PO Project Overview - Revision history

Cooperl: /* Project Description */

2019-02-19T23:28:42Z

Project Description

Rwalls: /* POC Curators */

2012-03-27T13:07:54Z

POC Curators

Rwalls at 13:07, 27 March 2012

2012-03-27T13:07:16Z

Rwalls: /* Data Representation */

2012-03-27T13:04:06Z

Data Representation

Rwalls: /* Project Description */

2012-03-27T13:02:17Z

Project Description

Shuly at 02:16, 4 December 2008

2008-12-04T02:16:52Z

Shuly at 02:15, 4 December 2008

2008-12-04T02:15:27Z

Shuly at 01:37, 26 November 2008

2008-11-26T01:37:22Z

Shuly at 23:53, 25 November 2008

2008-11-25T23:53:44Z

Shuly at 23:17, 25 November 2008

2008-11-25T23:17:09Z

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 * <big>'''Plant Anatomical Entites'''</big>  A controlled vocabulary of plant's morphological and anatomical structures representing organ, tissue and cell types and their relationships. Examples are stamen, gynoecium, petal, parenchyma, guard cell, etc.
-* <big>'''Plant Structure Sevelopmental Stages'''</big>  A controlled vocabulary of growth and developmental stages in various plants and their relationships. Examples are germination, seedling, flowering, etc.
+* <big>'''Plant Structure Developmental Stages'''</big>  A controlled vocabulary of growth and developmental stages in various plants and their relationships. Examples are germination, seedling, flowering, etc.
 These controlled vocabularies (arranged in a single ontology) are based on internationally published/accepted terminology and definitions.

@@ Line 42: / Line 42: @@
 ==POC Curators==
-See a list of the [Plant Ontology curators].
+See a list of the [[Plant Ontology curators]].
 [[Category:Documents]]

@@ Line 1: / Line 1: @@
 ==Project Description==
-The main goal of the project is to provide controlled vocabularies for the following plant-specific knowledge domains namely,
+The main goal of the project is to provide controlled vocabularies for the following plant-specific knowledge domains:
-* <big>'''Plant Anatomical Entites'''</big> A controlled vocabulary of plant's morphological and anatomical structures representing organ, tissue and cell types and their relationships. Examples are stamen, gynoecium, petal, parenchyma, guard cell, etc.
+* <big>'''Plant Anatomical Entites'''</big>  A controlled vocabulary of plant's morphological and anatomical structures representing organ, tissue and cell types and their relationships. Examples are stamen, gynoecium, petal, parenchyma, guard cell, etc.
-* <big>'''Plant Structure Sevelopmental Stages'''</big> A controlled vocabulary of growth and developmental stages in various plants and their relationships. Examples are germination, seedling, flowering, etc.
+* <big>'''Plant Structure Sevelopmental Stages'''</big>  A controlled vocabulary of growth and developmental stages in various plants and their relationships. Examples are germination, seedling, flowering, etc.
-These controlled vocabularies (arranged in a single ontology) is based on internationally published/accepted terminology and definitions.
+These controlled vocabularies (arranged in a single ontology) are based on internationally published/accepted terminology and definitions.
-In order to facilitate the use of the controlled vocabularies as attributes in other ontologies being developed by collaborating databases e.g. Open Biological Ontology ([http://obo.sourceforge.net/ OBO]), the PO controlled vocabularies, arranged in ontologies, will facilitate the attribution process and querying at different levels of granularity. The PO controlled vocabularies will also facilitate the execution of uniform queries across participating databases, thereby facilitating interoperability of plant-based databases.
+In order to facilitate the use of the controlled vocabularies as attributes in other ontologies being developed by collaborating databases, e.g., the [http://www.obofoundry.org/ Open Biological and Biomedical Ontology  (OBO) Foundry], the PO facilitates the attribution process and querying at different levels of granularity. The PO also facilitates the execution of uniform queries across participating databases, thereby facilitating interoperability of plant-based databases.
 The members of the Plant Ontology Consortium would facilitate the sharing of information and tools developed by the Plant Ontology Consortium. However, each database which utilizes the Plant Ontology information will be able to chose how it will use the information (i.e. a non-federated approach to utilizing PO information will be practiced).
@@ Line 15: / Line 16: @@
 It is considered extremely important that the terms used in the controlled vocabularies be obtained/derived from internationally published sources and/or usage. Every term in the controlled vocabulary will be accompanied by an appropriate/internationally accepted definition. The definitions provided for the terms will indicate a traceable source for the definition (e.g. ISBN number). If the definition has been modified then the reference will also include a personal signature or identifier of the developer/curator/provider. Synonyms should be indicated wherever available. This standard will contribute to an authoritative product thus encouraging wide spread usage of the ontologies and will foster consistency in the annotation of data by database curators.
 ==Data Representation==
@@ Line 42: / Line 39: @@
 Every term has a unique alphanumeric identifier to be used as a database cross-reference [/docs/numbers/number.html identifier] in collaborating databases.
 [[Category:Documents]]

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 '''Develops_from: ''' This relationship is used in the anatomy ontology to indicate the temporal relationship between a tissue or organ and its developmental predecessor. For example ectocarp develops_from ovary outer.
 Other attributes of terms can also be represented, namely synonym(s), unique identifier and database cross-reference.
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 Every term has a unique alphanumeric identifier to be used as a database cross-reference [/docs/numbers/number.html identifier] in collaborating databases.
 [[Category:Documents]]

@@ Line 3: / Line 3: @@
 The main goal of the project is to provide controlled vocabularies for the following plant-specific knowledge domains namely,
-* <big>'''Plant Structure'''</big> A controlled vocabulary of plant's morphological and anatomical structures representing organ, tissue and cell types and their relationships. Examples are stamen, gynoecium, petal, parenchyma, guard cell, etc.
+* <big>'''Plant Anatomical Entites'''</big> A controlled vocabulary of plant's morphological and anatomical structures representing organ, tissue and cell types and their relationships. Examples are stamen, gynoecium, petal, parenchyma, guard cell, etc.
-* <big>'''Growth and developmental stages'''</big> A controlled vocabulary of growth and developmental stages in various plants and their relationships. Examples are germination, seedling, flowering, etc.
+* <big>'''Plant Structure Sevelopmental Stages'''</big> A controlled vocabulary of growth and developmental stages in various plants and their relationships. Examples are germination, seedling, flowering, etc.
-These controlled vocabularies (arranged in ontologies) will be based on internationally published/accepted terminology and their definitions.
+These controlled vocabularies (arranged in a single ontology) is based on internationally published/accepted terminology and definitions.
 In order to facilitate the use of the controlled vocabularies as attributes in other ontologies being developed by collaborating databases e.g. Open Biological Ontology ([http://obo.sourceforge.net/ OBO]), the PO controlled vocabularies, arranged in ontologies, will facilitate the attribution process and querying at different levels of granularity. The PO controlled vocabularies will also facilitate the execution of uniform queries across participating databases, thereby facilitating interoperability of plant-based databases.
@@ Line 15: / Line 15: @@
 It is considered extremely important that the terms used in the controlled vocabularies be obtained/derived from internationally published sources and/or usage. Every term in the controlled vocabulary will be accompanied by an appropriate/internationally accepted definition. The definitions provided for the terms will indicate a traceable source for the definition (e.g. ISBN number). If the definition has been modified then the reference will also include a personal signature or identifier of the developer/curator/provider. Synonyms should be indicated wherever available. This standard will contribute to an authoritative product thus encouraging wide spread usage of the ontologies and will foster consistency in the annotation of data by database curators.
 ==Data Representation==

← Older revision		Revision as of 02:16, 4 December 2008
Line 66:		Line 66:
	Ontogenetic and phylogenetic information of various macromorphological systems pertinent to plants (i.e. roots, stems, leaves, inflorescence, fruit, seed) can be reflected in relevant ontologies. Clarification of the structure and placement of these ontologies can be provided by appropriate interpretation from published phylogenetic studies of plants. The information provided about characters/traits with the phylogenetic labels of synapomorphies, symplesiomorphies, apomorphies, could be valuable in determining/clarifying the structure of ontologies (notwithstanding the fact that this phylogenetic information is implicitly hypothetical). <br /><br />Furthermore, the role of ontogeny information is evaluated regarding its possible use to test information according to the True Path Rule. Such perspectives are used in developing the ontology of stoma development and structure and the ontology of female and male inflorescence and flower structure.		Ontogenetic and phylogenetic information of various macromorphological systems pertinent to plants (i.e. roots, stems, leaves, inflorescence, fruit, seed) can be reflected in relevant ontologies. Clarification of the structure and placement of these ontologies can be provided by appropriate interpretation from published phylogenetic studies of plants. The information provided about characters/traits with the phylogenetic labels of synapomorphies, symplesiomorphies, apomorphies, could be valuable in determining/clarifying the structure of ontologies (notwithstanding the fact that this phylogenetic information is implicitly hypothetical). <br /><br />Furthermore, the role of ontogeny information is evaluated regarding its possible use to test information according to the True Path Rule. Such perspectives are used in developing the ontology of stoma development and structure and the ontology of female and male inflorescence and flower structure.

−	[[Category:~~Documentation~~]]	+	[[Category:Documents]]

← Older revision		Revision as of 02:15, 4 December 2008
Line 65:		Line 65:

	Ontogenetic and phylogenetic information of various macromorphological systems pertinent to plants (i.e. roots, stems, leaves, inflorescence, fruit, seed) can be reflected in relevant ontologies. Clarification of the structure and placement of these ontologies can be provided by appropriate interpretation from published phylogenetic studies of plants. The information provided about characters/traits with the phylogenetic labels of synapomorphies, symplesiomorphies, apomorphies, could be valuable in determining/clarifying the structure of ontologies (notwithstanding the fact that this phylogenetic information is implicitly hypothetical). <br /><br />Furthermore, the role of ontogeny information is evaluated regarding its possible use to test information according to the True Path Rule. Such perspectives are used in developing the ontology of stoma development and structure and the ontology of female and male inflorescence and flower structure.		Ontogenetic and phylogenetic information of various macromorphological systems pertinent to plants (i.e. roots, stems, leaves, inflorescence, fruit, seed) can be reflected in relevant ontologies. Clarification of the structure and placement of these ontologies can be provided by appropriate interpretation from published phylogenetic studies of plants. The information provided about characters/traits with the phylogenetic labels of synapomorphies, symplesiomorphies, apomorphies, could be valuable in determining/clarifying the structure of ontologies (notwithstanding the fact that this phylogenetic information is implicitly hypothetical). <br /><br />Furthermore, the role of ontogeny information is evaluated regarding its possible use to test information according to the True Path Rule. Such perspectives are used in developing the ontology of stoma development and structure and the ontology of female and male inflorescence and flower structure.
		+
		+	[[Category:Documentation]]

@@ Line 1: / Line 1: @@
 <blockquote>
-<big>'''Project Description'''</big>
+==Project Description==
 The main goal of the project is to provide controlled vocabularies for the following plant-specific knowledge domains namely,
@@ Line 18: / Line 18: @@
 It is considered extremely important that the terms used in the controlled vocabularies be obtained/derived from internationally published sources and/or usage. Every term in the controlled vocabulary will be accompanied by an appropriate/internationally accepted definition. The definitions provided for the terms will indicate a traceable source for the definition (e.g. ISBN number). If the definition has been modified then the reference will also include a personal signature or identifier of the developer/curator/provider. Synonyms should be indicated wherever available. This standard will contribute to an authoritative product thus encouraging wide spread usage of the ontologies and will foster consistency in the annotation of data by database curators.
-<big>'''Data Representation:'''</big>
+==Data Representation==
 The PO Consortium adopted a simple data structure called the Directed Acyclic Graph (DAG). This structure is a type of hierarchy where the biological concepts are organized as a network tree structure in which the nodes at the top (root) of the tree are more general cases of specific terms at the bottom (leaves) of the structure.
@@ Line 67: / Line 67: @@
 Ontogenetic and phylogenetic information of various macromorphological systems pertinent to plants (i.e. roots, stems, leaves, inflorescence, fruit, seed) can be reflected in relevant ontologies. Clarification of the structure and placement of these ontologies can be provided by appropriate interpretation from published phylogenetic studies of plants. The information provided about characters/traits with the phylogenetic labels of synapomorphies, symplesiomorphies, apomorphies, could be valuable in determining/clarifying the structure of ontologies (notwithstanding the fact that this phylogenetic information is implicitly hypothetical). <br /><br />Furthermore, the role of ontogeny information is evaluated regarding its possible use to test information according to the True Path Rule. Such perspectives are used in developing the ontology of stoma development and structure and the ontology of female and male inflorescence and flower structure.