MIXS not showing labels and wrong CURIEs

[matentzn]

Describe the bug
A clear and concise description of what the bug is.

1. Label not shown
2. CURIE rendering is wrong for the MIXS namespace (123 instead of MIXS:123)
3. Definition is missing

see for more details here: GenomicsStandardsConsortium/mixs#1076 (comment)

To Reproduce

Steps to reproduce the behavior:

1. See https://www.ebi.ac.uk/ols4/ontologies/gscmixs/properties/https%253A%252F%252Fw3id.org%252Fmixs%252F0001107

Expected behavior
A clear and concise description of what you expected to happen.

You should see a label and CURIE.

Screenshots

Upload minimal complete example

Additional context

The RDF in the ontology looks like this:

MIXS:0001107 a owl:DatatypeProperty ;
    rdfs:label "samp_name" ;
    dcterms:title "sample name" ;
    schema1:keywords "sample" ;
    rdfs:range xsd:string ;
    skos:definition "A local identifier or name that for the material sample used for extracting nucleic acids, and subsequent sequencing. It can refer either to the original material collected or to any derived sub-samples. It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible. INSDC requires every sample name from a single Submitter to be unique. Use of a globally unique identifier for the field source_mat_id is recommended in addition to sample_name" ;
    skos:inScheme <https://w3id.org/mixs> ;
    MIXS:Preferred_unit "" .

My first instinct: OLS does not have MIXS: <https://w3id.org/mixs/> in its internal prefix map causing at least some of the rendering issues.

[jamesamcl]

Related to #792 - I will handle this one

[turbomam]

Thanks @jamesamcl . @Woolly-at-EBI and I were were wondering if we could have a short Zoom with you or one of your delegates.

The way I see it, there are two phases of getting MIxS into OLS:

• generating the OWL artifact with linkml tools
• importing the OWL artifact into OLS in an optional way

I think we have done a pretty good job of the OWL generation

• https://github.com/GenomicsStandardsConsortium/mixs/blob/main/project/owl/mixs.owl.ttl
• https://bioportal.bioontology.org/ontologies/MIXS?p=properties

But I feel clueless when it comes to configuring the import into OLS. And I am going to want to request the addition of this pretty soon:

https://github.com/berkeleybop/metpo

[turbomam]

According to Claude:

@jamesamcl you and your colleagues probably already know all of this

Root Causes of MIxS Display Issues in OLS

Problem 1: preferredPrefix is lowercase gscmixs instead of MIXS

Current config:
"preferredPrefix": "gscmixs"

Should be:
"preferredPrefix": "MIXS"

This is why CURIEs show as 0001107 instead of MIXS:0001107. The preferredPrefix controls how CURIEs are displayed.

---

Problem 2: base_uri uses a CURIE instead of a full URI

Current config:
"base_uri": ["MIXS:"]

Should be:
"base_uri": ["https://w3id.org/mixs/"]

Compare to EFO which correctly uses a full URI:
"base_uri": ["http://www.ebi.ac.uk/efo/EFO_"]

OLS uses base_uri to identify which terms belong to this ontology. Since MIXS: is a CURIE that OLS doesn't know how to expand, it can't properly match terms.

---

Problem 3: label_property includes owl:DatatypeProperty (a type, not a property!)

Current config:
"label_property": [
"owl:DatatypeProperty", ← THIS IS WRONG
"rdfs:label",
"dcterms:title",
"schema1:keywords"
]

owl:DatatypeProperty is the RDF type of MIxS terms (like MIXS:0001107 a owl:DatatypeProperty), not a property used for labels. Someone confused the type with label properties.

Should be:
"label_property": "rdfs:label"
or if you want dcterms:title as an alternative:
"label_property": ["rdfs:label", "dcterms:title"]

---

The actual term in the OWL file looks correct:

MIXS:0001107 a owl:DatatypeProperty ;
rdfs:label "samp_name" ;
dcterms:title "sample name" ;
skos:definition "A local identifier or name that for the material sample..." ;

The OWL file has rdfs:label and skos:definition correctly. The problem is entirely in the OLS config, not your gen-owl output.