SQL Queries
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Revision as of 21:05, 11 February 2011 (edit) YuliaBushmanova (Talk | contribs) (→Convert gene names to DDB_G IDs) ← Previous diff |
Revision as of 21:07, 11 February 2011 (edit) YuliaBushmanova (Talk | contribs) (→Notes for Genes containing word string) Next diff → |
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SELECT g.name, fp.value | SELECT g.name, fp.value | ||
FROM cgm_chado.featureprop fp | FROM cgm_chado.featureprop fp | ||
- | INNER JOIN cgm_chado.v_gene_features g ON g.feature_id = fp.feature_id | + | INNER JOIN cgm_chado.v_gene_features g ON g.feature_id = fp.feature_id |
- | INNER JOIN cgm_chado.cvterm ct ON fp.type_id = ct.cvterm_id | + | INNER JOIN cgm_chado.cvterm ct ON fp.type_id = ct.cvterm_id |
- | INNER JOIN cgm_chado.organism o ON o.organism_id = g.organism_id | + | INNER JOIN cgm_chado.organism o ON o.organism_id = g.organism_id |
WHERE o.common_name = 'dicty' | WHERE o.common_name = 'dicty' | ||
AND ct.name = 'public note' | AND ct.name = 'public note' |
Revision as of 21:07, 11 February 2011
Total GO
- Canonical query (excluding obsolete annotations)
SELECT COUNT(fcvt.feature_cvterm_id) annotations FROM cgm_chado.feature_cvterm fcvt JOIN cgm_chado.feature gene ON gene.feature_id = fcvt.feature_id JOIN cgm_chado.cvterm type ON type.cvterm_id = gene.TYPE_ID JOIN cgm_chado.cvterm GO ON GO.cvterm_id = fcvt.cvterm_id JOIN cgm_chado.cv ON cv.cv_id = GO.cv_id JOIN cgm_chado.organism ON organism.organism_id = gene.organism_id WHERE type.name = 'gene' AND gene.is_deleted = 0 AND cv.name IN('molecular_function', 'biological_process', 'cellular_component') AND GO.is_obsolete = 0 AND organism.common_name = 'dicty'
- Including obsolete annotations
SELECT COUNT(fcvt.feature_cvterm_id) annotations FROM cgm_chado.feature_cvterm fcvt JOIN cgm_chado.feature gene ON gene.feature_id = fcvt.feature_id JOIN cgm_chado.cvterm type ON type.cvterm_id = gene.TYPE_ID JOIN cgm_chado.cvterm GO ON GO.cvterm_id = fcvt.cvterm_id JOIN cgm_chado.cv ON cv.cv_id = GO.cv_id JOIN cgm_chado.organism ON organism.organism_id = gene.organism_id WHERE type.name = 'gene' AND gene.is_deleted = 0 AND cv.name IN('molecular_function', 'biological_process', 'cellular_component') AND organism.common_name = 'dicty'
- Only obsolete annotations
SELECT COUNT(fcvt.feature_cvterm_id) obsolete_annotations FROM cgm_chado.feature_cvterm fcvt JOIN cgm_chado.feature gene ON gene.feature_id = fcvt.feature_id JOIN cgm_chado.cvterm type ON type.cvterm_id = gene.TYPE_ID JOIN cgm_chado.cvterm GO ON GO.cvterm_id = fcvt.cvterm_id JOIN cgm_chado.organism ON organism.organism_id = gene.organism_id JOIN cgm_chado.cv ON cv.cv_id = GO.cv_id WHERE type.name = 'gene' AND gene.is_deleted = 0 AND cv.name IN('molecular_function', 'biological_process', 'cellular_component') AND GO.is_obsolete = 1 AND organism.common_name = 'dicty'
Total GO by aspect
- biological_process
SELECT COUNT(fcvt.feature_cvterm_id) process_annotations FROM cgm_chado.feature_cvterm fcvt JOIN cgm_chado.feature gene ON gene.feature_id = fcvt.feature_id JOIN cgm_chado.cvterm type ON type.cvterm_id = gene.TYPE_ID JOIN cgm_chado.cvterm GO ON GO.cvterm_id = fcvt.cvterm_id JOIN cgm_chado.cv ON cv.cv_id = GO.cv_id JOIN organism ON organism.organism_id = gene.organism_id WHERE type.name = 'gene' AND gene.is_deleted = 0 AND cv.name = 'biological_process' AND GO.is_obsolete = 0 AND organism.common_name = 'dicty'
- molecular_function
SELECT COUNT(fcvt.feature_cvterm_id) function_annotations FROM cgm_chado.feature_cvterm fcvt JOIN cgm_chado.feature gene ON gene.feature_id = fcvt.feature_id JOIN cgm_chado.cvterm type ON type.cvterm_id = gene.TYPE_ID JOIN cgm_chado.cvterm GO ON GO.cvterm_id = fcvt.cvterm_id JOIN cgm_chado.cv ON cv.cv_id = GO.cv_id JOIN organism ON organism.organism_id = gene.organism_id WHERE type.name = 'gene' AND gene.is_deleted = 0 AND cv.name = 'molecular_function' AND GO.is_obsolete = 0 AND organism.common_name = 'dicty'
- cellular_component
SELECT COUNT(fcvt.feature_cvterm_id) component_annotations FROM cgm_chado.feature_cvterm fcvt JOIN cgm_chado.feature gene ON gene.feature_id = fcvt.feature_id JOIN cgm_chado.cvterm type ON type.cvterm_id = gene.TYPE_ID JOIN cgm_chado.cvterm GO ON GO.cvterm_id = fcvt.cvterm_id JOIN cgm_chado.cv ON cv.cv_id = GO.cv_id JOIN organism ON organism.organism_id = gene.organism_id WHERE type.name = 'gene' AND gene.is_deleted = 0 AND cv.name = 'cellular_component' AND GO.is_obsolete = 0 AND organism.common_name = 'dicty'
GO non IEA by aspect
- Canonical query(all aspects)
SELECT cv.name aspect,count(fcvt.feature_cvterm_id) annotations FROM cgm_chado.feature_cvterm fcvt JOIN cgm_chado.feature gene ON gene.feature_id = fcvt.feature_id JOIN cgm_chado.cvterm type ON type.cvterm_id = gene.TYPE_ID JOIN cgm_chado.cvterm GO ON GO.cvterm_id = fcvt.cvterm_id JOIN cgm_chado.cv ON cv.cv_id = GO.cv_id JOIN cgm_chado.feature_cvtermprop fcvt_prop ON fcvt_prop.feature_cvterm_id=fcvt.feature_cvterm_id JOIN cgm_chado.cvterm evterm ON evterm.cvterm_id=fcvt_prop.type_id JOIN cgm_chado.cv ev ON ev.cv_id=evterm.cv_id JOIN organism ON organism.organism_id = gene.organism_id WHERE type.name = 'gene' ANd gene.is_deleted = 0 AND cv.name IN('molecular_function', 'biological_process', 'cellular_component') AND GO.is_obsolete = 0 AND ev.name like 'evidence_code%' AND evterm.name != 'inferred from electronic annotation' AND organism.common_name = 'dicty' GROUP BY cv.name ORDER BY annotations DESC
GO by evidence code
- Canonical query(all aspects)
SELECT evsyn.synonym_ evidence_code,count(fcvt.feature_cvterm_id) annotations FROM cgm_chado.feature_cvterm fcvt JOIN cgm_chado.feature gene ON gene.feature_id = fcvt.feature_id JOIN cgm_chado.cvterm type ON type.cvterm_id = gene.TYPE_ID JOIN cgm_chado.cvterm GO ON GO.cvterm_id = fcvt.cvterm_id JOIN cgm_chado.cv ON cv.cv_id = GO.cv_id JOIN cgm_chado.feature_cvtermprop fcvt_prop ON fcvt_prop.feature_cvterm_id=fcvt.feature_cvterm_id JOIN cgm_chado.cvterm evterm ON evterm.cvterm_id=fcvt_prop.type_id JOIN cgm_chado.cv ev ON ev.cv_id=evterm.cv_id JOIN cgm_chado.cvtermsynonym evsyn on evterm.cvterm_id=evsyn.cvterm_id JOIN cgm_chado.cvterm synterm on synterm.cvterm_id=evsyn.type_id JOIN organism ON organism.organism_id = gene.organism_id WHERE type.name = 'gene' AND gene.is_deleted = 0 AND organism.common_name = 'dicty' AND GO.is_obsolete = 0 AND ev.name like 'evidence_code%' AND synterm.name IN ('EXACT','RELATED') AND LENGTH(evsyn.synonym_) = 3 AND cv.name IN('molecular_function', 'biological_process', 'cellular_component') GROUP BY evsyn.synonym_ ORDER BY annotations DESC
- biological process only
SELECT evsyn.synonym_ evidence_code,count(fcvt.feature_cvterm_id) annotations FROM cgm_chado.feature_cvterm fcvt JOIN cgm_chado.feature gene ON gene.feature_id = fcvt.feature_id JOIN cgm_chado.cvterm type ON type.cvterm_id = gene.TYPE_ID JOIN cgm_chado.cvterm GO ON GO.cvterm_id = fcvt.cvterm_id JOIN cgm_chado.cv ON cv.cv_id = GO.cv_id JOIN cgm_chado.feature_cvtermprop fcvt_prop ON fcvt_prop.feature_cvterm_id=fcvt.feature_cvterm_id JOIN cgm_chado.cvterm evterm ON evterm.cvterm_id=fcvt_prop.type_id JOIN cgm_chado.cv ev ON ev.cv_id=evterm.cv_id JOIN cgm_chado.cvtermsynonym evsyn on evterm.cvterm_id=evsyn.cvterm_id JOIN cgm_chado.cvterm synterm on synterm.cvterm_id=evsyn.type_id JOIN organism ON organism.organism_id = gene.organism_id WHERE type.name = 'gene' AND gene.is_deleted = 0 AND GO.is_obsolete = 0 AND ev.name like 'evidence_code%' AND synterm.name IN ('EXACT','RELATED') AND LENGTH(evsyn.synonym_) = 3 AND organism.common_name = 'dicty' AND cv.name = 'biological_process' GROUP BY evsyn.synonym_ ORDER BY annotations DESC
- For other aspects replace biological_process (in cv.name) with either of molecular_function or cellular_component
New literatures by date
SELECT * from cgm_chado.pub WHERE created_at >= to_date('12/28/2010','MM/DD/YYYY') AND created_at <= to_date('01/04/2011','MM/DD/YYYY') AND pubplace = 'PUBMED' ORDER BY pub_id
- To retrieve only pubmed id
SELECT pub.uniquename pubmed from cgm_chado.pub WHERE created_at >= to_date('12/28/2010','MM/DD/YYYY') AND created_at <= to_date('01/04/2011','MM/DD/YYYY') AND pubplace = 'PUBMED' ORDER BY pub_id desc
Literature, all Annotations, Curator, from Distinct Reference
- By reference no
- Remember to replace 10060 with any other number
SELECT feat.name locus, fpub.pub_id reference_no,pubterm.name literature_topic, curator.name who_did_it,cpubprop.timecreated when FROM cgm_chado.feature_pub fpub JOIN cgm_chado.feature_pubprop fpubprop ON fpubprop.feature_pub_id=fpub.feature_pub_id JOIN cgm_chado.cvterm pubterm ON pubterm.cvterm_id=fpubprop.type_id JOIN cgm_chado.cv pubcv ON pubcv.cv_id=pubterm.cv_id JOIN cgm_chado.curator_feature_pubprop cpubprop ON cpubprop.feature_pubprop_id=fpubprop.feature_pubprop_id JOIN cgm_chado.curator ON curator.curator_id=cpubprop.curator_id JOIN cgm_chado.feature feat ON feat.feature_id = fpub.feature_id JOIN cgm_chado.organism ON organism.organism_id = feat.organism_id WHERE pubcv.name = 'dictyBase_literature_topic' AND organism.common_name = 'dicty' AND reference_no = 10060
- By curator
SELECT DISTINCT c.name who_did_it FROM cgm_chado.pub p INNER JOIN cgm_chado.feature_pub fp ON p.pub_id = fp.pub_id INNER JOIN cgm_chado.feature_pubprop fpp ON fpp.feature_pub_id = fp.feature_pub_id INNER JOIN cgm_chado.curator_feature_pubprop cfpp ON cfpp.feature_pubprop_id = fpp.feature_pubprop_id INNER JOIN cgm_chado.curator c ON c.curator_id = cfpp.curator_id WHERE p.pub_id = 10060
Find all lit topics associated with each gene, by paper
SELECT dx.accession, p.uniquename, stragg( ct.name ) AS Literature_Topics FROM cgm_chado.v_gene_features g INNER JOIN cgm_chado.dbxref dx ON g.dbxref_id = dx.dbxref_id INNER JOIN cgm_chado.feature_pub fp ON g.feature_id = fp.feature_id INNER JOIN cgm_chado.pub p ON fp.pub_id = p.pub_id INNER JOIN cgm_chado.feature_pubprop fpp ON fp.feature_pub_id = fpp.feature_pub_id INNER JOIN cgm_chado.cvterm ct ON fpp.type_id = ct.cvterm_id INNER JOIN cgm_chado.cv ON ct.cv_id = cv.cv_id INNER JOIN cgm_chado.organism o ON o.organism_id = g.organism_id WHERE o.common_name = 'dicty' AND p.pubplace = 'PUBMED' AND cv.name ='dictyBase_literature_topic' GROUP BY dx.accession, p.uniquename ORDER BY to_number(p.uniquename)
Notes for Genes containing word string
Replace 'public note' with 'private note for Private Notes. In this example notes containing UTR are searched.
SELECT g.name, fp.value FROM cgm_chado.featureprop fp INNER JOIN cgm_chado.v_gene_features g ON g.feature_id = fp.feature_id INNER JOIN cgm_chado.cvterm ct ON fp.type_id = ct.cvterm_id INNER JOIN cgm_chado.organism o ON o.organism_id = g.organism_id WHERE o.common_name = 'dicty' AND ct.name = 'public note' AND value LIKE '%UTR%'
Convert gene names to DDB_G IDs
SELECT g.name AS GENE_NAME, dx.accession AS DDB_G_ID FROM cgm_chado.v_gene_features g INNER JOIN cgm_chado.dbxref dx ON g.dbxref_id = dx.dbxref_id INNER JOIN cgm_chado.organism o ON o.organism_id = g.organism_id WHERE o.common_name = 'dicty' AND g.name IN ('rab14', 'rab11A' , 'rab21' )
Genes, Primary IDs from Genes with specific Gene Product
Substitute any gene product for 'TRANSCRIPT%'; the % can be omitted when gene product is distinct.
SELECT G.GENE_NAME, G.PRIMARY_FEATURE_DICTYBASEID FROM CGM_DDB.GENE_PRODUCT GP INNER JOIN CGM_DDB.LOCUS_GP LGP ON LGP.GENE_PRODUCT_NO = GP.GENE_PRODUCT_NO INNER JOIN CGM_CHADO.V_GENE_DICTYBASEID G ON LGP.LOCUS_NO = G.GENE_FEATURE_ID WHERE UPPER(GP.GENE_PRODUCT) LIKE UPPER('TRANSCRIPT%') GROUP BY G.GENE_NAME, G.PRIMARY_FEATURE_DICTYBASEID;
Genes, Primary IDs from Genes with automated Gene Product
SELECT G.GENE_NAME, G.PRIMARY_FEATURE_DICTYBASEID, GP.GENE_PRODUCT FROM CGM_DDB.GENE_PRODUCT GP INNER JOIN CGM_DDB.LOCUS_GP LGP ON LGP.GENE_PRODUCT_NO = GP.GENE_PRODUCT_NO INNER JOIN CGM_CHADO.V_GENE_DICTYBASEID G ON LGP.LOCUS_NO = G.GENE_FEATURE_ID WHERE GP.IS_AUTOMATED ='1' order by GP.GENE_PRODUCT
Pseudogene IDs
SELECT feature.uniquename FROM CGM_CHADO.feature INNER JOIN CGM_CHADO.cvterm ON cvterm.cvterm_id = feature.TYPE_ID WHERE cvterm.name = 'pseudogene' and feature.is_deleted = 0
To get also the Gene Name
SELECT psuedofeat.uniquename pseudogene,genefeat.name gene FROM CGM_CHADO.v_notdeleted_feature pseudofeat inner join CGM_CHADO.feature_relationship frel on frel.subject_id=pseudofeat.feature_id inner join CGM_CHADO.v_notdeleted_feature genefeat on frel.object_id=genefeat.feature_id inner join CGM_CHADO.cvterm on cvterm.cvterm_id=pseudofeat.type_id WHERE cvterm.name = 'pseudogene'
Genes with conflicting evidence
This query can also be used to find genes with support notes, such as 'genomic context'.
SELECT v.name, p.value FROM cgm_chado.featureprop p inner JOIN cgm_chado.V_VERIFIED_GENE_FEATURES v on p.feature_id=v.feature_id WHERE p.value like 'Conflicting evidence'
Genes with 'complete support'
SELECT v.name, p.value FROM cgm_chado.featureprop p inner JOIN cgm_chado.V_VERIFIED_GENE_FEATURES v on p.feature_id=v.feature_id where p.value like 'ESTs' or p.value like 'sequence similarity' AND not v.name in (SELECT v.name FROM cgm_chado.featureprop p inner JOIN cgm_chado.V_VERIFIED_GENE_FEATURES v on p.feature_id=v.feature_id WHERE p.value like 'Conflicting evidence' or p.value like 'Incomplete support')
Modified gene models by curator and date
Replace 'CGM_DDB_BOBD' with CGM_DDB_PFEY or CGM_DDB_PASC
SELECT v.name , v.timelastmodified FROM cgm_chado.V_VERIFIED_GENE_FEATURES v join cgm_chado.featureprop p on p.feature_id=v.feature_id WHERE v.created_by ='CGM_DDB_BOBD' and p.value like 'curator inference' ORDER BY v.timelastmodified
Genes with community annotations
SELECT f.name FROM cgm_chado.feature f JOIN cgm_chado.FEATUREPROP fp on f.feature_id = fp.feature_id WHERE fp.value like 'Has Wiki Page' ORDER BY f.name
Genes with community annotations on Gene Page (description)
SELECT f.name, p.value as descriptions FROM cgm_chado.featureprop p inner JOIN cgm_chado.v_gene_features l on l.feature_id=p.feature_id JOIN cgm_chado.feature f on f.feature_id = p.feature_id WHERE p.type_id=972 AND p.feature_id in ( SELECT feature_id FROM cgm_chado.FEATUREPROP WHERE value like 'Has Wiki Page' )
Map all primary DDB to GenBank Protein Accession
select d.accession, f.name, db.name from CGM_CHADO.v_primary_feature f inner join CGM_CHADO.feature_dbxref fd on fd.feature_id = f.feature_id inner join CGM_CHADO.dbxref d on d.dbxref_id = fd.dbxref_id inner join CGM_CHADO.db on d.db_id = db.db_id and db.name = 'DB:Protein Accession Number';
Genes, DDB IDs with Specific GO terms, created_by
Replace GO ID with any other; delete the 'and created_by..' if not restricted to curator; add 'order by..' after parenthesis to sort by gene_name etc.
SELECT * from cgm_chado.v_gene_dictybaseid WHERE gene_feature_id in (SELECT distinct locus_no from go_locus_goev WHERE goid = 6118 and created_by='CGM_DDB_PFEY')
Summaries
select fp.FEATURE_ID, p.paragraph_text from cgm_chado.featureprop fp JOIN cgm_ddb.paragraph p on TO_NCHAR(fp.value)= p.paragraph_no WHERE fp.type_id=984 and written_by ='CGM_DDB_KPIL' and not paragraph_text like '<summary%><curation_status>%' and exists (select * from cgm_chado.featureprop where type_id=984 and value like paragraph_no) order by date_created
Summary by Text string including Curation Status
SELECT p.created_by, FEATURE_ID as n FROM cgm_chado.featureprop fp JOIN cgm_ddb.paragraph p on TO_NCHAR(fp.value)= p.paragraph_no WHERE fp.type_id=984 AND paragraph_text like '%Basic%'
Number of PM references with GO and PHenotype annotations
SELECT TAB_NAME, PRIMARY_KEY, reference_no FROM reflink WHERE reference_no in ( SELECT reference_no FROM reference WHERE pubmed is not null )
Table must be cleaned up: In excel do "convert data to columns" and distangle the PRIMARY_KEY fields. Then put PMIDs in one column and sort, then delete duplicate PMID refs.
Strain Names, Systematic Names, Strain Description where strain name starts with a specific string (example 'JS')
SELECT strain_name, systematic_name, strain_description FROM stock_center WHERE strain_name like 'JS%' or systematic_name like 'JS%'
Can also search for specific strains by using 'equals'
SELECT strain_name, systematic_name, strain_description FROM cgm_ddb.stock_center WHERE strain_name = 'JS65' or systematic_name = 'JS65'
Strain Names, Synonyms, Systematic Names, Created_by, Strain Description
SELECT strain_name, stragg( name) as synonyms, systematic_name, created_by, strain_description FROM cgm_ddb.stock_center sc JOIN cgm_ddb.STRAIN_SYNONYM ss on ss.strain_id = sc.id JOIN cgm_chado.synonym_ cs on ss.synonym_id= cs.synonym_id GROUP BY strain_name, created_by, strain_description, systematic_name ORDER BY created_by, strain_name
Can also restrict the curator by adding
where created_by ='CGM_DDB_PASC'
before the GROUP BY statement
Strain Names, Created_by, Strain Description, Strain Characteristics
SELECT strain_name, systematic_name, strain_description, stragg( name) as Strain_characteristics FROM cgm_ddb.stock_center s join cgm_ddb.STRAIN_CHAR_CVTERM sc on s.id = sc.strain_id join cgm_chado.CVTERM cv on sc.CVTERM_ID = cv.CVTERM_ID where strain_description like '%null%' group by strain_name, systematic_name, strain_description
Strain Names, Created_by, by a specific plasmid
SELECT strain_name, plasmid, mutagenesis_method, created_by FROM cgm_ddb.stock_center WHERE plasmid like '%pEXP%' or plasmid like '%pExp%' ORDER BY created_by
Strain Names, Systematic Name, Strain Description, by a specific Strain Characteristic
SELECT strain_name, systematic_name, name, strain_description FROM stock_center s JOIN STRAIN_CHAR_CVTERM sc on s.id = sc.strain_id JOIN cgm_chado.CVTERM cv on sc.CVTERM_ID = cv.CVTERM_ID WHERE name ='multiple null mutant' ORDER BY strain_name
Strains annotated with a specific environment condition
SELECT strain_name, systematic_name, name as envt FROM cgm_ddb.stock_center s JOIN cgm_chado.phenstatement ps ON s.genotype_id = ps.genotype_id JOIN cgm_chado.cvterm cv ON cv.CVTERM_ID = ps.ENVIRONMENT_ID WHERE name ='in suspension'
Strains annotated with a specific assay
SELECT strain_name, systematic_name, name as assay FROM stock_center s JOIN cgm_chado.phenstatement ph on s.genotype_id = ph.genotype_id JOIN cgm_chado.phenotype p ON ph.phenotype_id = p.phenotype_id JOIN cgm_chado.cvterm cv ON cv.CVTERM_ID = p.assay_ID WHERE name ='electron microscopy'
Stock Center Orders by name
Substitute any name or use 'last_name' and order by anything, here by order ID.
SELECT * from cgm_ddb.stock_center_view WHERE first_name = 'Baskar' ORDER BY Order_ID
Order rows in a resultset
select name,uniquename,seqlen,residues,created_by from cgm_chado.feature order by timelastmodified asc|desc asc => should sort the result by ascending order desc => should sort the result by descending order
No of Colleagues
select count(COLLEAGUE_NO) ccount from cgm_ddb.COLLEAGUE;
Number of curated models
select count(*) as c from cgm_chado.V_VERIFIED_GENE_FEATURES v
Select feature types by dictyBase ID
select ncrna.uniquename FROM cgm_chado.feature ncrna join cgm_chado.cvterm nctype on nctype.cvterm_id=ncrna.type_id where nctype.name like '%snoRNA%' OR nctype.name = 'ncRNA' or nctype.name like 'class%RNA' or nctype.name = 'rRNA' or nctype.name = 'snRNA' OR nctype.name LIKE 'RNase%' OR nctype.name LIKE 'SRP%'
Select Feature types by dictyBase ID with gene name, gene products (bundled into one field by comma).
select gene.name, stragg (gp.gene_product) as gene_product, ncrna.uniquename FROM cgm_chado.feature ncrna join cgm_chado.cvterm nctype on nctype.cvterm_id=ncrna.type_id INNER JOIN cgm_chado.feature_relationship fr ON ncrna.feature_id = fr.subject_id INNER JOIN cgm_chado.cvterm rcvt ON rcvt.cvterm_id = fr.type_id INNER JOIN cgm_chado.feature gene ON gene.feature_id = fr.object_id INNER JOIN cgm_ddb.locus_gp lg ON lg.locus_no = gene.feature_id INNER JOIN cgm_ddb.gene_product gp ON lg.gene_product_no = gp.gene_product_no where nctype.name like '%snoRNA%' OR nctype.name = 'ncRNA' or nctype.name like 'class%RNA' or nctype.name = 'rRNA' or nctype.name = 'snRNA' OR nctype.name LIKE 'RNase%' OR nctype.name LIKE 'SRP%' group by gene.name, ncrna.uniquename
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