@fbraza/pi-cite 0.1.0 → 0.3.0

package/skills/literature/references/pubmed_common_queries.md

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+# Common PubMed Query Patterns
+
+This reference provides practical examples of common PubMed search patterns for various research scenarios.
+
+## General Research Queries
+
+### Finding Recent Research on a Topic
+```
+breast cancer[tiab] AND 2023:2024[dp]
+```
+
+### Systematic Reviews on a Topic
+```
+(diabetes[tiab] OR diabetes mellitus[mh]) AND systematic review[pt]
+```
+
+### Meta-Analyses
+```
+hypertension[tiab] AND meta-analysis[pt] AND 2020:2024[dp]
+```
+
+### Clinical Trials
+```
+alzheimer disease[mh] AND randomized controlled trial[pt]
+```
+
+### Finding Guidelines
+```
+asthma[tiab] AND (guideline[pt] OR practice guideline[pt])
+```
+
+## Disease-Specific Queries
+
+### Cancer Research
+```
+# General cancer screening
+cancer screening[tiab] AND systematic review[pt] AND 2020:2024[dp]
+
+# Specific cancer type with treatment
+lung cancer[tiab] AND immunotherapy[tiab] AND clinical trial[pt]
+
+# Cancer genetics
+breast neoplasms[mh] AND BRCA1[tiab] AND genetic testing[tiab]
+```
+
+### Cardiovascular Disease
+```
+# Heart disease prevention
+(heart disease[tiab] OR cardiovascular disease[mh]) AND prevention[tiab] AND 2022:2024[dp]
+
+# Stroke treatment
+stroke[mh] AND (thrombectomy[tiab] OR thrombolysis[tiab]) AND randomized controlled trial[pt]
+
+# Hypertension management
+hypertension[mh]/drug therapy AND comparative effectiveness[tiab]
+```
+
+### Infectious Diseases
+```
+# COVID-19 research
+COVID-19[tiab] AND (vaccine[tiab] OR vaccination[tiab]) AND 2023:2024[dp]
+
+# Antibiotic resistance
+(antibiotic resistance[tiab] OR drug resistance, bacterial[mh]) AND systematic review[pt]
+
+# Tuberculosis treatment
+tuberculosis[mh]/drug therapy AND (multidrug-resistant[tiab] OR MDR-TB[tiab])
+```
+
+### Neurological Disorders
+```
+# Alzheimer's disease
+alzheimer disease[mh] AND (diagnosis[sh] OR biomarkers[tiab]) AND 2020:2024[dp]
+
+# Parkinson's disease treatment
+parkinson disease[mh] AND treatment[tiab] AND clinical trial[pt]
+
+# Multiple sclerosis
+multiple sclerosis[mh] AND disease modifying[tiab] AND review[pt]
+```
+
+### Diabetes
+```
+# Type 2 diabetes management
+diabetes mellitus, type 2[mh] AND (lifestyle[tiab] OR diet[tiab]) AND randomized controlled trial[pt]
+
+# Diabetes complications
+diabetes mellitus[mh] AND (complications[sh] OR diabetic neuropathy[mh])
+
+# New diabetes drugs
+diabetes mellitus, type 2[mh] AND (GLP-1[tiab] OR SGLT2[tiab]) AND 2022:2024[dp]
+```
+
+## Drug and Treatment Research
+
+### Drug Efficacy Studies
+```
+# Compare two drugs
+(drug A[nm] OR drug B[nm]) AND condition[mh] AND comparative effectiveness[tiab]
+
+# Drug side effects
+medication name[nm] AND (adverse effects[sh] OR side effects[tiab])
+
+# Drug combination therapy
+(aspirin[nm] AND clopidogrel[nm]) AND acute coronary syndrome[mh]
+```
+
+### Treatment Comparisons
+```
+# Surgery vs medication
+condition[mh] AND (surgery[tiab] OR surgical[tiab]) AND (medication[tiab] OR drug therapy[sh]) AND comparative study[pt]
+
+# Different surgical approaches
+procedure[tiab] AND (laparoscopic[tiab] OR open surgery[tiab]) AND outcomes[tiab]
+```
+
+### Alternative Medicine
+```
+# Herbal supplements
+(herbal medicine[mh] OR phytotherapy[mh]) AND condition[tiab] AND clinical trial[pt]
+
+# Acupuncture
+acupuncture[mh] AND pain[tiab] AND randomized controlled trial[pt]
+```
+
+## Diagnostic Research
+
+### Diagnostic Tests
+```
+# Sensitivity and specificity
+test name[tiab] AND condition[tiab] AND (sensitivity[tiab] AND specificity[tiab])
+
+# Diagnostic imaging
+(MRI[tiab] OR magnetic resonance imaging[tiab]) AND brain tumor[tiab] AND diagnosis[sh]
+
+# Lab test evaluation
+biomarker name[tiab] AND disease[tiab] AND (diagnostic[tiab] OR screening[tiab])
+```
+
+### Screening Programs
+```
+# Cancer screening
+cancer type[tiab] AND screening[tiab] AND (cost effectiveness[tiab] OR benefit[tiab])
+
+# Population screening
+condition[tiab] AND mass screening[mh] AND public health[tiab]
+```
+
+## Population-Specific Queries
+
+### Pediatric Research
+```
+# Children with specific condition
+condition[tiab] AND (child[mh] OR pediatric[tiab]) AND treatment[tiab]
+
+# Age-specific
+disease[tiab] AND (infant[mh] OR child, preschool[mh])
+
+# Pediatric dosing
+drug name[nm] AND pediatric[tiab] AND (dosing[tiab] OR dose[tiab])
+```
+
+### Geriatric Research
+```
+# Elderly population
+condition[tiab] AND (aged[mh] OR elderly[tiab] OR geriatric[tiab])
+
+# Aging and disease
+aging[mh] AND disease[tiab] AND mechanism[tiab]
+
+# Polypharmacy
+polypharmacy[tiab] AND elderly[tiab] AND adverse effects[tiab]
+```
+
+### Pregnant Women
+```
+# Pregnancy and medications
+drug name[nm] AND (pregnancy[mh] OR pregnant women[tiab]) AND safety[tiab]
+
+# Pregnancy complications
+pregnancy complication[tiab] AND management[tiab]
+```
+
+### Sex-Specific Research
+```
+# Female-specific
+condition[tiab] AND female[mh] AND hormones[tiab]
+
+# Male-specific
+disease[tiab] AND male[mh] AND risk factors[tiab]
+
+# Sex differences
+condition[tiab] AND (sex factors[mh] OR gender differences[tiab])
+```
+
+## Epidemiology and Public Health
+
+### Prevalence Studies
+```
+disease[tiab] AND (prevalence[tiab] OR epidemiology[sh]) AND country/region[tiab]
+```
+
+### Incidence Studies
+```
+condition[tiab] AND incidence[tiab] AND population[tiab] AND 2020:2024[dp]
+```
+
+### Risk Factors
+```
+disease[mh] AND (risk factors[mh] OR etiology[sh]) AND cohort study[tiab]
+```
+
+### Global Health
+```
+disease[tiab] AND (developing countries[mh] OR low income[tiab]) AND burden[tiab]
+```
+
+### Health Disparities
+```
+condition[tiab] AND (health disparities[tiab] OR health equity[tiab]) AND minority groups[tiab]
+```
+
+## Methodology-Specific Queries
+
+### Research Methodology
+
+#### Cohort Studies
+```
+condition[tiab] AND cohort study[tiab] AND prospective[tiab]
+```
+
+#### Case-Control Studies
+```
+disease[tiab] AND case-control studies[mh] AND risk factors[tiab]
+```
+
+#### Cross-Sectional Studies
+```
+condition[tiab] AND cross-sectional studies[mh] AND prevalence[tiab]
+```
+
+### Statistical Methods
+```
+# Machine learning in medicine
+(machine learning[tiab] OR artificial intelligence[tiab]) AND diagnosis[tiab] AND validation[tiab]
+
+# Bayesian analysis
+condition[tiab] AND bayes theorem[mh] AND clinical decision[tiab]
+```
+
+### Genetic and Molecular Research
+```
+# GWAS studies
+disease[tiab] AND (genome-wide association study[tiab] OR GWAS[tiab])
+
+# Gene expression
+gene name[tiab] AND (gene expression[mh] OR mRNA[tiab]) AND disease[tiab]
+
+# Proteomics
+condition[tiab] AND proteomics[mh] AND biomarkers[tiab]
+
+# CRISPR research
+CRISPR[tiab] AND (gene editing[tiab] OR genome editing[tiab]) AND 2020:2024[dp]
+```
+
+## Author and Institution Queries
+
+### Finding Work by Specific Author
+```
+# Single author
+smith ja[au] AND cancer[tiab] AND 2023:2024[dp]
+
+# First author only
+jones m[1au] AND cardiology[tiab]
+
+# Multiple authors from same group
+(smith ja[au] OR jones m[au] OR wilson k[au]) AND research topic[tiab]
+```
+
+### Institution-Specific Research
+```
+# University affiliation
+harvard[affil] AND cancer research[tiab] AND 2023:2024[dp]
+
+# Hospital research
+"mayo clinic"[affil] AND clinical trial[pt]
+
+# Country-specific
+japan[affil] AND robotics[tiab] AND surgery[tiab]
+```
+
+## Journal-Specific Queries
+
+### High-Impact Journals
+```
+# Specific journal
+nature[ta] AND genetics[tiab] AND 2024[dp]
+
+# Multiple journals
+(nature[ta] OR science[ta] OR cell[ta]) AND immunology[tiab]
+
+# Journal with ISSN
+0028-4793[issn] AND clinical trial[pt]
+```
+
+## Citation and Reference Queries
+
+### Finding Specific Articles
+```
+# By PMID
+12345678[pmid]
+
+# By DOI
+10.1056/NEJMoa123456[doi]
+
+# By first author and year
+smith ja[1au] AND 2023[dp] AND cancer[tiab]
+```
+
+### Finding Cited Work
+```
+# Related articles
+Similar Articles feature from any PubMed result
+
+# By keyword in references
+Use "Cited by" links when available
+```
+
+## Advanced Combination Queries
+
+### Comprehensive Literature Review
+```
+(disease name[tiab] OR disease name[mh]) AND
+((treatment[tiab] OR therapy[tiab] OR management[tiab]) OR
+(diagnosis[tiab] OR screening[tiab]) OR
+(epidemiology[tiab] OR prevalence[tiab])) AND
+(systematic review[pt] OR meta-analysis[pt] OR review[pt]) AND
+2019:2024[dp] AND english[la]
+```
+
+### Precision Medicine Query
+```
+(precision medicine[tiab] OR personalized medicine[tiab] OR pharmacogenomics[mh]) AND
+cancer[tiab] AND
+(biomarkers[tiab] OR genetic testing[tiab]) AND
+clinical application[tiab] AND
+2020:2024[dp]
+```
+
+### Translational Research
+```
+(basic science[tiab] OR bench to bedside[tiab] OR translational medical research[mh]) AND
+disease[tiab] AND
+(clinical trial[pt] OR clinical application[tiab]) AND
+2020:2024[dp]
+```
+
+## Quality Filters
+
+### High-Quality Evidence
+```
+condition[tiab] AND
+(randomized controlled trial[pt] OR systematic review[pt] OR meta-analysis[pt]) AND
+humans[mh] AND
+english[la] AND
+2020:2024[dp]
+```
+
+### Free Full Text Articles
+```
+topic[tiab] AND free full text[sb] AND 2023:2024[dp]
+```
+
+### Articles with Abstracts
+```
+condition[tiab] AND hasabstract[text] AND review[pt]
+```
+
+## Staying Current
+
+### Latest Publications
+```
+topic[tiab] AND 2024[dp] AND english[la]
+```
+
+### Preprints and Early Access
+```
+topic[tiab] AND (epub ahead of print[tiab] OR publisher[sb])
+```
+
+### Setting Up Alerts
+```
+# Create search and save to My NCBI
+# Enable email alerts for new matching articles
+topic[tiab] AND (randomized controlled trial[pt] OR systematic review[pt])
+```
+
+## COVID-19 Specific Queries
+
+### Vaccine Research
+```
+(COVID-19[tiab] OR SARS-CoV-2[tiab]) AND
+(vaccine[tiab] OR vaccination[tiab]) AND
+(efficacy[tiab] OR effectiveness[tiab]) AND
+2023:2024[dp]
+```
+
+### Long COVID
+```
+(long covid[tiab] OR post-acute covid[tiab] OR PASC[tiab]) AND
+(symptoms[tiab] OR treatment[tiab])
+```
+
+### COVID Treatment
+```
+COVID-19[tiab] AND
+(antiviral[tiab] OR monoclonal antibody[tiab] OR treatment[tiab]) AND
+randomized controlled trial[pt]
+```
+
+## Tips for Constructing Queries
+
+### 1. PICO Framework
+Use PICO (Population, Intervention, Comparison, Outcome) to structure clinical queries:
+
+```
+P: diabetes mellitus, type 2[mh]
+I: metformin[nm]
+C: lifestyle modification[tiab]
+O: glycemic control[tiab]
+
+Query: diabetes mellitus, type 2[mh] AND (metformin[nm] OR lifestyle modification[tiab]) AND glycemic control[tiab]
+```
+
+### 2. Iterative Refinement
+Start broad, review results, refine:
+```
+1. diabetes → too broad
+2. diabetes mellitus type 2 → better
+3. diabetes mellitus, type 2[mh] AND metformin[nm] → more specific
+4. diabetes mellitus, type 2[mh] AND metformin[nm] AND randomized controlled trial[pt] → focused
+```
+
+### 3. Use Search History
+Combine previous searches in Advanced Search:
+```
+#1: diabetes mellitus, type 2[mh]
+#2: cardiovascular disease[mh]
+#3: #1 AND #2 AND risk factors[tiab]
+```
+
+### 4. Save Effective Searches
+Create My NCBI account to save successful queries for future use and set up automatic alerts.

package/skills/literature/references/pubmed_routine.md

@@ -0,0 +1,93 @@
+# PubMed E-utilities — Routine Quick-Reference
+
+Quick-start for routine literature searches (≤200 PMIDs, common field tags). For batch operations, history server, or all 9 endpoints → load `pubmed_api_reference.md`. For advanced search syntax → load `pubmed_search_syntax.md`. For query templates by scenario → load `pubmed_common_queries.md`.
+
+## Core Endpoints (Routine)
+
+| Endpoint | Purpose | When to use |
+|---|---|---|
+| `esearch.fcgi` | Search and retrieve PMIDs | Every PubMed search |
+| `efetch.fcgi` | Download full records / abstracts | Retrieving paper details |
+| `esummary.fcgi` | Get document summaries (title, authors, journal) | Quick metadata checks |
+
+## Search (ESearch)
+
+```
+https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi
+```
+
+**Parameters (routine):**
+```
+db=pubmed
+term=<query>
+retmax=<N>        # max results (default 20, max 10000 for routine queries)
+retmode=json
+sort=relevance    # or "pub_date", "first_author"
+datetype=pdat
+mindate=YYYY/MM/DD
+maxdate=YYYY/MM/DD
+```
+
+## Fetch Abstracts (EFetch)
+
+```
+https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi
+```
+
+**Parameters:**
+```
+db=pubmed
+id=<PMID1,PMID2,...>   # comma-separated, max ~200 for routine
+rettype=abstract       # or "medline", "xml", "uilist"
+retmode=text           # or "xml"
+```
+
+## Most-Used Field Tags
+
+| Tag | Meaning |
+|---|---|
+| `[tiab]` | Title or abstract (most common for keyword search) |
+| `[mh]` | MeSH term (includes narrower terms automatically) |
+| `[majr]` | MeSH term as major topic only |
+| `[pt]` | Publication type |
+| `[nm]` | Substance name (for drugs/compounds) |
+| `[au]` / `[1au]` / `[lastau]` | Author / first author / last author |
+| `[dp]` | Publication date |
+| `[la]` | Language |
+| `[affil]` | Affiliation |
+
+## Routine Query Patterns
+
+```
+# Systematic review with date range
+(topic[mh] OR topic[tiab]) AND systematic review[pt] AND 2020:2024[dp]
+
+# Free full-text RCTs on a drug for a disease
+drug[nm] AND disease[mh] AND randomized controlled trial[pt] AND free full text[sb]
+
+# PICO: Population + Intervention/Comparison + Outcome
+disease[mh] AND (drug_A[nm] OR drug_B[tiab]) AND outcome[tiab] AND randomized controlled trial[pt]
+
+# Gene + disease + expression
+gene_name[tiab] AND (gene expression[mh] OR mRNA[tiab]) AND disease[tiab]
+```
+
+## Python (Biopython)
+
+```python
+from Bio import Entrez
+Entrez.email = "your@email.com"
+
+handle = Entrez.esearch(db="pubmed", term="macrophage[mh] AND lung transplantation[mh]",
+                        retmax=200, usehistory="y")
+record = Entrez.read(handle)
+pmids = record["IdList"]
+
+fetch_handle = Entrez.efetch(db="pubmed", id=",".join(pmids),
+                              rettype="abstract", retmode="text")
+abstracts = fetch_handle.read()
+```
+
+## Rate Limits
+
+3 requests/sec without API key; 10/sec with NCBI API key. Add `api_key=YOUR_KEY` parameter for higher throughput.