Dec 5th, 2017 Ontology Working Group Meeting - Revision history

Cooperl at 20:19, 5 December 2017

2017-12-05T20:19:22Z

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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=

Cooperl: /* Agenda */

2017-12-05T20:16:58Z

Agenda

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	=Agenda=		=Agenda=

	~~Tuesday Dec 5th, 2017~~

	==December Planteome Release==		==December Planteome Release==
	* PECO release		* PECO release
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	Clean up and make gene level annotation		Clean up and make gene level annotation

	Maize V4 annotations		* Maize V4 annotations
	Map existing names to new V4 ids, along with aliases		** Map existing names to new V4 ids, along with aliases
	Protein coding genes		** Protein coding genes

	AM- Subcellular localization annotations for MaizeV4		* AM- Subcellular localization annotations for MaizeV4

	PSDS- look at reviewer’s comments		* PSDS- look at reviewer’s comments

	Sorghum gene expression atlas		* Sorghum gene expression atlas
	Sorghum GRIN phenotype annotations		* Sorghum GRIN phenotype annotations

	~~New~~ data files- check SVN		* Need list of new data files? - check SVN

	* TO- fixing priorities list- may not be able to get them all done		* TO- fixing priorities list- may not be able to get them all done
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	* ''Question from MAL to JE: Do you run reasoner on the Planteome.owl file? Owl tools should have quality checks?''		* ''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		* 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,		* Stress ontology- move to the repo?, names are weird- being scraped,
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	** Hold for next release, discuss further at future		** 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?

	~~Possible time for Marie to Corvallis?~~		* Annual report -EA- has added info to their doc, MAL will send us
	~~Time frame? 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		* DWS- new hire? Evo Devo genes to connect fruit ripening and flower development
	In situs		** In situs
	Utilize Noctua to build the annotations?		* Utilize Noctua to build the annotations?
	- Fruit types paper		- Fruit types paper
	- wound periderm, lenticels work		- wound periderm, lenticels work
	-DWS will follow up with BS		-DWS will follow up with BS
	Annual report - abstracts, meetings, people,		* Annual report - abstracts, meetings, people,

	Ideas for the renewal- submit by March or April? No set deadlines- May 15th at the latest		==Ideas for the renewal==
	Two panels per year- June, November		- submit by March or April? No set deadlines- May 15th at the latest
	NCE		* Two panels per year- June, November
			* NCE will only last 1 year, if that

Cooperl: /* Agenda */

2017-12-05T20:13:30Z

Agenda

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	Tuesday Dec 5th, 2017		Tuesday Dec 5th, 2017

	December Release		==December Planteome Release==
	PECO release		* PECO release
	Sorghum and yam mapping almost completed		* Sorghum and yam mapping almost completed
	~~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?~~

			===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-		* New rice iprscan data- fewer results were returned-
	Clean up and make gene level annotation		Clean up and make gene level annotation

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	New data files- check SVN		New data files- check SVN

	TO- fixing priorities list- may not be able to get them all done		* 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		* 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?''

	~~TO + PECO~~- ~~working~~ with ~~CM and MAL to fix~~ the ~~patterns~~, ~~imports~~		*Noctua- moved to live database, updated with the GO version, won’t recognize the catalog file

	~~Run reasoner on the Planteome.owl file? Owl tools should have quality checks?~~		* Stress ontology- move to the repo?, names are weird- being scraped,
			** Need to fix on a name, PSO
	~~Noctua- moved to live database, updated with the GO version, won’t recognize the catalog file~~		** Hold for next release, discuss further at future

	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

Cooperl: /* Agenda */

2017-12-05T20:11:07Z

Agenda

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 =Agenda=
-In progress...
+Tuesday Dec 5th, 2017
 ==Phenoscape Hackathon Dec. 11th-14th==

Cooperl: /* Agenda */

2017-12-04T20:41:00Z

Agenda

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		==Presentation of PhenoArche data management by INRA==
		* Has date been set yet? - propose the following dates: 23, 25 janvier et 6 février.

Cooperl: /* Agenda */

2017-12-04T20:36:53Z

Agenda

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	* 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





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

Cooperl: /* Phenoscape Hackathon Dec. 11th-14th */

2017-12-04T20:35:25Z

Phenoscape Hackathon Dec. 11th-14th

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	===[http://kb.phenoscape.org/#/home Phenoscape]===		===[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]

Cooperl: /* Phenoscape Hackathon Dec. 11th-14th */

2017-12-04T20:34:38Z

Phenoscape Hackathon Dec. 11th-14th

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	* LC and AM will attend		* LC and AM will attend

	===[http://kb.phenoscape.org/#/home Phenoscape~~.org/#/home~~]===		===[http://kb.phenoscape.org/#/home Phenoscape]===

	* [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]

Cooperl: /* Phenoscape Hackathon Dec. 11th-14th */

2017-12-04T20:34:06Z

Phenoscape Hackathon Dec. 11th-14th

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	==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.org/#/home]===

	* [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]

Cooperl: /* Goals of the Workshop */

2017-12-04T20:33:20Z

Goals of the Workshop

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	===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.