Sept 29th, 2015 Ontology Working Group Meeting - Revision history

Cooperl: /* 2. TermGenie Demo */

2015-11-05T20:06:39Z

2. TermGenie Demo

← Older revision		Revision as of 20:06, 5 November 2015
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	Don't use the template it give you (shown in red under the name)		Don't use the template it give you (shown in red under the name)
	select the little check-box, and click submit		select the little check-box, and click submit
	Now it waits for a "gate-keeper" to accept the term from the queue		- Now it waits for a "gate-keeper" to accept the term from the queue
	Gate-keeper reviews it (can edit), and performs the commit.		- Gate-keeper reviews it (can edit), and performs the commit, once accepted it will update the ontology on GitHub
	once accepted it will update the ontology on GitHub
	Works in GO		Works in GO
	* You can jump to different ontologies, select the upper level term you want it under, and hit "use template" (only works if there is an upper level term that your term conforms to.)		* You can jump to different ontologies, select the upper level term you want it under, and hit "use template" (only works if there is an upper level term that your term conforms to.)

Cooperl at 18:46, 19 October 2015

2015-10-19T18:46:20Z

← Older revision		Revision as of 18:46, 19 October 2015
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	* 2 curators from CIGAR coming		* 2 curators from CIGAR coming
	* EA: Could check with ICARDA and ICRISAT curators, if there is money and they are interested to come		* EA: Could check with ICARDA and ICRISAT curators, if there is money and they are interested to come
	** Suggested: ~~Kathleen Carrol (sp?)~~ - ICARDA, Morocco might come to the training. Worked on the lentil trait dictionary and was interested in getting trained. (She was apparently at the April workshop (not sure which one this is. Not at the Crop Ontology 2014 meeting in Montpellier).		** Suggested: Karthika Rajendra - ICARDA, Morocco might come to the training. Worked on the lentil trait dictionary and was interested in getting trained. (She was apparently at the April workshop (not sure which one this is. Not at the Crop Ontology 2014 meeting in Montpellier).
	** RS Hamilton- IRRI, very busy as he is also working at Rome office, but will be at the PAG meeting		** RS Hamilton- IRRI, very busy as he is also working at Rome office, but will be at the PAG meeting
	* CM will be there all week, so we can have the Protege training at any time in the week. Seth will come for a couple of days at the end of the week.		* CM will be there all week, so we can have the Protege training at any time in the week. Seth will come for a couple of days at the end of the week.

Cooperl: /* 2. TermGenie Demo */

2015-10-13T18:29:46Z

2. TermGenie Demo

← Older revision		Revision as of 18:29, 13 October 2015
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	== 2. TermGenie Demo ==		== 2. TermGenie Demo ==
	* TermGenie [http://geneontology.org/page/termgenie] is a tool for creating new ontology terms for either GO (Gene Ontology) or OBA (Ontology of Biological Attributes), as well as others. It uses a pattern-based approach to rapidly generate new terms and place them appropriately within the ontology structure. All terms are reviewed by a senior editor before the final commit to the ontology.		* TermGenie [http://geneontology.org/page/termgenie] is a tool for creating new ontology terms for either GO (Gene Ontology) or OBA (Ontology of Biological Attributes), as well as others. It uses a pattern-based approach to rapidly generate new terms and place them appropriately within the ontology structure. All terms are reviewed by a senior editor before the final commit to the ontology.

			Link to [https://github.com/geneontology/termgenie TermGenie GitHub]

	* Two instances of TermGenie exist: for OBA and GO:		* Two instances of TermGenie exist: for OBA and GO:

Cooperl: /* 2. TermGenie Demo */

2015-10-13T18:27:29Z

2. TermGenie Demo

← Older revision		Revision as of 18:27, 13 October 2015
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	== 2. TermGenie Demo ==		== 2. TermGenie Demo ==
	* A tool for creating new ontology terms for either GO (Gene Ontology) or OBA (Ontology of Biological Attributes). It uses a pattern-based approach to rapidly generate new terms and place them appropriately within the ontology structure. All terms are reviewed by a senior editor before the final commit to the ontology.		* TermGenie [http://geneontology.org/page/termgenie] is a tool for creating new ontology terms for either GO (Gene Ontology) or OBA (Ontology of Biological Attributes), as well as others. It uses a pattern-based approach to rapidly generate new terms and place them appropriately within the ontology structure. All terms are reviewed by a senior editor before the final commit to the ontology.

	* Two instances of TermGenie exist: for OBA and GO:		* Two instances of TermGenie exist: for OBA and GO:

Cooperl: /* 2. TermGenie Demo */

2015-10-13T18:14:53Z

2. TermGenie Demo

← Older revision		Revision as of 18:14, 13 October 2015
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	* Two instances of TermGenie exist: for OBA and GO:		* Two instances of TermGenie exist: for OBA and GO:
	** [http://go.termgenie.org/ TermGenie GO]		** [http://go.termgenie.org/ TermGenie GO]
			** [http://oba.termgenie.org/ TermGenie OBA]
	** [http://go.termgenie.org/ TermGenie OBA]

	* CM		* CM

Cooperl at 17:47, 13 October 2015

2015-10-13T17:47:12Z

← Older revision		Revision as of 17:47, 13 October 2015
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	** Suggested: Kathleen Carrol (sp?) - ICARDA, Morocco might come to the training. Worked on the lentil trait dictionary and was interested in getting trained. (She was apparently at the April workshop (not sure which one this is. Not at the Crop Ontology 2014 meeting in Montpellier).		** Suggested: Kathleen Carrol (sp?) - ICARDA, Morocco might come to the training. Worked on the lentil trait dictionary and was interested in getting trained. (She was apparently at the April workshop (not sure which one this is. Not at the Crop Ontology 2014 meeting in Montpellier).
	** RS Hamilton- IRRI, very busy as he is also working at Rome office, but will be at the PAG meeting		** RS Hamilton- IRRI, very busy as he is also working at Rome office, but will be at the PAG meeting
			* CM will be there all week, so we can have the Protege training at any time in the week. Seth will come for a couple of days at the end of the week.

	* CM will be there all week, so we can have the Protege training at any time in the week.

	== 2. TermGenie Demo ==		== 2. TermGenie Demo ==
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	* CM		* CM
	- log-in (anyone can sign up)- Firefox		* log-in (anyone can sign up)- Firefox
	~~- select~~ template (currently entity-quality)		* Select template (currently entity-quality)
	~~enter~~ the entity (pick it from the GO), the quality (from PATO), enter optional lit_ref, and DBXref		* Enter the entity (pick it from the GO), the quality (from PATO), enter optional lit_ref, and DBXref
	It checks for duplicates, or existing terms		It checks for duplicates, or existing terms
	Gives the label (add "trait") to the end. Also give a definition		Gives the label (add "trait") to the end. Also give a definition

Cooperl at 17:21, 13 October 2015

2015-10-13T17:21:12Z

← Older revision		Revision as of 17:21, 13 October 2015
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	==1. Training workshop in Corvallis==		==1. Training workshop in Corvallis==
	* Location: Corvallis, 2nd week of Nov		* Location: Corvallis, 2nd week of Nov
	* notes are on the wiki- dates, accommodations		* notes are on the wiki [[Planteome_Curator_workshop_Fall_2015]] - dates, accommodations
	* EA: Could check with ICARDA and ICRISAT curators, if there is money and they are interested to come
	** Suggested: Kathleen Carrol (sp?) - ICARDA, morocco might come to the training. Worked on the lentil trait dictionary and was interested in getting trained. (She was apparentaly at the April workshop (not sure which one this is. Not at the Crop Ontology 2014 meeting in Montpellier.
	** RS Hamilton

	* PJ said whomever is on the Planteome- has travel funds, and should go ahead and use them. We will book the others (CIP, etc...)		* PJ said whomever is on the Planteome- has travel funds, and should go ahead and use them. We will book the others (CIP, etc...)
	* 2 curators from CIGAR coming		* 2 curators from CIGAR coming
			* EA: Could check with ICARDA and ICRISAT curators, if there is money and they are interested to come
			** Suggested: Kathleen Carrol (sp?) - ICARDA, Morocco might come to the training. Worked on the lentil trait dictionary and was interested in getting trained. (She was apparently at the April workshop (not sure which one this is. Not at the Crop Ontology 2014 meeting in Montpellier).
			** RS Hamilton- IRRI, very busy as he is also working at Rome office, but will be at the PAG meeting


	* CM will be there all week, so we can have the Protege training at any time in the week.		* CM will be there all week, so we can have the Protege training at any time in the week.

Cooperl at 23:44, 12 October 2015

2015-10-12T23:44:58Z

← Older revision		Revision as of 23:44, 12 October 2015
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	* Location: Corvallis, 2nd week of Nov		* Location: Corvallis, 2nd week of Nov
	* notes are on the wiki- dates, accommodations		* notes are on the wiki- dates, accommodations
			* EA: Could check with ICARDA and ICRISAT curators, if there is money and they are interested to come
			** Suggested: Kathleen Carrol (sp?) - ICARDA, morocco might come to the training. Worked on the lentil trait dictionary and was interested in getting trained. (She was apparentaly at the April workshop (not sure which one this is. Not at the Crop Ontology 2014 meeting in Montpellier.
			** RS Hamilton

	* cathinle carrol (sp?) - ICARDA, morocco might come to the training. Worked on the lentil trait dictionary (EA)
	* PJ said whomever is on the Planteome- has travel funds, and should go ahead and use them. We will book the others (CIP, etc...)		* PJ said whomever is on the Planteome- has travel funds, and should go ahead and use them. We will book the others (CIP, etc...)
	* 2 curators from CIGAR coming		* 2 curators from CIGAR coming

Cooperl at 22:41, 12 October 2015

2015-10-12T22:41:52Z

← Older revision		Revision as of 22:41, 12 October 2015
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	==1. Training workshop in Corvallis==		==1. Training workshop in Corvallis==
	* Location: Corvallis, 2nd week of Nov		* Location: Corvallis, 2nd week of Nov
	* notes are on the wiki- dates, accommodations		* notes are on the wiki- dates, accommodations

	* cathinle carrol (sp?) - morocco might come to the training. (EA)		* cathinle carrol (sp?) - ICARDA, morocco might come to the training. Worked on the lentil trait dictionary (EA)
	* PJ said whomever is on the Planteome- has travel funds, and should go ahead and use them. We will book the others (CIP, etc...)		* PJ said whomever is on the Planteome- has travel funds, and should go ahead and use them. We will book the others (CIP, etc...)
	* 2 curators from CIGAR coming		* 2 curators from CIGAR coming

Cooperl: /* 3. Discussion About Plant Trait Ontology: */

2015-10-08T16:11:02Z

3. Discussion About Plant Trait Ontology:

← Older revision		Revision as of 16:11, 8 October 2015
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	Link from Chris: [http://wiki.obofoundry.org/wiki/index.php/PATO:plant_trait_xp]		Link from Chris: [http://wiki.obofoundry.org/wiki/index.php/PATO:plant_trait_xp PATO:plant_trait_xp]