ROBOT can export details about ontology entities as a table. At minimum, the
export command expects an input ontology (
--input), a set of column headers (
--header), and a file to write to (
robot export --input nucleus_part_of.owl \ --header "ID|LABEL" \ --export nucleus.csv
The following formats are currently supported:
tsv- tab-separated file, default format for unknown extensions
csv- comma-separated file
html- HTML table with with Bootstrap styling
html-list- HTML bullet list with Bootstrap styling
json- JSON file with values as arrays (except for ID/CURIE and IRI, which are single strings)
xlsx- Excel workbook with contents on first sheet
These can be specified with the
robot export --input nucleus_part_of.owl \ --header "LABEL|SubClass Of" \ --format html --export results/nucleus.html
If this option is not included,
export will predict the format based on the file extension:
robot export --input nucleus_part_of.owl \ --header "ID|LABEL|SubClasses" \ --export results/nucleus.json
--header option is a pipe-separated list of special keywords or properties used in the ontology. The columns in the
--header argument will exactly match the first line of the export file (the column headers).
--header types are supported:
IRI: creates an “IRI” column based on the full unique identifier
ID: creates an “ID” column based on the short form of the unique identifier (CURIE) - please note that all IRIs must have defined prefixes, or the full IRI will be returned.
LABEL: creates a “Label” column based on
rdfs:labelcan also be used in place of this column)
SYNONYMS: creates a “SYNONYMS” column based on all synonyms (oboInOwl exact, broad, narrow, related, or IAO alternative term)
SubClass Of: creates a “SubClass Of” column based on
SubClasses: creates a “SubClasses” column based on direct children of a class
Equivalent Class: creates an “Equivalent Classes” column based on
SubProperty Of: creates a “SubProperty Of” column based on
Equivalent Property: creates an “Equivalent Properties” column based on
Disjoint With: creates a “Disjoint With” column based on
Type: creates an “Instance Of” column based on
rdf:typefor named individuals or the OWL EntityType for all others (e.g.,
oboInOwl:hasDbXref). Any prefix used must be defined.
database_cross_reference). This label will also be used as the column header.
The first header in the
--header list is used to sort the rows of the export. You can change the column that is sorted on by including
--sort <header>. This can either be one header, or a pipe-separated list of headers that will be sorted in-order:
robot export --input nucleus_part_of.owl \ --header "ID|LABEL|SubClass Of" \ --sort "LABEL|SubClass Of" \ --export results/nucleus-sorted.csv
In the example above, the rows are first sorted on the
NAME field, and then sorted by
SubClass Of. This means that entities with the same parent will be grouped in alphabetical order.
--sort header starts with
^, the column will be sorted in reverse order.
robot export --input nucleus_part_of.owl \ --header "ID|LABEL|SubClass Of" \ --sort "^LABEL" \ --export results/nucleus-reversed.csv
All special keyword columns will include both named OWL objects (named classes, properties, and individuals) and anonymous expressions (class expressions, property expressions). When using another object or data property, the values will include both individuals and class expressions (from subclass or equivalent statements) in Manchester syntax. When using an annotation property, the literal value will be returned.
By default, multiple values in a cell are separated with a pipe character (
|). You can update this to anything you’d like with the
--split option. For example, you could separate with commas:
robot export --input nucleus_part_of.owl \ --header "NAME|SubClass Of" --split ", "
The output of any cell with multiple values is sorted in alphabetical order.
By default, the export includes details on the classes and individuals in an ontology. Properties are excluded. You can configure which types of entities you wish to include with the
--include <entity types> option. The
<entity types> argument is a space-, comma-, or tab-separated list of one or more of the following entity types:
For example, to return the details of individuals only:
robot --prefix "example: http://example.com/" \ export --input template.owl \ --header "ID|LABEL|Type" \ --include "individuals" \ --export results/individuals.csv
To return details of classes and properties:
robot export --input nucleus_part_of.owl \ --header "ID|LABEL|Type|SubClass Of|SubProperty Of" \ --include "classes properties" \ --export results/classes-properties.csv
--include option does not need to be specified if you are getting details on individuals and classes. If you do specify an
--include, it cannot be an empty string, as no entities will be included in the export.
Finally, the export will include both named entities and anonymous expressions (subclasses, equivalent classes, property expressions). You can change this with the
--entity-select ANY: include both named and anonymous expressions in all columns (default)
--entity-select NAMED: include only named entities in all columns
--entity-select ANONYMOUS: include only anonymous expressions in all columns
robot export --input nucleus_part_of.owl \ --header "LABEL|SubClass Of|part of" \ --entity-select NAMED \ --export results/nucleus.csv
Note that in the example above, the first two headers are special keywords and the third is the label of a property used in the ontology.
These export-wide defaults can be overridden in specific columns by including the keyword in a square-bracket-enclosed tag following the column name:
col name [ANY]: include both named entities and anonymous expressions in this column
col name [NAMED]: include only named entities in this column
col name [ANON]/
col name [ANONYMOUS]: include only anonymous expressions in this column
robot export --input nucleus.owl \ --header "ID|LABEL|SubClass Of [NAMED]|SubClass Of [ANON]|SubClass Of [ANY]" \ --export results/nucleus_export.csv
SubClass Of column in this output is different. The
SubClass Of [ANY] column is a combination of both
These tags can be combined with the rendering tags, for example:
robot export --input nucleus.owl \ --header "ID|LABEL|SubClass Of [NAME NAMED]|SubClass Of [ID NAMED]|SubClass Of [NAME ANON]|SubClass Of [ID ANON]" \ --export results/nucleus_logic.csv
It is not recommended to use the
ANON tag in combination with
LABEL, as if an entity used in an anonymous expression does not have a label, it will be rendered as an empty string. Additionally, the entity selection tags will have no effect on annotation property values.
Entities used in cell values are rendered by one of four different strategies:
NAME- render the entity by label (if label does not exist, entity is rendered by CURIE)
ID- render the entity by short form ID/CURIE
IRI- render the entity by full IRI
LABEL- render the entity by label ONLY (if label does not exist, entity is rendered as an empty string)
By default, values are rendered with the
NAME strategy. To update the strategy globally, you can use the
--entity-format option and provide one of the above values:
robot export --input nucleus_part_of.owl \ --header "ID|SubClass Of" \ --entity-format ID \ --entity-select NAMED \ --export results/nucleus-ids.csv
In the above example, all the “subclass of” values will be rendered by their short form ID.
You can also specify different rendering strategies for different columns by including the strategy name in a square-bracket-enclosed tag after the column name:
robot export --input nucleus_part_of.owl \ --header "rdfs:label|SubClass Of [ID]|SubClass Of [IRI]" \ --entity-select NAMED \ --export results/nucleus-iris.csv
These tags should not be used with the following default columns:
IRI as they will not change the rendered values.
These tags can be used for object and annotation property columns as well. When using these tags with annotation properties, the value in the cell will only change if the annotation value is an IRI. For literals, the annotation value will always be rendered the same, no matter what the tag is.
--entity-format values are:
--entity-select values are:
--include cannot be an empty string as there will be no entities to return details on. Note that classes and individuals are included by default and properties are excluded by default.
A property cannot be resolved, usually meaning that the label cannot be resolved. Ensure that the property label is defined in the input ontology or the column name provided is one of the special keywords.
A column header can only have one entity format tag in the square brackets after the column name.
A column header can only have one entity selection tag in the square brackets after the column name.
The following formats are currently supported:
xlsx. Please make sure you are using one of these formats.
The allowed tag values are: