PhyloSoC:Export ontology-based phenotype descriptions to EOL

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Revision as of 10:20, 17 June 2011 by Alexgansca (talk) (Week 3 (June 6 - June 13))
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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 available, use phenotype annotations to taxa in the OWL format.
  • Given two ore more taxa with phenotype annotations, find common anatomical structures between those.
  • 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.

This will be done using only the information in the provided taxa files.

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 presence of [phenotype_entity] or the absence of [phenotype_entity]".

Week 3 (June 6 - June 13)

  • Cover all the methods implemented so far with tests using the Ictalurus genus and the Ictalurus australis and Ictalurus punctatus taxa.
  • Clean all the code so far and pushed it to github.

Week 4 (June 13 - June 20)

  • At this point, I have extracted phenotypic traits and those can serve as a starting point for the project module that builds human-readable text for EoL.
  • Experiment different methods for building text from phenotype annotations. (Here additional information on this these annotations would be useful. Subtask : find out how I could obtain such information).
  • Begin writing code for this module.

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)