Difference between revisions of "Collaborative Phenotype Annotation"

From phenoscape
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=== MX versus Phenex ===
 
=== MX versus Phenex ===
The [http://mx.phenomix.org/index.php/Main_Page MX web application] is being enhanced with features for EQ annotation of character matrix data. Phenoscape may be interested in adopting this system for data curation. This page collects a list of pros and cons to help decide whether to adopt the MX web application or continue using the Phenex desktop software.
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The [http://mx.phenomix.org/index.php/Main_Page MX web application] is being enhanced with features for EQ annotation of character matrix data. Phenoscape may be interested in adopting this system for data curation. This page collects a list of pros and cons to help decide whether to adopt the MX web application or continue using the [[Phenex]] desktop software.
  
 
==== MX pros ====
 
==== MX pros ====
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* less independence for anonymous user - requires server management, project accounts
 
* less independence for anonymous user - requires server management, project accounts
  
==== Phenex pros ====
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==== [[Phenex]] pros ====
 
* outputs files ready for KB; workflow in place
 
* outputs files ready for KB; workflow in place
 
* integrates OBO-Edit code for ontology visualization and query
 
* integrates OBO-Edit code for ontology visualization and query
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* easy to point to customized versions of ontologies
 
* easy to point to customized versions of ontologies
  
==== Phenex cons ====
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==== [[Phenex]] cons ====
 
* less flexible interface
 
* less flexible interface
 
* requires use of version control system for collaboration
 
* requires use of version control system for collaboration

Revision as of 23:50, 10 September 2011

Requirements

A requirements and priorities document is in development and being reviewed by stakeholders.

Technology options

MX versus Phenex

The MX web application is being enhanced with features for EQ annotation of character matrix data. Phenoscape may be interested in adopting this system for data curation. This page collects a list of pros and cons to help decide whether to adopt the MX web application or continue using the Phenex desktop software.

MX pros

  • web based, central database
    • easy collaboration
    • record of who changed what
    • latest application version always running
  • many other features besides EQ annotation
  • easy to create new pages displaying various reports using data
  • initial development of phenotype categories for EQ
  • unify more of Jim's effort

MX cons

  • many other features besides EQ annotation
  • missing ontology visualization tools
  • EQ interface in flux - not quite ready for primetime
  • requires internet connection
  • output format suitable for KB ingestion must be coded
  • reliance on BioPortal web services for ontology data
  • less independence for anonymous user - requires server management, project accounts

Phenex pros

  • outputs files ready for KB; workflow in place
  • integrates OBO-Edit code for ontology visualization and query
  • "simple", targeted interface
  • easy to point to customized versions of ontologies

Phenex cons

  • less flexible interface
  • requires use of version control system for collaboration
  • tightly coupled to OBO format
  • updates must be manually downloaded and installed