Crop Ontology Pages - Revision history

Marieangelique.laporte at 09:55, 10 September 2015

2015-09-10T09:55:47Z

@@ Line 74: / Line 74: @@
 |}
 =OBO files=
 ==OBO file structure==

Marieangelique.laporte: /* Introduction to The Crop Ontology */

2015-06-22T11:24:43Z

Introduction to The Crop Ontology

← Older revision		Revision as of 11:24, 22 June 2015
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	The Crop Ontology website consists of 5 sections:		The Crop Ontology website consists of 5 sections:
	# Phenotypes and Traits Ontology		# Phenotypes and Traits Ontology
			##crop specific trait ontologies. contains also the methods and the scales of measurement
			## crop list: Maize, Rice, Wheat, Cassava, Cowpea, Chickpea, Potato, Sorghum, Soybean, Barley, Common Bean, Groundnut, Pearl millet, Pigeon Pea, Musa, Sweet Potato, Yam, Oat, Vitis
	# Plant Anatomy & Development Ontology		# Plant Anatomy & Development Ontology
			##Banana anatomy
			##Plant Ontology (PO)
			##Wheat Plant Anatomy and Development Ontology: Defines growth stages of wheat
	# General Germplasm Ontology		# General Germplasm Ontology
			##FAO/IPGRI Multi-Crop Passport Descriptor ontology : Adapted from FAO/Bioversity Multi-Crop Passport Descriptors, 2004
			##GCP Germplasm ontology: General germplasm descriptors
			##ICIS germplasm methods ontology: adaptation of the ICIS germplasm methods table
	# Location and Environmental Ontology		# Location and Environmental Ontology
			##Country and Location ontology: Official ISO 3166-1 alpha-2, alpha-3 and numeric country codes
			##Crop Research ontology: Describes experimental design, environmental conditions and methods associated with the crop study/experiment/trail and their evaluation
	# Structural and Functional Genomic Ontology		# Structural and Functional Genomic Ontology
			##Bioversity molecular markers ontology: Adapted from Descriptors for Genetic Markers Technologies (2004)

	===There are 3 ways of creating “ontologies” on the Crop Ontology website===		===There are 3 ways of creating “ontologies” on the Crop Ontology website===

Marieangelique.laporte: /* List of Crops and IDs */

2015-06-22T08:25:07Z

List of Crops and IDs

Show changes

Cooperl: /* List of Crops and IDs */

2015-06-10T18:44:27Z

List of Crops and IDs

← Older revision		Revision as of 18:44, 10 June 2015
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	\|-		\|-
	\| Maize		\| Maize
	\| ~~322~~		\| CO_322
	\|-		\|-
	\| Rice		\| Rice

Cooperl: /* List of Crops and IDs */

2015-06-08T21:25:36Z

List of Crops and IDs

← Older revision		Revision as of 21:25, 8 June 2015
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	\|}		\|}

	The trait ontologies start with 3XX whereas the anatomy ontologies start with 1XX.		Note: The trait ontologies start with 3XX whereas the anatomy ontologies start with 1XX.

	==Trait Template==		==Trait Template==

Cooperl: /* Introduction to The Crop Ontology */

2015-06-08T21:23:06Z

Introduction to The Crop Ontology

@@ Line 17: / Line 17: @@
 * The ontologies can be downloaded in various formats: CSV, OBO, SKOS and JSON. The structures of the different formats are described in the following sections.
 * Note that because there is no exact mapping between the different formats some compromises has been made. Not all the information is available in the different formats.
 ==Trait Template==

Cooperl: /* List of Crops and IDs */

2015-06-08T21:22:50Z

List of Crops and IDs

← Older revision		Revision as of 21:22, 8 June 2015
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	\|For Categorical: Class 4 - value = meaning\|\|Local Name (URI) + rdf: type skos:concept		\|For Categorical: Class 4 - value = meaning\|\|Local Name (URI) + rdf: type skos:concept
	\|}		\|}

	~~=List of Crops and IDs=~~
	~~According to the project timeline, the crops that will be linked to the reference ontologies are:~~
	~~{\| border="1" class="sortable"~~
	\|-
	~~! Crops~~
	~~! Prefixes~~
	\|-
	~~\| Maize~~
	~~\| 322~~
	\|-
	~~\| Rice~~
	~~\| 320~~
	\|-
	~~\| Wheat~~
	~~\| 321 (traits) and 121 (anatomy)~~
	\|-
	~~\| Cassava~~
	~~\| 334~~
	\|-
	~~\| Cowpea~~
	~~\| 340~~
	\|-
	~~\| Chickpea~~
	~~\| 338~~
	\|-
	~~\| Potato~~
	~~\| 330~~
	\|-
	~~\| Sorghum~~
	~~\| 324~~
	\|-
	~~\| Soybean~~
	~~\| 336~~
	\|-
	~~\| Barley~~
	~~\| 323~~
	\|-
	~~\| Common Bean~~
	~~\| 335~~
	\|-
	~~\| Groundnut~~
	~~\| 337~~
	\|-
	~~\| Pearl Millet~~
	~~\| 327~~
	\|-
	~~\| Pigeon Pea~~
	~~\| 341~~
	\|-
	~~\| Musa~~
	~~\| 325 (traits) and 125 (anatomy)~~
	\|-
	~~\| Sweet Potato~~
	~~\| 331~~
	\|-
	~~\| Yam~~
	~~\| 333~~
	\|-
	~~\| Other crops ?????~~
	\|
	\|}

	~~The trait ontologies start with 3XX whereas the anatomy ontologies start with 1XX.~~

Cooperl: /* SKOS files */

2015-06-08T21:22:01Z

SKOS files

← Older revision		Revision as of 21:22, 8 June 2015
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	\|For Categorical: Class 4 - value = meaning\|\|Term + name + is-a		\|For Categorical: Class 4 - value = meaning\|\|Term + name + is-a
	\|}		\|}



	=SKOS files=		=SKOS files=

Cooperl: /* OBO file structure */

2015-06-08T21:21:31Z

OBO file structure

← Older revision		Revision as of 21:21, 8 June 2015
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	==OBO file structure==		==OBO file structure==
	OBO files are created using the obo2owl library (which should sound familiar ;-)).		OBO files are created using the obo2owl library (which should sound familiar ;-)).

	The main issue with the Trait Template is that because different IDs can be created for the same “thing” (e.g. the term “cm” will get different IDs if different traits are measured in cm), different obo terms can have the same name (but different IDs).		The main issue with the Trait Template is that because different IDs can be created for the same “thing” (e.g. the term “cm” will get different IDs if different traits are measured in cm), different obo terms can have the same name (but different IDs).

	That is a problem when our users tried to import the OBO files in a Chado database.		That is a problem when our users tried to import the OBO files in a Chado database.

	Consequently, I created a little script that created OBO files where all the names are unique in a given namespace. The script has not be inserted in the website yet but it will be soon. Example of an OBO files on Github.		* Consequently, I created a little script that created OBO files where all the names are unique in a given namespace. The script has not be inserted in the website yet but it will be soon. Example of an OBO files on Github. (MAL)

	{\| border="1" class="sortable"		{\| border="1" class="sortable"

Cooperl: /* Structure of the Trait Template V5 (Léo is still working on it with Julian Pietragalla from CIMMYT) */

2015-06-08T21:20:28Z

Structure of the Trait Template V5 (Léo is still working on it with Julian Pietragalla from CIMMYT)

← Older revision		Revision as of 21:20, 8 June 2015
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	==Structure of the Trait Template V5 (Léo is still working on it with Julian Pietragalla from CIMMYT) ==		==Structure of the Trait Template V5 (Léo is still working on it with Julian Pietragalla from CIMMYT) ==
	Note the structure can still evolve. Template V5 is still a draft		Note the structure can still evolve. Template V5 is still a draft

	{\| {{table}}		{\| {{table}}
	\| align="center" style="background:#f0f0f0;"\|'''Column'''		\| align="center" style="background:#f0f0f0;"\|'''Column'''
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	\| Curation\|\|Comments for curation		\| Curation\|\|Comments for curation
	\|-		\|-
	\| Scientist\|\|Name of scientist submitting variable.		\| Scientist\|\|Name of scientist submitting variable
	\|-		\|-
	\| Institution\|\|Name of institution submitting variable		\| Institution\|\|Name of institution submitting variable
	\|-		\|-
	\| Language\|\|2 letter ISO code for language in which variable data is submitted.		\| Language\|\|2 letter ISO code for language in which variable data is submitted
	\|-		\|-
	\| Date\|\|Date the variable was submitted.		\| Date\|\|Date the variable was submitted
	\|-		\|-
	\| Crop\|\|Crop name.		\| Crop\|\|Crop name
	\|-		\|-
	\| Trait ID\|\|Term ID for trait as generated by the system. Use an existing ID to modify data for that trait. If left blank the system will automatically generate a new ID.		\| Trait ID\|\|Term ID for trait as generated by the system. Use an existing ID to modify data for that trait. If left blank the system will automatically generate a new ID.

← Older revision		Revision as of 21:22, 8 June 2015
Line 277:		Line 277:
	\|For Categorical: Class 4 - value = meaning\|\|Local Name (URI) + rdf: type skos:concept		\|For Categorical: Class 4 - value = meaning\|\|Local Name (URI) + rdf: type skos:concept
	\|}		\|}

	~~=List of Crops and IDs=~~
	~~According to the project timeline, the crops that will be linked to the reference ontologies are:~~
	~~{\| border="1" class="sortable"~~
	\|-
	~~! Crops~~
	~~! Prefixes~~
	\|-
	~~\| Maize~~
	~~\| 322~~
	\|-
	~~\| Rice~~
	~~\| 320~~
	\|-
	~~\| Wheat~~
	~~\| 321 (traits) and 121 (anatomy)~~
	\|-
	~~\| Cassava~~
	~~\| 334~~
	\|-
	~~\| Cowpea~~
	~~\| 340~~
	\|-
	~~\| Chickpea~~
	~~\| 338~~
	\|-
	~~\| Potato~~
	~~\| 330~~
	\|-
	~~\| Sorghum~~
	~~\| 324~~
	\|-
	~~\| Soybean~~
	~~\| 336~~
	\|-
	~~\| Barley~~
	~~\| 323~~
	\|-
	~~\| Common Bean~~
	~~\| 335~~
	\|-
	~~\| Groundnut~~
	~~\| 337~~
	\|-
	~~\| Pearl Millet~~
	~~\| 327~~
	\|-
	~~\| Pigeon Pea~~
	~~\| 341~~
	\|-
	~~\| Musa~~
	~~\| 325 (traits) and 125 (anatomy)~~
	\|-
	~~\| Sweet Potato~~
	~~\| 331~~
	\|-
	~~\| Yam~~
	~~\| 333~~
	\|-
	~~\| Other crops ?????~~
	\|
	\|}

	~~The trait ontologies start with 3XX whereas the anatomy ontologies start with 1XX.~~