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A Virtual File System for the PubChem Chemical Structure and Bioassay Database

A Virtual File System for the PubChem Chemical Structure and Bioassay Database. Wolf-D. Ihlenfeldt Xemistry GmbH K önigstein , Germany . PubChem on the Web. PubChem Project Mission.

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A Virtual File System for the PubChem Chemical Structure and Bioassay Database

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  1. A Virtual File System for the PubChem Chemical Structure and Bioassay Database Wolf-D. IhlenfeldtXemistry GmbH Königstein, Germany

  2. PubChem on the Web

  3. PubChem Project Mission • Provide comprehensive public access to screening data generated by NIH Roadmap Initiative and other public research projects • Link assay results, structures screened, literature references, basic computed properties, external information sources • Convenient and free queries and download of filtered structure and assay data for further research • Wait a moment - they call that convenient ?!?

  4. Problems with Interactive Data Retrieval in PubChem • Separation betweentext/data (Entrez) andstructurequerysystemswithinconsistentinterfaces • Dumbed-down structurequeryinterface, but overengineeredtextquerytools • ObscureEntrezsyntaxforcombining multiple subqueries • QuirkyEntrezapproachesregardingnumericalqueries, quoting, fieldnames, outputformats, historytitles, autoqueryexpansion… • Historyofhistoryproblems

  5. Interactive Data Retrieval in PubChem • Very limited customizationofdownloadabledatacontent • Fullstructuredatarecordonlyas ASN.1 blob, optionallywithgratutioushomebrew XML wrapper • SD-fileisincomplete, a structureapproximationand still not compatiblewithexactinterpretationof MDL standards • Nevertheless, well donesystemforbrowsing, but not forseriousdatacollection

  6. Routes to Programmatic Data Retrieval from PubChem Somedisconnectedcomponentsexist: • Entrez e-utilsBasic accesstoEntreztextdatabases, getstatus, retrieve ID sets, somerecorddataorsethistory via simple text-basedqueries • PubChemstructuredisplaypagesCan beabusedfordirectdownloadofsinglerecords in ASN.1 format, bypassingthe FTP waitqueue • PubChem Power User Gateway (PUG)XML/ASN.1 specificationforexecuting simple structurequeriesandgetting ID sets, history handle fromPubChemservers • Nodirect SQL serverdbaccessever, that‘spolicy!

  7. The Cactvs Toolkit • Universal scriptingenvironmentforchemicaldataprocessing • Framework ofchemicalobjects(ensembles, reactions, tables, …), dynamicallydefinedobjectpropertieswithassociatedcomputationmethods, andextensionmodules (I/O modulesfor different typesoffiles, databaseaccess, data type handlers, commandextensions,…) • Lazycomputation – requestsomedata on an object, and a way will befoundtogetitifpossible

  8. Cactvs and PubChem • Cactvs Toolkitlicensedby NCBI as integral componentofthePubChemsoftwaresuite • Usedforfile I/O, syntaxverification, propertycomputation, structuredepiction, structureidentification via hashcodes, interfaceto NIST InChI suite, fingerprints, sub/superstructure & formulasearchsystem, WWW structuresketching • OnlyexternallyavailabletoolkitthatunderstandsPubChemdatastructures (ASN.1 specsforsubstances, compounds, assays, and PUG) – includingliteraturereferences, conformerdata, etc.

  9. Basic PubChemIntegration • Ensemble object creation via CID:set eh [ens create $cid]Direct download and parsing of binary ASN.1 record via display page. Also supported as file I/O module. • Computation of CID and SIDs from structure:set cid [ens get $eh E_CID]set sidlist [ens get $eh E_SIDSET]Parsing of Entrez E-utils output from submission of InChI string as text search

  10. Basic PubChemIntegration • Compoundnamelookupsetiupacname [ensget $eh E_IUPAC_NAME]Directdownloadandparsingof XML CID displayrecord, extractingOpenEyecomputedname • CAS numberlookupsetcasno [ensget $eh E_CAS] Directdownloadandparsingof XML SID setdisplayrecordswhichcontaindepositor-suppliednames, usingpatternrecognition

  11. Initial PubChem Integration • CAS number I/O moduleset eh [molfile read $casfile]Look up CID as generic term via E-utils, download ASN.1 record via CID. Also supported as object creation commandset eh [ens create $cas]

  12. The PubChem Virtual File Project • ImprovedaccesstoPubChemdatabasemakeitindistinguishablefrom a local, read-onlystructurefile in Cactvs scriptingenvironment • Input functionstransparentlyreadstructuresandalltheirdatafromPubChem • Query functionsconvenientdevelopmentandarchivalofqueriesexceedingthecapabilitesof Web interfacesand PUG, maintainingstandard Cactvs queryandretrievalsyntax

  13. General Approach • Implementa Cactvs I/O moduleI/O modulesincorporatefunctiontableswithrichsetoffunctionsthatareautomaticallycalled in specificsituations, capabilityflags, documentationfields, etc. • Hidden, automaticuseofEntrez E-utilsand PUGRun asmanytasksaspossible on Entrez/PubChemstructuresearch, datadownloadandlocalprocessingonlyas last resort • Optimizeforsakeofefficiencyand just beingniceUsecachingtechniquestoreducenetworkandserverload, observe NCBI scriptaccessrules

  14. PubChem Virtual File I/O Code sample: • filex load pubchem19 • molfile open <pubchem>molfile0 • molfile count molfile012002343 • molfile read molfile0ens0 • ens props ens0…E_INCHI E_IUPAC_NAME E_NCBI_COMPOUND_ID E_EXACT_MASS E_TPSA E_SMILES E_SMILES/2…. • ens get ens0 E_CID1 • molfile read molfile0ens1 • molfile set molfile0 record 999999 Contact Entrez e-utils, get database status E-utils, get 5K sector of record-CID map, then single-record ASN.1 download via display page Single-record ASN.1 download via display page Try to load compressed CID use bit vector from xemistry.com, fallback are more e-utils queries for record/CID map sectors

  15. Simple PubChem Queries Code sample: set fh [molfile open <pubchem>] set cidlist [molfile scan $fh „structure >= $smarts“ \ {proplist E_CID}] Operations behind the scenes: • Set-up of PUG record • Post PUG, monitor return status • Cache CID result data • Direct access to result set, no structure download

  16. Intermediate PubChem Queries Code sample: set fh [molfile open <pubchem>] set enslist [molfile scan $fh \„or {structure = $smiles1} {structure = $smiles2}\ {structure = $smiles3}“ enslist] Operations behind the scenes: • Create and post PUG records, get history keys • Perform server-side e-utils result merge via history keys • Retrieve CID set • Download structures as ASN.1 blobs via CID

  17. Power PubChem Queries Code sample: setstfh [molfile open $mysdfile] setfh [molfile open <pubchem>] setth [molfilescan $fh \„and {structure ~>= $stfh 95} {formula >= \[M\]0} \ {E_NMOLECULES = 1} {E_STEREO_COUNT(1) >= 1}“ \{table E_CID score E_SMILES E_FORMULA recordimage} \ {} 1000] tablewrite $th similar_in_pubchem.xls Bioassayaccessisunfortunately not yetpartof PUG.

  18. Summary • Goal: MakePubChemfinallyconvenientlyaccessibleasdatasourceforlocalwork • Feature: Read alldatafromPubChemrecords, andfurthermanipulateittoyourheart‘scontent • Feature: Write andconservecomplexqueriesbeyondwhatyoucan do withthe Web interface • Feature: Export data in manymoreformatsthanpossible via the Web interface • Future: Sort out remainingproblemswithcachingandfieldaccess in complexqueries, use parallel PUG submissions, integrateassaydataaccess

  19. Availability • Is a standardcomponentof3.353 andlater CACTVS toolkitreleases • Free academicdownloadsfromwww.xemistry.comfor multiple platforms (Linux, MS Windows, MacOSX, Solaris, BSD) • Also partofbasiccommercialtoolkit, tobedistributedwithregularcustomerupdates

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