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Pronto

Pronto. Trish Whetzel Center for Bioinformatics University of Pennsylvania. What is Pronto?. System for ontology term proposals Consists of: Web service Facilitate term proposals by annotation applications Database backend Ontology storage and term curation information Mailing list

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Pronto

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  1. Pronto Trish Whetzel Center for Bioinformatics University of Pennsylvania

  2. What is Pronto? • System for ontology term proposals • Consists of: • Web service • Facilitate term proposals by annotation applications • Database backend • Ontology storage and term curation information • Mailing list • Notify the community of changes to terms • Web forms • Term proposals by people as singletons or batch term proposals

  3. Ontology Development Process • Phases • Development Phase • Use cases/Term Requirements • Card sorting, develop term hierarchy (is-a relations), term definitions • Build Ontology - add class restrictions, axioms, etc. • Production Phase • Use of ontology by other sources, e.g. databases, annotation applications, etc. • Add new terms as needed by community Pronto is designed for use during the production phase of ontology development

  4. Motivation • Enhanced functionality compared to the existing Sourceforge term tracker • Ability to collect information about a term proposal in a structured format • Term name • Definition • Parent Class of term • Synonyms • Programmatic access • Queries to display term status, term history, batch loading of approved terms into the ontology file • Web service for automated term submission from annotation applications

  5. Term Proposals

  6. New MO Term tracker Existing SourceforgeTerm Tracker

  7. MO TermTracker • Existing Features • Propose new terms • Update term name and/or definition • Display Status of terms • Search by • Class • Date • Submitter • Suggestions for other functions?

  8. Search By Class

  9. MO Term Service • Web Service • Definition: A Web Service is a software component that is described via WSDL and is capable of being accessed via standard network protocols such as but not limited to SOAP over HTTP. • SOAP - Simple Object Access Protocol • Definition: SOAP is a lightweight XML based protocol used for invoking web services and exchanging structured data and type information on the Web.

  10. MO Term Service cont. • Written in Java, can accept a SOAP object generated in any language • WSDL operations • e.g. AddTerm - load term proposals into the Pronto schema • AddTerm operation requires 6 parameters • Login • Password • Boolean to indicate if password is being sent encrypted • Term name • Definition • Parent Class

  11. Mock-up of MIAME-Express with Web Service Display Proposed Terms

  12. Example Web Service Client in PHP <?php require_once ('/world/www.cbil-https/htdocs/MOTerm/nusoap/lib/nusoap.php'); $params = array ( 'login' => $login, -> HIDDEN VARIABLE 'password' => $passwd, -> HIDDEN VARIABLE 'encrypted' => 'false', -> HIDDEN VARIABLE 'termName' => $_POST['term'], -> PROVIDED BY USER 'termDefinition' => $_POST['definition'], -> PROVIDED BY USER 'termParentClass' => $parentClass -> HIDDEN VARIABLE ); $serverpath = 'http://delphi:8090/axisDev/services/MoTermService?wsdl'; $client = new soapclient($serverpath, true); $result = $client->call('addTerm', $params); ?>

  13. Pronto Schema

  14. Future Additions • Batch upload of terms • Propose synonyms • Additional Web service operations? https://www.cbil.upenn.edu/MOTerm/

  15. Components applicable for development of OBI? • Batch loading of terms into the tracker • Batch loading of terms and annotations into the ontology file • Others?

  16. Jerric Gao Elisabetta Manduchi Junmin Liu Jonathan Schug Angel Pizarro Chris Stoeckert Use Cases and Beta testers Helen Parkinson Tina Boussard-Hernandez Pete Souda Stefan Weimann Ryan Brinkman Acknowledgements

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