Oct 25th, 2016 Ontology Working Group Meeting - Revision history

Cooperl: /* New Taxon constraints added to PO */

2016-10-25T19:22:22Z

New Taxon constraints added to PO

← Older revision		Revision as of 19:22, 25 October 2016
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	* ''Possible solutions: Use the GO union classes (see: http://purl.obolibrary.org/obo/go/extensions/go-taxon-groupings.owl)''		* ''Possible solutions: Use the GO union classes (see: http://purl.obolibrary.org/obo/go/extensions/go-taxon-groupings.owl)''
			** http://geneontology.org/ontology/extensions/go-taxon-groupings/

	* ''Or use weaker "present_in", or negative relations like "never_in"		* ''Or use weaker "present_in", or negative relations like "never_in"
	** ''For microspores, use a term for "heterosporous plants"- is it in NCBI? Doubtful''		** ''For microspores, use a term for "heterosporous plants"- is it in NCBI? Doubtful''

Cooperl: /* New Taxon constraints added to PO */

2016-10-25T19:20:21Z

New Taxon constraints added to PO

← Older revision		Revision as of 19:20, 25 October 2016
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	* BS Suggestion from 10-11-16: maybe we should be using the in_taxon relation, rather than the only_in_taxon relation		* BS Suggestion from 10-11-16: maybe we should be using the in_taxon relation, rather than the only_in_taxon relation

	* ''Possible solutions: Use the GO union classes (~~how do we do that??~~) or use weaker "present_in", or negative relations like "never_in"		* ''Possible solutions: Use the GO union classes (see: http://purl.obolibrary.org/obo/go/extensions/go-taxon-groupings.owl)''
			* ''Or use weaker "present_in", or negative relations like "never_in"
	** ''For microspores, use a term for "heterosporous plants"- is it in NCBI? Doubtful''		** ''For microspores, use a term for "heterosporous plants"- is it in NCBI? Doubtful''
	** ''Make our own taxonomy??? Not a good alternative''		** ''Make our own taxonomy??? Not a good alternative''

Cooperl: /* How to deal with the ones that are in more than one taxa (that do not have a common ancestor)- two ways: */

2016-10-25T18:42:55Z

How to deal with the ones that are in more than one taxa (that do not have a common ancestor)- two ways:

← Older revision		Revision as of 18:42, 25 October 2016
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	* BS Suggestion from 10-11-16: maybe we should be using the in_taxon relation, rather than the only_in_taxon relation		* BS Suggestion from 10-11-16: maybe we should be using the in_taxon relation, rather than the only_in_taxon relation

	* ''Possible solutions: Use the GO union classes (how do we do that??) or use weaker "present_in"		* ''Possible solutions: Use the GO union classes (how do we do that??) or use weaker "present_in", or negative relations like "never_in"
	or negative relations like "never_in"
	** ''For microspores, use a term for "heterosporous plants"- is it in NCBI? Doubtful''		** ''For microspores, use a term for "heterosporous plants"- is it in NCBI? Doubtful''
	** ''Make our own taxonomy??? Not a good alternative''		** ''Make our own taxonomy??? Not a good alternative''

Cooperl: /* How to deal with the ones that are in more than one taxa (that do not have a common ancestor)- two ways: */

2016-10-25T18:42:31Z

How to deal with the ones that are in more than one taxa (that do not have a common ancestor)- two ways:

← Older revision		Revision as of 18:42, 25 October 2016
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	* The other was is to use "X only_in_taxon (Y OR Z)", but this needs to be tested....		* The other was is to use "X only_in_taxon (Y OR Z)", but this needs to be tested....

	* Suggestion: maybe we should be using the in_taxon relation, rather than the only_in_taxon relation		* BS Suggestion from 10-11-16: maybe we should be using the in_taxon relation, rather than the only_in_taxon relation

			* ''Possible solutions: Use the GO union classes (how do we do that??) or use weaker "present_in"
			or negative relations like "never_in"
			** ''For microspores, use a term for "heterosporous plants"- is it in NCBI? Doubtful''
			** ''Make our own taxonomy??? Not a good alternative''
			** ''Taxonomies change frequently''

	== Suggest adding a new relation between the morphology trait and a quality trait ==		== Suggest adding a new relation between the morphology trait and a quality trait ==

Cooperl: /* Addition of fruit subclasses */

2016-10-25T18:20:35Z

Addition of fruit subclasses

← Older revision		Revision as of 18:20, 25 October 2016
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	* ''We will give DWS et al, access to modify pages on the planteome site, can put a picture of the structure on the page, with a link to the Amigo page for those terms. Will start with the fruit terms.''		* ''We will give DWS et al, access to modify pages on the planteome site, can put a picture of the structure on the page, with a link to the Amigo page for those terms. Will start with the fruit terms.''
	** Question- how can we link from the term page?		** Question- how can we link from the term page?
			== "Ghost seeds"==
			* How to create a terms to annotate the seed where the embryo has been removed?
			** microdissections add novel terms (eg: remove embryo from the seed, what do you call the remaining part? "ghost")

			* ''should we be concentrating on things that actually exist? These artificial structures might be a slippery slope''
			** '' PJ -counter argument - plant biology is drifting towards more artificial biology (think about mutants)''
			** ''CM - you can make a one-of term that contains the remaining terms, and that it is derived_from seed. Make sure to tag them appropriately''

	==New Taxon constraints added to PO==		==New Taxon constraints added to PO==

Cooperl: /* Suggest adding a new relation between the morphology trait and a quality trait */

2016-10-25T18:18:09Z

Suggest adding a new relation between the morphology trait and a quality trait

← Older revision		Revision as of 18:18, 25 October 2016
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	== Suggest adding a new relation between the morphology trait and a quality trait ==		== Suggest adding a new relation between the morphology trait and a quality trait ==
	~~Many of these are currently is_a children resulting in dual parentage, we also have some that are part_of, but this is technically not correct~~		- tabled for next meeting - see notes on Oct 11th

	~~e.g. pericarp texture (TO:0002623):~~
	* is_a pericarp morphology trait (TO:0000945)
	* is_a fruit quality trait (TO:0002728)

	* maybe we can use [http://www.ontobee.org/ontology/RO?iri=http://purl.obolibrary.org/obo/RO_0002326 contributes_to]
	* if and only if exists c', p' c part_of c' and c' capable_of p and c capable_of p' and p' part_of p then c contributes_to p

	= Upcoming Meetings and Workshops=		= Upcoming Meetings and Workshops=

Cooperl: /* Addition of fruit subclasses */

2016-10-25T18:16:56Z

Addition of fruit subclasses

← Older revision		Revision as of 18:16, 25 October 2016
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	* After Oct 11th meeting, we decided to add the specifc types of fruits to the PO		* After Oct 11th meeting, we decided to add the specifc types of fruits to the PO
	* Brandon and Dario have a working set- see: [https://docs.google.com/document/d/19iF4Q-fdEiX6GjUAC3V5KtGZ4BfvtX_5_NMZquuR2hU/edit Provisional fruit Hierarchy]		* Brandon and Dario have a working set- see: [https://docs.google.com/document/d/19iF4Q-fdEiX6GjUAC3V5KtGZ4BfvtX_5_NMZquuR2hU/edit Provisional fruit Hierarchy]

			* ''The goal is to create a framenwork that can be easily added to. (drupe-let, and other *-lets will go in as synonyms). The community has a lot of different opinions on the names of fruits.''

			* ''Would be great to have line art/pictures of the different fruit types

			* ''We will give DWS et al, access to modify pages on the planteome site, can put a picture of the structure on the page, with a link to the Amigo page for those terms. Will start with the fruit terms.''
			** Question- how can we link from the term page?

	==New Taxon constraints added to PO==		==New Taxon constraints added to PO==

Cooperl: /* Revisions to lenticel (PO:0000031) and new term for lenticel like structure on root tubers */

2016-10-25T18:12:29Z

Revisions to lenticel (PO:0000031) and new term for lenticel like structure on root tubers

← Older revision		Revision as of 18:12, 25 October 2016
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	* Propose slightly revised def'n:		* Propose slightly revised def'n:
	lenticel (PO:0000031): A portion of the shoot axis periderm (PO:0005048) characterized by the presence of intercellular spaces between the cells of the phellem (PO:0004003) and phelloderm (PO:0005050)		lenticel (PO:0000031): A portion of the shoot axis periderm (PO:0005048) characterized by the presence of intercellular spaces between the cells of the phellem (PO:0004003) and phelloderm (PO:0005050)
	~~maybe~~ put in comment: produced by the cork cambium (PO:0005599)		* put in comment: produced by the cork cambium (PO:0005599)

			''the "lenticels" look similar in potatoes and sweet potatoes, but they arise from a different structure. This leads to confusion. Has been moved to shoot-axis periderm (for the true stem lenticels). Roots have proto-zylem (star shape) - lateral roots arise opposite these protozylem poles.
			* ''root lenticels will be called 'root periderm scars'''
			*''PJ - add a comment on the lenticel term to improve the understanding of the difference in function of each. Also add broad synonym "root lenticel" to the new periderm scars''

	== root periderm scar- new==		== root periderm scar- new==

Cooperl: /* spine root terms for PO */

2016-10-25T18:07:52Z

spine root terms for PO

← Older revision		Revision as of 18:07, 25 October 2016
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	* lateral root spine (PO:0030088): A lateral root (PO:0020121) that is sclerified, pointed, and lacks indeterminate growth and nutritive function.		* lateral root spine (PO:0030088): A lateral root (PO:0020121) that is sclerified, pointed, and lacks indeterminate growth and nutritive function.

			''Comments: remove "indeterminate growth" and 'nutritive function' from the def'n of 'root' term" because the root spines do not grow indeterminate manner. and Some roots don't serve this function-- eg palm tree brace roots

	==Revisions to lenticel (PO:0000031) and new term for lenticel like structure on root tubers ==		==Revisions to lenticel (PO:0000031) and new term for lenticel like structure on root tubers ==

Cooperl: /* Planteome Ontology WG Zoom Meeting */

2016-10-25T18:06:13Z

Planteome Ontology WG Zoom Meeting

← Older revision		Revision as of 18:06, 25 October 2016
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	* Recordings:		* Recordings:
	** [[File:Ontology Working Group meeting-video 10-25-2016.mp4\|thumbnail\|Ontology Working Group meeting-video 10-25-2016.mp4]]		** [[File:Ontology Working Group meeting-video 10-25-2016.mp4\|thumbnail\|Ontology Working Group meeting-video 10-25-2016.mp4]]
	**		** [[File:Ontology Working Group meeting-audio 10-25-2016.m4a\|thumbnail\|Ontology Working Group meeting-audio 10-25-2016.m4a]]
	[[File:Ontology Working Group meeting-audio 10-25-2016.m4a\|thumbnail\|Ontology Working Group meeting-audio 10-25-2016.m4a]]

	==spine root terms for PO==		==spine root terms for PO==