POC Conf. Call 4-19-11 - Revision history

Cooperl: /* Tech issues: */

2011-04-25T23:49:25Z

Tech issues:

Cooperl: /* Tech issues: */

2011-04-25T22:52:18Z

Tech issues:

Cooperl: /* plant embryo (PO:0009009) */

2011-04-25T17:45:53Z

plant embryo (PO:0009009)

Cooperl: /* cultured plant embryo and its children */

2011-04-25T17:38:16Z

cultured plant embryo and its children

Cooperl: /* cultured plant embryo and its children */

2011-04-25T17:33:20Z

cultured plant embryo and its children

Cooperl: /* plant embryo (PO:0009009) */

2011-04-25T17:29:00Z

plant embryo (PO:0009009)

Cooperl: /* plant embryo (PO:0009009) */

2011-04-25T17:27:33Z

plant embryo (PO:0009009)

Cooperl: /* plant embryo (PO:0009009) */

2011-04-25T17:24:34Z

plant embryo (PO:0009009)

Cooperl: /* Tech issues: */

2011-04-25T16:33:16Z

Tech issues:

Cooperl: /* Tech issues: */

2011-04-25T16:28:48Z

Tech issues:

@@ Line 51: / Line 51: @@
 ''BS brought up the topic of review for OBO Foundry acceptance. He suggested that the PO can be submitted for OBO Foundry membership within the next weeks''
-''Asked if we have one ontology or two? We have one, because all have same id space. We have been using the word 'namespace' to mean a branch of the ontology, which is really a line in the obo stanza generated by OboEdit. Namespace may mean something different in the Obo Foundry. The default namespace for the PO is still plant ontology.   We should be careful in how we refer to parts of the PO. For example, GO has been merged into one file, but old literature says there were three ontologies, so that is how people still talk about it. BS will send a copy of OBO foundry principles so we can check if we are in compliance and what needs to be done.''
+''Asked if we have one ontology or two? We have one, because all have same id space (PO). We have been using the word 'namespace' to mean a branch of the ontology, which is really a line in the obo stanza generated by OboEdit. Namespace may mean something different in the Obo Foundry. The default namespace for the PO is still plant ontology.   We should be careful in how we refer to parts of the PO. For example, GO has been merged into one file, but old literature says there were three ontologies, so that is how people still talk about it. BS will send a copy of OBO foundry principles so we can check if we are in compliance and what needs to be done.''
 ''By email after the call: BS sent us a link to the list of principles: [[http://www.obofoundry.org/wiki/index.php/OBO_Foundry_Principles OBO_Foundry_Principles]] and then CM sent:"Use the list here":  [[http://www.obofoundry.org/wiki/index.php/Category:Accepted Accepted]]''

@@ Line 27: / Line 27: @@
 '''* progress on has_parts?'''
-''Currently, the existing has parts in the ontology do not seem to be causing any problems, now thta we removed the reciprocal relations.  The problem still exists that the annotations do not flow in the right direction. ''
+''Currently, the existing has parts in the ontology do not seem to be causing any problems, now that we removed the reciprocal relations.  The problem still exists that the annotations do not flow in the right direction. ''
 ''JE still needs a test file that has fewer terms and annotations, because testing with the live version takes about 10 hours to load.''

@@ Line 105: / Line 105: @@
 ''DS pointed out that somatic or adventitious embryos are all embryos that are derived from apogamy, so we could use the word apogamy in the definition for clarity.''
-''Adventitious embryo should be merged into the new term 'somatic (plant) embryo'?  Need to work on the definition of 'somatic (plant) embryo'.  Do we need 'plant' in the name?''
+''Adventitious embryo should be merged into the new term 'somatic plant embryo'  Need to work on the definition of 'somatic plant embryo'.''
 *Note: Adventitious embryos, somatic embryos, embryos that arise through apogamy, and cultured haploid embryos, embryos cannot be considered in the sporophytic phase (as it it defined now), since they are not the product of fertilization.

← Older revision		Revision as of 17:38, 25 April 2011
Line 138:		Line 138:
	new proposed def’n: A plant embryo arising from previously differentiated somatic cells ''in vitro'', rather than from the zygote or from gametes.		new proposed def’n: A plant embryo arising from previously differentiated somatic cells ''in vitro'', rather than from the zygote or from gametes.

−	is_a: plant embryo, need a new term "somatic (plant) embryo"	+	''is_a: plant embryo, and need a new term "somatic (plant) embryo"''

@@ Line 126: / Line 126: @@
 PJ:  We should we have a cultured zygotic embryo, any annotation to cultured ZE should go there
@@ Line 136: / Line 138: @@
 new proposed def’n: A plant embryo arising from previously differentiated somatic cells ''in vitro'', rather than from the zygote or from gametes.
-is_a: plant embryo
+is_a: plant embryo, need a new term "somatic (plant) embryo"
-See new proposed definition of embryo above.
+''See new proposed definition of embryo above.''
 ==[http://sourceforge.net/tracker/index.php?func=detail&aid=3132547&group_id=76834&atid=835555 embryonic plant structures]==

@@ Line 79: / Line 79: @@
 ''new proposed comment: An embryo is generally formed after the first division of a zygote, but in the case of adventitious embryos, somatic embryos, other embryos that arise through apogamy, and cultured haploid embryos, it is formed after the division of a single cell that is not a zygote. The end of the embryonic phase varies among taxa. In seed plants, the embryonic phase ends with germination. In pteridophytes, the embryonic phase ends with the formation of the first true leaf after the cotyledon(s). In bryophytes, the embryonic phase ends when the apical cell stops dividing and the sporangium begins to develop.''
@@ Line 90: / Line 88: @@
 '''Other issues:'''
-Adventitious embryos, somatic embryos, embryos that arise through apogamy, and cultured haploid embryos, embryos cannot be considered in the sporophytic phase (as it it defined now), since they are not the product of fertilization.
+*on 4-12-11, PJ suggested we could add zygotic embryo- the one in the seed and also a cultured one.  Also, we need haploid embryo as child of cultured embryo?  Do haploid embryos ever form in nature?
-Suggest that we rework the definition of [https://sourceforge.net/tracker/index.php?func=detail&aid=3030027&group_id=76834&atid=835555 sporophytic phase] with a comment about apogamy.  see SF tracker and/or future meeting:
+''We discussed whether or not the original intent was to describe an embryo derived from a zygote and grown in culture?  BS suggested it would be better to call it: "cultured zygote-derived (plant) embryo",  as the name 'zygotic embryo' is a little misleading, because it implies that it is an embryo that is a zygote. May want to rename "zygote-derived embryo" or similar, but should keep (cultured) zygotic embryo as synonym because it is widely used.''''
+'''*adventitious embryo''' (PO:0004537): Embryo derived directly from nucellus cells without involving embryo sac cells
 Is this always true?  Need to check on it.
@@ Line 108: / Line 105: @@
 ''DS pointed out that somatic or adventitious embryos are all embryos that are derived from apogamy, so we could use the word apogamy in the definition for clarity.''
-''BS pointed out that the name 'zygotic embryo' is a little misleading, because it implies that it is an embryo that is a zygote. May want to rename "zygote-derived embryo" or similar, but should keep zygotic embryo as synonym because it is widely use.''
 ==[https://sourceforge.net/tracker/?func=add&group_id=76834&atid=835555 cultured plant embryo and its children]==

@@ Line 44: / Line 44: @@
 -Will also need to be changed on the AmiGO Browser (eg search page)- how difficult is this?
-''JE was able to modiy the drop down menu on the Amigo browser to say "plant anatomy" instead of "plant structure" while we spoke.''
+''JE was able to modify the drop down menu on the Amigo browser to say "plant anatomy" instead of "plant structure" while we spoke.''
 '''*Review for OBO Foundry Acceptance'''
-''BS brought up the topic of review for OBO Foundry acceptance. Asked if we have one ontology or two? We have one, because all have same id space. We have been using the word namespace to mean a branch of the ontology, which is really a line in the obo stanza generated by OboEdit. Namespace may mean something different in the Obo Foundry. The default namespace for the PO is still plant ontology.   We should be careful in how we refer to parts of the PO. For example, GO has been merged into one file, but old literature says there were three ontologies, so that is how people still talk about it. BS will send a copy of OBO foundry principles so we can check if we are in compliance and what needs to be done.''
+''BS brought up the topic of review for OBO Foundry acceptance. He suggested that the PO can be submitted for OBO Foundry membership within the next weeks''
-''By email after the call: BS sent us a link to the list of principles: [[http://www.obofoundry.org/wiki/index.php/OBO_Foundry_Principles OBO_Foundry_Principles]] and then CM sent:"Use the list here":  [[http://www.obofoundry.org/wiki/index.php/Category:Accepted Accepted]]
+''By email after the call: BS sent us a link to the list of principles: [[http://www.obofoundry.org/wiki/index.php/OBO_Foundry_Principles OBO_Foundry_Principles]] and then CM sent:"Use the list here":  [[http://www.obofoundry.org/wiki/index.php/Category:Accepted Accepted]]''
 =Issues arising from last week's meeting:=