From 37568f5da56622c2fd5dd74499a696d38fafbc68 Mon Sep 17 00:00:00 2001 From: Dan O'Donovan <dan.odonovan@gmail.com> Date: Tue, 14 Nov 2023 10:20:27 +0000 Subject: [PATCH] docs: notes on results of commands --- README.md | 36 ++++++++++++++++++++++++++++++++++++ 1 file changed, 36 insertions(+) diff --git a/README.md b/README.md index 3e7f412..25a9ca3 100644 --- a/README.md +++ b/README.md @@ -65,6 +65,34 @@ healx-chains \ --predictions-filter-file data/parkinson-disease-filter/predictions.txt \ --explanations-filter-file data/parkinson-disease-filter/prioritised-edge-types.txt ``` +Results are written to an evidence chains file `results/evidence-chains.jsonl` in the JSONL format. Each line contains +a generated "chain" prediction with the following example structure + +```json +{ + "prediction": "methixene_COMPOUND", + "prediction_score": 0.08924107199497017, + "start_node": "methixene_COMPOUND", + "end_node": "parkinson_disease_DISEASE", + "metapath": [ + { + "label": "COMPOUND_inhibits_GENE", + "reversed": false + }, + { + "label": "DISEASE_associates_GENE", + "reversed": true + } + ], + "path_score": 0.005949453701297636, + "path": [ + "methixene_COMPOUND", + "htr2c_GENE", + "parkinson_disease_DISEASE" + ] +} +``` +we can expect to find thousands of chains in this file. ### Filter the chains for Parkinson Disease @@ -79,3 +107,11 @@ healx-filter \ data/parkinson-disease-filter/prioritised-edge-types.txt \ --filtered-evidence-chains-file filtered-evidence-chains.txt ``` + +which will produce a filtered evidence chains file in text format, `filtered-evidence-chains.txt` - one line per text +chain. An example of one of the lines from this file are + +``` +AMANTADINE inhibits CHRNA3 participates NEUROACTIVE_LIGAND-RECEPTOR_INTERACTION involves CABERGOLINE in_trial_for PARKINSON_DISEASE +``` +.