POC Conf. Call 12-28-10 - Revision history

Cooperl: /* Issues arising from new terms: */

2011-01-03T22:37:42Z

Issues arising from new terms:

Cooperl: /* PO Next release */

2011-01-03T17:39:14Z

PO Next release

Cooperl: /* 'sensu' terms */

2011-01-03T17:38:00Z

'sensu' terms

Rwalls: /* Musa shoot terms */

2011-01-03T14:03:29Z

Musa shoot terms

Rwalls: /* Musa fruit terms */

2011-01-03T13:58:04Z

Musa fruit terms

Rwalls: /* Musa flower terms */

2011-01-03T13:47:58Z

Musa flower terms

Rwalls: /* Issues arising from new terms: */

2011-01-03T13:39:49Z

Issues arising from new terms:

Rwalls: /* Musa fruit terms */

2010-12-30T20:29:56Z

Musa fruit terms

Rwalls: /* Musa fruit terms */

2010-12-30T20:27:45Z

Musa fruit terms

Rwalls: /* Musa fruit terms */

2010-12-30T20:13:22Z

Musa fruit terms

@@ Line 51: / Line 51: @@
 ''PJ: add reference to CO where they are being referred to, LC will check with Rosemary/Elizabeth about the changes that were discussed @ CO- using PO terms rather than CO?''
-''see [[GCP_Crop_Ontology]]''
+''see ''[[http://pantheon.generationcp.org/index.php?option=com_content&task=view&id=20&Itemid=37 GCP_Crop_Ontology]]
 ''GCP used numbers like: CO_125:0000012. CO is already in use for Cell Ontology, so need to use numerical suffix to distinguish Crop Ontology from Cell Ontology. Different numerical suffixes refer to different crops. Will add xrefs to GCP terms for Musa as: CO_125:0000012.''

@@ Line 215: / Line 215: @@
 - complete changes discussed this week, put on Beta browser after Justin E returns from vacation (tomorrow?)
-''The next set of items should be slated for the nest round of revisions, so we can deal with the annotations, documentation, TIPs paper and preparing for PAG.  and also we need to do an 'internal' review before releasing it early in the New Year.''
+''The next set of items should be slated for the next round of revisions, so we can deal with the annotations, documentation, TIPs paper and preparing for PAG.  Also we need to do an 'internal' review before releasing it early in the New Year.''
 - look for annotations that need to be moved:
@@ Line 224: / Line 224: @@
-''RW will focus on doing the changes to the PSO that have been discussed in the last 2 weeks.  Will be done by Thursday, Dec 30th?''
+''RW will focus on doing the changes to the PSO that have been discussed in the last 2 weeks.  Will be done by Thursday, Dec 30th, then it will be loaded on the beta browser''
 ===TIPS proposal===

@@ Line 209: / Line 209: @@
 ''Accepted, approved by PJ, who was not on the call on 12-22''
-''Also, check that we have subset: Poaceae "Term used for grasses", we do''
+''Also, checked that we have subset: Poaceae "Term used for grasses", we do''
 ===PO Next release===

@@ Line 178: / Line 178: @@
 ''Note: 'sucker shoot' is a synonym of PO:0004544 : root-borne shoot system, ''
-''need both root-borne and shoot-borne suckers.''
+''need both root-borne and shoot-borne suckers. Important point is that suckers come from buds (adventitious or axillary) at the older or basal of the plant''
@@ Line 184: / Line 184: @@
 Could this be a collective phyllome structure (it is only composed of petioles, not phyllomes)? If not, we could make it a collective plant structure. If this structure is unique to Musa, we should call it "Musa pseudostem," but maybe it occurs in other taxa?
@@ Line 191: / Line 193: @@
-''add notes here...''
+''Will add new terms for leaf sheath ab/adaxial epidermis. Pseudostem underlayers will be narrow synonym of leaf sheath abaxial epidermis..''
 ''Note: need to check with Rosemary/Elizabeth whether we should use 'banana' or 'Musa'?  ''Musa'' is the Genus name.''

@@ Line 115: / Line 115: @@
 *'''bunch''': The descriptive term for all the fruits along the rachis. part_of CO_125.0000048 ! inflorescence. Syn: "infructescence" BROAD
-This could be a narrow synonym of infructescence (PO:0006342). Not sure what they mean by rachis in this definition - probably the main axis of the infructescence.
+This could be a narrow synonym of infructescence (PO:0006342). Rachis in this definition refers the main axis of the infructescence.
 ''synonym of infructescence, subset Musa''
@@ Line 146: / Line 146: @@
 ''secondary infructescence: A reproductive shoot system that is part of an infructescence and has a  second order infructescence branch and any shoot axes and fruits that arise from that branch. part_of infructescence, has_part infructescence branch, fruit''
@@ Line 153: / Line 155: @@
 Probably should just annotate to whatever part of the flower it is that remains (petal, tepal, etc.)
-''revised term names and proposed def'ns:'' persistent sepal, petal or tepal:  ...''  Common in persimmons, eggplant, tomatoes, peppers, tomatillos, etc
+''Persistent phyllomes are common in persimmons, eggplant, tomatoes, peppers, tomatillos, etc. Need new terms that can have part_of relations to fruit rather than flowers.''
-''sepal is part of the flower, add comment that it may persist in fruit''
+''sepal is part of the flower, add comment that it may persist in fruit.''
 ===Musa shoot terms===

@@ Line 68: / Line 68: @@
 is_a shoot system, part_of inflorescence
 ''Revised term name and def'n:''
@@ Line 93: / Line 95: @@
-''This will go in as a synonym of inflorescence bud.''
+''Male bud will be a synonym of inflorescence bud, with a reference to the crop ontology.''
 ===[https://sourceforge.net/tracker/?func=detail&aid=3147080&group_id=76834&atid=835555 Inflorescence and infructescence]===

@@ Line 53: / Line 53: @@
 ''see [[GCP_Crop_Ontology]]''
-''GCP used numbers like: CO_125.0000012, but CO is already in use for Cell Ontology, and this has too many digits in the numerical portion, will add xrefs to GCP terms as: CO_125:0000012.''
+''GCP used numbers like: CO_125:0000012. CO is already in use for Cell Ontology, so need to use numerical suffix to distinguish Crop Ontology from Cell Ontology. Different numerical suffixes refer to different crops. Will add xrefs to GCP terms for Musa as: CO_125:0000012.''
 ===Musa flower terms===

@@ Line 135: / Line 135: @@
 ''A Musa inflorescence is a raceme of cymes (not compound spike)''
-''There was some debate about whether or not to name the sub-inflorescences that arise from the first order branches primary inflorescence or secondary inflorescence. We decided it should be consistent with how we describe branching orders. We don't actually have terms for different branching orders yet, but the stem is defined as the primary (not zero order) axis of the plant, which makes the first-order branches secondary axes. We do have terms for inflorescence branch orders. For example, an inflorescence branch is "Any branch forming from a primary or the higher order inflorescence axis," while a second order inflorescence branch is "Any branch forming from a primary or first order inflorescence branch." Similar for third order inflorescence branch. We don't actually have terms for first order inflorescence branch or the primary axis, so I don't know if the first order branch refers to the main axis or a branch from this axis. These definitions are ambiguous, but since they have annotation attached to them, I cannot change them until I know what they mean.''
+''There was some debate about whether or not to name the sub-inflorescences that arise from the first order branches primary inflorescence or secondary inflorescence. We decided it should be consistent with how we describe branching orders. We don't actually have terms for different branching orders yet, but the stem is defined as the primary (not zero order) axis of the plant, which makes the first-order branches secondary axes. We do have terms for inflorescence branch orders. For example, an inflorescence branch is "Any branch forming from the primary or the higher order inflorescence axis," while a second order inflorescence branch is "Any branch forming from a primary or first order inflorescence branch." Similar for third order inflorescence branch. We don't actually have terms for first order inflorescence branch or the primary axis, so I don't know if the first order branch refers to the main axis or a branch from this axis. These definitions are ambiguous, but since they have annotation attached to them, I cannot change them until I know what they mean.''
 ''I am creating new terms for secondary inflorescence and secondary infructescence. Can change names and definitions and add higher orders later if needed.''