Maria del Mar Quiroga

Warnings using metaspades

5

I'm trying to assemble some publicly available metagenomic data using metaspades. The data is here: https://www.omicsdi.org/dataset/omics_ena_project/PRJNA379494. I'm testing the first set of paired-end reads: SRR5351712_1 and SRR5351712_2. I was able...

`git update git-for-windows` has been deprecated: https://stackoverflow.com/questions/13790592/how-to-upgrade-git-on-windows-to-the-latest-version#:~:text=If%20you%20type%20git%20update,git%2Dfor%2Dwindows%20instead.

Grammar, clarity and other updates

1

Fix up typos, grammar and improve clarity for lessons 1, 2, and 4. Replace function to calculate the volume of a cube with a function more relevant to Social Sciences.

R version of the coordination network toolkit?

1

Hi team, This looks like a really interesting toolkit, but we have not been able to use it much as we are primarily R users. Is there any possibility of...

Empty tei output for Elsevier xml files

8

Hi again, I'm getting empty tei xml outputs from GROBID for all of our Elsevier xml files, wondering if anybody could take a look?

Funding statement missed by Pub2TEI for xml from Taylor and Francis

3

When I use Pub2TEI on the xml fie for https://www.tandfonline.com/doi/xml/10.1080/15427560.2014.942420, the funding statement is not getting copied over to the output xml. Does this happen to have an easy fix?...

Conflict of interests missing from xml output

5

Hi, We are looking into using Grobid for a project to look into conflict of interest, funding, and other transparency statements in published articles. These statements are put in different...

Trial registration statement missing from xml output

3

Hi again, Another "error case". For the published pdf for https://pubmed.ncbi.nlm.nih.gov/27917460/ (not the freely available author manuscript), the "Trial Registration" located just under the abstract on page 1 is missing...

GROBID detects funding information, but funder is left out in tei xml output

5

Hi, Me again, sorry! I have another potential error case where the funder is correctly identified, but the name of the funder is left out of the TEI/XML output in...

GROBID splits sentences, puts second half in a figure description

6

Potential error case, not sure if open access (i.e., can be used for training). For the PDF file from: https://link.springer.com/article/10.1007/s12144-016-9469-4. The PDF looks like this:  Whereas GROBID appears to...