--- name: pubmed-database-9f03c6d6357d description: >- Search PubMed for scientific literature, including published clinical trials. Fetch abstracts and full text. Link published research to biological databases (gene, protein, nucleotide, PubChem) to discover associations between papers and specific compounds or genes. Verify medical spelling, match raw citations, and cache result sets for bulk processing. Interfaces NCBI E-utilities and PMC BioC APIs. --- # PubMed API ## Prerequisites 1. **`uv`**: Read the `uv` skill and follow its Setup instructions to ensure `uv` is installed and on PATH. 2. **User Notification**: If LICENSE_NOTIFICATION.txt does not already exist in this skill directory then (1) prominently notify the user to check the terms at https://pubmed.ncbi.nlm.nih.gov/disclaimer/ and https://www.ncbi.nlm.nih.gov/home/about/policies/ and to always check the license of the papers retrieved by the skill for any restrictions, then (2) create the file recording the notification text and timestamp. 3. **`.env` file**: Make sure the `.env` file exists in your home directory. Create one if it does not exist. 4. **`NCBI_API_KEY`** (optional): Raises the NCBI E-utilities rate limit from 3 to 10 requests/second. The skill works without it, but a key is recommended if the user plans many queries or encounters a 429 error. The user can obtain one for free by registering at https://www.ncbi.nlm.nih.gov/account/settings/ 5. **`USER_EMAIL`** (optional but recommended): Identifies the caller to NCBI (recommended by their Terms of Use). If the variables are missing from `.env`, do NOT ask the user to paste them into the chat (this would leak keys into the agent's context). Instead, give the user these commands — **substituting `ENV_FILE` with the resolved literal path to the `.env` file**: ```bash printf "Enter NCBI API key (typing hidden): " && read -s key && echo && echo "NCBI_API_KEY=$key" >> "ENV_FILE" && echo "Saved." ``` ```bash printf "Enter contact email: " && read email && echo "USER_EMAIL=$email" >> "ENV_FILE" && echo "Saved." ``` The scripts load credentials automatically via `dotenv`. **NEVER** read, print, or inspect the `.env` file or its variables (e.g. no `cat`, `grep`, `echo`, `printenv`, or `os.environ.get` on keys). Credentials must stay out of the agent's context. This skill provides CLI access to the NCBI PubMed and PubMed Central APIs via `scripts/pubmed_api.py` — a single CLI with 10 functions covering search, fetch, linking, full text, spelling, discovery, citation matching, and caching. ## Core Rules - **API Use**: Always use the provided wrapper `scripts/pubmed_api.py` which manages rate limits automatically and prevents API abuse. Setting the `NCBI_API_KEY` environment variable raises the rate limit from 3 to 10 requests/second. Querying the API any other way (e.g. via curl, wget, or hand-written code) is strictly forbidden. - **JSON Processing**: Use `jq` to filter and transform JSON output (or python equivalents if `jq` is not available) to prevent hallucinations and context overflow. - **Temporary Files**: To avoid polluting the working directory with JSON files, use a temporary directory inside the current directory. When running multiple agents or tasks in parallel, ensure each uses a unique subdirectory name (e.g., `tmp_$TASK_ID/`) to avoid file collisions. - **Notification**: If this skill is used, ensure this is mentioned in the output AND list the URLs of all papers that were used in producing the output. ## Structure of the skill folder - `SKILL.md` - This file - `scripts/pubmed_api.py` - The skill CLI - `references/` - Directory with detailed function specifications - `advanced-linking.md` - `advanced-search.md` - `bulk-workflows.md` - `citation-matching.md` - `cross-database-linking.md` - `fetch-and-resolve.md` - `search-and-discovery.md` - `utilities.md` ## CLI Usage ```bash uv run scripts/pubmed_api.py [--flag value ...] ``` - **Positional Arguments**: Arguments are positional; list arguments are passed as comma-separated strings without spaces (e.g. `"35113657,31234568"`). - **Flag Options**: Optional arguments can be passed as `--flag value` instead of positional args. - **Output Handling**: On success, JSON is written to `output_file`. On error, the process exits with a non-zero code and no output file is written. ### Example Usage ```bash uv run scripts/pubmed_api.py ./search_results.json search_pubmed "BRCA1" --max_results 5 cat ./search_results.json | jq '.[]' -r uv run scripts/pubmed_api.py ./abstracts.json fetch_article_abstracts "35113657" cat ./abstracts.json | jq '.[0].title' -r ``` ## Essential Recipes **Join PMIDs for the next call (most common chaining pattern):** ```bash cat ./search_results.json | jq -r 'join(",")' ``` **Slim abstracts to essential fields and truncate long abstracts:** ```bash cat ./abstracts.json | jq '[.[] | {pmid, title, snippet: (.abstract // "")[:500]}]' ``` **Filter by keyword (null-safe):** ```bash cat ./abstracts.json | jq '[.[] | select((.title // "") | contains("Review"))]' ``` ### Context Management & Accuracy When processing larger result sets (>10 abstracts): 1. **Filter Early**: Use `jq` to verify keywords in abstracts *before* reading the full JSON into context. 2. **Slimming**: Extract only `title` and `abstract` fields unless explicitly instructed otherwise. Author lists and metadata contribute to noise. 3. **Bulk Operations (N > 10)**: Avoid fetching or processing IDs one-by-one. The API and History Server are designed for bulk retrieval. Fetch all data in a **single turn** and use shell pipelines to slim the results before reading into context. This prevents turn exhaustion and context overflow. 4. **Grounding**: Never use internal knowledge to provide specific identifiers (PMIDs, CIDs, Gene IDs) if no results are found. Report the tool's output accurately to ensure results are grounded in the current database state. 5. **Search Termination**: When asked to find papers that may not exist, limit exploration to 3–5 high-quality, varied search queries. If no results match after these attempts, conclude that no papers meet the criteria rather than continuing to iterate — unless explicitly instructed to be thorough. ## Functions > **⚠️ MANDATORY**: You **MUST** read the linked reference file for a function > group **before calling any function** in that group. The tables below only > describe *what* each function does — not *how* to call it. Argument names, > argument order, flags, and output schemas are **only** documented in the > reference files. **Do NOT guess or infer arguments from function names.** If > you call a function without first reading its reference, you **will** produce > incorrect invocations. ### [Search](references/search-and-discovery.md) - `search_pubmed`: Find PMIDs matching a free-text or structured NCBI query. - `global_database_discovery`: Count how many records match a query across every NCBI database. ### [Fetch & Resolve](references/fetch-and-resolve.md) - `fetch_article_abstracts`: Retrieve metadata and abstracts for a batch of PMIDs. - `get_full_text_pmc`: Retrieve open-access full text from PMC. - `fetch_database_summary`: Resolve opaque UIDs from any NCBI database into human-readable metadata. ### [Cross-Database Linking](references/cross-database-linking.md) - `find_linked_biological_data`: Find records in other NCBI databases linked to a source record. - `discover_available_links`: List all available ELink linknames for a given record. ### [Bulk Workflows](references/bulk-workflows.md) When working with **more than ~10 PMIDs**, avoid processing IDs one-by-one. Upload them to the NCBI History Server via `cache_results_history` to get a session handle (`webenv` + `query_key`), then pass that handle to `fetch_article_abstracts` or `find_linked_biological_data` for a single bulk call. Chain with `jq` shell pipelines to slim results before reading into context. This prevents turn exhaustion and context overflow. See the reference for complete workflow recipes (search→fetch, cross-db exploration, citation resolution, and bulk retrieval with data slimming). - `cache_results_history`: Upload PMIDs to the NCBI History Server for bulk retrieval. ### [Utilities](references/utilities.md) - `verify_medical_spelling`: Spell-check biomedical terms before searching. - `match_raw_citations`: Resolve incomplete bibliographic citations to PMIDs. --- Source attribution: mkurman Original project: https://github.com/mkurman/zorai/blob/ddf914fecff90c98e7064d15af63a64101babd23/skills/scientific-skills-gdm/pubmed_database/SKILL.md License: Apache-2.0 License information: https://www.apache.org/licenses/LICENSE-2.0 Original upstream instructions; downloaded from Mega AI Hub. ## Upstream license notice Apache License Version 2.0, January 2004 http://www.apache.org/licenses/ TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION 1. Definitions. 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See the License for the specific language governing permissions and limitations under the License. # Mega AI Hub resource metadata Creator / publisher: mkurman Original project: https://github.com/mkurman/zorai/blob/ddf914fecff90c98e7064d15af63a64101babd23/skills/scientific-skills-gdm/pubmed_database/SKILL.md Attribution basis: Source repository record Fields of work: Education & Research, Healthcare & Life Sciences, Data & Analytics Roles: Researcher, Clinical Research, Data Analyst Specialties: API Tools: Pubmed Api Country applicability: Country not specified Classification basis: Source category, role and specialization labels Instruction SHA-256: 808d0abe14f735e77830de866f807c4831670c730e49adbb1f987e278ad60f85