{ "cells": [ { "cell_type": "code", "execution_count": 1, "metadata": {}, "outputs": [], "source": [ "import pandas as pd\n", "from OpenAITools.JRCTTools import fetch_clinical_trials, extract_jrct_links, create_dataframe_from_urls, reorder_columns" ] }, { "cell_type": "code", "execution_count": 2, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "検索ボタンがクリックできないため、JavaScriptでクリックします。\n", "1 ページ目を処理しました。\n", "2 ページ目を処理しました。\n", "3 ページ目を処理しました。\n", "4 ページ目を処理しました。\n", "5 ページ目を処理しました。\n", "6 ページ目を処理しました。\n", "7 ページ目を処理しました。\n", "8 ページ目を処理しました。\n", "9 ページ目を処理しました。\n", "10 ページ目を処理しました。\n", "11 ページ目を処理しました。\n", "12 ページ目を処理しました。\n", "13 ページ目を処理しました。\n", "14 ページ目を処理しました。\n", "15 ページ目を処理しました。\n", "16 ページ目を処理しました。\n", "17 ページ目を処理しました。\n", "次のページはありません。全ての結果を取得しました。\n" ] } ], "source": [ "# fetch_clinical_trialsを使って検索結果を取得\n", "results = fetch_clinical_trials(disease_name=\"がん 神経膠腫 骨髄腫 黒色腫 肉腫 間質腫瘍 膠芽腫 内分泌腫瘍 パジェット ラブドイド 癌 固形腫瘍 リンパ腫 中皮腫 新生物 SCLC\", freeword=\"\"\n", " ,include_not_yet_recruiting=True,\n", " include_suspended=True,\n", " specific_clinical_research=True,\n", " corporate_clinical_trial=True,\n", " physician_initiated_clinical_trial=True)" ] }, { "cell_type": "code", "execution_count": 3, "metadata": {}, "outputs": [ { "data": { "text/plain": [ "827" ] }, "execution_count": 3, "metadata": {}, "output_type": "execute_result" } ], "source": [ "len(results)" ] }, { "cell_type": "code", "execution_count": 7, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Processing URL: https://jrct.niph.go.jp/latest-detail/jRCT2021240039\n", "Waiting for 15 seconds before the next request...\n", "Processing URL: https://jrct.niph.go.jp/latest-detail/jRCT1030240513\n", "Waiting for 15 seconds before the next request...\n", "Processing URL: https://jrct.niph.go.jp/latest-detail/jRCTs022240038\n", "Waiting for 15 seconds before the next request...\n", "Processing URL: 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for 15 seconds before the next request...\n", "Processing URL: https://jrct.niph.go.jp/latest-detail/jRCT1091220221\n", "Waiting for 15 seconds before the next request...\n", "Processing URL: https://jrct.niph.go.jp/latest-detail/jRCT1080222856\n", "Waiting for 15 seconds before the next request...\n", "Processing URL: https://jrct.niph.go.jp/latest-detail/jRCT2080221970\n", "Waiting for 15 seconds before the next request...\n" ] } ], "source": [ " # jRCT詳細リンクを作成\n", "jrct_links = extract_jrct_links(results)\n", "\n", " # 詳細リンクからデータフレームを作成\n", "df = create_dataframe_from_urls(jrct_links,delay=15)" ] }, { "cell_type": "code", "execution_count": 8, "metadata": {}, "outputs": [], "source": [ "# 整列後の DataFrame を作成\n", "sorted_df = reorder_columns(df)" ] }, { "cell_type": "code", "execution_count": 9, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "/var/folders/yw/qz00x75d7kb98f7vm8dkhkvw0000gn/T/ipykernel_94701/3932068550.py:1: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n", " sorted_df['JRCT ID'] = [result[0] for result in results]\n", "/var/folders/yw/qz00x75d7kb98f7vm8dkhkvw0000gn/T/ipykernel_94701/3932068550.py:2: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n", " sorted_df['Title'] = [result[1] for result in results]\n", "/var/folders/yw/qz00x75d7kb98f7vm8dkhkvw0000gn/T/ipykernel_94701/3932068550.py:3: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n", " sorted_df['Target'] = [result[2] for result in results]\n" ] } ], "source": [ "sorted_df['JRCT ID'] = [result[0] for result in results]\n", "sorted_df['Title'] = [result[1] for result in results]\n", "sorted_df['Target'] = [result[2] for result in results]" ] }, { "cell_type": "code", "execution_count": 10, "metadata": {}, "outputs": [], "source": [ "new_order = [\"JRCT ID\", 'NCT No', 'JapicCTI No',\"Title\",'Target'] + [col for col in sorted_df.columns if col not in [\"JRCT ID\", 'NCT No', 'JapicCTI No',\"Title\",'Target']]" ] }, { "cell_type": "code", "execution_count": 11, "metadata": {}, "outputs": [], "source": [ "sorted_df = sorted_df[new_order]" ] }, { "cell_type": "code", "execution_count": 12, "metadata": {}, "outputs": [ { "data": { "text/html": [ "
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JRCT IDNCT NoJapicCTI NoTitleTarget研究・治験の目的試験等のフェーズ試験の種類無作為化盲検化...assignmentpurposeInclusion CriteriaExclusion CriteriaAge MinimumAge MaximumGenderDiscontinuation CriteriaKeywordIntervention(s)
0jRCT2021240039NCT06632951None[M25-204]転移性尿路上皮癌患者を対象に，livmoniplimab とbudigal...尿路上皮癌主要目的：全生存期間（以下「OS」）を指標として，livmoniplimab と budig...2None無作為化比較非盲検...parallel assignmenttreatment purpose-Participant has histologically or cytological...-Participant has received more than 1 prior ch...18age old overNo limitBothNaN-Arm 1: Livmoniplimab (Dose A) + Budigalimab\\r...
1jRCT1030240513NoneNone進行がん患者に対する可聴領域外のハイレゾ自然音源が与える生体情報や癒しの変化を評価する\\n探...がん進行がん患者を対象に、可聴領域外のハイレゾ自然音源を介入とした音楽療法が、無音と比較して、疲...None介入研究無作為化比較単盲検...parallel assignmentsupportive careEligible participants must meet the following ...Exclusion criteria apply if any of the followi...18age old overNo limitNaNcancer,Participants will be exposed to either sounds ...
2jRCTs022240038NoneNone手術支援ロボットを用いた遠隔手術支援の臨床応用消化器癌消化器がんの患者のうち、内視鏡手術用支援機器を用いる手術の適応がある患者を対象として、遠隔地...None介入研究単一群非盲検...single assignmenttreatment purpose1) Patients with gastrointestinal cancer using...1) Difficulty of curative resection\\r\\n2) Diff...20age old overNo limitBothNaNTelesurgery, robotTelesurgcal support via communication lines fr...
3jRCT1041240134NoneNone乳がん患者におけるアベマシクリブによる下痢症状に対するロペラミド予防投与の有効性検証試験乳癌アベマシクリブに起因する下痢に対しロペラミドを予防内服することでアベマシクリブの減量を回避することNone介入研究単一群非盲検...single assignmenttreatment purpose1)Patients with hormone receptor-positive, HER...1)Patients with severe complications (e.g., in...18age old overNo limitBothNaNAdminister 1 mg of loperamide at the onset of ...
4jRCT2031240512NoneNoneフッ化ピリミジン製剤及びプラチナ製剤を含む一次治療に不応・不耐となった切除不能進行・再発胃癌...切除不能進行・再発胃癌フッ化ピリミジン・プラチナ系薬剤に不応・不耐の切除不能進行・再発胃癌被験者を対象として、ベバ...1None無作為化比較非盲検...parallel assignmenttreatment purpose1)\\tAge between 18 and 75 years.\\r\\n2)\\tPerfor...1)\\tPrior treatment history with paclitaxel, r...18age old over75age old underBothNaNSafety Part (Dose Escalation):\\r\\nLevel 0: Bev...
..................................................................
1141jRCT1091220254NoneNone肺動静脈分離3D-CT angiographyにおけるヨード造影剤量低減の検討肺がんNoneNoneNoneNone単盲検...YesNoneNoneNoneAge Month Week Day Hour No limitAge Month Week Day Hour No limitBothNaNIntervention type:DRUG\\nName of intervention: ...
1142jRCT1090220224NoneNone体幹部神経ブロック後のレボブピバカインの血中濃度の変化下腹部消化器がんNoneNoneNoneNone非盲検...NoneNoneNone20Age Month Week Day Hour overAge Month Week Day Hour No limitBothNaNIntervention type:\\nName of intervention:\\nDos...
1143jRCT1091220221NoneNoneヨード造影剤と生理食塩水の混合溶液を用いたtest injectionによる混合割合と造影効...肺がんNoneNoneNoneNone非盲検...NoNoneNoneNoneAge Month Week Day Hour No limitAge Month Week Day Hour No limitBothNaNIntervention type:DRUG\\nName of intervention:N...
1144jRCT1080222856NoneJapicCTI-152908レンビマカプセル特定使用成績調査実施計画書−根治切除不能な甲状腺癌患者における安全性及び有効...根治切除不能な甲状腺癌NoneNone観察研究NoneNone...NoneNoneNoneNoneNoneNoneBothNaNinvestigational material(s)\\nGeneric name etc ...
1145jRCT2080221970NoneJapicCTI-122016進行／再発副腎皮質癌に対するgemcitabine、capecitabine併用化学療法副腎皮質癌NoneNone介入研究NoneNone...NoneNoneNoneNoneNoneNoneBothNaN
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1146 rows × 38 columns

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" ], "text/plain": [ " JRCT ID NCT No JapicCTI No \\\n", "0 jRCT2021240039 NCT06632951 None \n", "1 jRCT1030240513 None None \n", "2 jRCTs022240038 None None \n", "3 jRCT1041240134 None None \n", "4 jRCT2031240512 None None \n", "... ... ... ... \n", "1141 jRCT1091220254 None None \n", "1142 jRCT1090220224 None None \n", "1143 jRCT1091220221 None None \n", "1144 jRCT1080222856 None JapicCTI-152908 \n", "1145 jRCT2080221970 None JapicCTI-122016 \n", "\n", " Title Target \\\n", "0 [M25-204]転移性尿路上皮癌患者を対象に，livmoniplimab とbudigal... 尿路上皮癌 \n", "1 進行がん患者に対する可聴領域外のハイレゾ自然音源が与える生体情報や癒しの変化を評価する\\n探... がん \n", "2 手術支援ロボットを用いた遠隔手術支援の臨床応用 消化器癌 \n", "3 乳がん患者におけるアベマシクリブによる下痢症状に対するロペラミド予防投与の有効性検証試験 乳癌 \n", "4 フッ化ピリミジン製剤及びプラチナ製剤を含む一次治療に不応・不耐となった切除不能進行・再発胃癌... 切除不能進行・再発胃癌 \n", "... ... ... \n", "1141 肺動静脈分離3D-CT angiographyにおけるヨード造影剤量低減の検討 肺がん \n", "1142 体幹部神経ブロック後のレボブピバカインの血中濃度の変化 下腹部消化器がん \n", "1143 ヨード造影剤と生理食塩水の混合溶液を用いたtest injectionによる混合割合と造影効... 肺がん \n", "1144 レンビマカプセル特定使用成績調査実施計画書−根治切除不能な甲状腺癌患者における安全性及び有効... 根治切除不能な甲状腺癌 \n", "1145 進行／再発副腎皮質癌に対するgemcitabine、capecitabine併用化学療法 副腎皮質癌 \n", "\n", " 研究・治験の目的 試験等のフェーズ 試験の種類 \\\n", "0 主要目的：全生存期間（以下「OS」）を指標として，livmoniplimab と budig... 2 None \n", "1 進行がん患者を対象に、可聴領域外のハイレゾ自然音源を介入とした音楽療法が、無音と比較して、疲... None 介入研究 \n", "2 消化器がんの患者のうち、内視鏡手術用支援機器を用いる手術の適応がある患者を対象として、遠隔地... None 介入研究 \n", "3 アベマシクリブに起因する下痢に対しロペラミドを予防内服することでアベマシクリブの減量を回避すること None 介入研究 \n", "4 フッ化ピリミジン・プラチナ系薬剤に不応・不耐の切除不能進行・再発胃癌被験者を対象として、ベバ... 1 None \n", "... ... ... ... \n", "1141 None None None \n", "1142 None None None \n", "1143 None None None \n", "1144 None None 観察研究 \n", "1145 None None 介入研究 \n", "\n", " 無作為化 盲検化 ... assignment purpose \\\n", "0 無作為化比較 非盲検 ... parallel assignment treatment purpose \n", "1 無作為化比較 単盲検 ... parallel assignment supportive care \n", "2 単一群 非盲検 ... single assignment treatment purpose \n", "3 単一群 非盲検 ... single assignment treatment purpose \n", "4 無作為化比較 非盲検 ... parallel assignment treatment purpose \n", "... ... ... ... ... ... \n", "1141 None 単盲検 ... Yes None \n", "1142 None 非盲検 ... None \n", "1143 None 非盲検 ... No None \n", "1144 None None ... None None \n", "1145 None None ... None None \n", "\n", " Inclusion Criteria \\\n", "0 -Participant has histologically or cytological... \n", "1 Eligible participants must meet the following ... \n", "2 1) Patients with gastrointestinal cancer using... \n", "3 1)Patients with hormone receptor-positive, HER... \n", "4 1)\\tAge between 18 and 75 years.\\r\\n2)\\tPerfor... \n", "... ... \n", "1141 None \n", "1142 None \n", "1143 None \n", "1144 None \n", "1145 None \n", "\n", " Exclusion Criteria \\\n", "0 -Participant has received more than 1 prior ch... \n", "1 Exclusion criteria apply if any of the followi... \n", "2 1) Difficulty of curative resection\\r\\n2) Diff... \n", "3 1)Patients with severe complications (e.g., in... \n", "4 1)\\tPrior treatment history with paclitaxel, r... \n", "... ... \n", "1141 None \n", "1142 None \n", "1143 None \n", "1144 None \n", "1145 None \n", "\n", " Age Minimum Age Maximum \\\n", "0 18age old over No limit \n", "1 18age old over No limit \n", "2 20age old over No limit \n", "3 18age old over No limit \n", "4 18age old over 75age old under \n", "... ... ... \n", "1141 Age Month Week Day Hour No limit Age Month Week Day Hour No limit \n", "1142 20Age Month Week Day Hour over Age Month Week Day Hour No limit \n", "1143 Age Month Week Day Hour No limit Age Month Week Day Hour No limit \n", "1144 None None \n", "1145 None None \n", "\n", " Gender Discontinuation Criteria Keyword \\\n", "0 Both NaN \n", "1 NaN cancer, \n", "2 Both NaN Telesurgery, robot \n", "3 Both NaN \n", "4 Both NaN \n", "... ... ... ... \n", "1141 Both NaN \n", "1142 Both NaN \n", "1143 Both NaN \n", "1144 Both NaN \n", "1145 Both NaN \n", "\n", " Intervention(s) \n", "0 -Arm 1: Livmoniplimab (Dose A) + Budigalimab\\r... \n", "1 Participants will be exposed to either sounds ... \n", "2 Telesurgcal support via communication lines fr... \n", "3 Administer 1 mg of loperamide at the onset of ... \n", "4 Safety Part (Dose Escalation):\\r\\nLevel 0: Bev... \n", "... ... \n", "1141 Intervention type:DRUG\\nName of intervention: ... \n", "1142 Intervention type:\\nName of intervention:\\nDos... \n", "1143 Intervention type:DRUG\\nName of intervention:N... \n", "1144 investigational material(s)\\nGeneric name etc ... \n", "1145 \n", "\n", "[1146 rows x 38 columns]" ] }, "execution_count": 12, "metadata": {}, "output_type": "execute_result" } ], "source": [ "sorted_df" ] }, { "cell_type": "code", "execution_count": 13, "metadata": {}, "outputs": [], "source": [ "sorted_df.to_csv('../JRCT20241208Cancer.csv')" ] }, { "cell_type": "code", "execution_count": 14, "metadata": {}, "outputs": [ { "data": { "text/plain": [ "array(['NCT06632951', None, 'NCT06692738', 'NCT06573294', 'NCT06627647',\n", " 'NCT06549595', 'NCT06660654', 'NCT06496178', 'NCT06608927',\n", " 'NCT04898634', 'NCT06393374', 'NCT06312176', 'NCT06629779',\n", " 'NCT06698042', 'NCT06561386', 'NCT05445778', 'NCT06509906',\n", " 'NCT06598306', 'NCT05605899', 'NCT06486441', 'NCT06435429',\n", " 'NCT06586515', 'NCT06551142', 'NCT06077760', 'NCT06622941',\n", " 'NCT06564844', 'NCT06360354', 'NCT06622226', 'NCT05580562',\n", " 'NCT06346392', 'NCT06581432', 'NCT06561685', 'NCT06555744',\n", " 'NCT05730036', 'NCT06551324', 'NCT04777851', 'NCT06413706',\n", " 'NCT06417814', 'NCT03423628', 'NCT06528093', 'NCT06465069',\n", " 'NCT06333951', nan, 'NCT06526793', 'NCT06312137', 'NCT04547166',\n", " 'NCT06431594', 'NCT06497556', 'NCT06400472', 'NCT06526819',\n", " 'NCT06012435', 'NCT06421935', 'NCT05424822', 'NCT06452277',\n", " 'NCT06508658', 'NCT06305754', 'NCT03313778', 'NCT04895709',\n", " 'NCT04852887', 'NCT06467357', 'NCT06353386', 'NCT06282575',\n", " 'NCT06223516', 'NCT06318273', 'NCT06170788', 'NCT06191744',\n", " 'NCT06345729', 'NCT06422143', 'NCT06459180', 'NCT06356129',\n", " 'NCT06470438', 'NCT05201066', 'NCT04482309', 'NCT06095583',\n", " 'NCT06428409', 'NCT05456256', 'NCT06535893', 'NCT06158841',\n", " 'NCT06356311', 'NCT06211036', 'NCT06074588', 'NCT06131398',\n", " 'NCT06319820', 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'NCT05654623', 'NCT05347485', 'NCT05319730',\n", " 'NCT05572515', 'NCT05253651', 'NCT05629585', 'NCT05546476',\n", " 'NCT05623020', 'NCT05619744', 'NCT04892173', 'NCT05567185',\n", " 'NCT05257083', 'NCT05498428', 'NCT05261399', 'NCT05555732',\n", " 'NCT05489211', 'NCT05277051', 'NCT05206357', 'NCT05565378',\n", " 'NCT05259839', 'NCT05397496', 'NCT05464030', 'NCT05325866',\n", " 'NCT05440786', 'NCT05275868', 'NCT05307705', 'NCT05481437',\n", " 'NCT05099172', 'NCT05337137', 'NCT05137847', 'NCT05298423',\n", " 'NCT05201781', 'NCT05067283', 'NCT05238922', 'NCT04707248',\n", " 'NCT05317416', 'NCT05301842', 'NCT05322577', 'NCT04928846',\n", " 'NCT04862663', 'NCT04771078', 'NCT05094336', 'NCT05211895',\n", " 'NCT05111626', 'NCT04960709', 'NCT05221840', 'NCT05365581',\n", " 'NCT05083169', 'NCT03888105', 'NCT03960840', 'NCT05123482',\n", " 'NCT05061823', 'NCT06535009', 'NCT05114746', 'NCT05048797',\n", " 'NCT02912949', 'NCT04803994', 'NCT05091346', 'NCT05029882',\n", " 'NCT05005403', 'NCT04819100', 'NCT04857372', 'NCT05034887',\n", " 'NCT03438474', 'NCT05021562', 'NCT05012618', 'NCT03398655',\n", " 'NCT04956640', 'NCT05064618', 'NCT04949256', 'NCT04923893',\n", " 'NCT04975997', 'NCT03609359', 'NCT04886804', 'NCT04185883',\n", " 'NCT04452591', 'NCT04711252', 'NCT04777994', 'NCT04660344',\n", " 'NCT04612751', 'NCT04400591', 'NCT03711032', 'NCT04221542',\n", " 'NCT04661007', 'NCT04640623', 'NCT04649073', 'NCT04606446',\n", " 'NCT03769506', 'NCT04683250', 'NCT04379596', 'NCT03899155',\n", " 'NCT04542824', 'NCT04189614', 'NCT04429087', 'NCT04417465',\n", " 'NCT04328948', 'NCT04419532', 'NCT04211337', 'NCT04210115',\n", " 'NCT03899792', 'NCT03768063', 'NCT03969004', 'NCT04145622',\n", " 'NCT04094311', 'NCT04288999', 'NCT03260491', 'NCT04008797',\n", " 'NCT03821935', 'NCT03818893', 'NCT02609776', 'NCT03444701',\n", " 'NCT03401385'], dtype=object)" ] }, "execution_count": 14, "metadata": {}, "output_type": "execute_result" } ], "source": [ "sorted_df['NCT No'].unique()" ] 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