Guidance on writing clinical description for Condition Phenotypes
Gowtham A. Rao
2024-10-02
Source:vignettes/GuidanceOnClinicalDescriptionForConditionPhenotypes.Rmd
GuidanceOnClinicalDescriptionForConditionPhenotypes.RmdPhenotypeLibrary is part of HADES.
Note: This document is a DRAFT guidance. We request a succinct clinical description, tailored for individuals with a background in medical terminology, informatics, or clinical practice, to enable a shared comprehension of the clinical concept being modeled in the phenotype. While the following structure is recommended, all fields are OPTIONAL.
The clinical description often encompasses medical technical terms pertinent to general pathophysiology, steering clear of extensive molecular biology discussions. The target audience, potentially comprising clinicians, is not presumed to have a research methods background. The goal is not to replicate a medical textbook chapter but to elucidate the clinical idea succinctly.
This document serves as a valuable input for the phenotyper—the individual responsible for developing and evaluating the cohort definition. If the phenotyper is utilizing Atlas for cohort creation, the clinical description is anticipated to guide and furnish justifications for the concept set expression, alongside the rules for entry event criteria, inclusion rules, and exit criteria. Please adhere to the following structure where possible and appropriate:
Condition: [Name for the Clinical idea]
Clinical Overview
Disease Overview
Provide an introduction, including if possible a definition from reputable scientific sources like medical textbooks, pubmed articles, medical dictionaries, or clinical guidelines in the form - ‘it is defined as.’ Assess whether there’s a consensus understanding among medical professionals, explaining your reasoning. Also provide an opinion if this condition is of special interest in pharmacovigilance and explain why. Add any relevant history or etymology of the condition to provide context.
Drug Induced Conditions
If the idea ‘Drug induced Condition’ is commonly used in pharmacovigilance, if possible please provide a definition for ‘Drug induced Condition’ in the form of ‘it is defined as’. Please compare the condition to ‘Drug induced Condition’. Please highlight key ideas that differentiate between the two, with special focus on what makes it ‘Drug - induced’ vs not drug induced.
Defining Features
List enumerate the typical signs, symptoms or defining patient features. For each item, explain their importance for medical professionals evaluating patients presenting with the given condition. Identify and highlight any of the enumerated features that are considered either characteristic or pathognomonic for this condition. Please indicate if any of these features are contraindicatives of Drug induced Condition. Add a separate special note on Drug induced Condition.
Synonyms and Subtypes
Synonyms
Please list medical terms that serve as specific synonyms for the same condition. For each term, provide context explaining the situations in which these synonyms are typically employed. Additionally, include any layman terms that describe the condition, but only if these terms are lexically or semantically distinct from the medical terms listed.
Management
Diagnosis
Outline the evaluation, by making a list of relevant tests. Provide examples of potential results. Explain their utility for medical assessment of patients with the given condition. Please report if any of the subtypes of the condition have a uniquely different diagnostic evaluation. Add a separate special note on Drug induced Condition.
Treatment
Current Standards
List current treatment option(s) that are considered standard of care. These are what have been or are being offered in the last 5 years.
Differential Diagnoses; Co-occurrent, Ambiguous and Mutually Exclusive Conditions
Differential Diagnosis
List conditions that might be confused with the condition under discussion and are commonly considered a differential diagnosis. For each item, highlight the differences in mechanisms and treatment strategies, include co-occurrence information, explain the importance for a medical professional. Add a separate special note on Drug induced Condition.
Diseases Commonly Co-occurrent
List conditions that might co-occur in the same patient with the condition under discussion. For each item, highlight the differences in mechanisms and treatment strategies, include co-occurrence information, explain the importance for a medical professional. Add a separate special note on Drug induced Condition.
Medical Conditions and Diseases that are Ambiguous
Highlight clinical conditions that are confusingly similar, elucidating why they might cause confusion. Exclude subtypes of the condition under discussion here. Add a separate special note on Drug induced Condition.
Exclusions
List any conditions, diagnostic procedures or treatments that rule out the diagnosis of the condition under discussion. For each item, explain why ruling these out are crucial. Add a separate special note on Drug induced Condition.
Mutually Exclusive Conditions
Identify specific conditions or treatments that when co-occurring in the patient, make the occurrence of the condition under discussion unlikely. Explain why these are not expected to co-occur with the condition and why when this mutually exclusive condition occurs the person is less likely to have the condition. Add a separate special note on Drug induced Condition.
Using GPT to generate clinical description
The above text may be generated using a GPT prompt.
Replace XXXXXXXX with ‘Acute new onset ST Elevated Myocardial Infarction’ while processing this prompt. Generate a detailed report on XXXXXXXX, serving as a guide for pharmacovigilance professionals evaluating the causal relationship between drug exposure and this condition. The document should incorporate standard technical language from the fields of medicine, pharmacology, and molecular biology.
Document Creation Guidelines:
Sequential Processing: Respond to prompts sequentially.
Contextual Allocation: Save pertinent information for future, more relevant sub-prompts.
Redundancy Minimization: Avoid repetition of content and phrasing.
Prompt Completion: Cease processing upon completing each sub-prompt.
Disclaimers: Omit disclaimers about technology limitations.
Abbreviations. Please don’t create de novo abbreviations. Please only use abbreviations if those are used in scientific publications.
After each sub-prompt, await my command, typically ‘next,’ before proceeding to the subsequent sub-prompt.
Sub-prompts
1: # 1.0.0. CLINICAL OVERVIEW: ## 1.1.0. Disease Overview: Provide an introduction, including if possible a definition from reputable scientific sources like medical textbooks, pubmed articles, medical dictionaries, or clinical guidelines in the form - ‘it is defined as.’ Assess whether there’s a consensus understanding among medical professionals, explaining your reasoning. Also provide an opinion if this XXXXXXXX is of special interest in pharmacovigilance and explain why. Add any relevant history or etymology of XXXXXXXX to provide context. In my follow-up, I will ask for synonyms, presentation, diagnostic evaluation, differential diagnosis, treatment plan, prognosis, exclusions, subtypes. So please don’t cover those topics here.
2: ### 1.1.1. Drug induced XXXXXXXX: If the idea ‘Drug induced XXXXXXXX’ is commonly used in pharmacovigilance, if possible please provide a definition for ‘Drug induced XXXXXXXX’ in the form of ‘it is defined as’. Please compare XXXXXXXX to ‘Drug induced XXXXXXXX’. Please highlight key ideas that differentiate between the two, with special focus on what makes it ‘Drug - induced’ vs not drug induced.
3: ## 1.2.0. Defining features: List enumerate the typical signs, symptoms or defining patient features. For each item, explain their importance for medical professionals evaluating patients presenting with the given XXXXXXXX. Identify and highlight any of the enumerated features that are considered either characteristic or pathognomonic for this XXXXXXXX. Please indicate if any of these features are contraindicatives of Drug induced XXXXXXXX. Add a separate special note on Drug induced XXXXXXXX.
4: ## 1.3.0. Synonyms and subtypes ### 1.3.1. Synonyms Please list medical terms that serve as specific synonyms for the same XXXXXXXX. For each term, provide context explaining the situations in which these synonyms are typically employed. Additionally, include any layman terms that describe XXXXXXXX, but only if these terms are lexically or semantically distinct from the medical terms listed.### 1.3.2. Disease subtypes Describe any subtypes, dedicating no more than two sentences to the essential characteristics of each. Add a separate special note on Drug induced XXXXXXXX.
5: ## 1.4. Management ### 1.4.1. Diagnosis Outline the evaluation, by making a list of relevant tests. Provide examples of potential results. Explain their utility for medical assessment of patients with the given XXXXXXXX. Please report if any of the subtypes of XXXXXXXX have a uniquely different diagnostic evaluation. Add a separate special note on Drug induced XXXXXXXX.
6: ### 1.4.2. Treatment #### 1.4.2.1. Current Standards: where you should list current treatment option(s) that are considered standard of care. These are what have been or are being offered in the last 5 years. #### 1.4.2.2. Previous Standards: where you should list previous treatment option(s) that are no longer offered. These were offered more than 5 years ago, but are not offered anymore. Please provide a time-frame for when it was a standard. #### 1.4.2.3. Treatment evolution: Explain how the standard of care may have evolved over time. #### 1.4.2.4. Unique treatment plans]: Please report if any of the subtypes of XXXXXXXX have a uniquely different treatment plan. Add a separate special note on Drug induced XXXXXXXX.
7: ### 1.4.3. Prognosis: #### 1.4.3.1. Short Term prognosis: Provide the patient’s short-term clinical outcome (within 3 months post-diagnosis). #### 1.4.3.2. Long Term prognosis: Provide the patients long-term (1 year or more) clinical outcome. Please report if any of the subtypes of XXXXXXXX have a uniquely different prognosis. Add a separate special note on Drug induced XXXXXXXX.
9: ## 1.5.0. Differential diagnoses; co-occurrent, ambiguous and mutually exclusive conditions: ### 1.5.1. Differential diagnosis: List conditions that might be confused with XXXXXXXX and are commonly considered a differential diagnosis. For each item, highlight the differences in mechanisms and treatment strategies, include co-occurrence information, explain the importance for a medical professional. Add a separate special note on Drug induced XXXXXXXX.
10: ### 1.5.2. Diseases commonly co-occurrent: List conditions that might co-occur in the same patient with XXXXXXXX. For each item, highlight the differences in mechanisms and treatment strategies, include co-occurrence information, explain the importance for a medical professional. Add a separate special note on Drug induced XXXXXXXX.
11: ### 1.5.3. Medical conditions and diseases that are ambiguous: Highlight clinical conditions that are confusingly similar, elucidating why they might cause confusion. Exclude subtypes of XXXXXXXX here. Add a separate special note on Drug induced XXXXXXXX.
12: 1.5.4. Exclusions: List any conditions, diagnostic procedures or treatments that rule out the diagnosis of XXXXXXXX. For each item, explain why ruling these out are crucial. Add a separate special note on Drug induced XXXXXXXX.
13: ### 1.5.5. Mutually Exclusive Conditions: Identify specific conditions or treatments that when co-occurring in the patient, make the occurrence of XXXXXXXX unlikely. Explain why these are not expected to co-occur with XXXXXXXX and why when this mutually exclusive condition occurs the person is less likely to have XXXXXXXX. Add a separate special note on Drug induced XXXXXXXX.
14: ## 1.6.0. Patient Profile: Provide one or more short case narratives of a patient with XXXXXXXX for three levels of diagnostic certainty: suspected case, probable case, definite case. If possible use formats used in the field like the SOAP format. Add a separate special note on Drug induced XXXXXXXX.”