Apr. 26th, 2016 Ontology Working Group Meeting - Revision history

Cooperl: /* = AgroVoc */

2017-02-07T21:54:44Z

= AgroVoc

← Older revision		Revision as of 21:54, 7 February 2017
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	* Integrates environmental aspects		* Integrates environmental aspects

	=== AgroVoc==		== AgroVoc==
	* SKOS vocabulary		* SKOS vocabulary
	* something that might be useful for PSO relationships and interactions; 1370 is_Pathogen_Of links		* something that might be useful for PSO relationships and interactions; 1370 is_Pathogen_Of links

Cooperl at 23:36, 23 May 2016

2016-05-23T23:36:13Z

← Older revision		Revision as of 23:36, 23 May 2016
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	http://icbo.cgrb.oregonstate.edu/ICBO_submission		http://icbo.cgrb.oregonstate.edu/ICBO_submission

	'''Deadline is May ~~17th~~'''		'''Deadline is May 5th'''

	Proposed Topics, with suggested lead:		Proposed Topics, with suggested lead:

Cooperl: /* 3. ICBO 2016 Call for Papers is open */

2016-05-23T21:35:47Z

3. ICBO 2016 Call for Papers is open

← Older revision		Revision as of 21:35, 23 May 2016
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	http://icbo.cgrb.oregonstate.edu/ICBO_submission		http://icbo.cgrb.oregonstate.edu/ICBO_submission

	'''Deadline is May ~~5th~~'''		'''Deadline is May 17th'''

	Proposed Topics, with suggested lead:		Proposed Topics, with suggested lead:

Cooperl: /* Potential collaborators */

2016-04-27T21:03:00Z

Potential collaborators

← Older revision		Revision as of 21:03, 27 April 2016
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	* KE Lin (Rijk Zwaan): works on vegetable varieties. Interested in the approach in order to map his species specific breeders traits.		* KE Lin (Rijk Zwaan): works on vegetable varieties. Interested in the approach in order to map his species specific breeders traits.
	* Sebastien Briois (Syngenta): was interested in using Planteome data.		* Sebastien Briois (Syngenta): was interested in using Planteome data.
	* Melissa ~~Haedel~~ (OHSU): phenopackets to annotate the breeders data. (see below)		* Melissa Haendel (OHSU): phenopackets to annotate the breeders data. (see below)

	*Follow ups:		*Follow ups:
	**Everything should be under Creative Commons licensing, so all that's required for use is a 'thank you' on the web page where Planteome data is used		**Everything should be under Creative Commons licensing, so all that's required for use is a 'thank you' on the web page where Planteome data is used
	**PJ would like to set up a meeting with some of the possible collaborators		**PJ would like to set up a meeting with some of the possible collaborators

	===Talks of Interest:===		===Talks of Interest:===

Cooperl: /* = AgroVoc */

2016-04-26T18:46:14Z

= AgroVoc

← Older revision		Revision as of 18:46, 26 April 2016
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	** is GACS intended as an uberon or PO/TO life effort that serves as a reference unifying multiple sources?		** is GACS intended as an uberon or PO/TO life effort that serves as a reference unifying multiple sources?
	* I'm not completely sure it's an improvement, e.g. spikelet in GACS: http://tester-os-kktest.lib.helsinki.fi/gacsdemo/agrovoc/en/page/c_7301 vs. spikelet in AGROVOC: http://aims.fao.org/skosmos/agrovoc/en/page/c_7301; As you can see the AGROVOC one is richer as it has partOf relationships, etc		* I'm not completely sure it's an improvement, e.g. spikelet in GACS: http://tester-os-kktest.lib.helsinki.fi/gacsdemo/agrovoc/en/page/c_7301 vs. spikelet in AGROVOC: http://aims.fao.org/skosmos/agrovoc/en/page/c_7301; As you can see the AGROVOC one is richer as it has partOf relationships, etc
	* Of course, both could import PO in this particular case, but keeping their own language translations. Hopefully the PhenoHarmonIS meeting will be the first step in the OBO and FAO etc communities learning from each other)		* Of course, both could import PO in this particular case, but keeping their own language translations. Hopefully the PhenoHarmonIS meeting will be the first step in the OBO and FAO etc communities learning from each other

	==2. Update on the plans for the PhenoHarmonIS Meeting in Montpellier, 9-13 May 2016==		==2. Update on the plans for the PhenoHarmonIS Meeting in Montpellier, 9-13 May 2016==

Cooperl: /* PhenoPackets: */

2016-04-26T18:45:35Z

PhenoPackets:

← Older revision		Revision as of 18:45, 26 April 2016
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	* Integrates environmental aspects		* Integrates environmental aspects

	* ~~AgroVoc -~~ something that might be useful for PSO relationships and interactions		=== AgroVoc==
	* GACS - ~~AgroVoc plus NATL~~ and ~~CABT~~		* SKOS vocabulary
	** ~~less complex~~		* something that might be useful for PSO relationships and interactions; 1370 is_Pathogen_Of links
	** ~~includes AgroVoc~~		* CM has been experimenting with aligning it to our ontologies; interested to convert it to OWL version using OBO conventions
			* See: https://github.com/cmungall/agrovoc-obo
			* Looks like Cyril is involved, I'm aware of his work on GMOD/Chado: https://rd-alliance.org/groups/agrisemantics-wg.html

			* Marie, is there a repository for GACS? Are you involved in any of the mapping work? Found this: http://tester-os-kktest.lib.helsinki.fi/gacsdemo/en/
			** Mentioned in these slides: http://www.slideshare.net/CIARD_AIMS/from-gacs-to-agrisemantics-steps-forward-towards-interoperability-of-data-for-agriculture-and-nutrition-by-caterina-caracciolo; Lots of common interest, e.g. slide 10
			** It seems agrisemantics is one step beyond GACS, but having difficulties finding anything concrete - is it at the early stages?
			** is GACS intended as an uberon or PO/TO life effort that serves as a reference unifying multiple sources?
			* I'm not completely sure it's an improvement, e.g. spikelet in GACS: http://tester-os-kktest.lib.helsinki.fi/gacsdemo/agrovoc/en/page/c_7301 vs. spikelet in AGROVOC: http://aims.fao.org/skosmos/agrovoc/en/page/c_7301; As you can see the AGROVOC one is richer as it has partOf relationships, etc
			* Of course, both could import PO in this particular case, but keeping their own language translations. Hopefully the PhenoHarmonIS meeting will be the first step in the OBO and FAO etc communities learning from each other)

	==2. Update on the plans for the PhenoHarmonIS Meeting in Montpellier, 9-13 May 2016==		==2. Update on the plans for the PhenoHarmonIS Meeting in Montpellier, 9-13 May 2016==

Cooperl: /* Other Items */

2016-04-26T18:34:15Z

Other Items

← Older revision		Revision as of 18:34, 26 April 2016
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	==Other Items==		==Other Items==
	Tabled from previous meetings:		Tabled from previous meetings: Did not get a chance to cover today

	===OBA development- Chris Mungall===		===OBA development- Chris Mungall===

Cooperl: /* 4. Plant Trait Ontology updates */

2016-04-26T18:33:40Z

4. Plant Trait Ontology updates

← Older revision		Revision as of 18:33, 26 April 2016
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	* Recent revisions and changes to the equivalence axioms etc		* Recent revisions and changes to the equivalence axioms etc

	* Plans to do release		* Plans to do release.....

	Link to Google doc: [https://docs.google.com/document/d/1cBIVlPzVt0RFPIUbcPjpXABcfhh3MKwUf8gjR1kaAbY/edit?usp=sharing TO Issues: Number_of Traits]		Link to Google doc: [https://docs.google.com/document/d/1cBIVlPzVt0RFPIUbcPjpXABcfhh3MKwUf8gjR1kaAbY/edit?usp=sharing TO Issues: Number_of Traits]
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	''Or should this be whole plant????''		''Or should this be whole plant????''

			=== Comments:===
			* CM: prefers simpler definition, not G-D format?
			* BS thinks it is OK
			* Compare with OBA, use YAML
			* Look at example from the Planteome workshop- ????

	==5. AmiGO2 Update: ==		==5. AmiGO2 Update: ==

Cooperl: /* 4. Plant Trait Ontology updates */

2016-04-26T18:30:26Z

4. Plant Trait Ontology updates

@@ Line 111: / Line 111: @@
 * intersection_of: inheres_in PO:0000XYZ ! plant part being counted
 * intersection_of: occurs_in PO:0025025 ! root system-  this is for the part of the plant which has the multiple parts, could also be ‘whole plant’
 ==5. AmiGO2 Update: ==

Cooperl: /* 4. Plant Trait Ontology updates */

2016-04-26T18:25:42Z

4. Plant Trait Ontology updates

← Older revision		Revision as of 18:25, 26 April 2016
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	Link to Google doc: [https://docs.google.com/document/d/1cBIVlPzVt0RFPIUbcPjpXABcfhh3MKwUf8gjR1kaAbY/edit?usp=sharing TO Issues: Number_of Traits]		Link to Google doc: [https://docs.google.com/document/d/1cBIVlPzVt0RFPIUbcPjpXABcfhh3MKwUf8gjR1kaAbY/edit?usp=sharing TO Issues: Number_of Traits]

	Number_of Traits		Number_of Traits: General format- (OBO file stanza)

	General format:
	(OBO file stanza)

	* intersection_of: PATO:0001555 ! has number of		* intersection_of: PATO:0001555 ! has number of
	* intersection_of: inheres_in PO:0000XYZ ! plant part being counted		* intersection_of: inheres_in PO:0000XYZ ! plant part being counted