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Publication data and build pipeline

The publication system separates portable citation data from website-only metadata while preserving BibTeX as the source used for the CV.

Data flow

bibliography/publications.bib
        +
publication_metadata/*.yml
        +
_people/*.md
        |
        v
scripts/build_publications.py
        |
        +--> _papers/<BibTeXKey>.yml
        +--> pub.bib
        |
        +--> scripts/build_cv.py
                 +--> cv/generated/publications.tex
                 +--> assets/ABoyle_CV.pdf

Authoritative files

  • bibliography/publications.bib: authors, title, journal, year, volume, pages, DOI, PMID, URLs, abstract, and other citation fields.
  • publication_metadata/*.yml: Michigan umid relationships and website-only fields.
  • _people/*.md: canonical member names and profile URLs.

Generated files

  • _papers/*.yml: records consumed by Jekyll.
  • pub.bib: combined bibliography offered as a website download.
  • cv/generated/publications.tex: CV publication list generated from the same records.
  • assets/ABoyle_CV.pdf: compiled CV deployed with the site.

Never edit a generated paper file, pub.bib, or cv/generated/publications.tex directly.

Citation keys

Each BibTeX key is a permanent, filename-safe identifier:

FirstAuthorYearMnemonic

Examples:

Dong2023RegulomeDB2
McDonald2021Cas9MobileElements
VanDeynze2025HMMSTR
SMaHTNetwork2025SomaticMutationBenchmarking

Keys must match ^[A-Za-z][A-Za-z0-9]*$, be unique without regard to filename case, and remain unchanged when a preprint becomes a journal article. The generated filename is exactly _papers/<BibTeXKey>.yml.

Adding or updating a publication

  1. Add or edit the entry in bibliography/publications.bib.

  2. For a new key, create a sidecar:

    python3 scripts/scaffold_publication_metadata.py --bibkey NewKey2026

  3. Review the inferred members list. The scaffold is conservative and cannot infer consortium participation or every historical author name.

  4. Add any website-only fields described below.

  5. Regenerate and test:

    make publications
make cv
make check

  6. Commit the BibTeX, sidecar, generated _papers record, pub.bib, generated CV TeX, and updated CV PDF.

When bibliography/publications.bib changes, the GitHub Actions workflow performs the same website and CV generation and commits changed generated files after a direct push. The workflow can also be started manually.

Minimal sidecar

bibkey: VanDeynze2025HMMSTR
members:
  - kvandeyn
  - crmumm
  - apboyle

bibkey must match one BibTeX entry. members contains Michigan umid values from _people in byline order when practical.

Historical or publication-specific names

Do not add name aliases to _people. Map a specific byline in the relevant sidecar:

bibkey: Mumm2023OnRamp
members:
  - melyssae
  - apboyle
author_member_map:
  melyssae: "Drexel, Melissa L"

The mapping value may be the exact BibTeX author name or a zero-based author index. Every mapped umid must also appear in members.

Consortium and other non-byline participation

When a lab member participated through a group author but is not individually named in the BibTeX byline:

members:
  - apboyle
member_roles:
  apboyle: consortium

Supported non-byline roles are consortium, contributor, group_author, and non_byline. The main Publications page displays a Consortium badge if any member role is consortium. An individual member page can show that person’s role without inserting a false personal byline.

Website-only links

Citation fields should remain in BibTeX where possible. Sidecar links are for supplemental resources:

links:
  code: https://github.com/example/tool
  data: https://example.org/dataset
  protocol: https://example.org/protocol
  news:
    - /papers/2026/01/01/example/

news is normalized to a list. Article, PDF, and preprint URLs should normally be BibTeX fields rather than duplicated in links.

Featured publications

The Publications page shows up to four records with featured: true, newest first:

featured: true
topics:
  - Tandem repeats
  - Long-read sequencing
  - Neurogenetics
summary: >-
  A concise plain-language description of the central result and why it matters.
teaser: /assets/images/publications/VanDeynze2025HMMSTR.png

The teaser should be a screenshot of the full first page of the paper, tightly cropped to the page boundary. The CSS scales the full page into the card without cropping it.

Optional overrides

These fields are accepted when citation information cannot be represented appropriately in BibTeX:

status: preprint          # published, preprint, or in_press
publication_type: article # article, chapter, or conference
PMID: "12345678"
biorxiv: https://...
abstract: >-
  Optional website-specific abstract override.

Prefer to maintain DOI, PMID, URLs, dates, abstracts, journal, volume, and pages in BibTeX.

Generated paper schema

Every generated record contains:

generated: true
bibkey: StableKey2026
title: Paper title
author_list:
  - citation_name: Boyle AP
    member_url: /people/Alan_Boyle/
    member_name: Alan P. Boyle, Ph.D.
    equal_contrib: true       # only when present
    co_senior: true           # only when present
year: 2026
sort_date: 2026-06-28
members:
  - apboyle
bibtex: |
  @article{StableKey2026,
    ...
  }

Optional generated fields are limited to those used by the current templates: status, publication_type, journal, volume, number, pages, doi, PMID, primary_url, pdf, biorxiv, links, member_roles, abstract, featured, topics, summary, and teaser.

The full author list is always serialized and displayed. There is no short or collapsible author representation.

Validation rules

The build rejects or warns about:

  • Unsafe or duplicate BibTeX keys.
  • Duplicate DOIs.
  • Missing sidecars or orphaned sidecars.
  • Unknown or duplicate member umid values.
  • Members that cannot be matched to the byline without an override or non-byline role.
  • Invalid status, publication type, or role values.
  • Duplicate filenames on case-insensitive filesystems.
  • Deprecated slug, legacy_bibkeys, person alias fields, and obsolete generated assets.
  • Stale or missing generated records in --check mode.

Run strict validation with:

python3 scripts/build_publications.py --check --strict

CV integration

The CV does not parse a separate bibliography or maintain its own author-name list. scripts/build_cv.py uses the validated publication records and the sidecar member mappings. Alan Boyle is bolded by umid: apboyle; other byline members are underlined. Non-byline consortium roles remain associated with member pages but are not inserted into the CV author list. See CV.md.