Plant Ontology Response to OBO Foundry Review - Revision history

Cooperl: moved OBO Foundry Review and Response- Oct, 2013 to Plant Ontology Response to OBO Foundry Review

2013-10-21T21:53:47Z

moved OBO Foundry Review and Response- Oct, 2013 to Plant Ontology Response to OBO Foundry Review

Cooperl: /* Principle 5: Clearly Delineated Content */

2013-10-21T16:31:39Z

Principle 5: Clearly Delineated Content

Cooperl: /* Principle 5: Clearly Delineated Content */

2013-10-21T16:31:09Z

Principle 5: Clearly Delineated Content

Cooperl: /* Principle 5: Clearly Delineated Content */

2013-10-21T16:30:34Z

Principle 5: Clearly Delineated Content

Cooperl: /* Principle 5: Clearly Delineated Content */

2013-10-21T16:28:15Z

Principle 5: Clearly Delineated Content

Cooperl at 16:24, 21 October 2013

2013-10-21T16:24:47Z

Cooperl at 16:24, 21 October 2013

2013-10-21T16:24:29Z

Cooperl: /* Principle 11: Single Locus of Authority */

2013-10-20T23:49:04Z

Principle 11: Single Locus of Authority

Cooperl: /* Principle 9: Plurality of Users */

2013-10-20T23:48:21Z

Principle 9: Plurality of Users

Cooperl: /* Principle 8: Documentation */

2013-10-20T23:47:26Z

Principle 8: Documentation

@@ Line 120: / Line 120: @@
 ''Reply: Currently: ''
-* ''plant structure (PO:0009011):  An anatomical structure that is or was part of a plant, or was derived from a part of a plant.
+* ''plant structure (PO:0009011):  An anatomical structure that is or was part of a plant, or was derived from a part of a plant. Comment: 'Part' includes both proper parts and the whole plant. CARO:0000003 anatomical structure is defined as: Material anatomical entity that has inherent 3D shape and is generated by coordinated expression of the organism's own genome.''
 * '' portion of plant substance (PO:0025161): A portion of organism substance that is or was part of a plant.Comment: Refers to portion of organism substance (CARO:0000004) which is defined as: Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body. For plants, the word "body" refers to a whole plant or part thereof.  Can include substances like latex, xylem sap, phloem sap, resin, mucilage, oil, cuticle, cutin, sporopollenin.''

@@ Line 103: / Line 103: @@
 ''Reply:''
-*'' CARO:0000000 anatomical entity: Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species.''
+*''anatomical entity (CARO:0000000): Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species.''
 * ''plant anatomical entity (PO:0025131): An anatomical entity that is or was part of a plant. Comment: Includes both material entities such as plant structures and immaterial entities such as plant anatomical spaces.''

@@ Line 122: / Line 122: @@
 * ''plant structure (PO:0009011):  An anatomical structure that is or was part of a plant, or was derived from a part of a plant.
 Comment: 'Part' includes both proper parts and the whole plant. CARO:0000003 anatomical structure is defined as: Material anatomical entity that has inherent 3D shape and is generated by coordinated expression of the organism's own genome.''
 * '' portion of plant substance (PO:0025161): A portion of organism substance that is or was part of a plant.Comment: Refers to portion of organism substance (CARO:0000004) which is defined as: Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body. For plants, the word "body" refers to a whole plant or part thereof.  Can include substances like latex, xylem sap, phloem sap, resin, mucilage, oil, cuticle, cutin, sporopollenin.''
 ''The first is an “anatomical structure” while the second is a “portion of organism substance”.  Since the PO is developed in OBOF, we added the comments to clarify that these are indeed referencing the CARO terms, which differentiate them.  We also used the CARO ID as a DBXref.''
-''The new version suggests that ‘portion of plant substance’ is a plant anatomical entity and is part of some other plant structure. e.g. Cuticular wax. (http://www.plantontology.org/amigo/go.cgi?action=dotty&view=details&search_constraint=terms&query=PO:0025386). This ontology graph is similar to the one we see for ‘cytoplasm’ in GO (http://amigo.geneontology.org/cgi-bin/amigo/browse.cgi?action=set-tree&term=GO:0005737).''
+''The current PO version defines ‘portion of plant substance’ is a plant anatomical entity and is part of some other plant structure. e.g. cuticular wax. (http://www.plantontology.org/amigo/go.cgi?action=dotty&view=details&search_constraint=terms&query=PO:0025386). This ontology graph is similar to the one we see for ‘cytoplasm’ in GO (http://amigo.geneontology.org/cgi-bin/amigo/browse.cgi?action=set-tree&term=GO:0005737).''

← Older revision		Revision as of 16:28, 21 October 2013
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	''In the PO, we include anatomical entities that were part of a plant since many plant parts are no longer connected to the parent plant, for example grains or other fruits, wood, or leaves.''		''In the PO, we include anatomical entities that were part of a plant since many plant parts are no longer connected to the parent plant, for example grains or other fruits, wood, or leaves.''

−	''We could add a comment or Xref to refer to the OBI or ERO terms, but the problem with this is that the various plant parts are not representative of the whole plant nor are they always intended for input during an investigation. Also the OBI entities specimen and sample from an organism applies to the samples that were put together for isolating some features, in this case an RNA, DNA, protein etc. In our cases of annotation the whole body can be a specimen. Therefore, to keep the confusion of samples away and not mix it up with the OBI, we went to the intended path. ~~On the other note. Is OBI funded and what’s the status of its maintenance and updates?~~''	+	''We could add a comment or Xref to refer to the OBI or ERO terms, but the problem with this is that the various plant parts are not representative of the whole plant nor are they always intended for input during an investigation. Also the OBI entities specimen and sample from an organism applies to the samples that were put together for isolating some features, in this case an RNA, DNA, protein etc. In our cases of annotation the whole body can be a specimen. Therefore, to keep the confusion of samples away and not mix it up with the OBI, we went to the intended path.''

@@ Line 9: / Line 9: @@
 '''Summary of Review Findings'''
-In general, we found that the Plant Ontology is a good ontology, largely following the principles as laid down by the Foundry. We have some specific recommendations for improvements but found no major significant shortfalls in the offering. The following table summarises the findings of this review on a per principle basis, and detailed discussion of each point follows.
+"In general, we found that the Plant Ontology is a good ontology, largely following the principles as laid down by the Foundry. We have some specific recommendations for improvements but found no major significant shortfalls in the offering. The following table summarizes the findings of this review on a per principle basis, and detailed discussion of each point follows."
 {| {{table}}

← Older revision	Revision as of 21:53, 21 October 2013
(No difference)

← Older revision		Revision as of 16:24, 21 October 2013
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	Domain of ontology: Plant anatomy, morphology and growth and development and their association to plant genomics data for all plants.		Domain of ontology: Plant anatomy, morphology and growth and development and their association to plant genomics data for all plants.
−
−	~~Our specific recommendations are contained in the report below. Thank you for participating in the OBO Foundry review process.~~

	'''Summary of Review Findings'''		'''Summary of Review Findings'''

← Older revision		Revision as of 23:49, 20 October 2013
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	"The PO has specified a single locus of authority."		"The PO has specified a single locus of authority."
		+
		+	==Principle 12: Naming Conventions==
		+	"Pass"
		+
		+	"The PO uses singular nouns for naming the entities contained in the ontology. Names are unambiguous. Some terms, such as 'fruit', have an exceptionally high number of alternative IDs. Use of alternative IDs should be minimised wherever possible. However, it is understood that this scenario can arise for valid reasons having to do with legacy, therefore it is not specifically penalised."
		+
		+	==Principle 16: Maintenance==
		+	"Pass"
		+
		+	"By their own admission, the PO is committed to the maintenance of the ontology in the light of scientific advance. The tracker and SVN repository show a history of ongoing maintenance that serves as sufficient grounds for optimism about continued performance into the future."

← Older revision		Revision as of 23:48, 20 October 2013
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	"The ontology contains a plurality of users as evidenced by the wealth of citations to the main publications in which the project has been presented (three top papers each cited >50 times)."		"The ontology contains a plurality of users as evidenced by the wealth of citations to the main publications in which the project has been presented (three top papers each cited >50 times)."
		+
		+	==Principle 10: Collaboration==
		+	"Pass"
		+
		+	"The ontology has established many important collaborations and serves as a hub for the exchange of data and annotations in the domain as evidenced by the discussion contained in the paper Plant Ontology paper (Comparative and Functional Genomics 6 (7-8) 2005, p 388-397) and by the many citations. The PO developers have furthermore also participated in conferences and attended meetings hosted by developers of ontologies in other, related domains. Finally, the PO has offered a tracker to encourage community participation. The SourceForge tracker has 537 requests in total and there is evidence of continuous and recent responsiveness by the PO team to these requests."
		+
		+	==Principle 11: Single Locus of Authority==
		+	"Pass"
		+
		+	"The PO has specified a single locus of authority."

← Older revision		Revision as of 23:47, 20 October 2013
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	''Reply: As we are developing the PO in OBO, we currently do not have the capability to make these URLS, except for in the AmiGO browser, where they are converted to links. They can be located by searching the tracker for the number of interest, although the easier route is through the browser.''		''Reply: As we are developing the PO in OBO, we currently do not have the capability to make these URLS, except for in the AmiGO browser, where they are converted to links. They can be located by searching the tracker for the number of interest, although the easier route is through the browser.''
		+
		+	==Principle 9: Plurality of Users==
		+	"Pass"
		+
		+	"The ontology contains a plurality of users as evidenced by the wealth of citations to the main publications in which the project has been presented (three top papers each cited >50 times)."