xref_config.ini 89.2 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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#                                                                      #
########################################################################

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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     =
data_uri        = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/current/gff/dmel-all-*.gff.gz

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[source ARRAY_EMBL_MMC1_20k_v1::anopheles_gambiae]
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# Used by anopheles_gambiae
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name            = ARRAY_EMBL_MMC1_20k_v1
download        = Y
order           = 40
priority        = 1
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prio_descr      =
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parser          = VbDirectParser
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release_uri     =
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data_uri        = file:Anopheles_gambiae/EMBL/EMBL_MMC1_20k_v1.txt
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[source ARRAY_EMBL_MMC2_12k_v1::anopheles_gambiae]
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# Used by anopheles_gambiae
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name            = ARRAY_EMBL_MMC2_12k_v1
download        = Y
order           = 40
priority        = 1
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prio_descr      =
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parser          = VbDirectParser
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release_uri     =
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data_uri        = file:Anopheles_gambiae/EMBL/EMBL_MMC2_12k_v1.txt
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[source ARRAY_JHSPH_AG_GAMBER_15k_v1::anopheles_gambiae]
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# Used by anopheles_gambiae
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name            = ARRAY_JHSPH_AG_GAMBER_15k_v1
download        = Y
order           = 40
priority        = 1
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prio_descr      =
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parser          = VbDirectParser
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release_uri     =
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data_uri        = file:Anopheles_gambiae/JHSPH/JHSPH_AG_GAMBER_15k_v1.txt
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[source ARRAY_JHSPH_GAM3_0_21k_v1::anopheles_gambiae]
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# Used by anopheles_gambiae
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name            = ARRAY_JHSPH_GAM3_0_21k_v1
download        = Y
order           = 40
priority        = 1
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prio_descr      =
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parser          = VbDirectParser
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release_uri     =
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data_uri        = file:Anopheles_gambiae/JHSPH/JHSPH_GAM3.0_21k_v1.txt
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[source ARRAY_JHU_AEG1.0_20k_v1::aedes_aegypti]
# Used by aedes_aegypti
name            = ARRAY_JHU_AEG1.0_20k_v1
download        = Y
order           = 40
priority        = 1
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prio_descr      =
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parser          = VbDirectParser
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release_uri     =
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data_uri        = file:Aedes_aegypti/JHU/JHU_AEG1.0_20k_v1.txt
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[source ARRAY_LIV_AEGDETOX_0_25k_v1::aedes_aegypti]
# Used by aedes_aegypti
name            = ARRAY_LIV_AEGDETOX_0_25k_v1
download        = Y
order           = 40
priority        = 1
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prio_descr      =
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parser          = VbDirectParser
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release_uri     =
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data_uri        = file:Aedes_aegypti/LIV/LIV_AEGDETOX_0.25k_v1.txt
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[source ARRAY_LIV_GAMDETOX_0_25k_v1::anopheles_gambiae]
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# Used by anopheles_gambiae
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name            = ARRAY_LIV_GAMDETOX_0_25k_v1
download        = Y
order           = 40
priority        = 1
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prio_descr      =
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parser          = VbDirectParser
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release_uri     =
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data_uri        = file:Anopheles_gambiae/LIV/LIV_GAMDETOX_0.25k_v1.txt
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[source ARRAY_LIV_GAMDETOX_0_25k_v2::anopheles_gambiae]
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# Used by anopheles_gambiae
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name            = ARRAY_LIV_GAMDETOX_0_25k_v2
download        = Y
order           = 40
priority        = 1
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prio_descr      =
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parser          = VbDirectParser
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release_uri     =
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data_uri        = file:Anopheles_gambiae/LIV/LIV_GAMDETOX_0.25k_v2.txt
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[source ARRAY_ND_TIGRTC_9_6K_v1::aedes_aegypti]
# Used by aedes_aegypti
name            = ARRAY_ND_TIGRTC_9_6K_v1
download        = Y
order           = 40
priority        = 1
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prio_descr      =
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parser          = VbDirectParser
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release_uri     =
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data_uri        = file:Aedes_aegypti/ND/ND_TIGRTC_9.6k_v1.txt
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[source ARRAY_UCR_GillMgMT_0_2K_v2::aedes_aegypti]
# Used by aedes_aegypti
name            = ARRAY_UCR_GillMgMT_0_2K_v2
download        = Y
order           = 40
priority        = 1
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prio_descr      =
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parser          = VbDirectParser
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release_uri     =
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data_uri        = file:Aedes_aegypti/UCR/UCR_GillMgMT_0.2k_v2.txt
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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 AgilentCGH::homo_sapiens]
# Used by homo_sapiens
name            = AgilentCGH
download        = Y
order           = 50
priority        = 1
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prio_descr      =
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parser          = AgilentParser
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release_uri     =
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data_uri        = file:AgilentCGH/HumanCGH.fasta
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[source AgilentProbe::danio_rerio]
# Used by danio_rerio
name            = AgilentProbe
download        = Y
order           = 50
priority        = 1
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prio_descr      =
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parser          = AgilentParser
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release_uri     =
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data_uri        = file:AgilentProbe/ZebrafishExpression.fasta
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[source AgilentProbe::homo_sapiens]
# Used by homo_sapiens
name            = AgilentProbe
download        = Y
order           = 50
priority        = 1
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prio_descr      =
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parser          = AgilentParser
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release_uri     =
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data_uri        = file:AgilentProbe/HumanExpression.fasta
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[source AgilentProbe::mus_musculus]
# Used by mus_musculus
name            = AgilentProbe
download        = Y
order           = 50
priority        = 1
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prio_descr      =
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parser          = AgilentParser
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release_uri     =
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data_uri        = file:AgilentProbe/MouseExpression.fasta
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[source AgilentProbe::rattus_norvegicus]
# Used by rattus_norvegicus
name            = AgilentProbe
download        = Y
order           = 50
priority        = 1
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prio_descr      =
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parser          = AgilentParser
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release_uri     =
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data_uri        = file:AgilentProbe/RatExpression.fasta
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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
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prio_descr      =
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parser          = AnophelesSymbolParser
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release_uri     =
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data_uri        = file:Anopheles_symbol/GeneName_translation_UniqID.txt
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[source bdgpinsituexpr::drosophila_melanogaster]
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# Used by drosophila_melanogaster
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name            = bdgpinsituexpr
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download        = N
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order           = 50
priority        = 1
prio_descr      = BDGP in situ gene expression
parser          = Flybase_dmel_GFFv3_Parser
release_uri     =
data_uri        = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/current/gff/dmel-all-*.gff.gz

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[source CCDS::MULTI]
# Used by homo_sapiens, 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        = file:CCDS/CCDS.txt
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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_Pep/consensus-proteins_xref.fasta
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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_trans/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 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
parser          = Flybase_dmel_GFFv3_Parser
release_uri     =
data_uri        = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/current/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      =
#parser          = Flybase_dmel_GFFv3_Parser
#release_uri     =
#data_uri        = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/current/gff/dmel-all-*.gff.gz

#[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      =
#parser          = Flybase_dmel_GFFv3_Parser
#release_uri     =
#data_uri        = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/current/gff/dmel-all-*.gff.gz

#[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      =
#parser          = Flybase_dmel_GFFv3_Parser
#release_uri     =
#data_uri        = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/current/gff/dmel-all-*.gff.gz

#[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      =
#parser          = Flybase_dmel_GFFv3_Parser
#release_uri     =
#data_uri        = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/current/gff/dmel-all-*.gff.gz
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[source EntrezGene::MULTI]
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# Used by aedes_aegypti, anopheles_gambiae, apis_mellifera, bos_taurus, caenorhabditis_elegans, canis_familiaris, ciona_intestinalis, ciona_savignyi, danio_rerio, dasypus_novemcinctus, drosophila_melanogaster, echinops_telfairi, erinaceus_europaeus, equus_caballus, felis_catus, gallus_gallus, gasterosteus_aculeatus, homo_sapiens, 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, takifugu_rubripes, tupaia_belangeri, xenopus_tropicalis
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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 Ens_Ag_gene::drosophila_melanogaster]
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# Used by drosophila_melanogaster
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#name            = Ens_Ag_gene
#download        = N
#order           = 50
#priority        = 1
#prio_descr      = Ensembl mosquito gene predictions
#parser          = Flybase_dmel_GFFv3_Parser
#release_uri     =
#data_uri        = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/current/gff/dmel-all-*.gff.gz

#[source Ens_Am_gene::drosophila_melanogaster]
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# Used by drosophila_melanogaster
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#name            = Ens_Am_gene
#download        = N
#order           = 50
#priority        = 1
#prio_descr      = Ensembl bee gene predictions
#parser          = Flybase_dmel_GFFv3_Parser
#release_uri     =
#data_uri        = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/current/gff/dmel-all-*.gff.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     =
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
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order           = 100
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priority        = 1
prio_descr      = ID assigned by FlyBase
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parser          = FlybaseParser
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release_uri     =
data_uri        = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/current/gff/dmel-all-*.gff.gz

[source flybase_transcript_id::drosophila_melanogaster]
# Used by drosophila_melanogaster
name            = flybase_transcript_id
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download        = N
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order           = 50
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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
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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
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name            = FlyBaseCGID_gene
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download        = N
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order           = 50
priority        = 1
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prio_descr      = FlyBase_Annotation_IDs
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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
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name            = FlyBaseCGID_transcript
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download        = N
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order           = 50
priority        = 1
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prio_descr      = FlyBase_Annotation_IDs
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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
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name            = FlyBaseCGID_translation
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download        = N
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order           = 50
priority        = 1
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prio_descr      = FlyBase_Annotation_IDs
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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
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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     =
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
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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     =
data_uri        = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/current/gff/dmel-all-*.gff.gz

[source FlyBaseName_translations::drosophila_melanogaster]
# Used by drosophila_melanogaster
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name            = FlyBaseName_translation
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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     =
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
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download        = N
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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


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[source GO::MULTI]
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# Used by aedes_aegypti, anopheles_gambiae, apis_mellifera, bos_taurus, canis_familiaris, ciona_intestinalis, ciona_savignyi, dasypus_novemcinctus, drosophila_melanogaster, echinops_telfairi, erinaceus_europaeus, equus_caballus, felis_catus, gallus_gallus, gasterosteus_aculeatus, loxodonta_africana, macaca_mulatta, monodelphis_domestica, myotis_lucifugus, ochotona_princeps, ornithorhynchus_anatinus, oryctolagus_cuniculus, oryzias_latipes, pan_troglodytes, pongo_pygmaeus,saccharomyces_cerevisiae, spermophilus_tridecemlineatus, takifugu_rubripes, tupaia_belangeri
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name            = GO
download        = Y
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order           = 80
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priority        = 1
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prio_descr      = main
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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

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[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

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[source GO::caenorhabditis_elegans]
# Used by caenorhabditis_elegans
name            = GO
download        = Y
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order           = 85
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priority        = 1
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prio_descr      = main
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parser          = GOParser
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release_uri     =
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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
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order           = 85
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priority        = 1
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prio_descr      = main
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parser          = GOParser
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release_uri     =
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data_uri        = ftp://ftp.geneontology.org/pub/go/gene-associations/gene_association.zfin.gz

[source GO::homo_sapiens]
# Used by homo_sapiens
name            = GO
download        = Y
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order           = 85
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priority        = 1
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prio_descr      = main
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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

[source GO::mus_musculus]
# Used by mus_musculus
name            = GO
download        = Y
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order           = 85
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priority        = 1
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prio_descr      = main
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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
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[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

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[source GO::rattus_norvegicus]
# Used by rattus_norvegicus
name            = GO
download        = Y
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order           = 85
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priority        = 1
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prio_descr      = main
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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

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[source HGNC::homo_sapiens]
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# Used by homo_sapiens
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name            = HGNC
download        = Y
order           = 30
priority        = 1
prio_descr      = havana
parser          = HGNC_ENSGParser
release_uri     =
data_uri        = file:HGNC/HGNC_TO_ENSG

[source HGNC::homo_sapiens#01]
# Used by homo_sapiens
name            = HGNC
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download        = Y
order           = 51
priority        = 2
prio_descr      = ccds
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parser          = HGNC_CCDSParser
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release_uri     =
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data_uri        = file:HGNC/CCDS_TO_HGNC

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[source HGNC::homo_sapiens#02]
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# Used by homo_sapiens
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name            = HGNC
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download        = Y
order           = 29
priority        = 3
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prio_descr      = entrezgene_manual
parser          = HGNCParser
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release_uri     =
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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&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
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[source HGNC::homo_sapiens#03]
# Used by #01
name            = HGNC
download        = N
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order           = 30
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priority        = 4
prio_descr      = refseq_manual
parser          = HGNC_ENSGParser
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release_uri     =
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data_uri        = file:HGNC/HGNC_TO_ENSG
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[source HGNC::homo_sapiens#04]
# used by #01 which produces HGNC refseq and entrezgene types
name            = HGNC
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download        = N
order           = 30
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priority        = 5
prio_descr      = entrezgene_mapped
parser          = HGNC_ENSGParser
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release_uri     =
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data_uri        = file:HGNC/HGNC_TO_ENSG
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[source HGNC::homo_sapiens#05]
# used by #01 which produces HGNC refseq and entrezgene types
name            = HGNC
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download        = N
order           = 30
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priority        = 6
prio_descr      = refseq_mapped
parser          = HGNC_ENSGParser
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release_uri     =
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data_uri        = file:HGNC/HGNC_TO_ENSG
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[source HGNC::homo_sapiens#06]
# used by uniprotParser
name            = HGNC
download        = N
order           = 30
priority        = 7
prio_descr      = uniprot
parser          = uniprotparser
release_uri     =
data_uri        = see_uniprot

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

[source IMGT/GENE_DB::mus_musculus]
# Used by mus_musculus
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name            = IMGT/GENE_DB
download        = Y
order           = 40
priority        = 1
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prio_descr      =
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parser          = SegmentParser
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release_uri     =
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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
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prio_descr      =
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parser          = SegmentParser
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release_uri     =
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data_uri        = file:Homo_sapiens/Segments/Seg_xrefs.txt
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[source IMGT/LIGM_DB::mus_musculus]
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# Special source used by SegmentParser.  This source is not
# used directly by any species.  Data is created by the source
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# 'IMGT/GENE_DB::mus_musculus'.
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name            = IMGT/LIGM_DB
download        = N
order           = 40
priority        = 1
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prio_descr      =
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parser          = SegmentParser
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release_uri     =
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data_uri        = file:Mus_musculus/Segments/Seg_xrefs.txt
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[source IPI::bos_taurus]
# Used by bos_taurus
name            = IPI
download        = Y
order           = 30
priority        = 1
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prio_descr      =
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parser          = IPIParser
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release_uri     =
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data_uri        = ftp://ftp.ebi.ac.uk/pub/databases/IPI/current/ipi.BOVIn.fasta.gz

[source IPI::gallus_gallus]
# Used by gallus_gallus
name            = IPI
download        = Y
order           = 30
priority        = 1
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prio_descr      =
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parser          = IPIParser
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release_uri     =
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data_uri        = ftp://ftp.ebi.ac.uk/pub/databases/IPI/current/ipi.CHICK.fasta.gz

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[source IPI::danio_rerio]
# Used by danio_rerio
name            = IPI
download        = Y
order           = 30
priority        = 1
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prio_descr      =
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parser          = IPIParser
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release_uri     =
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data_uri        = ftp://ftp.ebi.ac.uk/pub/databases/IPI/current/ipi.BRARE.fasta.gz

[source IPI::homo_sapiens]
# Used by homo_sapiens
name            = IPI
download        = Y
order           = 30
priority        = 1
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prio_descr      =
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parser          = IPIParser
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release_uri     =
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data_uri        = ftp://ftp.ebi.ac.uk/pub/databases/IPI/current/ipi.HUMAN.fasta.gz

[source IPI::mus_musculus]
# Used by mus_musculus
name            = IPI
download        = Y
order           = 30
priority        = 1
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prio_descr      =
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parser          = IPIParser
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release_uri     =
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data_uri        = ftp://ftp.ebi.ac.uk/pub/databases/IPI/current/ipi.MOUSE.fasta.gz

[source IPI::rattus_norvegicus]
# Used by rattus_norvegicus
name            = IPI
download        = Y
order           = 30
priority        = 1
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prio_descr      =
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parser          = IPIParser
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release_uri     =
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data_uri        = ftp://ftp.ebi.ac.uk/pub/databases/IPI/current/ipi.RAT.fasta.gz

[source Illumina_V1::homo_sapiens]
# Used by homo_sapiens
name            = Illumina_V1
download        = Y
order           = 50
priority        = 1
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prio_descr      =
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parser          = FastaParser
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release_uri     =
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data_uri        = file:Illumina_V1/Human_WG-6.fa
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[source Illumina_V1::mus_musculus]
# Used by mus_musculus
name            = Illumina_V1
download        = Y
order           = 50
priority        = 1
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prio_descr      =
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parser          = FastaParser
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release_uri     =
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data_uri        = file:Illumina_V1/Mouse-6_V1.fa
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[source Illumina_V2::homo_sapiens]
# Used by homo_sapiens
name            = Illumina_V2
download        = Y
order           = 50
priority        = 1
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prio_descr      =
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parser          = IlluminaParser
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release_uri     =
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data_uri        = file:Illumina_V2/Human-6_v2_sequence.csv
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[source Interpro::MULTI]
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# Used by aedes_aegypti, anopheles_gambiae, apis_mellifera, bos_taurus, caenorhabditis_elegans, canis_familiaris, ciona_intestinalis, ciona_savignyi, danio_rerio, dasypus_novemcinctus, echinops_telfairi, erinaceus_europaeus, equus_caballus, felis_catus, gallus_gallus, gasterosteus_aculeatus, homo_sapiens, loxodonta_africana, macaca_mulatta, monodelphis_domestica, mus_musculus, myotis_lucifugus, ochotona_princeps, ornithorhynchus_anatinus, oryctolagus_cuniculus, pan_troglodytes,pongo_pygmaeus, oryzias_latipes, rattus_norvegicus, saccharomyces_cerevisiae, spermophilus_tridecemlineatus, takifugu_rubripes, tupaia_belangeri, xenopus_tropicalis
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name            = Interpro
download        = Y
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order           = 70
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priority        = 1
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prio_descr      =
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parser          = InterproParser
release_uri     = ftp://ftp.ebi.ac.uk/pub/databases/interpro/release_notes.txt
data_uri        = ftp://ftp.ebi.ac.uk/pub/databases/interpro/interpro.xml.gz

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[source MIM_GENE::homo_sapiens]
# MIM parse loads data as MIM_GENE or MIM_MORBID not as MIM
name            = MIM_GENE
download        = N
order           = 40
priority        = 1
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prio_descr      =
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parser          = MIMParser
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release_uri     =
data_uri        =
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[source MIM_MORBID::homo_sapiens]
# MIM parse loads data as MIM_GENE or MIM_MORBID not as MIM
name            = MIM_MORBID
download        = N
order           = 40
priority        = 1
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prio_descr      =
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parser          = MIMParser
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release_uri     =
data_uri        =
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[source MIM::homo_sapiens]
# Used by homo_sapiens
name            = MIM
download        = Y
order           = 10
priority        = 1
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prio_descr      =
859
parser          = MIMParser
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release_uri     =
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data_uri        = ftp://ftp.ncbi.nih.gov/repository/OMIM/omim.txt.Z

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863
[source MGI::mus_musculus]
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# Used by mus_musculus
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name            = MGI
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download        = Y
order           = 30
priority        = 1
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prio_descr      =
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parser          = MGDParser
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release_uri     =
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data_uri        = ftp://ftp.informatics.jax.org/pub/reports/MRK_SwissProt_TrEMBL.rpt
data_uri        = ftp://ftp.informatics.jax.org/pub/reports/MRK_Synonym.sql.rpt

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[source OTTT::MULTI]
# Used by homo_sapiens, mus_musculus
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name            = OTTT
download        = Y
order           = 50
priority        = 1
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prio_descr      =
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parser          = OTTTParser
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release_uri     =
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data_uri        = file:OTTT/OTTT.txt
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[source RGD::rattus_norvegicus]
# Used by rattus_norvegicus
name            = RGD
download        = Y
order           = 30
priority        = 1
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prio_descr      =
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parser          = RGDParser
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release_uri     =
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data_uri        = ftp://rgd.mcw.edu/pub/data_release/GENES_RAT