Mar 1st, 2016 Ontology Working Group Meeting - Revision history

Cooperl: /* Tentative Schedule */

2016-03-07T19:34:08Z

Tentative Schedule

← Older revision		Revision as of 19:34, 7 March 2016
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	===== Tentative Schedule =====		===== Tentative Schedule =====
	* Day 1: morning - Austin present Planteome		* Monday Day 1: morning - Austin present Planteome
	* Day 2: show how lentil and cassava data has been annotated		* Tuesday Day 2: show how lentil and cassava data has been annotated
	* GAF2 format - column 16 - not unstructured, it has data relationships included		* GAF2 format - column 16 - not unstructured, it has data relationships included

Cooperl: /* Changes and updates in the IBP files */

2016-03-07T19:33:05Z

Changes and updates in the IBP files

← Older revision		Revision as of 19:33, 7 March 2016
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	* need to be clear on our naming for the purl.		* need to be clear on our naming for the purl.
	* PURLS are stored here: https://github.com/OBOFoundry/purl.obolibrary.org/blob/master/config/to.yml		* PURLS are stored here: https://github.com/OBOFoundry/purl.obolibrary.org/blob/master/config/to.yml
	* from the chat: MAL should us ontology:to/ibp-FOO-traits/FOO.owl		* from the chat: MAL should use ontology:to/ibp-FOO-traits/FOO.owl

	== Update on AmiGO APIs- Justin Elser ==		== Update on AmiGO APIs- Justin Elser ==

Cooperl: /* Changes and updates in the IBP files */

2016-03-07T19:32:07Z

Changes and updates in the IBP files

← Older revision		Revision as of 19:32, 7 March 2016
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	==Changes and updates in the IBP files ==		==Changes and updates in the IBP files ==
	* Review of progress with building the version of ~~Amigo~~ with the CO classes merged in		* Review of progress with building the Planteome version of AmiGO with the CO classes merged in

	* Three files are currently integrated: rice, cassava, lentil		* Three files are currently integrated: rice, cassava, lentil

Cooperl: /* Tentative Schedule */

2016-03-02T22:46:36Z

Tentative Schedule

← Older revision		Revision as of 22:46, 2 March 2016
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	* 64K mutant lines with phenotype data		* 64K mutant lines with phenotype data
	* C3-C4 mutant collection- any data on this would be awesome to get as well.		* C3-C4 mutant collection- any data on this would be awesome to get as well.


			===Genomic & Opensource Breeding Informatics Initiative (GOBII)===
			* what is GOBII (http://cbsugobii05.tc.cornell.edu/wordpress/) - learn as much about it as possible
			** creates field books and templates in a standard way for phenotype collection, more about providing tools than collecting data. push for them to use TO/CO ontologies in these GOBII


	===== Tentative Schedule =====		===== Tentative Schedule =====
	* Day 1 morning - Austin present Planteome		* Day 1: morning - Austin present Planteome
	* Day 2- show how lentil and cassava data has been annotated		* Day 2: show how lentil and cassava data has been annotated
	* GAF2 format - column 16 - not unstructured, it has data relationships included		* GAF2 format - column 16 - not unstructured, it has data relationships included

	* what is GOBII (http://cbsugobii05.tc.cornell.edu/wordpress/) - learn as much about it as possible
	** creates fieldbooks and templates in a standard way for phenotype collection, more about providing tools than collecting data. push for them to use TO/CO ontologies in these GOBI
	* Visit to genebank, fields, see the phenotyping platform		* Visit to genebank, fields, see the phenotyping platform
	* They are doing some automating phenotyping with UAVs- plant physiology, soil physiology		* They are doing some automating phenotyping with UAVs- plant physiology, soil physiology

Cooperl: /* Notes: */

2016-03-02T22:43:32Z

Notes:

← Older revision		Revision as of 22:43, 2 March 2016
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	* Goal is to have the data annotated, and have the trait dictionary in its final version		* Goal is to have the data annotated, and have the trait dictionary in its final version
	** add breeding traits to the TD, currently only genebank traits are in there.		** add breeding traits to the TD, currently only genebank traits are in there.

	* data annotation- Identify datasets for Planteome		* data annotation- Identify datasets for Planteome
	* genebank data, breeding database, "breeding for rice"- similar to data in BMS		* genebank data, breeding database, "breeding for rice"- similar to data in BMS
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	* IRGC packets http://www.irgcis.irri.org:81/grc/SearchData.htm		* IRGC packets http://www.irgcis.irri.org:81/grc/SearchData.htm
	* ~~ir64~~ mutant collection -another database		* IR64 mutant collection -another database, plus any other high throughput phenotyping data

	~~IR64 mutant collection~~
	~~C4 rice~~
	any other high throughput phenotyping data
	* 64K mutant lines with phenotype data		* 64K mutant lines with phenotype data
	* C3-C4 mutant collection- any data on this would be awesome to get as well.		* C3-C4 mutant collection- any data on this would be awesome to get as well.

	===== Tentative Schedule =====		===== Tentative Schedule =====
	* ~~day~~ 1 morning - Austin present Planteome		* Day 1 morning - Austin present Planteome
	* Day 2- show how lentil and cassava data ~~got~~ annotated		* Day 2- show how lentil and cassava data has been annotated
	* GAF2 format - column 16 - not unstructured, it has data relationships included		* GAF2 format - column 16 - not unstructured, it has data relationships included

	* what is ~~GOBI~~- learn as much about ~~GOBI~~ as possible		* what is GOBII (http://cbsugobii05.tc.cornell.edu/wordpress/) - learn as much about it as possible
	** creates fieldbooks and templates in a standard way for phenotype collection, more about providing tools than collecting data. push for them to use TO/CO ontologies in these GOBI		** creates fieldbooks and templates in a standard way for phenotype collection, more about providing tools than collecting data. push for them to use TO/CO ontologies in these GOBI
	* Visit to genebank, fields, see the phenotyping platform		* Visit to genebank, fields, see the phenotyping platform

Cooperl: /* schedule */

2016-03-02T22:41:00Z

schedule

← Older revision		Revision as of 22:41, 2 March 2016
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	* 64K mutant lines with phenotype data		* 64K mutant lines with phenotype data
	* C3-C4 mutant collection- any data on this would be awesome to get as well.		* C3-C4 mutant collection- any data on this would be awesome to get as well.
	===== ~~schedule~~ =====		===== Tentative Schedule =====
	* day 1 morning - Austin present Planteome		* day 1 morning - Austin present Planteome
	* Day 2- show how lentil and cassava data got annotated		* Day 2- show how lentil and cassava data got annotated

Cooperl: /* Notes: */

2016-03-02T22:39:23Z

Notes:

← Older revision		Revision as of 22:39, 2 March 2016
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	* data annotation- Identify datasets for Planteome		* data annotation- Identify datasets for Planteome
	* genebank data, breeding database, "breeding for rice"- similar to data in BMS		* genebank data, breeding database, "breeding for rice"- similar to data in BMS
			** http://www.irgcis.irri.org:81/grc/AboutIRGCIS.htm

	* 3K genomes of rice in another database, PJ - no trait data, only sequencing data		* 3K genomes of rice in another database, PJ - no trait data, only sequencing data
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	* ANYTHING they have to include, we will get included, very first pass will be similar to casava and lentil		* ANYTHING they have to include, we will get included, very first pass will be similar to casava and lentil
	* Anything that doesn't fit in the first pass, get the data, and we can evaluate how to make the additional data fit the GAF2 form (they might not be comfortable with giving ALL the data, but get what I can- access to images would be great		* Anything that doesn't fit in the first pass, get the data, and we can evaluate how to make the additional data fit the GAF2 form (they might not be comfortable with giving ALL the data, but get what I can- access to images would be great
	* ~~irgc~~ packets
	* ~~ir64mutant~~ collection -another database		* IRGC packets http://www.irgcis.irri.org:81/grc/SearchData.htm
			* ir64 mutant collection -another database

			IR64 mutant collection
			C4 rice
			any other high throughput phenotyping data
	* 64K mutant lines with phenotype data		* 64K mutant lines with phenotype data
	* C3-C4 mutant collection- any data on this would be awesome to get as well.		* C3-C4 mutant collection- any data on this would be awesome to get as well.

Cooperl: /* Other AmiGO Issues: */

2016-03-02T22:08:14Z

Other AmiGO Issues:

← Older revision		Revision as of 22:08, 2 March 2016
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	* purls needed again (catalogs can fix this -xml format)		* purls needed again (catalogs can fix this -xml format)
	* do a redirect within the catalogs		* do a redirect within the catalogs
	* put the catalog on ~~gitup~~ that maps all logical definitions onto the dev versions, the catalog can also insure that protege pulls the dev versions of all the imported ontologies		* put the catalog on GitHub that maps all logical definitions onto the dev versions, the catalog can also insure that protege pulls the dev versions of all the imported ontologies

	* more frequent releases will insure that TO doesn't reference updated PO terms, before the PO gets released, the idea is to eventually release PO/TO/etc simultaneously.		* more frequent releases will insure that TO doesn't reference updated PO terms, before the PO gets released, the idea is to eventually release PO/TO/etc simultaneously.
	* Ideally releases would be monthly		* Ideally releases would be monthly

	* iPlant mirror working at:		* iPlant mirror working at: http://draco.cyverse.org/amigo

	** some issues, like slow response- say something to iplant folks.		** some issues, like slow response- say something to iplant folks.

Cooperl: /* Changes and updates in the IBP files */

2016-03-02T22:03:01Z

Changes and updates in the IBP files

← Older revision		Revision as of 22:03, 2 March 2016
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	* wheat- ''newly mapped and will be added soon, once the issues of the id numbers are resolved''		* wheat- ''newly mapped and will be added soon, once the issues of the id numbers are resolved''
	** Latest changes: added the crop common name to all terms, removed the categorical classes (ie: Agronomical Traits), made all CO class names in lower case		** Latest changes: added the crop common name to all terms, removed the categorical classes (ie: Agronomical Traits), made all CO class names in lower case
			* The mappings to TO (is_a) are on the trait class, but there are still some on the cassava variables, as it appeared on the browser. These were originally put in since the variable was not connected, but can now be removed.
			* In cassava file, the variable has an is_a relationship to the trait, since the variable_of, method_of and scale_of relations are not being displayed. This is a workaround to get the variable to show as a child (should revert to actual relationships when we can get it sorted out in AmiGO)

	* ~~In cassava file, the variable has an is_a relationship to the trait, since the variable_of, method_of and scale_of relations are not being displayed~~		*Note: funny synonyms in AmiGO cause weird behavior with autocomplete ''(not sure what this means..)''
	* The mappings to TO are on the trait class,but there are still some on the variables, as it appeared on the browser. These were originally put in since the variable was not connected, but can now be removed.
	* This is a workaround to get the variable to show as a child (should revert to actual relationships when we can get it sorted out in AmiGO)
	* funny synonyms in AmiGO cause weird behavior with autocomplete

	* Questions and discussions:		* Questions and discussions:

Cooperl: /* schedule */

2016-03-02T00:55:24Z

schedule

← Older revision		Revision as of 00:55, 2 March 2016
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	* day 1 morning - Austin present Planteome		* day 1 morning - Austin present Planteome
	* Day 2- show how lentil and cassava data got annotated		* Day 2- show how lentil and cassava data got annotated
	* GAF2 format - column 16 - not unstructured		* GAF2 format - column 16 - not unstructured, it has data relationships included
	it has data relationships included
	learn as much about GOBI as possible		* what is GOBI- learn as much about GOBI as possible
	~~what is GOBI~~		** creates fieldbooks and templates in a standard way for phenotype collection, more about providing tools than collecting data. push for them to use TO/CO ontologies in these GOBI
	creates fieldbooks and templates in a standard way for phenotype collection		* Visit to genebank, fields, see the phenotyping platform
	more about providing tools than collecting data.		* They are doing some automating phenotyping with UAVs- plant physiology, soil physiology
	push for them to use TO/CO ontologies in these GOBI
	~~visit~~ to genebank
	~~visit to~~ fields
	~~visit to~~ see the phenotyping platform
	They are doing some automating phenotyping with UAVs
	plant physiology
	soil physiology
	Bottom line: Look at all the data they are collecting, and see if we can get those things integrated in our workflow		Bottom line: Look at all the data they are collecting, and see if we can get those things integrated in our workflow
	we want to attempt to get a meeting with "homebase"		we want to attempt to get a meeting with "homebase"
	8 hours ahead - could meet Wednesday (0800) Philippines = Tuesday (1600) Corvallis
			* 8 hours ahead - could meet Wednesday (0800) Philippines = Tuesday (1600) Corvallis
	Austin work with their staff to get the phenotyping data format		Austin work with their staff to get the phenotyping data format
	find exact ID of their varieties- need the EXACT seed packet ID		find exact ID of their varieties- need the EXACT seed packet ID, publicly available IDs to link out to from Planteome, basically need to find out how they store data
	publicly available IDs to link out to from Planteome
	basically need to find out how they store data
	~~ICBO -abstract~~
	~~another workshop before or after ICBO~~
	~~invite people back to Corvallis~~

	== 5. [http://www.phenotypercn.org/?page_id=2750 Phenotype RCN meeting February 26-28, 2016] ==		== 5. [http://www.phenotypercn.org/?page_id=2750 Phenotype RCN meeting February 26-28, 2016] ==