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)  #
#                                                                      #
########################################################################

[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/current/gff/dmel-all-*.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        = file:/lustre/scratch103/ensembl/gk4/flybase/dere_1.3/seqdata/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        = file:/lustre/scratch103/ensembl/gk4/flybase/dvir_1.2/seqdata/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/current/gff/dmel-all-*.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-*.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/current/gff/dmel-all-*.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-*.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/current/gff/dmel-all-*.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-*.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        = file:/lustre/scratch103/ensembl/gk4/flybase/dsim_1.3/seqdata/dsim-all-r1.3.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        = file:/lustre/scratch103/ensembl/gk4/flybase/dsec_1.3/seqdata/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        = file:/lustre/scratch103/ensembl/gk4/flybase/dmoj_1.3/seqdata/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        = file:/lustre/scratch103/ensembl/gk4/flybase/dvir_1.2/seqdata/dvir-all-r1.2.gff.gz

[source AFFY_DrosGenome1::drosophila_melanogaster]
# Used by drosophila_melanogaster
name            = AFFY_DrosGenome1
download        = N
order           = 50
priority        = 1
prio_descr      =
parser          = Flybase_dmel_GFFv3_Parser
release_uri     =
data_uri        = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/current/gff/dmel-all-*.gff.gz

[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

[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/Varsplic::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
release_uri     =
data_uri        = file:VB_Community_Annotation/Aedes_VB_Community_Annotation.fa

[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 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

#[source Anopheles_symbol::anopheles_gambiae]
# Used by anopheles_gambiae
#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
download        = Y
order           = 40
priority        = 1
prio_descr      =
parser          = VBCommunitySymbolParser
release_uri     =
data_uri        = file:VB_Community_Annotation/xref_Anopheles_symbol_lookup

[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 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/current/gff/dmel-all-*.gff.gz

#[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     =
data_uri        = script:host=>genebuild7,dbname=>db8_human_cdsonly_22sept2010,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=>genebuild7,dbname=>db8_mouse_cdsonly_22sept2010,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.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


[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/current/gff/dmel-all-*.gff.gz

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

#[source DGRC-2::drosophila_melanogaster]
# Used by drosophila_melanogaster
#name            = DGRC-2
#download        = N
#order           = 50
#priority        = 1
#prio_descr      =
#parser          = FlybaseParser
#release_uri     =
#data_uri        = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/current/gff/dmel-all-*.gff.gz

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

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

[source EntrezGene::MULTI]
# 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_pygmaeus,  rattus_norvegicus, saccharomyces_cerevisiae, spermophilus_tridecemlineatus, 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]
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
release_uri     =
data_uri        = ftp://fantom.gsc.riken.jp/FANTOM3/DDBJ/DDBJ_fantom3_HTC_accession.txt.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          = Flybase_dmel_GFFv3_Parser
release_uri     =
data_uri        = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/current/gff/dmel-all-*.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
release_uri     =
data_uri        = file:/lustre/scratch103/ensembl/gk4/flybase/dmel_5.25/seqdata/gff/dmel-all-r5.25.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
release_uri     =
data_uri        = file:/lustre/scratch103/ensembl/gk4/flybase/dpse_2.8/seqdata/dpse-all-r2.8.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
release_uri     =
data_uri        = file:/lustre/scratch103/ensembl/gk4/flybase/dgri_1.3/seqdata/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
release_uri     =
data_uri        = file:/lustre/scratch103/ensembl/gk4/flybase/dwil_1.3/seqdata/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
release_uri     =
data_uri        = file:/lustre/scratch103/ensembl/gk4/flybase/dana_1.3/seqdata/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
release_uri     =
data_uri        = file:/lustre/scratch103/ensembl/gk4/flybase/dyak_1.3/seqdata/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
release_uri     =
data_uri        = file:/lustre/scratch103/ensembl/gk4/flybase/dsim_1.3/seqdata/dsim-all-r1.3.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
release_uri     =
data_uri        = file:/lustre/scratch103/ensembl/gk4/flybase/dsec_1.3/seqdata/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
release_uri     =
data_uri        = file:/lustre/scratch103/ensembl/gk4/flybase/dere_1.3/seqdata/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
release_uri     =
data_uri        = file:/lustre/scratch103/ensembl/gk4/flybase/dper_1.3/seqdata/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
release_uri     =
data_uri        = file:/lustre/scratch103/ensembl/gk4/flybase/dmoj_1.3/seqdata/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
release_uri     =
data_uri        = file:/lustre/scratch103/ensembl/gk4/flybase/dvir_1.2/seqdata/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          = Flybase_dmel_GFFv3_Parser
release_uri     =
data_uri        = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/current/gff/dmel-all-*.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          = Flybase_dmel_GFFv3_Parser
release_uri     =
data_uri        = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/current/gff/dmel-all-*.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          = Flybase_dmel_GFFv3_Parser
release_uri     =
data_uri        = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/current/gff/dmel-all-*.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          = Flybase_dmel_GFFv3_Parser
release_uri     =
data_uri        = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/current/gff/dmel-all-*.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          = Flybase_dmel_GFFv3_Parser
release_uri     =
data_uri        = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/current/gff/dmel-all-*.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          = Flybase_dmel_GFFv3_Parser
release_uri     =
data_uri        = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/current/gff/dmel-all-*.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          = Flybase_dmel_GFFv3_Parser
release_uri     =
data_uri        = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/current/gff/dmel-all-*.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          = Flybase_dmel_GFFv3_Parser
release_uri     =
data_uri        = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/current/gff/dmel-all-*.gff.gz

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

[source GO::MULTI]
# 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_pygmaeus,saccharomyces_cerevisiae, spermophilus_tridecemlineatus, taeniopygia_guttata, takifugu_rubripes, tupaia_belangeri,phaeodactylum_tricornutum,thalassiosira_pseudonana
name            = GO
download        = Y
order           = 80
priority        = 1
prio_descr      = main
parser          = GOParser
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
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
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
release_uri     =
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
order           = 85
priority        = 1
prio_descr      = main
parser          = GOParser
release_uri     =
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
release_uri     =
data_uri        = script:
#data_uri        = script:host=>ens-staging1,dbname=>ensembl_ontology_61,

[source goslim_goa::EG]
# Used by Ensembl Genomes
name            = goslim_goa
download        = Y
order           = 120
priority        = 1
prio_descr      = main
parser          = GOSlimParser
release_uri     =
data_uri        = script:host=>mysql-eg-staging-1,port=>4160,dbname=>ensembl_ontology_61,

[source GO::homo_sapiens]
# Used by homo_sapiens
name            = GO
download        = Y
order           = 85
priority        = 1
prio_descr      = main
parser          = GOParser
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
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
release_uri     = http://www.ebi.ac.uk/GOA/MOUSE_release.html
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

[source GO::mus_musculus#01]
 # Used by mus_musculus
 name            = GO
 download        = Y
 order           = 85
 priority        = 1
 prio_descr      = goga
 parser          = GOParser
 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
release_uri     = http://www.ebi.ac.uk/GOA/rat_release.html
data_uri        = ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/RAT/gene_association.goa_rat.gz
data_uri        = http://archive.geneontology.org/latest-termdb/go_daily-termdb.obo-xml.gz

[source GO::saccharomyces_cerevisiae]
# Used by saccharomyces_cerevisiae
name            = GO
download        = Y
order           = 85
priority        = 1
prio_descr      = main
parser          = GOParser
release_uri     =
data_uri        = ftp://ftp.geneontology.org/pub/go/gene-associations/gene_association.sgd.gz
data_uri        = http://archive.geneontology.org/latest-termdb/go_daily-termdb.obo-xml.gz

[source HPA::homo_sapiens]
# Used by homo_sapiens
name            = HPA
download        = Y
order           = 50
priority        = 1
prio_descr      = Human Protein Atlas (HPA) database
parser          = HPAParser
release_uri     = 
data_uri        = http://www.proteinatlas.org/download/xref.php

#[source IMGT_HLA::homo_sapiens]
# Used by homo_sapiens
#name            = IMGT_HLA
#download        = Y
#order           = 100
#priority        = 1
#prio_descr      = HLA Nomenclature database
#parser          = HLAParser
#release_uri     = 
#data_uri        = http://hla.alleles.org/xrefs/embl.txt

[source LRG_HGNC_notransfer]
name            = LRG_HGNC_notransfer
download        = N
order           = 30
priority        = 5
prio_descr      = 
parser          = HGNCParser
release_uri     =
data_uri        =

[source HGNC::homo_sapiens#01]
# Used by homo_sapiens
name            = HGNC
download        = Y
order           = 30
#order 51
priority        = 2
prio_descr      = ccds
parser          = HGNC_CCDSParser
release_uri     =
data_uri        = script:wget=>http://www.genenames.org/cgi-bin/hgnc_downloads.cgi?title=HGNC+output+data&hgnc_dbtag=on&col=gd_hgnc_id&col=gd_status&col=gd_ccds_ids&status=Approved&status_opt=2&level=pri&=on&where=&order_by=gd_app_sym_sort&limit=&format=text&submit=submit&.cgifields=&.cgifields=level&.cgifields=chr&.cgifields=status&.cgifields=hgnc_dbtag,host=>genebuild7,dbname=>db8_human_cdsonly_22sept2010,


[source HGNC::homo_sapiens#07]
# used by #02 
name            = HGNC
download        = N
order           = 30
priority        = 1
prio_descr      = ensembl_manual
parser          = HGNCParser
release_uri     =
data_uri        = 

[source HGNC::homo_sapiens]
# Used by homo_sapiens
name            = HGNC
download        = Y
order           = 30
priority        = 3
prio_descr      = vega
parser          = HGNC_ENSTParser
release_uri     =
data_uri        = script:
#data_uri        = script:vuser=>ensro,vhost=>ens-research,vdbname=>st3_homo_sapiens_vega_59_20100903,vport=>3306,cuser=>ensro,chost=>ens-staging1,cport=>3306,cdbname=>homo_sapiens_core_61_37f,


[source HGNC::homo_sapiens#02]
# Used by homo_sapiens
name            = HGNC
download        = Y
order           = 29
priority        = 4
prio_descr      = entrezgene_manual
parser          = HGNCParser
release_uri     =
data_uri        = http://www.genenames.org/cgi-bin/hgnc_downloads.cgi?title=Genew+output+data&col=gd_hgnc_id&col=gd_app_sym&col=gd_app_name&col=gd_prev_sym&col=gd_aliases&col=gd_pub_eg_id&col=gd_pub_refseq_ids&col=md_eg_id&col=md_refseq_id&col=gd_pub_ensembl_id&col=md_prot_id&col=gd_lsdb_links&status=Approved&status=Approved+Non-Human&status_opt=3&=on&where=&order_by=gd_hgnc_id&limit=&format=text&submit=submit&.cgifields=&.cgifields=status&.cgifields=chr


[source HGNC::homo_sapiens#03]
# Used by #02
name            = HGNC
download        = N
order           = 30
priority        = 5
prio_descr      = refseq_manual
parser          = HGNCParser
release_uri     =
data_uri        =

[source HGNC::homo_sapiens#09]
# used by #02 
name            = HGNC
download        = N
order           = 30
priority        = 5
prio_descr      = swissprot_manual
parser          = HGNCParser
release_uri     =
data_uri        = 

[source HGNC::homo_sapiens#04]
# used by #02 which produces HGNC refseq and entrezgene types
name            = HGNC
download        = N
order           = 30
priority        = 6
prio_descr      = entrezgene_mapped
parser          = HGNCParser
release_uri     =
data_uri        =

[source HGNC::homo_sapiens#05]
# used by #02 which produces HGNC refseq and entrezgene types
name            = HGNC
download        = N
order           = 30
priority        = 7
prio_descr      = refseq_mapped
parser          = HGNCParser
release_uri     =
data_uri        =

[source HGNC::homo_sapiens#06]
# used by uniprotParser
name            = HGNC
download        = N
order           = 30
priority        = 8
prio_descr      = uniprot
parser          = uniprotparser
release_uri     =
data_uri        = see_uniprot

[source HGNC::homo_sapiens#08]
# used by #02 
name            = HGNC
download        = N
order           = 30
priority        = 100
prio_descr      = desc_only
parser          = HGNCParser
release_uri     =
data_uri        = 


[source IKMCs_KOs::mus_musculus]
name            = IKMCs_KOs
download        = Y
order           = 40
priority        = 1
prio_descr      =
parser          = IKMCParser
release_uri     =
data_uri        = script:

[source IKMCs_No_products_available_yet::mus_musculus]
name            = IKMCs_No_products_available_yet
download        = N
order           = 40
priority        = 1
prio_descr      =
parser          = IKMCParser
release_uri     =
data_uri        = 

[source IKMCs_Vector_available::mus_musculus]
name            = IKMCs_Vector_available
download        = N
order           = 40
priority        = 1
prio_descr      =
parser          = IKMCParser
release_uri     =
data_uri        = 

[source IKMCs_ES_cells_available::mus_musculus]
name            = IKMCs_ES_cells_available
download        = N
order           = 40
priority        = 1
prio_descr      =
parser          = IKMCParser
release_uri     =
data_uri        = 

[source IKMCs_Mice_available::mus_musculus]
name            = IKMCs_Mice_available
download        = N
order           = 40
priority        = 1
prio_descr      =
parser          = IKMCParser
release_uri     =
data_uri        = 


[source IMGT/GENE_DB::homo_sapiens]
# Used by homo_sapiens
name            = IMGT/GENE_DB
download        = Y
order           = 40
priority        = 1
prio_descr      =
parser          = SegmentParser
release_uri     =
data_uri        = file:Homo_sapiens/Segments/Seg_xrefs.txt

[source IMGT/GENE_DB::mus_musculus]
# Used by mus_musculus
name            = IMGT/GENE_DB
download        = Y
order           = 40
priority        = 1
prio_descr      =
parser          = SegmentParser
release_uri     =
data_uri        = file:Mus_musculus/Segments/Seg_xrefs.txt

[source IMGT/LIGM_DB::homo_sapiens]
# Special source used by SegmentParser.  This source is not
# used directly by any species.  Data is created by the source
# 'IMGT/GENE_DB::homo_sapiens'.
name            = IMGT/LIGM_DB
download        = N
order           = 40
priority        = 1