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Commit 6c9eb151 authored by Magali Ruffier's avatar Magali Ruffier
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ENSCORESW-2818: remove historical vega sources

parent c0d38d06
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4 merge requests!342Feature/schema update 96,!282Feature/xref config cleanup,!342Feature/schema update 96,!282Feature/xref config cleanup
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misc-scripts/xref_mapping/xref_config.ini
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− 168
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......@@ -1173,18 +1173,6 @@ 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 = VegaOfficialNameParser
release_uri =
data_uri = script:source=>HGNC,host=>mysql-ens-sta-1,port=>4519,
#data_uri = script:source=>HGNC,chost=>ens-production,cdbname=>mr6_human_core,vdbhost=>ens-production,vdbname=>mr6_human_vega,
[source HGNC::homo_sapiens#02]
# Used by homo_sapiens
......@@ -1443,18 +1431,6 @@ parser = MGIParser
release_uri =
data_uri = http://www.informatics.jax.org/downloads/reports/MRK_ENSEMBL.rpt
[source MGI::mus_musculus#02]
# Used by mus_musculus
name = MGI
download = Y
order = 45
priority = 2
prio_descr = vega
parser = VegaOfficialNameParser
release_uri =
data_uri = script:source=>MGI,host=>mysql-ens-sta-1,port=>4519,
#data_uri = script:source=>MGI,chost=>ens-production,cdbname=>mr6_mouse_core,vhost=>ens-production,vdbname=>mr6_mouse_vega,
[source MGI::mus_musculus#05]
# Used by mus_musculus
name = MGI
......@@ -1490,35 +1466,6 @@ dependent_on = HGNC
release_uri =
data_uri = http://www.orphadata.org/data/xml/en_product6.xml
[source OTTT::homo_sapiens]
#
# NOW taken when merging done with havana
#
# Used by homo_sapiens
name = OTTT
download = N
order = 50
priority = 1
prio_descr =
parser = OTTTParser
release_uri =
data_uri =
#data_uri = script:host=>ens-staging,port=>3306,dbname=>homo_sapiens_vega_55_37,
[source OTTT::mus_musculus]
#
# NOW taken when merging done with havana
#
# Used by mus_musculus
name = OTTT
download = N
order = 50
priority = 1
prio_descr =
parser = OTTTParser
release_uri =
data_uri =
[source Reactome::MULTI]
# Used by all species
name = Reactome
......@@ -1582,18 +1529,6 @@ parser = done_in_RGDParser
release_uri =
data_uri =
[source RGD::rattus_norvegicus#01]
# Used by homo_sapiens
name = RGD
download = Y
order = 30
priority = 3
prio_descr = vega
parser = VegaOfficialNameParser
release_uri =
data_uri = script:source=>RGD,host=>mysql-ens-sta-1,port=>4519,
#data_uri = script:source=>RGD,chost=>genebuild3,cdbname=>db8_rattus_norvegicus_core_77_5,vhost=>genebuild6,vdbname=>db8_rat_vega_77,
[source RGD_trans_name]
name = RGD_trans_name
download = N
......@@ -1603,17 +1538,6 @@ prio_descr =
parser = done_in_official_naming
release_uri =
[source RGD_curated_transcript::mus_musculus]
name = RGD_curated_transcript_notransfer
download = Y
order = 49
priority = 1
prio_descr =
parser = curated_transcriptParser
release_uri =
data_uri = script:source=>RGD,host=>mysql-ens-sta-1,port=>4519,
#data_uri = script:source=>RGD,chost=>ens-staging2,cdbname=>rattus_norvegicus_core_77_5,vdbname=>db8_rat_vega_77,vhost=>genebuild6,
[source RefSeq_dna::MULTI-vertebrate]
# Used by vertebrates
name = RefSeq_dna
......@@ -3639,39 +3563,6 @@ parser = ChecksumParser
release_uri =
data_uri = ftp://ftp.ebi.ac.uk/pub/databases/RNAcentral/current_release/md5/md5.tsv.gz
[source HGNC_curated_transcript::homo_sapiens]
name = HGNC_curated_transcript_notransfer
download = Y
order = 49
priority = 1
prio_descr = curated with transcript number postfix
parser = curated_transcriptParser
release_uri =
data_uri = script:source=>HGNC,host=>mysql-ens-sta-1,port=>4519,
#data_uri = script:source=>HGNC,chost=>ens-production,cdbname=>mr6_human_core,vdbname=>mr6_human_vega,vhost=>ens-production,
[source PIGGY_curated_transcript::sus_scrofa]
name = PIGGY_curated_transcript_notransfer
download = Y
order = 49
priority = 1
prio_descr = curated with transcript number postfix
parser = curated_transcriptParser
release_uri =
data_uri = script:source=>PIGGY,host=>mysql-ens-sta-1,port=>4519,
#data_uri = script:source=>PIGGY,chost=>ens-production,cdbname=>mr6_pig_core,vdbname=>mr6_pig_vega,vhost=>ens-production,
[source PIGGY::sus_scrofa]
# Used by sus_scrofa
name = PIGGY
download = Y
order = 30
priority = 1
prio_descr = vega
parser = VegaOfficialNameParser
release_uri =
data_uri = script:host=>mysql-ens-sta-1,port=>4519,
[source PIGGY_trans_name]
name = PIGGY_trans_name
download = N
......@@ -3717,18 +3608,6 @@ prio_descr =
parser = done_in_official_naming
release_uri =
[source MGI_curated_transcript::mus_musculus]
name = MGI_curated_transcript_notransfer
download = Y
order = 49
priority = 1
prio_descr =
parser = curated_transcriptParser
release_uri =
data_uri = script:source=>MGI,host=>mysql-ens-sta-1,port=>4519,
#data_uri = script:source=>MGI,chost=>ens-production,cdbname=>mr6_mouse_core,vdbname=>mr6_pig_vega,vhost=>ens-production,
[source MGI_automatic_transcript::mus_musculus]
name = MGI_automatic_transcript_notransfer
download = N
......@@ -3760,17 +3639,6 @@ parser = comes via official naming
release_uri =
data_uri =
[source Clone_based_vega_transcript::homo_sapiens]
name = Clone_based_vega_transcript
download = N
order = 50
priority = 1
prio_descr =
parser = HGNC_curated_transcriptParser
release_uri =
data_uri = loaded as part of HGNC_curated_transcript
[source Clone_based_ensembl_transcript::homo_sapiens]
name = Clone_based_ensembl_transcript
download = N
......@@ -3780,16 +3648,6 @@ prio_descr =
parser = done_in_official_naming
release_uri =
[source Clone_based_vega_gene::homo_sapiens]
name = Clone_based_vega_gene
download = N
order = 50
priority = 1
prio_descr =
parser = done_in_official_naming
release_uri =
[source Clone_based_ensembl_gene::homo_sapiens]
name = Clone_based_ensembl_gene
download = N
......@@ -3824,18 +3682,6 @@ data_uri = http://zfin.org/data_transfer/Downloads/uniprot.txt
data_uri = http://zfin.org/data_transfer/Downloads/aliases.txt
data_uri = http://zfin.org/data_transfer/Downloads/gene_seq.txt
[source ZFIN_ID::danio_rerio#02]
# Used by danio_rerio
name = ZFIN_ID
download = Y
order = 30
priority = 2
prio_descr = vega
parser = VegaOfficialNameParser
release_uri =
data_uri = script:source=>ZFIN_ID,host=>mysql-ens-sta-1,port=>4519,
#data_uri = script:source=>ZFIN_ID,chost=>ens-production,cdbname=>mr6_danio_core,vhost=>ens-production,vdbname=>mr6_danio_vega,
[source ZFIN_ID::danio_rerio#03]
# Used by danio_rerio
name = ZFIN_ID
......@@ -3848,17 +3694,6 @@ release_uri =
#data_uri = http://zfin.org/data_transfer/Downloads/genetic_markers.txt
data_uri = ftp://zfin.org/pub/transfer/MEOW/zfin_genes.txt
[source ZFIN_ID_curated_transcript::danio_rerio]
name = ZFIN_ID_curated_transcript_notransfer
download = Y
order = 49
priority = 1
prio_descr = curated with transcript number postfix
parser = curated_transcriptParser
release_uri =
data_uri = script:source=>ZFIN_ID,host=>mysql-ens-sta-1,port=>4519,
#data_uri = script:source=>ZFIN_ID,chost=>ens-production,cdbname=>mr6_danio_core,vdbname=>mr6_pig_vega,vhost=>ens-production,
[source ZFIN_ID_trans_name]
name = ZFIN_ID_trans_name
download = N
......@@ -6377,7 +6212,6 @@ aliases = mmusculus, mouse, musmusculus
source = CCDS::mus_musculus
source = EntrezGene::MULTI
source = MGI::mus_musculus#01
source = MGI::mus_musculus#02
source = MGI::mus_musculus#03
source = MGI::mus_musculus#05
source = Reactome::MULTI
......@@ -6748,7 +6582,6 @@ source = EntrezGene::MULTI
source = Reactome::MULTI
source = RNACentral::MULTI
source = RGD::rattus_norvegicus
source = RGD::rattus_norvegicus#01
source = RGD::rattus_norvegicus#02
source = RefSeq_dna::rattus_norvegicus
source = RefSeq_peptide::rattus_norvegicus
......@@ -7302,7 +7135,6 @@ source = UniParc::MULTI
source = RFAM::MULTI
source = miRBase::MULTI
source = ArrayExpress::MULTI
source = PIGGY::sus_scrofa
[species aegilops_tauschii]
taxonomy_id = 37682
......
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