1. uriexpr_contains

This is a filter function. It allows to select mappings depending on whether a URI Expression contains a given value in one of its slots.

It takes (at least) three arguments:

• the URI Expression whose contents should be tested; placeholders are expanded in this argument, which will be typically be set to a mapping’s subject or object ID;
• the name of a URI Expression slot;
• the expected value of that slot.

The function may take additional pairs of arguments to check several slots in the same call.

For example, a mapping with the following subject ID:

https://example.org/schema/0001/(disease:'MONDO:1234',phenotype:'HP:5678')

would be selected by the following filter (assuming the MONDO prefix name has been duly declared):

uriexpr_contains(%{subject_id}, 'disease', MONDO:*) -> ...;

2. uriexpr_slot_value

This is a format modifier function that allows to extract the value of a particular slot within a URI Expression.

It takes a single mandatory argument, which is the name of the slot whose value should be extracted.

For example, assuming the same subject ID as in the previous section, the following placeholder:

the following placeholder

"%{subject_id|uriexpr_slot_value(phenotype)}"

will insert the value HP:5678. Note that if the HP prefix name is declared, the value of the slot will be expanded to its full-length form. Append the short modifier if you specifically want the short form of the identifier.

3. uriexpr_expand

This is a format modifier function that is specific to the SSSOM/T-OWL dialect. It expands a URI Expression value into a OWL class expression according to a pre-defined template.

The template must be declared at the beginning of the SSSOM/T-OWL ruleset using the uriexpr_declare_format directive, which expects two arguments:

• the name of the URI Expression schema (the first part of the URI Expression),
• and the template to use for URI Expressions that follow that schema; in that template, names enclosed in curly brackets (like this: {name}) represent the slots of the URI Expression.

Here is a complete example:

prefix SCHEMA: <http://example.org/schema/>
prefix BFO:    <http://purl.obolibrary.org/obo/BFO_>
prefix MONDO:  <http://purl.obolibrary.org/obo/MONDO_>
prefix HP:     <http://purl.obolibrary.org/obo/HP_>
prefix DO:     <http://purl.obolibrary.org/obo/DOID_>

uriexpr_declare_format(SCHEMA:0001, "(<{disease}> and (BFO:0000051 some <{phenotype}>))");

subject==SCHEMA:0001* -> create_axiom("%object_id EquivalentTo: %{subject_id|uriexpr_expand}");

When applied to the following mapping:

that ruleset would create the following axiom:

DO:3333 EquivalentTo: MONDO:1234 and (BFO:0000051 some HP:5678)

4. uriexpr_toext

This is a preprocessor function that allows to encode the components of a URI Expression into a mapping’s extension slots.

It takes a single argument which is the URI Expression to encode. Placeholders are expanded in that argument.

If the argument does indeed contain a URI Expression, the value of each component in that expression will be stored into a SSSOM extension slot whose property name will be formed by concatenating the name of the URI Expression schema and the name of the slot.

The function has no effect is the argument does not contain a URI Expression.

For example, a mapping with the following subject ID:

https://example.org/schema/0001/(disease:'MONDO:1234',phenotype:'HP:5678')

would be turned into an identical mapping but with two additional extension slots:

• a slot identified by the property https://example.org/schema/0001/disease, containing the value http://purl.obolibrary.org/obo/MONDO_1234;
• and a slot identified by the property https://example.org/schema/0001/phenotype, containing the value http://purl.obolibrary.org/obo/HP_5678.