Plant Disease Ontology (PDO) - Revision history

Cooperl at 17:12, 10 April 2013

2013-04-10T17:12:45Z

Cooperl: /* Conversion of ontology file to owl from OBO: At the Protege Short Course: */

2013-04-10T17:08:40Z

Conversion of ontology file to owl from OBO: At the Protege Short Course:

Cooperl at 17:04, 10 April 2013

2013-04-10T17:04:58Z

Cooperl at 16:52, 10 April 2013

2013-04-10T16:52:39Z

Cooperl at 23:07, 9 June 2012

2012-06-09T23:07:30Z

Cooperl at 23:07, 9 June 2012

2012-06-09T23:07:08Z

Cooperl at 22:26, 16 May 2012

2012-05-16T22:26:30Z

Cooperl at 22:26, 16 May 2012

2012-05-16T22:26:19Z

Cooperl: Created page with 'This page will hold notes on the Plant Disease Ontology (PDO) being developed by the PO'

2012-05-16T22:21:51Z

Created page with 'This page will hold notes on the Plant Disease Ontology (PDO) being developed by the PO'

New page

This page will hold notes on the Plant Disease Ontology (PDO) being developed by the PO

@@ Line 1: / Line 1: @@
-This page will hold notes on the Plant Disease Ontology (PDO) being developed by the PO
+Notes on the Plant Disease Ontology (PDO) being developed by the PO
 Issues under discussion:
 *use of common names to describe the diseases and are caused by a variety of pathogens: e.g. [http://www.apsnet.org/publications/commonnames/Pages/Rice.aspx Pecky Rice]

← Older revision		Revision as of 17:08, 10 April 2013
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	*use of common names to describe the diseases and are caused by a variety of pathogens: e.g. [http://www.apsnet.org/publications/commonnames/Pages/Rice.aspx Pecky Rice]		*use of common names to describe the diseases and are caused by a variety of pathogens: e.g. [http://www.apsnet.org/publications/commonnames/Pages/Rice.aspx Pecky Rice]
−
−	~~=Conversion of ontology file to owl from OBO: At the Protege Short Course:=~~
−	*Imported the plant_disease_ontology.obo file, version 1553. Had to do something to make the names appear as the labels, rather than the PDO:id. At the time Tim Redmond said there was some sort of bug, but he worked around it.
−	*need to figure out how to do it again, maybe redo the import and replicate?
−	*We also set the numbering system so we could add terms (entities) and have them be assigned a PDIO:id- how did we do that???
−
−	* The PDO:Ids are not showing up in the annotations- how do I get them to display?
−	~~eg. causal agent PDO:0000015~~
−
−
−	~~==What else did we did:==~~
−	*Created object properties: inverse of each other:
−	~~-'causal agent of' and has_causal_agent~~
−	~~- has_part and part_of~~
−	*Also created:
−	~~- isa_primary_host~~
−	**probably should make the naming consistent with underscores
−
−
−	~~===Fixing problem of spp. as causal agents===~~
−	*fungal spp. (PDO:0000070) made it a subclass of fungal biotic causal agent (PDO:0000026) with the class restrictions (?correct term?),:
−	* has_part only 'fungal species'
−	* has_part some 'fungal species'
−
−	*Pythium spp. (PDO:0000064)
−	~~-made this class Equivalent to 'fungal spp.' and (has_part only 'Pythium sp.')~~
−
−	*Created the new class 'Pythium sp.' and made the two individual Pythium sp.subclasses of it: Pythium dissotocum and Pythium spinosum. Not sure how to see the new PDO:id.
−
−	~~Can do the same with the other two classes: Curvularia spp. and Fusarium spp.~~

← Older revision		Revision as of 17:04, 10 April 2013
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	This page will hold notes on the Plant Disease Ontology (PDO) being developed by the PO		This page will hold notes on the Plant Disease Ontology (PDO) being developed by the PO
−
−
−
−
−

	Issues under discussion:		Issues under discussion:

← Older revision		Revision as of 16:52, 10 April 2013
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	This page will hold notes on the Plant Disease Ontology (PDO) being developed by the PO		This page will hold notes on the Plant Disease Ontology (PDO) being developed by the PO
		+
		+
		+
		+
		+

	Issues under discussion:		Issues under discussion:

@@ Line 5: / Line 5: @@
 *use of common names to describe the diseases and are caused by a variety of pathogens: e.g. [http://www.apsnet.org/publications/commonnames/Pages/Rice.aspx Pecky Rice]
-Conversion of ontology file to owl from OBO: At the Protege Short Course:
+=Conversion of ontology file to owl from OBO: At the Protege Short Course:=
 *Imported the plant_disease_ontology.obo file, version 1553.  Had to do something to make the names appear as the labels, rather than the PDO:id. At the time Tim Redmond said there was some sort of bug, but he worked around it.
 *need to figure out how to do it again, maybe redo the import and replicate?
@@ Line 14: / Line 14: @@
-=What else did we did:=
+==What else did we did:==
 *Created object properties: inverse of each other:
 -'causal agent of' and has_causal_agent
@@ Line 23: / Line 23: @@
-==Fixing problem of spp. as causal agents==
+===Fixing problem of spp. as causal agents===
 *fungal spp. (PDO:0000070) made it a subclass of fungal biotic causal agent (PDO:0000026) with the class restrictions (?correct term?),:
 * has_part only 'fungal species'

← Older revision		Revision as of 23:07, 9 June 2012
Line 5:		Line 5:
	*use of common names to describe the diseases and are caused by a variety of pathogens: e.g. [http://www.apsnet.org/publications/commonnames/Pages/Rice.aspx Pecky Rice]		*use of common names to describe the diseases and are caused by a variety of pathogens: e.g. [http://www.apsnet.org/publications/commonnames/Pages/Rice.aspx Pecky Rice]

−	*	+	Conversion of ontology file to owl from OBO: At the Protege Short Course:
		+	*Imported the plant_disease_ontology.obo file, version 1553. Had to do something to make the names appear as the labels, rather than the PDO:id. At the time Tim Redmond said there was some sort of bug, but he worked around it.
		+	*need to figure out how to do it again, maybe redo the import and replicate?
		+	*We also set the numbering system so we could add terms (entities) and have them be assigned a PDIO:id- how did we do that???
		+
		+	* The PDO:Ids are not showing up in the annotations- how do I get them to display?
		+	eg. causal agent PDO:0000015
		+
		+
		+	=What else did we did:=
		+	*Created object properties: inverse of each other:
		+	-'causal agent of' and has_causal_agent
		+	- has_part and part_of
		+	*Also created:
		+	- isa_primary_host
		+	**probably should make the naming consistent with underscores
		+
		+
		+	==Fixing problem of spp. as causal agents==
		+	*fungal spp. (PDO:0000070) made it a subclass of fungal biotic causal agent (PDO:0000026) with the class restrictions (?correct term?),:
		+	* has_part only 'fungal species'
		+	* has_part some 'fungal species'
		+
		+	*Pythium spp. (PDO:0000064)
		+	-made this class Equivalent to 'fungal spp.' and (has_part only 'Pythium sp.')
		+
		+	*Created the new class 'Pythium sp.' and made the two individual Pythium sp.subclasses of it: Pythium dissotocum and Pythium spinosum. Not sure how to see the new PDO:id.
		+
		+	Can do the same with the other two classes: Curvularia spp. and Fusarium spp.

← Older revision		Revision as of 22:26, 16 May 2012
Line 1:		Line 1:
	This page will hold notes on the Plant Disease Ontology (PDO) being developed by the PO		This page will hold notes on the Plant Disease Ontology (PDO) being developed by the PO
		+
		+	Issues under discussion:
		+
		+	*use of common names to describe the diseases and are caused by a variety of pathogens:
		+	e.g. [http://www.apsnet.org/publications/commonnames/Pages/Rice.aspx Pecky Rice]
		+
		+	*