Crop Ontology Pages

Introduction

The Crop Ontology website 5 sections:

1. General Germplasm Ontology
2. Phenotypes and Traits Ontology
3. Structural and Functional Genomic Ontology
4. Location and Environmental Ontology
5. Plant Anatomy & Development Ontology

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

• First, one can choose to upload a Trait Dictionary in Excel. 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 (Note,

• OBO files can be uploaded as well. They can be used to create ontologies in any of the 5 sections.
• Finally, ontologies can be built from scratch using the website dedicated interface.

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.

Trait Template

Structure of the Trait Template V4

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 columns). 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.

The Trait Template V4 columns are:

• IBFieldbook
• Name of submitting scientist
• Institution
• Language of submission (only in ISO 2 letter codes)
• Date of submission
• Crop
• Name of Trait
• Abbreviated name
• Synonyms (separate by commas)
• Trait ID for modification, Blank for New
• Description of Trait
• How is this trait routinely used?
• Trait Class
• Method ID for modification, Blank for new
• Name of Method
• Describe how measured (method)
• Growth Stage
• Bibliographic Reference
• Comments
• Scale ID for modification, Blank for new
• Type of Measure (Continuous, Discrete or Categorical)
• For Continuous: units of measurement
• For Continuous: reporting units (if different from measurement)
• For Continuous: minimum
• For Continuous: maximum
• For Discrete: Name of scale or units of measurement
• For Categorical: Name of rating scale
• For Categorical: Class 1 - value = meaning
• For Categorical: Class 2 - value = meaning
• For Categorical: Class 3 - value = meaning
• For Categorical: Class 4 - value = meaning
• For Categorical: Class 5 - value = meaning

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

Column	Description
Curation	Comments for curation
Scientist	Name of scientist submitting variable.
Institution	Name of institution submitting variable
Language	2 letter ISO code for language in which variable data is submitted.
Date	Date the variable was submitted.
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	Trait name (property)
Entity	A trait must follow the convention "Trait" = "Entity" + "Attribute", eg for "grain colour", attribute = "grain"
Attribute	eg for "grain colour", entity = "colour"
Trait synonyms	Acronym/abbreviated name.
Trait abbreviation	Recommended trait name abbreviation
Trait abbreviation synonyms	Other trait name abbreviations
Trait description	Textual description of trait.
Trait class	General class to which trait belongs.
Trait status	recommended, standard, obsolete,
Trait Xref	Cross reference of the trait e.g., Xref to TO
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.
Method	(Short) method name.
Method description	Textual description of method.
Formula	For computational methods, express the formula using variable names
Method class	Measurement, Counting, Rating, Estimation, Scoring, Computation
Method reference	Biobliographical reference describing method.
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.
Scale name	[Guidelines to be defined for naming the scale]
Scale class	Numerical, Nominal, Ordinal, Text, Code, Time, Duration
Decimal places	For numerical, number of decimal places of report
Lower limit	Minimum value (used for validation) for numerical and date
Upper limit	Maximum value (used for validation).
Scale Xref	Cross reference to the scale, eg to a unit repository like "improved UO"
Categorie i	Class value and meaning of the category "i" with "i" a positive integer
Variable name	Name of the variable, it follows a naming convention described in guidelines
Variable synonyms	Other names given to this variable
Context of use	Indication of how trait is routinely used. If several context of use, separate with ","
Growth stage	Growthstage at which measurement is made. Follow standards. If variable used in time series, leave blank
Variable status	Obsolete, Legacy, Standard // institution1, institution2, Recommended, Experimental, Revision
CV Term ID	ID generated by BMS
Variable Xref

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.

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

List of Crops and IDs

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

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.