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Adding more notebook examples of associations (#636)
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* Adding more notebook examples of associations

Adding hpoa g2d as a source

* regenerated notebook

* regenerated notebook

* lint
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@cmungall
cmungall authored Aug 17, 2023
1 parent 4a306aa commit 678dfdd
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1,378 changes: 323 additions & 1,055 deletions notebooks/Commands/Associations.ipynb
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235 changes: 235 additions & 0 deletions notebooks/Commands/TermsetSimilarity.ipynb
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{
"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
}
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