Software and Utilities: Difference between revisions

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The purpose of the <b>Software and Utilities</b> group is to support both the GOC and the user community with technical, software, bioinformatics and computer-science related matters. In addition, this group will help drive the GOC through the research and provision of new computational technologies and methodologies relating to ontologies and ontology-based data analysis. This group is responsible for creating, clarifying and extending the common model that underpins all of GO. Ontology development tools are necessary for the [[Ontology Development]] group to perform its function. In addition, the [[Annotation Outreach]] group and wider community need means of exploring and utilizing GO and existing annotations. This group complements all the other groups.
[[Category:Software]]
 
For the legacy page, see [[Software_and_Utilities_(Archived)]] and [[Software and Utilities group summary]]


[[Software and Utilities group summary]]


==Meetings==
==Meetings==


*[[Database_Meeting_21_Nov_2006]]
See the GO calendar
 
Core meetings:
 
* biweekly all-day thursday LBL hack days (anyone can zoom in)
* biweekly Noctua calls
* adhoc zooms between developers as needed
 
Also:


==Projects==
* updates on go-managers calls
* ontology engineering team join ontology calls
* most devs join annotation calls
 
==Mail List==
 
* godev-internal on groups.io


===OBO-Edit===
==Resources==


*[http://www.oboedit.org OBO-Edit home page]
===Documentation===


Technical articles:
* [[Intersections in the OBO-Edit datamodel]]
* [[OBO Parser - Getting Started]]
* [[Reasoner Overview]]
* [[OBO-Edit Datamodel Interfaces Diagram]]


===AmiGO===
===Trackers===


[[:Category:AmiGO working group|AmiGO working group]]
===People===


===GO database and go-perl===
The following people dedicate some portion of their time to the GO project


Main page: http://www.godatabase.org
* Seth Carbon LBL (Manager, Noctua, AmiGO, Solr, Infrastructure)
* Eric Douglass LBL (Triplestore, Ontology Engineering and Semantic Tools, Pipeline)
* Nathan Dunn LBL (Tools, AGR integration)
* Ben Good LBL (Noctua, Pathway integration)
* Marcin Joachimiak LBL, (Bioinformatics)
* HyeongSik Kim LBL (OWL, Solr)
* Chris Mungall LBL (PI)
* Deepak Unni LBL (BioLink API)


go-dev: http://www.godatabase.org/dev/
* Laurent-Phillippe Albou USC (LBL affiliate) (Bioinformatics, Networks)
* Dustin Ebert USC (Pipeline, GO-CAMs)
* Huaiyu Mi USC (Panther, PAINT Pipeline)
* Tremayne Mushayahama USC (Noctua)
* Anushya Muruganujan USC (Panther, PAINT, Enrichment)


* Jim Balhoff RENCI (Noctua, Ontology Engineering)


[[:Category:go-dev Code Org|go-dev Code Org]] : Thoughts on the organization of go-dev source.
==Wiki==


[[ GoDB loading ]] Proposal for refactoring go-full loads
All software-and-utilities pages on the wiki should go in the wikispace SWUG (SoftWare Utilities Group)


===SO===


Main page: http://www.sequenceontology.org
==Projects==


====MiSO====
All projects are managed via GitHub projects. For a list of all, see the [https://github.com/orgs/geneontology/projects GO github projects page]
CVS http://song.cvs.sourceforge.net/song/software/scripts/miSO


browser http://song.sf.net/SO_view/index.html
=== GitHub Repos ===


====Cross-products in SO====
* https://github.com/geneontology/noctua
* https://github.com/geneontology/amigo
* https://github.com/biolink/ontobio/
* https://github.com/owlcollab/owltools
 
===AmiGO===


SO contains cross-product definitions of many composite terms. See
* https://github.com/geneontology/amigo
[[SO Cross Products]] for the methodology.
* [[AmiGO_Manual:_Overview]]
* [[AmiGO_Manual:_Installation]]
* [http://sourceforge.net/tracker/?group_id=36855&atid=494390 AmiGO Requests]
* [http://sourceforge.net/tracker/?group_id=36855&atid=908269 AmiGO bug reports]


===Obol===
===Noctua===


http://www.fruitfly.org/~cjm/obol
* [[Noctua]] Curator docs
* https://github.com/geneontology/noctua
* [https://docs.google.com/document/d/1w3mkF1RQIzwROOCMTkqjYaOn8ZbdsW52t-xA4DKt0vg/edit#heading=h.du3v9zif59jp Noctua Technical Stack]

Latest revision as of 09:47, 9 April 2019


For the legacy page, see Software_and_Utilities_(Archived) and Software and Utilities group summary


Meetings

See the GO calendar

Core meetings:

  • biweekly all-day thursday LBL hack days (anyone can zoom in)
  • biweekly Noctua calls
  • adhoc zooms between developers as needed

Also:

  • updates on go-managers calls
  • ontology engineering team join ontology calls
  • most devs join annotation calls

Mail List

  • godev-internal on groups.io

Resources

Documentation

Trackers

People

The following people dedicate some portion of their time to the GO project

  • Seth Carbon LBL (Manager, Noctua, AmiGO, Solr, Infrastructure)
  • Eric Douglass LBL (Triplestore, Ontology Engineering and Semantic Tools, Pipeline)
  • Nathan Dunn LBL (Tools, AGR integration)
  • Ben Good LBL (Noctua, Pathway integration)
  • Marcin Joachimiak LBL, (Bioinformatics)
  • HyeongSik Kim LBL (OWL, Solr)
  • Chris Mungall LBL (PI)
  • Deepak Unni LBL (BioLink API)
  • Laurent-Phillippe Albou USC (LBL affiliate) (Bioinformatics, Networks)
  • Dustin Ebert USC (Pipeline, GO-CAMs)
  • Huaiyu Mi USC (Panther, PAINT Pipeline)
  • Tremayne Mushayahama USC (Noctua)
  • Anushya Muruganujan USC (Panther, PAINT, Enrichment)
  • Jim Balhoff RENCI (Noctua, Ontology Engineering)

Wiki

All software-and-utilities pages on the wiki should go in the wikispace SWUG (SoftWare Utilities Group)


Projects

All projects are managed via GitHub projects. For a list of all, see the GO github projects page

GitHub Repos

AmiGO

Noctua

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