xref_config.ini

# $Id$

##########################################################################
# SOURCES                                                                #
#                                                                        #
# Keys:                                                                  #
#   name          - name of this source (required)                       #
#   download      - must be downloaded (Y or N, required)                #
#   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'                             #
#   parser        - the parser to be used (required)                     #
#   release_uri   - URI pointing to release information (optional)       #
#   data_uri      - URI pointing to the data files (multiple, required)  #
#   dependent_on  - Comma separated list of sources which must be loaded #
#                   first.                                               #
#                   Note that if species does not have xrefs from a      #
#                   master source specified in this list than the        #
#                   dependency is ignored                                #
#                                                                        #
##########################################################################

[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        =

[source AFFY_DrosGenome1::drosophila_melanogaster]
# Used by drosophila_melanogaster
name            = AFFY_DrosGenome1
download        = N
order           = 50
priority        = 1
prio_descr      =
parser          = FlybaseParser
release_uri     =
data_uri        = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r5.46_FB2012_04/gff/dmel-all-r5.46.gff.gz

[source BDGP_insitu_expr::drosophila_melanogaster]
# Used by drosophila_melanogaster
name            = BDGP_insitu_expr
download        = N
order           = 50
priority        = 1
prio_descr      = BDGP in situ gene expression
parser          = FlybaseParser
release_uri     =
data_uri        = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r5.46_FB2012_04/gff/dmel-all-r5.46.gff.gz

[source BioGRID::drosophila_melanogaster]
# Used by drosophila_melanogaster
name            = BioGRID
download        = N
order           = 50
priority        = 1
prio_descr      =
parser          = FlybaseParser
release_uri     =
data_uri        = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r5.46_FB2012_04/gff/dmel-all-r5.46.gff.gz

[source DEDb::drosophila_melanogaster]
# Used by drosophila_melanogaster
name            = DEDb
download        = N
order           = 50
priority        = 1
prio_descr      = Drosophila melanogaster Exon DataBase
parser          = FlybaseParser
release_uri     =
data_uri        = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r5.46_FB2012_04/gff/dmel-all-r5.46.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     =
data_uri        = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r5.46_FB2012_04/gff/dmel-all-r5.46.gff.gz

[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-r2.29.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     =
data_uri        = ftp://ftp.flybase.org/genomes/dsim/current/gff/dsim-all-r1.4.gff.gz

[source EPD::drosophila_sechellia]
# 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.org/releases/current/dsec_r1.3/gff/dsec-all-r1.3.gff.gz

[source EPD::drosophila_mojavensis]
# 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.org/releases/current/dmoj_r1.3/gff/dmoj-all-r1.3.gff.gz

[source EPD::drosophila_virilis]
# 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.org/releases/current/dvir_r1.2/gff/dvir-all-r1.2.gff.gz

[source FlyAtlas::drosophila_melanogaster]
# Used by drosophila_melanogaster
name            = FlyAtlas
download        = N
order           = 50
priority        = 1
prio_descr      =
parser          = FlybaseParser
release_uri     =
data_uri        = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r5.46_FB2012_04/gff/dmel-all-r5.46.gff.gz

[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-r2.29.gff.gz

[source FlyExpress::drosophila_melanogaster]
# Used by drosophila_melanogaster
name            = FlyExpress
download        = N
order           = 50
priority        = 1
prio_descr      =
parser          = FlybaseParser
release_uri     =
data_uri        = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r5.46_FB2012_04/gff/dmel-all-r5.46.gff.gz

[source FlyReactome::drosophila_melanogaster]
# Used by drosophila_melanogaster
name            = FlyReactome
download        = N
order           = 50
priority        = 1
prio_descr      =
parser          = FlybaseParser
release_uri     =
data_uri        = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r5.46_FB2012_04/gff/dmel-all-r5.46.gff.gz

[source GenomeRNAi::drosophila_melanogaster]
# Used by drosophila_melanogaster
name            = GenomeRNAi
download        = N
order           = 50
priority        = 1
prio_descr      =
parser          = FlybaseParser
release_uri     =
data_uri        = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r5.46_FB2012_04/gff/dmel-all-r5.46.gff.gz

[source InteractiveFly::drosophila_melanogaster]
# Used by drosophila_melanogaster
name            = InteractiveFly
download        = N
order           = 50
priority        = 1
prio_descr      =
parser          = FlybaseParser
release_uri     =
data_uri        = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r5.46_FB2012_04/gff/dmel-all-r5.46.gff.gz

[source MEROPS::drosophila_melanogaster]
# 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_melanogaster/dmel_r5.46_FB2012_04/gff/dmel-all-r5.46.gff.gz

[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     =
data_uri        = ftp://ftp.flybase.org/releases/current/dere_1.3/gff/dere-all-r1.3.gff.gz

[source MEROPS::drosophila_virilis]
# 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.org/releases/current/dvir_1.2/gff/dvir-all-r1.2.gff.gz

[source miRBase::drosophila_melanogaster]
# 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_melanogaster/dmel_r5.46_FB2012_04/gff/dmel-all-r5.46.gff.gz

[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-r2.29.gff.gz

[source MitoDrome::drosophila_melanogaster]
# Used by drosophila_melanogaster
name            = MitoDrome
download        = N
order           = 50
priority        = 1
prio_descr      =
parser          = FlybaseParser
release_uri     =
data_uri        = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r5.46_FB2012_04/gff/dmel-all-r5.46.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     =
data_uri        = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r5.46_FB2012_04/gff/dmel-all-r5.46.gff.gz

[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-r2.29.gff.gz

[source flybase_annotation_id::drosophila_melanogaster]
# Used by drosophila_melanogaster
name            = flybase_annotation_id
download        = N
order           = 50
priority        = 1
prio_descr      = Annotation ID assigned by FlyBase
parser          = FlybaseParser
release_uri     =
data_uri        = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r5.46_FB2012_04/gff/dmel-all-r5.46.gff.gz

[source flybase_gene_id::drosophila_melanogaster]
# Used by drosophila_melanogaster
name            = flybase_gene_id
download        = Y
order           = 100
priority        = 1
prio_descr      = ID assigned by FlyBase
parser          = FlybaseParser
dependent_on    = Uniprot/SPTREMBL,Uniprot/SWISSPROT,Interpro
release_uri     =
data_uri        = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r5.46_FB2012_04/gff/dmel-all-r5.46.gff.gz

[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
dependent_on    = Uniprot/SPTREMBL,Uniprot/SWISSPROT,Interpro
release_uri     =
data_uri        = ftp://ftp.flybase.net/genomes/Drosophila_pseudoobscura/current/gff/dpse-all-r2.29.gff.gz

[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
dependent_on    = Uniprot/SPTREMBL,Uniprot/SWISSPROT,Interpro
release_uri     =
data_uri        = ftp://ftp.flybase.org/releases/current/dgri_r1.3/gff/dgri-all-r1.3.gff.gz

[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
dependent_on    = Uniprot/SPTREMBL,Uniprot/SWISSPROT,Interpro
release_uri     =
data_uri        = ftp://ftp.flybase.org/releases/current/dwil_r1.3/gff/dwil-all-r1.3.gff.gz

[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
dependent_on    = Uniprot/SPTREMBL,Uniprot/SWISSPROT,Interpro
release_uri     =
data_uri        = ftp://ftp.flybase.org/releases/current/dana_r1.3/gff/dana-all-r1.3.gff.gz

[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
dependent_on    = Uniprot/SPTREMBL,Uniprot/SWISSPROT,Interpro
release_uri     =
data_uri        = ftp://ftp.flybase.org/releases/current/dyak_r1.3/gff/dyak-all-r1.3.gff.gz

[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
dependent_on    = Uniprot/SPTREMBL,Uniprot/SWISSPROT,Interpro
release_uri     =
data_uri        = ftp://ftp.flybase.org/genomes/dsim/current/gff/dsim-all-r1.4.gff.gz

[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
dependent_on    = Uniprot/SPTREMBL,Uniprot/SWISSPROT,Interpro
release_uri     =
data_uri        = ftp://ftp.flybase.org/releases/current/dsec_r1.3/gff/dsec-all-r1.3.gff.gz

[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
dependent_on    = Uniprot/SPTREMBL,Uniprot/SWISSPROT,Interpro
release_uri     =
data_uri        = ftp://ftp.flybase.org/releases/current/dere_r1.3/gff/dere-all-r1.3.gff.gz

[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
dependent_on    = Uniprot/SPTREMBL,Uniprot/SWISSPROT,Interpro
release_uri     =
data_uri        = ftp://ftp.flybase.org/releases/current/dper_r1.3/gff/dper-all-r1.3.gff.gz

[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
dependent_on    = Uniprot/SPTREMBL,Uniprot/SWISSPROT,Interpro
release_uri     =
data_uri        = ftp://ftp.flybase.org/releases/current/dmoj_r1.3/gff/dmoj-all-r1.3.gff.gz

[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
dependent_on    = Uniprot/SPTREMBL,Uniprot/SWISSPROT,Interpro
release_uri     =
data_uri        = ftp://ftp.flybase.org/releases/current/dvir_r1.2/gff/dvir-all-r1.2.gff.gz

[source flybase_transcript_id::drosophila_melanogaster]
# Used by drosophila_melanogaster
name            = flybase_transcript_id
download        = N
order           = 50
priority        = 1
prio_descr      = ID assigned by FlyBase
parser          = FlybaseParser
release_uri     =
data_uri        = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r5.46_FB2012_04/gff/dmel-all-r5.46.gff.gz

[source flybase_translation_id::drosophila_melanogaster]
# Used by drosophila_melanogaster
name            = flybase_translation_id
download        = N
order           = 50
priority        = 1
prio_descr      = ID assigned by FlyBase
parser          = FlybaseParser
release_uri     =
data_uri        = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r5.46_FB2012_04/gff/dmel-all-r5.46.gff.gz

[source FlyBaseCGID_gene::drosophila_melanogaster]
# Used by drosophila_melanogaster
name            = FlyBaseCGID_gene
download        = N
order           = 50
priority        = 1
prio_descr      = FlyBase_Annotation_IDs
parser          = FlybaseParser
release_uri     =
data_uri        = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r5.46_FB2012_04/gff/dmel-all-r5.46.gff.gz

[source FlyBaseCGID_transcript::drosophila_melanogaster]
# Used by drosophila_melanogaster
name            = FlyBaseCGID_transcript
download        = N
order           = 50
priority        = 1
prio_descr      = FlyBase_Annotation_IDs
parser          = FlybaseParser
release_uri     =
data_uri        = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r5.46_FB2012_04/gff/dmel-all-r5.46.gff.gz

[source FlyBaseCGID_translation::drosophila_melanogaster]
# Used by drosophila_melanogaster
name            = FlyBaseCGID_translation
download        = N
order           = 50
priority        = 1
prio_descr      = FlyBase_Annotation_IDs
parser          = FlybaseParser
release_uri     =
data_uri        = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r5.46_FB2012_04/gff/dmel-all-r5.46.gff.gz

[source FlyBaseName_gene::drosophila_melanogaster]
# Used by drosophila_melanogaster
name            = FlyBaseName_gene
download        = N
order           = 50
priority        = 1
prio_descr      = Name assigned to gene in FlyBase gff
parser          = FlybaseParser
release_uri     =
data_uri        = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r5.46_FB2012_04/gff/dmel-all-r5.46.gff.gz

[source FlyBaseName_transcript::drosophila_melanogaster]
# Used by drosophila_melanogaster
name            = FlyBaseName_transcript
download        = N
order           = 50
priority        = 1
prio_descr      = Name assigned to transcript in FlyBase gff
parser          = FlybaseParser
release_uri     =
data_uri        = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r5.46_FB2012_04/gff/dmel-all-r5.46.gff.gz

[source FlyBaseName_translations::drosophila_melanogaster]
# Used by drosophila_melanogaster
name            = FlyBaseName_translation
download        = N
order           = 50
priority        = 1
prio_descr      = Name assigned to translation in FlyBase gff
parser          = FlybaseParser
release_uri     =
data_uri        = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r5.46_FB2012_04/gff/dmel-all-r5.46.gff.gz

[source PHIbase::MULTI]
name            = PHIbase
download        = Y
order           = 50
priority        = 1
prio_descr      =
parser          = PHIbaseParser
dependent_on    = Uniprot/SWISSPROT,Uniprot/SPTREMBL
release_uri     =
data_uri        = http://www.phi-base.org/PHI-export.php



[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
source 		= ArrayExpress::EG

[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
source          = goslim_goa::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
source          = Uniprot/SWISSPROT::DIRECT
source          = RFAM::MULTI
source		= miRBase::MULTI
source 		= ArrayExpress::MULTI

[source VB_Community_Annotation::aedes_aegypti]
# Used by aedes_aegypti
name            = VB_Community_Annotation
download        = Y
order           = 40
priority        = 1
prio_descr      =
#parser          = AedesCAPParser
parser          = VBCommunitySymbolParser
release_uri     =
data_uri        = file:VB_Community_Annotation/Aedes_VB_Community_Annotation.fa

[source VB_Community_Annotation_Synonym::aedes_aegypti]
# Used by aedes_aegypti
name            = VB_Community_Annotation_Synonym
download        = Y
order           = 40
priority        = 1
prio_descr      =
#parser          = AedesCAPParser
dependent_on    = VB_Community_Annotation
parser          = VBCommunitySynonymParser
release_uri     =
data_uri        = file:VB_Community_Annotation/Aedes_aegypti_synonym.txt

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

[source VB_Community_Annotation_Synonym::culex_quinquefasciatus]
# Used by culex_quinquefasciatus
name            = VB_Community_Annotation_Synonym
download        = Y
order           = 40
priority        = 1
prio_descr      =
dependent_on    = VB_Community_Annotation
parser          = VBCommunitySynonymParser
release_uri     =
data_uri        = file:VB_Community_Annotation/Culex_quinquefasciatus_synonyms.txt

[source VB_Community_Annotation::ixodes_scapularis]
# Used by ixodes_scapularis
name            = VB_Community_Annotation
download        = Y
order           = 40
priority        = 1
prio_descr      =
parser          = VBCommunitySymbolParser
release_uri     =
data_uri        = file:VB_Community_Annotation/Ixodes_scapularis_symbols.txt

[source AedesGenBank::aedes_aegypti]
# Used by aedes_aegypti
name            = AedesGenBank
download        = Y
order           = 30
priority        = 1
prio_descr      =
parser          = AedesGenBankParser
release_uri     =
data_uri        = file:AedesGenBank/Aedes_proteinID.fa

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

[source VB_Community_Annotation_Synonym::anopheles_gambiae]
# Used by anopheles_gambiae
name            = VB_Community_Annotation_Synonym
download        = Y
order           = 40
priority        = 1
prio_descr      =
dependent_on    = VB_Community_Annotation
parser          = VBCommunitySynonymParser
release_uri     =
data_uri        = file:VB_Community_Annotation/Anopheles_gambiae_synonyms.txt

[source ImmunoDB::anopheles_gambiae]
# Used by anopheles_gambiae
name            = ImmunoDB
download        = Y
order           = 40
priority        = 1
prio_descr      =
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

[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

[source VB_RNA_Description::anopheles_gambiae]
# Used by anopheles_gambiae
name            = VB_RNA_Description
download        = Y
order           = 40
priority        = 1
prio_descr      =
parser          = VBRNADescriptionParser
release_uri     =
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

[source VB_External_Description::ixodes_scapularis]
# Used by ixodes_scapularis
name            = VB_External_Description
download        = Y
order           = 40
priority        = 1
prio_descr      =
parser          = VBExternalDescriptionParser
release_uri     =
data_uri        = file:VB_External_Description/IscaW1-1_gene_description.txt

[source ArrayExpress::MULTI]
# Used by all ensembl species
name            = ArrayExpress
download        = Y
order           = 50
priority        = 1
prio_descr      =
parser          = ArrayExpressParser
release_uri     =
data_uri        = script:wget=>http://www.ebi.ac.uk/gxa/dataExport/organisms,project=>ensembl,
#data_uri        = script:wget=>http://www.ebi.ac.uk/gxa/dataExport/organisms,project=>ensembl,host=>ens-production,dbname=>mr6_human_core,

[source ArrayExpress::EG]
name            = ArrayExpress
download        = Y
order           = 50
priority        = 1
prio_descr      =
parser          = ArrayExpressParser
release_uri     =
data_uri        = script:wget=>http://www.ebi.ac.uk/gxa/dataExport/organisms,project=>ensemblgenomes,


[source CCDS::homo_sapiens]
# Used by homo_sapiens
name            = CCDS
download        = Y
order           = 10
priority        = 1
prio_descr      =
parser          = CCDSParser
release_uri     =
data_uri        = script:host=>ens-livemirror,dbname=>ccds_human_71,tran_name=>ENST,

[source CCDS::mus_musculus]
# Used by mus_musculus
name            = CCDS
download        = Y
order           = 10
priority        = 1
prio_descr      =
parser          = CCDSParser
release_uri     =
data_uri        = script:host=>ens-livemirror,dbname=>ccds_mouse_70,tran_name=>ENSMUST,

[source Celera_Pep::anopheles_gambiae]
# Used by anopheles_gambiae
name            = Celera_Pep
download        = Y
order           = 40
priority        = 1
prio_descr      =
parser          = CeleraProteinParser
release_uri     =
data_uri        = file:Celera/Anopheles_Celera_consensus-proteins_xref.fasta

[source Celera_Gene::anopheles_gambiae]
name            = Celera_Gene
download        = N
order           = 40
priority        = 1
prio_descr      =
parser          = CeleraProteinParser

[source Celera_Trans::anopheles_gambiae]
# Used by anopheles_gambiae
name            = Celera_Trans
download        = Y
order           = 40
priority        = 1
prio_descr      =
parser          = CeleraTranscriptParser
release_uri     =
data_uri        = file:Celera/Anopheles_Celera_consensus-transcripts_xref.fasta

[source Codelink::homo_sapiens]
# Used by homo_sapiens
name            = Codelink
download        = Y
order           = 50
priority        = 1
prio_descr      =
parser          = CodelinkParser
release_uri     =
data_uri        = file:Codelink/GEHC_Amersham_CodeLink_HWG_300026.fna

[source Codelink::mus_musculus]
# Used by mus_musculus
name            = Codelink
download        = Y
order           = 50
priority        = 1
prio_descr      =
parser          = CodelinkParser
release_uri     =
data_uri        = file:Codelink/GEHC_Amersham_CodeLink_MWG_300033.fna

[source Codelink::rattus_norvegicus]
# Used by rattus_norvegicus
name            = Codelink
download        = Y
order           = 50
priority        = 1
prio_descr      =
parser          = CodelinkParser
release_uri     =
data_uri        = file:Codelink/GEHC_Amersham_CodeLink_RWG_300031.fna


[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.dbass.soton.ac.uk/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.dbass.soton.ac.uk/dbass3/download.asp?item=gene

[source EntrezGene::MULTI]
# Used by aedes_aegypti, anolis_carolinensis, anopheles_gambiae, acyrthosiphon_pisum, apis_mellifera, bos_taurus, caenorhabditis_elegans, canis_familiaris, cavia_porcellus, 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, ictidomys_tridecemlineatus, sus_scrofa, taeniopygia_guttata, takifugu_rubripes, tupaia_belangeri, xenopus_tropicalis,phaeodactylum_tricornutum,thalassiosira_pseudonana
name            = EntrezGene
download        = Y
order           = 10
priority        = 1
prio_descr      =
parser          = EntrezGeneParser
release_uri     =
data_uri        = ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene_info.gz

[source WikiGene::MULTI]
# used via the EntrezGeneParser, for all species
name            = WikiGene
download        = N
order           = 100
priority        = 1
prio_descr      =
parser          = EntrezGeneParser
release_uri     =
data_uri        = comes via EntrezGene


[source Fantom::mus_musculus]
# Used by mus_muscullus
name            = Fantom
download        = Y
order           = 100
priority        = 1
prio_descr      =
parser          = FantomParser
dependent_on    = Uniprot/SPTREMBL,Uniprot/SWISSPROT
release_uri     =
data_uri        = ftp://fantom.gsc.riken.jp/FANTOM3/DDBJ/DDBJ_fantom3_HTC_accession.txt.gz

[source GO::MULTI]
# Used by aedes_aegypti, anolis_carolinensis, anopheles_gambiae, acyrthosiphon_pisum, apis_mellifera, bos_taurus, canis_familiaris, cavia_porcellus, 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, ictidomys_tridecemlineatus, sus_scrofa, taeniopygia_guttata, takifugu_rubripes, tupaia_belangeri,phaeodactylum_tricornutum,thalassiosira_pseudonana
name            = GO
download        = Y
order           = 80
priority        = 1
prio_descr      = main
parser          = GOParser
dependent_on    = Uniprot/SPTREMBL,Uniprot/SWISSPROT,RefSeq_dna,RefSeq_peptide,SGD
release_uri     = http://www.ebi.ac.uk/GOA/uniprot_release
data_uri        = ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/UNIPROT/gene_association.goa_uniprot.gz
data_uri        = http://archive.geneontology.org/latest-termdb/go_daily-termdb.obo-xml.gz

[source InterproGO::MULTI]
# Used by all
name            = GO
download        = Y
order           = 85
priority        = 2
prio_descr      = interpro
parser          = InterproGoParser
dependent_on    = GO
release_uri     =
data_uri        = http://www.geneontology.org/external2go/interpro2go

[source GO::caenorhabditis_elegans]
# Used by caenorhabditis_elegans
name            = GO
download        = Y
order           = 85
priority        = 1
prio_descr      = main
parser          = GOParser
dependent_on    = Uniprot/SPTREMBL,Uniprot/SWISSPROT,RefSeq_dna,RefSeq_peptide,wormbase_all
release_uri     =
data_uri        = ftp://ftp.geneontology.org/pub/go/gene-associations/gene_association.wb.gz


[source GO::caenorhabditis_elegans_gene]
# Used by caenorhabditis_elegans
name            = GO_to_gene
download        = Y
order           = 85
priority        = 1
prio_descr      = main
parser          = Use by GOParser
dependent_on    =
release_uri     =
data_uri        =


[source GO::danio_rerio]
# Used by danio_rerio
name            = GO
download        = Y
order           = 85
priority        = 1
prio_descr      = main
parser          = GOParser
dependent_on    = Uniprot/SPTREMBL,Uniprot/SWISSPROT,RefSeq_dna,RefSeq_peptide
release_uri     = http://www.ebi.ac.uk/GOA/zebrafish_release
data_uri        = ftp://ftp.geneontology.org/pub/go/gene-associations/gene_association.zfin.gz
data_uri        = http://archive.geneontology.org/latest-termdb/go_daily-termdb.obo-xml.gz

[source goslim_goa::MULTI]
# Used by all
name            = goslim_goa
download        = Y
order           = 120
priority        = 1
prio_descr      = main
parser          = GOSlimParser
dependent_on    = GO
release_uri     =
#data_uri        = script:
data_uri        = script:host=>ens-staging1,dbname=>ensembl_ontology_71,

[source goslim_goa::EG]
# Used by Ensembl Genomes
name            = goslim_goa
download        = Y
order           = 120
priority        = 1
prio_descr      = main
parser          = GOSlimParser
dependent_on    = GO
release_uri     =
data_uri        = script:host=>mysql-eg-pan-1.ebi.ac.uk,port=>4276,dbname=>ensemblgenomes_ontology_16_69,

[source GO::homo_sapiens]
# Used by homo_sapiens
name            = GO
download        = Y
order           = 85
priority        = 1
prio_descr      = main
parser          = GOParser
dependent_on    = Uniprot/SPTREMBL,Uniprot/SWISSPROT,RefSeq_dna,RefSeq_peptide
release_uri     = http://www.ebi.ac.uk/GOA/human_release
data_uri        = ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/HUMAN/gene_association.goa_human.gz
data_uri        = http://archive.geneontology.org/latest-termdb/go_daily-termdb.obo-xml.gz

[source GO::mus_musculus]
# Used by mus_musculus
name            = GO
download        = Y
order           = 85
priority        = 1
prio_descr      = main
parser          = GOParser
dependent_on    = Uniprot/SPTREMBL,Uniprot/SWISSPROT,RefSeq_dna,RefSeq_peptide
release_uri     = http://www.ebi.ac.uk/GOA/MOUSE_release
data_uri        = ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/MOUSE/gene_association.goa_mouse.gz
data_uri        = http://archive.geneontology.org/latest-termdb/go_daily-termdb.obo-xml.gz

# TODO This has been removed because of the issues it causes with mappings linked to Genes and not to Translations
# [source GO::mus_musculus#01]
# # Used by mus_musculus
# name            = GO
# download        = Y
# order           = 85
# priority        = 1
# prio_descr      = goga
# parser          = GOParser
# dependent_on    = Uniprot/SPTREMBL,Uniprot/SWISSPROT,RefSeq_dna,RefSeq_peptide
# release_uri     =
# data_uri        = http://www.geneontology.org/cgi-bin/downloadGOGA.pl/gene_association.mgi.gz
# data_uri        = http://archive.geneontology.org/latest-termdb/go_daily-termdb.obo-xml.gz

[source GO::rattus_norvegicus]
# Used by rattus_norvegicus
name            = GO
download        = Y
order           = 85
priority        = 1
prio_descr      = main
parser          = GOParser
dependent_on    = Uniprot/SPTREMBL,Uniprot/SWISSPROT,RefSeq_dna,RefSeq_peptide
release_uri     = http://www.ebi.ac.uk/GOA/rat_release