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Add a required `references` list to `ProblemMetadata`: the publications a problem is based on, each with its `doi` and a `bibtex` entry. The first entry is the main publication, its BibTeX key is the problem ID (checked by `bmp-check-metadata`). `get_bibtex()` aggregates the main publications' entries; the site build writes them to `references.bib`. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
DOIs are taken from the SBML model annotations (for `Giordano_Nature2020` and `Zhao_QuantBiol2020`, which only have PubMed IDs, via NCBI E-utilities). The BibTeX entries were generated from the Crossref API records (fetched 2026-10-22) without manual edits; only HTML entities were decoded, non-breaking spaces replaced, `&` escaped, and page ranges written with `--`. Article numbers are used as `pages` where there are no pages. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Corrections verified against the publications' full texts:
* `Bachmann_MSB2011`: `pages` `MSB201150` -> `516` ("Molecular Systems
Biology 7; Article number 516")
* `Chen_MSB2009`: `pages` `MSB200874` -> `239` ("Molecular Systems
Biology 5; Article number 239")
* `Fujita_SciSignal2010`: add missing `pages` `ra56` ("Volume 3 Issue
132 ra56")
* `Borghans_BiophysChem1997`: author "JoséA.M." -> "José A.M." ("José
A.M. Borghans"); title: add the missing separator between title and
subtitle, which the paper sets on separate lines (". " as in PubMed,
PMID 17029867)
* `Zhao_QuantBiol2020`: title: U+2010 hyphen -> "-" in "COVID-19"
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
BibTeX treats "A.M." as a single name part, so abbreviating styles
(e.g. `abbrv`) drop the second initial ("J. A. Borghans" instead of
"J. A. M. Borghans"). Affects `Borghans_BiophysChem1997` and
`Rahman_MBS2016`.
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Bibliography styles that convert titles to sentence case (e.g. `plain`,
or biblatex with `\MakeSentenceCase`) would otherwise lowercase them
("dna", "covid-19", "italy"). Only acronyms, gene/protein names, proper
nouns, and single capital letters are braced; other capitalized words
are left for the style to handle.
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Some journals print initials without periods ("Martin E Böhm"), and
Crossref has them that way. In BibTeX, initials should end with a
period; otherwise styles that print full given names show "Martin E
Böhm", and JabRef reports the names as not in standard BibTeX format.
Affects `Bachmann_MSB2011`, `Chen_MSB2009`, `Smith_BMCSystBiol2013`,
and `Weber_BMC2015`.
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
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Adds the source publication(s) of each problem to
metadata.yamlas a requiredreferenceslist, each entry withdoiandbibtex. The first entry is the main publication; its BibTeX key is the problem ID.bmp-check-metadatachecks the DOI format, thatbibtexis a single entry with a matchingdoifield, and the key.Further changes:
get_bibtex()combines the entries; the site build writes them toreferences.bibnext toindex.html, linked from the overview page.The data were added in reviewable steps (see individual commits):
Giordano_Nature2020andZhao_QuantBiol2020via PubMed).All entries were processed with BibTeX (
plain,abbrv) and biblatex/biber (--validate-datamodel) without warnings.The SBML reference annotations are left as they are; for now, there is no check that they agree with
metadata.yaml.Relates to #308.
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