Genome Catalogue

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Genome Catalogue

• Tanya Gray
• Centre for Ecology Hydrology, Oxford
• 11th September 2006

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Genome Catalogue

• Software
• User Functionality
• How to be involved

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Software

• Open Source Software
• Apache Tomcat
• eXist XML database
• Orbeon Presentation Server
• Developed as a generic application
• deployment MICheck, Genome Catalogue
• relevant when asking for a new feature add to
  generic version or specific to the Genome
  Catalogue?

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Software
Apache Tomcat Server
eXist XML database
Orbeon Presentation Server
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Software

• XML schema archive
• upload XML schema
• transformation of schema to input forms, html
  reports, summary pages, term list
• Reports saved as XML instances
• validate against XML schema

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User Functionality

• Public Functions
• browse reports in XML, HTML
• download most recent XML schema
• search reports
• create a user account
• view user activity

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User Functionality ctd./

• Restricted-access Functions
• create reports (edit/delete reports you have
  created)
• upload XML schema files
• generate forms from a selected XML schema
• add/delete terms from XML schema and assign status

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How to be involved

• Create a user account
• add/edit/delete genome reports,
• add/delete terms assign status to terms
• GSC Wiki
• GSC Technical Implementation Working Group
• GSC SourceForge Functions
• mailing lists
• feature request
• bug report

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Genome Catalogue - Create a user account

• location http//darwin.nox.ac.uk/gsc/gcat
• create a user account to add genome reports and
  review terms

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GSC Wiki

• Location
• http//darwin.nerc-oxford.ac.uk/gc_wiki
• Access
• Unrestricted
• Purpose
• Record of useful information, resources, FAQs,
  etc

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SourceForge

• Project Web site
• http//sourceforge.net/projects/gensc/
• Functions
• Mailing Lists
• Feature Request Tracker
• Bug Report Tracker

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SourceForge Mailing Lists

• Gensc-wgs-all (54)
• For working groups to discuss checklist content
  and completion of case studies
• Gensc-devel (16)
• Discuss implementation and development of the
  MIGS specification
• Gensc-coord (1) new
• For GSC coordinators
• Gensc-announce (0) new
• Announcements relating to the GSC

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SourceForge Feature Tracker

• Location
• https//sourceforge.net/tracker/?group_id153365a
  tid787478
• Submit and track feature requests for the Genome
  Catalogue
• Can be submitted anonymously or with SourceForge
  user account

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SourceForge Bug Report Tracker

• Location
• https//sourceforge.net/tracker/?group_id153365a
  tid787475
• Report and track resolution of bugs identified in
  the Genome Catalogue
• Reports can be sent anonymously or with
  SourceForge user account

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GSC Technical Implementation Working Group

• First GSC Technical Implementation Working Group
  workshop held in December 2005
• Further workshops to be held to discuss technical
  implementation including discussions on
• ontology development
• metadata exchange
• user interface design

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Community Involvement