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| TEMPLATE_v3 = '''We now have a following <document> in the medical field: | |
| """ | |
| {} | |
| """ | |
| You are an expert in biomedical research. | |
| You are asked to answer the following <question>s based on the <document>, the <question>s and their <instruction>s and <rule>s are as follows: | |
| - "Question 1": | |
| - "question": "What is the <animal type> of this study?" | |
| - "instruction": "This task is to find the <animal type> according to the <document>." | |
| - "definition": | |
| - "animal type": "The rodent type used in the article" | |
| - "rule": "<answer> of <animal type> should be one of the two choices {{mice/rats}} or both" | |
| - "Question 2": | |
| - "question": "What is the <exposure age> of this study?" | |
| - "instruction": "This task is to find the <exposure age> according to the <document>." | |
| - "definition": | |
| - "exposure age": "The age when the animals were exposed to anesthetics. There are two kinds of <exposure age>: <postnatal day> and <gestational day>" | |
| - "postnatal day": "<postnatal day> means the days after the animals were born. For example, 'postnatal day <int>' means the animals were born for <int> day. 'postnatal day <int>' is sometimes shortened to 'PND <int>' or 'pnd <int>', which still means 'postnatal day <int>', after birth. 'postnatal day <int>' is sometimes shortened to 'p<int>', which still means 'postnatal day <int>', after birth" | |
| - "gestational day": "<gestational day> means the days after the animals were pregnant. For example, 'gestational day <int>' means the animals were pregnant for <int> day. 'gestational day <int>' is sometimes abbreviated as 'E <int>', 'E' meaning before birth" | |
| - "rule": "<answer> of <exposure age> should be expressed as one of {{'postnatal day <int>'/'gestational day <int>'}}. For Example: "postnatal day 7", "Gestational day 21" | |
| - "Question 3": | |
| - "question": "Is there any <behavior test> done in this study?" | |
| - "instruction": "This task is to find whether there are any <behavior test> in the study according to the <document>." | |
| - "definition": | |
| - "behavior test": "If there are any of the <behavior tests> described and done in the article, which mentioned as: 'Open field test', 'Morris water task', 'fear conditioning test', 'Dark/light avoidance'; 'passive/active avoidance test'; 'elevated maze', 'Forced swim test', 'Object recognition test', 'Social interaction/preference'." | |
| - "rule": "<answer> to <behavior test> should be one of the two choices {{Yes/No}}." | |
| - "Question 4": | |
| - "question": "What's the <intervention>s of this study? | |
| - "instruction": "This task is to find the <intervention>s according to the <document>." | |
| - "definition": | |
| - "intervention": "The <intervention>s are anesthetic drugs, which in one of {{"isoflurane"/"sevoflurane"/"desflurane"/"ketamine"/"propofol"/"Midazolam"/"Nitrous oxide“}}." | |
| - "rule": "There are one or two <intervention>s in the <document>. Please find them all and answer the <question>. If there is only one <intervention>, the second one is 'None'." | |
| - "Question 5": | |
| - "question": "What's the <genetic chain> of this study?" | |
| - "instruction": "This task is to find the <genetic chain> according to the <document>." | |
| - "definition": | |
| - "genetic chain": "The <genetic chain> is the genetic type of the animals being used in the article." | |
| - "rule": "Please do as the following examples: 'C57BL/6', 'C57BL/6J' should be extracted as 'C57BL/6'; 'Sprague Dawley', 'Sprague-Dawley', 'SD' should be extracted as 'Sprague Dawley'; 'CD-1' should be extracted as 'CD-1'; 'Wistar/ST' should be extracted as 'Wistar/ST'; 'Wistar' should be extracted as 'Wistar'; 'FMR-1 KO' should be extracted as 'FMR-1 KO'." | |
| Here is the instrucrtions for all the <question>s: | |
| 1. Please select the <original sentences> related the "behavior tests" from the <document> for each <question>. | |
| 2. Please use the <original sentences> to answer the <question> by following the <rule> and <instruction> accroding to the <definition>. | |
| 3. Please provide <original sentences> coming from the <document>. | |
| 4. Output the <answer> in the following JSON format: | |
| {{ | |
| "Question 1": {{ | |
| "answer": "{{mice/rats/both}}", | |
| "original sentences": [] | |
| }}, | |
| "Question 2": {{ | |
| "answer": "{{postnatal day <int>/gestational day <int>}}", | |
| "original sentences": [] | |
| }}, | |
| "Question 3": {{ | |
| "answer": "{{Yes/No}}", | |
| "original sentences": [] | |
| }}, | |
| "Question 4": | |
| {{ | |
| {{intervention 1}}: {{ | |
| "answer": "{{intervention 1}}]", | |
| "original sentences": [] | |
| }} | |
| {{intervention 2}}: {{ | |
| "answer": "{{intervention 2}}", | |
| "original sentences": [] | |
| }} | |
| }}, | |
| "Question 5": {{ | |
| "answer": "{{genetic chain}}", | |
| "original sentences": [] | |
| }} | |
| }} | |
| ''' | |
| TEMPLATE_v2 = '''We now have a following <document> in the medical field: | |
| """ | |
| {} | |
| """ | |
| We have some introduction here: | |
| 1. DOI: The DOI link for the article, usually can be found in the first line of the .txt file for the article. E.g., “DOI: 10.3892/mmr.2019.10397”. | |
| 2. Citation ID: The number in the file name. E.g., “1134”. | |
| 3. First author: The last name in the file name. E.g., “Guan”. | |
| 4. Year: The year in the file name. E.g., “2019”. | |
| 5. Animal type: The rodent type used in the article, should be one of the choices: mice, rats. E.g., “rats”. | |
| 6. Exposure age: The age when the animals were exposed to anesthetics, should be mentioned as "PND1", "PND7","postnatal day 7", "Gestational day 21", etc, which should be extract as: 'PND XX' , 'Gestational day xx'. E.g., “PND7”. | |
| 7. Behavior test: Whether there is any behavior test in the article, should be one of the choices: "Y", "N". "Y" is chosen if there are any of the behavior tests described and done in the article, which mentioned as: "Open field test", "Morris water task", "fear conditioning test", "Dark/light avoidance"; "passive/active avoidance test"; "elevated maze", "Forced swim test", "Object recognition test", "Social interaction/preference“. E.g., “N”. | |
| 8. Intervention 1 & Intervention 2: Intervention 1 and Intervention 2 are both anesthetic drugs, which listed as: "isoflurane", "sevoflurane", "desflurane", "ketamine", "propofol", "Midazolam", "Nitrous oxide“. If none, put “NA”. E.g., “propofol”. | |
| 9. Genetic chain: Genetic chain is the genetic type of the animals being used in the article, here is the examples: | |
| "C57BL/6", "C57BL/6J" should be extracted as "C57BL/6"; "Sprague Dawley", "Sprague-Dawley", "SD" should be extracted as "Sprague Dawley"; "CD-1" should be extracted as "CD-1"; "Wistar/ST" should be extracted as "Wistar/ST"; "Wistar" should be extracted as "Wistar"; "FMR-1 KO" should be extracted as "FMR-1 KO“. E.g., “Sprague Dawley”. | |
| We have some <question>s begin with "Question" here: | |
| """ | |
| {} | |
| """ | |
| Please finish the following task: | |
| 1. Please select the <original sentences> related the each <question> from the <document>. | |
| 2. Please use the <original sentences> to answer the <question>. | |
| 3. Please provide <original sentences> coming from the <document>. | |
| 4. Output the <answer> in the following json format: | |
| {{ | |
| "Question 1": {{ | |
| "question": {{}}, | |
| "answer": {{}}, | |
| "original sentences": [] | |
| }}, | |
| "Question 2": {{ | |
| "question": {{}}, | |
| "answer": {{}}, | |
| "original sentences": [] | |
| }}, | |
| ... | |
| }} | |
| ''' | |
| TEMPLATE_v1 = '''We now have a following <document> in the medical field: | |
| """ | |
| {} | |
| """ | |
| We have some <question>s begin with "Question" here: | |
| """ | |
| {} | |
| """ | |
| Please finish the following task: | |
| 1. Please select the <original sentences> related the each <question> from the <document>. | |
| 2. Please use the <original sentences> to answer the <question>. | |
| 3. Please provide <original sentences> coming from the <document>. | |
| 4. Output the <answer> in the following json format: | |
| {{ | |
| "Question 1": {{ | |
| "question": {{}}, | |
| "answer": {{}}, | |
| "original sentences": [] | |
| }}, | |
| "Question 2": {{ | |
| "question": {{}}, | |
| "answer": {{}}, | |
| "original sentences": [] | |
| }}, | |
| ... | |
| }} | |
| ''' | |
| QUESTIONS = [ | |
| "What is the DOI of this study?", | |
| "What is the Citation ID of this study?", | |
| "What is the First author of this study?", | |
| "What is the year of this study?", | |
| "What is the animal type of this study?", | |
| "What is the exposure age of this study?", | |
| "Is there any behavior test done in this study?", | |
| "What's the Intervention 1's name of this study?(anesthetics only)", | |
| "What's the Intervention 2's name of this study?(anesthetics only)", | |
| "What's the genetic chain of this study?", | |
| "Input question", | |
| ] | |
| QUESTIONS = [ f'Question {id_ +1 }: {q}' for id_, q in enumerate(QUESTIONS) if 'Input question' not in q] | |
| QUESTIONS = '\n'.join(QUESTIONS) |