POC Conf. Call 3-29-11 - Revision history

Cooperl: /* Use of ontology id's in definitions */

2011-04-12T16:29:10Z

Use of ontology id's in definitions

Rwalls: /* New terms and proposed definitions from last week's meeting */

2011-04-01T14:53:56Z

New terms and proposed definitions from last week's meeting

Rwalls: /* New terms and proposed definitions from last week's meeting */

2011-03-31T11:05:42Z

New terms and proposed definitions from last week's meeting

Rwalls: /* New terms and proposed definitions from last week's meeting */

2011-03-31T10:58:40Z

New terms and proposed definitions from last week's meeting

Cooperl: /* participates_in relation */

2011-03-30T18:57:54Z

participates_in relation

Cooperl: /* participates_in relation */

2011-03-30T18:56:57Z

participates_in relation

Cooperl: /* participates_in relation */

2011-03-30T18:55:46Z

participates_in relation

Cooperl: /* has_part relation */

2011-03-30T18:54:03Z

has_part relation

Cooperl: /* Rename Plant Structure Ontology (PSO) to Plant Anatomy Ontology (PAO)? */

2011-03-30T18:42:40Z

Rename Plant Structure Ontology (PSO) to Plant Anatomy Ontology (PAO)?

Cooperl: /* has_part relation */

2011-03-30T18:40:58Z

has_part relation

@@ Line 42: / Line 42: @@
 ''As a general guideline, whenever we use a definition from another ontology for a term, but alter it to fit PO, we should put the other ontology ID '''plus''' POC:curators into the definition dbxrefs.  This gives credit to the source of the definition''
-''Note: We should check that the browser will automatically create the xrefs, or we can also add them there.  We should request CARO to the GO Dbx database, along with SourceForge and PATO.  Does CARO/PATO need to have a website in order to do so?  We could use the link to Bioportal''
+''Note: We should check that the browser will automatically create the hyperlinks, or we can also add them there.  We should request CARO to the GO Dbx database, along with SourceForge and PATO.''
 ''LC: I added a statement and example explaining this to our [[PO_Developers_Guide]].''

← Older revision		Revision as of 14:53, 1 April 2011
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−	'''[https://sourceforge.net/tracker/?func=detail&aid=3257963& pollen]''': A microgametophyte that is located in a pollen sac.	+	'''[https://sourceforge.net/tracker/index.php?func=detail&aid=3257963&group_id=76834&atid=835555 pollen]''': A microgametophyte that is located in a pollen sac.

	Comment: Produces pollen sperm cells.		Comment: Produces pollen sperm cells.

← Older revision		Revision as of 11:05, 31 March 2011
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−	'''[https://sourceforge.net/tracker/index.php?func=detail&aid=3028397&group_id=76834&atid=835555 embryo sac]''' (existing term, PO:0025074): A megagametophyte that is ~~contained~~ in an ovule in an ovary.	+	'''[https://sourceforge.net/tracker/index.php?func=detail&aid=3028397&group_id=76834&atid=835555 embryo sac]''' (existing term, PO:0025074): A megagametophyte that is located in an ovule in an ovary.

	Comment: Produces an embryo sac egg cell.		Comment: Produces an embryo sac egg cell.

@@ Line 219: / Line 219: @@
-'''[https://sourceforge.net/tracker/?func=detail&aid=3257959&group_id=76834&atid=835555 megagametophyte]''': A whole plant in the gametophytic phase that produces only egg cells.
+'''[https://sourceforge.net/tracker/?func=detail&aid=3257959&group_id=76834&atid=835555 megagametophyte]'''(PO:0025279): A whole plant in the gametophytic phase that produces only egg cells.
 Comment: Megagametophytes in bryophytes only produce egg cells, but do not develop from megaspores, because there is no heterospory in bryophytes. In some pteridophytes, megagametophytes develop from megaspores. In angiosperms, ''Gnetum'' and ''Weltwischia'' the megagametophyte is greatly reduced. The megagametophyte in angiosperms is an embryo sac.
-'''[https://sourceforge.net/tracker/?func=detail&aid=3257959&group_id=76834&atid=835555 microgametophyte]''': A whole plant in the gametophytic phase that produces only sperm cells.
+'''[https://sourceforge.net/tracker/?func=detail&aid=3257959&group_id=76834&atid=835555 microgametophyte]''' (PO:0025280): A whole plant in the gametophytic phase that produces only sperm cells.
 Comment: Microgametophytes in bryophytes only produce sperm cells, but do not develop from microspores, because there is no heterospory in bryophytes. In some pteridophytes, microgametophytes develop from microspores. In seed plants the male gametophyte is reduced to a pollen grain.

@@ Line 149: / Line 149: @@
-this gives the reasoner the information that an apical cell participates in gametophyte phase via the part_of relation
+- this gives the reasoner the information that an apical cell participates_in gametophyte phase via the part_of relation
 (really this axiom should be in RO, and there should be some mechanism where you can just import it but things are a bit primitive right now)
@@ Line 155: / Line 155: @@
 RW: I did this and it worked.
-''Should we request this feature on the OE tracker?''
+''LC: Should we request this feature on the OBO-Edit tracker?''
 ''It is okay to continue to add the participates_in relations to the developers' file. PJ prepared an icon using the letters P-i in green, which we can put on the browser.''

← Older revision		Revision as of 18:56, 30 March 2011
Line 154:		Line 154:

	RW: I did this and it worked.		RW: I did this and it worked.
		+
		+	''Should we request this feature on the OE tracker?''

	''It is okay to continue to add the participates_in relations to the developers' file. PJ prepared an icon using the letters P-i in green, which we can put on the browser.''		''It is okay to continue to add the participates_in relations to the developers' file. PJ prepared an icon using the letters P-i in green, which we can put on the browser.''

@@ Line 119: / Line 119: @@
 ''For the time being, we can continue to use has_part relations, but we will have to revisit how to deal with them before the next release.''
-==participates_in relation==
+==''participates_in'' relation==
 Need to get these in.  Should we make a test file to see if these are going to cause issues?
@@ Line 126: / Line 126: @@
-'''Question:''' If a parent term (e.g., plant gametangium) has a participates_in relation, do we need to specify participates_in relation for all its children (e.g., archegonium and antheridium), or will the reasoner know to apply the relation to the children?
+'''Question:''' If a parent term (e.g., plant gametangium) has a ''participates_in relation'', do we need to specify ''participates_in'' relation for all its children (e.g., archegonium and antheridium), or will the reasoner know to apply the relation to the children?
 Should not need it for children if it is transitive:
-A is_a  B, and B participates_in C, then A participates_in C
+A is_a  B, and B ''participates_in'' C, then A ''participates_in'' C
 and
-A part_of B, and B  participates_in C, then A participates_in C
+A ''part_of'' B, and B  ''participates_in'' C, then A ''participates_in'' C
 '''Answer''' (from Chris Mungall): participation isn't transitive. (''in OboEdit by default'')

← Older revision		Revision as of 18:54, 30 March 2011
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	==''has_part'' relation==		==''has_part'' relation==
		+
		+	For more details- please see the [[POC Technical Issues Page]]

	How will we deal with has_part relation? for this release? for future releases?		How will we deal with has_part relation? for this release? for future releases?

@@ Line 27: / Line 27: @@
 ''We should check with CM to see if we should change the namespace, which is currently plant_structure to plant_anatomy, and what the ramifications of such a change would be.''
-''This name Plant Structure ontology is used on the PO webpage and in other spots where the individual files are linked to (such as Bioportal)- so it should also change in those places''
+''This name Plant Structure ontology is used on the PO webpage and in other spots where the individual files are linked to (such as Bioportal)- so it should also change in those places.  Will need to be changed on the AmiGO Browser''
 ==Use of ontology id's in definitions==

@@ Line 96: / Line 96: @@
 ''We will work further on this and discuss this more next week''
-==has_part relation==
+==''has_part'' relation==
 How will we deal with has_part relation? for this release? for future releases?
@@ Line 111: / Line 111: @@
 Report from JE @ tests and annotations etc:
-''PJ created some smaller ontology files with has_part relations to test in the beta browser. JE confirmed that they load fine, which means that the has_part relation does not interfere with loading. We still have the issue of how annotations pass through the has_part relations. PJ and JE are working on it with CM. For the time being, we can continue to use has_part relations, but we will have to revisit how to deal with them before the next release.''
+''PJ created some smaller ontology files with has_part relations to test in the beta browser. JE confirmed that they load fine, which means that the has_part relation does not interfere with loading. We still have the issue of how annotations pass through the has_part relations. PJ and JE are working on it with CM.''
 ==participates_in relation==