Difference between revisions of "Roadmap for first iteration"
From phenoscape
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===Cartik=== | ===Cartik=== | ||
* Set up Eclipse project for Restlet based web service application on personal machine, commit to OBD-WS SVN. | * Set up Eclipse project for Restlet based web service application on personal machine, commit to OBD-WS SVN. | ||
| − | * Begin implementing | + | * Begin implementing dummy term info and autocomplete services. |
| − | |||
| − | |||
| − | |||
| − | |||
==Nov. 17-21== | ==Nov. 17-21== | ||
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===Cartik=== | ===Cartik=== | ||
| − | |||
| − | |||
* Deploy OBD-WS application; continue deploying in-progress builds. | * Deploy OBD-WS application; continue deploying in-progress builds. | ||
** Package as WAR, deploy on Eryops. | ** Package as WAR, deploy on Eryops. | ||
| − | ** Include | + | ** 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== | ==Nov. 24-28== | ||
| Line 39: | Line 32: | ||
* mostly on vacation | * mostly on vacation | ||
===Cartik=== | ===Cartik=== | ||
| − | * | + | * Complete Term Info service |
| − | * | + | * Complete Autocomplete service. |
| + | * Provide dummy Anatomy, Taxon, and Gene data service(s). | ||
==Dec. 1-5== | ==Dec. 1-5== | ||
| Line 47: | Line 41: | ||
* Begin using autocomplete and term info services in all so-far developed user interfaces. | * Begin using autocomplete and term info services in all so-far developed user interfaces. | ||
===Cartik=== | ===Cartik=== | ||
| − | * | + | * 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 | ||
| + | * 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== | ==Dec. 8-12== | ||
| Line 56: | Line 53: | ||
* Begin implementing taxon user interface. | * Begin implementing taxon user interface. | ||
===Cartik=== | ===Cartik=== | ||
| + | * Complete ZFIN data loading tasks. | ||
| + | * Implement data service(s) related to Anatomy (requirements documented Nov. 17-21). | ||
==Dec. 15-19== | ==Dec. 15-19== | ||
| Line 61: | Line 60: | ||
* Complete taxon user interface. | * Complete taxon user interface. | ||
* Implement and complete gene 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=== | ===Cartik=== | ||
| + | * Complete Taxon data services. | ||
| + | * Completely implement Gene data services. | ||
| + | |||
==Outcome== | ==Outcome== | ||
===Query UI=== | ===Query UI=== | ||
Revision as of 21:46, 11 November 2008
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
- Document interface design requirements on wiki
- Investigate and begin documenting additional data service needs required by interface
- Start Rails web interface project; commit to SVN.
- Write EQ count script, as per Paula's request, using Ruby; provide results to Phenoscape mailing list.
Cartik
- Set up Eclipse project for Restlet based web service application on personal machine, commit to OBD-WS SVN.
- Begin implementing dummy term info and autocomplete services.
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
- 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
- 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)
