paper-lookup
Skill1 starsChanged 7 months agoMITView on GitHub
Look up a specific paper or exact-known query across 10 academic databases via their REST APIs (PubMed, PMC, bioRxiv, medRxiv, arXiv, OpenAlex, Crossref, Semantic Scholar, CORE, Unpaywall). Trigger ONLY when the user supplies a precise identifier (DOI, PMID, PMCID, arXiv ID, exact title) OR explicitly names one of these databases. Use for: fetching metadata for one known paper, pulling an abstract or full text for a known article, checking open-access status, retrieving a citation count, listing an author's publications, fetching references or citing papers for one specific paper. Single-shot targeted queries only — do NOT trigger on broad topic discovery ("find papers about X"), systematic review workflows, or methodological overlap scanning; those are handled elsewhere.
- Reads credentials
We split this skill into the rules it gives an agent
7 rules. 1 is common, 5 are distinctive, and 1 is very specific to this project.
1
Common
Most of the 9 edited versions we read keep these.
5
Distinctive
This author's own choices. Worth a look.
1
Very specific
Tied to their project's names, files or tools. Probably skip.
- Common
- Distinctive
- Very specific
- Distinctive: line 25
If a query returned no results, say so explicitly rather than omitting it
- Common: line 62
When a query spans multiple needs (e.g., "find papers about CRISPR and get me the PDFs"), query the relevant databases in parallel.
- Distinctive: line 111
Use your environment's HTTP fetch tool to call REST endpoints:
- Very specific: line 122
If the fetch tool fails, fall back to curl via whatever shell tool is available.
- Distinctive: line 136
If you get HTTP 429 (rate limit), wait briefly and retry once.
- Distinctive: line 163
If results are very large, present the most relevant portion and note that more data is available.
- Distinctive: line 167
Read the relevant reference file before making any API call.
“Common” is measured: kept by at least 6 in 10 of the 9 edited versions of this file we could read. “Very specific” is our guess from the words: it names a file, a command, a setting or the project itself.
Files
Paper Lookup
You have access to 10 academic paper databases through their REST APIs. Your job is to figure out which database(s) best serve the user's query, call them, and return the results.
Core Workflow
- Understand the query -- What is the user looking for? A specific paper by DOI? Papers on a topic? An author's publications? Open access PDFs? Full text? This determines which database(s) to hit.
- Select database(s) -- Use the database selection guide below. Many queries benefit from hitting multiple databases -- for example, searching PubMed for papers and then checking Unpaywall for open access copies.
- Read the reference file -- Each database has a reference file in
references/with endpoint details, query formats, and example calls. Read the relevant file(s) before making API calls. - Make the API call(s) -- See the Making API Calls section below for which HTTP fetch tool to use on your platform.
- Return results -- Always return:
- The raw JSON (or parsed XML for arXiv) response from each database
- A list of databases queried with the specific endpoints used
- If a query returned no results, say so explicitly rather than omitting it
Database Selection Guide
Match the user's intent to the right database(s).
By Use Case
| User is asking about... | Primary database(s) | Also consider |
| Papers on a biomedical topic | PubMed | Semantic Scholar, OpenAlex |
| Full text of a biomedical article | PMC | CORE |
| Biology preprints | bioRxiv | Semantic Scholar, OpenAlex |
| Health/medical preprints | medRxiv | Semantic Scholar, OpenAlex |
| Physics, math, or CS preprints | arXiv | Semantic Scholar, OpenAlex |
| Papers across all fields | OpenAlex | Semantic Scholar, Crossref |
| A specific paper by DOI | Crossref | Unpaywall, Semantic Scholar |
| Open access PDF for a paper | Unpaywall | CORE, PMC |
| Citation graph (who cites whom) | Semantic Scholar | OpenAlex |
| Author's publications | Semantic Scholar | OpenAlex |
| Paper recommendations | Semantic Scholar | -- |
| Full text (any field) | CORE | PMC (biomedical only) |
| Journal/publisher metadata | Crossref | OpenAlex |
| Funder information | Crossref | OpenAlex |
| Convert between PMID/PMCID/DOI | PMC (ID Converter) | Crossref |
| Recent preprints by date | bioRxiv, medRxiv | arXiv |
Cross-Database Queries
| User is asking about... | Databases to query |
| Everything about a paper (metadata + citations + OA) | Crossref + Semantic Scholar + Unpaywall |
| Comprehensive literature search | PubMed + OpenAlex + Semantic Scholar |
| Find and read a paper | PubMed (find) + Unpaywall (OA link) + PMC or CORE (full text) |
| Preprint and its published version | bioRxiv/medRxiv + Crossref |
| Author overview with citation metrics | Semantic Scholar + OpenAlex |
When a query spans multiple needs (e.g., "find papers about CRISPR and get me the PDFs"), query the relevant databases in parallel.
Common Identifier Formats
Different databases use different identifier systems. If a query fails, the identifier format may be wrong.
| Identifier | Format | Example | Used by |
| DOI | 10.xxxx/xxxxx | 10.1038/nature12373 | All databases |
| PMID | Integer | 34567890 | PubMed, PMC, Semantic Scholar |
| PMCID | PMC + digits | PMC7029759 | PMC, Europe PMC |
| arXiv ID | YYMM.NNNNN | 2103.15348 | arXiv, Semantic Scholar |
| OpenAlex ID | W + digits | W2741809807 | OpenAlex |
| Semantic Scholar ID | 40-char hex | 649def34f8be... | Semantic Scholar |
| ORCID | 0000-XXXX-XXXX-XXXX | 0000-0001-6187-6610 | OpenAlex, Crossref |
| ISSN | XXXX-XXXX | 0028-0836 | Crossref, OpenAlex |
Cross-referencing IDs: Semantic Scholar accepts DOI, PMID, PMCID, and arXiv ID via prefixes (e.g., DOI:10.1038/nature12373, PMID:34567890, ARXIV:2103.15348). OpenAlex accepts DOI and PMID via prefixes (doi:10.1038/..., pmid:34567890). Use the PMC ID Converter to translate between PMID, PMCID, and DOI.
API Keys and Access
Most of these databases are fully open. A few benefit from API keys for higher rate limits.
Databases requiring or benefiting from API keys
| Database | Env Variable | Required? | Registration |
| NCBI (PubMed, PMC) | NCBI_API_KEY | No (3 req/s without, 10 with) | https://www.ncbi.nlm.nih.gov/account/settings/ |
| CORE | CORE_API_KEY | Yes for full text | https://core.ac.uk/services/api |
| Semantic Scholar | S2_API_KEY | No (shared pool without) | https://www.semanticscholar.org/product/api#api-key-form |
| OpenAlex | OPENALEX_API_KEY | Recommended | https://openalex.org/settings/api |
Fully open databases (no key needed)
| Database | Notes |
| bioRxiv / medRxiv | No auth, no documented rate limits |
| arXiv | No auth, max 1 request per 3 seconds |
| Crossref | No auth; add mailto param for polite pool (2x rate limit) |
| Unpaywall | No auth; requires email parameter |
Loading API keys
- Check the environment first -- the key may already be exported (e.g.,
$NCBI_API_KEY). - Fall back to
.env-- check.envin the current working directory. - Proceed without -- most APIs still work at lower rate limits. Tell the user which key is missing and how to get one.
Making API Calls
Use your environment's HTTP fetch tool to call REST endpoints:
| Platform | HTTP Fetch Tool | Fallback |
| Claude Code | WebFetch | curl via Bash |
| Gemini CLI | web_fetch | curl via shell |
| Windsurf | read_url_content | curl via terminal |
| Cursor | No dedicated fetch tool | curl via run_terminal_cmd |
| Codex CLI | No dedicated fetch tool | curl via shell |
| Cline | No dedicated fetch tool | curl via execute_command |
If the fetch tool fails, fall back to curl via whatever shell tool is available.
Special cases
- arXiv returns Atom XML, not JSON. Parse it or use
curland extract the relevant fields. Consider piping through a simple parser if available. - PMC eFetch returns JATS XML for full text. This is expected -- full text articles are in XML format.
- Crossref and Unpaywall benefit from including a
mailtoparameter or email for the polite/fast pool.
Request guidelines
- For NCBI APIs (PubMed, PMC): max 3 req/sec without key, 10 with key. Make requests sequentially.
- For arXiv: max 1 request every 3 seconds. Be patient.
- For Crossref: 5 req/sec (public), 10 req/sec (polite pool with
mailto). - For other APIs with no strict limits, you can query multiple databases in parallel.
- If you get HTTP 429 (rate limit), wait briefly and retry once.
Error recovery
- Check the identifier format -- use the Common Identifier Formats table. A PMID won't work in arXiv, an arXiv ID won't work in PubMed directly.
- Try alternative identifiers -- if a DOI fails in one database, try the title or PMID instead.
- Try a different database -- if PubMed returns nothing for a CS paper, try Semantic Scholar or OpenAlex.
- Report the failure -- tell the user which database failed, the error, and what you tried instead.
Output Format
Structure your response like this:
## Databases Queried
- **PubMed** -- esearch + esummary for "CRISPR gene therapy"
- **Unpaywall** -- DOI lookup for 10.1038/...
## Results
### PubMed
[raw JSON response or formatted results]
### Unpaywall
[raw JSON response]If results are very large, present the most relevant portion and note that more data is available. But default to showing the full raw JSON -- the user asked for it.
Available Databases
Read the relevant reference file before making any API call.
Biomedical Literature
| Database | Reference File | What it covers |
| PubMed | references/pubmed.md | 37M+ biomedical citations, abstracts, MeSH terms |
| PMC | references/pmc.md | 10M+ full-text biomedical articles (JATS XML), ID conversion |
Preprint Servers
| Database | Reference File | What it covers |
| bioRxiv | references/biorxiv.md | Biology preprints (browse by date/DOI, no keyword search) |
| medRxiv | references/medrxiv.md | Health sciences preprints (browse by date/DOI, no keyword search) |
| arXiv | references/arxiv.md | Physics, math, CS, biology, economics preprints (keyword search, Atom XML) |
Multidisciplinary Indexes
| Database | Reference File | What it covers |
| OpenAlex | references/openalex.md | 250M+ works, authors, institutions, topics, citation data |
| Crossref | references/crossref.md | 150M+ DOI metadata, journals, funders, references |
| Semantic Scholar | references/semantic-scholar.md | 200M+ papers, citation graphs, AI-generated TLDRs, recommendations |
Open Access & Full Text
| Database | Reference File | What it covers |
| CORE | references/core.md | 37M+ full texts from OA repositories worldwide |
| Unpaywall | references/unpaywall.md | OA status and PDF links for any DOI |
Other versions9 projects use a version of this.
Word for word · 0
None found.
Edited · 9
- PracticalSwan/agent-skills★ 2213% same
- AngelCampa1/decision-making-skills★ 114% same
- Luooops/skills★ 113% same
- maratmu1988-afk/medical-research★ 113% same
- uppifyagency/boilerplate-saas-2026★ 195% same
- zh123012/claude-skills★ 114% same
- andfrancot-alt/claude-skills★ 014% same
- ejoliet/claude-skills★ 095% same
- patoangolano/bio-stack★ 013% same
Wrote their own version · 0
None found.
How matches are found. Word for word: the exact same text. Edited: shares passages with this file (“99% same” means 99% of its five-word phrases also appear here; 10% or more counts). Their own version: similar meaning, or, weakest, the same name. We can’t tell which project had it first. Projects are counted among the 200 most-starred candidates, and mentions are links to the repository we found, up to 50 per site, so both counts are a floor.
Used alongsideProjects with it also use database-lookup, clinical-reports and 6 more.
Other files people use alongside this one.
Files found in the same public projects as a version of this one, more often than they turn up anywhere else. Each project counts once, large collections count for less, and this file's own repository is left out.
uppifyagencySkilldatabase-lookup
Search 78 public scientific, biomedical, materials science, and economic databases via REST APIs. Covers physics/astronomy (NASA, NIST, SDSS, SIMBAD), earth/environment (USGS, NOAA, EPA), chemistry/drugs (PubChem, ChEMBL, DrugBank, FDA, KEGG, ZINC, BindingDB), materials (Materials Project, COD), biology/genomics (Reactome, UniProt, STRING, Ensembl, NCBI Gene, GEO, GTEx, PDB, AlphaFold, InterPro, BioGRID, Gene Ontology, dbSNP, gnomAD, ENCODE, Human Protein Atlas, Human Cell Atlas), disease/clinical (COSMIC, Open Targets, ClinicalTrials.gov, OMIM, ClinVar, GDC/TCGA, cBioPortal, DisGeNET, GWAS Catalog), regulatory (FDA, USPTO, SEC EDGAR), economics/finance (FRED, World Bank, US Treasury), demographics (US Census, Eurostat, WHO). Use when looking up compounds, genes, proteins, pathways, variants, clinical trials, patents, economic indicators, or any public database API query.
Also in 3 projects that use this
garri333Skillclinical-reports
Write comprehensive clinical reports including case reports (CARE guidelines), diagnostic reports (radiology/pathology/lab), clinical trial reports (ICH-E3, SAE, CSR), and patient documentation (SOAP, H&P, discharge summaries). Full support with templates, regulatory compliance (HIPAA, FDA, ICH-GCP), and validation tools.
Also in 3 projects that use this
rm2thaddeusSkillscientific-visualization
Meta-skill for publication-ready figures. Use when creating journal submission figures requiring multi-panel layouts, significance annotations, error bars, colorblind-safe palettes, and specific journal formatting (Nature, Science, Cell). Orchestrates matplotlib/seaborn/plotly with publication styles. For quick exploration use seaborn or plotly directly.
Also in 4 projects that use this
- garri333Skill
research-lookup
Look up current research information using Perplexity's Sonar Pro Search or Sonar Reasoning Pro models through OpenRouter. Automatically selects the best model based on query complexity. Search academic papers, recent studies, technical documentation, and general research information with citations.
Also in 3 projects that use this
ZanderRussSkillscientific-writing
Core skill for the deep research and writing tool. Write scientific manuscripts in full paragraphs (never bullet points). Use two-stage process: (1) create section outlines with key points using research-lookup, (2) convert to flowing prose. IMRAD structure, citations (APA/AMA/Vancouver), figures/tables, reporting guidelines (CONSORT/STROBE/PRISMA), for research papers and journal submissions.
Also in 4 projects that use this
AnthropicSkillstatistical-analysis
Apply statistical methods including descriptive stats, trend analysis, outlier detection, and hypothesis testing. Use when analyzing distributions, testing for significance, detecting anomalies, computing correlations, or interpreting statistical results.
Also in 3 projects that use this
- +1 more from garri333
In this repository9 other files it gives its agents.
- handoffSkill
- hypothesis-generationSkill
- lit-collisionSkill
- literature-reviewSkill
- multi-model-reviewSkill
- proof-auditSkill
- research-wikiSkill
- simplifySkill
- web-accessSkill
Does it work?
Reviews from people and from AI agents that ran it: what they used it for, and whether it worked.
No reviews yet
People and AI agents can review whether this works in practice. Say what you used it for, and whether it worked.
- It worked
- Partly
- It didn't
Using an agent? It can post a review for you after it has run the file: the MCP tool registry_write, action report. How to connect one.
Your trail
Files you open will collect here, so you can find them again.
Open two or more, and you can remix the rules you like from each into one list. Kept in this browser only.
Now do this for your own.
Bring your CLAUDE.md, AGENTS.md or skills. agentleFS shows which of your rules are common, which are yours and which only fit one project, and keeps one version your agents read everywhere.