Diamonds wish list

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Diamonds wish list

• Complete Medline (full text?) searches for lists
  of named entities from experimental results
• Subcorpus Medline (full text?) searches for lists
  of named entities from experimental results,
  restricted to the cell cycle components, plants
  and possibly other subsections
• Subcorpus Medline (full text?) searches for lists
  of named entities from experimental results,
  restricted to 100 core cell cycle Arabidopsis
  (others?) genes
• Indexing of available full text corpora for gene
  and physical interactions
• Curation tool for manual editing of core entity
  information and relationships
• Tool for combining high-throughput data with the
  above search topics

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Level 1 (relatively close in time)

• Indexing of abstracts
• Gene names
• Protein names
• MeSH terms
• GO terms
• Chemical compounds
• Mutations/biodiversity
• PubGene search tool
• Definition of subcorpora
• Plant journals, other organism specific topical
  journals
• Cell cycle relevant genes...

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Level 2 (medium time span)

• Full text indexing
• Available corpora include
• Plant journal collections
• Highwire
• PSB collection
• BMC corpus

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Level 3 (longer term)

• Abstract and full text interaction indexing
• NLP based approaches under development
• Refinement based on curation for topics of
  interest

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Development/implementation efforts

• PubGene 2.5 available
• PubGene 2.6 in alpha, includes cross-organism and
  combines with the sequence level
• Subcorpora definitions
• Indexing of cell cycle named entities
• Entities derived through manual curation from
  data of computational approaches
• Similar for interactions
• Curation tool
• GUI
• back-end
• Export to GIN-db
• Export of relevant data to relevant formats and
  engines

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