PDRO ontology shows reduced search results for "acetaminophen"

[jvendetti]

Received the following problem report from an end user on the support list:

I use the Prescription of Drugs Ontology (PDRO) through REDCap, and REDCap's ontology service is managed through BioPortal.

I noticed around a month ago that the values in the Prescription of Drugs Ontology (PDRO) are suddenly very limited. For example, in both REDCap and on the BioPortal widget demonstration, if I start typing "acetaminophen," while I used to get a variety of options from DRON and CHEBI showing different brands, dosages, etc, now I only see two options: paracetamol and antidote to paracetamol poisoning.

The following REST call shows the two search results the user refers to:

https://data.bioontology.org/search?q=acetaminophen&ontologies=PDRO&display_context=false&display_links=false

Screenshot of the same results displayed in the Rails application:

[jvendetti]

This ontology has a complex set of imports. The top-level pdro.owl file has 12 direct imports, and ~70 indirect imports. A complete reprocessing of the ontology shows a number of imports are missing (no longer available at the advertised location):

http://purl.obolibrary.org/obo/dron/components/dron-ingredient.owl
http://purl.obolibrary.org/obo/dron/components/dron-ndc.owl
http://purl.obolibrary.org/obo/dron/components/dron-obsolete.owl
http://purl.obolibrary.org/obo/dron/components/dron-rxnorm.owl
http://purl.obolibrary.org/obo/dron/imports/apollo_sv_import.owl
http://purl.obolibrary.org/obo/dron/imports/bfo_import.owl
http://purl.obolibrary.org/obo/dron/imports/go_import.owl
http://purl.obolibrary.org/obo/dron/imports/iao_import.owl
http://purl.obolibrary.org/obo/dron/imports/obi_import.owl
http://purl.obolibrary.org/obo/dron/imports/ogms_import.owl
http://purl.obolibrary.org/obo/dron/imports/omo_import.owl
http://purl.obolibrary.org/obo/dron/imports/pato_import.owl
http://purl.obolibrary.org/obo/dron/imports/pr_import.owl
http://purl.obolibrary.org/obo/dron/imports/ro_import.owl
http://purl.obolibrary.org/obo/dron/imports/uo_import.owl
http://purl.obolibrary.org/obo/obi/dev/import/CLO_imports.owl
http://purl.obolibrary.org/obo/obi/dev/import/CL_imports.owl
http://purl.obolibrary.org/obo/obi/dev/import/IAO_imports.owl
http://purl.obolibrary.org/obo/obi/dev/import/UBERON_imports.owl
http://purl.obolibrary.org/obo/obi/dev/import/VO_imports.owl
http://purl.obolibrary.org/obo/iao/iao-edit.owl
http://purl.obolibrary.org/obo/ro/core-subset.owl

It's also worth noting that the Protege ontology editor shows similar search results as BioPortal, i.e., matching against classes with IDs of CHEBI:74529 and CHEBI:46195 because "acetaminophen" is present in either a synonym or definition attached to the those classes:

[jvendetti]

Graphical representation of the direct and indirect imports for this ontology:

[pfabry]

Hi,

I am one of the contributors to the PDRO ontology. We were also contacted by the same user regarding this issue. I must admit that I am quite surprised both by the nature of the problem and by the volume of imported content that you report for PDRO.

1. Reduced search results for "acetaminophen"

PDRO is an ontology of informational entities related to drug prescriptions, such as dosages, routes of administration, frequencies of administration, and other prescribing information. PDRO does not itself contain drug products or drug names such as "acetaminophen." However, it imports selected classes from ontologies such as DRON and CHEBI, which do contain such entities.

I am not familiar with the details of how the BioPortal browser handles imported content. For example, if a user accesses the class "drug product" through PDRO, does BioPortal expose all subclasses asserted in DRON, even when they are not explicitly referenced in PDRO? If so, I suspect that the issue may be related to a recent DRON update that introduced two distinct classes: DRON:00000074 ("drug product") and DRON:00000005 ("clinical drug product"). Drug names now appear to be classified under the latter.

As a result, when a user searches for "acetaminophen," they may only retrieve the CHEBI class and no longer find the corresponding DRON entries through the "drug product" hierarchy. However, this raises another question: although the label and modeling appear to have changed, the IRI has remained the same. I would therefore not have expected this change to affect search results, so I may be missing some aspect of how BioPortal indexes imported content.

2. PDRO imports

I am genuinely surprised by the number of imported classes reported for PDRO. While browsing the ontology through its BioPortal page, I also encountered classes that appear entirely unrelated to PDRO, such as "astronomical body part" and "outer space."

Furthermore, downloading the ontology through the "Download latest submission" option produces an ontology containing more than 20,000 classes and approximately 250,000 axioms, which is vastly larger than the ontology we maintain.

For comparison, the current version of PDRO is available on GitHub:

https://github.com/OpenLHS/PDRO

This repository contains the merged ontology. The imported ontologies are stored locally here:

https://github.com/OpenLHS/PDRO/tree/master/src/imports

There are currently 14 import modules, which is admittedly a substantial number. However, the ontology itself contains only about 310 classes and 3,300 axioms. The figures reported by BioPortal therefore seem inconsistent with the actual contents of the ontology.

We have unfortunately had limited time to maintain and update PDRO in recent years, and a comprehensive revision would require resources that are not currently available. Nevertheless, a relatively straightforward improvement would be to update the DRON import in PDRO to resolve the apparent inconsistencies between "drug product" and "clinical drug product."

Please let me know whether this could be a plausible explanation for the issue you are observing, or whether there are additional details from the BioPortal side that might help clarify the situation.

Regards,

Paul