SWUG Timeline 2010-2011 (Archived): Difference between revisions

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Automatically generated from excel file in cvs
Automatically generated from excel file in cvs
[http://www.geneontology.org/timelines/SWUG-timeline-2010-to-2011.txt timelines/SWUG-timeline-2010-to-2011.txt]
[http://www.geneontology.org/timelines/SWUG-timeline-2010-to-2011.txt
timelines/SWUG-timeline-2010-to-2011.txt]
 
'''Do not edit this table directly'''
 
(NOT YET COMPLETE, IN PROGRESS)
 
 
{|class="wikitable" style="text-align:center" border="1"
{|class="wikitable" style="text-align:center" border="1"
|-
|-
! [[PROJECT]]
! [[PROJECT]]
! LEAD/PERSONNEL
! LEAD/PERSONNEL
! Groups
! Jul-10
! Jul-10
! Aug-10
! Aug-10
Line 24: Line 32:
! Dec-11
! Dec-11
|-
|-
| [[Term Submission Tool]]
| [[]]
|-
| [[Compositional Term Submission Tool]]
| Chris
| Chris
| [[Ontology Development]]
|  [[#v1]] beta, [[#curator_testing]]
|  [[#v1]] beta, [[#curator_testing]]
|  [[#v1]] release, regulation rollout
|  [[#v1]] release, regulation rollout; [[#v1_report]]
|  [[#integrate_autocomplete]] (dep: [[Full Text Indexing]]
|  [[#integrate_autocomplete]] (dep: [[Full Text Indexing]]
| rollout [[#additional_templates]] as required
| rollout [[#additional_templates]] as required
Line 33: Line 44:
| rollout [[#additional_templates]] as required
| rollout [[#additional_templates]] as required
| rollout [[#additional_templates]] as required; plan [[#v2]] in java/OWL
| rollout [[#additional_templates]] as required; plan [[#v2]] in java/OWL
| OWL reasoner benchmarks
| OWL [[#Reasoner_Benchmarks]]
| Complete feasibility study - java/OWLAPI port (dep: [[Transition to OWL]])
| Complete feasibility study - java/OWLAPI port (dep: [[Transition to OWL]])
| Prototype java/OWLAPI version (TBD: assign developer)
| Prototype java/OWLAPI version (TBD: assign developer)
Line 46: Line 57:
| [[OBO-Edit MIREOT support]]
| [[OBO-Edit MIREOT support]]
| Amina
| Amina
| [[Ontology Development]]
| beta with isa closure support
|
| release of 2.1, with isa closure support
|
| evaluate future requirements
|-
|-
| [[Transition to OWL]]
| [[Transition to OWL]]
| Chris
| Chris
| [[Ontology Development]]
|  
|  
| obof1.4 guide DRAFT release
| [[#obof1.4_guide]] DRAFT release
| obof1.4 guide DRAFT collect comments
| [[#obof1.4_guidee]] DRAFT collect comments
| obof1.4 formal spec DRAFT release
| [[#obof1.4_syntax]] spec DRAFT release
| obof1.4 feature freeze
| obof1.4 feature freeze
| obo abstract syntax to OWL2 mapping, incl IAO
| obo abstract syntax to [[#OWL2_mapping,]] incl IAO
| obof1.4 formal spec  release
| obof1.4 formal spec  release
| java OBO parser spec
| [[#Java_OBO_Parser]] spec
|  
|  
| java OBO parser impl (TBD: assign developer)
| [[#Java_OBO_Parser]] impl (TBD: assign developer)
| JUnit test suite
| [[#JUnit_Test_Suite]]
| OBO Parser to OWLAPIv3 bridge
| OBO Parser to [[#OWLAPI_Bridge]]
| Integrate bridge into P4
| [[#Integration]] - add bridge to P4
|-
| [[]]
|-
|-
| [[]]
| [[]]
Line 69: Line 85:
| [[Full Text Indexing]]
| [[Full Text Indexing]]
| Seth
| Seth
| [[Category:AmiGO_Hub]]
| Evaulate Solr
| Evaulate Solr
| Install Solr on labs
| Install Solr on labs
| GO-Solr Index engine
| GO-Solr Index engine
|  
| GO-Solr Index engine optimizations
| Integrate into labs: queries
| Integrate into labs: queries
| Integrate into labs: autocomplete
| Integrate into labs: autocomplete
| Public version using Solr for queries
| Public version with autocomplete
| Advanced queries via solr (labs)
|-
| [[Col16 in AmiGO]]
| Seth
| [[Annotation_Advocacy_and_Coordination]] [[Category:AmiGO_Hub]]
|
| db storage plan
| load c16 into db, labs
| load c16 into db, public
| display c16, labs
|  
|  
| Public version with autocomplete
| query on c16, labs
| display c16, public
|-
|-
| [[Relation Filtering in AmiGO]]
| [[Relation Filtering in AmiGO]]
| Seth
| Seth
| [[Category:AmiGO_Hub]]
| Release [[#database_reasoner]]
| Release [[#database_reasoner]]
|
| Relation Filtering in [[#map2slim]]
|
| Relation Filtering in [[#Term_Enrichment]]
|
|
| Relation Filtering in main display
|-
|-
| [[AmiGO and QuickGO Integration]]
| [[AmiGO and QuickGO Integration]]
| Seth; Tony
| Seth; Tony
| [[Category:AmiGO_Hub]]
|  
|  
|  
|  
| QuickGO graph views in AmiGO (labs)
| QuickGO [[#graph]] views in AmiGO (labs)
|  
|  
| Feasibility study of deeper integration
| Feasibility study of deeper integration
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| [[RefGenome Views]]
| [[RefGenome Views]]
| Seth
| Seth
| [[Category:AmiGO_Hub]] [[Reference Geome]]
|  
|  
| basic js Phylo viewer in AmiGO labs
| basic js Phylo viewer in AmiGO labs
|
|
|
|
|
|
|
| Grid view integrated with js phylo view
|-
|-
| [[RefGenome Reports]]
| [[RefGenome Reports]]
| Sven; Mary, Seth
| Sven; Mary, Seth
|  
| [[Category:AmiGO_Hub]] [[Reference Geome]]
| load gp2pthr family info
| basic html reports in labs
| basic html reports in labs
| gp2family in pulic release
| load full pthr tree
| example tree queries in GOOSE
|-
|-
| [[IndiGO Annotation Editor]]
| [[IndiGO Annotation Editor]]
| Seth; Tony
| Seth; Tony
| [[Annotation_Advocacy_and_Coordination]]
| Evaluation of protein2go functionality
| Evaluation of protein2go functionality
|  
|  
|  
|  
| Feasibility study
| Feasibility study
|
| specification of REST API for ontology info
| specification of REST API for annotation create/update
|-
|-
| [[GO Galaxy Environment]]
| [[GO Galaxy Environment]]
| Seth; Amelia
| Seth; Amelia
| [[Category:AmiGO_Hub]]
| alpha on labs
| alpha on labs
|  
|  
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| [[Taxon Constraint Engine]]
| [[Taxon Constraint Engine]]
| Chris, Amelia
| Chris, Amelia
| [[Annotation_Advocacy_and_Coordination]] [[Ontology Development]]
| v1 running weekly
| v1 running weekly
|  [[#v1]] maintenance
|  [[#v1]] maintenance
Line 127: Line 185:
|  [[#v1]] maintenance
|  [[#v1]] maintenance
|  
|  
| feasibility: web editing of taxon constraints
| plan v2 in java/OWL  (dep: [[Transition to OWL]])
|
| prototype java/OWL version
|  
|  
| plan v2 in java/OWL (dep: [[Transition to OWL]])
| production java/OWL version
| web interface and editing of constraints
|-
|-
| [[Function to Process Inference Engine]]
| [[Function to Process Inference Engine]]
| Chris
| Chris
| [[Annotation_Advocacy_and_Coordination]] [[Ontology Development]]
| v1 running weekly
| v1 running weekly
|  [[#v1]] maintenance
|  [[#v1]] maintenance
Line 139: Line 203:
|  
|  
| plan v2 in java/OWL (dep: [[Transition to OWL]])
| plan v2 in java/OWL (dep: [[Transition to OWL]])
|
|
| prototype java/OWL version
|
|
| production java/OWL version
|-
|-
| [[Additional Expressivity in GO Annotations]]
| [[Additional Expressivity in GO Annotations]]
| Amelia
| [[Annotation_Advocacy_and_Coordination]] [[Ontology Development]]
| GAF2 publishing
| feasibility: integrating pathway/GO data
| LEGO feasibility
|-
|-
| [[]]
| [[Annotation Rule Engine]]
| Amelia
| [[Annotation_Advocacy_and_Coordination]] [[Ontology Development]]
| Collect rules on wiki
| Specify XML format
| Collect rules into XML
|
| alpha version of rule engine
| integrate SQL rules into engine
| integrate scripting rules into engine
| evaluate OWLAPI, SPARQL, RIF for use in rules engine
| OWL inferences
|-
|-
| [[Incremental Database Loading]]
| [[Incremental Database Loading]]
| Ben
| Ben
| [[Annotation_Advocacy_and_Coordination]]
|  [[#benchmarks]]
|
| java parsers implemented
| java bulkload dumpers
| sql loader
|-
|-
| [[Virtualization]]
| [[Virtualization]]
| Seth+Ben
| Seth+Ben
| [[Category:AmiGO_Hub]]
|
|
|  [[#feasibility_study]]
|
|
| create test VM
|
|
| Distribute VM
|-
|-
| [[]]
| [[Advanced AmiGO Displays]]
| Seth
|
| N-matrix alpha on labs
|
|
|
| Ontology-annotation grid view (labs)
| integration with N-matrix amigo environment
|-
|-
| [[]]
| [[Schema Overhaul]]
| Chris
|
|
|
|
| plan
|-
|-
| [[]]
| [[AmiGO overhaul]]
| Seth
|-
|-
| [[]]
| [[]]
|-
|-
| [[]]
| [[ONGOING]]
|-
| [[]]
|-
| [[]]
|-
| [[]]
|-
| [[]]
|-
|-
| [[OBO Edit Development]]
| [[OBO Edit Development]]
| Amina
| Amina
| ONGOING
| [[Ontology Development]]
| 2.1 betas
| 2.1 stable beta testing
| 2.1 public
| determine 2.2 requirements
| evaluate P4 architecture
| implement simultaneous obo/owl save in P4
| autodetect of file changes in OE
| feasibility study of OE as P4 plugin
|-
|-
| [[AmiGO Development]]
| [[AmiGO Development]]
| Seth
| Seth
| ONGOING
| [[Category:AmiGO_Hub]]
|  [[#1_8]] labs
|  [[#1_8]] public
|-
|-
| [[PAINT Development]]
| [[PAINT Development]]
| Suzi
| Suzi
| ONGOING
| [[Reference Geome]]
|-
|-
| [[Production]]
| [[Production]]
| Ben
| Ben
|
| ONGOING
| ONGOING
| ONGOING
| ONGOING
| ONGOING
| ONGOING
| ONGOING
| ONGOING
| ONGOING
| ONGOING
| ONGOING
| ONGOING
| ONGOING
| ONGOING
| ONGOING
| ONGOING
|-
|-
| [[Website]]
| [[Website]]
| Amela
| Amela
|
| ONGOING
| ONGOING
| ONGOING
| ONGOING
| ONGOING
| ONGOING
| ONGOING
| ONGOING
| ONGOING
| ONGOING
| ONGOING
| ONGOING
| ONGOING
| ONGOING
| ONGOING
| ONGOING
| ONGOING
|-
|-
| [[Schema]]
| [[]]
| Chris
|-
|-
| [[]]
| [[]]
|}[[Category:SWUG Projects]]
|}
[[Category:SWUG Projects]]
[[Category:Timelines]]

Revision as of 20:37, 9 August 2010

Automatically generated from excel file in cvs [http://www.geneontology.org/timelines/SWUG-timeline-2010-to-2011.txt timelines/SWUG-timeline-2010-to-2011.txt]

Do not edit this table directly

(NOT YET COMPLETE, IN PROGRESS)


PROJECT LEAD/PERSONNEL Groups Jul-10 Aug-10 Sep-10 Oct-10 Nov-10 Dec-10 Jan-11 Feb-11 Mar-11 Apr-11 May-11 Jun-11 Jul-11 Aug-11 Sep-11 Oct-11 Nov-11 Dec-11
[[]]
Compositional Term Submission Tool Chris Ontology Development #v1 beta, #curator_testing #v1 release, regulation rollout; #v1_report #integrate_autocomplete (dep: Full Text Indexing rollout #additional_templates as required rollout #additional_templates as required rollout #additional_templates as required rollout #additional_templates as required; plan #v2 in java/OWL OWL #Reasoner_Benchmarks Complete feasibility study - java/OWLAPI port (dep: Transition to OWL) Prototype java/OWLAPI version (TBD: assign developer) Junit test suite beta java/OWLAPI version {TBD: assign developer} production java/OWLAPI version {TBD: assign developer}
OBO-Edit MIREOT support Amina Ontology Development beta with isa closure support release of 2.1, with isa closure support evaluate future requirements
Transition to OWL Chris Ontology Development #obof1.4_guide DRAFT release #obof1.4_guidee DRAFT collect comments #obof1.4_syntax spec DRAFT release obof1.4 feature freeze obo abstract syntax to #OWL2_mapping, incl IAO obof1.4 formal spec release #Java_OBO_Parser spec #Java_OBO_Parser impl (TBD: assign developer) #JUnit_Test_Suite OBO Parser to #OWLAPI_Bridge #Integration - add bridge to P4
[[]]
Full Text Indexing Seth Evaulate Solr Install Solr on labs GO-Solr Index engine GO-Solr Index engine optimizations Integrate into labs: queries Integrate into labs: autocomplete Public version using Solr for queries Public version with autocomplete Advanced queries via solr (labs)
Col16 in AmiGO Seth Annotation_Advocacy_and_Coordination db storage plan load c16 into db, labs load c16 into db, public display c16, labs query on c16, labs display c16, public
Relation Filtering in AmiGO Seth Release #database_reasoner Relation Filtering in #map2slim Relation Filtering in #Term_Enrichment Relation Filtering in main display
AmiGO and QuickGO Integration Seth; Tony QuickGO #graph views in AmiGO (labs) Feasibility study of deeper integration TBD
RefGenome Views Seth Reference Geome basic js Phylo viewer in AmiGO labs Grid view integrated with js phylo view
RefGenome Reports Sven; Mary, Seth Reference Geome load gp2pthr family info basic html reports in labs gp2family in pulic release load full pthr tree example tree queries in GOOSE
IndiGO Annotation Editor Seth; Tony Annotation_Advocacy_and_Coordination Evaluation of protein2go functionality Feasibility study specification of REST API for ontology info specification of REST API for annotation create/update
GO Galaxy Environment Seth; Amelia alpha on labs map2slim GAF fetching enrichment AmiGO integration (labs) obo2owl visualization AmiGO integration (public)
Taxon Constraint Engine Chris, Amelia Annotation_Advocacy_and_Coordination Ontology Development v1 running weekly #v1 maintenance #v1 maintenance #v1 maintenance feasibility: web editing of taxon constraints plan v2 in java/OWL (dep: Transition to OWL) prototype java/OWL version production java/OWL version web interface and editing of constraints
Function to Process Inference Engine Chris Annotation_Advocacy_and_Coordination Ontology Development v1 running weekly #v1 maintenance #v1 maintenance #v1 maintenance plan v2 in java/OWL (dep: Transition to OWL) prototype java/OWL version production java/OWL version
Additional Expressivity in GO Annotations Amelia Annotation_Advocacy_and_Coordination Ontology Development GAF2 publishing feasibility: integrating pathway/GO data LEGO feasibility
Annotation Rule Engine Amelia Annotation_Advocacy_and_Coordination Ontology Development Collect rules on wiki Specify XML format Collect rules into XML alpha version of rule engine integrate SQL rules into engine integrate scripting rules into engine evaluate OWLAPI, SPARQL, RIF for use in rules engine OWL inferences
Incremental Database Loading Ben Annotation_Advocacy_and_Coordination #benchmarks java parsers implemented java bulkload dumpers sql loader
Virtualization Seth+Ben #feasibility_study create test VM Distribute VM
Advanced AmiGO Displays Seth N-matrix alpha on labs Ontology-annotation grid view (labs) integration with N-matrix amigo environment
Schema Overhaul Chris plan
AmiGO overhaul Seth
[[]]
ONGOING
OBO Edit Development Amina Ontology Development 2.1 betas 2.1 stable beta testing 2.1 public determine 2.2 requirements evaluate P4 architecture implement simultaneous obo/owl save in P4 autodetect of file changes in OE feasibility study of OE as P4 plugin
AmiGO Development Seth #1_8 labs #1_8 public
PAINT Development Suzi Reference Geome
Production Ben ONGOING ONGOING ONGOING ONGOING ONGOING ONGOING ONGOING ONGOING ONGOING ONGOING ONGOING ONGOING ONGOING ONGOING ONGOING
Website Amela ONGOING ONGOING ONGOING ONGOING ONGOING ONGOING ONGOING ONGOING ONGOING ONGOING ONGOING ONGOING ONGOING ONGOING ONGOING ONGOING
[[]]
[[]]
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