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mediKanren 2

Prerequisites

Loading databases

Running queries

Lightweight reasoning

Relations for lightweight reasoning are defined in lw-reasoning.rkt, and are currently under development and subject to change.

Here is an example of getting synonyms and subclasses:

(require "lw-reasoning.rkt")

(define meformin "CHEBI:6801")

;; get diseases/phenotypes treated by meformin and its synonyms
(define treated-diseases
  (run* disease-or-phen
    (fresh (drug)
      (kgx-synonym drug meformin)
      (triple drug "biolink:treats" disease-or-phen)
      (conde ((is-a disease-or-phen "biolink:PhenotypicFeature")) ; *
             ((is-a disease-or-phen "biolink:Disease"))))))

(get-names-ls treated-diseases)

;; get subclasses
(get-names-ls
 (apply append
        (map (lambda (disease)
               (run* d (subclass-of+ d disease)))
             treated-diseases)))

TRAPI service

Running the TRAPI service:

racket server.rkt

exposes the following endpoints on port 8384:

/pmi/v1/query, duplicated on /query

Main TRAPI endpoint, accepts TRAPI 1.1 requests. Requests are run one at a time, on a first-received basis, and are limited to 10 minutes query time.

/

Simple Web UI for testing queries.

/health

Simple health check: runs a trivial query and reports on query time. If other queries are running and/or queued to be run, this query will return only after the others have terminated or timed out.