Nov 24th, 2015 Ontology Working Group Meeting - Revision history

Cooperl: /* Planteome Ontology WG Zoom Meeting: */

2015-11-25T00:25:17Z

Planteome Ontology WG Zoom Meeting:

← Older revision		Revision as of 00:25, 25 November 2015
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	* Attendees: AM, MAL, LC, PJ, JE, CM and EA		* Attendees: AM, MAL, LC, PJ, JE, CM and EA
	* Regrets: JD		* Regrets: JD
			* [[File:Ontology_WG_Meeting_video_11-24-15.mp4\|thumb\|Ontology WG 11-24-15 video]]
			* [[File:Ontology_WG_Meeting_audio_only_11-24-15.m4a\|thumb\|Ontology WG 10-24-15 audio]]

	=Review of recent Planteome Developers' Workshop, Nov 9th-13th, 2015 Corvallis, OR =		=Review of recent Planteome Developers' Workshop, Nov 9th-13th, 2015 Corvallis, OR =

Cooperl: /* Planteome Ontology WG Zoom Meeting: */

2015-11-25T00:17:45Z

Planteome Ontology WG Zoom Meeting:

← Older revision		Revision as of 00:17, 25 November 2015
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	Date: Tuesday Nov. 24th, 2015		Date: Tuesday Nov. 24th, 2015
	Time: 9am PST (GMT-8)		Time: 9am PST (GMT-8)

	* <sup>Connection details: '''Join from PC, Mac, Linux, iOS or Android: https://zoom.us/j/551476918</sup>'''		* <sup>Connection details: '''Join from PC, Mac, Linux, iOS or Android: https://zoom.us/j/551476918</sup>'''

	Attendees: AM, MAL, LC, PJ, JE, CM and EA		* Attendees: AM, MAL, LC, PJ, JE, CM and EA
			* Regrets: JD
	Regrets: JD

	=Review of recent Planteome Developers' Workshop, Nov 9th-13th, 2015 Corvallis, OR =		=Review of recent Planteome Developers' Workshop, Nov 9th-13th, 2015 Corvallis, OR =

Cooperl: /* AmiGO2 Demo- TO with CO lentils */

2015-11-24T23:21:50Z

AmiGO2 Demo- TO with CO lentils

← Older revision		Revision as of 23:21, 24 November 2015
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	* The demo is a proof-of-concept for mapping .xls to our browser. Automation will be necessary. Possibly could convert our g-sheet to .csv for the perl script that CM will make to do that automatically.		* The demo is a proof-of-concept for mapping .xls to our browser. Automation will be necessary. Possibly could convert our g-sheet to .csv for the perl script that CM will make to do that automatically.

	[[File:Visualize.png\|~~framed~~\|Plant Height - TO with CO-Lentils]]		[[File:Visualize.png\|thumbnail\|center\|Plant Height - TO with CO-Lentils]]

	=Next Meeting: Tuesday Dec. 8th=		=Next Meeting: Tuesday Dec. 8th=

Cooperl: /* AmiGO2 Demo- TO with CO lentils */

2015-11-24T23:20:30Z

AmiGO2 Demo- TO with CO lentils

← Older revision		Revision as of 23:20, 24 November 2015
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	* The demo is a proof-of-concept for mapping .xls to our browser. Automation will be necessary. Possibly could convert our g-sheet to .csv for the perl script that CM will make to do that automatically.		* The demo is a proof-of-concept for mapping .xls to our browser. Automation will be necessary. Possibly could convert our g-sheet to .csv for the perl script that CM will make to do that automatically.

			[[File:Visualize.png\|framed\|Plant Height - TO with CO-Lentils]]
	[[File:Visualize.png\|~~thumbnail~~\|Plant Height - TO with CO-Lentils]]

	=Next Meeting: Tuesday Dec. 8th=		=Next Meeting: Tuesday Dec. 8th=

Cooperl: /* AmiGO2 Demo- TO with CO lentils */

2015-11-24T23:19:25Z

AmiGO2 Demo- TO with CO lentils

← Older revision		Revision as of 23:19, 24 November 2015
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	* The demo is a proof-of-concept for mapping .xls to our browser. Automation will be necessary. Possibly could convert our g-sheet to .csv for the perl script that CM will make to do that automatically.		* The demo is a proof-of-concept for mapping .xls to our browser. Automation will be necessary. Possibly could convert our g-sheet to .csv for the perl script that CM will make to do that automatically.


			[[File:Visualize.png\|thumbnail\|Plant Height - TO with CO-Lentils]]

	=Next Meeting: Tuesday Dec. 8th=		=Next Meeting: Tuesday Dec. 8th=

Cooperl: /* AmiGO2 Demo- TO with CO lentils */

2015-11-24T23:15:49Z

AmiGO2 Demo- TO with CO lentils

← Older revision		Revision as of 23:15, 24 November 2015
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	* The demo is a proof-of-concept for mapping .xls to our browser. Automation will be necessary. Possibly could convert our g-sheet to .csv for the perl script that CM will make to do that automatically.		* The demo is a proof-of-concept for mapping .xls to our browser. Automation will be necessary. Possibly could convert our g-sheet to .csv for the perl script that CM will make to do that automatically.


			=Next Meeting: Tuesday Dec. 8th=

Cooperl: /* AmiGO2 */

2015-11-24T23:14:48Z

AmiGO2

← Older revision		Revision as of 23:14, 24 November 2015
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	5. Once term is added, the final term will be posted on GitHub issue and it will be closed.		5. Once term is added, the final term will be posted on GitHub issue and it will be closed.

	=AmiGO2=		=AmiGO2 Demo- TO with CO lentils=
	A demonstration version of the AmiGO2.0 Planteome browser has been set up with the TO and the lentil ontology, along with the mappings to the equivalent classes.		* A demonstration version of the AmiGO2.0 Planteome browser has been set up with the TO and the lentil ontology, along with the mappings to the equivalent classes.
			* You can view it at: http://dev.planteome.org
			* Example: [http://dev.planteome.org/amigo/term/CO_339:0000114 plant height trait]
			** Files loaded: dev version of TO: plant-trait-ontology.obo from github and the

	~~You can view it at: http://dev.planteome.org~~		* from CM: I made a file called 'ibp-lentil-traits/merged.owl' which is the combination of CO_339 (OWL file?) plus bridging axioms derived from Pankaj's excel spreadsheet.
			** [https://raw.githubusercontent.com/Planteome/plant-trait-ontology/master/ext/lentil-traits.owl ibp-lentil-traits/merged.owl]
	~~Example: [http://dev.planteome.org/amigo/term/CO_339:0000114 plant height trait]~~

	* ~~Files loaded: dev version of TO: plant-trait-ontology.obo~~ from ~~github and the~~

	~~Chris Mungall wrote~~:
	> I made a file called ibp-lentil-traits/merged.owl which is the combination of CO_339 plus bridging axioms derived from Pankaj's excel
	https://raw.githubusercontent.com/Planteome/plant-trait-ontology/master/ext/lentil-traits.owl

	* The demo is a proof-of-concept for mapping .xls to our browser. Automation will be necessary. Possibly could convert our g-sheet to .csv for the perl script that CM will make to do that automatically.		* The demo is a proof-of-concept for mapping .xls to our browser. Automation will be necessary. Possibly could convert our g-sheet to .csv for the perl script that CM will make to do that automatically.

Cooperl: /* AmiGO2 */

2015-11-24T23:12:32Z

AmiGO2

← Older revision		Revision as of 23:12, 24 November 2015
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	> I made a file called ibp-lentil-traits/merged.owl which is the combination of CO_339 plus bridging axioms derived from Pankaj's excel		> I made a file called ibp-lentil-traits/merged.owl which is the combination of CO_339 plus bridging axioms derived from Pankaj's excel
	https://raw.githubusercontent.com/Planteome/plant-trait-ontology/master/ext/lentil-traits.owl		https://raw.githubusercontent.com/Planteome/plant-trait-ontology/master/ext/lentil-traits.owl

			* The demo is a proof-of-concept for mapping .xls to our browser. Automation will be necessary. Possibly could convert our g-sheet to .csv for the perl script that CM will make to do that automatically.

Cooperl: /* AmiGO2 */

2015-11-24T22:41:17Z

AmiGO2

← Older revision		Revision as of 22:41, 24 November 2015
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	Example: [http://dev.planteome.org/amigo/term/CO_339:0000114 plant height trait]		Example: [http://dev.planteome.org/amigo/term/CO_339:0000114 plant height trait]

	~~==Questions~~ and ~~Comments~~: ==		* Files loaded: dev version of TO: plant-trait-ontology.obo from github and the

			Chris Mungall wrote:
			> I made a file called ibp-lentil-traits/merged.owl which is the combination of CO_339 plus bridging axioms derived from Pankaj's excel
			https://raw.githubusercontent.com/Planteome/plant-trait-ontology/master/ext/lentil-traits.owl

Cooperl: /* TermGenie */

2015-11-24T22:36:06Z

TermGenie

← Older revision		Revision as of 22:36, 24 November 2015
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	* Proposed workflow for requesting terms through TermGenie-TO		* Proposed workflow for requesting terms through TermGenie-TO
	1. Sign up for a persona account (for new requesters - from TermGenie page)		1. Sign up for a persona account (for new requesters - from TermGenie page)

	2. Add a ticket to the TO tracker, include persona username (email address), requesting TG permission. CM will add you as a user		2. Add a ticket to the TO tracker, include persona username (email address), requesting TG permission. CM will add you as a user

	3. Requests should yield an id automatically, then the term will go into the moderation queue		3. Requests should yield an id automatically, then the term will go into the moderation queue

	4. If there are questions, discussion should be on the GitHub issue, not through emails.		4. If there are questions, discussion should be on the GitHub issue, not through emails.

	5. Once term is added, the final term will be posted on GitHub issue and it will be closed.		5. Once term is added, the final term will be posted on GitHub issue and it will be closed.