GROBID transition

[draciti]

Analysis on additional papers:

Valerio: I debugged the text extraction and modified GROBID parameters to include section names (headers) as sentences.

I also checked all the other issues you reported, and they are mostly GROBID extraction errors on the Cell Press STAR Protocols paper format, which was generating a lot of errors also with the old extraction method based on heuristics. See my replies below:

Daniela: General comments: for all papers below I spot-checked sentences from each section (e.g. abstract, introduction, results, figure legends, discussion)

00065855 Checked random sentences from each section, all good. The only sentences that were not extracted were section headers, e.g. 3.1. Method development for quantification of GSH-NEM and GSSG via LC-MS/MS

• FIXED - added section names to extracted sentences

00065849 It worked great!

00065841 Sentences in SUMMARY not extracted

• NOT FIXED - GROBID extraction error

Section headers not extracted, e.g.: scRNA-seq of aging C. Elegans

• FIXED - added section names to extracted sentences

Or extracted in tandem with another sentence: Cell-type-specific regulation and TF activity Differential gene expression across cell types is driven by factors that regulate mRNA production and stability.

• NOT FIXED - GROBID extraction error

Some sentences are not extracted: e.g. Gene expression drift is a common correlate of aging.

• NOT FIXED - GROBID extraction error

00065836 Headers not extracted, but not all. e.g.: 'Plasmid and cell line generation'; 'Fluorescence imaging'

• FIXED - added section names to extracted sentences

An example of an header that was extracted: Recovery of protein synthesis after DNA damage depends on transcription-couple

• NOTE - This is also a sentence in a figure legend and was extracted for that reason, but now all section headers are added

Lots of sentences on Page 10 (paragraph Prospects and limitations of the RPS assay) were not extracted.

• NOT FIXED - The first sentence in the section is missing the second half, but all the other sentences look ok to me.

00065832 It did not extract the section 'Before you begin' culturing worms starting from: 'Here, we present protocols to determine binding between..' To '..and FLAG- tagged nuclear hormone receptors.' Starting on the following page, same section, the extraction worked.

• NOT FIXED - GROBID extraction error

Other bits were not extracted. Eg.:

• CRITICAL: It is imperative that all samples be exposed to each temperature for the same amount of time for consistent results.

  15. Transfer each sample into ice-chilled 1.5 mL microcentrifuge tubes and spin at 20,000 3 g for 20 min at 4 C.
• 19. Load samples into four NuPage 12% Bis-Tris gels, 17-well, 1.0 mm in 13 MES SDS running buffer. Run at 100 V constant for about 2 h. Note: The amount of protein to be loaded for gel electrophoresis will depend on the efficacy of the primary antibody. For FLAG-tagged proteins, we have had success with loading 10– 15 mL of the protein/LDS/b-ME mixture.

• NOT FIXED - GROBID extraction error

[draciti]

Daniela to test 5 additional papers, then move to production

[draciti]

Tested 5 more papers, results below. Let me know if we need more

General question: When we click on ‘Sentence level classification’, does it process also the supplementary material or only the main PDF? If only the main PDF we can think of adding a separate button for processing the supplementals

00065854 blob:https://literature.alliancegenome.org/90d4ee65-cfbf-4359-a7d8-b51d7a0faa1e

Abstract not extracted but the display of the abstract is peculiar, almost like in a separate box Other than that, it worked great!

00065853 First sentence of the introduction not captured, probably because there is a charachter (T) that spans two rows: THE brain is one of the most studied and complex systems of the biological systems, because neurological disorders are closely related to changes in brain structure Other sentences in the paragraph look fine

First sentence of figure caption #1 not captured, but it is not even possible to copy-paste manually Caption of table III also problematic

00065850 NOTE: It did not extract any sentence

00065847 It worked great

00065846 It worked great

[valearna]

Is this still ongoing @draciti ? Can we close this issue?

[draciti]

We can close this @valearna , GROBID is working pretty well!