🧬 Aging Wiki

retrieving-papers

Properties1
aliasespaper retrieval, DOI resolution

2 min read

SOP: retrieving papers

The wiki references every primary source by DOI (and PMID/PMC where available). The DOI is the canonical identifier — papers are referenced by DOI, never by a local file path. This SOP covers discovery (finding the right paper) and full-text resolution.

Discovery — finding papers by topic (use the web)

For term-based citation discovery, query the public literature APIs (via WebFetch or curl):

  • PubMed eutils — https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=<query>&retmode=json&retmax=20
  • Semantic Scholar — https://api.semanticscholar.org/graph/v1/paper/search?query=<query>&fields=title,authors,year,externalIds,citationCount&limit=10 (returns DOIs + citation counts; useful for high-impact filtering)
  • Crossref — https://api.crossref.org/works?query=<query>&rows=10&select=DOI,title,author,issued,is-referenced-by-count
  • Europe PMC — https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=<query>&format=json&pageSize=10

Metadata for a known DOI

  • Authors — curl -s "https://api.crossref.org/works/<DOI>" | jq -r '.message.author[] | "\(.given) \(.family)"'
  • Abstract — Crossref’s .message.abstract (often present), or the publisher landing page.
  • Open-access status / full text — Europe PMC and the Unpaywall API (https://api.unpaywall.org/v2/<DOI>?email=<you>) report OA status and an open PDF URL when one exists.

Full-text resolution

Reading the full PDF (needed for a verification pass — see verifying-extraction) requires resolving the DOI to a local file. This is handled by a private local tooling layer documented in CLAUDE.local.md (git-ignored, not part of this public repo). Nothing in the wiki content depends on a specific tool: on a fresh clone without that layer, substitute your own DOI→PDF resolution (institutional access, Unpaywall, PMC OA, preprint servers).

When no full text is available (paywalled, no OA copy):

  • Check PMC for an author manuscript: https://www.ncbi.nlm.nih.gov/pmc/articles/?term=<DOI>
  • Check preprint servers (bioRxiv, arXiv, medRxiv).
  • Still record the DOI in the study page frontmatter, cite from the abstract, and tag #gap/no-fulltext-access. Keep verified: false until the full text can be read.

When recording a study in the wiki

Always include the DOI (and PMID/PMC if available) in the study page frontmatter, even when the PDF isn’t available. See extracting-evidence for what to extract and adding-a-claim for citation format.

See also

Graph View

Backlinks