Curation Tool

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Curation Tool

• DIAMONDS WP2PubGene, Tor-Kristian
  Jenssentkj_at_pubgene.com

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Performed work

• Database design and implementation
• Article data
• Dictionary data
• User annotations and other user data
• Design and implementation of support programs for
  data management
• Java curation tool data server
• Java curation tool client with GUI

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Curation tool overview

• Background Tool for knowledge base construction
• Use scenario Manual curator, e.g.,
  re-constructing pathway or interaction networks
  from literature
• Feature highlights
• Multi-user, concurrent server-client system
• Client with graphical user interface
• Server built with tomcat servlets and
  web-services on top of relational database
  (MySQL)
• Includes PubGene text-indexing information
• Search functionality
• Association/Interaction/Relationship editing
  genes, proteins from model organisms
• Includes extensive dictionaries/ontologies

4
Technical specifications

• Fully implemented in java (version 1.5)
• GUI application (client) distributed as jar
• Data server separated from underlying relational
  database (MySQL5) by data API level
• Data server combines tomcat servlets and java web
  services
• User data separated from other data (article,
  dictionaries, etc.)
• XML for data transport format for flexibility
  and compatibility
• CVS for version control and secure storage of
  development project

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Data model

• A general concept of association An association
  is a binding between physical entities or
  components
• Entity occurrence or reference typical entities
  are genes, proteins, etc.
• Genes and proteins are linked to organism
• Associations can be ordered or un-ordered
• Associations can be nested
• Main associations up-regulates, complexes
  with
• Secondary associations cellular or temporal
  specification

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User workspace

• List of working articles articles can be added
  and removed from this list
• Article search by keyword and entity occurrence
• List of user annotations
• Annotations can be shared among annotators
  adding of comments/votes etc.
• Annotations are submitted to central storage
  server
• User workspace available from anywhere
• Article locking allows multiple concurrent users

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Article search
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Entity search

• Search for entity by name and entity type
• Upon identification of correct entity, retrieve
  article list according to PubGene index

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Main window
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Panels
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Dictionaries
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Next steps

• Full text articles
• Improve article navigation/search
• Dictionary editing
• Additional dictionaries
• Additional indexes
• Refine curation tool user data model
• Database views/filters
• restrict to cell cycle genes/proteins