PhyloSoC:Export ontology-based phenotype descriptions to EOL

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Revision as of 10:24, 30 May 2011 by Alexgansca (talk) (Week 2 (May 30 - June 6))
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Jim Balhoff (primary)

Chris Mungall

Matt Yoder

Cyndy Parr

Project description

Short abstract

This project involves developing a system that will map the phenotypic data from an OBD database to the EOL transfer schema. This implies determining what phenotypic information can be used and creating human-readable segments of text that can be integrated in a Encyclopedia of Life page.


Details regarding the development of this project will be posted on the Ontophenotype blog.

Project plan

Community Bonding Period

  • Subscribe to recommended mailing lists Done
  • Start github repository and check git settings and connectivity Done
  • Start project blog Done

Week 1 (May 23 - May 30)

  • Write a parser for the Phenoscape data in the JSON format. Done

Week 2 (May 30 - June 6)

  • If availebe, use phenotype annotations to taxa in the OWL format.
  • Given two ore more taxa with phenotype annotations, find common anatomical structures between those.
 This will be done using only the information in the provided taxa files.
  • Given a starting taxon and other taxa, find the phenotype data that differentiates the first taxon from the others. In other words, find what makes a taxon anatomically particular compared to others.

It would be interesting to present such information in an EOL page. For example, in a section about a species morphology, a phrase like "This species sets apart from the others in the [species_genus] by the lack of [phenotype_entity]." could be automatically generated. Another example is for a genus page : "A common denominator for this genus is the presents of [phenotype_entity] or the absence of [phenotype_entity]".

Week 3 (June 6 - June 13)

Week 4 (June 13 - June 20)

Week 5 (June 20 - June 27)

Week 6 (June 27 - July 4)

Week 7 (July 4 - July 11)

Week 8 (July 11 - July 18)

Week 9 (July 18 - July 25)

Week 10 (July 25 - August 1)

Week 11 (August 1 - August 8)

Week 12 (August 8 - August 15)