{ "cells": [ { "cell_type": "markdown", "id": "4eee119c-f6cf-4d06-b7f2-cc90bcdbeb3c", "metadata": {}, "source": [ "# HPO CLI Examples\n", "\n", "The Human Phenotype Ontology (HPO) provides a standardized vocabulary of phenotypic abnormalities encountered in human disease. Each term in the HPO describes a phenotypic abnormality, such as Atrial septal defect. \n", "\n", "__OBO URL__ https://obofoundry.org/ontology/hp" ] }, { "cell_type": "markdown", "id": "e174fee2-18c6-4fc5-aa39-19ca83aa5680", "metadata": {}, "source": [ "## Initial configuration\n", "\n", "Here we set up alias and convenience functions for use in this Jupyter notebook.\n", "\n", "First we will set up an alias for accessing the sqlite version of HPO.\n", "\n", "__Note__ this only works in a Jupyter notebook context. On the command line, instead do\n", "`alias hp=runoak -i sqlite:obo:hp`" ] }, { "cell_type": "code", "id": "ec1bbc3d-7c2f-4625-a604-093409dcbab7", "metadata": { "ExecuteTime": { "end_time": "2024-10-17T00:54:58.292851Z", "start_time": "2024-10-17T00:54:58.289874Z" } }, "source": [ "from openpyxl.styles.builtins import output\n", "\n", "alias hp runoak -i sqlite:obo:hp" ], "outputs": [], "execution_count": 7 }, { "metadata": { "ExecuteTime": { "end_time": "2024-10-17T00:53:44.605639Z", "start_time": "2024-10-17T00:53:44.463758Z" } }, "cell_type": "code", "source": "!mkdir -p output", "id": "faeea5610c6b9c35", "outputs": [], "execution_count": 4 }, { "metadata": { "ExecuteTime": { "end_time": "2024-10-17T00:54:13.859665Z", "start_time": "2024-10-17T00:54:13.856511Z" } }, "cell_type": "code", "source": "import pandas as pd", "id": "5ed2084fe1c2904a", "outputs": [], "execution_count": 6 }, { "metadata": {}, "cell_type": "markdown", "source": "## Summary Statistics", "id": "fece60d46efbc6f2" }, { "cell_type": "code", "id": "1d662c04-e674-4979-8ee9-c8984041eebc", "metadata": { "ExecuteTime": { "end_time": "2024-10-17T00:59:06.657869Z", "start_time": "2024-10-17T00:56:36.331268Z" } }, "source": "hp statistics --group-by-prefix -O csv -o output/stats.tsv", "outputs": [], "execution_count": 9 }, { "metadata": { "ExecuteTime": { "end_time": "2024-10-17T00:59:06.708622Z", "start_time": "2024-10-17T00:59:06.668852Z" } }, "cell_type": "code", "source": "pd.read_csv(\"output/stats.tsv\", sep=\"\\t\")", "id": "94099917b1139784", "outputs": [ { "data": { "text/plain": [ " id compared_with agents class_count deprecated_class_count \\\n", "0 BFO NaN NaN 11 0 \n", "1 BSPO NaN NaN 0 0 \n", "2 CHEBI NaN NaN 1849 1 \n", "3 CL NaN NaN 1151 1 \n", "4 GO NaN NaN 2563 2 \n", "5 HP NaN NaN 19434 446 \n", "6 HsapDv NaN NaN 12 7 \n", "7 IAO NaN NaN 0 0 \n", "8 MPATH NaN NaN 75 0 \n", "9 NBO NaN NaN 64 0 \n", "10 OMO NaN NaN 0 0 \n", "11 PATO NaN NaN 567 0 \n", "12 PR NaN NaN 206 0 \n", "13 RO NaN NaN 1 0 \n", "14 UBERON NaN NaN 5605 0 \n", "15 dce NaN NaN 0 0 \n", "16 dcterms NaN NaN 0 0 \n", "17 obo NaN NaN 0 0 \n", "18 oio NaN NaN 0 0 \n", "19 owl NaN NaN 0 0 \n", "20 rdfs NaN NaN 0 0 \n", "\n", " non_deprecated_class_count class_count_with_text_definitions \\\n", "0 11 0 \n", "1 0 0 \n", "2 1848 1447 \n", "3 1150 1118 \n", "4 2561 2563 \n", "5 18988 16398 \n", "6 5 12 \n", "7 0 0 \n", "8 75 73 \n", "9 64 22 \n", "10 0 0 \n", "11 567 562 \n", "12 206 206 \n", "13 1 1 \n", "14 5605 5130 \n", "15 0 0 \n", "16 0 0 \n", "17 0 0 \n", "18 0 0 \n", "19 0 0 \n", "20 0 0 \n", "\n", " class_count_without_text_definitions object_property_count \\\n", "0 11 6 \n", "1 0 26 \n", "2 402 0 \n", "3 33 3 \n", "4 0 0 \n", "5 3036 0 \n", "6 0 0 \n", "7 0 0 \n", "8 2 0 \n", "9 42 0 \n", "10 0 0 \n", "11 5 0 \n", "12 0 0 \n", "13 0 158 \n", "14 475 0 \n", "15 0 0 \n", "16 0 0 \n", "17 0 32 \n", "18 0 0 \n", "19 0 0 \n", "20 0 0 \n", "\n", " annotation_property_count ... 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\n", "17 NaN NaN \n", "18 NaN NaN \n", "19 NaN NaN \n", "20 NaN NaN \n", "\n", " class_count_by_subset_organ_slim class_count_by_subset_pheno_slim \\\n", "0 NaN NaN \n", "1 NaN NaN \n", "2 NaN NaN \n", "3 NaN NaN \n", "4 NaN NaN \n", "5 NaN NaN \n", "6 NaN NaN \n", "7 NaN NaN \n", "8 NaN NaN \n", "9 NaN NaN \n", "10 NaN NaN \n", "11 NaN NaN \n", "12 NaN NaN \n", "13 NaN NaN \n", "14 135.0 1724.0 \n", "15 NaN NaN \n", "16 NaN NaN \n", "17 NaN NaN \n", "18 NaN NaN \n", "19 NaN NaN \n", "20 NaN NaN \n", "\n", " class_count_by_subset_phenotype_rcn class_count_by_subset_uberon_slim \\\n", "0 NaN NaN \n", "1 NaN NaN \n", "2 NaN NaN \n", "3 NaN NaN \n", "4 NaN NaN \n", "5 NaN NaN \n", "6 NaN NaN \n", "7 NaN NaN \n", "8 NaN NaN \n", "9 NaN NaN \n", "10 NaN NaN \n", "11 NaN NaN \n", "12 NaN NaN \n", "13 NaN NaN \n", "14 8.0 899.0 \n", "15 NaN NaN \n", "16 NaN NaN \n", "17 NaN NaN \n", "18 NaN NaN \n", "19 NaN NaN \n", "20 NaN NaN \n", "\n", " class_count_by_subset_unverified_taxonomic_grouping \\\n", "0 NaN \n", "1 NaN \n", "2 NaN \n", "3 NaN \n", "4 NaN \n", "5 NaN \n", "6 NaN \n", "7 NaN \n", "8 NaN \n", "9 NaN \n", "10 NaN \n", "11 NaN \n", "12 NaN \n", "13 NaN \n", "14 2.0 \n", "15 NaN \n", "16 NaN \n", "17 NaN \n", "18 NaN \n", "19 NaN \n", "20 NaN \n", "\n", " class_count_by_subset_upper_level class_count_by_subset_vertebrate_core \n", "0 NaN NaN \n", "1 NaN NaN \n", "2 NaN NaN \n", "3 NaN NaN \n", "4 NaN NaN \n", "5 NaN NaN \n", "6 NaN NaN \n", "7 NaN NaN \n", "8 NaN NaN \n", "9 NaN NaN \n", "10 NaN NaN \n", "11 NaN NaN \n", "12 NaN NaN \n", "13 NaN NaN \n", "14 50.0 462.0 \n", "15 NaN NaN \n", "16 NaN NaN \n", "17 NaN NaN \n", "18 NaN NaN \n", "19 NaN NaN \n", "20 NaN NaN \n", "\n", "[21 rows x 541 columns]" ], "text/html": [ "
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idcompared_withagentsclass_countdeprecated_class_countnon_deprecated_class_countclass_count_with_text_definitionsclass_count_without_text_definitionsobject_property_countannotation_property_count...class_count_by_subset_inconsistent_with_fmaclass_count_by_subset_major_organclass_count_by_subset_non_informativeclass_count_by_subset_organ_slimclass_count_by_subset_pheno_slimclass_count_by_subset_phenotype_rcnclass_count_by_subset_uberon_slimclass_count_by_subset_unverified_taxonomic_groupingclass_count_by_subset_upper_levelclass_count_by_subset_vertebrate_core
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3CLNaNNaN11511115011183330...NaNNaNNaNNaNNaNNaNNaNNaNNaNNaN
4GONaNNaN2563225612563000...NaNNaNNaNNaNNaNNaNNaNNaNNaNNaN
5HPNaNNaN194344461898816398303601...NaNNaNNaNNaNNaNNaNNaNNaNNaNNaN
6HsapDvNaNNaN127512000...NaNNaNNaNNaNNaNNaNNaNNaNNaNNaN
7IAONaNNaN0000004...NaNNaNNaNNaNNaNNaNNaNNaNNaNNaN
8MPATHNaNNaN7507573200...NaNNaNNaNNaNNaNNaNNaNNaNNaNNaN
9NBONaNNaN64064224200...NaNNaNNaNNaNNaNNaNNaNNaNNaNNaN
10OMONaNNaN0000004...NaNNaNNaNNaNNaNNaNNaNNaNNaNNaN
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12PRNaNNaN2060206206000...NaNNaNNaNNaNNaNNaNNaNNaNNaNNaN
13RONaNNaN101101582...NaNNaNNaNNaNNaNNaNNaNNaNNaNNaN
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21 rows × 541 columns

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" ] }, "execution_count": 10, "metadata": {}, "output_type": "execute_result" } ], "execution_count": 10 }, { "metadata": {}, "cell_type": "markdown", "source": "## Lookup by Label", "id": "f5ed0b8f0c8dbe79" }, { "metadata": { "ExecuteTime": { "end_time": "2024-10-17T01:04:34.057941Z", "start_time": "2024-10-17T01:04:31.020906Z" } }, "cell_type": "code", "source": "hp info 'Tibial bowing'", "id": "d9ad636a9b0e68b0", "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "HP:0002982 ! Tibial bowing\r\n" ] } ], "execution_count": 25 }, { "metadata": { "ExecuteTime": { "end_time": "2024-10-17T01:04:56.329580Z", "start_time": "2024-10-17T01:04:53.645524Z" } }, "cell_type": "code", "source": "hp info 'Short tibia' 'Tibial bowing'", "id": "3c06a722d00370dd", "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "HP:0005736 ! Short tibia\r\n", "HP:0002982 ! Tibial bowing\r\n" ] } ], "execution_count": 26 }, { "metadata": {}, "cell_type": "markdown", "source": [ "## Search\n", "\n", "We can use the OAK search syntax to find labels with a partial match to \"tibia\"" ], "id": "4d8582151a89d3ba" }, { "cell_type": "code", "id": "79d50f29-4bdc-4f34-9ecb-ace887ea2f67", "metadata": { "ExecuteTime": { "end_time": "2024-10-17T00:59:09.769326Z", "start_time": "2024-10-17T00:59:06.835242Z" } }, "source": [ "hp info l~tibia" ], "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "HP:0002982 ! Tibial bowing\r\n", "HP:0002992 ! Abnormal tibia morphology\r\n", "HP:0003832 ! Abnormality of the tibial plateaux\r\n", "HP:0003833 ! Laterally deficient tibial plateaux\r\n", "HP:0005028 ! Widened proximal tibial metaphyses\r\n", "HP:0005736 ! Short tibia\r\n", "HP:0005766 ! Disproportionate shortening of the tibia\r\n", "HP:0005772 ! Aplasia/Hypoplasia of the tibia\r\n", "HP:0005892 ! Proximal tibial and fibular fusion\r\n", "HP:0005929 ! Synostosis involving the tibia\r\n", "HP:0006379 ! Proximal tibial hypoplasia\r\n", "HP:0006390 ! Anterior tibial bowing\r\n", "HP:0006413 ! Broad tibial metaphyses\r\n", "HP:0006414 ! Distal tibial bowing\r\n", "HP:0006423 ! Peg-like central prominence of distal tibial metaphyses\r\n", "HP:0006426 ! Rudimentary to absent tibiae\r\n", "HP:0006436 ! obsolete Shortening of the tibia\r\n", "HP:0006456 ! Irregular proximal tibial epiphyses\r\n", "HP:0006491 ! Abnormal tibial metaphysis morphology\r\n", "HP:0006508 ! Abnormality of tibial epiphyses\r\n", "HP:0008963 ! Tibialis muscle weakness\r\n", "HP:0009556 ! Absent tibia\r\n", "HP:0009736 ! Tibial pseudarthrosis\r\n", "HP:0010504 ! Increased length of the tibia\r\n", "HP:0010591 ! Abnormality of the proximal tibial epiphysis\r\n", "HP:0010592 ! Abnormality of the distal tibial epiphysis\r\n", "HP:0011399 ! Tibialis anterior muscle atrophy\r\n", "HP:0012221 ! Pretibial blistering\r\n", "HP:0012284 ! Small proximal tibial epiphyses\r\n", "HP:0012564 ! Premature epimetaphyseal fusion in tibia\r\n", "HP:0030292 ! Tibial metaphyseal irregularity\r\n", "HP:0030294 ! Metaphyseal chondromatosis of tibia\r\n", "HP:0030308 ! Flared distal tibial metaphysis\r\n", "HP:0031173 ! Tibial spur\r\n", "HP:0031260 ! Triangular tibia\r\n", "HP:0031305 ! Tibial arterial calcification\r\n", "HP:0032538 ! Pretibial dimple\r\n", "HP:0034372 ! Internal tibial torsion\r\n", "HP:0034373 ! External tibial torsion\r\n", "HP:0034517 ! Pretibial hyperpigmentation\r\n", "HP:0041089 ! Avulsion fractured tibia\r\n", "HP:0041143 ! Fractured tibia\r\n", "HP:0100341 ! Tibial deviation of the 4th toe\r\n", "HP:0100343 ! Tibial deviation of the 3rd toe\r\n", "HP:0100345 ! Tibial deviation of the 2nd toe\r\n", "HP:0100347 ! Tibial deviation of the 5th toe\r\n", "HP:0100499 ! Tibial deviation of toes\r\n", "HP:0100694 ! Tibial torsion\r\n", "HP:0200028 ! Pretibial myxedema\r\n", "HP:6000778 ! Cone-shaped distal tibial epiphysis\r\n", "HP:6000809 ! Thickened tibial cortex\r\n", "HP:6000867 ! Delayed tibial epiphyseal ossification\r\n", "HP:6000886 ! Enlarged distal tibial epiphysis\r\n", "HP:6000951 ! Flared proximal tibial metaphysis\r\n", "UBERON:0000313 ! portion of cartilage tissue in tibia\r\n", "UBERON:0000979 ! tibia\r\n", "UBERON:0001323 ! tibial nerve\r\n", "UBERON:0001385 ! tibialis anterior\r\n", "UBERON:0001545 ! anterior tibial vein\r\n", "UBERON:0001546 ! posterior tibial vein\r\n", "UBERON:0001667 ! tibialis posterior\r\n", "UBERON:0004098 ! tibial plateaux\r\n", "UBERON:0004383 ! epiphysis of tibia\r\n", "UBERON:0004405 ! distal epiphysis of tibia\r\n", "UBERON:0004499 ! skeletal muscle tissue of tibialis anterior\r\n", "UBERON:0007610 ! tibial artery\r\n", "UBERON:0008230 ! tibialis\r\n", "UBERON:0008772 ! proximal epiphysis of tibia\r\n", "UBERON:0009989 ! condyle of tibia\r\n", "UBERON:0010370 ! tibial vein\r\n", "UBERON:0010849 ! tibia cartilage element\r\n", "UBERON:0010850 ! tibia pre-cartilage condensation\r\n", "UBERON:0013280 ! diaphysis of tibia\r\n", "UBERON:0013750 ! metaphysis of tibia\r\n", "UBERON:0015004 ! tibia endochondral element\r\n", "UBERON:7500062 ! tibial tuberosity\r\n" ] } ], "execution_count": 11 }, { "metadata": {}, "cell_type": "markdown", "source": "Note that the OWL version of HP includes merged imports of parts of other ontologies. To constrain search to only HPO we can do a conjunction query with ID space:", "id": "20b20f5ebda9a5c8" }, { "metadata": { "ExecuteTime": { "end_time": "2024-10-17T01:06:21.557747Z", "start_time": "2024-10-17T01:06:18.841679Z" } }, "cell_type": "code", "source": "hp info l~tibia .and i^HP:", "id": "6d1b81a8ec5f9744", "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "HP:0002982 ! Tibial bowing\r\n", "HP:0002992 ! Abnormal tibia morphology\r\n", "HP:0003832 ! Abnormality of the tibial plateaux\r\n", "HP:0003833 ! Laterally deficient tibial plateaux\r\n", "HP:0005028 ! Widened proximal tibial metaphyses\r\n", "HP:0005736 ! Short tibia\r\n", "HP:0005766 ! Disproportionate shortening of the tibia\r\n", "HP:0005772 ! Aplasia/Hypoplasia of the tibia\r\n", "HP:0005892 ! Proximal tibial and fibular fusion\r\n", "HP:0005929 ! Synostosis involving the tibia\r\n", "HP:0006379 ! Proximal tibial hypoplasia\r\n", "HP:0006390 ! Anterior tibial bowing\r\n", "HP:0006413 ! Broad tibial metaphyses\r\n", "HP:0006414 ! Distal tibial bowing\r\n", "HP:0006423 ! Peg-like central prominence of distal tibial metaphyses\r\n", "HP:0006426 ! Rudimentary to absent tibiae\r\n", "HP:0006436 ! obsolete Shortening of the tibia\r\n", "HP:0006456 ! Irregular proximal tibial epiphyses\r\n", "HP:0006491 ! Abnormal tibial metaphysis morphology\r\n", "HP:0006508 ! Abnormality of tibial epiphyses\r\n", "HP:0008963 ! Tibialis muscle weakness\r\n", "HP:0009556 ! Absent tibia\r\n", "HP:0009736 ! Tibial pseudarthrosis\r\n", "HP:0010504 ! Increased length of the tibia\r\n", "HP:0010591 ! Abnormality of the proximal tibial epiphysis\r\n", "HP:0010592 ! Abnormality of the distal tibial epiphysis\r\n", "HP:0011399 ! Tibialis anterior muscle atrophy\r\n", "HP:0012221 ! Pretibial blistering\r\n", "HP:0012284 ! Small proximal tibial epiphyses\r\n", "HP:0012564 ! Premature epimetaphyseal fusion in tibia\r\n", "HP:0030292 ! Tibial metaphyseal irregularity\r\n", "HP:0030294 ! Metaphyseal chondromatosis of tibia\r\n", "HP:0030308 ! Flared distal tibial metaphysis\r\n", "HP:0031173 ! Tibial spur\r\n", "HP:0031260 ! Triangular tibia\r\n", "HP:0031305 ! Tibial arterial calcification\r\n", "HP:0032538 ! Pretibial dimple\r\n", "HP:0034372 ! Internal tibial torsion\r\n", "HP:0034373 ! External tibial torsion\r\n", "HP:0034517 ! Pretibial hyperpigmentation\r\n", "HP:0041089 ! Avulsion fractured tibia\r\n", "HP:0041143 ! Fractured tibia\r\n", "HP:0100341 ! Tibial deviation of the 4th toe\r\n", "HP:0100343 ! Tibial deviation of the 3rd toe\r\n", "HP:0100345 ! Tibial deviation of the 2nd toe\r\n", "HP:0100347 ! Tibial deviation of the 5th toe\r\n", "HP:0100499 ! Tibial deviation of toes\r\n", "HP:0100694 ! Tibial torsion\r\n", "HP:0200028 ! Pretibial myxedema\r\n", "HP:6000778 ! Cone-shaped distal tibial epiphysis\r\n", "HP:6000809 ! Thickened tibial cortex\r\n", "HP:6000867 ! Delayed tibial epiphyseal ossification\r\n", "HP:6000886 ! Enlarged distal tibial epiphysis\r\n", "HP:6000951 ! Flared proximal tibial metaphysis\r\n" ] } ], "execution_count": 27 }, { "metadata": { "ExecuteTime": { "end_time": "2024-10-17T00:59:12.659707Z", "start_time": "2024-10-17T00:59:10.076525Z" } }, "cell_type": "code", "source": "hp labels l~tibia > output/search-tibia.tsv", "id": "22260f44e229a640", "outputs": [], "execution_count": 12 }, { "metadata": { "ExecuteTime": { "end_time": "2024-10-17T00:59:12.676194Z", "start_time": "2024-10-17T00:59:12.665053Z" } }, "cell_type": "code", "source": "pd.read_csv(\"output/search-tibia.tsv\", sep=\"\\t\")", "id": "fde8fbb20de12453", "outputs": [ { "data": { "text/plain": [ " id label\n", "0 HP:0002982 Tibial bowing\n", "1 HP:0002992 Abnormal tibia morphology\n", "2 HP:0003832 Abnormality of the tibial plateaux\n", "3 HP:0003833 Laterally deficient tibial plateaux\n", "4 HP:0005028 Widened proximal tibial metaphyses\n", ".. ... ...\n", "71 UBERON:0010850 tibia pre-cartilage condensation\n", "72 UBERON:0013280 diaphysis of tibia\n", "73 UBERON:0013750 metaphysis of tibia\n", "74 UBERON:0015004 tibia endochondral element\n", "75 UBERON:7500062 tibial tuberosity\n", "\n", "[76 rows x 2 columns]" ], "text/html": [ "
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idlabel
0HP:0002982Tibial bowing
1HP:0002992Abnormal tibia morphology
2HP:0003832Abnormality of the tibial plateaux
3HP:0003833Laterally deficient tibial plateaux
4HP:0005028Widened proximal tibial metaphyses
.........
71UBERON:0010850tibia pre-cartilage condensation
72UBERON:0013280diaphysis of tibia
73UBERON:0013750metaphysis of tibia
74UBERON:0015004tibia endochondral element
75UBERON:7500062tibial tuberosity
\n", "

76 rows × 2 columns

\n", "
" ] }, "execution_count": 13, "metadata": {}, "output_type": "execute_result" } ], "execution_count": 13 }, { "metadata": {}, "cell_type": "markdown", "source": "## Basic Lookup", "id": "79a536c19df9b5e1" }, { "cell_type": "code", "id": "bbf2ea5f-6521-4980-a63f-95c35ccbb740", "metadata": { "ExecuteTime": { "end_time": "2024-10-17T00:59:15.273664Z", "start_time": "2024-10-17T00:59:12.713563Z" } }, "source": [ "hp info HP:0002982" ], "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "HP:0002982 ! Tibial bowing\r\n" ] } ], "execution_count": 14 }, { "cell_type": "code", "id": "f2e60d50-e16b-41a7-ade5-4bb7c6d9a96c", "metadata": { "ExecuteTime": { "end_time": "2024-10-17T00:59:40.521901Z", "start_time": "2024-10-17T00:59:36.905939Z" } }, "source": "hp info HP:0002982 -O obo", "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\r\n", "[Term]\r\n", "id: HP:0002982\r\n", "name: Tibial bowing\r\n", "def: \"A bending or abnormal curvature of the tibia.\" [orcid:0000-0002-0736-9199]\r\n", "xref: UMLS:C1837081\r\n", "subset: hposlim_core\r\n", "synonym: \"Bowed shankbone\" EXACT [orcid:0000-0001-5208-3432]\r\n", "synonym: \"Bowed shinbone\" EXACT [orcid:0000-0001-5208-3432]\r\n", "synonym: \"Bowed tibia\" EXACT []\r\n", "synonym: \"Bowing of the tibia\" EXACT []\r\n", "is_a: HP:0002979 ! Bowing of the legs\r\n", "is_a: HP:0002992 ! Abnormal tibia morphology\r\n", "\r\n" ] } ], "execution_count": 17 }, { "metadata": {}, "cell_type": "markdown", "source": "## Basic Graph Operations", "id": "d6d0a10e8ff153e3" }, { "metadata": { "ExecuteTime": { "end_time": "2024-10-17T01:00:44.023410Z", "start_time": "2024-10-17T01:00:41.454890Z" } }, "cell_type": "code", "source": "hp ancestors --predicates rdfs:subClassOf HP:0002982 ", "id": "d45d5f6e69b2a64b", "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "id\tlabel\r\n", "HP:0000001\tAll\r\n", "HP:0000118\tPhenotypic abnormality\r\n", "HP:0000924\tAbnormality of the skeletal system\r\n", "HP:0000940\tAbnormal diaphysis morphology\r\n", "HP:0002813\tAbnormal limb bone morphology\r\n", "HP:0002814\tAbnormality of the lower limb\r\n", "HP:0002979\tBowing of the legs\r\n", "HP:0002981\tAbnormality of the calf\r\n", "HP:0002982\tTibial bowing\r\n", "HP:0002992\tAbnormal tibia morphology\r\n", "HP:0006487\tBowing of the long bones\r\n", "HP:0011314\tAbnormal long bone morphology\r\n", "HP:0011842\tAbnormal skeletal morphology\r\n", "HP:0011844\tAbnormal appendicular skeleton morphology\r\n", "HP:0033127\tAbnormality of the musculoskeletal system\r\n", "HP:0040064\tAbnormality of limbs\r\n", "HP:0040068\tAbnormality of limb bone\r\n", "HP:0040069\tAbnormal lower limb bone morphology\r\n" ] } ], "execution_count": 21 }, { "metadata": { "ExecuteTime": { "end_time": "2024-10-17T01:00:03.856250Z", "start_time": "2024-10-17T01:00:00.774742Z" } }, "cell_type": "code", "source": "hp descendants -p i HP:0002982", "id": "5f7f3b2c61b834a2", "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "HP:0002982 ! Tibial bowing\r\n", "HP:0006390 ! Anterior tibial bowing\r\n", "HP:0006414 ! Distal tibial bowing\r\n" ] } ], "execution_count": 19 }, { "metadata": {}, "cell_type": "markdown", "source": "## Relationships", "id": "4b545378b6995db5" }, { "metadata": { "ExecuteTime": { "end_time": "2024-10-17T01:02:57.575884Z", "start_time": "2024-10-17T01:02:53.697838Z" } }, "cell_type": "code", "source": "hp relationships HP:0002982 ", "id": "33c57f23d3e8602d", "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "subject\tpredicate\tobject\tsubject_label\tpredicate_label\tobject_label\r\n", "HP:0002982\trdfs:subClassOf\tHP:0002979\tTibial bowing\tNone\tBowing of the legs\r\n", "HP:0002982\trdfs:subClassOf\tHP:0002992\tTibial bowing\tNone\tAbnormal tibia morphology\r\n" ] } ], "execution_count": 24 }, { "metadata": {}, "cell_type": "markdown", "source": "## Trees", "id": "b399e28b351ccb9c" }, { "metadata": { "ExecuteTime": { "end_time": "2024-10-17T01:01:16.005721Z", "start_time": "2024-10-17T01:01:08.639428Z" } }, "cell_type": "code", "source": "hp tree -p i --down HP:0002982 ", "id": "4ce800ba9dac209e", "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "* [] HP:0000001 ! All\r\n", " * [i] HP:0000118 ! Phenotypic abnormality\r\n", " * [i] HP:0033127 ! Abnormality of the musculoskeletal system\r\n", " * [i] HP:0000924 ! Abnormality of the skeletal system\r\n", " * [i] HP:0011842 ! Abnormal skeletal morphology\r\n", " * [i] HP:0011844 ! Abnormal appendicular skeleton morphology\r\n", " * [i] HP:0011314 ! Abnormal long bone morphology\r\n", " * [i] HP:0000940 ! Abnormal diaphysis morphology\r\n", " * [i] HP:0006487 ! Bowing of the long bones\r\n", " * [i] HP:0002979 ! Bowing of the legs\r\n", " * [i] **HP:0002982 ! Tibial bowing**\r\n", " * [i] HP:0006414 ! Distal tibial bowing\r\n", " * [i] HP:0006390 ! Anterior tibial bowing\r\n", " * [i] HP:0002813 ! Abnormal limb bone morphology\r\n", " * [i] HP:0000940 ! Abnormal diaphysis morphology\r\n", " * [i] HP:0006487 ! Bowing of the long bones\r\n", " * [i] HP:0002979 ! Bowing of the legs\r\n", " * [i] **HP:0002982 ! Tibial bowing**\r\n", " * [i] HP:0006414 ! Distal tibial bowing\r\n", " * [i] HP:0006390 ! Anterior tibial bowing\r\n", " * [i] HP:0040069 ! Abnormal lower limb bone morphology\r\n", " * [i] HP:0002992 ! Abnormal tibia morphology\r\n", " * [i] **HP:0002982 ! Tibial bowing**\r\n", " * [i] HP:0006414 ! Distal tibial bowing\r\n", " * [i] HP:0006390 ! Anterior tibial bowing\r\n", " * [i] HP:0040068 ! Abnormality of limb bone\r\n", " * [i] HP:0002813 ! Abnormal limb bone morphology\r\n", " * [i] HP:0000940 ! Abnormal diaphysis morphology\r\n", " * [i] HP:0006487 ! Bowing of the long bones\r\n", " * [i] HP:0002979 ! Bowing of the legs\r\n", " * [i] **HP:0002982 ! Tibial bowing**\r\n", " * [i] HP:0006414 ! Distal tibial bowing\r\n", " * [i] HP:0006390 ! Anterior tibial bowing\r\n", " * [i] HP:0040069 ! Abnormal lower limb bone morphology\r\n", " * [i] HP:0002992 ! Abnormal tibia morphology\r\n", " * [i] **HP:0002982 ! Tibial bowing**\r\n", " * [i] HP:0006414 ! Distal tibial bowing\r\n", " * [i] HP:0006390 ! Anterior tibial bowing\r\n", " * [i] HP:0040064 ! Abnormality of limbs\r\n", " * [i] HP:0040068 ! Abnormality of limb bone\r\n", " * [i] HP:0002813 ! Abnormal limb bone morphology\r\n", " * [i] HP:0000940 ! Abnormal diaphysis morphology\r\n", " * [i] HP:0006487 ! Bowing of the long bones\r\n", " * [i] HP:0002979 ! Bowing of the legs\r\n", " * [i] **HP:0002982 ! Tibial bowing**\r\n", " * [i] HP:0006414 ! Distal tibial bowing\r\n", " * [i] HP:0006390 ! Anterior tibial bowing\r\n", " * [i] HP:0040069 ! Abnormal lower limb bone morphology\r\n", " * [i] HP:0002992 ! Abnormal tibia morphology\r\n", " * [i] **HP:0002982 ! Tibial bowing**\r\n", " * [i] HP:0006414 ! Distal tibial bowing\r\n", " * [i] HP:0006390 ! Anterior tibial bowing\r\n", " * [i] HP:0002814 ! Abnormality of the lower limb\r\n", " * [i] HP:0002981 ! Abnormality of the calf\r\n", " * [i] HP:0002979 ! Bowing of the legs\r\n", " * [i] **HP:0002982 ! Tibial bowing**\r\n", " * [i] HP:0006414 ! Distal tibial bowing\r\n", " * [i] HP:0006390 ! Anterior tibial bowing\r\n", " * [i] HP:0002992 ! Abnormal tibia morphology\r\n", " * [i] **HP:0002982 ! Tibial bowing**\r\n", " * [i] HP:0006414 ! Distal tibial bowing\r\n", " * [i] HP:0006390 ! Anterior tibial bowing\r\n", " * [i] HP:0040069 ! Abnormal lower limb bone morphology\r\n", " * [i] HP:0002992 ! Abnormal tibia morphology\r\n", " * [i] **HP:0002982 ! Tibial bowing**\r\n", " * [i] HP:0006414 ! Distal tibial bowing\r\n", " * [i] HP:0006390 ! Anterior tibial bowing\r\n" ] } ], "execution_count": 22 }, { "metadata": {}, "cell_type": "markdown", "source": "## Graph Visualization", "id": "11d16a4c5113c921" }, { "metadata": { "ExecuteTime": { "end_time": "2024-10-17T01:02:09.317262Z", "start_time": "2024-10-17T01:02:03.729111Z" } }, "cell_type": "code", "source": "hp viz -p i HP:0002982 -o output/graph-tb.png ", "id": "71b491731093b36b", "outputs": [], "execution_count": 23 }, { "metadata": {}, "cell_type": "markdown", "source": "![img](output/graph-tb.png)", "id": "8cc65d1ab3bf5e28" }, { "metadata": {}, "cell_type": "markdown", "source": "## Semantic Similarity", "id": "1c40f0564220ebfa" }, { "metadata": { "ExecuteTime": { "end_time": "2024-10-17T01:07:13.952975Z", "start_time": "2024-10-17T01:07:08.421317Z" } }, "cell_type": "code", "source": "hp similarity \"Tibial bowing\" @ \"Short tibia\"", "id": "e95d52165a48a437", "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "subject_id: HP:0002982\r\n", "subject_label: Tibial bowing\r\n", "object_id: HP:0005736\r\n", "object_label: Short tibia\r\n", "ancestor_id: HP:0002992\r\n", "ancestor_label: Abnormal tibia morphology\r\n", "object_information_content: 13.359841052540446\r\n", "subject_information_content: 13.359841052540446\r\n", "ancestor_information_content: 9.659401334399353\r\n", "jaccard_similarity: 0.56\r\n", "phenodigm_score: 2.325782609631356\r\n" ] } ], "execution_count": 29 }, { "metadata": {}, "cell_type": "markdown", "source": "## Associations", "id": "afbc08fb26450f6" }, { "metadata": { "ExecuteTime": { "end_time": "2024-10-17T01:09:56.134494Z", "start_time": "2024-10-17T01:09:54.421851Z" } }, "cell_type": "code", "source": "!curl -L -s http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt > output/hpoa_g2p.tsv\n", "id": "95f57128c7389f15", "outputs": [], "execution_count": 32 }, { "metadata": { "ExecuteTime": { "end_time": "2024-10-17T01:15:31.470527Z", "start_time": "2024-10-17T01:15:15.187327Z" } }, "cell_type": "code", "source": "hp -G hpoa_g2p -g output/hpoa_g2p.tsv associations -Q subject NCBIGene:8192 -O csv > output/assocs-query.tsv", "id": "5d68d254c22bbf7e", "outputs": [], "execution_count": 36 }, { "metadata": { "ExecuteTime": { "end_time": "2024-10-17T01:15:31.494992Z", "start_time": "2024-10-17T01:15:31.475954Z" } }, "cell_type": "code", "source": "pd.read_csv(\"output/assocs-query.tsv\", sep=\"\\t\")", "id": "33bd92f81c4e860c", "outputs": [ { "data": { "text/plain": [ " subject predicate object property_values subject_label \\\n", "0 NCBIGene:8192 NaN HP:0001250 NaN CLPP \n", "1 NCBIGene:8192 NaN HP:0000013 NaN CLPP \n", "2 NCBIGene:8192 NaN HP:0000007 NaN CLPP \n", "3 NCBIGene:8192 NaN HP:0010464 NaN CLPP \n", "4 NCBIGene:8192 NaN HP:0008232 NaN CLPP \n", "5 NCBIGene:8192 NaN HP:0011969 NaN CLPP \n", "6 NCBIGene:8192 NaN HP:0004322 NaN CLPP \n", "7 NCBIGene:8192 NaN HP:0000786 NaN CLPP \n", "8 NCBIGene:8192 NaN HP:0000815 NaN CLPP \n", "9 NCBIGene:8192 NaN HP:0000252 NaN CLPP \n", "10 NCBIGene:8192 NaN HP:0000407 NaN CLPP \n", "\n", " predicate_label object_label \\\n", "0 NaN Seizure \n", "1 NaN Hypoplasia of the uterus \n", "2 NaN Autosomal recessive inheritance \n", "3 NaN Streak ovary \n", "4 NaN Elevated circulating follicle stimulating horm... \n", "5 NaN Elevated circulating luteinizing hormone level \n", "6 NaN Short stature \n", "7 NaN Primary amenorrhea \n", "8 NaN Hypergonadotropic hypogonadism \n", "9 NaN Microcephaly \n", "10 NaN Sensorineural hearing impairment \n", "\n", " negated publications evidence_type supporting_objects \\\n", "0 NaN NaN NaN NaN \n", "1 NaN NaN NaN NaN \n", "2 NaN NaN NaN NaN \n", "3 NaN NaN NaN NaN \n", "4 NaN NaN NaN NaN \n", "5 NaN NaN NaN NaN \n", "6 NaN NaN NaN NaN \n", "7 NaN NaN NaN NaN \n", "8 NaN NaN NaN NaN \n", "9 NaN NaN NaN NaN \n", "10 NaN NaN NaN NaN \n", "\n", " primary_knowledge_source aggregator_knowledge_source subject_closure \\\n", "0 NaN NaN NaN \n", "1 NaN NaN NaN \n", "2 NaN NaN NaN \n", "3 NaN NaN NaN \n", "4 NaN NaN NaN \n", "5 NaN NaN NaN \n", "6 NaN NaN NaN \n", "7 NaN NaN NaN \n", "8 NaN NaN NaN \n", "9 NaN NaN NaN \n", "10 NaN NaN NaN \n", "\n", " subject_closure_label object_closure object_closure_label comments \n", "0 NaN NaN NaN NaN \n", "1 NaN NaN NaN NaN \n", "2 NaN NaN NaN NaN \n", "3 NaN NaN NaN NaN \n", "4 NaN NaN NaN NaN \n", "5 NaN NaN NaN NaN \n", "6 NaN NaN NaN NaN \n", "7 NaN NaN NaN NaN \n", "8 NaN NaN NaN NaN \n", "9 NaN NaN NaN NaN \n", "10 NaN NaN NaN NaN " ], "text/html": [ "
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0NCBIGene:8192NaNHP:0001250NaNCLPPNaNSeizureNaNNaNNaNNaNNaNNaNNaNNaNNaNNaNNaN
1NCBIGene:8192NaNHP:0000013NaNCLPPNaNHypoplasia of the uterusNaNNaNNaNNaNNaNNaNNaNNaNNaNNaNNaN
2NCBIGene:8192NaNHP:0000007NaNCLPPNaNAutosomal recessive inheritanceNaNNaNNaNNaNNaNNaNNaNNaNNaNNaNNaN
3NCBIGene:8192NaNHP:0010464NaNCLPPNaNStreak ovaryNaNNaNNaNNaNNaNNaNNaNNaNNaNNaNNaN
4NCBIGene:8192NaNHP:0008232NaNCLPPNaNElevated circulating follicle stimulating horm...NaNNaNNaNNaNNaNNaNNaNNaNNaNNaNNaN
5NCBIGene:8192NaNHP:0011969NaNCLPPNaNElevated circulating luteinizing hormone levelNaNNaNNaNNaNNaNNaNNaNNaNNaNNaNNaN
6NCBIGene:8192NaNHP:0004322NaNCLPPNaNShort statureNaNNaNNaNNaNNaNNaNNaNNaNNaNNaNNaN
7NCBIGene:8192NaNHP:0000786NaNCLPPNaNPrimary amenorrheaNaNNaNNaNNaNNaNNaNNaNNaNNaNNaNNaN
8NCBIGene:8192NaNHP:0000815NaNCLPPNaNHypergonadotropic hypogonadismNaNNaNNaNNaNNaNNaNNaNNaNNaNNaNNaN
9NCBIGene:8192NaNHP:0000252NaNCLPPNaNMicrocephalyNaNNaNNaNNaNNaNNaNNaNNaNNaNNaNNaN
10NCBIGene:8192NaNHP:0000407NaNCLPPNaNSensorineural hearing impairmentNaNNaNNaNNaNNaNNaNNaNNaNNaNNaNNaN
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