Compositional Term Submission Tool: Difference between revisions
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(aka [[TermGenie]]) | |||
Project lead: Chris | Project lead: Chris | ||
Coordinates with: ontology-editors | Coordinates with: ontology-editors | ||
== Purpose == | |||
An increasing number of terms coming in from sourceforge are automatable compositional terms - particularly regulation terms. Ontology editors waste time performing manual tasks that could be automated, and curators experience a bottleneck during annotation. | |||
The compositional term request system allows annotators to use a web template system to instantaneously get the term they require, provided it conforms to an existing pre-determined template. A reasoner is used to place the term automatically in the hierarchy. | |||
Documentation for the system is available here: [[TermGenie]] | |||
== Groups == | |||
* [[Ontology_Development]] | |||
== Project Dependencies == | |||
* [[Full_Text_Indexing]] (soft dependency) | |||
* [[Transition to OWL]] (for [[#v2]]) | |||
== Status == | |||
[[#v1]] is available to curators, currently on regulation requests are live | |||
* http://berkeleybop.org/obo/quickterm/GO | |||
== Deliverables == | == Deliverables == | ||
=== v1 === | |||
v1 is obo-format dependent, uses a custom reasoner, and relies on various ad-hoc scripts | |||
==== v1 report ==== | |||
v1 is | A report on the v1 implementation is available: | ||
* [[Compositional Term Submission Tool v1 Report]] | |||
== v2 == | === v2 === | ||
v2 will be a port of [[#v1]] | v2 will be a port of [[#v1]] | ||
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* works off of OBO or OWL files | * works off of OBO or OWL files | ||
* uses OWLAPIv3 | * uses OWLAPIv3 | ||
* runs in TomCat | * runs in TomCat/Jetty | ||
* uses OWL reasoners | * uses OWL reasoners | ||
Dependencies: [[Transition to OWL]] | Dependencies: [[Transition to OWL]] | ||
=== Benchmarks === | See: [[TermGenie2]] | ||
==== Reasoner Benchmarks ==== | |||
Need to test various OWL reasoners, simulate evolution of GO | Need to test various OWL reasoners, simulate evolution of GO | ||
== | ==== Feasibility Study ==== | ||
== | |||
Determine feasibility of java version | |||
[[Category:SWUG Projects]] | [[Category:SWUG Projects]] |
Latest revision as of 17:27, 14 June 2011
(aka TermGenie)
Project lead: Chris
Coordinates with: ontology-editors
Purpose
An increasing number of terms coming in from sourceforge are automatable compositional terms - particularly regulation terms. Ontology editors waste time performing manual tasks that could be automated, and curators experience a bottleneck during annotation.
The compositional term request system allows annotators to use a web template system to instantaneously get the term they require, provided it conforms to an existing pre-determined template. A reasoner is used to place the term automatically in the hierarchy.
Documentation for the system is available here: TermGenie
Groups
Project Dependencies
- Full_Text_Indexing (soft dependency)
- Transition to OWL (for #v2)
Status
#v1 is available to curators, currently on regulation requests are live
Deliverables
v1
v1 is obo-format dependent, uses a custom reasoner, and relies on various ad-hoc scripts
v1 report
A report on the v1 implementation is available:
v2
v2 will be a port of #v1
- implemented in Java
- works off of OBO or OWL files
- uses OWLAPIv3
- runs in TomCat/Jetty
- uses OWL reasoners
Dependencies: Transition to OWL
See: TermGenie2
Reasoner Benchmarks
Need to test various OWL reasoners, simulate evolution of GO
Feasibility Study
Determine feasibility of java version