These are some general-purpose utility scripts that can be used to convert trait ontologies between various different formats that are used internally to manage the traits, by the Crop Ontology website, and by the breeDBase backend.
Trait Workbook: An Excel workbook containing separate worksheets for each data type: Variables, Traits, Methods, Scales, Trait Classes, and Ontology Root Information. This file is used internally to edit and/or add new traits.
Trait Dictionary: A semi-colon separated flat text file used by the Crop Ontology website. Each row of a Trait Dictionary is an observation variable and contains the complete trait, method and scale information for the variable.
OBO: A text file format used by OBO-Edit to store ontology information.
Each data type (Variable, Trait, Method, Scale) is represented by a
[Term] block and their relationships are defined by is_a, method_of,
scale_of and variable_of terms.
-
The standard-obo file contains separate namespaces for each data type
-
The sgn-obo file uses a single namespace for the root elements, variables and traits
The following documents contain information on the general steps and workflow of creating a new ontology from scratch or working with an existing
create_tw.pl - Create a Trait Workbook from an existing Trait Dictionary
NAME
create_tw.pl
SYNOPSIS
Usage: perl create_tw.pl -d namespace -n name -r root -o output [-v] [input]
Options/Arguments:
-d the default ontology namespace. This will be used when
generating an obo file (ex sugar_kelp_trait).
-n the ontology display name. A human-readable name for the
ontology (ex Sugar Kelp Traits).
-r the ontology root id. Most likely the Crop Ontology ID (ex
CO_360).
-o the output location of the trait workbook excel file (xlsx
extension).
-v verbose output
input specify the Crop Ontology Root ID (ex: CO_360) to download the
trait dictionary from cropontology.org OR the file path to an
existing trait dictionary. If no input is provided, a new trait
workbook will be created containing an example variable, trait,
and scale.
DESCRIPTION
This will create a 'Trait Workbook' Excel file from an existing Crop
Ontology 'Trait Dictionary'. A Trait Dictionary is a flat text file
containing all of the trait information available on the Crop Ontology
website. The Trait Dictionary can be specified by it's CO ID (such as
CO_360) and downloaded from the Crop Ontology website OR by a file path
to an existing Trait Dictionary file.
The resulting Trait Workbook will contain the worksheets 'Variables',
'Traits', 'Methods', 'Scales', 'Trait Classes' and 'Root'. Some columns
will have conditional formatting applied that will highlight duplicated
values. The 'Trait name', 'Method name' and 'Scale name' columns in the
'Variables' worksheet will highlight names of elements that do not match
existing elements.
The Trait Workbook file can be used by the build_traits.pl script to
build a Trait Dictionary and/or OBO file.
AUTHOR
David Waring <[email protected]>
build_traits.pl - Build a Trait Dictionary and/or Standard-OBO file from a Trait Workbook
NAME
build_traits.pl
SYNOPSIS
Usage: perl build_traits.pl [-o output -u username] [-t output] [-i
institution] [-c category count] [-fv] file
Options/Arguments:
-o specify the output location for the generic obo file
-u specify the username of the person generating the file(s)
required when generating an obo file
-t specify the output location for the trait dictionary file
-i filter the output to contain only the variables used by the
specified institution
-c specify the number of scale categories that are defined in the
trait workbook (default=10)
-f force the generation of the files (ignore the unique and
required checks)
-q trait dictionary file: enclose the values with double quotes
(and change double quotes in the value to two double quotes)
-v verbose output
file file path to the trait workbook
DESCRIPTION
Build a trait dictionary (a flat text file containg all of the trait
information used by the Crop Ontology website) and/or standard obo file
(generalized ontology text file) from a "trait workbook" (an Excel
workbook containing worksheets for a trait ontology's "Variables",
"Traits", "Methods", "Scales", "Trait Classes" and "Root" information).
AUTHOR
David Waring <[email protected]>
convert_obo.pl - Convert a Standard-OBO file to an SGN-OBO file
NAME
convert_obo.pl
SYNOPSIS
Usage: perl convert_obo.pl -d namespace [-n namespace]
[--remove-synoynms] -o output [-v] input
Example: perl convert_obo.pl -d barley_traits -n barley_traits_trait -n
barley_traits_variable -o sgn.obo standard.obo
Options/Arguments:
--default, -d
The default / root namespace. This is the namespace that the
other namespaces ([{default}_trait, {default}_variable] or
namespaces provided as -n args) will be converted to. This is
the namespace that will have to be given to the gmod scriptswhen
loading an ontology into breedbase.
--namespace, -n
The namespace(s) from the standard-obo file to renamed to the
default (-d) namespace in the output obo file. This option can
be used more than once to specify multiple namespaces to
include. To load an ontology into breedbase, this should include
the namespaces of the ontology root term, trait classes, traits,
and variables.
By default, this script will use the {default namespace},
{default namespace}_trait, and {default namepspace}_variable
namespaces to convert if none are given here.
--remove-synoynms
When this flag is set, variable synonyms will be removed from
the .obo file. We've noticed that if a variable has any
synonyms, the synonyms will be preferred over the actual name
when the traits are fetched via BrAPI to be used in the Field
Book app.
--output, -o
specify the output location for the sgn-obo file
--verbose, -v
verbose output
input specify the location of the input standard-obo file
DESCRIPTION
Convert a standard-obo file into an sgn-obo file to be loaded into a
breeDBase instance.
This will rename all of the specified standard-obo namespaces into the
single default namespace.
AUTHOR
David Waring <[email protected]>
- JSON
- Excel::Writer::XLSX
- Excel::Writer::XLSX::Utility
- Spreadsheet::Read
- Spreadsheet::ParseXLSX
- Text::CSV_XS
- DateTime::Format::Excel
curlmust be installed to download a Trait Dictionary from the Crop Ontology website.