Roadmap for first iteration
From phenoscape
This is a development roadmap for the first production iteration of the Phenoscape database and web interface, for introduction at the SICB 2009 meeting.
Contents
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
- 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
- [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):
- ZFIN phenotype curations have been loaded into OBD database on Cartik's laptop along with 71 NeXML files from Phenoscape project
- ZFIN curations use PHENOSCAPE:exhibits and PHENOSCAPE:hasAllele relations
- Database size is 1.6 GB after running the OBD reasoner
- Database upload to Darwin to be commenced on the morrow (Nov 21, 2008)
- 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
- 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)