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Chem2Bio2RDF

Some notes.

cheminfov:

From http://i571.wikispaces.com/2D+chemical+database+searching+systems:

psql -U cicc3 -d chord or psql -U cicc3 -d gnova create table gnovatest (smiles VARCHAR(200), name VARCHAR(50), logp real, fkey BIT(166));

\d gnovatest

INSERT INTO gnovatest (smiles, name, logp) VALUES ( 'CC(=O)Nc1ccc(O)cc1', 'Acetaminophen', 0.27 ); INSERT INTO gnovatest (smiles, name, logp) VALUES ( 'CC(C)NCC(O)COc1ccccc1CC=C', 'Alprenolol', 2.81); INSERT INTO gnovatest (smiles, name, logp) VALUES ( 'CC(N)Cc1ccccc1', 'Amphetamine', 1.76 ); INSERT INTO gnovatest (smiles, name, logp) VALUES ( 'CC(CS)C(=O)N1CCCC1C(=O)O', 'Captopril', 0.84 ); INSERT INTO gnovatest (smiles, name, logp) VALUES ( 'CN(C)CCCN1c2ccccc2Sc3ccc(Cl)cc13', 'Chlorpromazine', 5.20 ); INSERT INTO gnovatest (smiles, name, logp) VALUES ( 'OC(=O)Cc1ccccc1Nc2c(Cl)cccc2Cl', 'Diclofenac', 4.02 ); INSERT INTO gnovatest (smiles, name, logp) VALUES ( 'NCC1(CC(=O)O)CCCCC1', 'Gabapentin', -1.37 ); INSERT INTO gnovatest (smiles, name, logp) VALUES ( 'COC(=O)c1ccccc1O', 'Salicylate', 2.60 );

update gnovatest set fkey = public166keys(smiles);

select smiles,name,logp from gnovatest; select * from gnovatest;

select smiles,name,logp from gnovatest where matches(smiles, '*C(=O)O');

select smiles,name,logp from gnovatest where (matches(smiles, '*C(=O)O') AND (logp>1.0));

select smiles,name,logp from gnovatest where tanimoto(fkey, public166keys('CC(=O)Oc1ccccc1C(=O)O')) > 0.6;

drop table gnovatest;

\dt

select count(*) from public.chembl_02_compounds ;

select table_name from information_schema.tables where table_schema='public' AND table_name LIKE 'chembl%' ;

\d+ public.chembl_02_compounds

$ cat describe_chembl.sql \d+ public.chembl_02_activities \d+ public.chembl_02_assay2target \d+ public.chembl_02_assay_type \d+ public.chembl_02_assays \d+ public.chembl_02_compound_properties \d+ public.chembl_02_compound_records \d+ public.chembl_02_compound_synonyms \d+ public.chembl_02_compounds \d+ public.chembl_02_confidence_score_lookup \d+ public.chembl_02_docs \d+ public.chembl_02_relationship_type \d+ public.chembl_02_source \d+ public.chembl_02_target_class \d+ public.chembl_02_target_dictionary \d+ public.chembl_02_target_type

How to dump specific dataset from pg? In C2B2R, all data is in database "chord", schema "public", in sets of tables such as:

drugbank drugbank_drug drugbank_drug_sp drugbank_drugtarget drugbank_drugtarget_sp drugbank_target drugbank_target_seq

pg_dump -U cicc3 \ --schema=public \ -t drugbank \ -t drugbank_drug \ -t drugbank_drug_sp \ -t drugbank_drugtarget \ -t drugbank_drugtarget_sp \ -t drugbank_target \ -t drugbank_target_seq \ -v \ chord \ > drugbank-pgdump.sql

On cheminfov, in the PostgreSQL instance, all data is in database "chord" (this was a design choice and not required). The schema "gnova" provides gNova Chord functionality as usual in accordance with Chord documentation. (Another database could have been used.) All data is in the schema "public" within database "chord", another design choice. Each dataset (drugbank, chembl, etc.) could have been implemented as a distinct schema.

Oops! Missed some drugbank tables. The list is:

chord=> select table_name from information_schema.tables where table_schema='public' and table_name ilike '%drugbank%' ORDER BY table_name; table_name ---------------------------------- c2b2r_DrugBankDrug c2b2r_drugbankdrug_042011 c2b2r_DrugBankDrugDrug c2b2r_drugbankdrug_substructure c2b2r_drugbankdrugtarget_042011 c2b2r_DrugBankTarget c2b2r_drugbanktarget_042011 ctd_disease_drugbank ctd_gene_drugbank doid_drugbank drugbank drugbank_drug drugbank_drug_sp drugbank_drugtarget drugbank_drugtarget_sp drugbank_target drugbank_target_seq gene_drugbank goid_drugbank huge_genopedia_gene_drugbank huge_phenopedia_disease_drugbank (21 rows)

(Non-trivial to associate tables with source datasets!)

Not all tables in d2rq mapping, so some are unused?:

Not in mapping, so irrelevant?

huge_genopedia_gene_drugbank huge_phenopedia_disease_drugbank c2b2r_drugbankdrug_042011 c2b2r_drugbankdrugtarget_042011 c2b2r_drugbanktarget_042011 ctd_disease_drugbank ctd_gene_drugbank doid_drugbank goid_drugbank gene_drugbank

grants$ gunzip -c chembl_13-mysqldump-pgcompatible.sql.gz | ~/c2b2r_fix_chembl_mysqldump.py | gzip -c > chembl_13-mysqldump-pgcompatible-fixed.sql.gz

c2b2r_fix_chembl_mysqldump.py: lines: 4945 c2b2r_fix_chembl_mysqldump.py: lines fixed: 4162