*** FOR RESEARCH PURPOSES ONLY ***
Proof-of-concept for reasoning over the SemMedDB knowledge base, using miniKanren + heuristics + indexing.
./code/study-imatinib.rkt contains the most iteresting examples currently.
TODO: add SemMedDB files, along with terms of use information for SemMedDB.
TODO: add simple instructions for running the queries.
https://download.racket-lang.org/
You'll need to obtain the full data from: https://skr3.nlm.nih.gov/SemMedDB/
A small sample, code/sample_semmed.csv, is provided to demonstrate the format expected for processing.
Given semmed.csv, Run these commands from the code directory:
mkdir semmed
racket csv-semmed-ordered-unique-enum.rkt semmed.csv semmed
racket csv-semmed-simplify.rkt semmed.csv semmed
racket semmed-index-predicate.rkt semmed
Depending on the size of the CSV you're using, these commands could take up to a few hours to process all records.
The GUI is a convenient way to express some forms of simple queries. For more power, see the section on running queries programmatically.
From the code directory, run racket gui-simple.rkt to start the GUI.
As you interact, the console will display additional information in some cases.
- When clicking on results, the corresponding PubMed URLs will be printed for your convenience. If you're running on OSX within iTerm2, you can CMD+click a URL to open it in the browser.
- When querying with synthetic predicates such as
increases[*]/decreases[*], the results will not be displayed in the GUI, but will instead be continuously streamed to the console.
Start with code/tacrine.rkt code/imatinib-query.rkt, which includes queries taken from code/study-imatinib.rkt, and also includes a high-level description of the queries.
Take a look at the various study-*.rkt files in the code directory for examples. You can run these from the command line, e.g., racket study-imatinib.rkt.
To write your own queries, either as a new *.rkt file or interactively, start with:
(require "mk-db.rkt")
to load the database and its indices (this will take several seconds, so be patient). Once loaded, you will have access to the full underlying miniKanren language, plus the new semmed-specific relations:
(concepto c)
(fuzzy-concepto name c)
(cuio c cui)
(cui*o c cui*)
(edgeo `(,subject-concept ,object-concept ,predicate ,subject-type ,object-type ,pubref))
which you can compose freely in queries. Being that mediKanren is an embedded DSL, you also have access to Racket for metaprogramming.