Skip to content

biblio_pdf_fetch_oa for 11 papers missing PDFs/docling fulltext in pixecog bib library.

Context: pixecog has 36 bib entries in bib/pixecog.bib. 25 have docling fulltext extraction. The remaining 11 are missing PDFs entirely (docling_batch reports 0 pending — meaning no PDFs exist to process). Need to fetch open-access PDFs for these 11 papers so docling can extract their fulltext for RAG.

Steps: 1. Run biblio_library_quality() in pixecog to identify the 11 citekeys without fulltext 2. For each, run biblio_pdf_fetch_oa("") to attempt OA PDF download 3. After PDFs are fetched, run biblio_docling_batch() to extract fulltext 4. Re-run biblio_compile() to update compiled.bib


Source context: pixecog

PixEcog (pixecog): Neuropixels and ECoG dataset and analysis

Recent commits:

80d9ee0 Fix mkdocs build warnings: bibtex config, include-markdown delimiters, dead nav/links, abbreviated citation keys, false-positive citations, merge modkey.bib
0d1ff72 Publish TTL notebook HTMLs (investigate_ttl_artifact, ttl_artifact_removal)
56cc377 [DATALAD] Added subdataset

README:


type: readme


Quick Start for Collaborators

Follow this checklist to get started with Pixecog documentation and workflows.

🐀 Pixecog Project — Compact Overview

Core principles

  • One immutable BIDS raw dataset (raw/) as the canonical baseline
  • Each analysis pipeline ha