ciona savignyi added

misc-scripts/xref_mapping/sql/populate_metadata.sql

@@ -24,6 +24,7 @@ INSERT INTO species (species_id, taxonomy_id, name, aliases) VALUES (4932, 4932,
 INSERT INTO species (species_id, taxonomy_id, name, aliases) VALUES (7460, 7460,  'apis_mellifera',  'apismellifera,honeybee,amellifera');
 
 INSERT INTO species (species_id, taxonomy_id, name, aliases) VALUES (7719, 7719,  'ciona_intestinalis', 'cionaintestinalis,cintestinalis,seasquirt'); 
+INSERT INTO species (species_id, taxonomy_id, name, aliases) VALUES (51511, 51511,'ciona_savignyi',     'ciona_savi,csav,savi'); 
 
 # Serveral strains of anopheles have different taxonomy IDs
 INSERT INTO species (species_id, taxonomy_id, name, aliases) VALUES (7165,7165, 'anopheles_gambiae', 'mosquito,anopheles,agambiae,anophelesgambiae');
@@ -334,7 +335,7 @@ INSERT INTO source_url (source_id, species_id, url, checksum, file_modified_date
 ##      Agilent
 INSERT INTO source_url (source_id, species_id, url, checksum, file_modified_date, upload_date, parser) VALUES (2700, 10090,'LOCAL:AgilentProbe/MouseExpression.fasta', '', now(), now(), "AgilentParser");
 
-##      ncRNA's presently inhouse.
+##      ncRNAs presently inhouse.
 INSERT INTO source_url (source_id, species_id, url, checksum, file_modified_date, upload_date, parser) VALUES (4000, 10090,'LOCAL:ncRNA/ncRNA.txt', '', now(), now(), "ncRNAParser");
 
 
@@ -372,7 +373,7 @@ INSERT INTO source_url (source_id, species_id, url, checksum, file_modified_date
 ##      Agilent
 INSERT INTO source_url (source_id, species_id, url, checksum, file_modified_date, upload_date, parser) VALUES (2700, 10116,'LOCAL:AgilentProbe/RatExpression.fasta', '', now(), now(), "AgilentParser");
 
-##      ncRNA's presently inhouse.
+##      ncRNAs presently inhouse.
 INSERT INTO source_url (source_id, species_id, url, checksum, file_modified_date, upload_date, parser) VALUES (4000, 10116,'LOCAL:ncRNA/ncRNA.txt', '', now(), now(), "ncRNAParser");
 
 # --------------------------------------------------------------------------------
@@ -622,6 +623,110 @@ VALUES (2611, 7719,'ftp://ftp.jgi-psf.org/pub/JGI_data/Ciona/v2.0/FM1.aa.fasta.g
 
 
 
+#### Ciona savignyi 
+
+## Uniprot
+INSERT INTO source_url (source_id, species_id, url, file_modified_date, upload_date, parser) VALUES\
+ (1, 7719, 'ftp://ftp.ebi.ac.uk/pub/databases/uniprot/knowledgebase/uniprot_sprot.dat.gz', now(), now(), "UniProtParser");
+INSERT INTO source_url (source_id, species_id, url, file_modified_date, upload_date, parser) VALUES\
+ (2, 7719, 'ftp://ftp.ebi.ac.uk/pub/databases/uniprot/knowledgebase/uniprot_trembl.dat.gz', now(), now(), "UniProtParser");
+INSERT INTO source_url (source_id, species_id, url, checksum, file_modified_date, upload_date, parser) VALUES (3000, 7719, 'ftp://ftp.ebi.ac.uk/pub/databases/uniprot/knowledgebase/uniprot_sprot_varsplic.fasta.gz', '', now(), now(), "UniProtVarSplicParser");
+
+##       refseq ftp://ftp.ncbi.nih.gov/refseq/release/vertebrate_other/ *gpff
+INSERT INTO source_url (source_id, species_id, url, file_modified_date, upload_date, parser) VALUES\
+(3, 7719,'ftp://ftp.ncbi.nih.gov/refseq/release/vertebrate_other/vertebrate_other1.protein.gpff.gz',  now(), now(), "RefSeqGPFFParser");
+INSERT INTO source_url (source_id, species_id, url, file_modified_date, upload_date, parser) VALUES\
+(3, 7719,'ftp://ftp.ncbi.nih.gov/refseq/release/vertebrate_other/vertebrate_other2.protein.gpff.gz',  now(), now(), "RefSeqGPFFParser");
+INSERT INTO source_url (source_id, species_id, url, file_modified_date, upload_date, parser) VALUES\
+(3, 7719,'ftp://ftp.ncbi.nih.gov/refseq/release/vertebrate_other/vertebrate_other3.protein.gpff.gz',  now(), now(), "RefSeqGPFFParser");
+INSERT INTO source_url (source_id, species_id, url, file_modified_date, upload_date, parser) VALUES\
+(3, 7719,'ftp://ftp.ncbi.nih.gov/refseq/release/vertebrate_other/vertebrate_other4.protein.gpff.gz',  now(), now(), "RefSeqGPFFParser");
+INSERT INTO source_url (source_id, species_id, url, file_modified_date, upload_date, parser) VALUES\
+(3, 7719,'ftp://ftp.ncbi.nih.gov/refseq/release/vertebrate_other/vertebrate_other5.protein.gpff.gz',  now(), now(), "RefSeqGPFFParser");
+INSERT INTO source_url (source_id, species_id, url, file_modified_date, upload_date, parser) VALUES\
+(3, 7719,'ftp://ftp.ncbi.nih.gov/refseq/release/vertebrate_other/vertebrate_other6.protein.gpff.gz',  now(), now(), "RefSeqGPFFParser");
+INSERT INTO source_url (source_id, species_id, url, file_modified_date, upload_date, parser) VALUES\
+(3, 7719,'ftp://ftp.ncbi.nih.gov/refseq/release/vertebrate_other/vertebrate_other7.protein.gpff.gz',  now(), now(), "RefSeqGPFFParser"); 
+
+##       refseq ftp://ftp.ncbi.nih.gov/refseq/release/vertebrate_other/ *rna*fna*
+INSERT INTO source_url (source_id, species_id, url, file_modified_date, upload_date, parser) VALUES\
+ (4, 7719,'ftp://ftp.ncbi.nih.gov/refseq/release/vertebrate_other/vertebrate_other1.rna.fna.gz',  now(), now(), "RefSeqParser");
+INSERT INTO source_url (source_id, species_id, url, file_modified_date, upload_date, parser) VALUES\
+ (4, 7719,'ftp://ftp.ncbi.nih.gov/refseq/release/vertebrate_other/vertebrate_other2.rna.fna.gz',  now(), now(), "RefSeqParser");
+INSERT INTO source_url (source_id, species_id, url, file_modified_date, upload_date, parser) VALUES\
+ (4, 7719,'ftp://ftp.ncbi.nih.gov/refseq/release/vertebrate_other/vertebrate_other3.rna.fna.gz',  now(), now(), "RefSeqParser");
+INSERT INTO source_url (source_id, species_id, url, file_modified_date, upload_date, parser) VALUES\
+ (4, 7719,'ftp://ftp.ncbi.nih.gov/refseq/release/vertebrate_other/vertebrate_other4.rna.fna.gz',  now(), now(), "RefSeqParser");
+INSERT INTO source_url (source_id, species_id, url, file_modified_date, upload_date, parser) VALUES\
+ (4, 7719,'ftp://ftp.ncbi.nih.gov/refseq/release/vertebrate_other/vertebrate_other5.rna.fna.gz',  now(), now(), "RefSeqParser");
+INSERT INTO source_url (source_id, species_id, url, file_modified_date, upload_date, parser) VALUES\
+ (4, 7719,'ftp://ftp.ncbi.nih.gov/refseq/release/vertebrate_other/vertebrate_other6.rna.fna.gz',  now(), now(), "RefSeqParser");
+INSERT INTO source_url (source_id, species_id, url, file_modified_date, upload_date, parser) VALUES\
+ (4, 7719,'ftp://ftp.ncbi.nih.gov/refseq/release/vertebrate_other/vertebrate_other7.rna.fna.gz',  now(), now(), "RefSeqParser"); 
+
+
+INSERT INTO source_url (source_id, species_id, url, file_modified_date, upload_date, parser)\
+VALUES (3,7227,'ftp://ftp.ncbi.nih.gov/refseq/release/invertebrate/invertebrate1.protein.gpff.gz',now(),now(),'RefSeqGPFFParser');
+
+INSERT INTO source_url (source_id, species_id, url, file_modified_date, upload_date, parser)\
+VALUES (3,7227,'ftp://ftp.ncbi.nih.gov/refseq/release/invertebrate/invertebrate2.protein.gpff.gz',now(),now(),'RefSeqGPFFParser');
+
+INSERT INTO source_url (source_id, species_id, url, file_modified_date, upload_date, parser)\
+VALUES (3,7227,'ftp://ftp.ncbi.nih.gov/refseq/release/invertebrate/invertebrate3.protein.gpff.gz',now(),now(),'RefSeqGPFFParser');
+
+INSERT INTO source_url (source_id, species_id, url, file_modified_date, upload_date, parser)\
+VALUES (3,7227,'ftp://ftp.ncbi.nih.gov/refseq/release/invertebrate/invertebrate4.protein.gpff.gz',now(),now(),'RefSeqGPFFParser');
+
+INSERT INTO source_url (source_id, species_id, url, file_modified_date, upload_date, parser)\
+VALUES (3,7227,'ftp://ftp.ncbi.nih.gov/refseq/release/invertebrate/invertebrate5.protein.gpff.gz',now(),now(),'RefSeqGPFFParser');
+
+INSERT INTO source_url (source_id, species_id, url, file_modified_date, upload_date, parser)\
+VALUES (3,7227,'ftp://ftp.ncbi.nih.gov/refseq/release/invertebrate/invertebrate6.protein.gpff.gz',now(),now(),'RefSeqGPFFParser');
+
+INSERT INTO source_url (source_id, species_id, url, file_modified_date, upload_date, parser)\
+VALUES (3,7227,'ftp://ftp.ncbi.nih.gov/refseq/release/invertebrate/invertebrate7.protein.gpff.gz',now(),now(),'RefSeqGPFFParser');
+
+INSERT INTO source_url (source_id, species_id, url, file_modified_date, upload_date, parser)\
+VALUES (3,7227,'ftp://ftp.ncbi.nih.gov/refseq/release/invertebrate/invertebrate8.protein.gpff.gz',now(),now(),'RefSeqGPFFParser');
+
+INSERT INTO source_url (source_id, species_id, url, file_modified_date, upload_date, parser)\
+VALUES (3,7227,'ftp://ftp.ncbi.nih.gov/refseq/release/invertebrate/invertebrate9.protein.gpff.gz',now(),now(),'RefSeqGPFFParser');
+
+INSERT INTO source_url (source_id, species_id, url, file_modified_date, upload_date, parser)\
+VALUES (3,7227,'ftp://ftp.ncbi.nih.gov/refseq/release/invertebrate/invertebrate10.protein.gpff.gz',now(),now(),'RefSeqGPFFParser');
+
+INSERT INTO source_url (source_id, species_id, url, file_modified_date, upload_date, parser)\
+VALUES (3,7227,'ftp://ftp.ncbi.nih.gov/refseq/release/invertebrate/invertebrate11protein.gpff.gz',now(),now(),'RefSeqGPFFParser');
+
+INSERT INTO source_url (source_id, species_id, url, file_modified_date, upload_date, parser)\
+VALUES (3,7227,'ftp://ftp.ncbi.nih.gov/refseq/release/invertebrate/invertebrate12.protein.gpff.gz',now(),now(),'RefSeqGPFFParser');
+
+INSERT INTO source_url (source_id, species_id, url, file_modified_date, upload_date, parser)\
+VALUES (3,7227,'ftp://ftp.ncbi.nih.gov/refseq/release/invertebrate/invertebrate13.protein.gpff.gz',now(),now(),'RefSeqGPFFParser');
+
+INSERT INTO source_url (source_id, species_id, url, file_modified_date, upload_date, parser)\
+VALUES (3,7227,'ftp://ftp.ncbi.nih.gov/refseq/release/invertebrate/invertebrate14.protein.gpff.gz',now(),now(),'RefSeqGPFFParser');
+
+INSERT INTO source_url (source_id, species_id, url, file_modified_date, upload_date, parser)\
+VALUES (3,7227,'ftp://ftp.ncbi.nih.gov/refseq/release/invertebrate/invertebrate15.protein.gpff.gz',now(),now(),'RefSeqGPFFParser');
+
+
+##       GO
+INSERT INTO source_url (source_id, species_id, url, file_modified_date, upload_date, parser) VALUES\
+(1070, 7719,'ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/UNIPROT/gene_association.goa_uniprot.gz', now(), now(), "GOParser");
+
+##      Interpro
+INSERT INTO source_url (source_id, species_id, url, file_modified_date, upload_date, parser) VALUES\
+(1300, 7719,'ftp://ftp.ebi.ac.uk/pub/databases/interpro/interpro.xml.gz', now(), now(), "InterproParser");
+
+##      UniGene
+INSERT INTO source_url (source_id, species_id, url, file_modified_date, upload_date, parser) VALUES\
+(6, 7719,'ftp://ftp.ncbi.nih.gov/repository/UniGene/Ciona_savignyi/Csa.seq.uniq.gz ftp://ftp.ncbi.nih.gov/repository/UniGene/Ciona_savignyi/Csa.data.gz',  now(), now(), "UniGeneParser");
+
+
+
+
+
 # --------------------------------------------------------------------------------
 
 ###### Anopheles