--- name: scientific-db-pubmed-database-5b4c406c73b0 description: Direct PubMed and NCBI E-utilities search workflows for biomedical literature, MeSH queries, PMID lookup, citation retrieval, and API-backed literature monitoring. Use when a task needs biomedical literature from PubMed rather than general web search. metadata: origin: community --- # PubMed Database Use this skill when a task needs biomedical literature from PubMed rather than general web search. ## When to Use - Searching MEDLINE or life-sciences literature. - Building PubMed queries with MeSH terms, field tags, dates, or article types. - Looking up PMIDs, abstracts, publication metadata, or related citations. - Running systematic-review search passes that need repeatable search strings. - Using NCBI E-utilities directly from Python, shell, or another HTTP client. ## Query Construction Start with the research question, split it into concepts, then combine concepts with Boolean operators. ```text concept_1 AND concept_2 AND filter synonym_a OR synonym_b NOT exclusion_term ``` Useful PubMed field tags: - `[ti]`: title - `[ab]`: abstract - `[tiab]`: title or abstract - `[au]`: author - `[ta]`: journal title abbreviation - `[mh]`: MeSH term - `[majr]`: major MeSH topic - `[pt]`: publication type - `[dp]`: date of publication - `[la]`: language Examples: ```text diabetes mellitus[mh] AND treatment[tiab] AND systematic review[pt] AND 2023:2026[dp] (metformin[nm] OR insulin[nm]) AND diabetes mellitus, type 2[mh] AND randomized controlled trial[pt] smith ja[au] AND cancer[tiab] AND 2026[dp] AND english[la] ``` ## MeSH and Subheadings Prefer MeSH when the concept has a stable controlled-vocabulary term. Combine MeSH with title/abstract terms when the topic is new or terminology varies. Correct subheading syntax puts the subheading before the field tag: ```text diabetes mellitus, type 2/drug therapy[mh] cardiovascular diseases/prevention & control[mh] ``` Use `[majr]` only when the topic must be central to the paper. It can improve precision but may miss relevant work. ## Filters Publication types: - `clinical trial[pt]` - `meta-analysis[pt]` - `randomized controlled trial[pt]` - `review[pt]` - `systematic review[pt]` - `guideline[pt]` Date filters: ```text 2026[dp] 2020:2026[dp] 2026/03/15[dp] ``` Availability filters: ```text free full text[sb] hasabstract[text] ``` ## E-utilities Workflow NCBI E-utilities supports repeatable API workflows: 1. `esearch.fcgi`: search and return PMIDs. 2. `esummary.fcgi`: return lightweight article metadata. 3. `efetch.fcgi`: fetch abstracts or full records in XML, MEDLINE, or text. 4. `elink.fcgi`: find related articles and linked resources. Use an email and API key for production scripts. Store API keys in environment variables, never in committed files or command history. ```python import os import time import requests BASE = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils" def esearch(query: str, retmax: int = 20) -> list[str]: params = { "db": "pubmed", "term": query, "retmode": "json", "retmax": retmax, "tool": "ecc-pubmed-search", "email": os.environ.get("NCBI_EMAIL", ""), } api_key = os.environ.get("NCBI_API_KEY") if api_key: params["api_key"] = api_key response = requests.get(f"{BASE}/esearch.fcgi", params=params, timeout=30) response.raise_for_status() time.sleep(0.35) return response.json()["esearchresult"]["idlist"] pmids = esearch("hypertension[mh] AND randomized controlled trial[pt] AND 2024:2026[dp]") print(pmids) ``` For batches, prefer NCBI history server parameters (`usehistory=y`, `WebEnv`, `query_key`) instead of passing very long PMID lists through URLs. ## Output Discipline For each search pass, record: - exact search string - database searched - date searched - filters used - result count - export format - any manual exclusions Example: ```markdown | Database | Date searched | Query | Filters | Results | | --- | --- | --- | --- | ---: | | PubMed | 2026-05-11 | `sickle cell disease[mh] AND CRISPR[tiab]` | 2020:2026[dp], English | 42 | ``` ## Review Checklist - Are field tags valid PubMed tags? - Are MeSH terms paired with free-text synonyms for newer topics? - Is the date range explicit and appropriate? - Does the search log include enough detail to reproduce the query? - Are API keys loaded from the environment? - Does HTTP code call `raise_for_status()` or otherwise handle non-200 responses before parsing? - Are rate limits respected? ## References - [PubMed help](https://pubmed.ncbi.nlm.nih.gov/help/) - [NCBI E-utilities documentation](https://www.ncbi.nlm.nih.gov/books/NBK25501/) - [NCBI API key guidance](https://support.nlm.nih.gov/kbArticle/?pn=KA-05317) - NCBI support: --- Source attribution: affaan-m Original project: https://github.com/affaan-m/everything-claude-code/blob/25278e7d7b6cf6e6a4e7a6c8e10f14ff22f0eb5b/skills/scientific-db-pubmed-database/SKILL.md License: MIT License information: https://opensource.org/license/mit Original upstream instructions; downloaded from Mega AI Hub. ## Upstream license notice MIT License Copyright (c) 2026 Affaan Mustafa Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. # Mega AI Hub resource metadata Creator / publisher: affaan-m Original project: https://github.com/affaan-m/everything-claude-code/blob/25278e7d7b6cf6e6a4e7a6c8e10f14ff22f0eb5b/skills/scientific-db-pubmed-database/SKILL.md Attribution basis: Source repository record Fields of work: Data & Analytics, Education & Research, Healthcare & Life Sciences Roles: Clinical Research, Data Analyst, Researcher Specialties: API Tools: Ncbi E Utilities, Pubmed Country applicability: Country not specified Classification basis: Source catalog labels Instruction SHA-256: 345e081fd995c2ab8c6f3e2062363d2d67b4f3e5cd58d49475c33c71a0e18237