Difference between revisions of "Roadmap for first iteration"

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==Nov. 10-14==
 
==Nov. 10-14==
 
===Jim===
 
===Jim===
−
* Document interface design requirements on wiki
+
* '''[Complete]''' Document interface design requirements on wiki
−
* Investigate additional data service needs required by interface
+
** See [[Web_UI_first_iteration|overview]] and [[Web_UI_mockups|mockup drawings]].
−
* Start Rails web interface project
+
** These will continue to be updated.
−
* Write EQ count script using Ruby
+
* '''[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.
 +
 
 
===Cartik===
 
===Cartik===
−
* Set up Eclipse project for Restlet based web service application in OBD-WS
+
* '''[Complete]''' Set up Eclipse project for Restlet based web service application on personal machine, commit to OBD-WS SVN.
−
* Begin implementing Term Info service
+
** Cartik and Jim worked together on this and discussed the basics of Restlet applications.
−
* Write code to parse ZFIN phenotype data and load into OBD
+
** Can be found in SVN at https://obo.svn.sourceforge.net/svnroot/obo/OBD-WS/trunk
−
** See http://zfin.org/zf_info/downloads.html#phenotype
+
* '''[Complete]''' Begin implementing dummy term info and autocomplete services.
−
** Data: http://zfin.org/data_transfer/Downloads/pheno_obo.txt
 
−
** should use "exhibits" relation
 
  
 
==Nov. 17-21==
 
==Nov. 17-21==
 
===Jim===
 
===Jim===
−
* Document data retrieval web service specifications
+
* '''[Ongoing]''' Document data retrieval web service specifications
−
** Anatomy
+
** Anatomy '''[Done]'''
−
** Taxon
+
** Taxon '''[Postponed]'''
−
** Genes
+
** Genes '''[Done]'''
−
* Implement Rails app skeleton and begin coding front page
+
* '''[Complete]''' Implement Rails app skeleton and code front page
−
* Implement reusable JavaScript term info panel
+
* '''[Complete]''' Implement reusable JavaScript term info panel and embed in front page search interface.
−
* Address file merging issues with Paula.
+
* '''[Postponed to after SICB]''' Address NEXUS/Phenote file merging issues with Paula. Provide problematic files as NeXML to Paula and Wasila.
  
 
===Cartik===
 
===Cartik===
−
* Complete Term Info service
+
* '''[Complete]''' Deploy OBD-WS application; continue deploying in-progress builds.
−
* Deploy OBD-WS application; continue deploying in-progress builds.
+
** Package as WAR, deploy on Eryops.
−
** Include real or dummy info and autocomplete services.
+
** Include dummy autocomplete and term info services.
−
* Enhance OBD data loader pipeline to perform pre-processing of ZFA ontology, replacing xrefs with is_a links to TAO
+
* '''[Complete]''' Begin implementing live Term Info service within OBD-WS application.
−
** These xrefs seem to still be in TAO - may have to fix that or work around
+
* '''[Complete]''' Begin implementing live Autocomplete service within OBD-WS application.
−
* Implement autocomplete service
 
  
 
==Nov. 24-28==
 
==Nov. 24-28==
 
===Jim===
 
===Jim===
−
* mostly on vacation
+
* '''[Complete]''' mostly on vacation
 
===Cartik===
 
===Cartik===
−
* Provide dummy Anatomy data service(s).
+
* '''[Complete]''' Complete Term Info service
−
* Implement data service(s) related to Anatomy (requirements documented Nov. 17-21).
+
* '''[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).
  
 
==Dec. 1-5==
 
==Dec. 1-5==
 
===Jim===
 
===Jim===
−
* Implement anatomy UI.
+
* '''[Done]''' Implement anatomy UI.
−
* Begin using autocomplete and term info services in all so-far developed user interfaces.
+
* '''[Complete]''' Begin using autocomplete and term info services in all so-far developed user interfaces.
 +
 
 
===Cartik===
 
===Cartik===
−
* Provide all defined services as dummy services if not yet implemented.
+
* '''[Complete 2008-11-20]''' Write code to parse ZFIN phenotype data and load into OBD
−
* Complete implementing Anatomy data services.
+
** See http://zfin.org/zf_info/downloads.html#phenotype
−
* Begin implementing Taxon data services.
+
** 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
  
 
==Dec. 8-12==
 
==Dec. 8-12==
 
===Jim===
 
===Jim===
−
* Complete anatomy user interface.
+
* '''[Done]''' Complete anatomy user interface.
−
* Begin implementing taxon user interface.
+
* '''[Ongoing]''' Begin implementing taxon user interface - changed to Gene interface
 +
 
 
===Cartik===
 
===Cartik===
 +
* '''[Complete]''' Complete ZFIN data loading tasks.
 +
* '''[First version deployed 12-12-2008]'''Implement data service(s) related to Anatomy (requirements documented Nov. 17-21).
 +
** ''NOTES''
 +
**# Next version deployed on Dec 14, 2008
 +
**# Tested on Eryops by Cartik on Dec 14
 +
**# To be verified by Jim
  
 
==Dec. 15-19==
 
==Dec. 15-19==
 
===Jim===
 
===Jim===
−
* Complete taxon user interface.
+
* Complete taxon user interface. '''[Postponed]'''
−
* Implement gene user interface.
+
* '''[Ongoing]''' Implement and complete gene user interface.
  
 
===Cartik===
 
===Cartik===
 +
* '''[Complete]'''Complete implementing Anatomy data services.
 +
* '''[Complete]'''Begin implementing Taxon data services - changed to Gene.
 +
 +
==Dec. 22 - Jan. 2 (2 weeks)==
 +
===Jim===
 +
* Mostly on vacation.
 +
===Cartik===
 +
* '''[Postponed]'''Complete Taxon data services.
 +
* '''[Complete]'''Completely implement Gene data services.
 +
** ''NOTES''
 +
**# 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
 +
 
==Outcome==
 
==Outcome==
 
===Query UI===
 
===Query UI===
Line 71: Line 108:
 
* ZFIN annotations (tab-delimited)
 
* ZFIN annotations (tab-delimited)
  
−
[[Category:Informatics]]
+
[[Category:Archive]]

Latest revision as of 19:27, 11 October 2011

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] 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.

Cartik

  • [Complete] Set up Eclipse project for Restlet based web service application on personal machine, commit to OBD-WS SVN.
  • [Complete] Begin implementing dummy term info and autocomplete services.

Nov. 17-21

Jim

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

Cartik

  • [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.

Nov. 24-28

Jim

  • [Complete] mostly on vacation

Cartik

  • [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).

Dec. 1-5

Jim

  • [Done] Implement anatomy UI.
  • [Complete] 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
    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
  • [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)
    1. Is a links corresponding to DbXref links between ZFA and TAO terms have been added to Phenoscape database
    2. Is a links are added correctly irrespective of direction of DbXref link between ZFA and TAO terms
    3. New Phenoscape database will be loaded into Darwin tomorrow via PGSQL dump

Dec. 8-12

Jim

  • [Done] Complete anatomy user interface.
  • [Ongoing] Begin implementing taxon user interface - changed to Gene interface

Cartik

  • [Complete] Complete ZFIN data loading tasks.
  • [First version deployed 12-12-2008]Implement data service(s) related to Anatomy (requirements documented Nov. 17-21).
    • NOTES
      1. Next version deployed on Dec 14, 2008
      2. Tested on Eryops by Cartik on Dec 14
      3. To be verified by Jim

Dec. 15-19

Jim

  • Complete taxon user interface. [Postponed]
  • [Ongoing] Implement and complete gene user interface.

Cartik

  • [Complete]Complete implementing Anatomy data services.
  • [Complete]Begin implementing Taxon data services - changed to Gene.

Dec. 22 - Jan. 2 (2 weeks)

Jim

  • Mostly on vacation.

Cartik

  • [Postponed]Complete Taxon data services.
  • [Complete]Completely implement Gene data services.
    • NOTES
      1. First few versions of anatomy data services have been implemented and deployed on Eryops as of Dec 20
      2. First version of gene data services has been implemented and deployed on Eryops as of Dec 20

Outcome

Query UI

  • Anatomy
  • Taxon
  • Gene

Data Content

  • Ontologies
  • Anatomy ontologies linkage
  • Phenoscape annotations (NeXML)
  • ZFIN annotations (tab-delimited)
Retrieved from "https://wiki.phenoscape.org/wg/phenoscape/index.php?title=Roadmap_for_first_iteration&oldid=9083"