2. 1 Péter Kovács May, 2005 Compound storage / retrieval with JChem Cartridge for Oracle

3. 2 Slide 2 Compound storage / retrieval with JChem Cartridge for Oracle May 2005 Contents Purpose of JChem Cartridge Constituents of the JChem Cartridge API Normal Tables vs. JChem Tables Architecture of JChem Cartridge

4. 3 Slide 3 Compound storage / retrieval with JChem Cartridge for Oracle May 2005 Purpose of JChem Cartridge Access JChem functionality using SQL: SELECT count(*) FROM nci WHERE jc_contains(structure, 'Brc1cnc2ccccc12') = 1 Access JChem in any programming environment offering Oracle connectivity (Visual Basic, Java, Perl, PHP, Python, Apache mod_plsql...). Execute SQL queries efficiently using extensible indexes Precompute chemical information on structures by creating jc_idxtype indexes: CREATE INDEX jcxnci ON nci(structure) INDEXTYPE IS jc_idxtype The jc_idxtype implementation scans the indexed column for eligible structures in one single uninterrupted operation: domain index scan

5. 4 Slide 4 Compound storage / retrieval with JChem Cartridge for Oracle May 2005 Elements of the JChem Cartridge API Operators ( jc_... ) and their functional forms ( jcf_... ) Index parameters and default properties DML operators for JChem tables Support functions for user defined operators

6. 5 Slide 5 Compound storage / retrieval with JChem Cartridge for Oracle May 2005 Operators and their functional forms I. Typical operator: jc_ (, ) Operator for substructure search: jc_contains(, ) Swiss-army-knife search operator: jc_compare(,, )

7. 6 Slide 6 Compound storage / retrieval with JChem Cartridge for Oracle May 2005 Operators and their functional forms II. Chemical Terms The Lipinski-rule in chemical terms: SELECT count(*) FROM nci_3m WHERE jc_compare(structure, 'O=C1ONC(N1c2ccccc2)-c3ccccc3','sep=! t:s!ctFilter:(mass() <= 500) && (logP() <= 5) && (donorCount() <= 5) && (acceptorCount() <= 10)') = 1 Presently, about 100 functions including topological and physiochemical descriptors. Users can define their own functions.

8. 7 Slide 7 Compound storage / retrieval with JChem Cartridge for Oracle May 2005 Operators and their functional forms III. Chemical Terms and Query Filter: SELECT id, purchase_date FROM compounds_instock WHERE jc_compare(structure, 'C(=S)([N][N])[S]', 'sep=! t:t!simThreshold:0.9!ctFilter:logp()>1!filterQuery:select rowid from compounds_instock where purchase_date > DATE ''2002-01-01''') = 1 Filter queries allow to execute search on a subset of a table's rows and execute the performance sensitive chemical computations in domain index scan mode. Dynamic generation of static images: SELECT jc_molconvertb(structure, 'png -2') FROM nci where id = :1 Avaliable image formats: png, jpeg, svg, powray, ppm PNG

9. 8 Slide 8 Compound storage / retrieval with JChem Cartridge for Oracle May 2005 Index parameters Index parameters affect: Fingerprint attributes Standardizer configuration Table space and storage options of the index table Generate index jcxnci using structures in the table stfp_keys as structural keys: CREATE INDEX jcxnci ON nci(structure) INDEXTYPE IS jc_idxtype PARAMETERS('STRUCTURALFP_CONFIG=select structure from stfp_keys') Strip hydrogens and use Daylight-style aromatization during index creation: CREATE INDEX jcxnci ON nci(structure) INDEXTYPE IS jc_idxtype PARAMETERS('STD_CONFIG=dehydrogenize:optional..aromatize:d')

10. 9 Slide 9 Compound storage / retrieval with JChem Cartridge for Oracle May 2005 Default properties Used for SQL statements where no information from JChem indexes is available. Sample SQL statement without index information: SELECT jc_contains('O=C1C=CNC=C1', 'n1ccccc1') FROM dual Set default properties: CALL jc_set_default_property('standardizerConfig', 'aromatize:d')

11. 10 Slide 10 Compound storage / retrieval with JChem Cartridge for Oracle May 2005 Supported Column Types VARCHAR2 columns Targets and queries are VARCHAR2. Operator names: jc_contains, jc_compare, jc_equals... BLOB columns Targets and queries are BLOB. Operator names: jc_containsb, jc_compareb, jc_equalsb... Exceptions: jc_molconvertb: takes VARCHAR2, returns BLOB jc_molconvertbb: takes BLOB, returns BLOB

12. 11 Slide 11 Compound storage / retrieval with JChem Cartridge for Oracle May 2005 Supported Table Types Regular Table : nci_1k JChem Table (generated by jcman or API) : jc_nci_1k CREATE INDEX jcxnci_1k... Index table: jcxnci_1k_jcx CREATE INDEX jcxjc_nci_1k... Rowid of the base table ( nci_1k )

13. 12 Slide 12 Compound storage / retrieval with JChem Cartridge for Oracle May 2005 Regular Tables vs. JChem Tables Regular tables – base table and index table are physically distinct – index properties are specified as index parameters JChem tables – base table and index table are physically the same – most of the index properties are specified during table creation (jcman or Java API) Pros & Cons: –inserts from outside the database are faster with JChem tables than with regular tables –JChem tables require Java API or the jcman command line tool (for table creation) and Java API or special cartridge functions for INSERTs, UPDATEs and DELETEs; standard SQL can be used with regular tables in all cases.

14. 13 Slide 13 Compound storage / retrieval with JChem Cartridge for Oracle May 2005 JChem Indexes with JChem Tables VARCHAR2 Index creation: CREATE INDEX jcxjc_nci ON jc_nci(cd_smiles) INDEXTYPE IS jc_idxtype Search: SELECT jc_contains(cd_smiles, 'n1ccccc1') FROM jc_nci BLOB Index creation: CREATE INDEX jcxjc_nci ON jc_nci(cd_structure) INDEXTYPE IS jc_idxtype Search: SELECT jc_contains(cd_structure, 'n1ccccc1') FROM jc_nci

15. 14 Slide 14 Compound storage / retrieval with JChem Cartridge for Oracle May 2005 JChem Cartridge Architecture I. Computation intensive operations performed in a separate JVM (currently Tomcat) Advantages: fast execution (optimized native code) starting point for distributed architecture JChem Server Search Oracle JChem Cartridge Cache JChem Core Cache JChem Streams JChem Base Update HTTP JDBC

16. 15 Slide 15 Compound storage / retrieval with JChem Cartridge for Oracle May 2005 JChem Cartridge Architecture II. Type Of Database Access Single Session: One SQL statement accesses the database through one single database session –Used for inserting and updating to maintain strict transaction semantics –Computation is still done in Tomcat (for performance) Dual Session: One SQL statement accesses the database through multiple database sessions –Used for searching (for performance and code-reuse reasons) –Only committed changes are seen –Ex Machina mechanism to maintain user identity across sessions acting on behalf of the same operation

17. 16 Slide 16 Compound storage / retrieval with JChem Cartridge for Oracle May 2005 JChem Cartridge Architecture III. Single Session Database Access JChem Server Search Engine Oracle JChem Cartridge SQL Plus/any DB application Index Table jc_insert Cache Index Table... JChem StreamsJChem Streams Adapter JChem Core Execution Engine 2. 3. 4. 5. 1. 6. 7. 8. 9. 10. 11.

18. 17 Slide 17 Compound storage / retrieval with JChem Cartridge for Oracle May 2005 JChem Cartridge Architecture IV. Dual Session Database Access JChem Server Search Engine Oracle JChem Cartridge SQL Plus/any DB application Index Table Cache jc_contains Cache Index Table... JChem StreamsJChem Streams Adapter JChem Core 7. 2. 3.4. 5. 6. Execution Engine 1. 8. 10. 11. 12. 9.

19. 18 Slide 18 Compound storage / retrieval with JChem Cartridge for Oracle May 2005 JChem Cartridge Architecture V. Dual Session Semantics Transaction context differing across session Changes must be committed to include them in searches Security context disrupted across sessions: Two options: Configure super user with many privileges Use jchem_core_pkg.use_password( password VARCHAR2) for primary database sessions

20. 19 Slide 19 Compound storage / retrieval with JChem Cartridge for Oracle May 2005 Performance Table containing 3003012 structures (12xNCI) in VARCHAR2 colums with 3GHz dual Xeon with 2GB system memory Index creation (regular tables): 5801 seconds Import w/o duplicate filtering (JChem-tables): 13104 seconds Substructure search results: Query StructureHit Count Time (milliseconds) JChem-tablesRegular tables C1CN1c2cnnc3c(cncc23)C4=CSC=C40364374 O=C1ONC(N1c2ccccc2)c3ccccc3204456467 [#8]-c1c(N=N)c(cc2cc(ccc12)S([#8])(=O)=O)S([#8])(=O)=O118810171042 C(Sc1ncnc2ncnc12)c3ccccc317529801016 [#7]C1=CC=NC2=C1C=CC(Cl)=C2463219872074 c1ncc2ncnc2n1498481587316446 Clc1ccccc12743566045963139

21. 20 Slide 20 Compound storage / retrieval with JChem Cartridge for Oracle May 2005 Future plans Support more features already included or planned in JChem Base: Pharmacophore similarity search Custom descriptor (e.g. BCUT, scalar) and metric at similarity search Coordination bond support Tautomeric search support Other S-groups

22. 21 Slide 21 Compound storage / retrieval with JChem Cartridge for Oracle May 2005 Summary JChem Cartridge for Oracle allows to access the rich functionality of JChem Base in a flexible and efficient manner. JChem Cartridge for Oracle uses creative solutions to broaden the applicability of JChem's core functions while preserving key benefits of the Java platform.

23. 22 Slide 22 Compound storage / retrieval with JChem Cartridge for Oracle May 2005 Links Documentation –www.jchem.com/doc/admin/cartridge.html –www.jchem.com/doc/guide/cartridge/index.html Forum –www.chemaxon.hu/forum/forum7.html Brochure –www.chemaxon.com/brochures/JChem_Cartridg e.pdf

24. 23 Slide 23 Compound storage / retrieval with JChem Cartridge for Oracle May 2005 Máramaros köz 3/a Budapest, 1037 Hungary info@chemaxon.com www.chemaxon.com Thank you for your attention