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

misc-scripts/xref_mapping/xref_config.ini

@@ -207,6 +207,7 @@ release_uri     =
 data_uri        = http://www.phi-base.org/PHI-export.php
 
 
+
 [species anas_platyrhynchos]
 taxonomy_id     = 8839
 aliases         = duck, mallard, mallard duck, mallard ducks, anas platyrhynchos, anas boschas, anas domesticus
@@ -1761,6 +1762,41 @@ parser          = RefSeqGPFFParser
 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
 
+[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]
 # Used by canis_familiaris
@@ -2018,6 +2054,42 @@ parser          = RefSeqGPFFParser
 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
 
+[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]
 # Used by canis_familiaris
@@ -2180,7 +2252,7 @@ priority        = 1
 prio_descr      =
 parser          = PomBaseParser
 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]
 # Special source used in UCSCParser.  No species uses this source.
@@ -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.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]
 # Used by caenorhabditis_elegans
 name            = UniGene
@@ -3542,11 +3662,11 @@ taxonomy_id     = 7029
 aliases         = apisum, acyrthosiphon, acyrthosiphonpisum, pea aphid
 source          = EntrezGene::MULTI
 source          = GO::MULTI
-source          = goslim_goa::MULTI
+source          = goslim_goa::EG
 source          = InterproGO::MULTI
 source          = Interpro::MULTI
-source					= RefSeq_dna::MULTI-invertebrate
-source					= RefSeq_peptide::MULTI-invertebrate
+source	        = RefSeq_dna::MULTI-invertebrate
+source	        = RefSeq_peptide::MULTI-invertebrate
 source          = UniGene::acyrthosiphon_pisum
 source          = Uniprot/SPTREMBL::MULTI
 source          = Uniprot/SWISSPROT::MULTI
@@ -3592,8 +3712,7 @@ source		= AnoXcel::anopheles_gambiae
 taxonomy_id     = 7460
 aliases         = amellifera, apismellifera, honeybee
 source          = EntrezGene::MULTI
-source          = GO::MULTI
-source          = goslim_goa::MULTI
+source          = goslim_goa::EG
 source          = InterproGO::MULTI
 source          = Interpro::MULTI
 source          = RefSeq_dna::apis_mellifera
@@ -5344,3 +5463,93 @@ source          = Uniprot/SPTREMBL::MULTI
 source          = Uniprot/SWISSPROT::MULTI
 #source          = ncRNA::MULTI
 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
+
+