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Adds paper/paper.md (Whedon-format draft seeded from the README statement of need), paper/paper.bib (six seed entries flagged for DOI verification), and paper/INSTRUCTIONS.md for collaborators. Gates: - tests/test_paper.py: front matter, citation resolution, and JOSS word budgets, running in CI (python-test), as the paper-checks pre-commit hook, and via make paper-check - .github/workflows/paper.yml: path-filtered compile of paper.pdf from the JOSS paperdraft resources, uploaded as an artifact - Makefile: paper-check / paper-image / paper-pdf / paper targets The paperdraft build patches the archived whedon sources (registry-qualified base image, frozen TeXLive 2021 repo, vestigial biblatex strip); the Makefile and workflow versions must stay in sync.
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test_docs_source_of_truth requires every .PHONY Makefile target in the CONTRIBUTING.md Task runner table and every workflow described once in the llms.txt GitHub Workflows entry with matching purpose terms; paper.yml's compile step now names itself a test build so the entry reads naturally.
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@jaredroach and @gglusman this is where we're supposed to work on and edit the JOSS paper for Tablassert. I still need to scaffold out the paper but I'd imagine us here commenting. Making edits as commits to this branch, etc... I'll update y'all here when I do anything |
Replaces the scaffold's TODO seed text with a complete draft across all JOSS-required sections (Summary, Statement of need, State of the field, Software design, Research impact statement, AI usage disclosure stub, Acknowledgements stub, References). Research impact states lineage facts with status caveats: MicrobiomeKG precursor use, current MOKG builds, DAKP releases, pending translator-ingests integration, KRAKEN graph consumption, rare-disease graph in preparation. paper.bib: every published entry re-verified against Crossref/arXiv/ bioRxiv or upstream CITATION.cff/release metadata; replaces four wrong scaffold DOIs (biolink-model, translator, babel, kgx) and fixes the MicrobiomeKG author order; adds koza, redb, kraken, dakp, drug-approvals, ingests entries. Gates: paper-check now enforces the JOSS-required section list and the official 750-1750 word body budget (scaffold capped at a self-imposed 1000); markdownlint overrides MD025 for paper/paper.md because the JOSS template puts every section at heading level 1. Verified: pytest full suite 1229 passed, pyright clean, ruff clean, markdownlint clean, html-validate clean, paper.pdf compiles to 3 pages with resolved citations.
… field Front matter now uses the JOSS affiliation-index convention with an affiliations list; the previous full-string affiliations made authblk collapse the rendered author block to the last author (verified in the compiled PDF). KGX is cited with title only since it has no CITATION.cff or registry-verified author list. CITATION.cff author order updated to match.
- AI usage disclosure: pi agent, model inventory, validation methods, funding - paper/benchmarks: fullmap vs hosted SRI name resolution; Tablassert vs Koza - State of the field: LinkML, NameRes service distinct from BABEL - Software design: column context, filtering, tie-breakers, taxon allowlist trade-off, exact-match resolution rationale, SapBERT BABEL checkpoint, output validation passes, DAKP audit scale - Bibliography: fix koza version, add kgx authors, add NameRes, LinkML, MOKG dataset, graph monorepo, ingests PR 550 references - Research impact: deployed MOKG graphs use Tablassert
…ap sizes - Move benchmark numbers into a Benchmarks section - validate-kgx vs KGX schema-driven validate; --prune repair mode - Fullmap sizes: 44.5 GB prebuilt (BABEL 22.2.0), 24.7 GB local store - Trim to stay inside the JOSS body budget
The 24.7 GB figure was only the primary redb file; the store is one primary plus 16 shard files, 92,881,358,848 bytes uncompressed. Benchmark README now carries the per-component breakdown.
…pher, OntoWeaver, Monarch JOSS's official template lists only Summary, Statement of need, State of the field, Software design, Research impact, AI usage disclosure, Acknowledgements, and References, so the standalone Benchmarks section is folded into Software design where the numbers support design claims. New citations replace the LinkML repo entry with the GigaScience paper and add BioCypher (Nat Biotechnol 2023), OntoWeaver/BioCypher tabular-to-KG mapping (FUSION 2024), and Monarch 2024 (NAR) to State of the field. Trim AI disclosure redundancy to stay inside the 1750-word budget.
Adds Caufield et al., Bioinformatics 40:btae104 (2024), contrasted as free-text zero-shot extraction against Tablassert's structured-table sources. Compensating trims keep the body inside the JOSS word budget.
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@jaredroach the paper is at a stage where I want you to take a look at it. This links to the JOSS requirements. This links to a render of the draft. Let me know if you're satisfied with the contributions section. Please flag any typos or unclear wording. Feedback on the narrative, and especially the statement of need and research sections, would be amazing too. @gglusman is busy until Wednesday, so you have my full attention for comments you make here or on Slack until then. Also, feel free to make updates and commit them to the branch. |
Corrected capitalization in acknowledgements section.
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What
Scaffolds the JOSS paper in
paper/(tracked, not ignored) and wires it into the repo's gates:paper/paper.md: Whedon-format draft, seeded from the README statement of needpaper/paper.bib: six seed entriespaper/INSTRUCTIONS.md: collaborator guidance (word budgets, figures, submission flow)tests/test_paper.py: front matter / citation resolution / word-budget gate (runs in CIpython-test, as thepaper-checkspre-commit hook, and viamake paper-check).github/workflows/paper.yml: path-filtered compile ofpaper.pdffrom the JOSS paperdraft resources, uploaded as a PR artifactMakefile:paper-check/paper-image/paper-pdf/paperVerified locally:
make papercompiles a valid PDF with resolved citations;make paper-pdfis idempotent (stamp + Docker layer cache); the Paper workflow will run on this PR sincepaper/**changed.Checklist before submission to review-joss
TODO(collaborators)section inpaper/paper.md(Statement of need, State of the field, Acknowledgements)% TODO: verifyentry inpaper/paper.bib(title, authors, year, DOI)paper/figures/and uncomment the Figures placeholderCITATION.cff)make paperpasses locallyNotes
paper-imagebuilds the paperdraft image from the archived (frozen 2024-04-16) openjournals/whedon sources with three patches (registry-qualified base, frozen TeXLive 2021 repo, vestigial biblatex strip). Makefile and workflow copies must stay in sync.paper/*.pdfand.paperdraft/are git-ignored.