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ROBOT is licensed under the
BSD 3-Clause License.
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Template

Contents

  1. Overview
  2. Template Strings
    1. Generic Template Strings
    2. Class Template Strings
    3. Property Template Strings
    4. Individual Template Strings
  3. Merging (--merge-before, --merge-after)
  4. Examples

Overview

ROBOT can convert tables to OWL format using templates. See template.csv for an example. The approach extends the QTT method described in Overcoming the ontology enrichment bottleneck with Quick Term Templates.

ROBOT can read comma-separated values (.csv) or tab-separated values (.tsv or .tab):

robot template --template template.csv \
  --prefix "ex: http://example.com/" \
  --ontology-iri "https://github.com/ontodev/robot/examples/template.owl" \
  --output results/template.owl

Each template file must be set up in the following format:

  1. Headers: ROBOT expects the first row to contain column names for every column used in the data. These are used to make error messages more helpful.
  2. Templates: ROBOT expects the second row to contain template strings for each column that will be used in the OWL conversion. See below for details on template strings.
  3. Data: ROBOT expects each of the remaining rows to correspond to a term (a class, property, or individual).

Template Options

The template command accepts an optional input ontology, either using the --input option or from the previous command in a chain. If an input ontology is given, its rdfs:labels will be used when parsing the template. The --template or -t option specifies the CSV or TSV template file. Multiple templates are allowed, and the order of templates is significant. You can also specify the normal --prefix options, the --output-iri and --version-iri, and the usual --output options. See Merging for the three different merge options, and details on how they control the output of the command.

A template may have multiple errors in different rows and columns. By default, template will fail on the first error encountered. If you wish to proceed with errors, use --force true. This will log all row parse errors to STDERR and attempt to create an ontology anyway. Be aware that the output ontology may be missing axioms.

Template Strings

Generic Template Strings

Sometimes you want to include zero or more values in a single spreadsheet cell, for example when you want to allow for multiple annotations or have separate logical axioms. If a template string also contains SPLIT=|, then ROBOT will use the | character to split the contents of a cell in that column and add an annotation for each result (if there are any). Instead of | you can specify a string of characters of your choice – other than pure whitespace – to split on (e.g. SPLIT=, ).

Class Template Strings

(A CI template string tells ROBOT to read the cell value as an IRI and assert it as the CLASS_TYPE. This is included for legacy support, and the other class template strings are preferred.)

Example of Class Template Strings

Label Entity Type Superclass Disjoint Classes Equivalent axioms
LABEL TYPE SC % DC % EC part_of some %
Class 2 class Class 1    
Class 3 class     Class 2
Class 4 class equivalent Class 3  

Class 2 will be a subclass of Class 1. Class 3 will be equivalent to part_of some 'Class 2' and Class 4 will be disjoint with Class 3.

Manchester expressions can also be used within the cells. To avoid ambiguity, it’s best to enclose expressions in parentheses:

Label Parent
LABEL SC %
Class 4  
Class 5 (part_of some ‘Class 4’)

In this template, Class 5 would be a subclass of part_of some 'Class 4'.

Property Template Strings

Example of Property Template Strings

ID Entity Type Characteristic Super Property Domain Range
ID TYPE CHARACTERISTIC SP % DOMAIN RANGE
OP:1 owl:ObjectProperty   Property 1 Class 1 Class 2
DP:1 owl:DataProperty functional Property 2 Class 2 xsd:string

Individual Template Strings

If the TYPE is a defined class, owl:Individual, or owl:NamedIndividual, an instance will be created. If the TYPE does not include a defined class, that instance will have no class assertions. You may include a SPLIT= in TYPE if you wish to provide more than one class assertion for an individual.

Example of Individual Template Strings

Label Entity Type Property Assertions Different Individuals
LABEL TYPE I part_of DI %
Individual 1 Class 1 Individual 2  
Individual 2 Class 1   Individual 1

Merging

The template command has three options for merging, which are especially useful when chaining commands. First some terminology:

The three options can differ in which ontology is saved for the --output option and which is sent to the next command in the chain:

option --output output
no merge result result
merge before merged merged
merge after result merged

These three options are particularly useful when chaining commands. For instance, the merge-after option lets you save the result ontology separately, then send the merged ontology to the next command. See merge for more information on merge options, including --collapse-import-closure and --include-annotations.

If the command includes --ancestors, the result ontology will include the ancestors (from the input ontology) of the result ontology terms. Only the labels of the ancestors will be included.

Examples

Create an output ontology that includes the input ontology and the terms defined in the template:

robot template --merge-before --input edit.owl \
  --template template.csv --output results/template.owl

Create two outputs – the templated terms (uberon_template.owl) and the input ontology merged with the output ontology with an annotation (uberon_v2.owl):

robot template --merge-after \
  --input edit.owl \
  --template uberon_template.csv \
  --output results/uberon_template.owl \
  annotate --annotation rdfs:comment "UBERON with new terms" \
  --output results/uberon_v2.owl

Create an output ontology that consists of the template terms plus their dependencies (uberon_template_2.owl):

robot template --ancestors --input edit.owl \
  --template uberon_template.csv \
  --ontology-iri "https://github.com/ontodev/robot/examples/uberon_template_2.owl" \
  --output results/uberon_template_2.owl

Create an output ontology that includes the input ontology and the terms defined in the template, but keep the import statements* (test_template.owl):

robot template --merge-before \
  --input test.owl \
  --collapse-import-closure false \
  --template uberon_template.csv \
  --output results/test_template.owl

* NOTE: the imports would be merged into the output if --collapse-import-closure true is included instead.

Further examples can be found in the OBI repository


Error Messages

Annotation Property Characteristic Error

Annotation properties should not have any value in the CHARACTERISTIC column, if it exists. This type of logic for annotation properties is not supported in OWL.

Annotation Property Error

The annotation property provided could not be resolved. Check your template to ensure the provided annotation property is in a correct IRI or CURIE format. For legibility, using CURIEs is recommended, but you must ensure that the prefix is defined.

A rdfs:label
A http://www.w3.org/2000/01/rdf-schema#label

Annotation Property Type Error

The only valid PROPERTY_TYPE for an annotation property is subproperty. Other types of logic for annotation properties are not supported in OWL. If this column is left blank, it will default to subproperty.

Axiom Annotation Error

An axiom annotation is an annotation on an axiom, either a class axiom or another annotation. Because of this, any time >A is used, an annotation must be in the previous column. Any time >C is used, a class expression must be in the previous column.

A rdfs:label,>A rdfs:comment
C %,>C rdfs:comment

Class Type Error

The valid CLASS_TYPE values are: subclass, equivalent, and disjoint.

Class Type Split Error

A class row may only use one of: subclass, equivalent, and disjoint. To add other types of axioms on an OWL class, use a separate row.

Column Mismatch Error

There number of header columns (first row) must be equal to the number of template string columns (second row).

Data Property Characteristic Error

The only valid CHARACTERISTIC value for a data property is functional. Other types of property characteristics for data properties are not supported in OWL.

Datatype Error

The datatype provided in an AT template string could not be resolved. Check your template to ensure the provided datatype is in a correct IRI or CURIE format. For legibility, using CURIEs is recommended, but you must ensure that the prefix is defined.

AT rdfs:label^^xsd:string
AT rdfs:label^^http://www.w3.org/2001/XMLSchema#string

File Type Error

The --template option accepts the following file types: CSV, TSV, or TAB.

ID Error

Each template must have an ID column. Keep in mind that if the template has an ID column, but it is not filled in for a row, that row will be skipped.

Individual Type Error

The valid INDIVIDUAL_TYPE values are: named, same, and different.

Individual Type Split Error

An individual row may only use one of: named, same, and different. To add other types of axioms on an OWL individual, use a separate row.

IRI Error

The IRI provided as the value (in a row) to an AI template string could not be resolved as an IRI. Check your template to ensure the provided value is in a correct IRI or CURIE format. If using CURIEs, remember to ensure the prefix is defined.

Language Format Error

The template string for an AL annotation must always include @.

AL rdfs:label@en

Manchester Parse Error

The provided value cannot be parsed and may not be in proper Manchester syntax. See Manchester Syntax for more details. If you are using labels, make sure the labels are defined in the --input ontology or using the LABEL column. Also ensure that all properties use a label instead of a CURIE or IRI.

Merge Error

--merge-before and --merge-after cannot be used simultaneously.

Missing Template Error

You must specify at least one template with --template to proceed.

Missing Type Error

If no CLASS_TYPE column is included, ROBOT will default to using subclass. If a CLASS_TYPE column is included, though, each row must include a specified class type. If the CLASS_TYPE is left empty, this error message will be returned.

Multiple Property Type Error

While the PROPERTY_TYPE column may include multiple types, only one of the logical types is allowed in each column: subproperty, equivalent, disjoint, or (for object properties only) inverse. To add other types of axioms on an OWL property, use a separate row.

Null ID Error

An IRI cannot be created from the provided ID. This is most likely because the ID is not formatted properly, as an IRI or a CURIE.

Property Type Error

The valid PROPERTY_TYPE values are: subproperty, equivalent, disjoint, and (for object properties only) inverse.

Template File Error

The template cannot be found in the current directory. Make sure the file exists and your path is correct.

Typed Format Error

The template string for an AT annotation must always include ^^.

AT rdfs:label^^xsd:string

Unknown Characteristic Error

An invalid CHARACTERISTIC value was passed. If you are providing multiple characteristics, make sure to include SPLIT= in your template string. Valid characteristics are:

Unknown Template Error

Valid template strings are limited to the described above. If a different template string is provided, this error message will be returned.