POC Conf. Call 6-7-11 - Revision history

Cooperl: /* Action Items: */

2011-06-24T21:37:42Z

Action Items:

Cooperl: /* Action Items: */

2011-06-24T21:33:55Z

Action Items:

Cooperl: /* Action Items: */

2011-06-24T21:24:59Z

Action Items:

Cooperl: /* Proposal: move all leaf parts to part_of leaf */

2011-06-24T21:22:52Z

Proposal: move all leaf parts to part_of leaf

Cooperl: /* Proposal: move all leaf parts to part_of leaf */

2011-06-24T21:14:30Z

Proposal: move all leaf parts to part_of leaf

Cooperl: /* Proposal: move all leaf parts (be they part_of vascular leaf, part_of non-vascular leaf or part_of leaf) to be part_of leaf */

2011-06-24T21:10:13Z

Proposal: move all leaf parts (be they part_of vascular leaf, part_of non-vascular leaf or part_of leaf) to be part_of leaf

Cooperl: /* Actions: */

2011-06-24T20:58:21Z

Actions:

Cooperl: /* Discussion: */

2011-06-24T20:57:59Z

Discussion:

Cooperl: /* Discussion + Action? */

2011-06-24T20:57:44Z

Discussion + Action?

Cooperl: /* Proposal: move all leaf parts (be they part_of vascular leaf, part_of non-vascular leaf or part_of leaf) to be part_of leaf */

2011-06-24T20:57:20Z

Proposal: move all leaf parts (be they part_of vascular leaf, part_of non-vascular leaf or part_of leaf) to be part_of leaf

@@ Line 129: / Line 129: @@
 ==Action Items:==
-* Need to make a list of all the part_of children of each VL and NVL''
+* Need to make a list of all the part_of children of each VL and NVL
-*Rather than setting a strict policy about when to inflate or not, we should probably consider it on a case by case basis
+* Need to work on the definition of rosette and cauline leaves
-* It is important that we have the script for transferring annotation up and running, and that we test out whether or not we can use column 16 for associating leaf types '''before''' we meet with them
+* Rather than setting a strict policy about when to inflate or not, we should probably consider it on a case by case basis
-* We also need to consider processing of the annotation files that happens with each release.''
+* We need to have the script for transferring the annotations up and running, and that we test out whether or not we can use column 16 for associating leaf types '''before''' we meet with them
-* We need a demo to show TAIR
+* We also need to consider processing of the annotation files that happens with each release
-* We can use the ontology file to generate a list of the part_of leaf, including those that are part_of only vascular or non-vascular leaves.''
+* Add a disjoint between NVL and VL
-* Add a disjoint between NVL and VL
+* We need a demo to show TAIR
-* Set up a meeting with TAIR to explain to them why we don't want to add all of the specific terms, and to work them on a solution
+* Set up a meeting with TAIR to explain to them why we don't want to add all of the specific terms, and to work them on the solution
 ==List of annotations on terms that are part_of leaf==

@@ Line 129: / Line 129: @@
 ==Action Items:==
-*Set up a meeting with TAIR to explain to them why we don't want to add all of the specific terms, and to work them on a solution
+* Need to make a list of all the part_of children of each VL and NVL''
 *Rather than setting a strict policy about when to inflate or not, we should probably consider it on a case by case basis
@@ Line 142: / Line 143: @@
 * Add a disjoint between NVL and VL
 ==List of annotations on terms that are part_of leaf==

@@ Line 129: / Line 129: @@
 ==Action Items:==
-''We should set up a meeting with TAIR to explain to them why we don't want to add all of the specific terms, and to work them on a solution.''
+*Set up a meeting with TAIR to explain to them why we don't want to add all of the specific terms, and to work them on a solution
-''Rather than setting a strict policy about when to inflate or not, we should probably consider it on a case by case basis.''
+*Rather than setting a strict policy about when to inflate or not, we should probably consider it on a case by case basis
-''It is important that we have the script for transferring annotation up and running, and that we test out whether or not we can use column 16 for associating leaf types '''before''' we meet with them.''
+* It is important that we have the script for transferring annotation up and running, and that we test out whether or not we can use column 16 for associating leaf types '''before''' we meet with them
-''We also need to consider processing of the annotation files that happens with each release.''
+* We also need to consider processing of the annotation files that happens with each release.''
-''We need a demo to show TAIR.''
+* We need a demo to show TAIR
-''We can use the ontology file to generate a list of the part_of leaf, including those that are part_of only vascular or non-vascular leaves.''
+* We can use the ontology file to generate a list of the part_of leaf, including those that are part_of only vascular or non-vascular leaves.''
 ==List of annotations on terms that are part_of leaf==

@@ Line 117: / Line 117: @@
 ''PJ suggested that we could use disjoint_from relation, for example: have leaf vascular system be a part_of leaf (instead of part_of vascular leaf) then make it disjoint_from non-vascular leaf.''
-eg Leaf vein part of leaf, disjoint between leaf vein and NVL.  Does this work?
+eg. leaf vein part_of_leaf, disjoint between leaf vein and NVL.  Does this work?
 ==Action Items:==

← Older revision		Revision as of 21:14, 24 June 2011
Line 116:		Line 116:

	''PJ suggested that we could use disjoint_from relation, for example: have leaf vascular system be a part_of leaf (instead of part_of vascular leaf) then make it disjoint_from non-vascular leaf.''		''PJ suggested that we could use disjoint_from relation, for example: have leaf vascular system be a part_of leaf (instead of part_of vascular leaf) then make it disjoint_from non-vascular leaf.''
		+
		+	eg Leaf vein part of leaf, disjoint between leaf vein and NVL. Does this work?

	==Action Items:==		==Action Items:==

@@ Line 102: / Line 102: @@
 ''Also, we need to work on the definitions of rosette leaf and cauline leaf. Should link them to growth stages, because (at least in Arabidopsis and other Brassicaceae) they are the same leaves at different times.''
-===Proposal: move all leaf parts (be they part_of vascular leaf, part_of non-vascular leaf or part_of leaf) to be part_of leaf===
+===Proposal: move all leaf parts to part_of leaf===
-''-This was proposed so that users could find all of the parts in one place. This might also force them to make the second annotation to the type of leaf.
+''-This was proposed so that users could find all of the parts in one place. This might also force them to make the second annotation to the type of leaf. ''
-PJ suggested that we could use disjoint_from relation, for example: have leaf vascular system be a part_of leaf (instead of part_of vascular leaf) then make it disjoint_from non-vascular leaf.''
 ''Would this prevent curators from making an association to the wrong type of leaf?''
 ''Problem with this is that we intentionally omit information that we know to be true (e.g., we would leave out leaf vascular system part_of vascular leaf). That is not necessarily bad, but we need to have a good reason for it.''
 ==Action Items:==

← Older revision		Revision as of 20:57, 24 June 2011
Line 94:		Line 94:

	''BS: We need to work with TAIR to avoid alienating them, as they are important contributors to the annotation database and may just go create their own mini-ontology to satisfy their needs if we cannot provide it. ''		''BS: We need to work with TAIR to avoid alienating them, as they are important contributors to the annotation database and may just go create their own mini-ontology to satisfy their needs if we cannot provide it. ''
−

	===rosette leaf and cauline leaf===		===rosette leaf and cauline leaf===

@@ Line 74: / Line 74: @@
 ''Comment from BS: This is a common problem for many ontologies and there is no single or standard way to deal with it. It would not do any harm to add those extra terms, as long as you are careful.  It is messy but would not hurt anything. Annotators like pre-composed terms.  On the other hand post-compositional terms (compound terms created 'on-the-fly') are better, but then if an annotation is attached to it it becomes a pre-composed term.  Treat each case on its own merit. ''
-==Discussion + Action?==
+==Discussion:==
 See notes on [[Summary_of_Changes_to_PO_May_2011#Changes_to_children_of_leaf_.28PO:0025034.29]]