SWUG Timeline 2010-2011 (Archived): Difference between revisions
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Automatically generated from excel file in cvs | [[Category:SWUG Projects]][[Category:Archived]] | ||
[[Category:Software]] [[Category:Timelines]] | |||
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''' | '''Do not edit this table directly''' | ||
{|class="wikitable" style="text-align:center" border="1" | {|class="wikitable" style="text-align:center" border="1" | ||
Line 12: | Line 11: | ||
! LEAD/PERSONNEL | ! LEAD/PERSONNEL | ||
! Groups | ! Groups | ||
! Jul | ! 10-Jul | ||
! Aug | ! 10-Aug | ||
! Sep | ! 10-Sep | ||
! Oct | ! 10-Oct | ||
! Nov | ! 10-Nov | ||
! Dec | ! 10-Dec | ||
! Jan | ! 11-Jan | ||
! Feb | ! 11-Feb | ||
! Mar | ! 11-Mar | ||
! Apr | ! 11-Apr | ||
! May | ! 11-May | ||
! Jun | ! 11-Jun | ||
! Jul | ! 11-Jul | ||
! Aug | ! 11-Aug | ||
! Sep | ! 11-Sep | ||
! Oct | ! 11-Oct | ||
! Nov | ! 11-Nov | ||
! Dec | ! 11-Dec | ||
|- | |- | ||
| [[]] | | [[]] | ||
Line 36: | Line 35: | ||
| Chris | | Chris | ||
| [[Ontology Development]] | | [[Ontology Development]] | ||
| [[#v1]] beta, [[#curator_testing]] | | [[Compositional Term Submission Tool#v1|v1]] beta, [[Compositional Term Submission Tool#curator_testing|curator_testing]] DONE | ||
| [[#v1]] release, regulation rollout; [[#v1_report]] | | [[Compositional Term Submission Tool#v1|v1]] release, regulation rollout DONE; [[Compositional Term Submission Tool#v1_report|v1_report]] DONE | ||
| [[#integrate_autocomplete]] (dep: [[Full Text Indexing]] | | [[Compositional Term Submission Tool#integrate_autocomplete|integrate_autocomplete]] (dep: [[Full Text Indexing]] | ||
| rollout [[#additional_templates]] as required | | rollout [[Compositional Term Submission Tool#additional_templates|additional_templates]] as required | ||
| rollout [[#additional_templates]] as required | | rollout [[Compositional Term Submission Tool#additional_templates|additional_templates]] as required | ||
| rollout [[#additional_templates]] as required | | rollout [[Compositional Term Submission Tool#additional_templates|additional_templates]] as required | ||
| rollout [[#additional_templates]] as required; plan [[#v2]] in java/OWL | | rollout [[Compositional Term Submission Tool#additional_templates|additional_templates]] as required; plan [[Compositional Term Submission Tool#v2|v2]] in java/OWL | ||
| OWL [[#Reasoner_Benchmarks]] | | OWL [[Compositional Term Submission Tool#Reasoner_Benchmarks|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 57: | Line 56: | ||
| Amina | | Amina | ||
| [[Ontology Development]] | | [[Ontology Development]] | ||
| beta with isa closure support | | beta with isa closure support DONE | ||
| | | | ||
| release of 2.1, with isa closure support | | release of 2.1, with isa closure support | ||
Line 67: | Line 66: | ||
| [[Ontology Development]] | | [[Ontology Development]] | ||
| | | | ||
| [[#obof1.4_guide]] DRAFT release | | [[Transition to OWL#obof1.4_guide|obof1.4_guide]] DRAFT release DONE | ||
| [[#obof1. | | [[Transition to OWL#obof1.4_guide|obof1.4_guide]] DRAFT collect comments | ||
| [[#obof1.4_syntax]] spec DRAFT release | | [[Transition to OWL#obof1.4_syntax|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 [[Transition to OWL#OWL2_mapping,|OWL2_mapping,]] incl IAO | ||
| obof1.4 formal spec release | | obof1.4 formal spec release | ||
| [[#Java_OBO_Parser]] spec | | [[Transition to OWL#Java_OBO_Parser|Java_OBO_Parser]] spec | ||
| | | | ||
| [[#Java_OBO_Parser]] impl (TBD: assign developer) | | [[Transition to OWL#Java_OBO_Parser|Java_OBO_Parser]] impl (TBD: assign developer) | ||
| [[#JUnit_Test_Suite]] | | [[Transition to OWL#JUnit_Test_Suite|JUnit_Test_Suite]] | ||
| OBO Parser to [[#OWLAPI_Bridge]] | | OBO Parser to [[Transition to OWL#OWLAPI_Bridge|OWLAPI_Bridge]] | ||
| [[#Integration]] - add bridge to P4 | | [[Transition to OWL#Integration|Integration]] - add bridge to P4 | ||
|- | |- | ||
| [[]] | | [[]] | ||
Line 85: | Line 84: | ||
| Seth | | Seth | ||
| [[Category:AmiGO_Hub]] | | [[Category:AmiGO_Hub]] | ||
| Evaulate Solr | | Evaulate Solr DONE | ||
| Install Solr on labs | | Install Solr on labs DONE | ||
| GO-Solr Index engine | | GO-Solr Index engine | ||
| GO-Solr Index engine optimizations | | GO-Solr Index engine optimizations | ||
Line 95: | Line 94: | ||
| Advanced queries via solr (labs) | | Advanced queries via solr (labs) | ||
|- | |- | ||
| [[Col16 | | [[AmiGO Col16 Display]] | ||
| Seth | | Amelia, Seth | ||
| [[Annotation_Advocacy_and_Coordination]] [[Category:AmiGO_Hub]] | | [[Annotation_Advocacy_and_Coordination]] [[Category:AmiGO_Hub]] | ||
| | | | ||
Line 106: | Line 105: | ||
| query on c16, labs | | query on c16, labs | ||
| display c16, public | | display c16, public | ||
|- | |||
| [[AmiGO Col17 Display]] | |||
| Amelia, Seth | |||
| [[Annotation_Advocacy_and_Coordination]] [[Category:AmiGO_Hub]] | |||
| | |||
| db storage plan | |||
| load c17 into db, labs | |||
| load c17 into db, public | |||
| display c17, labs | |||
| | |||
| query on c17, labs | |||
| display c17, public | |||
|- | |- | ||
| [[Relation Filtering in AmiGO]] | | [[Relation Filtering in AmiGO]] | ||
| Seth | | Seth | ||
| [[Category:AmiGO_Hub]] | | [[Category:AmiGO_Hub]] | ||
| Release [[#database_reasoner]] | | Release [[Relation Filtering in AmiGO#database_reasoner|database_reasoner]] DONE | ||
| | | | ||
| Relation Filtering in [[#map2slim]] | | Relation Filtering in [[Relation Filtering in AmiGO#map2slim|map2slim]] | ||
| | | | ||
| Relation Filtering in [[#Term_Enrichment]] | | Relation Filtering in [[Relation Filtering in AmiGO#Term_Enrichment|Term_Enrichment]] | ||
| | | | ||
| | | | ||
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| | | | ||
| | | | ||
| QuickGO [[#graph]] views in AmiGO (labs) | | QuickGO [[AmiGO and QuickGO Integration#graph|graph]] views in AmiGO (labs) | ||
| | | | ||
| Feasibility study of deeper integration | | Feasibility study of deeper integration | ||
| TBD | | TBD | ||
|- | |- | ||
| [[ | | [[AmiGO Phylotrees]] | ||
| Seth | | Seth | ||
| [[Category:AmiGO_Hub]] [[Reference Geome]] | | [[Category:AmiGO_Hub]] [[Reference Geome]] | ||
| | | | ||
| basic js Phylo viewer in AmiGO labs | | basic js Phylo viewer in AmiGO labs DONE | ||
| | | | ||
| | | | ||
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| Grid view integrated with js phylo view | | Grid view integrated with js phylo view | ||
|- | |- | ||
| [[ | | [[Reference Genome Data Management and Reporting]] | ||
| Sven; Mary, Seth | | Sven; Mary, Seth | ||
| [[Category:AmiGO_Hub]] [[Reference Geome]] | | [[Category:AmiGO_Hub]] [[Reference Geome]] | ||
| load gp2pthr family info | | load gp2pthr family info DONE | ||
| basic html reports in labs | | basic html reports in labs | ||
| gp2family in pulic release | | gp2family in pulic release | ||
Line 155: | Line 166: | ||
| Seth; Tony | | Seth; Tony | ||
| [[Annotation_Advocacy_and_Coordination]] | | [[Annotation_Advocacy_and_Coordination]] | ||
| Evaluation of protein2go | | Evaluation of protein2go architecture DONE | ||
| | | | ||
| | | | ||
Line 166: | Line 177: | ||
| Seth; Amelia | | Seth; Amelia | ||
| [[Category:AmiGO_Hub]] | | [[Category:AmiGO_Hub]] | ||
| alpha on labs | | alpha on labs DONE | ||
| | | | ||
| map2slim | | map2slim | ||
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| AmiGO integration (public) | | AmiGO integration (public) | ||
|- | |- | ||
| [[Taxon Constraint Engine]] | | [[Taxon Constraint Check Engine]] | ||
| Chris, Amelia | | Chris, Amelia | ||
| [[Annotation_Advocacy_and_Coordination]] [[Ontology Development]] | | [[Annotation_Advocacy_and_Coordination]] [[Ontology Development]] | ||
| v1 running weekly | | v1 running weekly DONE | ||
| [[#v1]] maintenance | | [[Taxon Constraint Check Engine#v1|v1]] maintenance | ||
| [[#v1]] maintenance | | [[Taxon Constraint Check Engine#v1|v1]] maintenance | ||
| [[#v1]] maintenance | | [[Taxon Constraint Check Engine#v1|v1]] maintenance | ||
| | | | ||
| feasibility: web editing of taxon constraints | | feasibility: web editing of taxon constraints | ||
Line 195: | Line 206: | ||
| Chris | | Chris | ||
| [[Annotation_Advocacy_and_Coordination]] [[Ontology Development]] | | [[Annotation_Advocacy_and_Coordination]] [[Ontology Development]] | ||
| v1 running weekly | | v1 running weekly DONE | ||
| [[#v1]] maintenance | | [[Function to Process Inference Engine#v1|v1]] maintenance | ||
| [[#v1]] maintenance | | [[Function to Process Inference Engine#v1|v1]] maintenance | ||
| [[#v1]] maintenance | | [[Function to Process Inference Engine#v1|v1]] maintenance | ||
| | | | ||
| | | | ||
Line 209: | Line 220: | ||
| production java/OWL version | | production java/OWL version | ||
|- | |- | ||
| [[ | | [[Increasing Expressivity in GO Annotations]] | ||
| Amelia | | Amelia | ||
| [[Annotation_Advocacy_and_Coordination]] [[Ontology Development]] | | [[Annotation_Advocacy_and_Coordination]] [[Ontology Development]] | ||
| GAF2 publishing | | GAF2 publishing DONE | ||
| feasibility: integrating pathway/GO data | | feasibility: integrating pathway/GO data | ||
| LEGO feasibility | | LEGO feasibility | ||
Line 219: | Line 230: | ||
| Amelia | | Amelia | ||
| [[Annotation_Advocacy_and_Coordination]] [[Ontology Development]] | | [[Annotation_Advocacy_and_Coordination]] [[Ontology Development]] | ||
| Collect rules on wiki | | Collect rules on wiki DONE | ||
| Specify XML format | | Specify XML format | ||
| Collect rules into XML | | Collect rules into XML | ||
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| Ben | | Ben | ||
| [[Annotation_Advocacy_and_Coordination]] | | [[Annotation_Advocacy_and_Coordination]] | ||
| [[#benchmarks]] | | [[Incremental Database Loading#benchmarks|benchmarks]] | ||
| | | | ||
| java parsers implemented | | java parsers implemented | ||
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| | | | ||
| | | | ||
| [[#feasibility_study]] | | [[Virtualization#feasibility_study|feasibility_study]] | ||
| | | | ||
| | | | ||
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| [[Advanced AmiGO Displays]] | | [[Advanced AmiGO Displays]] | ||
| Seth | | Seth | ||
| | | [[Category:AmiGO_Hub]] | ||
| N-matrix alpha on labs | | N-matrix alpha on labs DONE | ||
| | | | ||
| | | | ||
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| [[AmiGO overhaul]] | | [[AmiGO overhaul]] | ||
| Seth | | Seth | ||
| [[Category:AmiGO_Hub]] | |||
|- | |- | ||
| [[]] | | [[]] | ||
Line 276: | Line 288: | ||
| [[ONGOING]] | | [[ONGOING]] | ||
|- | |- | ||
| [[OBO Edit Development]] | | [[OBO-Edit 2 Development]] | ||
| Amina | | Amina | ||
| [[Ontology Development]] | | [[Ontology Development]] | ||
| 2.1 betas | | 2.1 betas DONE | ||
| 2.1 stable beta testing | | 2.1 stable beta testing | ||
| 2.1 public | | 2.1 public | ||
Line 291: | Line 303: | ||
| Seth | | Seth | ||
| [[Category:AmiGO_Hub]] | | [[Category:AmiGO_Hub]] | ||
| [[#1_8]] labs | | [[AmiGO Development#1_8|1_8]] labs DONE | ||
| [[#1_8]] public | | [[AmiGO Development#1_8|1_8]] public | ||
|- | |- | ||
| [[PAINT Development]] | | [[PAINT Development]] | ||
Line 300: | Line 312: | ||
| [[Production]] | | [[Production]] | ||
| Ben | | Ben | ||
| | | [[Category:AmiGO_Hub]] | ||
| ONGOING | | ONGOING | ||
| ONGOING | | ONGOING | ||
| ONGOING | | ONGOING | ||
| svn support | |||
| ONGOING | | ONGOING | ||
| ONGOING | | ONGOING | ||
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| ONGOING | | ONGOING | ||
|- | |- | ||
| [[Website]] | | [[Website Maintenance]] | ||
| | | Amelia | ||
| | | [[:Category:Web_Presence_Working_Group]] | ||
| ONGOING | | ONGOING | ||
| ONGOING | | ONGOING | ||
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| ONGOING | | ONGOING | ||
| ONGOING | | ONGOING | ||
|} | |} | ||
Revision as of 10:27, 8 April 2019
Automatically generated from excel file in cvs: timelines/SWUG-timeline-2010-to-2011.txt
Do not edit this table directly
PROJECT | LEAD/PERSONNEL | Groups | 10-Jul | 10-Aug | 10-Sep | 10-Oct | 10-Nov | 10-Dec | 11-Jan | 11-Feb | 11-Mar | 11-Apr | 11-May | 11-Jun | 11-Jul | 11-Aug | 11-Sep | 11-Oct | 11-Nov | 11-Dec |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
[[]] | ||||||||||||||||||||
Compositional Term Submission Tool | Chris | Ontology Development | v1 beta, curator_testing DONE | v1 release, regulation rollout DONE; v1_report DONE | 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 DONE | release of 2.1, with isa closure support | evaluate future requirements | |||||||||||||||
Transition to OWL | Chris | Ontology Development | obof1.4_guide DRAFT release DONE | obof1.4_guide 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 DONE | Install Solr on labs DONE | 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) | ||||||||||
AmiGO Col16 Display | Amelia, 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 | ||||||||||||
AmiGO Col17 Display | Amelia, Seth | Annotation_Advocacy_and_Coordination | db storage plan | load c17 into db, labs | load c17 into db, public | display c17, labs | query on c17, labs | display c17, public | ||||||||||||
Relation Filtering in AmiGO | Seth | Release database_reasoner DONE | 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 | ||||||||||||||||
AmiGO Phylotrees | Seth | Reference Geome | basic js Phylo viewer in AmiGO labs DONE | Grid view integrated with js phylo view | ||||||||||||||||
Reference Genome Data Management and Reporting | Sven; Mary, Seth | Reference Geome | load gp2pthr family info DONE | 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 architecture DONE | 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 DONE | map2slim | GAF fetching | enrichment | AmiGO integration (labs) | obo2owl | visualization | AmiGO integration (public) | |||||||||||
Taxon Constraint Check Engine | Chris, Amelia | Annotation_Advocacy_and_Coordination Ontology Development | v1 running weekly DONE | 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 DONE | v1 maintenance | v1 maintenance | v1 maintenance | plan v2 in java/OWL (dep: Transition to OWL) | prototype java/OWL version | production java/OWL version | |||||||||||
Increasing Expressivity in GO Annotations | Amelia | Annotation_Advocacy_and_Coordination Ontology Development | GAF2 publishing DONE | feasibility: integrating pathway/GO data | LEGO feasibility | |||||||||||||||
Annotation Rule Engine | Amelia | Annotation_Advocacy_and_Coordination Ontology Development | Collect rules on wiki DONE | 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 DONE | Ontology-annotation grid view (labs) | integration with N-matrix amigo environment | ||||||||||||||||
Schema Overhaul | Chris | plan | ||||||||||||||||||
AmiGO overhaul | Seth | |||||||||||||||||||
[[]] | ||||||||||||||||||||
ONGOING | ||||||||||||||||||||
OBO-Edit 2 Development | Amina | Ontology Development | 2.1 betas DONE | 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 DONE | 1_8 public | |||||||||||||||||
PAINT Development | Suzi | Reference Geome | ||||||||||||||||||
Production | Ben | ONGOING | ONGOING | ONGOING | svn support | ONGOING | ONGOING | ONGOING | ONGOING | ONGOING | ONGOING | ONGOING | ONGOING | ONGOING | ONGOING | ONGOING | ||||
Website Maintenance | Amelia | Category:Web_Presence_Working_Group | ONGOING | ONGOING | ONGOING | ONGOING | ONGOING | ONGOING | ONGOING | ONGOING | ONGOING | ONGOING | ONGOING | ONGOING | ONGOING | ONGOING | ONGOING | ONGOING |