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==Introduction to [http://www.cropontology.org/ The Crop Ontology]==


The Crop Ontology website consists of 5 sections:
# 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
##Banana anatomy
##Plant Ontology (PO)
##Wheat Plant Anatomy and Development Ontology: Defines growth stages of wheat
# 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
##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
##Bioversity molecular markers ontology: Adapted from Descriptors for Genetic Markers Technologies (2004)


=Trait Template=
===There are 3 ways of creating “ontologies” on the Crop Ontology website===
==Structure of the Trait Template V4==
# Upload a Trait Dictionary (TD) in Excel. (Note, the TD is only used to store and load information about traits, thus it cannot be used for uploading ontologies that would belong to the other categories)
So far, the Trait Template V4 is uploaded into the CO website. The Trait Template is used to gather information on traits along with their methods and scales of measurement. For each trait, some meta-information is added (5 first column). An (unique) ID is created by the system for each trait, method and scale (several IDs are created when the scale is categorical). But for now, if two methods or scales are the same (seed length and leaf length are measured in centimeters), different IDs are created, which is far from being ideal or even ontologically correct.  
#  Upload an OBO file. They can be used to create ontologies in any of the 5 sections 
The Trait Template V4 columns are:
# Ontologies can be built from scratch using the website dedicated interface. ''Are there any examples of these?''
*IBFieldbook
 
*Name of submitting scientist
===Storage and Downloading===
*Institution
* Once the files are uploaded or some terms are submitted using the web interface, the data are stored in a noSQL database (Google App Engine Datastore).
*Language of submission (only in ISO 2 letter codes)
* 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.
*Date of submission
* 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.
*Crop
 
*Name of Trait
=List of Crops and IDs=
*Abbreviated name  
According to the project timeline, the crops that will be linked to the reference ontologies are:
*Synonyms (separate by commas)
{| {{table}}
*Trait ID for modification, Blank for New
| align="center" style="background:#f0f0f0;"|'''CROPS'''
*Description of Trait
| align="center" style="background:#f0f0f0;"|'''Crop Ids'''
*How is this trait routinely used?
| align="center" style="background:#f0f0f0;"|'''Prefixes'''
*Trait Class
| align="center" style="background:#f0f0f0;"|'''Map to prefixes recommended by Chris'''
*Method ID for modification, Blank for new
|-
*Name of Method
| Maize||322||CO_322||IBPCO:322xxxx
*Describe how measured (method)
|-
*Growth Stage
| Rice||320||CO_320||IBPCO:320xxxx
*Bibliographic Reference
|-
*Comments
| Wheat||321||CO_321||IBPCO:321xxxx
*Scale ID for modification, Blank for new
|-
*Type of Measure (Continuous, Discrete or Categorical)
| Cassava||334||CO_334||IBPCO:334xxxx
*For Continuous: units of measurement
|-
*For Continuous: reporting units (if different from measurement)
| Cowpea||340||CO_340||IBPCO:340xxxx
*For Continuous: minimum
|-
*For Continuous: maximum
| Chickpea||338||CO_338||IBPCO:338xxxx
*For Discrete: Name of scale or units of measurement
|-
*For Categorical: Name of rating scale
| Potato||330||CO_330||IBPCO:330xxxx
*For Categorical: Class 1 - value = meaning
|-
*For Categorical: Class 2 - value = meaning  
| Sorghum||324||CO_324||IBPCO:324xxxx
*For Categorical: Class 3 - value = meaning
|-
*For Categorical: Class 4 - value = meaning
| Soybean||336||CO_336||IBPCO:336xxxx
*For Categorical: Class 5 - value = meaning
|-
| Barley||323||CO_323||IBPCO:323xxxx
|-
| Common Bean||335||CO_335||IBPCO:335xxxx
|-
| Groundnut||337||CO_337||IBPCO:337xxxx
|-
| Pearl millet||327||CO_327||IBPCO:327xxxx
|-
| Pigeon Pea||341||CO_341||IBPCO:341xxxx
|-
| Musa||325 (traits) and 125 (anatomy)||CO_325 and CO_125||IBPCO:325xxxx and IBPCO:125xxxx
|-
| Sweet Potato||331||CO_331||IBPCO:331xxxx
|-
| Yam||333||CO_333||IBPCO:333xxxx
|-
| Other crops ???||||||
|}
 
=Trait Dictionary V5=
== Mapping TD to OBO ==
{| {{table}}
| align="center" style="background:#f0f0f0;"|'''TDv5 Elements'''
| align="center" style="background:#f0f0f0;"|'''Description'''
| align="center" style="background:#f0f0f0;"|'''Stored in CO website'''
| align="center" style="background:#f0f0f0;"|'''OBO element'''
|-
| Curation||Comments for curation||NO||NO
|-
| 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.||Yes||Ontology ID (trait namespace)
|-
| Trait||Trait name (property)||Yes||name (trait namespace)
|-
| Entity||A trait must follow the convention "Trait" = "Entity" + "Attribute", eg for "grain colour", attribute = "grain"||Yes||Crossproduct to PO
|-
| Attribute||eg for "grain colour", entity = "colour"||Yes||Crossproduct to PATO
|-
| Trait synonyms||Acronym/abbreviated name.||Yes||synonym (trait namespace)
|-
| Trait abbreviation||Trait name abbreviation. If several abbrevations, separate with comas. The recommended abbreviation must be the first in the list.||Yes||synonym (trait namespace)
|-
| Trait description||Textual description of trait.||Yes||def (trait namespace)
|-
| Trait class||General class to which trait belongs. Concensus trait classes are morphological, phenological, agronomical, physiological, abiotic stress, biotic stress, biochemical, quality traits and fertility traits||Yes||is_a
|-
| Trait status||Status of the trait. Trait can be tagged as recommended, standard for , deprecated, legacy||Yes||is_obsolete
|-
| Trait Xref||Cross reference of the trait e.g., Xref to TO||Yes||xref
|-
| Method ID|| Term ID for method as generated by the system. Use an existing ID to modify data for that method. If left blank the system will automatically generate a new ID. ||Yes||id
|-
| Method|| (Short) method name. ||Yes||name (method namespace)
|-
| Method description|| Textual description of method. ||Yes||def (method namespace)
|-
| Formula|| For computational methods, express the formula using variable names ||Yes||NO
|-
| Method class|| Measurement, Counting, Estimation, Computation ||Yes||NO
|-
| Method reference|| Biobliographical reference describing method. ||Yes||Xref
|-
| Scale id||Term ID for scale as generated by the system. Use an existing ID to modify data for that scale. If left blank the system will automatically generate a new ID.||Yes||id
|-
| Scale name||[Guidelines to be defined for naming the scale]||Yes||name (scale namespace)
|-
| Scale class||Numerical, Nominal, Ordinal, Text, Code, Time, Duration||Yes||NO
|-
| Decimal places||For numerical, number of decimal places of report||Yes||NO
|-
| Lower limit||Minimum value (used for validation) for numerical and date||Yes||NO
|-
| Upper limit||Maximum value (used for validation).||Yes||NO
|-
| Scale Xref||Cross reference to the scale, eg to a unit repository like "improved UO"||Yes||Xref
|-
| Category n||If the scale is categorical, class value and meaning of the n-th category. It possible to create as many category columns as necessary, as long as they are called "Category "||Yes||Yes
|-
| Variable ID||Term ID for method as generated by the system. Use an existing ID to modify data for that method. If left blank the system will automatically generate a new ID.||Yes||Ontology ID (variable namespace)
|-
| Variable name (abbreviated)||Name of the variable following the convetion __. Variable name must be unique.||Yes||synonym (variable namespace)
|-
| Variable synonyms||Other names given to this variable||Yes||synonym (variable namespace)
|-
| Context of use||Indication of how trait is routinely used. If several context of use, separate with ","||Yes||NO
|-
| Growth stage|| Growthstage at which measurement is made. Follow standards. If variable used in time series, leave blank ||Yes||NO
|-
| Variable status||Obsolete, Legacy, Standard for , Recommended, Experimental, Revision||Yes||is_obsolete
|-
| CV Term ID||ID generated by BMS||Yes||NO
|-
| Variable Xref||||Yes||Xref
|-
| Scientist||Name of scientist submitting variable.||Yes||NO
|-
| Institution||Name of institution submitting variable||Yes||NO
|-
| Language||2 letter ISO code for language in which variable data is submitted.||Yes||NO
|-
| Date||Date the variable was submitted.||Yes||NO
|-
| Crop||Crop name.||Yes||Yes
|-
| Full variable name||||||customized name. For new variables -> concatenation of  by  in
|-
| variable definition||||||T:  /n M:  /n S:
|}
=OBO files=
==OBO file structure==
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).
 
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. (MAL)
 
{| border="1" class="sortable"
!TD column!!OBO element
|-
|Crop||Used for setting up the namespace
|-
|Name of Trait||name
|-
|Trait ID for modification, Blank for New||Term + id
|-
|Description of Trait||definition
|-
|Trait Class||Term +id + name + is-a
|-
|Language of submission (only in ISO 2 letter codes)||We have only English OBO files.
|-
|Name of submitting scientist||created_by
|-
|Institution||Not used
|-
|Date of submission||creation_date
|-
|Abbreviated name||synonym [EXACT]
|-
|Synonyms (separate by commas)||synonym [EXACT]
|-
|How is this trait routinely used||Not used
|-
|Name of method||name
|-
|Method ID for modification, Blank for New||Term + id + method_of
|-
|Describe how measured (method||definition
|-
|Bibliographic Reference||xref
|-
|Growth Stage||Not used
|-
|Comments||Not used
|-
|Scale ID for modification, Blank for New||Term + id + scale_of
|-
|Type of Measure (Continuous, Discrete or Categorical||Not used
|-
|For Continuous: units of measurement||name
|-
|For Discrete: Name of scale or units of measurement||name
|-
|For Categorical: Name of rating scale||name
|-
|For Categorical: Class 1 - value = meaning||Term + name + is-a
|-
|For Categorical: Class 2 - value = meaning ||Term + name + is-a
|-
|For Categorical: Class 3 - value = meaning||Term + name + is-a
|-
|For Categorical: Class 4 - value = meaning||Term + name + is-a
|}
 
 
 
=SKOS files=
==SKOS file structure==
{| border="1" class="sortable"
!TD column!!SKOS
|-
|Crop||Used for setting up the namespace
|-
|Name of Trait||skos:prefLabel
|-
|Trait ID for modification, Blank for New||Local Name (URI) + rdf: type skos:concept
|-
|Description of Trait||skos:definition
|-
|Trait Class||rdf:type Skos:Concept + skos:broader
|-
|Language of submission (only in ISO 2 letter codes)||xml:lang of the literals. SKOS files are multilingual (if we have the info)
|-
|Name of submitting scientist||foaf:Person (not set so far but will be soon)
|-
|Institution||foaf:Organization (not set so far but will be soon)
|-
|Date of submission||dc:date (not set so far but will be soon)
|-
|Abbreviated name||skos:altLabel
|-
|Synonyms (separate by commas)||skos:altLabel
|-
|How is this trait routinely used||Not used
|-
|Name of method||skos:prefLabel
|-
|Method ID for modification, Blank for New||Local Name (URI) + rdf: type skos:concept
|-
|Describe how measured (method||skos:definition
|-
|Bibliographic Reference||Not set (dc: bibliographicCitation?)
|-
|Growth Stage||skos:related (not set so far)
|-
|Comments||skos:editorialNote
|-
|Scale ID for modification, Blank for New||Local Name (URI) + rdf: type skos:concept
|-
|Type of Measure (Continuous, Discrete or Categorical||Not used
|-
|For Continuous: units of measurement||skos:prefLabel
|-
|For Discrete: Name of scale or units of measurement||skos:prefLabel
|-
|For Categorical: Name of rating scale||skos:prefLabel
|-
|For Categorical: Class 1 - value = meaning||Local Name (URI) + rdf: type skos:concept
|-
|For Categorical: Class 2 - value = meaning ||Local Name (URI) + rdf: type skos:concept
|-
|For Categorical: Class 3 - value = meaning||Local Name (URI) + rdf: type skos:concept
|-
|For Categorical: Class 4 - value = meaning||Local Name (URI) + rdf: type skos:concept
|}

Latest revision as of 09:55, 10 September 2015

Introduction to The Crop Ontology

The Crop Ontology website consists of 5 sections:

  1. Phenotypes and Traits Ontology
    1. crop specific trait ontologies. contains also the methods and the scales of measurement
    2. 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
  2. Plant Anatomy & Development Ontology
    1. Banana anatomy
    2. Plant Ontology (PO)
    3. Wheat Plant Anatomy and Development Ontology: Defines growth stages of wheat
  3. General Germplasm Ontology
    1. FAO/IPGRI Multi-Crop Passport Descriptor ontology : Adapted from FAO/Bioversity Multi-Crop Passport Descriptors, 2004
    2. GCP Germplasm ontology: General germplasm descriptors
    3. ICIS germplasm methods ontology: adaptation of the ICIS germplasm methods table
  4. Location and Environmental Ontology
    1. Country and Location ontology: Official ISO 3166-1 alpha-2, alpha-3 and numeric country codes
    2. Crop Research ontology: Describes experimental design, environmental conditions and methods associated with the crop study/experiment/trail and their evaluation
  5. Structural and Functional Genomic Ontology
    1. Bioversity molecular markers ontology: Adapted from Descriptors for Genetic Markers Technologies (2004)

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

  1. Upload a Trait Dictionary (TD) in Excel. (Note, the TD is only used to store and load information about traits, thus it cannot be used for uploading ontologies that would belong to the other categories)
  2. Upload an OBO file. They can be used to create ontologies in any of the 5 sections
  3. Ontologies can be built from scratch using the website dedicated interface. Are there any examples of these?

Storage and Downloading

  • Once the files are uploaded or some terms are submitted using the web interface, the data are stored in a noSQL database (Google App Engine Datastore).
  • 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.

List of Crops and IDs

According to the project timeline, the crops that will be linked to the reference ontologies are:

CROPS Crop Ids Prefixes Map to prefixes recommended by Chris
Maize 322 CO_322 IBPCO:322xxxx
Rice 320 CO_320 IBPCO:320xxxx
Wheat 321 CO_321 IBPCO:321xxxx
Cassava 334 CO_334 IBPCO:334xxxx
Cowpea 340 CO_340 IBPCO:340xxxx
Chickpea 338 CO_338 IBPCO:338xxxx
Potato 330 CO_330 IBPCO:330xxxx
Sorghum 324 CO_324 IBPCO:324xxxx
Soybean 336 CO_336 IBPCO:336xxxx
Barley 323 CO_323 IBPCO:323xxxx
Common Bean 335 CO_335 IBPCO:335xxxx
Groundnut 337 CO_337 IBPCO:337xxxx
Pearl millet 327 CO_327 IBPCO:327xxxx
Pigeon Pea 341 CO_341 IBPCO:341xxxx
Musa 325 (traits) and 125 (anatomy) CO_325 and CO_125 IBPCO:325xxxx and IBPCO:125xxxx
Sweet Potato 331 CO_331 IBPCO:331xxxx
Yam 333 CO_333 IBPCO:333xxxx
Other crops ???

Trait Dictionary V5

Mapping TD to OBO

TDv5 Elements Description Stored in CO website OBO element
Curation Comments for curation NO NO
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. Yes Ontology ID (trait namespace)
Trait Trait name (property) Yes name (trait namespace)
Entity A trait must follow the convention "Trait" = "Entity" + "Attribute", eg for "grain colour", attribute = "grain" Yes Crossproduct to PO
Attribute eg for "grain colour", entity = "colour" Yes Crossproduct to PATO
Trait synonyms Acronym/abbreviated name. Yes synonym (trait namespace)
Trait abbreviation Trait name abbreviation. If several abbrevations, separate with comas. The recommended abbreviation must be the first in the list. Yes synonym (trait namespace)
Trait description Textual description of trait. Yes def (trait namespace)
Trait class General class to which trait belongs. Concensus trait classes are morphological, phenological, agronomical, physiological, abiotic stress, biotic stress, biochemical, quality traits and fertility traits Yes is_a
Trait status Status of the trait. Trait can be tagged as recommended, standard for , deprecated, legacy Yes is_obsolete
Trait Xref Cross reference of the trait e.g., Xref to TO Yes xref
Method ID Term ID for method as generated by the system. Use an existing ID to modify data for that method. If left blank the system will automatically generate a new ID. Yes id
Method (Short) method name. Yes name (method namespace)
Method description Textual description of method. Yes def (method namespace)
Formula For computational methods, express the formula using variable names Yes NO
Method class Measurement, Counting, Estimation, Computation Yes NO
Method reference Biobliographical reference describing method. Yes Xref
Scale id Term ID for scale as generated by the system. Use an existing ID to modify data for that scale. If left blank the system will automatically generate a new ID. Yes id
Scale name [Guidelines to be defined for naming the scale] Yes name (scale namespace)
Scale class Numerical, Nominal, Ordinal, Text, Code, Time, Duration Yes NO
Decimal places For numerical, number of decimal places of report Yes NO
Lower limit Minimum value (used for validation) for numerical and date Yes NO
Upper limit Maximum value (used for validation). Yes NO
Scale Xref Cross reference to the scale, eg to a unit repository like "improved UO" Yes Xref
Category n If the scale is categorical, class value and meaning of the n-th category. It possible to create as many category columns as necessary, as long as they are called "Category " Yes Yes
Variable ID Term ID for method as generated by the system. Use an existing ID to modify data for that method. If left blank the system will automatically generate a new ID. Yes Ontology ID (variable namespace)
Variable name (abbreviated) Name of the variable following the convetion __. Variable name must be unique. Yes synonym (variable namespace)
Variable synonyms Other names given to this variable Yes synonym (variable namespace)
Context of use Indication of how trait is routinely used. If several context of use, separate with "," Yes NO
Growth stage Growthstage at which measurement is made. Follow standards. If variable used in time series, leave blank Yes NO
Variable status Obsolete, Legacy, Standard for , Recommended, Experimental, Revision Yes is_obsolete
CV Term ID ID generated by BMS Yes NO
Variable Xref Yes Xref
Scientist Name of scientist submitting variable. Yes NO
Institution Name of institution submitting variable Yes NO
Language 2 letter ISO code for language in which variable data is submitted. Yes NO
Date Date the variable was submitted. Yes NO
Crop Crop name. Yes Yes
Full variable name customized name. For new variables -> concatenation of by in
variable definition T: /n M: /n S:

OBO files

OBO file structure

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).

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. (MAL)
TD column OBO element
Crop Used for setting up the namespace
Name of Trait name
Trait ID for modification, Blank for New Term + id
Description of Trait definition
Trait Class Term +id + name + is-a
Language of submission (only in ISO 2 letter codes) We have only English OBO files.
Name of submitting scientist created_by
Institution Not used
Date of submission creation_date
Abbreviated name synonym [EXACT]
Synonyms (separate by commas) synonym [EXACT]
How is this trait routinely used Not used
Name of method name
Method ID for modification, Blank for New Term + id + method_of
Describe how measured (method definition
Bibliographic Reference xref
Growth Stage Not used
Comments Not used
Scale ID for modification, Blank for New Term + id + scale_of
Type of Measure (Continuous, Discrete or Categorical Not used
For Continuous: units of measurement name
For Discrete: Name of scale or units of measurement name
For Categorical: Name of rating scale name
For Categorical: Class 1 - value = meaning Term + name + is-a
For Categorical: Class 2 - value = meaning Term + name + is-a
For Categorical: Class 3 - value = meaning Term + name + is-a
For Categorical: Class 4 - value = meaning Term + name + is-a


SKOS files

SKOS file structure

TD column SKOS
Crop Used for setting up the namespace
Name of Trait skos:prefLabel
Trait ID for modification, Blank for New Local Name (URI) + rdf: type skos:concept
Description of Trait skos:definition
Trait Class rdf:type Skos:Concept + skos:broader
Language of submission (only in ISO 2 letter codes) xml:lang of the literals. SKOS files are multilingual (if we have the info)
Name of submitting scientist foaf:Person (not set so far but will be soon)
Institution foaf:Organization (not set so far but will be soon)
Date of submission dc:date (not set so far but will be soon)
Abbreviated name skos:altLabel
Synonyms (separate by commas) skos:altLabel
How is this trait routinely used Not used
Name of method skos:prefLabel
Method ID for modification, Blank for New Local Name (URI) + rdf: type skos:concept
Describe how measured (method skos:definition
Bibliographic Reference Not set (dc: bibliographicCitation?)
Growth Stage skos:related (not set so far)
Comments skos:editorialNote
Scale ID for modification, Blank for New Local Name (URI) + rdf: type skos:concept
Type of Measure (Continuous, Discrete or Categorical Not used
For Continuous: units of measurement skos:prefLabel
For Discrete: Name of scale or units of measurement skos:prefLabel
For Categorical: Name of rating scale skos:prefLabel
For Categorical: Class 1 - value = meaning Local Name (URI) + rdf: type skos:concept
For Categorical: Class 2 - value = meaning Local Name (URI) + rdf: type skos:concept
For Categorical: Class 3 - value = meaning Local Name (URI) + rdf: type skos:concept
For Categorical: Class 4 - value = meaning Local Name (URI) + rdf: type skos:concept
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