"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ }
+ ],
+ "source": [
+ "# Explore most frequent n features in measurement table\n",
+ "feature_counts = omop.feature_statistics(source='measurement', number=20)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 5,
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/html": [
+ "\n",
+ "\n",
+ "
\n",
+ " \n",
+ " \n",
+ " feature_name \n",
+ " measurement_concept_id_1 \n",
+ " measurement_concept_id_2 \n",
+ " count \n",
+ " \n",
+ " \n",
+ " \n",
+ " \n",
+ " 0 \n",
+ " Respiratory Rate \n",
+ " 2000030002 \n",
+ " 3024171 \n",
+ " 19776 \n",
+ " \n",
+ " \n",
+ " 1 \n",
+ " Heart Rate \n",
+ " 2000030001 \n",
+ " 3027018 \n",
+ " 19319 \n",
+ " \n",
+ " \n",
+ " 2 \n",
+ " O2 saturation pulseoxymetry \n",
+ " 2000030003 \n",
+ " 40762499 \n",
+ " 17683 \n",
+ " \n",
+ " \n",
+ " 3 \n",
+ " Heart Rhythm \n",
+ " 2000030004 \n",
+ " 3022318 \n",
+ " 12441 \n",
+ " \n",
+ " \n",
+ " 4 \n",
+ " ART BP Mean \n",
+ " 2000030096 \n",
+ " 3027598 \n",
+ " 9738 \n",
+ " \n",
+ " \n",
+ " 5 \n",
+ " Arterial Blood Pressure systolic \n",
+ " 2000030009 \n",
+ " 3004249 \n",
+ " 9661 \n",
+ " \n",
+ " \n",
+ " 6 \n",
+ " Manual Blood Pressure Diastolic Right \n",
+ " 2000030157 \n",
+ " 3012888 \n",
+ " 9660 \n",
+ " \n",
+ " \n",
+ " 7 \n",
+ " Non Invasive Blood Pressure diastolic \n",
+ " 2000030006 \n",
+ " 21492240 \n",
+ " 8373 \n",
+ " \n",
+ " \n",
+ " 8 \n",
+ " Non Invasive Blood Pressure systolic \n",
+ " 2000030005 \n",
+ " 21492239 \n",
+ " 8371 \n",
+ " \n",
+ " \n",
+ " 9 \n",
+ " Non Invasive Blood Pressure mean \n",
+ " 2000030007 \n",
+ " 21492241 \n",
+ " 8366 \n",
+ " \n",
+ " \n",
+ " 10 \n",
+ " 0 \n",
+ " 0 \n",
+ " 0 \n",
+ " 6850 \n",
+ " \n",
+ " \n",
+ " 11 \n",
+ " Temperature Celsius \n",
+ " 2000030092 \n",
+ " 3020891 \n",
+ " 4057 \n",
+ " \n",
+ " \n",
+ " 12 \n",
+ " Potassium (serum) \n",
+ " 2000030062 \n",
+ " 3023103 \n",
+ " 3970 \n",
+ " \n",
+ " \n",
+ " 13 \n",
+ " Sodium (serum) \n",
+ " 2000030063 \n",
+ " 3019550 \n",
+ " 3954 \n",
+ " \n",
+ " \n",
+ " 14 \n",
+ " Chloride (serum) \n",
+ " 2000030064 \n",
+ " 3014576 \n",
+ " 3933 \n",
+ " \n",
+ " \n",
+ " 15 \n",
+ " Creatinine (serum) \n",
+ " 2000030068 \n",
+ " 3016723 \n",
+ " 3886 \n",
+ " \n",
+ " \n",
+ " 16 \n",
+ " Hemoglobin|Blood|Blood Gas \n",
+ " 2000001008 \n",
+ " 3000963 \n",
+ " 3778 \n",
+ " \n",
+ " \n",
+ " 17 \n",
+ " HCO3 (serum) \n",
+ " 2000030069 \n",
+ " 3016293 \n",
+ " 3763 \n",
+ " \n",
+ " \n",
+ " 18 \n",
+ " Glucose (serum) \n",
+ " 2000030072 \n",
+ " 3004501 \n",
+ " 3597 \n",
+ " \n",
+ " \n",
+ " 19 \n",
+ " GCS - Eye Opening \n",
+ " 2000030013 \n",
+ " 3016335 \n",
+ " 3268 \n",
+ " \n",
+ " \n",
+ "
\n",
+ "
Detected: feature Pain Level Response , feature ID 3034263 in concept table, match socre = 1 . \n",
+ " \n"
+ ],
+ "text/plain": [
+ "Detected: feature \u001b[32mPain Level Response\u001b[0m, feature ID \u001b[1;32m3034263\u001b[0m in concept table, match socre = \u001b[1;32m1\u001b[0m\u001b[32m.\u001b[0m\n"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ },
+ {
+ "data": {
+ "text/html": [
+ "Detected: feature Pain Level Acceptable , feature ID 4138763 in concept table, match socre = 1 . \n",
+ " \n"
+ ],
+ "text/plain": [
+ "Detected: feature \u001b[32mPain Level Acceptable\u001b[0m, feature ID \u001b[1;32m4138763\u001b[0m in concept table, match socre = \u001b[1;32m1\u001b[0m\u001b[32m.\u001b[0m\n"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ },
+ {
+ "data": {
+ "text/html": [
+ "Detected: feature Pain Present , feature ID 40757693 in concept table, match socre = 1 . \n",
+ " \n"
+ ],
+ "text/plain": [
+ "Detected: feature \u001b[32mPain Present\u001b[0m, feature ID \u001b[1;32m40757693\u001b[0m in concept table, match socre = \u001b[1;32m1\u001b[0m\u001b[32m.\u001b[0m\n"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ },
+ {
+ "data": {
+ "text/html": [
+ "Detected: feature Temperature Site , feature ID 3024265 in concept table, match socre = 1 . \n",
+ " \n"
+ ],
+ "text/plain": [
+ "Detected: feature \u001b[32mTemperature Site\u001b[0m, feature ID \u001b[1;32m3024265\u001b[0m in concept table, match socre = \u001b[1;32m1\u001b[0m\u001b[32m.\u001b[0m\n"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ },
+ {
+ "data": {
+ "text/html": [
+ "Detected: feature Oral Care , feature ID 3039006 in concept table, match socre = 1 . \n",
+ " \n"
+ ],
+ "text/plain": [
+ "Detected: feature \u001b[32mOral Care\u001b[0m, feature ID \u001b[1;32m3039006\u001b[0m in concept table, match socre = \u001b[1;32m1\u001b[0m\u001b[32m.\u001b[0m\n"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ },
+ {
+ "data": {
+ "text/html": [
+ "Detected: feature Bowel Sounds , feature ID 4337265 in concept table, match socre = 1 . \n",
+ " \n"
+ ],
+ "text/plain": [
+ "Detected: feature \u001b[32mBowel Sounds\u001b[0m, feature ID \u001b[1;32m4337265\u001b[0m in concept table, match socre = \u001b[1;32m1\u001b[0m\u001b[32m.\u001b[0m\n"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ },
+ {
+ "data": {
+ "text/html": [
+ "Detected: feature Past medical history , feature ID 3001062 in concept table, match socre = 1 . \n",
+ " \n"
+ ],
+ "text/plain": [
+ "Detected: feature \u001b[32mPast medical history\u001b[0m, feature ID \u001b[1;32m3001062\u001b[0m in concept table, match socre = \u001b[1;32m1\u001b[0m\u001b[32m.\u001b[0m\n"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ },
+ {
+ "data": {
+ "text/html": [
+ "Detected: feature Respiratory Effort , feature ID 21492835 in concept table, match socre = 1 . \n",
+ " \n"
+ ],
+ "text/plain": [
+ "Detected: feature \u001b[32mRespiratory Effort\u001b[0m, feature ID \u001b[1;32m21492835\u001b[0m in concept table, match socre = \u001b[1;32m1\u001b[0m\u001b[32m.\u001b[0m\n"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ },
+ {
+ "data": {
+ "text/html": [
+ "Detected: feature Code Status , feature ID 4127294 in concept table, match socre = 1 . \n",
+ " \n"
+ ],
+ "text/plain": [
+ "Detected: feature \u001b[32mCode Status\u001b[0m, feature ID \u001b[1;32m4127294\u001b[0m in concept table, match socre = \u001b[1;32m1\u001b[0m\u001b[32m.\u001b[0m\n"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ },
+ {
+ "data": {
+ "text/html": [
+ "Detected: feature Pain Management , feature ID 4192791 in concept table, match socre = 1 . \n",
+ " \n"
+ ],
+ "text/plain": [
+ "Detected: feature \u001b[32mPain Management\u001b[0m, feature ID \u001b[1;32m4192791\u001b[0m in concept table, match socre = \u001b[1;32m1\u001b[0m\u001b[32m.\u001b[0m\n"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ },
+ {
+ "data": {
+ "text/html": [
+ "Detected: feature O2 Delivery Device( s ) , feature ID 4036936 in concept table, match socre = 1 . \n",
+ " \n"
+ ],
+ "text/plain": [
+ "Detected: feature \u001b[32mO2 Delivery \u001b[0m\u001b[1;32mDevice\u001b[0m\u001b[1;32m(\u001b[0m\u001b[32ms\u001b[0m\u001b[1;32m)\u001b[0m, feature ID \u001b[1;32m4036936\u001b[0m in concept table, match socre = \u001b[1;32m1\u001b[0m\u001b[32m.\u001b[0m\n"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ },
+ {
+ "data": {
+ "text/html": [
+ "Detected: feature Fall , feature ID 436583 in concept table, match socre = 1 . \n",
+ " \n"
+ ],
+ "text/plain": [
+ "Detected: feature \u001b[32mFall\u001b[0m, feature ID \u001b[1;32m436583\u001b[0m in concept table, match socre = \u001b[1;32m1\u001b[0m\u001b[32m.\u001b[0m\n"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ },
+ {
+ "data": {
+ "text/html": [
+ "Detected: feature Ventilator Type , feature ID 3007397 in concept table, match socre = 1 . \n",
+ " \n"
+ ],
+ "text/plain": [
+ "Detected: feature \u001b[32mVentilator Type\u001b[0m, feature ID \u001b[1;32m3007397\u001b[0m in concept table, match socre = \u001b[1;32m1\u001b[0m\u001b[32m.\u001b[0m\n"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ },
+ {
+ "data": {
+ "text/html": [
+ "Detected: feature Family updated by MD , feature ID 46273928 in concept table, match socre = 1 . \n",
+ " \n"
+ ],
+ "text/plain": [
+ "Detected: feature \u001b[32mFamily updated by MD\u001b[0m, feature ID \u001b[1;32m46273928\u001b[0m in concept table, match socre = \u001b[1;32m1\u001b[0m\u001b[32m.\u001b[0m\n"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ },
+ {
+ "data": {
+ "text/html": [
+ "Detected: feature SVV ( Arterial ) , feature ID 37116693 in concept table, match socre = 1 . \n",
+ " \n"
+ ],
+ "text/plain": [
+ "Detected: feature \u001b[32mSVV \u001b[0m\u001b[1;32m(\u001b[0m\u001b[32mArterial\u001b[0m\u001b[1;32m)\u001b[0m, feature ID \u001b[1;32m37116693\u001b[0m in concept table, match socre = \u001b[1;32m1\u001b[0m\u001b[32m.\u001b[0m\n"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ },
+ {
+ "data": {
+ "text/html": [
+ "Detected: feature Tobacco Use History , feature ID 3012697 in concept table, match socre = 1 . \n",
+ " \n"
+ ],
+ "text/plain": [
+ "Detected: feature \u001b[32mTobacco Use History\u001b[0m, feature ID \u001b[1;32m3012697\u001b[0m in concept table, match socre = \u001b[1;32m1\u001b[0m\u001b[32m.\u001b[0m\n"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ },
+ {
+ "data": {
+ "text/html": [
+ "Detected: feature Family meeting attempted, unable , feature ID 46272666 in concept table, match socre = 1 . \n",
+ " \n"
+ ],
+ "text/plain": [
+ "Detected: feature \u001b[32mFamily meeting attempted, unable\u001b[0m, feature ID \u001b[1;32m46272666\u001b[0m in concept table, match socre = \u001b[1;32m1\u001b[0m\u001b[32m.\u001b[0m\n"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ },
+ {
+ "data": {
+ "text/html": [
+ "Detected: feature OR Sent , feature ID 4162219 in concept table, match socre = 1 . \n",
+ " \n"
+ ],
+ "text/plain": [
+ "Detected: feature \u001b[32mOR Sent\u001b[0m, feature ID \u001b[1;32m4162219\u001b[0m in concept table, match socre = \u001b[1;32m1\u001b[0m\u001b[32m.\u001b[0m\n"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ },
+ {
+ "data": {
+ "text/html": [
+ "Detected: feature MRSA SCREEN , feature ID 37397888 in concept table, match socre = 1 . \n",
+ " \n"
+ ],
+ "text/plain": [
+ "Detected: feature \u001b[32mMRSA SCREEN\u001b[0m, feature ID \u001b[1;32m37397888\u001b[0m in concept table, match socre = \u001b[1;32m1\u001b[0m\u001b[32m.\u001b[0m\n"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ },
+ {
+ "data": {
+ "text/html": [
+ "Detected: feature OR Received , feature ID 4265599 in concept table, match socre = 1 . \n",
+ " \n"
+ ],
+ "text/plain": [
+ "Detected: feature \u001b[32mOR Received\u001b[0m, feature ID \u001b[1;32m4265599\u001b[0m in concept table, match socre = \u001b[1;32m1\u001b[0m\u001b[32m.\u001b[0m\n"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ },
+ {
+ "data": {
+ "text/html": [
+ "Detected: feature ICP Line Insertion Date , feature ID 4048955 in concept table, match socre = 1 . \n",
+ " \n"
+ ],
+ "text/plain": [
+ "Detected: feature \u001b[32mICP Line Insertion Date\u001b[0m, feature ID \u001b[1;32m4048955\u001b[0m in concept table, match socre = \u001b[1;32m1\u001b[0m\u001b[32m.\u001b[0m\n"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ },
+ {
+ "data": {
+ "text/html": [
+ "Couldn't find concept [ 4215685 , 440922 , 44784283 , 4296248 , 2617452 , 4214956 , 4251171 , 40766231 , 40758030 , 46235654 ,\n",
+ "435928 , 443345 , 4179084 , 4310926 , 4306655 , 4207283 , 46273937 , 4119499 , 4323360 , 4311079 , 4239756 , 4203722 , 433942 , \n",
+ "4256640 , 440279 , 4324190 , 4179963 , 40479553 , 46272451 , 440927 , 4060985 , 439221 , 4314870 , 432789 , 4233464 , 433930 , \n",
+ "46272450 , 45766277 , 4276526 , 4135421 , 437165 , 4167217 , 441764 , 4180749 , 46272734 , 37016200 , 4060705 , 4168834 , \n",
+ "4182335 , 4179242 , 441749 , 4019967 , 4143274 , 4178782 , 4014023 , 4324321 , 4323345 , 439228 , 441192 , 439222 , 439996 , \n",
+ "46274064 , 4059907 , 36717001 , 4095498 , 43021271 , 4005823 , 46270032 , 4148407 , 46274011 , 4315085 , 441751 , 436882 , \n",
+ "441744 , 4279614 , 4144274 , 438046 , 4322482 , 44782983 , 443367 , 4162908 , 438950 , 4022569 , 42539646 , 4140830 , 4324181 , \n",
+ "441207 , 43020581 , 4139934 , 4168192 , 40481022 , 433658 , 443370 , 4096435 , 4152408 , 4147565 , 4060084 , 4305831 , \n",
+ "43021273 , 4059910 , 437175 , 36716245 , 436315 , 439371 , 4310065 , 42709971 , 4058728 , 4311077 , 4190634 , 4305297 , \n",
+ "4325851 , 437483 , 4216727 , 4334494 , 441206 , 40481819 , 4312972 , 443340 , 4327107 , 4144292 , 4310928 , 442165 , 4330220 , \n",
+ "443548 , 4179214 , 37016166 , 437738 , 4323344 , 4175576 , 436292 ] in concept table!\n",
+ " \n"
+ ],
+ "text/plain": [
+ "Couldn't find concept \u001b[1m[\u001b[0m\u001b[1;36m4215685\u001b[0m, \u001b[1;36m440922\u001b[0m, \u001b[1;36m44784283\u001b[0m, \u001b[1;36m4296248\u001b[0m, \u001b[1;36m2617452\u001b[0m, \u001b[1;36m4214956\u001b[0m, \u001b[1;36m4251171\u001b[0m, \u001b[1;36m40766231\u001b[0m, \u001b[1;36m40758030\u001b[0m, \u001b[1;36m46235654\u001b[0m,\n",
+ "\u001b[1;36m435928\u001b[0m, \u001b[1;36m443345\u001b[0m, \u001b[1;36m4179084\u001b[0m, \u001b[1;36m4310926\u001b[0m, \u001b[1;36m4306655\u001b[0m, \u001b[1;36m4207283\u001b[0m, \u001b[1;36m46273937\u001b[0m, \u001b[1;36m4119499\u001b[0m, \u001b[1;36m4323360\u001b[0m, \u001b[1;36m4311079\u001b[0m, \u001b[1;36m4239756\u001b[0m, \u001b[1;36m4203722\u001b[0m, \u001b[1;36m433942\u001b[0m, \n",
+ "\u001b[1;36m4256640\u001b[0m, \u001b[1;36m440279\u001b[0m, \u001b[1;36m4324190\u001b[0m, \u001b[1;36m4179963\u001b[0m, \u001b[1;36m40479553\u001b[0m, \u001b[1;36m46272451\u001b[0m, \u001b[1;36m440927\u001b[0m, \u001b[1;36m4060985\u001b[0m, \u001b[1;36m439221\u001b[0m, \u001b[1;36m4314870\u001b[0m, \u001b[1;36m432789\u001b[0m, \u001b[1;36m4233464\u001b[0m, \u001b[1;36m433930\u001b[0m, \n",
+ "\u001b[1;36m46272450\u001b[0m, \u001b[1;36m45766277\u001b[0m, \u001b[1;36m4276526\u001b[0m, \u001b[1;36m4135421\u001b[0m, \u001b[1;36m437165\u001b[0m, \u001b[1;36m4167217\u001b[0m, \u001b[1;36m441764\u001b[0m, \u001b[1;36m4180749\u001b[0m, \u001b[1;36m46272734\u001b[0m, \u001b[1;36m37016200\u001b[0m, \u001b[1;36m4060705\u001b[0m, \u001b[1;36m4168834\u001b[0m, \n",
+ "\u001b[1;36m4182335\u001b[0m, \u001b[1;36m4179242\u001b[0m, \u001b[1;36m441749\u001b[0m, \u001b[1;36m4019967\u001b[0m, \u001b[1;36m4143274\u001b[0m, \u001b[1;36m4178782\u001b[0m, \u001b[1;36m4014023\u001b[0m, \u001b[1;36m4324321\u001b[0m, \u001b[1;36m4323345\u001b[0m, \u001b[1;36m439228\u001b[0m, \u001b[1;36m441192\u001b[0m, \u001b[1;36m439222\u001b[0m, \u001b[1;36m439996\u001b[0m, \n",
+ "\u001b[1;36m46274064\u001b[0m, \u001b[1;36m4059907\u001b[0m, \u001b[1;36m36717001\u001b[0m, \u001b[1;36m4095498\u001b[0m, \u001b[1;36m43021271\u001b[0m, \u001b[1;36m4005823\u001b[0m, \u001b[1;36m46270032\u001b[0m, \u001b[1;36m4148407\u001b[0m, \u001b[1;36m46274011\u001b[0m, \u001b[1;36m4315085\u001b[0m, \u001b[1;36m441751\u001b[0m, \u001b[1;36m436882\u001b[0m, \n",
+ "\u001b[1;36m441744\u001b[0m, \u001b[1;36m4279614\u001b[0m, \u001b[1;36m4144274\u001b[0m, \u001b[1;36m438046\u001b[0m, \u001b[1;36m4322482\u001b[0m, \u001b[1;36m44782983\u001b[0m, \u001b[1;36m443367\u001b[0m, \u001b[1;36m4162908\u001b[0m, \u001b[1;36m438950\u001b[0m, \u001b[1;36m4022569\u001b[0m, \u001b[1;36m42539646\u001b[0m, \u001b[1;36m4140830\u001b[0m, \u001b[1;36m4324181\u001b[0m, \n",
+ "\u001b[1;36m441207\u001b[0m, \u001b[1;36m43020581\u001b[0m, \u001b[1;36m4139934\u001b[0m, \u001b[1;36m4168192\u001b[0m, \u001b[1;36m40481022\u001b[0m, \u001b[1;36m433658\u001b[0m, \u001b[1;36m443370\u001b[0m, \u001b[1;36m4096435\u001b[0m, \u001b[1;36m4152408\u001b[0m, \u001b[1;36m4147565\u001b[0m, \u001b[1;36m4060084\u001b[0m, \u001b[1;36m4305831\u001b[0m, \n",
+ "\u001b[1;36m43021273\u001b[0m, \u001b[1;36m4059910\u001b[0m, \u001b[1;36m437175\u001b[0m, \u001b[1;36m36716245\u001b[0m, \u001b[1;36m436315\u001b[0m, \u001b[1;36m439371\u001b[0m, \u001b[1;36m4310065\u001b[0m, \u001b[1;36m42709971\u001b[0m, \u001b[1;36m4058728\u001b[0m, \u001b[1;36m4311077\u001b[0m, \u001b[1;36m4190634\u001b[0m, \u001b[1;36m4305297\u001b[0m, \n",
+ "\u001b[1;36m4325851\u001b[0m, \u001b[1;36m437483\u001b[0m, \u001b[1;36m4216727\u001b[0m, \u001b[1;36m4334494\u001b[0m, \u001b[1;36m441206\u001b[0m, \u001b[1;36m40481819\u001b[0m, \u001b[1;36m4312972\u001b[0m, \u001b[1;36m443340\u001b[0m, \u001b[1;36m4327107\u001b[0m, \u001b[1;36m4144292\u001b[0m, \u001b[1;36m4310928\u001b[0m, \u001b[1;36m442165\u001b[0m, \u001b[1;36m4330220\u001b[0m, \n",
+ "\u001b[1;36m443548\u001b[0m, \u001b[1;36m4179214\u001b[0m, \u001b[1;36m37016166\u001b[0m, \u001b[1;36m437738\u001b[0m, \u001b[1;36m4323344\u001b[0m, \u001b[1;36m4175576\u001b[0m, \u001b[1;36m436292\u001b[0m\u001b[1m]\u001b[0m in concept table!\n"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ }
+ ],
+ "source": [
+ "adata = omop.extract_features(adata, source='observation', map_concept=True, add_aggregation_to_X=False, verbose=True, remove_empty_column=True, columns_in_source_table = ['observation_id', 'observation_datetime', 'observation_type_concept_id', 'value_as_number'])"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 16,
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "AnnData object with n_obs × n_vars = 852 × 2\n",
+ " obs: 'discharge_to_concept_id', 'death_date', 'ethnicity_source_concept_id', 'visit_start_date', 'gender_source_concept_id', 'discharge_to_source_value', 'provider_id_y', 'visit_source_concept_id', 'death_type_concept_id', 'cause_source_value', 'care_site_id_x', 'preceding_visit_occurrence_id', 'race_source_value', 'admitting_source_value', 'cause_concept_id', 'visit_source_value', 'gender_concept_id', 'race_concept_id', 'care_site_id_y', 'admitting_source_concept_id', 'birth_datetime', 'location_id', 'race_source_concept_id', 'visit_type_concept_id', 'provider_id_x', 'visit_start_datetime', 'visit_concept_id', 'cause_source_concept_id', 'visit_end_datetime', 'day_of_birth', 'visit_end_date', 'death_datetime', 'ethnicity_source_value', 'ethnicity_concept_id', 'person_source_value', 'month_of_birth'\n",
+ " uns: 'numerical_columns', 'non_numerical_columns'\n",
+ " layers: 'original'"
+ ]
+ },
+ "execution_count": 16,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "adata"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 17,
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "discharge_to_concept_id Int64\n",
+ "death_date category\n",
+ "ethnicity_source_concept_id Int64\n",
+ "visit_start_date category\n",
+ "gender_source_concept_id Int64\n",
+ "discharge_to_source_value category\n",
+ "provider_id_y Int64\n",
+ "visit_source_concept_id Int64\n",
+ "death_type_concept_id Int64\n",
+ "cause_source_value category\n",
+ "care_site_id_x Int64\n",
+ "preceding_visit_occurrence_id Int64\n",
+ "race_source_value category\n",
+ "admitting_source_value category\n",
+ "cause_concept_id Int64\n",
+ "visit_source_value category\n",
+ "gender_concept_id Int64\n",
+ "race_concept_id Int64\n",
+ "care_site_id_y Int64\n",
+ "admitting_source_concept_id Int64\n",
+ "birth_datetime category\n",
+ "location_id Int64\n",
+ "race_source_concept_id Int64\n",
+ "visit_type_concept_id Int64\n",
+ "provider_id_x Int64\n",
+ "visit_start_datetime category\n",
+ "visit_concept_id Int64\n",
+ "cause_source_concept_id Int64\n",
+ "visit_end_datetime category\n",
+ "day_of_birth Int64\n",
+ "visit_end_date category\n",
+ "death_datetime category\n",
+ "ethnicity_source_value category\n",
+ "ethnicity_concept_id Int64\n",
+ "person_source_value category\n",
+ "month_of_birth Int64\n",
+ "dtype: object"
+ ]
+ },
+ "execution_count": 17,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "adata.obs.dtypes"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 7,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "adata1 = adata.copy()"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 4,
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/html": [
+ "Trying to extarct the following features: [ 40762499 ] \n",
+ " \n"
+ ],
+ "text/plain": [
+ "Trying to extarct the following features: \u001b[1m[\u001b[0m\u001b[1;36m40762499\u001b[0m\u001b[1m]\u001b[0m\n"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ },
+ {
+ "data": {
+ "text/html": [
+ "Detected: feature O2 saturation pulseoxymetry , feature ID 40762499 in concept table, match socre = 1 . \n",
+ " \n"
+ ],
+ "text/plain": [
+ "Detected: feature \u001b[32mO2 saturation pulseoxymetry\u001b[0m, feature ID \u001b[1;32m40762499\u001b[0m in concept table, match socre = \u001b[1;32m1\u001b[0m\u001b[32m.\u001b[0m\n"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ },
+ {
+ "name": "stderr",
+ "output_type": "stream",
+ "text": [
+ "/opt/anaconda3/envs/ehrapy_latents/lib/python3.9/site-packages/anndata/utils.py:334: ExperimentalFeatureWarning: Support for Awkward Arrays is currently experimental. Behavior may change in the future. Please report any issues you may encounter!\n",
+ " warnings.warn(msg, category, stacklevel=stacklevel)\n"
+ ]
+ }
+ ],
+ "source": [
+ "adata = omop.extract_features(adata, source='measurement', features=[40762499], map_concept=True, add_aggregation_to_X=False, verbose=True, remove_empty_column=True)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "adata = omop.extract_features(adata, source='observation', features=[2000030003], map_concept=True, add_aggregation_to_X=False, verbose=True, remove_empty_column=True)"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "## Feature Extraction"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 17,
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/html": [
+ "Detected: feature O2 saturation pulseoxymetry , feature ID 2000030003 in concept table, feature ID 40762499 in \n",
+ "concept relationship table, match socre = 1 . \n",
+ " \n"
+ ],
+ "text/plain": [
+ "Detected: feature \u001b[32mO2 saturation pulseoxymetry\u001b[0m, feature ID \u001b[1;32m2000030003\u001b[0m in concept table, feature ID \u001b[1;32m40762499\u001b[0m in \n",
+ "concept relationship table, match socre = \u001b[1;32m1\u001b[0m\u001b[32m.\u001b[0m\n"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ },
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "extracting features\n",
+ "\u001b[1;35m2024-01-02 17:00:32,078\u001b[0m - \u001b[1;34mroot\u001b[0m \u001b[1;30mINFO - Added `['O2 saturation pulseoxymetry_min', 'O2 saturation pulseoxymetry_max', 'O2 saturation pulseoxymetry_mean']` columns to `obs`.\u001b[0m\n",
+ "\u001b[1;35m2024-01-02 17:00:32,080\u001b[0m - \u001b[1;34mroot\u001b[0m \u001b[1;30mINFO - Added `['O2 saturation pulseoxymetry_min', 'O2 saturation pulseoxymetry_max', 'O2 saturation pulseoxymetry_mean']` features to `X`.\u001b[0m\n"
+ ]
+ }
+ ],
+ "source": [
+ "# Extract features from tables\n",
+ "# Different sources are supported: measurement, observation\n",
+ "\n",
+ "# Could use feature ID \n",
+ "adata = omop.extract_features(adata, source='measurement', features=[2000030003], map_concept=True, add_aggregation_to_X=True, add_all_data=True, verbose=True)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 18,
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/html": [
+ "Detected: feature Base Excess|Blood|Blood Gas , feature ID 2000001002 in concept table, feature ID 3012501 in \n",
+ "concept relationship table, match socre = 1.0 . \n",
+ " \n"
+ ],
+ "text/plain": [
+ "Detected: feature \u001b[32mBase Excess|Blood|Blood Gas\u001b[0m, feature ID \u001b[1;32m2000001002\u001b[0m in concept table, feature ID \u001b[1;32m3012501\u001b[0m in \n",
+ "concept relationship table, match socre = \u001b[1;32m1.0\u001b[0m\u001b[32m.\u001b[0m\n"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ },
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "extracting features\n",
+ "\u001b[1;35m2024-01-02 17:00:35,969\u001b[0m - \u001b[1;34mroot\u001b[0m \u001b[1;30mINFO - Added `['Base Excess|Blood|Blood Gas_min', 'Base Excess|Blood|Blood Gas_max', 'Base Excess|Blood|Blood Gas_mean']` columns to `obs`.\u001b[0m\n",
+ "\u001b[1;35m2024-01-02 17:00:35,970\u001b[0m - \u001b[1;34mroot\u001b[0m \u001b[1;30mINFO - Added `['Base Excess|Blood|Blood Gas_min', 'Base Excess|Blood|Blood Gas_max', 'Base Excess|Blood|Blood Gas_mean']` features to `X`.\u001b[0m\n"
+ ]
+ }
+ ],
+ "source": [
+ "# Could use feature name\n",
+ "adata = omop.extract_features(adata, source='measurement', features=[\"Base Excess|Blood|Blood Gas\"], map_concept=True, add_aggregation_to_X=True, add_all_data=True, verbose=True)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 65,
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/html": [
+ "\n",
+ "\n",
+ "
\n",
+ " \n",
+ " \n",
+ " Unit \n",
+ " domain_id \n",
+ " concept_class_id \n",
+ " concept_code \n",
+ " \n",
+ " \n",
+ " \n",
+ " \n",
+ " year_of_birth \n",
+ " NaN \n",
+ " NaN \n",
+ " NaN \n",
+ " NaN \n",
+ " \n",
+ " \n",
+ " gender_source_value \n",
+ " NaN \n",
+ " NaN \n",
+ " NaN \n",
+ " NaN \n",
+ " \n",
+ " \n",
+ " O2 saturation pulseoxymetry_min \n",
+ " NaN \n",
+ " NaN \n",
+ " NaN \n",
+ " NaN \n",
+ " \n",
+ " \n",
+ " O2 saturation pulseoxymetry_max \n",
+ " NaN \n",
+ " NaN \n",
+ " NaN \n",
+ " NaN \n",
+ " \n",
+ " \n",
+ " O2 saturation pulseoxymetry_mean \n",
+ " NaN \n",
+ " NaN \n",
+ " NaN \n",
+ " NaN \n",
+ " \n",
+ " \n",
+ " Base Excess|Blood|Blood Gas_min \n",
+ " mEq/L \n",
+ " Measurement \n",
+ " Lab Test \n",
+ " 50802 \n",
+ " \n",
+ " \n",
+ " Base Excess|Blood|Blood Gas_max \n",
+ " mEq/L \n",
+ " Measurement \n",
+ " Lab Test \n",
+ " 50802 \n",
+ " \n",
+ " \n",
+ " Base Excess|Blood|Blood Gas_mean \n",
+ " mEq/L \n",
+ " Measurement \n",
+ " Lab Test \n",
+ " 50802 \n",
+ " \n",
+ " \n",
+ "
\n",
+ "