Commit dfaa18aa authored by Arnaud Kerhornou's avatar Arnaud Kerhornou
Browse files

Updated the metazoan set of species, adding tribolium_castaneum...

Updated the metazoan set of species, adding tribolium_castaneum strongylocentrotus_purpuratus nematostella_vectensis bombyx_mori amphimedon_queenslandica atta_cephalotes
parent be7aa3b2
...@@ -207,6 +207,7 @@ release_uri = ...@@ -207,6 +207,7 @@ release_uri =
data_uri = http://www.phi-base.org/PHI-export.php data_uri = http://www.phi-base.org/PHI-export.php
[species anas_platyrhynchos] [species anas_platyrhynchos]
taxonomy_id = 8839 taxonomy_id = 8839
aliases = duck, mallard, mallard duck, mallard ducks, anas platyrhynchos, anas boschas, anas domesticus aliases = duck, mallard, mallard duck, mallard ducks, anas platyrhynchos, anas boschas, anas domesticus
...@@ -1761,6 +1762,41 @@ parser = RefSeqGPFFParser ...@@ -1761,6 +1762,41 @@ parser = RefSeqGPFFParser
release_uri = ftp://ftp.ncbi.nih.gov/refseq/release/release-notes/RefSeq-release*.txt release_uri = ftp://ftp.ncbi.nih.gov/refseq/release/release-notes/RefSeq-release*.txt
data_uri = ftp://ftp.ncbi.nih.gov/genomes/Sus_scrofa/RNA/rna.gbk.gz data_uri = ftp://ftp.ncbi.nih.gov/genomes/Sus_scrofa/RNA/rna.gbk.gz
[source RefSeq_dna::strongylocentrotus_purpuratus]
# Used by strongylocentrotus_purpuratus
name = RefSeq_dna
download = Y
order = 20
priority = 2
prio_descr = refseq
parser = RefSeqGPFFParser
release_uri = ftp://ftp.ncbi.nih.gov/refseq/release/release-notes/RefSeq-release*.txt
data_uri = ftp://ftp.ncbi.nih.gov/genomes/Strongylocentrotus_purpuratus/RNA/rna.gbk.gz
[source RefSeq_dna::amphimedon_queenslandica]
# Used by amphimedon_queenslandica
name = RefSeq_dna
download = Y
order = 20
priority = 2
prio_descr = refseq
parser = RefSeqGPFFParser
release_uri = ftp://ftp.ncbi.nih.gov/refseq/release/release-notes/RefSeq-release*.txt
data_uri = ftp://ftp.ncbi.nih.gov/genomes/Amphimedon_queenslandica/RNA/rna.gbk.gz
[source RefSeq_dna::tribolium_castaneum]
# Used by tribolium_castaneum
name = RefSeq_dna
download = Y
order = 20
priority = 2
prio_descr = refseq
parser = RefSeqGPFFParser
release_uri = ftp://ftp.ncbi.nih.gov/refseq/release/release-notes/RefSeq-release*.txt
data_uri = ftp://ftp.ncbi.nih.gov/genomes/Tribolium_castaneum/RNA/rna.gbk.gz
[source RefSeq_dna::canis_familiaris] [source RefSeq_dna::canis_familiaris]
# Used by canis_familiaris # Used by canis_familiaris
...@@ -2018,6 +2054,42 @@ parser = RefSeqGPFFParser ...@@ -2018,6 +2054,42 @@ parser = RefSeqGPFFParser
release_uri = ftp://ftp.ncbi.nih.gov/refseq/release/release-notes/RefSeq-release*.txt release_uri = ftp://ftp.ncbi.nih.gov/refseq/release/release-notes/RefSeq-release*.txt
data_uri = ftp://ftp.ncbi.nih.gov/genomes/Sus_scrofa/protein/protein.gbk.gz data_uri = ftp://ftp.ncbi.nih.gov/genomes/Sus_scrofa/protein/protein.gbk.gz
[source RefSeq_peptide::amphimedon_queenslandica]
# Used by amphimedon_queenslandica
name = RefSeq_peptide
download = Y
order = 20
priority = 1
prio_descr =
parser = RefSeqGPFFParser
release_uri = ftp://ftp.ncbi.nih.gov/refseq/release/release-notes/RefSeq-release*.txt
data_uri = ftp://ftp.ncbi.nih.gov/genomes/Amphimedon_queenslandica/protein/protein.gbk.gz
[source RefSeq_peptide::strongylocentrotus_purpuratus]
# Used by strongylocentrotus_purpuratus
name = RefSeq_peptide
download = Y
order = 20
priority = 1
prio_descr =
parser = RefSeqGPFFParser
release_uri = ftp://ftp.ncbi.nih.gov/refseq/release/release-notes/RefSeq-release*.txt
data_uri = ftp://ftp.ncbi.nih.gov/genomes/Strongylocentrotus_purpuratus/protein/protein.gbk.gz
[source RefSeq_peptide::tribolium_castaneum]
# Used by tribolium_castaneum
name = RefSeq_peptide
download = Y
order = 20
priority = 1
prio_descr =
parser = RefSeqGPFFParser
release_uri = ftp://ftp.ncbi.nih.gov/refseq/release/release-notes/RefSeq-release*.txt
data_uri = ftp://ftp.ncbi.nih.gov/genomes/Tribolium_castaneum/protein/protein.gbk.gz
[source RefSeq_peptide::canis_familiaris] [source RefSeq_peptide::canis_familiaris]
# Used by canis_familiaris # Used by canis_familiaris
...@@ -2180,7 +2252,7 @@ priority = 1 ...@@ -2180,7 +2252,7 @@ priority = 1
prio_descr = prio_descr =
parser = PomBaseParser parser = PomBaseParser
release_uri = release_uri =
data_uri = http://www.ebi.ac.uk/~mcdowall/PomBaseFeatureDescriptions.txt data_uri = http://www.ebi.ac.uk/~mcdowall/PomBaseFeatureDescriptions_For-v65.txt
[source UCSC::MULTI] [source UCSC::MULTI]
# Special source used in UCSCParser. No species uses this source. # Special source used in UCSCParser. No species uses this source.
...@@ -2297,6 +2369,54 @@ release_uri = ...@@ -2297,6 +2369,54 @@ release_uri =
data_uri = ftp://ftp.ncbi.nih.gov/repository/UniGene/Sus_scrofa/Ssc.seq.uniq.gz data_uri = ftp://ftp.ncbi.nih.gov/repository/UniGene/Sus_scrofa/Ssc.seq.uniq.gz
data_uri = ftp://ftp.ncbi.nih.gov/repository/UniGene/Sus_scrofa/Ssc.data.gz data_uri = ftp://ftp.ncbi.nih.gov/repository/UniGene/Sus_scrofa/Ssc.data.gz
[source UniGene::bombyx_mori]
# Used by bombyx_mori
name = UniGene
download = Y
order = 30
priority = 1
prio_descr =
parser = UniGeneParser
release_uri =
data_uri = ftp://ftp.ncbi.nih.gov/repository/UniGene/Bombyx_mori/Bmo.seq.uniq.gz
data_uri = ftp://ftp.ncbi.nih.gov/repository/UniGene/Bombyx_mori/Bmo.data.gz
[source UniGene::nematostella_vectensis]
# Used by nematostella_vectensis
name = UniGene
download = Y
order = 30
priority = 1
prio_descr =
parser = UniGeneParser
release_uri =
data_uri = ftp://ftp.ncbi.nih.gov/repository/UniGene/Nematostella_vectensis/Nve.seq.uniq.gz
data_uri = ftp://ftp.ncbi.nih.gov/repository/UniGene/Nematostella_vectensis/Nve.data.gz
[source UniGene::tribolium_castaneum]
# Used by tribolium_castaneum
name = UniGene
download = Y
order = 30
priority = 1
prio_descr =
parser = UniGeneParser
release_uri =
data_uri = ftp://ftp.ncbi.nih.gov/repository/UniGene/Tribolium_castaneum/Tca.seq.uniq.gz
data_uri = ftp://ftp.ncbi.nih.gov/repository/UniGene/Tribolium_castaneum/Tca.data.gz
[source UniGene::strongylocentrotus_purpuratus]
# Used by tribolium_castaneum
name = UniGene
download = Y
order = 30
priority = 1
prio_descr =
parser = UniGeneParser
release_uri =
data_uri = ftp://ftp.ncbi.nih.gov/repository/UniGene/Strongylocentrotus_purpuratus/Spu.seq.uniq.gz
data_uri = ftp://ftp.ncbi.nih.gov/repository/UniGene/Strongylocentrotus_purpuratus/Spu.data.gz
[source UniGene::caenorhabditis_elegans] [source UniGene::caenorhabditis_elegans]
# Used by caenorhabditis_elegans # Used by caenorhabditis_elegans
name = UniGene name = UniGene
...@@ -3542,11 +3662,11 @@ taxonomy_id = 7029 ...@@ -3542,11 +3662,11 @@ taxonomy_id = 7029
aliases = apisum, acyrthosiphon, acyrthosiphonpisum, pea aphid aliases = apisum, acyrthosiphon, acyrthosiphonpisum, pea aphid
source = EntrezGene::MULTI source = EntrezGene::MULTI
source = GO::MULTI source = GO::MULTI
source = goslim_goa::MULTI source = goslim_goa::EG
source = InterproGO::MULTI source = InterproGO::MULTI
source = Interpro::MULTI source = Interpro::MULTI
source = RefSeq_dna::MULTI-invertebrate source = RefSeq_dna::MULTI-invertebrate
source = RefSeq_peptide::MULTI-invertebrate source = RefSeq_peptide::MULTI-invertebrate
source = UniGene::acyrthosiphon_pisum source = UniGene::acyrthosiphon_pisum
source = Uniprot/SPTREMBL::MULTI source = Uniprot/SPTREMBL::MULTI
source = Uniprot/SWISSPROT::MULTI source = Uniprot/SWISSPROT::MULTI
...@@ -3592,8 +3712,7 @@ source = AnoXcel::anopheles_gambiae ...@@ -3592,8 +3712,7 @@ source = AnoXcel::anopheles_gambiae
taxonomy_id = 7460 taxonomy_id = 7460
aliases = amellifera, apismellifera, honeybee aliases = amellifera, apismellifera, honeybee
source = EntrezGene::MULTI source = EntrezGene::MULTI
source = GO::MULTI source = goslim_goa::EG
source = goslim_goa::MULTI
source = InterproGO::MULTI source = InterproGO::MULTI
source = Interpro::MULTI source = Interpro::MULTI
source = RefSeq_dna::apis_mellifera source = RefSeq_dna::apis_mellifera
...@@ -5344,3 +5463,93 @@ source = Uniprot/SPTREMBL::MULTI ...@@ -5344,3 +5463,93 @@ source = Uniprot/SPTREMBL::MULTI
source = Uniprot/SWISSPROT::MULTI source = Uniprot/SWISSPROT::MULTI
#source = ncRNA::MULTI #source = ncRNA::MULTI
source = goslim_goa::EG source = goslim_goa::EG
[species amphimedon_queenslandica]
taxonomy_id = 400682
aliases = sponge, aqueenslandica, amphimedon_queenslandica
source = EntrezGene::MULTI
source = goslim_goa::EG
source = GO::MULTI
source = InterproGO::MULTI
source = Interpro::MULTI
source = RefSeq_dna::amphimedon_queenslandica
source = RefSeq_peptide::amphimedon_queenslandica
source = Uniprot/SPTREMBL::MULTI
source = Uniprot/SWISSPROT::MULTI
[species atta_cephalotes]
taxonomy_id = 12957
aliases = ant, acephalotes, atta_cephalotes
source = EntrezGene::MULTI
source = goslim_goa::EG
source = GO::MULTI
source = InterproGO::MULTI
source = Interpro::MULTI
source = RefSeq_dna::MULTI-invertebrate
source = RefSeq_peptide::MULTI-invertebrate
source = Uniprot/SPTREMBL::MULTI
source = Uniprot/SWISSPROT::MULTI
[species bombyx_mori]
taxonomy_id = 7091
aliases = silkworm, silk moth, bmori, bombyx_mori
source = EntrezGene::MULTI
source = goslim_goa::EG
source = GO::MULTI
source = InterproGO::MULTI
source = Interpro::MULTI
source = RefSeq_dna::MULTI-invertebrate
source = RefSeq_peptide::MULTI-invertebrate
source = UniGene::bombyx_mori
source = Uniprot/SPTREMBL::MULTI
source = Uniprot/SWISSPROT::MULTI
[species nematostella_vectensis]
taxonomy_id = 45351
aliases = anemone, sea anemone, nvectensis, nematostella_vectensis
source = EntrezGene::MULTI
source = goslim_goa::EG
source = GO::MULTI
source = InterproGO::MULTI
source = Interpro::MULTI
source = RefSeq_dna::MULTI-invertebrate
source = RefSeq_peptide::MULTI-invertebrate
source = UniGene::nematostella_vectensis
source = Uniprot/SPTREMBL::MULTI
source = Uniprot/SWISSPROT::MULTI
[species strongylocentrotus_purpuratus]
taxonomy_id = 7668
aliases = sea urchin, spurpuratus, strongylocentrotus_purpuratus
source = EntrezGene::MULTI
source = goslim_goa::EG
source = GO::MULTI
source = InterproGO::MULTI
source = Interpro::MULTI
source = RefSeq_dna::strongylocentrotus_purpuratus
source = RefSeq_peptide::strongylocentrotus_purpuratus
source = UniGene::strongylocentrotus_purpuratus
source = Uniprot/SPTREMBL::MULTI
source = Uniprot/SWISSPROT::MULTI
[species tribolium_castaneum]
taxonomy_id = 7070
aliases = red flour beetle, tcastaneum, tribolium_castaneum
source = EntrezGene::MULTI
source = goslim_goa::EG
source = GO::MULTI
source = InterproGO::MULTI
source = Interpro::MULTI
source = RefSeq_dna::tribolium_castaneum
source = RefSeq_peptide::tribolium_castaneum
source = UniGene::tribolium_castaneum
source = Uniprot/SPTREMBL::MULTI
source = Uniprot/SWISSPROT::MULTI
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