PO Annotation Extensions (column 16) - Revision history

Cooperl: /* Other types of relations to PO terms */

2015-10-01T20:23:59Z

Other types of relations to PO terms

Cooperl: /* Other types of relations to PO terms */

2015-10-01T20:20:06Z

Other types of relations to PO terms

Cooperl: /* Annotation extensions to other PO terms */

2015-10-01T20:08:28Z

Annotation extensions to other PO terms

Cooperl: /* Annotation extensions to other PO terms */

2015-10-01T19:56:59Z

Annotation extensions to other PO terms

Cooperl: /* Plant structures that are part_of another plant structure */

2015-10-01T19:56:10Z

Plant structures that are part_of another plant structure

Cooperl: /* Introduction */

2015-10-01T19:55:20Z

Introduction

Cooperl: /* has_part */

2015-10-01T19:54:18Z

has_part

Cooperl: /* has_part */

2015-10-01T19:53:57Z

has_part

Cooperl: /* has_part */

2015-10-01T19:53:40Z

has_part

Cooperl: /* Technical issues */

2015-10-01T19:53:09Z

Technical issues

@@ Line 68: / Line 68: @@
 The other relations used in the PO are:
-* has_part
+* ''has_part''
-* develops_from
+* ''develops_from''
-* derives_from
+* ''derives_by_manipulation_from''
-* adjacent_to
+* ''adjacent_to''
-* The PO can only specify a relation between two classes when that relation is '''true for every instance in every taxon''' in which the two classes occur (the All-Some rule).
+====The PO can only specify a relation between two classes when that relation is '''true for every instance in every taxon''' in which the two classes occur (the All-Some rule).====
 * A ''has_part'' B: only specified when ''every A has as a part some B''

@@ Line 68: / Line 68: @@
 The other relations used in the PO are:
-*has_part
+* has_part
-*develops_from
+* develops_from
-*derives_from
+* derives_from
-*adjacent_to
+* adjacent_to
-The PO can only specify a relation between two classes when that relation is true for every instance in every taxon in which the two classes occur (the all-some rule). That is, A has_part Bis is only specified when every A has some B as part, and A develop_from B is only specified when every A develops from some B. Because of the diversity among different plant taxa, there are many cases where a relation is valid for some taxa but not others. Although the PO cannot specify these relations, they could be added as annotation extensions.
+* The PO can only specify a relation between two classes when that relation is '''true for every instance in every taxon''' in which the two classes occur (the All-Some rule).
 ====Examples:====

@@ Line 16: / Line 16: @@
 * Column 16 should be used when the appropriate ''part_of'' or ''participates_in'' relation is not specified, or cannot be inferred within the PO, for example, for creating specific ''part_of'' relations when only a general ''part_of'' relation exists, or for linking a structure to a specific growth or developmental stage.
-. Plant structures that are ''part_of'' another plant structure
+'''1. Plant structures that are ''part_of'' another plant structure'''
-* The anatomical entity (PAE; PO:0025131) branch of the PO is structured with general categories of structures that are parents to more specific child terms.
+* The ''plant anatomical entity'' (PAE; PO:0025131) branch of the PO is structured with general categories of structures that are parents to more specific child terms.
 * Examples,
-** vascular leaf and non-vascular leaf are children of leaf
+** ''vascular leaf'' and ''non-vascular leaf'' are children of ''leaf''
-** aerial tuber and subterranean tuber are children of tuber
+** ''aerial tuber'' and ''subterranean tuber'' are children of ''tuber''
 * Any plant structure that can only be a part of one of the specific children will have a ''part_of'' relation only to that specific child (for example, costa part_of non-vascular leaf and leaf vascular system part_of vascular leaf), while plant structures that can be part of more than one type of the specific children will have a part_of relation to the more general term (for example, leaf tip part_of leaf).

@@ Line 16: / Line 16: @@
 * Column 16 should be used when the appropriate ''part_of'' or ''participates_in'' relation is not specified, or cannot be inferred within the PO, for example, for creating specific ''part_of'' relations when only a general ''part_of'' relation exists, or for linking a structure to a specific growth or developmental stage.
-. Plant structures that are '''part_of''' another plant structure
+. Plant structures that are ''part_of'' another plant structure
 * The anatomical entity (PAE; PO:0025131) branch of the PO is structured with general categories of structures that are parents to more specific child terms.

@@ Line 16: / Line 16: @@
 * Column 16 should be used when the appropriate ''part_of'' or ''participates_in'' relation is not specified, or cannot be inferred within the PO, for example, for creating specific ''part_of'' relations when only a general ''part_of'' relation exists, or for linking a structure to a specific growth or developmental stage.
-===Plant structures that are '''part_of''' another plant structure===
+. Plant structures that are '''part_of''' another plant structure
 * The anatomical entity (PAE; PO:0025131) branch of the PO is structured with general categories of structures that are parents to more specific child terms.

@@ Line 6: / Line 6: @@
 * The use of annotation extensions in the PO is based on the usage developed by the GO. A discussion of GO's annotation extension column can be found on the [http://wiki.geneontology.org/index.php/Annotation_Extension GO Annotation_Extension Page].
-* If and when an annotator chooses to use column 16, they are effectively creating an "on-the-fly" [http://wiki.geneontology.org/index.php/Category:Cross_Products cross product] term. - ''Need to check this...''
+* If and when an annotator chooses to use column 16, they are effectively creating an "on-the-fly" [http://wiki.geneontology.org/index.php/Category:Cross_Products cross product] term. - ''Need to clarify this...''
 =Uses=

@@ Line 130: / Line 130: @@
 * For example, all ''flowers'' in maize occur as part of an ''ear inflorescence''. Therefore, any gene expressed in a ''flower'' in maize should be also be annotated to ''ear inflorescence''.
-* Since we don't have the relation ''flower'''' part_of inflorescence'', this will not happen automatically.
+* Since we don't have the relation ''flower'' ''part_of'' ''inflorescence'', this will not happen automatically.
 ==For other relation types==

@@ Line 128: / Line 128: @@
 * Column 16 provides a way to deal with this, provided annotators can be trained to '''create the correct part_of relation in column 16'''.
-* For example, all ''flowers'' in maize occur as part of an ''ear inflorescence''. Therefore, any gene expressed in a ''flower'' in maize should be also be annotated to '''ear inflorescence''' .
+* For example, all ''flowers'' in maize occur as part of an ''ear inflorescence''. Therefore, any gene expressed in a ''flower'' in maize should be also be annotated to ''ear inflorescence''.
 * Since we don't have the relation flower part_of inflorescence, this will not happen automatically.

← Older revision		Revision as of 19:53, 1 October 2015
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	GO specifies what types of Dbid's can go in column 16, but that include other GO id's, so clearly there is no strict restriction on using the same database as column 5.		GO specifies what types of Dbid's can go in column 16, but that include other GO id's, so clearly there is no strict restriction on using the same database as column 5.
		+
		+	In future versions of the AmiGO browser, it '''may''' automatically read the relation between column 5 (PO term) and column 16 in one row of an annotation file and create a new row that associates the annotation with the term in column 16.