Roadmap for first iteration

This is a development roadmap for the first production iteration of the Phenoscape database and web interface, for introduction at the SICB 2009 meeting.

Nov. 10-14

Jim

• Document interface design requirements on wiki
• [Begun 2008-11-14] Investigate and begin documenting additional data service needs required by interface
• Start Rails web interface project; commit to SVN.
• [Complete 2008-11-14] Write EQ count script, as per Paula's request, using Ruby; provide results to Phenoscape mailing list.

Cartik

• [Complete 2008-11-13] Set up Eclipse project for Restlet based web service application on personal machine, commit to OBD-WS SVN.
  • Cartik and Jim worked together on this and discussed the basics of Restlet applications.
  • Can be found in SVN at https://obo.svn.sourceforge.net/svnroot/obo/OBD-WS/trunk
• [Term info complete 2008-11-14] Begin implementing dummy term info and autocomplete services.
  • Term info query has been tested with the database on Cartik's laptop. Results are returned in JSON format as requested by Jim

Nov. 17-21

Jim

• Document data retrieval web service specifications
  • Anatomy
  • Taxon
  • Genes
• Implement Rails app skeleton and code front page
• Implement reusable JavaScript term info panel and embed in front page search interface.
• Address NEXUS/Phenote file merging issues with Paula. Provide problematic files as NeXML to Paula and Wasila.

Cartik

• Deploy OBD-WS application; continue deploying in-progress builds.
  • Package as WAR, deploy on Eryops.
  • Include dummy autocomplete and term info services.
• Begin implementing live Term Info service within OBD-WS application.
• Begin implementing live Autocomplete service within OBD-WS application.

Nov. 24-28

Jim

• mostly on vacation

Cartik

• Complete Term Info service
• Complete Autocomplete service.
• Provide dummy Anatomy, Taxon, and Gene data service(s).

Dec. 1-5

Jim

• Implement anatomy UI.
• Begin using autocomplete and term info services in all so-far developed user interfaces.

Cartik

• Write code to parse ZFIN phenotype data and load into OBD
  • See http://zfin.org/zf_info/downloads.html#phenotype
  • Data: http://zfin.org/data_transfer/Downloads/pheno_obo.txt
  • should use "exhibits" relation
• Enhance OBD data loader pipeline to perform pre-processing of ZFA ontology, replacing xrefs with is_a links to TAO
  • These xrefs seem to still be in TAO - may have to fix that or work around

Dec. 8-12

Jim

• Complete anatomy user interface.
• Begin implementing taxon user interface.

Cartik

• Complete ZFIN data loading tasks.
• Implement data service(s) related to Anatomy (requirements documented Nov. 17-21).

Dec. 15-19

Jim

• Complete taxon user interface.
• Implement and complete gene user interface.

Cartik

• Complete implementing Anatomy data services.
• Begin implementing Taxon data services.

Dec. 22 - Jan. 2 (2 weeks)

Jim

• Mostly on vacation.

Cartik

• Complete Taxon data services.
• Completely implement Gene data services.

Outcome

Query UI

• Anatomy
• Taxon
• Gene

Data Content

• Ontologies
• Anatomy ontologies linkage
• Phenoscape annotations (NeXML)
• ZFIN annotations (tab-delimited)