Getting Relationships

Hi. I have used pronto for the last few months. First of all, kudos to the coders, it's great work.

Coming to the issue I am facing, I initially thought that pronto is able to extract all the relationships mentioned in an owl file, no matter how convoluted (read reified) the relations are. But then, I recently understood that there are some limitations.

For example, while parsing Disease Ontology OWL file, I saw that some relations were extracted while others were not:
For the following class:
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A primary bacterial infectious disease that results_in infection, has_material_basis_in Listeria monocytogenes, which is transmitted_by ingestion of contaminated food or raw milk or transmitted_by congenital method. Ingestion of Listeria by pregnant women has_symptom nausea, has_symptom vomiting, has_symptom diarrhea, has_symptom fever, has_symptom malaise, has_symptom back pain, and has_symptom headache. Maternal infection with Listeria can result in chorioamnionitis, premature labor, spontaneous abortion, or stillbirth.
ICD10CM:A32
ICD9CM:027.0
MESH:D008088
NCI:C82994
SNOMEDCT_US_2021_03_01:186315001
UMLS_CUI:C0023860
Infection by Listeria monocytogenes
Listeria infection
disease_ontology
DOID:11573



listeriosis




A primary bacterial infectious disease that results_in infection, has_material_basis_in Listeria monocytogenes, which is transmitted_by ingestion of contaminated food or raw milk or transmitted_by congenital method. Ingestion of Listeria by pregnant women has_symptom nausea, has_symptom vomiting, has_symptom diarrhea, has_symptom fever, has_symptom malaise, has_symptom back pain, and has_symptom headache. Maternal infection with Listeria can result in chorioamnionitis, premature labor, spontaneous abortion, or stillbirth.

url:http://www.nlm.nih.gov/medlineplus/ency/article/001380.htm

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pronto was not able to extract these relations among others:
IDO_0000664 NCBITaxon_1637
IDO_0000664 NCBITaxon_1639

but pronto was able to extract these relations:
RO_0002452 SYMP_0000458
RO_0002452 SYMP_0000570
RO_0002452 SYMP_0019145

Can anyone point me to method/strategies using which I can extract all of these relations?
Thanks,
Krishanu