Demonstration and Queries

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Competency Question 1
What is the suggested pharmaceutical intervention for a given patient, Sam?

Explanation: Here we provide the resulting recommendation for the patient sam.
The ADA 2018 guidelines have a list of requirements for diagnosing a patient with diabetes, and these guidelines are to assist in detecting the extent of severity of the illness, and both the patient's comorbid conditions and their contraindications. These details will be used to provide pharmaceutical treatment suggestions for a patient. The suggestions are generated by the help of SWRL rules that a backed by the guidelines. After the rules generate the suggested treatment plan, they are returned to the physician using the SPARQL query. The query first searches for all the patients, then it matches the patients to all their treatment plans, then it does a regular expression filter for the specific patient (in this case Sam). it returns the name of the patient and the suggested pharmaceutical treatment plan.

Click here to see the full Treatment Document static demo

Competency Question 2
What are the toxicities of metformin and of drugs similar to metformin?

Explanation:In this question we are trying to provide a physician with a comprehensive list of possible toxicities to a suggested drug to a patient, in this case, metformin. In order to give the physician a broad sense of the toxicities, we are providing not only the possible toxicities of metformin, but also of a drug similar to metformin. Here we are assuming that drugs with the same primary target and with the same interaction with this target, are similar and will have related toxicities. Thus, to give a broader sense of the toxicity of the drug, metformin, we are assuming that it can also have the the toxicity of its similar drug. Therefore to answer our question, we first need to find a drug that is similar to metformin by target and target mechanism (query 1), list the toxicities of both metformin and its similar drug (query 2).

Click here to see the full Toxicity static demo

Competency Question 3
Do the ADA guidelines cover a diverse population, such that an African American diabetic patient on Metformin, can receive a recommendation?

Explanation: In this question we are trying to provide a physician with a comprehensive description of the characteristics, (in this case racial diversity) of patient groups utilized in research studies, exposing findings of effective treatment of diabetes with Metformin, or the long term effects of the same. A physician is probably interested to see if the study from our catalog, detailing the Long term effects of Metformin ( a treatment prescribed by the physician ) , is applicable to his/her patient solely on their African American descent. A query - Query1, is triggered to this particular study that matches the physician’s query criteria of “dbt:Intervention - dbt-i:Metformin” and “dbt:AfricanAmerican” to “dbt:ClinicalTrial” with a title of “Long-term Metformin Use and Vitamin B12 Deficiency in the Diabetes Prevention Program Outcomes Study”. However the query surfaces the results that the study doesn’t particularly have a clear stated African American population, and under the closed world assumption the physician is shown a AfricanAmerican racial percentage representation of 0.

However the physician is still curious to see the general applicability of his patient’s race to the populations of patients utilized in Metformin Clinical Trials, This time round just to ensure that the physician gets a clearer idea of the racial diversity, he/she makes a broader Cohort Q2 request to find all “dbt:Race” studied in “dbt:ClinicalTrial” with “dbt:PatientGroup” ( owl:Class of dbt:Patient in the alternate representation) administered a “dbt-i:Medicalntervention” of “dbt-i:Metformin”. The physician is shown race percentages of races - {White, AfricanAmerican, Asian, Other} represented in the only other study - “10-Year Follow-up of Intensive Glucose Control in Type 2 Diabetes“ ingested.

Note on Technical Representation: We have two methods of representing descriptive statistics in our project, one which doesn’t involve punning and reification and is realizable in the RDF world alone; and another which requires us to use N-Triples format and necessitates the need for defining descriptions and definitions on sets of patients represented as ‘ow:Class’es. Our alternate approach is inspired and borrowed from James McCusker et al’s paper on “A Provenance-Driven Semantics of Aggregation”. We have two query versions for our below two cohort queries, and each of them need to be run against the latest versions of our separate Individuals files - non-aggregative representation individuals file and alternate triple representation individuals file respectively. Please refer to queries from “Query for Alternate Representation” if utilizing the alternate N-Triples representation.

Example of alternate representation on a feature like age

  1. dbt-i:Sam a dbt:Patient;
  2. sio:hasAttribute [
  3. a dbt:Age;
  4. sio:hasValue 37
  5. ].
  6.  
  7.  
  8. dbt-i:MetforminConventionalTherapyPatient a owl:Class;
  9. rdfs:subClassOf dbt:Patient;
  10. sio:hasAttribute [
  11. a dbt:Age;
  12. sio:hasAttribute
  13. [ a sio:Mean; sio:hasValue 63],
  14. [ a sio:StandardDeviation; sio:hasValue 9]
  15. ].

In the above representation, we see how the same class dbt:Age can be used to represent age of a patient Sam, and descriptive statistics on age for a patient group adminstered Metformin with a conventional therapy.

Click here to see the full Cohort static demo

This was developed as a part of the Ontology Engineering course supervised by Prof. Deborah McGuinness and Ms. Elisa Kendall at RPI in Fall'18