From a6b3fab398f1004b8e55893d09470f28b1b23a2f Mon Sep 17 00:00:00 2001 From: steve-fischer-200 Date: Fri, 17 Nov 2023 17:57:36 -0500 Subject: [PATCH 01/16] compoundprops; aaseqinfo; epitopesummary --- .../lib/xml/tuningManager/apiTuningManager.xml | 17 ++++++++--------- 1 file changed, 8 insertions(+), 9 deletions(-) diff --git a/Model/lib/xml/tuningManager/apiTuningManager.xml b/Model/lib/xml/tuningManager/apiTuningManager.xml index 07f6c34721..be2d2fb042 100644 --- a/Model/lib/xml/tuningManager/apiTuningManager.xml +++ b/Model/lib/xml/tuningManager/apiTuningManager.xml @@ -1898,7 +1898,7 @@ tablespace indx - + Used by GeneTables.Epitopes to map a gene to its epitopes. @@ -1907,7 +1907,7 @@ tablespace indx - + @@ -5747,7 +5746,7 @@ tablespace indx - + Properties table for ChEBI Compounds. @@ -8488,7 +8487,7 @@ tablespace indx - + Info from dots.ExternalAaSequence records for BLAT alignments @@ -9406,4 +9405,4 @@ tablespace indx ]]> - \ No newline at end of file + From 76506ecda160fcb46eb7cf681221492626e9f40a Mon Sep 17 00:00:00 2001 From: steve-fischer-200 Date: Fri, 17 Nov 2023 18:18:14 -0500 Subject: [PATCH 02/16] genelocations --- Model/lib/xml/tuningManager/apiTuningManager.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Model/lib/xml/tuningManager/apiTuningManager.xml b/Model/lib/xml/tuningManager/apiTuningManager.xml index be2d2fb042..9c6cc7c6ec 100644 --- a/Model/lib/xml/tuningManager/apiTuningManager.xml +++ b/Model/lib/xml/tuningManager/apiTuningManager.xml @@ -8896,7 +8896,7 @@ tablespace indx - + semicolon-delimited list of formatted genomic locations for each gene From 6c54baefefbb41f07f11062f1cc6ff051f495e66 Mon Sep 17 00:00:00 2001 From: steve-fischer-200 Date: Fri, 17 Nov 2023 21:06:06 -0500 Subject: [PATCH 03/16] wip --- .../lib/xml/tuningManager/apiTuningManager.xml | 17 +++++++++++++---- 1 file changed, 13 insertions(+), 4 deletions(-) diff --git a/Model/lib/xml/tuningManager/apiTuningManager.xml b/Model/lib/xml/tuningManager/apiTuningManager.xml index 9c6cc7c6ec..bb30508ad4 100644 --- a/Model/lib/xml/tuningManager/apiTuningManager.xml +++ b/Model/lib/xml/tuningManager/apiTuningManager.xml @@ -1841,7 +1841,7 @@ tablespace indx - + This table maps IDs for a sequence onto the official ID of the sequence. It is analogous to GeneId, which does the same thing for genes. Used by genomic-sequence record queries, by the sequence retrieval tool, and by @@ -1862,7 +1862,16 @@ tablespace indx SELECT ns.source_id as id, ns.source_id as sequence FROM dots.NaSequence ns, sres.OntologyTerm oterm WHERE ns.sequence_ontology_id = oterm.ontology_term_id - AND oterm.name in ('random_sequence', 'contig', 'supercontig', 'chromosome','mitochondrial_chromosome','plastid_sequence','cloned_genomic','apicoplast_chromosome','maxicircle') + AND oterm.source_id in + ('SO:0000449', --random_sequence + 'SO:0000149', --contig + 'SO:0000148', --supercontig + 'SO:0000340', --chromosome + 'SO:0000819', --mitochondrial_chromosome + 'SO:0000740', --plastid_sequence + 'SO:0000791', --cloned_genomic + 'SO:0001259', --apicoplast_chromosome + 'SO:0000742') --maxicirle UNION SELECT dr.primary_identifier AS id, ns.source_id AS sequence FROM dots.NaSequence ns, dots.DbRefNaSequence drnf, @@ -8495,12 +8504,12 @@ tablespace indx From 6a033fee36ed60936e5663dfe4456f8cd40a73e9 Mon Sep 17 00:00:00 2001 From: steve-fischer-200 Date: Sat, 18 Nov 2023 17:08:52 -0500 Subject: [PATCH 04/16] wip --- .../xml/tuningManager/apiTuningManager.xml | 24 ++++++++----------- 1 file changed, 10 insertions(+), 14 deletions(-) diff --git a/Model/lib/xml/tuningManager/apiTuningManager.xml b/Model/lib/xml/tuningManager/apiTuningManager.xml index bb30508ad4..378deb7f0d 100644 --- a/Model/lib/xml/tuningManager/apiTuningManager.xml +++ b/Model/lib/xml/tuningManager/apiTuningManager.xml @@ -3253,11 +3253,10 @@ tablespace indx - + Each row represents one EST. Used widely in the model, and to make the tuning tables BlastTypes, OrganismAbbreviationBlast, and OrganismAttributes. - @@ -3266,12 +3265,10 @@ tablespace indx - - + @@ -8515,7 +8511,7 @@ tablespace indx From 122dab61bd0f24a8a632def6626ba5ea79c3a77b Mon Sep 17 00:00:00 2001 From: steve-fischer-200 Date: Mon, 27 Nov 2023 18:33:39 -0500 Subject: [PATCH 05/16] wip --- .../xml/tuningManager/apiTuningManager.xml | 130 ++++++++---------- 1 file changed, 58 insertions(+), 72 deletions(-) diff --git a/Model/lib/xml/tuningManager/apiTuningManager.xml b/Model/lib/xml/tuningManager/apiTuningManager.xml index 378deb7f0d..d300417935 100644 --- a/Model/lib/xml/tuningManager/apiTuningManager.xml +++ b/Model/lib/xml/tuningManager/apiTuningManager.xml @@ -1504,7 +1504,7 @@ tablespace indx - + GeneId maps any valid ID for a gene onto its official ID. These two quantities are stored in the "id" and "gene" columns, respectively. The "unique_mapping" column is set to 1 for IDs which map to only one gene. @@ -1534,7 +1534,8 @@ tablespace indx @@ -1732,7 +1732,7 @@ tablespace indx regexp_replace(id, '\.\d\d?$', '') as id, gene, unique_mapping, union_member, database_name FROM &prefixGeneId&1 - WHERE regexp_like(id, '(.*)\.\d\d?$')) + WHERE id SIMILAR TO '%.\d\d?') SELECT id, gene, 0 as unique_mapping, 'base ID' as union_member, database_name FROM munge WHERE id NOT IN (SELECT id FROM &prefixGeneId&1) @@ -1857,7 +1857,9 @@ tablespace indx - + Stores (transcript, sequence, distance from centromere) 3-tuples for transcripts that lie on a sequence for which we have a centomere location. @@ -1966,7 +1969,7 @@ tablespace indx @@ -2098,10 +2101,11 @@ tablespace indx - + Stores, for each transcript, a string containing the gene-relative coordinates of all its introns and UTRs. @@ -2893,7 +2897,8 @@ tablespace indx - - - @@ -3136,6 +3134,7 @@ tablespace indx Each record represents one SNP. Widely used in the model, as well as in the creation of several other tuning tables, Includes only NGS SNPs. + @@ -3156,9 +3155,9 @@ tablespace indx AS (SELECT feature_source_id, is_reversed, na_feature_id FROM apidb.FeatureLocation WHERE is_top_level = 1 and feature_type = 'GeneFeature') - SELECT chromosome_info.project_id, + SELECT '&ORG_ABBREV' as org_abbrev, + '&PROJECT_ID' as project_id, ed.name as dataset, - sequence.na_sequence_id, sequence.source_id as seq_source_id, snp.location, snp.source_id, @@ -3186,11 +3185,9 @@ tablespace indx coalesce(stop_codon_snps.has_stop_codon, 0) AS has_stop_codon, case when snp.reference_aa is null then 1 else 0 end as is_noncoding_snp, fl.feature_source_id as gene_source_id, - fl.na_feature_id as gene_na_feature_id, CASE fl.is_reversed WHEN 0 THEN 'forward' WHEN 1 THEN 'reverse' ELSE null END as gene_strand, CAST(SUBSTR(sequence.sequence, snp.location::integer - 30, 30) AS VARCHAR(30)) AS lflank, CAST(SUBSTR(sequence.sequence, snp.location::integer + 1, 30) AS VARCHAR(30)) AS rflank, - chromosome_info.organism as organism, chromosome_info.ncbi_tax_id, chromosome_info.chromosome, chromosome_info.chromosome_order_num @@ -3226,7 +3223,7 @@ tablespace indx @@ -3239,7 +3236,7 @@ tablespace indx @@ -3269,6 +3266,7 @@ tablespace indx - + Like dots.SimilaritySpan, except that for sequences that are mapped by SequencePiece into parts of other sequences, both locations are stored. Used by GBrowse, and also in the creation of the Blastx tuning table. @@ -4027,7 +4025,8 @@ tablespace indx - + SNP Chip only, such as Plasmo barcode, 3k_chp and hd_array Each record represents one SNP. Widely used in the model, as well as in the creation of several other tuning tables - @@ -4118,18 +4117,16 @@ tablespace indx - - - - @@ -4223,20 +4210,20 @@ tablespace indx - + this otherwise-unneeded tuning table, which depends on SnpAttributesDoTS, exists so that the view SnpChipAttributes can be created as a side-effect @@ -4582,26 +4569,23 @@ tablespace indx - - Each record stores the nucleotide sequence of an EST, for use by the + + Each record stores the nucleotide sequence of an EST, as well as project_id, for use by the relevant attribute query in the WDK EST record. Propagated to portal instances. - - @@ -5751,7 +5735,7 @@ tablespace indx - + Properties table for ChEBI Compounds. @@ -8500,7 +8484,8 @@ tablespace indx Date: Mon, 27 Nov 2023 18:57:53 -0500 Subject: [PATCH 06/16] wip --- Model/lib/xml/tuningManager/apiTuningManager.xml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Model/lib/xml/tuningManager/apiTuningManager.xml b/Model/lib/xml/tuningManager/apiTuningManager.xml index d300417935..5b92dd1e6a 100644 --- a/Model/lib/xml/tuningManager/apiTuningManager.xml +++ b/Model/lib/xml/tuningManager/apiTuningManager.xml @@ -3969,7 +3969,7 @@ tablespace indx - + Each record maps a gene onto a subcellular location. Used by GenesBySubcellularLocalization. @@ -3980,7 +3980,7 @@ tablespace indx Date: Tue, 28 Nov 2023 21:31:13 -0500 Subject: [PATCH 07/16] wip --- .../xml/tuningManager/apiTuningManager.xml | 139 +++--------------- 1 file changed, 17 insertions(+), 122 deletions(-) diff --git a/Model/lib/xml/tuningManager/apiTuningManager.xml b/Model/lib/xml/tuningManager/apiTuningManager.xml index 6e5b23a099..b92a0925c0 100644 --- a/Model/lib/xml/tuningManager/apiTuningManager.xml +++ b/Model/lib/xml/tuningManager/apiTuningManager.xml @@ -51,7 +51,7 @@ - + Locations and Sequence of Signal Peptide Domains (SignalP) @@ -65,12 +65,11 @@ @@ -1986,12 +1985,10 @@ tablespace indx - + The BFMV for proteins. Each protein gets a single record, which stores all its attributes. Used mainly to create TranscriptAttributes - - @@ -2006,100 +2003,16 @@ tablespace indx - - - - - - - - - - - - - - - From 9476a4412b5af3919292bcce4eb1643a8b1b212e Mon Sep 17 00:00:00 2001 From: steve-fischer-200 Date: Wed, 29 Nov 2023 19:31:03 -0500 Subject: [PATCH 08/16] wpa --- .../xml/tuningManager/apiTuningManager.xml | 177 +++--------------- 1 file changed, 30 insertions(+), 147 deletions(-) diff --git a/Model/lib/xml/tuningManager/apiTuningManager.xml b/Model/lib/xml/tuningManager/apiTuningManager.xml index b92a0925c0..738cbdb059 100644 --- a/Model/lib/xml/tuningManager/apiTuningManager.xml +++ b/Model/lib/xml/tuningManager/apiTuningManager.xml @@ -2110,7 +2110,7 @@ tablespace indx - + The BFMV for the gene record. Each gene gets a single record, which stores all its attributes. Used widely, in the model and elsewhere, for queries involving genes, as well as in the creation of more than a @@ -2120,9 +2120,7 @@ tablespace indx - - @@ -2177,11 +2175,11 @@ tablespace indx @@ -2492,7 +2451,7 @@ tablespace indx @@ -2500,49 +2459,26 @@ tablespace indx - - - - - - - - - - - + - - - - - - @@ -2630,7 +2512,7 @@ tablespace indx @@ -2892,7 +2774,7 @@ tablespace indx - + A single product string per gene @@ -2908,14 +2790,14 @@ tablespace indx from (select distinct gf.source_id, gfp.product from dots.GeneFeature gf, apidb.GeneFeatureProduct gfp where gfp.na_feature_id = gf.na_feature_id - and gfp.is_preferred = 1) + and gfp.is_preferred = 1) sub group by source_id), gfp_any as (select source_id, substr(STRING_AGG(product, ', ' order by product), 1, 4000) as product from (select distinct gf.source_id, gfp.product from dots.GeneFeature gf, apidb.GeneFeatureProduct gfp - where gfp.na_feature_id = gf.na_feature_id) + where gfp.na_feature_id = gf.na_feature_id) sub group by source_id), tp_preferred as (select source_id, @@ -2924,7 +2806,7 @@ tablespace indx from dots.GeneFeature gf, dots.Transcript t, apidb.TranscriptProduct tp where t.parent_id = gf.na_feature_id and tp.na_feature_id = t.na_feature_id - and tp.is_preferred = 1) + and tp.is_preferred = 1) sub group by source_id), gf_product as (select source_id, product @@ -2936,7 +2818,7 @@ tablespace indx from (select distinct gf.source_id, tp.product from dots.GeneFeature gf, dots.Transcript t, apidb.TranscriptProduct tp where t.parent_id = gf.na_feature_id - and tp.na_feature_id = t.na_feature_id) + and tp.na_feature_id = t.na_feature_id) sub group by source_id), t_product as (select source_id, @@ -2944,9 +2826,10 @@ tablespace indx from (select gf.source_id, t.product from dots.GeneFeature gf, dots.Transcript t where t.parent_id = gf.na_feature_id - and t.product is not null) - group by source_id) - select gf.source_id, + and t.product is not null) sub + group by source_id) + select '&ORG_ABBREV' as org_abbrev, + gf.source_id, coalesce(gfp_preferred.product, gfp_any.product, tp_preferred.product, gf.product, tp_any.product, t_product.product) as product @@ -3163,7 +3046,7 @@ tablespace indx - + Each record represents one SNP. Widely used in the model, as well as in the creation of several other tuning tables, Includes only NGS SNPs. @@ -3236,7 +3119,7 @@ tablespace indx WHERE edr.external_database_release_id = snp.external_database_release_id AND ed.external_database_id = edr.external_database_id AND sequence.na_sequence_id = snp.na_sequence_id - AND chromosome_info.na_sequence_id = snp.na_sequence_id + AND chromosome_info.source_id = sequence.source_id -- WAS chromosome_info.na_sequence_id = snp.na_sequence_id ORDER BY edr.external_database_release_id, sequence.na_sequence_id, snp.location ]]> From bf92776caf0204d485c8b3a93733eae7f3efd544 Mon Sep 17 00:00:00 2001 From: steve-fischer-200 Date: Thu, 30 Nov 2023 07:18:02 -0500 Subject: [PATCH 09/16] wip --- .../xml/tuningManager/apiTuningManager.xml | 45 ++++++++++--------- 1 file changed, 25 insertions(+), 20 deletions(-) diff --git a/Model/lib/xml/tuningManager/apiTuningManager.xml b/Model/lib/xml/tuningManager/apiTuningManager.xml index 738cbdb059..65adf51cac 100644 --- a/Model/lib/xml/tuningManager/apiTuningManager.xml +++ b/Model/lib/xml/tuningManager/apiTuningManager.xml @@ -3,7 +3,7 @@ - + Locations and Sequence of Transmembrane Domains (TMHMM) @@ -14,22 +14,22 @@ @@ -1435,7 +1435,7 @@ - + Each record maps a gene to a PDB structure. Used by the model to find genes that have a PDB structure and to find the PDB structures for a given gene. @@ -1443,14 +1443,15 @@ + - @@ -2216,6 +2217,7 @@ tablespace indx gloc.locations AS gene_locations, -- next the transcript attributes: t.source_id AS transcript_source_id, + t.na_feature_id as internal_feature_id, tso.source_id as transcript_so_id, CAST(coalesce(preferred_tx_product.product, any_tx_product.product, t.product, @@ -8620,12 +8622,13 @@ tablespace indx - + for TranscriptAttributes.InterproColumns + @@ -8655,7 +8658,7 @@ tablespace indx SELECT DISTINCT dr.primary_identifier as primary_id, dr.remark, xd1.name as interpro_name, ta.source_id - FROM TranscriptAttributes ta, dots.AaLocation al, + FROM TranscriptAttributes ta, dots.AaLocation al, dots.TranslatedAASequence tas, sres.ExternalDatabaseRelease xdr1, sres.ExternalDatabase xd1, sres.ExternalDatabaseRelease xdr3, sres.ExternalDatabase xd3, sres.DbRef dr, dots.DbRefAaFeature draf, dots.DomainFeature df @@ -8665,7 +8668,8 @@ tablespace indx 'PFAM', 'PIRSF', 'PROSITEPROFILES', 'SMART', 'SUPERFAMILY', 'TIGRFAM' ) - AND ta.aa_sequence_id = df.aa_sequence_id + AND ta.protein_source_id = tas.source_id + AND tas.aa_sequence_id = df.aa_sequence_id AND df.aa_feature_id = draf.aa_feature_id AND df.aa_feature_id = al.aa_feature_id AND draf.db_ref_id = dr.db_ref_id @@ -8676,7 +8680,8 @@ tablespace indx ) t GROUP BY source_id ) - SELECT source_id, + SELECT '&ORG_ABBREV' as org_abbrev, + source_id, substr(interpro_id, 1, 200)||substr(interpro2_id, 1, 200) as interpro_id, substr(interpro_description, 1, 3000)||substr(interpro2_description, 1, 3000) as interpro_description, substr(pfam_id, 1, 200) as pfam_id, From 7ab70161aa43c35cd771413db620d25d4abf6e60 Mon Sep 17 00:00:00 2001 From: steve-fischer-200 Date: Thu, 30 Nov 2023 15:22:42 -0500 Subject: [PATCH 10/16] wip --- .../xml/tuningManager/apiTuningManager.xml | 22 ++++++++++--------- 1 file changed, 12 insertions(+), 10 deletions(-) diff --git a/Model/lib/xml/tuningManager/apiTuningManager.xml b/Model/lib/xml/tuningManager/apiTuningManager.xml index 65adf51cac..9b546bdf86 100644 --- a/Model/lib/xml/tuningManager/apiTuningManager.xml +++ b/Model/lib/xml/tuningManager/apiTuningManager.xml @@ -634,7 +634,7 @@ - + GeneGoTerms: each row represents one GO term assignment to one gene, right from what was loaded. @@ -642,17 +642,18 @@ + @@ -2217,7 +2219,7 @@ tablespace indx gloc.locations AS gene_locations, -- next the transcript attributes: t.source_id AS transcript_source_id, - t.na_feature_id as internal_feature_id, + '&ORG_ABBREV_' || t.na_feature_id as internal_feature_id, tso.source_id as transcript_so_id, CAST(coalesce(preferred_tx_product.product, any_tx_product.product, t.product, @@ -2480,15 +2482,15 @@ tablespace indx TABLESPACE INDX ]]> - Date: Thu, 30 Nov 2023 15:56:01 -0500 Subject: [PATCH 11/16] wip --- .../xml/tuningManager/apiTuningManager.xml | 24 +++++++++---------- 1 file changed, 12 insertions(+), 12 deletions(-) diff --git a/Model/lib/xml/tuningManager/apiTuningManager.xml b/Model/lib/xml/tuningManager/apiTuningManager.xml index 9b546bdf86..7710ab92c4 100644 --- a/Model/lib/xml/tuningManager/apiTuningManager.xml +++ b/Model/lib/xml/tuningManager/apiTuningManager.xml @@ -29,7 +29,7 @@ , dots.translatedaafeature taf , dots.translatedaasequence tas , dots.transmembraneaafeature tmf - WHERE ta.internal_feature_id = taf.na_feature_id + WHERE ta.internal_feature_id = '&ORG_ABBREV_' || taf.na_feature_id AND taf.aa_sequence_id = tas.aa_sequence_id AND tas.aa_sequence_id = tmf.aa_sequence_id and tmf.aa_feature_id = aal.aa_feature_id @@ -675,8 +675,8 @@ , sres.ExternalDatabase xd3 , sres.DbRef dr , dots.DbRefAaFeature draf - , dots.DomainFeature df , dots.AASequence aas + , dots.DomainFeature df LEFT JOIN dots.DomainFeature df2 ON df.parent_id = df2.aa_feature_id WHERE xd3.name IN('InterproscanData_RSRC', 'INTERPRO', 'Prints', 'HAMAP', 'SFLD', 'TIGRFAM', 'SUPERFAMILY', 'Pfam', 'PIRSF', 'PROSITE patterns', 'Superfamily', 'PRINTS', 'InterProScan', 'PFAM', 'SMART', 'CDD', 'PANTHER') AND ta.protein_source_id = aas.source_id @@ -2183,6 +2183,7 @@ tablespace indx t.source_id, -- first the gene attributes: gf.source_id AS gene_source_id, + '&ORG_ABBREV_' || gf.na_feature_id AS gene_internal_feature_id, LEAST(nl.start_min, nl.end_max) AS gene_start_min, GREATEST(nl.start_min, nl.end_max) AS gene_end_max, COALESCE(preferred_name.name, any_name.name) AS gene_name, @@ -6791,7 +6792,7 @@ tablespace indx - + @@ -6800,29 +6801,28 @@ tablespace indx = 1.5 ) t GROUP BY gene_source_id, project_id, sequence_id, haplotype_block_name, - start_min, end_max, start_max, end_min, organism + start_min, end_max, start_max, end_min ]]> From c2133c7f354490ac684bbf5458eaf1cd641027f2 Mon Sep 17 00:00:00 2001 From: steve-fischer-200 Date: Thu, 30 Nov 2023 20:19:07 -0500 Subject: [PATCH 12/16] wip --- .../xml/tuningManager/apiTuningManager.xml | 151 ++++++------------ 1 file changed, 52 insertions(+), 99 deletions(-) diff --git a/Model/lib/xml/tuningManager/apiTuningManager.xml b/Model/lib/xml/tuningManager/apiTuningManager.xml index 7710ab92c4..7002c9b849 100644 --- a/Model/lib/xml/tuningManager/apiTuningManager.xml +++ b/Model/lib/xml/tuningManager/apiTuningManager.xml @@ -2248,7 +2248,7 @@ tablespace indx edr.version AS external_db_version, CAST(gsa.chromosome AS VARCHAR(20)) AS chromosome, gsa.so_id as sequence_so_id, - gsa.chromosome_order_num, gsa.source_id as na_seq_source_id, + gsa.chromosome_order_num, --next the protein attributes: pa.source_id AS protein_source_id, pa.cds_start as coding_start, @@ -2535,62 +2535,63 @@ tablespace indx = 20 - GROUP BY atr.gene_source_id, atr.source_id, atr.taxon_id, atr.organism, ltr.transcript_novelty, ltr.transcript_length + GROUP BY atr.gene_source_id, atr.source_id, atr.ncbi_tax_id, atr.organism, ltr.transcript_novelty, ltr.transcript_length ) t WHERE total_reads >= 5 UNION - SELECT atr.gene_source_id, atr.source_id, atr.taxon_id, + SELECT atr.gene_source_id, atr.source_id, atr.ncbi_tax_id, 'intron_junction' as ontology_term_name, it.string_value string_value, null as number_value FROM @@ -2610,7 +2611,7 @@ tablespace indx , TranscriptAttributes atr WHERE it.gene_source_id = atr.gene_source_id UNION - SELECT atr.gene_source_id, atr.source_id, atr.taxon_id, + SELECT atr.gene_source_id, atr.source_id, atr.ncbi_tax_id, 'Unique_reads' as ontology_term_name, null as string_value , gj.total_unique number_value FROM GeneIntronJunction gj @@ -2622,7 +2623,7 @@ tablespace indx @@ -2855,19 +2856,17 @@ tablespace indx - + The BFMV for the gene record. Each gene gets a single record, which stores all its attributes. - - - - - - - - - - - - - @@ -4300,7 +4251,7 @@ tablespace indx - + Each record stores the transcript sequence of one gene. Used by the gene record and the sequence retrieval tool. Propagated to the portal. @@ -4309,7 +4260,7 @@ tablespace indx @@ -4323,7 +4274,7 @@ tablespace indx - + Each record stores the coding sequence of one gene. Used by the gene record and the sequence retrieval tool. Propagated to the portal. @@ -4333,12 +4284,12 @@ tablespace indx @@ -4350,24 +4301,24 @@ tablespace indx - + Each record stores the coding sequence of one gene. Used by the gene record and the sequence retrieval tool, as well as by buildTrackOldAnnotationTT. Propagated to the portal. - @@ -8192,7 +8143,7 @@ tablespace indx - + Materialization of GeneTables.GeneModelDump. @@ -8204,10 +8155,12 @@ tablespace indx From 23f9573a2c0edd59c182c3bd1e0e9f8470cb4882 Mon Sep 17 00:00:00 2001 From: steve-fischer-200 Date: Fri, 1 Dec 2023 14:59:49 -0500 Subject: [PATCH 13/16] wip --- .../xml/tuningManager/apiTuningManager.xml | 101 +++++++++--------- 1 file changed, 51 insertions(+), 50 deletions(-) diff --git a/Model/lib/xml/tuningManager/apiTuningManager.xml b/Model/lib/xml/tuningManager/apiTuningManager.xml index 7002c9b849..911091155b 100644 --- a/Model/lib/xml/tuningManager/apiTuningManager.xml +++ b/Model/lib/xml/tuningManager/apiTuningManager.xml @@ -1023,7 +1023,7 @@ WITH profiles AS ( SELECT p.source_id, ga.project_id, - ga.sequence_id, + ga.na_sequence_source_id, d.name, row_number() over(partition by d.name order by ga.chromosome_order_num, p.profile_as_string desc) as rn @@ -2012,10 +2012,11 @@ tablespace indx SELECT '&ORG_ABBREV' as org_abbrev, '&PROJECT_ID' as project_id, - tas.source_id, + tas.source_id as source_id, -- not sure what is best, so keeping both these source_ids + tas.source_id as aa_sequence_source_id, t.source_id as transcript_source_id, gf.source_id as gene_source_id, - cdsl.sequence_source_id as cds_seq_source_id, + cdsl.sequence_source_id as na_sequence_source_id, cdsl.is_reversed, cdsl.start_min as cds_start, cdsl.end_max as cds_end, @@ -2101,12 +2102,12 @@ tablespace indx @@ -2180,7 +2181,6 @@ tablespace indx SELECT DISTINCT '&ORG_ABBREV' as org_abbrev, '&PROJECT_ID' as project_id, - t.source_id, -- first the gene attributes: gf.source_id AS gene_source_id, '&ORG_ABBREV_' || gf.na_feature_id AS gene_internal_feature_id, @@ -2219,7 +2219,7 @@ tablespace indx entrez_table.entrez_id AS gene_entrez_id, gloc.locations AS gene_locations, -- next the transcript attributes: - t.source_id AS transcript_source_id, + t.source_id, '&ORG_ABBREV_' || t.na_feature_id as internal_feature_id, tso.source_id as transcript_so_id, CAST(coalesce(preferred_tx_product.product, any_tx_product.product, @@ -2236,8 +2236,9 @@ tablespace indx CASE coalesce(tl.is_reversed, 0) WHEN 0 THEN 'forward' WHEN 1 THEN 'reverse' ELSE tl.is_reversed::varchar END AS strand, CASE t.is_pseudo WHEN null THEN 0 ELSE t.is_pseudo END as is_pseudo, transcript_exons.exon_count, - sns.length AS length, sns.source_id as spliced_na_seq_source_id, - CAST(gsa.source_id AS VARCHAR(50)) AS sequence_id, + sns.length AS length, + sns.source_id as spliced_na_seq_source_id, + CAST(gsa.source_id AS VARCHAR(50)) AS na_sequence_source_id, gsa.ncbi_tax_id, so.source_id as so_id, CAST(so.name AS VARCHAR(150)) AS so_term_name, @@ -2250,7 +2251,8 @@ tablespace indx gsa.so_id as sequence_so_id, gsa.chromosome_order_num, --next the protein attributes: - pa.source_id AS protein_source_id, + pa.source_id as protein_source_id, + pa.aa_sequence_source_id as aa_sequence_source_id, pa.cds_start as coding_start, pa.cds_end as coding_end, pa.cds_length, @@ -2456,7 +2458,7 @@ tablespace indx @@ -2479,7 +2481,7 @@ tablespace indx @@ -2502,7 +2504,7 @@ tablespace indx @@ -2517,7 +2519,7 @@ tablespace indx @@ -2871,7 +2873,7 @@ tablespace indx , gene_start_min AS start_min , gene_end_max AS end_max , CASE strand WHEN 'forward' THEN '+' WHEN 'reverse' THEN '-' ELSE null END as strand_plus_minus - , sequence_id + , na_sequence_source_id , gene_name AS name , COALESCE(aggregates.product, aggregates.transcript_product) as old_product , gp.product @@ -2953,21 +2955,21 @@ tablespace indx @@ -2995,7 +2997,7 @@ tablespace indx @@ -3030,7 +3032,7 @@ tablespace indx SELECT '&ORG_ABBREV' as org_abbrev, '&PROJECT_ID' as project_id, ed.name as dataset, - sequence.source_id as seq_source_id, + sequence.source_id as sequence_source_id, snp.location, snp.source_id, snp.reference_strain, @@ -3095,7 +3097,7 @@ tablespace indx @@ -3225,7 +3227,7 @@ tablespace indx WHERE e.na_sequence_id = ba.query_na_sequence_id AND aseq.na_sequence_id = ba.query_na_sequence_id AND sequence.na_sequence_id = ba.target_na_sequence_id - AND ga.sequence_id = sequence.source_id + AND ga.na_sequence_source_id = sequence.source_id AND least(ba.target_end, ga.gene_end_max) - greatest(ba.target_start, ga.gene_start_min) >= 0 AND query_sequence.na_sequence_id = ba.query_na_sequence_id AND query_sequence.sequence_ontology_id = so.ontology_term_id @@ -3918,7 +3920,7 @@ tablespace indx ed.name AS dataset, snp.name as type, ds.subtype as platform, - sequence.source_id AS seq_source_id, + sequence.source_id AS sequence_source_id, snp_loc.start_min, SUBSTR(snp.reference_strain, 1, 200) AS reference_strain, SUBSTR(snp.reference_na, 1, 200) AS reference_na, @@ -3988,7 +3990,7 @@ tablespace indx @@ -4041,48 +4043,47 @@ tablespace indx - + Each record stores a Blastp similarity of a gene. Used by the gene-page Blastp table. - + @@ -4312,18 +4313,18 @@ tablespace indx @@ -6611,15 +6612,15 @@ tablespace indx WITH rnaseqgenes AS ( SELECT p.DATASET_NAME , p.source_id as gene_source_id - , ga.sequence_id as sequence_id + , ga.na_sequence_source_id as sequence_id , row_number() over (partition by p.dataset_name - order by p.max_value, p.source_id, ga.sequence_id) as rn + order by p.max_value, p.source_id, ga.na_sequence_source_id) as rn FROM profile p, geneattributes ga WHERE dataset_type = 'transcript_expression' and dataset_subtype = 'rnaseq' AND p.source_id = ga.source_id ), proteomicsgenes as ( SELECT ga.gene_source_id, - ga.SEQUENCE_ID, + ga.na_sequence_source_id, ga.protein_source_id, d.name, row_number() over(partition by d.name @@ -6645,7 +6646,7 @@ tablespace indx , dnt.name , dsp.name as dataset_presenter_name , sa.source_id as sequence_source_id - , pg.sequence_id as p_sequence_source_id +G , pg.sequence_id as p_sequence_source_id , pg.gene_source_id as p_gene_id , pg.protein_source_id as p_protein_id , rg.sequence_id as r_sequence_source_id @@ -8161,7 +8162,7 @@ tablespace indx string_agg(transcript_id, ',' ORDER BY transcript_id) AS transcript_ids FROM ( SELECT distinct ta.source_id as transcript_id, ta.gene_source_id as source_id, - ta.sequence_id,gm.start_min as gm_start, gm.end_max as gm_end, + ta.na_sequence_source_id as sequence_id, gm.start_min as gm_start, gm.end_max as gm_end, gm.type, gl.is_reversed FROM apidb.FeatureLocation gl, dots.NaSequence s, @@ -8723,14 +8724,14 @@ tablespace indx @@ -9117,7 +9118,7 @@ tablespace indx AND d.external_database_release_id = edr.external_database_release_id AND db.db_ref_id = d.db_ref_id AND na.na_feature_id = db.na_feature_id - AND (ta.transcript_source_id = na.source_id OR ta.gene_source_id = na.source_id) + AND (ta.source_id = na.source_id OR ta.gene_source_id = na.source_id) ]]> From c64104aadb5342addef0e2c9437299b7ae7fc438 Mon Sep 17 00:00:00 2001 From: steve-fischer-200 Date: Mon, 11 Dec 2023 15:36:34 -0500 Subject: [PATCH 14/16] wrapped up org specific TTs --- .../xml/tuningManager/apiTuningManager.xml | 129 ++++++++++-------- 1 file changed, 69 insertions(+), 60 deletions(-) diff --git a/Model/lib/xml/tuningManager/apiTuningManager.xml b/Model/lib/xml/tuningManager/apiTuningManager.xml index 911091155b..13a6a7e02f 100644 --- a/Model/lib/xml/tuningManager/apiTuningManager.xml +++ b/Model/lib/xml/tuningManager/apiTuningManager.xml @@ -1049,7 +1049,7 @@ - @@ -2132,25 +2131,18 @@ tablespace indx - - - - - - - - + Each row represents a colocated EST alignment - gene pair. Used by the model, by generateGeneMetrics, and in the creation of the OrganismAttributes tuning table @@ -3205,16 +3197,22 @@ tablespace indx + = 0 AND query_sequence.na_sequence_id = ba.query_na_sequence_id AND query_sequence.sequence_ontology_id = so.ontology_term_id - AND so.name = 'EST' - AND ba.target_na_sequence_id = sequence.na_sequence_id + AND so.source_id = 'SO:0000345' --EST + AND ba.target_na_sequence_id = target_sequence.na_sequence_id + AND sequence.source_id = target_sequence.source_id + AND ba.query_taxon_id = t.taxon_id ]]> @@ -3697,22 +3706,22 @@ tablespace indx - + Used by gene queries, as well as by generateGeneMetrics. Also an input to OrganismAttributes. + @@ -4132,7 +4143,8 @@ tablespace indx - + Each record stores the nucleotide sequence for one genomic sequence that is "official" (in the sense that it can be instantiated as a WDK sequence record. Used by generatePathoLogicFile and the sequence retrieval tool Propagated to portal instances. - - @@ -8151,8 +8160,6 @@ G , pg.sequence_id as p_sequence_source_id - - - + for GeneTables.RodMalPhenotypeTable @@ -8422,7 +8429,7 @@ G , pg.sequence_id as p_sequence_source_id AS (SELECT DISTINCT ga.source_id, ga.project_id, pm.source_id as rmgmid, pm.pubmed_id, pm.modification_type as mod_type, pm.is_successful as suc_of_gen_mod, - pm.mutation_description, ot.name, + pm.mutation_description, ot.source_id as ontology_source_id, SUBSTR(pr.phenotype_post_composition, 4000, 1) as phenotype1, SUBSTR(pr.phenotype_post_composition, 4000, 4001) as phenotype2, pm.has_multiple_mutations AS multiple, na.NA_FEATURE_ID as id, @@ -8434,7 +8441,7 @@ G , pg.sequence_id as p_sequence_source_id apidb.NaFeaturePhenotypeModel na WHERE pm.phenotype_model_id = pr.phenotype_model_id AND na.phenotype_model_id = pm.phenotype_model_id - AND na.na_feature_id = ga.na_feature_id + AND '&ORG_ABBREV_' || na.na_feature_id = ga.internal_feature_id ), knockdown AS (SELECT DISTINCT genes.source_id, mods.phenotype_model_id as model_id @@ -8444,7 +8451,7 @@ G , pg.sequence_id as p_sequence_source_id AND m.phenotype_model_id = nod.phenotype_model_id AND mods.phenotype_model_id = nod.phenotype_model_id AND m.id != nod.na_feature_id - AND genes.na_feature_id = nod.na_feature_id + AND genes.internal_feature_id = '&ORG_ABBREV_' || nod.na_feature_id AND m.source_id != genes.source_id -- AND mods.has_multiple_mutations = 1 ), @@ -8459,7 +8466,7 @@ G , pg.sequence_id as p_sequence_source_id ELSE 'YES' END AS suc_of_gen_mod, CAST(m.mutation_description AS VARCHAR(150)) AS mutation_description, - CAST(string_agg(m.name, ', ' ORDER BY m.name) + CAST(string_agg(m.ontology_source_id, ', ' ORDER BY m.ontology_source_id) AS VARCHAR(250)) AS life_cycle_stage, CONCAT(phenotype1,phenotype2) AS phenotype, m.phenotype_model_id @@ -8468,7 +8475,7 @@ G , pg.sequence_id as p_sequence_source_id m.suc_of_gen_mod, m.mutation_description, m.phenotype1, m.phenotype2,m.phenotype_model_id ) - SELECT results.*, + SELECT '&ORG_ABBREV' as org_abbrev, results.*, CAST(knockdown.source_id AS VARCHAR(30)) as other_source_id FROM results LEFT JOIN knockdown ON results.phenotype_model_id = knockdown.model_id @@ -8713,6 +8720,7 @@ G , pg.sequence_id as p_sequence_source_id + @@ -8723,8 +8731,8 @@ G , pg.sequence_id as p_sequence_source_id @@ -9051,7 +9060,7 @@ G , pg.sequence_id as p_sequence_source_id - + Links AlphaFold entries to gene ids where Uniprot ids are directly assigned @@ -9073,7 +9082,7 @@ G , pg.sequence_id as p_sequence_source_id Date: Fri, 29 Dec 2023 09:11:08 -0500 Subject: [PATCH 15/16] w.i.p. --- Model/lib/xml/tuningManager/apiTuningManager.xml | 16 ++++++++-------- Model/vp2TuningTablesEffort/tableGroups.yml | 15 +++++++++++++++ 2 files changed, 23 insertions(+), 8 deletions(-) diff --git a/Model/lib/xml/tuningManager/apiTuningManager.xml b/Model/lib/xml/tuningManager/apiTuningManager.xml index 13a6a7e02f..a497d051dd 100644 --- a/Model/lib/xml/tuningManager/apiTuningManager.xml +++ b/Model/lib/xml/tuningManager/apiTuningManager.xml @@ -169,7 +169,7 @@ - + Attributes for Metabolic Pathways @@ -580,7 +580,7 @@ - + the max and min depth of each ontology term in OntologyRelationship. Used by the GoTermSummary tuning table @@ -5537,7 +5537,7 @@ tablespace indx - + Properties table for ChEBI Compounds. @@ -5574,7 +5574,7 @@ tablespace indx - + The BFMV for the compound WDK record type. Used by the model for the compound record and queries, as well as in the creation of the PathwayCompounds tuning table. Propagated to portal instances. @@ -5610,7 +5610,7 @@ tablespace indx - + Alias table for Compounds. Compound column is the source_id from CompoundAttributes (chEBI_ID). ID can have this same ID, or mapping KEGG ID, or Name, or Synonym. @@ -5659,7 +5659,7 @@ tablespace indx - + Each record represents a 5-tuple of (reaction, compound, pathway, enzyme, type). Used extensively in the model for pathway-related queries, as well as by getImageMap.pl. @@ -5763,7 +5763,7 @@ tablespace indx - + Aggregates reactions irrespective of pathway. Required to determine if BioCyc reactions are reversible. Used extensively in the model in conjunction with pathwaycompounds for pathway related queries @@ -6291,7 +6291,7 @@ tablespace indx - + for use in GenesByReactionCompounds question diff --git a/Model/vp2TuningTablesEffort/tableGroups.yml b/Model/vp2TuningTablesEffort/tableGroups.yml index 00950515ae..f8291b0ec6 100644 --- a/Model/vp2TuningTablesEffort/tableGroups.yml +++ b/Model/vp2TuningTablesEffort/tableGroups.yml @@ -2,6 +2,7 @@ ID: 1 queries: datasetVQ.extDbNames tables: apidb.datasource +comment: do not need apidb.datasource (redundant) --- ID: 2 queries: organismVQ.CNV @@ -14,58 +15,72 @@ tables: 'apidb.datasource, sres.taxon, sres.taxonname' ID: 4 queries: GeneId.GenesBySequenceSourceId tables: apidb.featurelocation +comment: add a view for this. should include onto source id. --- ID: 5 queries: SequenceTables.Centromere tables: 'apidb.featurelocation, sres.ontologyterm' +comment: use above view --- ID: 6 queries: 'GeneVQ.MetadataQuery_ncraOR74A_phenotype_GeneImage_NAFeaturePhenotypeImage_RSRC, GeneVQ.OntologyQuery_ncraOR74A_phenotype_GeneImage_NAFeaturePhenotypeImage_RSRC, GeneVQ.MetadataQuery_PHI-base_curated_phenotype_NAFeaturePhenotypeGeneric_RSRC, GeneVQ.OntologyQuery_PHI-base_curated_phenotype_NAFeaturePhenotypeGeneric_RSRC' tables: 'apidb.nafeaturephenotype, study.study, study.studylink' +comment: create new view. should be able to join the study stuff in orgDB. (not CNV, SNP, antibodymicroarry, chipchip, chipseq) --- ID: 7 queries: GeneId.GenesByOldAnnotation tables: apidb.oldannotation +comment: create new view. is this only used by jbrowse, if so, use gff instead. --- ID: 8 queries: 'GeneVQ.MetadataQuery_pberANKA_phenotype_Bushnell_functional_profiling_RSRC, GeneVQ.PhenotypeGrowthRate' tables: apidb.phenotypegrowthrate +comment: create new view. --- ID: 9 queries: GeneVQ.MetadataQuery_ncraOR74A_phenotype_knockout_mutants_RSRC tables: apidb.phenotypemutants +comment: create new view. --- ID: 10 queries: 'GeneVQ.MetadataQuery_PhenotypeScore, GeneVQ.OntologyQuery_PhenotypeScore' tables: 'apidb.phenotypescore, sres.externaldatabase, sres.externaldatabaserelease, study.protocolappnode, study.study, study.studylink' +comment: create new tuning table. this is pure orgDB. --- ID: 11 queries: GeneVQ.PhenotypeScoreDataset tables: 'apidb.phenotypescore, sres.externaldatabase, sres.externaldatabaserelease, study.study, study.studylink' +comment: same table as above --- ID: 12 queries: rflpGenotypeVQ.withIsolates tables: apidb.rflpgenotype +comment: make new view --- ID: 13 queries: CommentTables.GeneComments tables: 'apidbtuning.annotatedgenomesummary, apidbtuning.geneattributes, apidbtuning.transcriptattributes, dots.dbrefnafeature, sres.dbref, sres.externaldatabase, sres.externaldatabaserelease' +comment: what is this query doing? --- ID: 14 queries: GeneAttributes.OrganismAbbrev tables: 'apidbtuning.apolloid, apidbtuning.geneattributes, apidb.organism' +comment: create view for apidb.organism. --- ID: 15 queries: GeneId.GenesByChIPchip tables: 'apidbtuning.chipchiptranscript, study.protocolappnode' +comment: ? --- ID: 16 queries: CompoundAttributes.DefaultStructure tables: 'apidbtuning.compoundattributes, apidbtuning.compoundid, chebi.structures' +comment: need tuning view for chebi --- ID: 17 queries: 'CompoundTables.MassSpecGraphsDataTableTriTryp, CompoundTables.MassSpecGraphsDataTablePlasmoDB' tables: 'apidbtuning.compoundattributes, apidbtuning.datasetpresenter, apidb.compoundmassspecresult, apidb.compoundpeaks, apidb.compoundpeakschebi, chebi.compounds, study.protocolappnode' +comment: talk to kathryn. might be extra cruft in the mass spec queries --- ID: 18 queries: CompoundIds.CompoundsByPathway From 2de4cdadbe3736160ab7bc8182ddd0712bc480a9 Mon Sep 17 00:00:00 2001 From: steve-fischer-200 Date: Tue, 9 Jan 2024 12:41:52 -0500 Subject: [PATCH 16/16] add tuningViews and nonTuningTables --- .../vp2TuningTablesEffort/findNonTuningTables | 16 ++++ Model/vp2TuningTablesEffort/nonTuningTables | 87 +++++++++++++++++++ Model/vp2TuningTablesEffort/tableGroups.yml | 4 + 3 files changed, 107 insertions(+) create mode 100755 Model/vp2TuningTablesEffort/findNonTuningTables create mode 100644 Model/vp2TuningTablesEffort/nonTuningTables diff --git a/Model/vp2TuningTablesEffort/findNonTuningTables b/Model/vp2TuningTablesEffort/findNonTuningTables new file mode 100755 index 0000000000..5a62dca2a8 --- /dev/null +++ b/Model/vp2TuningTablesEffort/findNonTuningTables @@ -0,0 +1,16 @@ +#!/usr/bin/perl +use strict; + +my %h; +while () { + next unless /^tables: '(.+)'/; + my @a = split(/, /, $1); + foreach my $t (@a) { + $h{$t} = 1; + } +} +foreach my $t (sort keys %h) { + next if $t =~/apidbtuning/; + print STDOUT "$t\n"; +} + diff --git a/Model/vp2TuningTablesEffort/nonTuningTables b/Model/vp2TuningTablesEffort/nonTuningTables new file mode 100644 index 0000000000..918487784d --- /dev/null +++ b/Model/vp2TuningTablesEffort/nonTuningTables @@ -0,0 +1,87 @@ +apidb.chrcopynumber +apidb.compoundmassspecresult +apidb.compoundpeaks +apidb.compoundpeakschebi +apidb.crisprphenotype +apidb.datasource +apidb.externalresourceurl +apidb.featurelocation +apidb.genefeatureproduct +apidb.geneinteraction +apidb.gff3 +apidb.massspecsummary +apidb.nafeaturehaploblock +apidb.nafeaturephenotype +apidb.nafeaturephenotypemodel +apidb.ontologytermresult +apidb.organism +apidb.pathwayreactionxref +apidb.phenotypegrowthrate +apidb.phenotypemodel +apidb.phenotyperesult +apidb.phenotypescore +apidb.rflpgenotype +apidb.seqedit +apidb.sequencevariation +apidb.transcriptproduct +chebi.chemical_data +chebi.compounds +chebi.names +chebi.structures +core.tableinfo +dots.aafeature +dots.aalocation +dots.aasequence +dots.aasequenceenzymeclass +dots.blatalignment +dots.chromosomeelementfeature +dots.dbrefaafeature +dots.dbrefnafeature +dots.dbrefnasequence +dots.domainfeature +dots.epitopefeature +dots.est +dots.externalnasequence +dots.genefeature +dots.goassocinstevidcode +dots.isolatefeature +dots.isolatesource +dots.lowcomplexityaafeature +dots.lowcomplexitynafeature +dots.massspecfeature +dots.motifaasequence +dots.nafeature +dots.nafeaturecomment +dots.nalocation +dots.nasequence +dots.secondarystructure +dots.secondarystructurecall +dots.similarity +dots.snpfeature +dots.tandemrepeatfeature +dots.transcript +dots.translatedaafeature +results.compoundmassspec +results.nafeaturediffresult +results.nafeatureexpression +results.nafeaturehostresponse +results.seqvariation +sres.bibliographicreference +sres.contact +sres.dbref +sres.enzymeclass +sres.externaldatabase +sres.externaldatabaserelease +sres.geneticcode +sres.ontologyrelationship +sres.ontologyterm +sres.pathway +sres.taxon +sres.taxonname +study.output +study.protocolappnode +study.protocolappparam +study.protocolparam +study.study +study.studybibref +study.studylink diff --git a/Model/vp2TuningTablesEffort/tableGroups.yml b/Model/vp2TuningTablesEffort/tableGroups.yml index f8291b0ec6..079684f73b 100644 --- a/Model/vp2TuningTablesEffort/tableGroups.yml +++ b/Model/vp2TuningTablesEffort/tableGroups.yml @@ -209,6 +209,7 @@ tables: 'apidbtuning.datasetpresenter, apidbtuning.externaldbdatasetpresenter, s ID: 49 queries: TranscriptAttributes.HasProteomics tables: 'apidbtuning.datasetpresenter, apidbtuning.geneattributes, apidb.datasource, apidb.massspecsummary, sres.externaldatabase, sres.externaldatabaserelease' +comment: DELETED --- ID: 50 queries: GeneAttributes.ProteinExpressionPtracks @@ -225,6 +226,7 @@ tables: 'apidbtuning.datasetpresenter, apidbtuning.msmodifiedpeptidesummary, api ID: 53 queries: TranscriptAttributes.ProteinGTracks tables: 'apidbtuning.datasetpresenter, apidbtuning.msmodifiedpeptidesummary, apidbtuning.transcriptattributes, apidb.datasource, apidb.massspecsummary, dots.secondarystructure, sres.externaldatabase, sres.externaldatabaserelease' +comment: DELETED --- ID: 54 queries: GeneId.GenesByISM @@ -281,6 +283,7 @@ tables: 'apidbtuning.gbrowsetracksorganism, apidbtuning.genomicseqattributes, ap ID: 67 queries: TranscriptAttributes.DnaGTracks tables: 'apidbtuning.gbrowsetracksorganism, apidbtuning.transcriptattributes, apidb.massspecsummary' +comment: DELETED --- ID: 68 queries: TranscriptAttributes.HasQuantitativeProteomics @@ -373,6 +376,7 @@ tables: 'apidbtuning.geneattributes, apidbtuning.taxonspecies, apidb.datasource, ID: 90 queries: GeneTables.PreferredProducts tables: 'apidbtuning.geneattributes, apidbtuning.transcriptattributes, apidb.genefeatureproduct, apidb.transcriptproduct, dots.genefeature, dots.goassocinstevidcode, dots.transcript, sres.ontologyterm' +comment: no longer used. --- ID: 91 queries: GeneAttributes.PbrowseOrganismAbbrev