pubmed_research_agent
Transform rough research ideas into a structured JSON plan with detailed prompts for execution. Organize project phases, literature search strategies, and data analysis to streamline biomedical research workflows.
Instructions
Generates a standardized JSON research plan outline from component details you provide. It accepts granular inputs for all research phases (conception, data collection, analysis, dissemination, cross-cutting concerns). If include_detailed_prompts_for_agent is true, the output plan will embed instructive prompts and detailed guidance notes to aid the research agent. The tool's primary function is to organize and structure your rough ideas into a formal, machine-readable plan. This plan is intended for further processing; as the research agent, you should then utilize your full suite of tools (e.g., file manipulation, get_pubmed_article_connections for literature/data search via PMID) to execute the outlined research, tailored to the user's request.
Input Schema
| Name | Required | Description | Default |
|---|---|---|---|
| cc_collaboration_strategy | No | If applicable, strategy for collaboration, communication, roles, and authorship. | |
| cc_ethical_considerations | No | Ethical considerations, IRB/IACUC approval plans, data privacy, RCR training. | |
| cc_record_keeping_and_data_management | No | Plan for record-keeping, version control, data storage, and DMP. | |
| include_detailed_prompts_for_agent | No | If true, the tool will add more detailed instructive prompts/guidance within the output fields for a research agent. If false (default), it will primarily structure the provided inputs with minimal additional prompting. | |
| organism_focus | No | Primary organism(s) or model systems (e.g., "Homo sapiens (iPSC-derived microglia)", "Mus musculus (5xFAD model)"). | |
| p1_blast_utilization_plan | No | If applicable, how sequence alignment services (e.g., NCBI BLAST) will be used (purpose, programs, databases). | |
| p1_controls_and_rigor | No | Description of key experimental controls and measures to ensure scientific rigor and reproducibility. | |
| p1_data_acquisition_plan_existing_data | No | Strategy for identifying and retrieving relevant existing datasets (databases, data types, tools). | |
| p1_data_acquisition_plan_new_data | No | Plan for generating novel data (data types, experimental models, key procedures, deposition plan). | |
| p1_experimental_paradigm | No | The overarching experimental design or study type (e.g., 'comparative multi-omics analysis', 'longitudinal cohort study'). | |
| p1_introduction_and_background | No | Brief overview of the research area, its significance, and relevant background information leading to this study. | |
| p1_knowledge_gap | No | Statement clearly identifying the specific gap in current knowledge this research addresses. | |
| p1_lit_review_databases_and_approach | No | Key databases (e.g., PubMed, EMBASE) and the search approach (e.g., iterative queries, snowballing). | |
| p1_literature_review_scope | No | The defined scope for the literature review (e.g., timeframes, study types, key themes). | |
| p1_methodological_challenges_and_mitigation | No | Anticipated methodological challenges and proposed mitigation strategies. | |
| p1_primary_hypothesis | No | The main, testable hypothesis. Should be clear, specific, and falsifiable. | |
| p1_pubmed_search_strategy_description | No | Description of the primary literature search strategy (e.g., for PubMed), including key terms and database considerations. | |
| p1_secondary_questions_or_hypotheses | No | Any secondary questions or hypotheses to be explored. | |
| p1_specific_research_question | No | The precise, focused primary research question the study will answer. | |
| p2_data_collection_methods_dry_lab | No | Execution details for data retrieval from databases (queries, tools, accessioning). | |
| p2_data_collection_methods_wet_lab | No | Specific wet-lab protocols if new data is generated (sample prep, treatments, instruments). | |
| p2_data_preprocessing_and_qc_plan | No | Pipeline for data cleaning, preprocessing (e.g., alignment, normalization), and quality control (metrics, thresholds, tools). | |
| p3_bioinformatics_pipeline_summary | No | Summary of the bioinformatics pipeline for high-throughput data analysis (tools, downstream analyses). | |
| p3_comparison_with_literature_plan | No | Strategy for contextualizing results with existing literature and addressing discrepancies. | |
| p3_data_analysis_strategy | No | Core statistical and computational methods to analyze data and test hypotheses (tests, software, ML models if any). | |
| p3_results_interpretation_framework | No | Framework for evaluating findings against hypotheses (statistical significance, biological relevance). | |
| p4_dissemination_data_deposition_plan | No | Strategy for depositing data in public repositories (types, repositories, FAIR principles). | |
| p4_dissemination_manuscript_plan | No | Plan for manuscript preparation (core message, target journal profile, key figures). | |
| p4_future_research_directions | No | Potential next steps, new questions, or translational applications arising from the research. | |
| p4_peer_review_and_publication_approach | No | Approach to journal submission and addressing peer review. | |
| primary_research_goal | Yes | The main scientific objective or central question the research aims to address (e.g., "To investigate the role of TREM2 in microglial response to amyloid-beta plaques"). | |
| project_title_suggestion | Yes | A concise and descriptive title for the research project. | |
| research_keywords | Yes | Core scientific keywords or MeSH terms defining the research domain (e.g., ["neuroinflammation", "Alzheimer's disease", "TREM2"]). |