Difference between revisions of "Roadmap for first iteration"

From phenoscape
(Jim)
 
(24 intermediate revisions by 3 users not shown)
Line 2: Line 2:
 
==Nov. 10-14==
 
==Nov. 10-14==
 
===Jim===
 
===Jim===
* '''[Complete 2008-11-18]''' Document interface design requirements on wiki
+
* '''[Complete]''' Document interface design requirements on wiki
 
** See [[Web_UI_first_iteration|overview]] and [[Web_UI_mockups|mockup drawings]].
 
** See [[Web_UI_first_iteration|overview]] and [[Web_UI_mockups|mockup drawings]].
 
** These will continue to be updated.
 
** These will continue to be updated.
* '''[Begun 2008-11-14]''' Investigate and begin documenting additional data service needs required by interface
+
* '''[Ongoing]''' Investigate and begin documenting additional data service needs required by interface
 
* '''[Complete]''' Start Rails web interface project; commit to SVN.
 
* '''[Complete]''' 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.
+
* '''[Complete]''' Write EQ count script, as per Paula's request, using Ruby; provide results to Phenoscape mailing list.
  
 
===Cartik===
 
===Cartik===
* '''[Complete 2008-11-13]''' Set up Eclipse project for Restlet based web service application on personal machine, commit to OBD-WS SVN.
+
* '''[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.
 
** 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
 
** 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.
+
* '''[Complete]''' 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==
 
==Nov. 17-21==
 
===Jim===
 
===Jim===
 
* '''[Ongoing]''' Document data retrieval web service specifications
 
* '''[Ongoing]''' Document data retrieval web service specifications
** Anatomy
+
** Anatomy '''[Done]'''
** Taxon
+
** Taxon '''[Postponed]'''
** Genes
+
** Genes '''[Done]'''
 
* '''[Complete]''' Implement Rails app skeleton and code front page
 
* '''[Complete]''' Implement Rails app skeleton and code front page
 
* '''[Complete]''' Implement reusable JavaScript term info panel and embed in front page search interface.
 
* '''[Complete]''' 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.
+
* '''[Postponed to after SICB]''' Address NEXUS/Phenote file merging issues with Paula. Provide problematic files as NeXML to Paula and Wasila.
  
 
===Cartik===
 
===Cartik===
* '''[First deployment on 2008-12-01]''' Deploy OBD-WS application; continue deploying in-progress builds.
+
* '''[Complete]''' Deploy OBD-WS application; continue deploying in-progress builds.
 
** Package as WAR, deploy on Eryops.
 
** Package as WAR, deploy on Eryops.
 
** Include dummy autocomplete and term info services.
 
** Include dummy autocomplete and term info services.
* Begin implementing live Term Info service within OBD-WS application. ''[Done]''
+
* '''[Complete]''' Begin implementing live Term Info service within OBD-WS application.
* Begin implementing live Autocomplete service within OBD-WS application. ''[Done]''
+
* '''[Complete]''' Begin implementing live Autocomplete service within OBD-WS application.
  
 
==Nov. 24-28==
 
==Nov. 24-28==
 
===Jim===
 
===Jim===
* mostly on vacation
+
* '''[Complete]''' mostly on vacation
 
===Cartik===
 
===Cartik===
*'''[Complete term info and autocomplete services 2008-11-26]'''
+
* '''[Complete]''' Complete Term Info service
** Complete Term Info service ''[Done]''
+
* '''[Complete]''' Complete Autocomplete service.
** Complete Autocomplete service. ''[Done]''
+
** ''NOTES (December 9, 2008)'': Term info search and autocomplete services have been tested on Phenoscape database on Eryops.
** ''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
+
** Results for autocomplete are returned in JSON format and have been verified by Jim
* Provide dummy Anatomy, Taxon, and Gene data service(s).
+
* '''[Abandoned]''' Provide dummy Anatomy, Taxon, and Gene data service(s).
  
 
==Dec. 1-5==
 
==Dec. 1-5==
 
===Jim===
 
===Jim===
* '''[Ongoing]''' Implement anatomy UI.
+
* '''[Done]''' Implement anatomy UI.
 
* '''[Complete]''' 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.
  
Line 59: Line 58:
 
*# Database upload to Darwin complete (Nov 21, 2008)
 
*# 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
 
*# 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
+
* '''[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
 
** 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 ZFIN data loading tasks. ''[Done]''
+
* '''[Complete]''' Complete ZFIN data loading tasks.
* Implement data service(s) related to Anatomy (requirements documented Nov. 17-21).
+
* '''[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 and complete gene user interface.
+
* '''[Ongoing]''' Implement and complete gene user interface.
 +
 
 
===Cartik===
 
===Cartik===
* Complete implementing Anatomy data services.
+
* '''[Complete]'''Complete implementing Anatomy data services.
* Begin implementing Taxon data services.
+
* '''[Complete]'''Begin implementing Taxon data services - changed to Gene.
  
 
==Dec. 22 - Jan. 2 (2 weeks)==
 
==Dec. 22 - Jan. 2 (2 weeks)==
Line 82: Line 91:
 
* Mostly on vacation.
 
* Mostly on vacation.
 
===Cartik===
 
===Cartik===
* Complete Taxon data services.
+
* '''[Postponed]'''Complete Taxon data services.
* Completely implement Gene 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==
Line 96: 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)