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@caufieldjh caufieldjh released this 02 Nov 18:45
· 4 commits to main since this release
v0.5.1
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Learn about vigilant mode.

Under 0.5.0 a quote has to start and end on whole words. That exposed text the extractors had welded together, where a correct quote now failed. This release stops the welds (#163).

Fixes

  • Crossref abstracts (DOI). JATS titles, sections and paragraphs, plus HTML div and br, are now blank-line-separated paragraphs. Before, <jats:title>Abstract</jats:title><jats:sec><jats:title>Disease overview</jats:title><jats:p>Acute… became AbstractDisease overviewAcute.
  • PubMed abstracts. A section heading welded onto its sentence becomes a Heading: label. That covers inline <b>Background</b>Neuroblastoma and headings PubMed stores with no markup (exposures.ConclusionsPoison). Only listed, title-case headings directly followed by a capital letter count. Bold that isn't welded, such as <b>IL</b>-6, is left alone.
  • PMC XML citation markers. A <xref ref-type="bibr">, or a <sup> holding only such markers, now gets a space before it. So FOXL2<sup>8</sup> no longer reads as FOXL28, and PGE2.<sup>41</sup> no longer as the decimal pge2.41. It also gets a space after it, except before a dash, so a range like [1-3] keeps its dash.
  • PMC XML lead-in labels. A paragraph's bold label welded to the next word (<bold>R 2.6</bold>We recommend) is set off from it.
  • Matching. The trailing-citation allowance also accepts superscript digits, so small ears matches small ears¹⁻³. As before, it applies only after a quote ending in a letter.

Existing caches are not refreshed automatically

EXTRACTOR_CACHE_VERSION is unchanged on purpose. Bumping it would re-fetch every cached reference on the next validation. So an entry cached before 0.5.1 keeps its welded text until you re-fetch it with linkml-reference-validator cache reference <ID> --force, which means results depend on when an entry was cached.

Check what a forced re-fetch gives back before keeping it. Full text that came from a PDF or publisher HTML can come back as an abstract only. In one re-fetch of 453 references, 66 came back abstract-only or empty.

Full changelog: v0.5.0...v0.5.1

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