N
order           = 50
priority        = 1
prio_descr      =
parser          = FlybaseParser
release_uri     =
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data_uri        = ftp://ftp.flybase.org/releases/current/dsec_r1.3/gff/dsec-all-r1.3.gff.gz
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[source EPD::drosophila_mojavensis]
# Used by the 12 drosophila genomes
name            = EPD
download        = N
order           = 50
priority        = 1
prio_descr      =
parser          = FlybaseParser
release_uri     =
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data_uri        = ftp://ftp.flybase.org/releases/current/dmoj_r1.3/gff/dmoj-all-r1.3.gff.gz
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[source EPD::drosophila_virilis]
# Used by the 12 drosophila genomes
name            = EPD
download        = N
order           = 50
priority        = 1
prio_descr      =
parser          = FlybaseParser
release_uri     =
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data_uri        = ftp://ftp.flybase.org/releases/current/dvir_r1.2/gff/dvir-all-r1.2.gff.gz
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[source AFFY_DrosGenome1::drosophila_melanogaster]
# Used by drosophila_melanogaster
name            = AFFY_DrosGenome1
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download        = N
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order           = 50
priority        = 1
prio_descr      =
parser          = Flybase_dmel_GFFv3_Parser
release_uri     =
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data_uri        = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r5.39_FB2011_07/gff/dmel-all-*.gff.gz
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[source PHIbase::MULTI]
name            = PHIbase
download        = Y
order           = 50
priority        = 1
prio_descr      =
parser          = PHIbaseParser
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dependent       = Uniprot/SWISSPROT,Uniprot/SPTREMBL
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release_uri     = 
data_uri        = http://www.phi-base.org/PHI-export.php


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[species anas_platyrhynchos]
taxonomy_id     = 8839
aliases         = duck, mallard, mallard duck, mallard ducks, anas platyrhynchos, anas boschas, anas domesticus
source          = EntrezGene::MULTI
source          = GO::MULTI
source          = InterproGO::MULTI
source          = Interpro::MULTI
source          = RefSeq_dna::MULTI-vertebrate_other
source          = RefSeq_peptide::MULTI-vertebrate_other
source          = Uniprot/SPTREMBL::MULTI
source          = Uniprot/SWISSPROT::MULTI

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[species anolis_carolinensis]
taxonomy_id     = 28377
aliases         = anole, green anole lizard, green anole, american anole, redthroated anole, anoliscarolinensis, anolis_carolinensis
source          = EntrezGene::MULTI
source          = GO::MULTI
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source          = goslim_goa::MULTI
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source          = InterproGO::MULTI
source          = Interpro::MULTI
source          = RefSeq_dna::MULTI-vertebrate_other
source          = RefSeq_peptide::MULTI-vertebrate_other
source          = Uniprot/SPTREMBL::MULTI
source          = Uniprot/SWISSPROT::MULTI
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#source          = Uniprot/Varsplic::MULTI
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[source VB_Community_Annotation::aedes_aegypti]
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# Used by aedes_aegypti
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name            = VB_Community_Annotation
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download        = Y
order           = 40
priority        = 1
prio_descr      =
parser          = AedesCAPParser
release_uri     =
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data_uri        = file:VB_Community_Annotation/Aedes_VB_Community_Annotation.fa
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[source AedesGenBank::aedes_aegypti]
# Used by aedes_aegypti
name            = AedesGenBank
download        = Y
order           = 30
priority        = 1
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prio_descr      =
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parser          = AedesGenBankParser
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release_uri     =
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data_uri        = file:AedesGenBank/Aedes_proteinID.fa
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[source Ixodes_ManualAnnotation::ixodes_scapularis]
# Used by ixodes_scapularis
name            = Ixodes_ManualAnnotation
download        = Y
order           = 40
priority        = 1
prio_descr      =
parser          = IxodesCAPParser
release_uri     =
data_uri        = file:Ixodes_scapularis/ixodes_CAP.fa

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#[source Anopheles_symbol::anopheles_gambiae]
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# Used by anopheles_gambiae
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#name            = Anopheles_symbol
#download        = Y
#order           = 40
#priority        = 1
#prio_descr      =
#parser          = AnophelesSymbolParser
#release_uri     =
#data_uri        = file:Anopheles_symbol/GeneName_translation_UniqID.txt

[source VB_Community_Annotation::anopheles_gambiae]
# Used by anopheles_gambiae
name            = VB_Community_Annotation
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download        = Y
order           = 40
priority        = 1
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prio_descr      =
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parser          = VBCommunitySymbolParser
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release_uri     =
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data_uri        = file:VB_Community_Annotation/xref_Anopheles_symbol_lookup
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[source ImmunoDB::anopheles_gambiae]
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# Used by anopheles_gambiae
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name            = ImmunoDB
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download        = Y
order           = 40
priority        = 1
prio_descr      =
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parser          = ImmunoDBParser
release_uri     =
data_uri        = file:ImmunoDB/Anopheles_ImmunoDB.txt

[source ImmunoDB::aedes_aegypti]
# Used by aedes_aegypti
name            = ImmunoDB
download        = Y
order           = 40
priority        = 1
prio_descr      =
parser          = ImmunoDBParser
release_uri     =
data_uri        = file:ImmunoDB/Aedes_ImmunoDB.txt

[source ImmunoDB::culex_quinquefasciatus]
# Used by culex_quinquefasciatus
name            = ImmunoDB
download        = Y
order           = 40
priority        = 1
prio_descr      =
parser          = ImmunoDBParser
release_uri     =
data_uri        = file:ImmunoDB/Culex_ImmunoDB.txt

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[source AnoXcel::anopheles_gambiae]
# Used by anopheles_gambiae
name            = AnoXcel
download        = Y
order           = 40
priority        = 1
prio_descr      =
parser          = AnoXcelParser
release_uri     =
data_uri        = file:AnoXcel/anoXcel3.6-Xrefs.txt

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[source VB_RNA_Description::anopheles_gambiae]
# Used by anopheles_gambiae
name            = VB_RNA_Description
download        = Y
order           = 40
priority        = 1
prio_descr      =
parser          = VBRNADescriptionParser
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release_uri     =
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data_uri        = file:VB_RNA_Description/An_AgamP3-5_ncRNA_description_lookup.txt

[source VB_RNA_Description::aedes_aegypti]
# Used by aedes_aegypti
name            = VB_RNA_Description
download        = Y
order           = 40
priority        = 1
prio_descr      =
parser          = VBRNADescriptionParser
release_uri     =
data_uri        = file:VB_RNA_Description/AaegL1-2_RNA_description.txt

[source VB_RNA_Description::culex_quinquefasciatus]
# Used by culex_quinquefasciatus
name            = VB_RNA_Description
download        = Y
order           = 40
priority        = 1
prio_descr      =
parser          = VBRNADescriptionParser
release_uri     =
data_uri        = file:VB_RNA_Description/CpipJ1-2_RNA_description.txt

[source VB_External_Description::aedes_aegypti]
# Used by aedes_aegypti
name            = VB_External_Description
download        = Y
order           = 40
priority        = 1
prio_descr      =
parser          = VBExternalDescriptionParser
release_uri     =
data_uri        = file:VB_External_Description/AaegL1-2_gene_description.txt

[source VB_External_Description::culex_quinquefasciatus]
# Used by culex_quinquefasciatus
name            = VB_External_Description
download        = Y
order           = 40
priority        = 1
prio_descr      =
parser          = VBExternalDescriptionParser
release_uri     =
data_uri        = file:VB_External_Description/CpipJ1-2_gene_description.txt
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[source BDGP_insitu_expr::drosophila_melanogaster]
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# Used by drosophila_melanogaster
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name            = BDGP_insitu_expr
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download        = N
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order           = 50
priority        = 1
prio_descr      = BDGP in situ gene expression
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parser          = FlybaseParser
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release_uri     =
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data_uri        = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r5.39_FB2011_07/gff/dmel-all-*.gff.gz
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#[source CCDS::MULTI]
## Used by homo_sapiens, mus_musculus
#name            = CCDS
#download        = Y
#order           = 10
#priority        = 1
#prio_descr      =
#parser          = CCDSParser
#release_uri     =
#data_uri        = file:CCDS/CCDS.txt

[source CCDS::homo_sapiens]
# Used by homo_sapiens
name            = CCDS
download        = Y
order           = 10
priority        = 1
prio_descr      =
parser          = CCDSParser
release_uri     =
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data_uri        = script:host=>ens-livemirror,dbname=>ccds_human_65,tran_name=>ENST,
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[source CCDS::mus_musculus]
# Used by mus_musculus
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name            = CCDS
download        = Y
order           = 10
priority        = 1
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prio_descr      =
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parser          = CCDSParser
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release_uri     =
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data_uri        = script:host=>ens-livemirror,dbname=>ccds_mouse_65,tran_name=>ENSMUST,
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[source Celera_Pep::anopheles_gambiae]
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# Used by anopheles_gambiae
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name            = Celera_Pep
download        = Y
order           = 40
priority        = 1
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prio_descr      =
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parser          = CeleraProteinParser
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release_uri     =
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data_uri        = file:Celera/Anopheles_Celera_consensus-proteins_xref.fasta
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[source Celera_Gene::anopheles_gambiae]
name            = Celera_Gene
download        = N
order           = 40
priority        = 1
prio_descr      =
parser          = CeleraProteinParser

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[source Celera_Trans::anopheles_gambiae]
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# Used by anopheles_gambiae
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name            = Celera_Trans
download        = Y
order           = 40
priority        = 1
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prio_descr      =
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parser          = CeleraTranscriptParser
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release_uri     =
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data_uri        = file:Celera/Anopheles_Celera_consensus-transcripts_xref.fasta
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[source Codelink::homo_sapiens]
# Used by homo_sapiens
name            = Codelink
download        = Y
order           = 50
priority        = 1
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prio_descr      =
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parser          = CodelinkParser
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release_uri     =
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data_uri        = file:Codelink/GEHC_Amersham_CodeLink_HWG_300026.fna
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[source Codelink::mus_musculus]
# Used by mus_musculus
name            = Codelink
download        = Y
order           = 50
priority        = 1
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prio_descr      =
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parser          = CodelinkParser
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release_uri     =
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data_uri        = file:Codelink/GEHC_Amersham_CodeLink_MWG_300033.fna
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[source Codelink::rattus_norvegicus]
# Used by rattus_norvegicus
name            = Codelink
download        = Y
order           = 50
priority        = 1
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prio_descr      =
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parser          = CodelinkParser
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release_uri     =
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data_uri        = file:Codelink/GEHC_Amersham_CodeLink_RWG_300031.fna
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[source DBASS5::homo_sapiens]
# Used by homo_sapiens
name            = DBASS5
download        = Y
order           = 50
priority        = 1
prio_descr      = Database of aberrant 5\' splice sites.
parser          = DBASSParser
release_uri     = 
data_uri        = http://www.som.soton.ac.uk/research/geneticsdiv/dbass5/download.aspx?item=gene

[source DBASS3::homo_sapiens]
# Used by homo_sapiens
name            = DBASS3
download        = Y
order           = 50
priority        = 1
prio_descr      = Database of aberrant 3\' splice sites.
parser          = DBASSParser
release_uri     = 
data_uri        = http://www.som.soton.ac.uk/research/geneticsdiv/dbass3/download.asp?item=gene


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[source DEDb::drosophila_melanogaster]
# Used by drosophila_melanogaster
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name            = DEDb
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download        = N
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order           = 50
priority        = 1
prio_descr      = Drosophila melanogaster Exon DataBase
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parser          = FlybaseParser
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release_uri     =
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data_uri        = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r5.39_FB2011_07/gff/dmel-all-*.gff.gz
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#[source DGRC-1::drosophila_melanogaster]
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# Used by drosophila_melanogaster
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#name            = DGRC-1
#download        = N
#order           = 50
#priority        = 1
#prio_descr      =
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#parser          = FlybaseParser
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#release_uri     =
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#data_uri        = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r5.39_FB2011_07/gff/dmel-all-*.gff.gz
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#[source DGRC-2::drosophila_melanogaster]
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# Used by drosophila_melanogaster
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#name            = DGRC-2
#download        = N
#order           = 50
#priority        = 1
#prio_descr      =
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#parser          = FlybaseParser
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#release_uri     =
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#data_uri        = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r5.39_FB2011_07/gff/dmel-all-*.gff.gz
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#[source DRSC::drosophila_melanogaster]
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# Used by drosophila_melanogaster
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#name            = DRSC
#download        = N
#order           = 50
#priority        = 1
#prio_descr      =
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#parser          = FlybaseParser
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#release_uri     =
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#data_uri        = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r5.39_FB2011_07/gff/dmel-all-*.gff.gz
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#[source DrosDel::drosophila_melanogaster]
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# Used by drosophila_melanogaster
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#name            = DrosDel
#download        = N
#order           = 50
#priority        = 1
#prio_descr      =
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#parser          = FlybaseParser
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#release_uri     =
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#data_uri        = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r5.39_FB2011_07/gff/dmel-all-*.gff.gz
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[source EntrezGene::MULTI]
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# Used by aedes_aegypti, anolis_carolinensis, anopheles_gambiae, acyrthosiphon_pisum, apis_mellifera, bos_taurus, caenorhabditis_elegans, canis_familiaris, ciona_intestinalis, ciona_savignyi, danio_rerio, dasypus_novemcinctus, drosophila_melanogaster, drosophila_pseudoobscura, echinops_telfairi, erinaceus_europaeus, equus_caballus, felis_catus, gallus_gallus, gasterosteus_aculeatus, gorilla_gorilla, homo_sapiens, ixodes_scappularis, loxodonta_africana, macaca_mulatta, monodelphis_domestica, mus_musculus, myotis_lucifugus, ochotona_princeps, oryctolagus_cuniculus, oryzias_latipes, pan_troglodytes, pongo_abelii,  rattus_norvegicus, saccharomyces_cerevisiae, spermophilus_tridecemlineatus, sus_scrofa, taeniopygia_guttata, takifugu_rubripes, tupaia_belangeri, xenopus_tropicalis,phaeodactylum_tricornutum,thalassiosira_pseudonana
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name            = EntrezGene
download        = Y
order           = 10
priority        = 1
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prio_descr      =
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parser          = EntrezGeneParser
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release_uri     =
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data_uri        = ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene_info.gz

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[source WikiGene::MULTI]
name            = WikiGene
download        = N
order           = 100
priority        = 1
prio_descr      =
parser          = EntrezGeneParser
release_uri     =
data_uri        = comes via EntrezGene


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[source Fantom::mus_musculus]
# Used by mus_muscullus
name            = Fantom
download        = Y
order           = 100
priority        = 1
prio_descr      =
parser          = FantomParser
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dependent       = Uniprot/SPTREMBL,Uniprot/SWISSPROT::MULTI
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release_uri     =
data_uri        = ftp://fantom.gsc.riken.jp/FANTOM3/DDBJ/DDBJ_fantom3_HTC_accession.txt.gz
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[source flybase_annotation_id::drosophila_melanogaster]
# Used by drosophila_melanogaster
name            = flybase_annotation_id
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download        = N
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order           = 50
priority        = 1
prio_descr      = Annotation ID assigned by FlyBase
parser          = Flybase_dmel_GFFv3_Parser
release_uri     =
620
data_uri        = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r5.39_FB2011_07/gff/dmel-all-*.gff.gz
621 622 623 624 625

[source flybase_gene_id::drosophila_melanogaster]
# Used by drosophila_melanogaster
name            = flybase_gene_id
download        = Y
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626
order           = 100
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priority        = 1
prio_descr      = ID assigned by FlyBase
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parser          = FlybaseParser
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dependent       = Uniprot/SPTREMBL,Uniprot/SWISSPROT,Interpro
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release_uri     =
632
data_uri        = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r5.39_FB2011_07/gff/dmel-all-*.gff.gz
633 634 635 636 637 638 639 640 641

[source flybase_gene_id::drosophila_pseudoobscura]
# Used by drosophila_pseudoobscura
name            = flybase_gene_id
download        = Y
order           = 100
priority        = 1
prio_descr      = ID assigned by FlyBase
parser          = FlybaseParser
642
dependent       = Uniprot/SPTREMBL,Uniprot/SWISSPROT,Interpro
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release_uri     =
644
data_uri        = ftp://ftp.flybase.net/genomes/Drosophila_pseudoobscura/current/gff/dpse-all-*.gff.gz
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[source flybase_gene_id::drosophila_grimshawi]
# Used by drosophila_grimshawi
name            = flybase_gene_id
download        = Y
order           = 100
priority        = 1
prio_descr      = ID assigned by FlyBase
parser          = FlybaseParser
654
dependent       = Uniprot/SPTREMBL,Uniprot/SWISSPROT,Interpro
655
release_uri     =
656
data_uri        = ftp://ftp.flybase.org/releases/current/dgri_r1.3/gff/dgri-all-r1.3.gff.gz
657 658 659 660 661 662 663 664 665

[source flybase_gene_id::drosophila_willistoni]
# Used by drosophila_willistoni
name            = flybase_gene_id
download        = Y
order           = 100
priority        = 1
prio_descr      = ID assigned by FlyBase
parser          = FlybaseParser
666
dependent       = Uniprot/SPTREMBL,Uniprot/SWISSPROT,Interpro
667
release_uri     =
668
data_uri        = ftp://ftp.flybase.org/releases/current/dwil_r1.3/gff/dwil-all-r1.3.gff.gz
669 670 671 672 673 674 675 676 677

[source flybase_gene_id::drosophila_ananassae]
# Used by drosophila_ananassae
name            = flybase_gene_id
download        = Y
order           = 100
priority        = 1
prio_descr      = ID assigned by FlyBase
parser          = FlybaseParser
678
dependent       = Uniprot/SPTREMBL,Uniprot/SWISSPROT,Interpro
679
release_uri     =
680
data_uri        = ftp://ftp.flybase.org/releases/current/dana_r1.3/gff/dana-all-r1.3.gff.gz
681 682 683 684 685 686 687 688 689

[source flybase_gene_id::drosophila_yakuba]
# Used by drosophila_yakuba
name            = flybase_gene_id
download        = Y
order           = 100
priority        = 1
prio_descr      = ID assigned by FlyBase
parser          = FlybaseParser
690
dependent       = Uniprot/SPTREMBL,Uniprot/SWISSPROT,Interpro
691
release_uri     =
692
data_uri        = ftp://ftp.flybase.org/releases/current/dyak_r1.3/gff/dyak-all-r1.3.gff.gz
693 694 695 696 697 698 699 700 701

[source flybase_gene_id::drosophila_simulans]
# Used by drosophila_simulans
name            = flybase_gene_id
download        = Y
order           = 100
priority        = 1
prio_descr      = ID assigned by FlyBase
parser          = FlybaseParser
702
dependent       = Uniprot/SPTREMBL,Uniprot/SWISSPROT,Interpro
703
release_uri     =
704
data_uri        = ftp://ftp.flybase.org/releases/current/dsim_r1.3/gff/dsim-all-r1.3.gff.gz
705 706 707 708 709 710 711 712 713

[source flybase_gene_id::drosophila_sechellia]
# Used by drosophila_sechellia
name            = flybase_gene_id
download        = Y
order           = 100
priority        = 1
prio_descr      = ID assigned by FlyBase
parser          = FlybaseParser
714
dependent       = Uniprot/SPTREMBL,Uniprot/SWISSPROT,Interpro
715
release_uri     =
716 717
data_uri        = ftp://ftp.flybase.org/releases/current/dsec_r1.3/gff/dsec-all-r1.3.gff.gz

718 719 720 721 722 723 724 725 726

[source flybase_gene_id::drosophila_erecta]
# Used by drosophila_erecta
name            = flybase_gene_id
download        = Y
order           = 100
priority        = 1
prio_descr      = ID assigned by FlyBase
parser          = FlybaseParser
727
dependent       = Uniprot/SPTREMBL,Uniprot/SWISSPROT,Interpro
728
release_uri     =
729
data_uri        = ftp://ftp.flybase.org/releases/current/dere_r1.3/gff/dere-all-r1.3.gff.gz
730 731 732 733 734 735 736 737 738

[source flybase_gene_id::drosophila_persimilis]
# Used by drosophila_persimilis
name            = flybase_gene_id
download        = Y
order           = 100
priority        = 1
prio_descr      = ID assigned by FlyBase
parser          = FlybaseParser
739
dependent       = Uniprot/SPTREMBL,Uniprot/SWISSPROT,Interpro
740
release_uri     =
741
data_uri        = ftp://ftp.flybase.org/releases/current/dper_r1.3/gff/dper-all-r1.3.gff.gz
742 743 744 745 746 747 748 749 750

[source flybase_gene_id::drosophila_mojavensis]
# Used by drosophila_mojavensis
name            = flybase_gene_id
download        = Y
order           = 100
priority        = 1
prio_descr      = ID assigned by FlyBase
parser          = FlybaseParser
751
dependent       = Uniprot/SPTREMBL,Uniprot/SWISSPROT,Interpro
752
release_uri     =
753
data_uri        = ftp://ftp.flybase.org/releases/current/dmoj_r1.3/gff/dmoj-all-r1.3.gff.gz
754 755 756 757 758 759 760 761 762

[source flybase_gene_id::drosophila_virilis]
# Used by drosophila_virilis
name            = flybase_gene_id
download        = Y
order           = 100
priority        = 1
prio_descr      = ID assigned by FlyBase
parser          = FlybaseParser
763
dependent       = Uniprot/SPTREMBL,Uniprot/SWISSPROT,Interpro
764
release_uri     =
765
data_uri        = ftp://ftp.flybase.org/releases/current/dvir_r1.2/gff/dvir-all-r1.2.gff.gz
766 767 768 769

[source flybase_transcript_id::drosophila_melanogaster]
# Used by drosophila_melanogaster
name            = flybase_transcript_id
770
download        = N
771
order           = 50
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priority        = 1
prio_descr      = ID assigned by FlyBase
parser          = Flybase_dmel_GFFv3_Parser
release_uri     =
776
data_uri        = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r5.39_FB2011_07/gff/dmel-all-*.gff.gz
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[source flybase_translation_id::drosophila_melanogaster]
# Used by drosophila_melanogaster
name            = flybase_translation_id
download        = N
order           = 50
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priority        = 1
prio_descr      = ID assigned by FlyBase
parser          = Flybase_dmel_GFFv3_Parser
release_uri     =
787
data_uri        = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r5.39_FB2011_07/gff/dmel-all-*.gff.gz
788 789 790

[source FlyBaseCGID_gene::drosophila_melanogaster]
# Used by drosophila_melanogaster
791
name            = FlyBaseCGID_gene
792
download        = N
793 794
order           = 50
priority        = 1
795
prio_descr      = FlyBase_Annotation_IDs
796 797
parser          = Flybase_dmel_GFFv3_Parser
release_uri     =
798
data_uri        = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r5.39_FB2011_07/gff/dmel-all-*.gff.gz
799 800 801

[source FlyBaseCGID_transcript::drosophila_melanogaster]
# Used by drosophila_melanogaster
802
name            = FlyBaseCGID_transcript
803
download        = N
804 805
order           = 50
priority        = 1
806
prio_descr      = FlyBase_Annotation_IDs
807 808
parser          = Flybase_dmel_GFFv3_Parser
release_uri     =
809
data_uri        = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r5.39_FB2011_07/gff/dmel-all-*.gff.gz
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[source FlyBaseCGID_translation::drosophila_melanogaster]
# Used by drosophila_melanogaster
813
name            = FlyBaseCGID_translation
814
download        = N
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order           = 50
priority        = 1
817
prio_descr      = FlyBase_Annotation_IDs
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parser          = Flybase_dmel_GFFv3_Parser
release_uri     =
820
data_uri        = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r5.39_FB2011_07/gff/dmel-all-*.gff.gz
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[source FlyBaseName_gene::drosophila_melanogaster]
# Used by drosophila_melanogaster
name            = FlyBaseName_gene
825
download        = N
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order           = 50
priority        = 1
prio_descr      = Name assigned to gene in FlyBase gff
parser          = Flybase_dmel_GFFv3_Parser
release_uri     =
831
data_uri        = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r5.39_FB2011_07/gff/dmel-all-*.gff.gz
832 833 834 835

[source FlyBaseName_transcript::drosophila_melanogaster]
# Used by drosophila_melanogaster
name            = FlyBaseName_transcript
836
download        = N
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order           = 50
priority        = 1
prio_descr      = Name assigned to transcript in FlyBase gff
parser          = Flybase_dmel_GFFv3_Parser
release_uri     =
842
data_uri        = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r5.39_FB2011_07/gff/dmel-all-*.gff.gz
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[source FlyBaseName_translations::drosophila_melanogaster]
# Used by drosophila_melanogaster
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name            = FlyBaseName_translation
847
download        = N
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order           = 50
priority        = 1
prio_descr      = Name assigned to translation in FlyBase gff
parser          = Flybase_dmel_GFFv3_Parser
release_uri     =
853
data_uri        = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r5.39_FB2011_07/gff/dmel-all-*.gff.gz
854 855 856 857

[source FlyGrid::drosophila_melanogaster]
# Used by drosophila_melanogaster
name            = FlyGrid
858
download        = N
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order           = 50
priority        = 1
prio_descr      =
862
parser          = FlybaseParser
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release_uri     =
864
data_uri        = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r5.39_FB2011_07/gff/dmel-all-*.gff.gz
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[source FlyReactome::drosophila_melanogaster]
# Used by drosophila_melanogaster
name            = FlyReactome
download        = N
order           = 50
priority        = 1
prio_descr      =
873 874
parser          = FlybaseParser
release_uri     =
875
data_uri        = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r5.39_FB2011_07/gff/dmel-all-*.gff.gz
876 877 878 879 880 881 882 883 884 885

[source BioGRID::drosophila_melanogaster]
# Used by drosophila_melanogaster
name            = BioGRID
download        = N
order           = 50
priority        = 1
prio_descr      =
parser          = FlybaseParser
release_uri     =
886
data_uri        = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r5.39_FB2011_07/gff/dmel-all-*.gff.gz
887 888 889 890 891 892 893 894 895 896

[source FlyExpress::drosophila_melanogaster]
# Used by drosophila_melanogaster
name            = FlyExpress
download        = N
order           = 50
priority        = 1
prio_descr      =
parser          = FlybaseParser
release_uri     =
897
data_uri        = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r5.39_FB2011_07/gff/dmel-all-*.gff.gz
898 899 900 901 902 903 904 905 906 907

[source GenomeRNAi::drosophila_melanogaster]
# Used by drosophila_melanogaster
name            = GenomeRNAi
download        = N
order           = 50
priority        = 1
prio_descr      =
parser          = FlybaseParser
release_uri     =
908
data_uri        = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r5.39_FB2011_07/gff/dmel-all-*.gff.gz
909 910 911 912 913 914 915 916 917 918

[source FlyAtlas::drosophila_melanogaster]
# Used by drosophila_melanogaster
name            = FlyAtlas
download        = N
order           = 50
priority        = 1
prio_descr      =
parser          = FlybaseParser
release_uri     =
919
data_uri        = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r5.39_FB2011_07/gff/dmel-all-*.gff.gz
920 921 922 923 924 925 926 927 928 929 930 931 932 933 934 935 936 937 938 939 940

[source FlyAtlas::drosophila_pseudoobscura]
# Used by drosophila_pseudoobscura
name            = FlyAtlas
download        = N
order           = 50
priority        = 1
prio_descr      =
parser          = FlybaseParser
release_uri     =
data_uri        = ftp://ftp.flybase.net/genomes/Drosophila_pseudoobscura/current/gff/dpse-all-*.gff.gz

[source InteractiveFly::drosophila_melanogaster]
# Used by drosophila_melanogaster
name            = InteractiveFly
download        = N
order           = 50
priority        = 1
prio_descr      =
parser          = FlybaseParser
release_uri     =
941
data_uri        = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r5.39_FB2011_07/gff/dmel-all-*.gff.gz
942 943 944 945 946 947 948 949 950

[source MitoDrome::drosophila_melanogaster]
# Used by drosophila_melanogaster
name            = MitoDrome
download        = N
order           = 50
priority        = 1
prio_descr      =
parser          = FlybaseParser
951
release_uri     =
952
data_uri        = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r5.39_FB2011_07/gff/dmel-all-*.gff.gz
953

954
[source GO::MULTI]
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955
# Used by aedes_aegypti, anolis_carolinensis, anopheles_gambiae, acyrthosiphon_pisum, apis_mellifera, bos_taurus, canis_familiaris, ciona_intestinalis, ciona_savignyi, dasypus_novemcinctus, drosophila_melanogaster, drosophila_pseudoobscura, drosophila_grimshawi, drosophila_willistoni, drosophila_ananassae, drosophila_yakuba, drosophila_simulans, drosophila_sechellia, drosophila_erecta, drosophila_persimilis, drosophila_mojavensis, drosophila_virilis, echinops_telfairi, erinaceus_europaeus, equus_caballus, felis_catus, gallus_gallus, gasterosteus_aculeatus, ixodes_scappularis, loxodonta_africana, macaca_mulatta, monodelphis_domestica, myotis_lucifugus, ochotona_princeps, ornithorhynchus_anatinus, oryctolagus_cuniculus, oryzias_latipes, pan_troglodytes, pongo_abelii, saccharomyces_cerevisiae, spermophilus_tridecemlineatus, sus_scrofa, taeniopygia_guttata, takifugu_rubripes, tupaia_belangeri,phaeodactylum_tricornutum,thalassiosira_pseudonana
956 957
name            = GO
download        = Y
958
order           = 80
959
priority        = 1
960
prio_descr      = main
961
parser          = GOParser
962
dependent       = Uniprot/SPTREMBL,Uniprot/SWISSPROT,RefSeq_dna,RefSeq_peptide,SGD
963 964
release_uri     = http://www.ebi.ac.uk/GOA/uniprot_release.html
data_uri        = ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/UNIPROT/gene_association.goa_uniprot.gz
965
data_uri        = http://archive.geneontology.org/latest-termdb/go_daily-termdb.obo-xml.gz
966

967 968 969 970 971 972 973 974
[source InterproGO::MULTI]
# Used by all
name            = GO
download        = Y
order           = 85
priority        = 2
prio_descr      = interpro
parser          = InterproGoParser
975
dependent       = GO
976 977 978
release_uri     =
data_uri        = http://www.geneontology.org/external2go/interpro2go

979 980 981 982
[source GO::caenorhabditis_elegans]
# Used by caenorhabditis_elegans
name            = GO
download        = Y
983
order           = 85
984
priority        = 1
985
prio_descr      = main
986
parser          = GOParser
987
dependent       = Uniprot/SPTREMBL,Uniprot/SWISSPROT,RefSeq_dna,RefSeq_peptide
988
release_uri     =
989 990 991 992 993 994
data_uri        = ftp://ftp.geneontology.org/pub/go/gene-associations/gene_association.wb.gz

[source GO::danio_rerio]
# Used by danio_rerio
name            = GO
download        = Y
995
order           = 85
996
priority        = 1
997
prio_descr      = main
998
parser          = GOParser
999
dependent       = Uniprot/SPTREMBL,Uniprot/SWISSPROT,RefSeq_dna,RefSeq_peptide
1000
release_uri     =
1001
data_uri        = ftp://ftp.geneontology.org/pub/go/gene-associations/gene_association.zfin.gz
1002
data_uri        = http://archive.geneontology.org/latest-termdb/go_daily-termdb.obo-xml.gz
1003

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1004
[source goslim_goa::MULTI]
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1005
# Used by all 
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name            = goslim_goa
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download        = Y
order           = 120
priority        = 1
prio_descr      = main
parser          = GOSlimParser
1012
dependent       = GO
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1013
release_uri     =
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1014
#data_uri        = script:
1015
data_uri        = script:host=>ens-staging1,dbname=>ensembl_ontology_65,
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1017 1018 1019 1020 1021 1022 1023 1024
[source goslim_goa::EG]
# Used by Ensembl Genomes
name            = goslim_goa
download        = Y
order           = 120
priority        = 1
prio_descr      = main
parser          = GOSlimParser
1025
dependent       = GO
1026
release_uri     =
1027
data_uri        = script:host=>mysql-eg-pan-1.ebi.ac.uk,port=>4276,dbname=>ensembl_ontology_65,
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1028

1029 1030 1031 1032
[source GO::homo_sapiens]
# Used by homo_sapiens
name            = GO
download        = Y
1033
order           = 85
1034
priority        = 1
1035
prio_descr      = main
1036
parser          = GOParser
1037
dependent       = Uniprot/SPTREMBL,Uniprot/SWISSPROT,RefSeq_dna,RefSeq_peptide
1038 1039
release_uri     = http://www.ebi.ac.uk/GOA/HUMAN_release.html
data_uri        = ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/HUMAN/gene_association.goa_human.gz
1040
data_uri        = http://archive.geneontology.org/latest-termdb/go_daily-termdb.obo-xml.gz
1041 1042 1043 1044 1045

[source GO::mus_musculus]
# Used by mus_musculus
name            = GO
download        = Y
1046
order           = 85
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