Bud - Revision history

Rwalls at 16:22, 27 September 2010

2010-09-27T16:22:38Z

Rwalls: /* 3. We needed the new term reproductive bud, which would be the parent of floral bud and inflorescence bud and we will keep and vegetative bud as another direct children of bud (this is the same option 2, but with the addition of reproductive bud):

2010-09-27T16:21:39Z

/* 3. We needed the new term reproductive bud, which would be the parent of floral bud and inflorescence bud and we will keep and vegetative bud as another direct children of bud (this is the same option 2, but with the addition of reproductive bud):

Rwalls at 16:20, 27 September 2010

2010-09-27T16:20:55Z

Rwalls: moved content from summary of changes page

2010-09-27T16:19:25Z

moved content from summary of changes page

New page

At the POC conference call on 6-23-10, we decided to obsolete the terms floral bud and reproductive bud. This was done to correct the problem of PO terms having multiple is_a parents (which is considered a bad practice in ontology design). However, this change did not work for our collaborators, since there were many existing annotations to the term floral bud (PO:0000056) that could not be moved to either terminal floral bud or axillary floral bud.

At the POC conference call on 9-22-10, we decided to use option #4, below (http://wiki.plantontology.org:8080/index.php/POC_Conf._Call_9-22-10#floral_bud_PO:0000056).

The ontology structure was as follows:[[File:Bud_terms-_old_version.jpg]]

bud

>axillary bud

>>axillary floral bud

>>axillary inflorescence bud

>>axillary vegetative bud

>floral bud

>>axillary floral bud

>>terminal floral bud

>inflorescence bud

>>axillary inflorescence bud

>>terminal inflorescence bud

>terminal bud

>>terminal floral bud?

>>terminal inflorescence bud

>>terminal vegetative bud

>vegetative bud

>>axillary vegetative bud

>>terminal inflorescence bud

This means that a term like terminal floral bud is_a terminal bud and is_a floral bud, or axillary vegetative bud is_a axillary bud and is_a vegetative bud, etc. This is useful is one wants to classify terms by different categories, but is not consistent with the goal of eliminating multiple inheritance.

Possible solutions were:

1. Make only axillary and terminal buds direct children of bud:[[File:Bud_terms_beta_2010.jpeg]]

bud

>axillary bud

>>axillary vegetative bud

>>axillary reproductive bud

>>>axillary floral bud

>>>axillary inflorescence bud

>terminal bud

>>terminal vegetative bud

>>terminal reproductive bud

>>>terminal floral bud

>>>terminal inflorescence bud

>>>terminal strobilus bud

At the POC conference call on 6-23-10, we chose option #1. This choice was made because early in bud development, you will always know if a bud is terminal or axillary, but you may not know yet if it is a floral, vegetative or inflorescence bud. This option has the advantage of removing multiple inheritance, but has the disadvantage of eliminating the potentially useful bin terms “floral bud” and “vegetative bud”.

We added the new terms: '''terminal reproductive bud''' and '''axillary reproductive bud''', so that terminal floral bud and terminal inflorescence bud are children of terminal reproductive bud, etc. These terms will allow for the inclusion of reproductive buds in non-flowering plants.

Other options considered:

2. Make only floral bud, inflorescence bud and vegetative bud direct children of bud. In this option, the terms axillary bud and terminal bud do not exist.

bud

>floral bud

>>axillary floral bud

>>terminal floral bud

>inflorescence bud

>>axillary inflorescence bud

>>terminal inflorescence bud

>vegetative bud

>>axillary vegetative bud

>>terminal inflorescence bud

3. We needed the new term reproductive bud, which would be the parent of floral bud and inflorescence bud and we will keep and vegetative bud as another direct children of bud (this is the same option 2, but with the addition of reproductive bud):

bud

>reproductive bud

>>floral bud

>>>axillary floral bud

>>>terminal floral bud

>>inflorescence bud

>>>axillary inflorescence bud

>>>terminal inflorescence bud

>>strobilus bud

>>>axillary strobilus bud

>>>terminal strobilus bud

>vegetative bud

>>axillary vegetative bud

>>terminal vegetative bud

4. Leave ontology as it is, and not worry about multiple inheritance (but of course add terms for reproductive bud and strobilus bud):

bud

>axillary bud

>>axillary vegetative bud

>>axillary reproductive bud

>>>axillary floral bud

>>>axillary inflorescence bud

>>>axillary strobilus bud

>terminal bud

>>terminal vegetative bud

>>terminal reproductive bud

>>>terminal floral bud

>>>terminal inflorescence bud

>>>terminal strobilus bud

>reproductive bud

>>floral bud

>>>terminal floral bud

>>>axillary floral bud

>>inflorescence bud

>>>terminal inflorescence bud

>>>axillary inflorescence bud

>>strobilus bud

>>>terminal strobilus bud

>>>axillary strobilus bud

>vegetative bud

>>axillary vegetative bud

>>terminal vegetative bud

← Older revision		Revision as of 16:22, 27 September 2010
Line 1:		Line 1:
	At the POC conference call on 6-23-10, we decided to obsolete the terms floral bud and reproductive bud. This was done to correct the problem of PO terms having multiple is_a parents (which is considered a bad practice in ontology design). However, this change did not work for our collaborators, since there were many existing annotations to the term floral bud (PO:0000056) that could not be moved to either terminal floral bud or axillary floral bud.		At the POC conference call on 6-23-10, we decided to obsolete the terms floral bud and reproductive bud. This was done to correct the problem of PO terms having multiple is_a parents (which is considered a bad practice in ontology design). However, this change did not work for our collaborators, since there were many existing annotations to the term floral bud (PO:0000056) that could not be moved to either terminal floral bud or axillary floral bud.

−	At the POC conference call on 9-22-10~~, we decided to use option #4, below~~ (http://wiki.plantontology.org:8080/index.php/POC_Conf._Call_9-22-10#floral_bud_PO:0000056).	+	At the POC conference call on 9-22-10 (http://wiki.plantontology.org:8080/index.php/POC_Conf._Call_9-22-10#floral_bud_PO:0000056), we decided to use option #4, below.

@@ Line 47: / Line 47: @@
 Possible solutions were:
-. Make only axillary and terminal buds direct children of bud:[[File:Bud_terms_beta_2010.jpeg]]
+===1. Make only axillary and terminal buds direct children of bud:===
 bud
@@ Line 82: / Line 84: @@
 Other options considered:
-. Make only floral bud, inflorescence bud and vegetative bud direct children of bud. In this option, the terms axillary bud and terminal bud do not exist.
+===2. Make only floral bud, inflorescence bud and vegetative bud direct children of bud. In this option, the terms axillary bud and terminal bud do not exist.===
@@ Line 110: / Line 112: @@
-. We needed the new term reproductive bud, which would be the parent of floral bud and inflorescence bud and we will keep and vegetative bud as another direct children of bud (this is the same option 2, but with the addition of reproductive bud):
+===3. We needed the new term reproductive bud, which would be the parent of floral bud and inflorescence bud and we will keep and vegetative bud as another direct children of bud (this is the same option 2, but with the addition of reproductive bud):===
@@ Line 147: / Line 149: @@
-. Leave ontology as it is, and not worry about multiple inheritance (but of course add terms for reproductive bud and strobilus bud):
+===4. Leave ontology as it is, and not worry about multiple inheritance (but of course add terms for reproductive bud and strobilus bud):===

@@ Line 122: / Line 122: @@
 >>floral bud
-  >>>axillary floral bud
+>>>axillary floral bud
-  >>>terminal floral bud
+>>>terminal floral bud
 >>inflorescence bud
-  >>>axillary inflorescence bud
+>>>axillary inflorescence bud
-  >>>terminal inflorescence bud
+>>>terminal inflorescence bud
 >>strobilus bud
-  >>>axillary strobilus bud
+>>>axillary strobilus bud
-  >>>terminal strobilus bud
+>>>terminal strobilus bud
 >vegetative bud
- >>axillary vegetative bud
+>>axillary vegetative bud
 ===4. Leave ontology as it is, and not worry about multiple inheritance (but of course add terms for reproductive bud and strobilus bud):===