-
Notifications
You must be signed in to change notification settings - Fork 29
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Adding more notebook examples of associations (#636)
* Adding more notebook examples of associations Adding hpoa g2d as a source * regenerated notebook * regenerated notebook * lint
- Loading branch information
Showing
23 changed files
with
109,217 additions
and
24,299 deletions.
There are no files selected for viewing
Large diffs are not rendered by default.
Oops, something went wrong.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,235 @@ | ||
{ | ||
"cells": [ | ||
{ | ||
"cell_type": "code", | ||
"execution_count": 1, | ||
"id": "c87fdb82", | ||
"metadata": {}, | ||
"outputs": [], | ||
"source": [ | ||
"alias hp runoak -i sqlite:obo:hp" | ||
] | ||
}, | ||
{ | ||
"cell_type": "code", | ||
"execution_count": 4, | ||
"id": "70661358", | ||
"metadata": {}, | ||
"outputs": [ | ||
{ | ||
"name": "stdout", | ||
"output_type": "stream", | ||
"text": [ | ||
"subject_termset:\r\n", | ||
" HP:0100752:\r\n", | ||
" id: HP:0100752\r\n", | ||
" label: Abnormal liver lobulation\r\n", | ||
" HP:0007042:\r\n", | ||
" id: HP:0007042\r\n", | ||
" label: Focal white matter lesions\r\n", | ||
"object_termset:\r\n", | ||
" HP:0006555:\r\n", | ||
" id: HP:0006555\r\n", | ||
" label: Diffuse hepatic steatosis\r\n", | ||
" HP:0025517:\r\n", | ||
" id: HP:0025517\r\n", | ||
" label: Hypoplastic hippocampus\r\n", | ||
"subject_best_matches:\r\n", | ||
" HP:0007042:\r\n", | ||
" match_source: HP:0007042\r\n", | ||
" score: 6.775984316965229\r\n", | ||
" similarity:\r\n", | ||
" subject_id: HP:0007042\r\n", | ||
" object_id: HP:0025517\r\n", | ||
" ancestor_id: HP:0100547\r\n", | ||
" ancestor_label: Abnormal forebrain morphology\r\n", | ||
" ancestor_information_content: 6.775984316965229\r\n", | ||
" jaccard_similarity: 0.5\r\n", | ||
" phenodigm_score: 1.8406499282814792\r\n", | ||
" match_source_label: Focal white matter lesions\r\n", | ||
" match_target: HP:0025517\r\n", | ||
" match_target_label: Hypoplastic hippocampus\r\n", | ||
" HP:0100752:\r\n", | ||
" match_source: HP:0100752\r\n", | ||
" score: 8.632074905566515\r\n", | ||
" similarity:\r\n", | ||
" subject_id: HP:0100752\r\n", | ||
" object_id: HP:0006555\r\n", | ||
" ancestor_id: HP:0410042\r\n", | ||
" ancestor_label: Abnormal liver morphology\r\n", | ||
" ancestor_information_content: 8.632074905566515\r\n", | ||
" jaccard_similarity: 0.5\r\n", | ||
" phenodigm_score: 2.0775075096815554\r\n", | ||
" match_source_label: Abnormal liver lobulation\r\n", | ||
" match_target: HP:0006555\r\n", | ||
" match_target_label: Diffuse hepatic steatosis\r\n", | ||
"object_best_matches:\r\n", | ||
" HP:0006555:\r\n", | ||
" match_source: HP:0006555\r\n", | ||
" score: 8.632074905566515\r\n", | ||
" similarity:\r\n", | ||
" subject_id: HP:0100752\r\n", | ||
" object_id: HP:0006555\r\n", | ||
" ancestor_id: HP:0410042\r\n", | ||
" ancestor_label: Abnormal liver morphology\r\n", | ||
" ancestor_information_content: 8.632074905566515\r\n", | ||
" jaccard_similarity: 0.5\r\n", | ||
" phenodigm_score: 2.0775075096815554\r\n", | ||
" match_source_label: Diffuse hepatic steatosis\r\n", | ||
" match_target: HP:0100752\r\n", | ||
" match_target_label: Abnormal liver lobulation\r\n", | ||
" HP:0025517:\r\n", | ||
" match_source: HP:0025517\r\n", | ||
" score: 6.775984316965229\r\n", | ||
" similarity:\r\n", | ||
" subject_id: HP:0007042\r\n", | ||
" object_id: HP:0025517\r\n", | ||
" ancestor_id: HP:0100547\r\n", | ||
" ancestor_label: Abnormal forebrain morphology\r\n", | ||
" ancestor_information_content: 6.775984316965229\r\n", | ||
" jaccard_similarity: 0.5\r\n", | ||
" phenodigm_score: 1.8406499282814792\r\n", | ||
" match_source_label: Hypoplastic hippocampus\r\n", | ||
" match_target: HP:0007042\r\n", | ||
" match_target_label: Focal white matter lesions\r\n", | ||
"average_score: 7.704029611265872\r\n", | ||
"best_score: 8.632074905566515\r\n" | ||
] | ||
} | ||
], | ||
"source": [ | ||
"hp termset-similarity \"Abnormal liver lobulation\" \"Focal white matter lesions\" @ \"Diffuse hepatic steatosis\" \"Hypoplastic hippocampus\"" | ||
] | ||
}, | ||
{ | ||
"cell_type": "code", | ||
"execution_count": 5, | ||
"id": "e1138d8f", | ||
"metadata": {}, | ||
"outputs": [], | ||
"source": [ | ||
"# alias hp2 runoak -i semsimian:sqlite:obo:hp" | ||
] | ||
}, | ||
{ | ||
"cell_type": "code", | ||
"execution_count": 7, | ||
"id": "8838921c", | ||
"metadata": {}, | ||
"outputs": [ | ||
{ | ||
"name": "stdout", | ||
"output_type": "stream", | ||
"text": [ | ||
"\u001b[2K[00:00:00] Building all X all pairwise similarity: \u001b[36m████████████████████████████████████████\u001b[34m\u001b[0m\u001b[0m 100%Building all X all pairwise similarity: \u001b[36m████████████████████░\u001b[34m░░░░░░░░░░░░░░░░░░░\u001b[0m\u001b[0m 50%subject_termset:\n", | ||
" HP:0100752:\n", | ||
" id: HP:0100752\n", | ||
" label: Abnormal liver lobulation\n", | ||
" HP:0007042:\n", | ||
" id: HP:0007042\n", | ||
" label: Focal white matter lesions\n", | ||
"object_termset:\n", | ||
" HP:0006555:\n", | ||
" id: HP:0006555\n", | ||
" label: Diffuse hepatic steatosis\n", | ||
" HP:0025517:\n", | ||
" id: HP:0025517\n", | ||
" label: Hypoplastic hippocampus\n", | ||
"subject_best_matches:\n", | ||
" HP:0100752:\n", | ||
" match_source: HP:0100752\n", | ||
" score: 8.634374534720992\n", | ||
" similarity:\n", | ||
" subject_id: HP:0100752\n", | ||
" object_id: HP:0006555\n", | ||
" ancestor_id: HP:0410042\n", | ||
" ancestor_label: Abnormal liver morphology\n", | ||
" ancestor_information_content: 8.634374534720992\n", | ||
" jaccard_similarity: 0.5\n", | ||
" phenodigm_score: 2.077784220596666\n", | ||
" match_source_label: Abnormal liver lobulation\n", | ||
" match_target: HP:0006555\n", | ||
" match_target_label: Diffuse hepatic steatosis\n", | ||
" HP:0007042:\n", | ||
" match_source: HP:0007042\n", | ||
" score: 6.778283946119706\n", | ||
" similarity:\n", | ||
" subject_id: HP:0007042\n", | ||
" object_id: HP:0025517\n", | ||
" ancestor_id: HP:0100547\n", | ||
" ancestor_label: Abnormal forebrain morphology\n", | ||
" ancestor_information_content: 6.778283946119706\n", | ||
" jaccard_similarity: 0.5\n", | ||
" phenodigm_score: 1.8409622410739046\n", | ||
" match_source_label: Focal white matter lesions\n", | ||
" match_target: HP:0025517\n", | ||
" match_target_label: Hypoplastic hippocampus\n", | ||
"object_best_matches:\n", | ||
" HP:0006555:\n", | ||
" match_source: HP:0006555\n", | ||
" score: 8.634374534720992\n", | ||
" similarity:\n", | ||
" subject_id: HP:0100752\n", | ||
" object_id: HP:0006555\n", | ||
" ancestor_id: HP:0410042\n", | ||
" ancestor_label: Abnormal liver morphology\n", | ||
" ancestor_information_content: 8.634374534720992\n", | ||
" jaccard_similarity: 0.5\n", | ||
" phenodigm_score: 2.077784220596666\n", | ||
" match_source_label: Diffuse hepatic steatosis\n", | ||
" match_target: HP:0100752\n", | ||
" match_target_label: Abnormal liver lobulation\n", | ||
" HP:0025517:\n", | ||
" match_source: HP:0025517\n", | ||
" score: 6.778283946119706\n", | ||
" similarity:\n", | ||
" subject_id: HP:0007042\n", | ||
" object_id: HP:0025517\n", | ||
" ancestor_id: HP:0100547\n", | ||
" ancestor_label: Abnormal forebrain morphology\n", | ||
" ancestor_information_content: 6.778283946119706\n", | ||
" jaccard_similarity: 0.5\n", | ||
" phenodigm_score: 1.8409622410739046\n", | ||
" match_source_label: Hypoplastic hippocampus\n", | ||
" match_target: HP:0007042\n", | ||
" match_target_label: Focal white matter lesions\n", | ||
"average_score: 7.706329240420349\n", | ||
"best_score: 8.634374534720992\n" | ||
] | ||
} | ||
], | ||
"source": [ | ||
"!runoak -i semsimian:sqlite:obo:hp termset-similarity \"Abnormal liver lobulation\" \"Focal white matter lesions\" @ \"Diffuse hepatic steatosis\" \"Hypoplastic hippocampus\"" | ||
] | ||
}, | ||
{ | ||
"cell_type": "code", | ||
"execution_count": null, | ||
"id": "0f43896e", | ||
"metadata": {}, | ||
"outputs": [], | ||
"source": [] | ||
} | ||
], | ||
"metadata": { | ||
"kernelspec": { | ||
"display_name": "Python 3 (ipykernel)", | ||
"language": "python", | ||
"name": "python3" | ||
}, | ||
"language_info": { | ||
"codemirror_mode": { | ||
"name": "ipython", | ||
"version": 3 | ||
}, | ||
"file_extension": ".py", | ||
"mimetype": "text/x-python", | ||
"name": "python", | ||
"nbconvert_exporter": "python", | ||
"pygments_lexer": "ipython3", | ||
"version": "3.9.5" | ||
} | ||
}, | ||
"nbformat": 4, | ||
"nbformat_minor": 5 | ||
} |
Oops, something went wrong.