Dec 5th, 2017 Ontology Working Group Meeting: Difference between revisions

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Join from PC, Mac, Linux, iOS or Android: https://zoom.us/j/639381573
Join from PC, Mac, Linux, iOS or Android: https://zoom.us/j/639381573
Meeting recordings:
* [[File:Ontology WG Meeting audio 12-05-2017.m4a|thumb|Ontology WG Meeting audio 12-05-2017]]
* [[File:Ontology WG Meeting video 12-05-2017.mp4|thumb|Ontology WG Meeting video 12-05-2017]]


=Agenda=
=Agenda=
==December Planteome Release==
* PECO release
* Sorghum and yam mapping almost completed
===Update on Annotations===
* Rice gene annotations- include? Subcellular localization annotations
*Rice annotations are at the transcriptome level- should be at the gene level
* AM: Master list for rice?
* New rice iprscan data- fewer results were returned-
Clean up and make gene level annotation
* Maize V4 annotations
** Map existing names to new V4 ids, along with aliases
** Protein coding genes
* AM- Subcellular localization annotations for MaizeV4
* PSDS- look at reviewer’s comments
* Sorghum gene expression atlas
* Sorghum GRIN phenotype annotations
* Need list of new data files? - check SVN
* TO- fixing priorities list- may not be able to get them all done
* Need to update the Planteome front page with widgets for Noctua and gene enrichment
* TO + PECO- working with CM and MAL to fix the patterns, imports
* ''Question from MAL to JE: Do you run reasoner on the Planteome.owl file? Owl tools should have quality checks?''
* Noctua- moved to live database, updated with the GO version, won’t recognize the catalog file
* Stress ontology- move to the repo?, names are weird- being scraped, 
** Need to fix on a name, PSO
** Hold for next release, discuss further at future
* Possible time for Marie to Corvallis?
Time frame? March? Last week feb- First week of March?
* Presentation from SupAgro- Jan 23rd?
* Annual report -EA- has added info to their doc, MAL will send us
* DWS- new hire? Evo Devo genes to connect fruit ripening and flower development
** In situs 
* Utilize Noctua to build the annotations?
- Fruit types paper
- wound periderm, lenticels work
-DWS will follow up with BS
* Annual report - abstracts, meetings, people,
==Ideas for the renewal==
- submit by March or April? No set deadlines- May 15th at the latest
* Two panels per year- June, November
* NCE will only last 1 year, if that


In progress...


==Phenoscape Hackathon Dec. 11th-14th==
==Phenoscape Hackathon Dec. 11th-14th==
*  LC and AM will attend
*  LC and AM will attend
===[http://kb.phenoscape.org/#/home Phenoscape]===
* A datastore of computable phenotypes for studies of evolution and genetics
* [https://github.com/phenoscape/KB-DataFest-2017/blob/master/workshop-description.md Phenoscape Workshop Description]
* [https://github.com/phenoscape/KB-DataFest-2017/blob/master/workshop-description.md Phenoscape Workshop Description]


===Goals of the Workshop===
===Goals of the Workshop===
To foster broader adoption, reuse, and interoperability of its flagship resource, the Phenoscape Knowledgebase (KB; http://kb.phenoscape.org).  
* To foster broader adoption, reuse, and interoperability of its flagship resource, the '''Phenoscape Knowledgebase''' (KB; http://kb.phenoscape.org).  
 
* The KB offers programmable (API) access to '''natural language phenotype descriptions''' annotated with formal ontologies so that machines can understand and compute with the semantics of descriptions at scale.
* The KB offers programmable (API) access to '''natural language phenotype descriptions''' annotated with formal ontologies so that machines can understand and compute with the semantics of descriptions at scale.
== Planteome Release==
Planned for Mid-Dec
==Presentation of PhenoArche data management by INRA==
* Has date been set yet? - propose the following dates:  23, 25 janvier et 6 février.


==Upcoming Events==
==Upcoming Events==

Latest revision as of 20:19, 5 December 2017

  • Date: Tuesday Dec 5th, 2017
  • Time: 8:15am PST (GMT-8)
  • Connection details:

Topic: Planteome Project's Zoom Meeting Time: Dec 5, 2017 8:15 AM Pacific Time (US and Canada)

Join from PC, Mac, Linux, iOS or Android: https://zoom.us/j/639381573

Meeting recordings:

Agenda

December Planteome Release

  • PECO release
  • Sorghum and yam mapping almost completed

Update on Annotations

  • Rice gene annotations- include? Subcellular localization annotations
  • Rice annotations are at the transcriptome level- should be at the gene level
  • AM: Master list for rice?
  • New rice iprscan data- fewer results were returned-

Clean up and make gene level annotation

  • Maize V4 annotations
    • Map existing names to new V4 ids, along with aliases
    • Protein coding genes
  • AM- Subcellular localization annotations for MaizeV4
  • PSDS- look at reviewer’s comments
  • Sorghum gene expression atlas
  • Sorghum GRIN phenotype annotations
  • Need list of new data files? - check SVN
  • TO- fixing priorities list- may not be able to get them all done
  • Need to update the Planteome front page with widgets for Noctua and gene enrichment
  • TO + PECO- working with CM and MAL to fix the patterns, imports
  • Question from MAL to JE: Do you run reasoner on the Planteome.owl file? Owl tools should have quality checks?
  • Noctua- moved to live database, updated with the GO version, won’t recognize the catalog file
  • Stress ontology- move to the repo?, names are weird- being scraped,
    • Need to fix on a name, PSO
    • Hold for next release, discuss further at future
  • Possible time for Marie to Corvallis?

Time frame? March? Last week feb- First week of March?

  • Presentation from SupAgro- Jan 23rd?
  • Annual report -EA- has added info to their doc, MAL will send us
  • DWS- new hire? Evo Devo genes to connect fruit ripening and flower development
    • In situs
  • Utilize Noctua to build the annotations?

- Fruit types paper - wound periderm, lenticels work -DWS will follow up with BS

  • Annual report - abstracts, meetings, people,

Ideas for the renewal

- submit by March or April? No set deadlines- May 15th at the latest

  • Two panels per year- June, November
  • NCE will only last 1 year, if that


Phenoscape Hackathon Dec. 11th-14th

  • LC and AM will attend

Phenoscape

  • A datastore of computable phenotypes for studies of evolution and genetics

Goals of the Workshop

  • To foster broader adoption, reuse, and interoperability of its flagship resource, the Phenoscape Knowledgebase (KB; http://kb.phenoscape.org).
  • The KB offers programmable (API) access to natural language phenotype descriptions annotated with formal ontologies so that machines can understand and compute with the semantics of descriptions at scale.

Planteome Release

Planned for Mid-Dec


Presentation of PhenoArche data management by INRA

  • Has date been set yet? - propose the following dates: 23, 25 janvier et 6 février.


Upcoming Events

  • Phenoscape Hackathon Dec. 11th-14th, LC and AM will attend
  • Plant and Animal Genome meeting January 2018
  • Phenoharmonis May 14th-18th, 2018
  • ICBO 2018- Corvallis, OR, August 6-10th

Next meeting: Jan 23rd

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