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.
- [Complete] Document interface design requirements on wiki
- [Ongoing] Investigate and begin documenting additional data service needs required by interface
- [Complete] Start Rails web interface project; commit to SVN.
- [Complete] Write EQ count script, as per Paula's request, using Ruby; provide results to Phenoscape mailing list.
- [Complete] 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
- [Complete] Begin implementing dummy term info and autocomplete services.
- [Ongoing] Document data retrieval web service specifications
- Anatomy [Done]
- Taxon [Postponed]
- Genes [Done]
- [Complete] Implement Rails app skeleton and code front page
- [Postponed to after SICB] Address NEXUS/Phenote file merging issues with Paula. Provide problematic files as NeXML to Paula and Wasila.
- [Complete] Deploy OBD-WS application; continue deploying in-progress builds.
- Package as WAR, deploy on Eryops.
- Include dummy autocomplete and term info services.
- [Complete] Begin implementing live Term Info service within OBD-WS application.
- [Complete] Begin implementing live Autocomplete service within OBD-WS application.
- [Complete] mostly on vacation
- [Complete] Complete Term Info service
- [Complete] Complete Autocomplete service.
- NOTES (December 9, 2008): Term info search and autocomplete services have been tested on Phenoscape database on Eryops.
- Results for autocomplete are returned in JSON format and have been verified by Jim
- [Abandoned] Provide dummy Anatomy, Taxon, and Gene data service(s).
- [Done] Implement anatomy UI.
- [Complete] Begin using autocomplete and term info services in all so-far developed user interfaces.
- [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 complete (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
- [Completed on 2008-12-10] 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
- NOTES (Date: Dec 10, 2008)
- Is a links corresponding to DbXref links between ZFA and TAO terms have been added to Phenoscape database
- Is a links are added correctly irrespective of direction of DbXref link between ZFA and TAO terms
- New Phenoscape database will be loaded into Darwin tomorrow via PGSQL dump
- [Done] Complete anatomy user interface.
- [Ongoing] Begin implementing taxon user interface - changed to Gene interface
- [Complete] Complete ZFIN data loading tasks.
- [First version deployed 12-12-2008]Implement data service(s) related to Anatomy (requirements documented Nov. 17-21).
- Next version deployed on Dec 14, 2008
- Tested on Eryops by Cartik on Dec 14
- To be verified by Jim
- Complete taxon user interface. [Postponed]
- [Ongoing] Implement and complete gene user interface.
- [Complete]Complete implementing Anatomy data services.
- [Complete]Begin implementing Taxon data services - changed to Gene.
Dec. 22 - Jan. 2 (2 weeks)
- Mostly on vacation.
- [Postponed]Complete Taxon data services.
- [Complete]Completely implement Gene data services.
- First few versions of anatomy data services have been implemented and deployed on Eryops as of Dec 20
- First version of gene data services has been implemented and deployed on Eryops as of Dec 20
- Anatomy ontologies linkage
- Phenoscape annotations (NeXML)
- ZFIN annotations (tab-delimited)