Crop Ontology Pages

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