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

• [Complete 2008-11-18] Document interface design requirements on wiki
  • See overview and mockup drawings.
  • These will continue to be updated.
• [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

• [First deployment on 2008-12-01] 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. [Done]
• Begin implementing live Autocomplete service within OBD-WS application. [Done]

Nov. 24-28

Jim

• mostly on vacation

Cartik

• [Complete term info and autocomplete services 2008-11-26]
  • Complete Term Info service [Done]
  • Complete Autocomplete service. [Done]
  • NOTES (November 26, 2008): Term info search and autocomplete services have been tested on Phenoscape database on Cartik's laptop. Results for autocomplete are returned in JSON format and need to be verified by Jim
• 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

• [Complete 2008-11-20] 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
  • NOTES (Date: Nov 20, 2008):
  1. ZFIN phenotype curations have been loaded into OBD database on Cartik's laptop along with 71 NeXML files from Phenoscape project
  2. ZFIN curations use PHENOSCAPE:exhibits and PHENOSCAPE:hasAllele relations
  3. Database size is 1.6 GB after running the OBD reasoner
  4. Database upload to Darwin complete (Nov 21, 2008)
  5. Loaded ZFIN data has been tested against OBD query engine and Term search engine. The latter is to be part of prototype to be demo'ed at SICB, Boston
• [Began work on 2008-11-30] 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. [Done]
• 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)