Pronto

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Pronto

• Trish Whetzel
• CBIL
• University of Pennsylvania

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What is Pronto?

• System for automated ontology term proposals by
  annotation applications and term
  proposals/curation by individuals
• Consists of
• Web Service
• Web forms
• Database backend
• Sourceforge mailing list

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Ontology Development Process

• Phases
• Development Phase
• Use cases/Term Requirements
• Card sorting, develop term hierarchy
• Build Ontology - add definitions, etc.
• Production Phase
• Use of ontology by other source, 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

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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
• Programmatic access
• Queries to display term status, term history
• Web service for automated term submission

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Term Proposals
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Existing SourceforgeTerm Tracker
New Mo Term tracker
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MO TermTracker

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

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Search By Class
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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.

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MO Term Service cont.

• Written in Java, can accept a SOAP object
  generated in any language
• WSDL currently contains 1 operation
• 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

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Mock-up of MIAME-Express with Web Service
Display Proposed Terms
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Example Web Service Client in PHP
lt?php require_once ('/world/www.cbil-https/htdocs/
MOTerm/nusoap/lib/nusoap.php') params array
( 'login' gt login, -gt HIDDEN
VARIABLE 'password' gt passwd,
-gt HIDDEN VARIABLE 'encrypted'
gt 'false', -gt HIDDEN VARIABLE
'termName' gt _POST'term', -gt PROVIDED BY
USER 'termDefinition' gt
_POST'definition', -gt PROVIDED BY USER
'termParentClass' gt parentClass -gt
HIDDEN VARIABLE ) serverpath
'http//delphi8090/axisDev/services/MoTermService
?wsdl' client new soapclient(serverpath,
true) result client-gtcall('addTerm',
params) ?gt
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Pronto Schema
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Future Additions

• New searches
• Batch upload of terms
• Use with other ontologies?
• Additional Web service operations?

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Acknowledgements

• Jerric Gao
• Elisabetta Manduchi
• Junmin Liu
• Jonathan Schug
• Angel Pizarro
• Chris Stoeckert

• Use Cases and Beta testers
• Helen Parkinson
• Tina Boussard-Hernandez
• Pete Souda

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