Curating Bioarchive publications

[ValWood]

I just spotted that some of the PMID publication in Canto are actually in Bioarchive, so

1. Do we want authors to be able to curate pubs when in BioArchive (I think yes, if they want to- pre publication curation is good)
2. BUT if so we need a way to migrate the annotation on a session to the eventual published version (A differnet PMID)

to discuss
@kimrutherford
@manulera

Also, I wondered if any of the sessions I have sent out already are BioArchive (Kim could you check Bioarchive pubs and their status with a query)

[kimrutherford]

BUT if so we need a way to migrate the annotation on a session to the eventual published version (A differnet PMID)

I'm hoping the PubMed ID for the bioRxiv version will be included in the XML metadata for the published version. If so hopefully we can automate the migration.

Kim could you check Bioarchive pubs and their status with a query

There are 12. Of those 3 have been sent to curators:

pmid	title	citation	publication_date	name	session_sent_date
PMID:34845452	Genome-wide characterization of SARS-CoV-2 cytopathogenic proteins in the search of antiviral targets.	bioRxiv 2021 Dec 14;	2021 12 14	Wrong organism
PMID:36747616	Anillin Related Mid1 as an Adaptive and Multimodal Contractile Ring Anchoring Protein: A Simulation Study.	bioRxiv 2023 Jan 27;	2023 01 27	Modelling
PMID:36778333	Microtubule competition and cell growth recenter the nucleus after anaphase in fission yeast.	bioRxiv 2023 Feb 01;	2023 02 01	Curatable
PMID:36798368	Quantifying yeast microtubules and spindles using the Toolkit for Automated Microtubule Tracking (TAMiT).	bioRxiv 2023 Feb 08;	2023 02 08	Method or reagent
PMID:36909652	Actin-microtubule crosstalk imparts stiffness to the contractile ring in fission yeast.	bioRxiv 2023 Mar 02;	2023 03 02	Curatable
PMID:36945633	H3K9 methylation enhances HP1-associated epigenetic silencing complex assembly and suppresses off-chromatin binding.	bioRxiv 2023 Mar 08;	2023 03 08	Curatable	2023-04-10 08:45:40
PMID:36945624	Comprehensive mutational analysis of the checkpoint signaling function of Rpa1/Ssb1 in fission yeast.	bioRxiv 2023 Mar 06;	2023 03 06	Curatable	2023-04-01 10:19:48
PMID:36945401	The minimal intrinsic stochasticity of constitutively expressed eukaryotic genes is sub-Poissonian.	bioRxiv 2023 Mar 08;	2023 03 08	Cell composition or WT feature
PMID:36993237	The fission yeast cytokinetic ring component Fic1 promotes septum formation.	bioRxiv 2023 Mar 14;	2023 03 14	Curatable	2023-04-01 09:15:33

[kimrutherford]

I'm hoping the PubMed ID for the bioRxiv version will be included in the XML metadata for the published version.

I had a look at this one:

PMID:34845452	Genome-wide characterization of SARS-CoV-2 cytopathogenic proteins in the search of antiviral targets.	bioRxiv 2021 Dec 14;	2021 12 14	Wrong organism

It's "Wrong organism" but it's now published.

This is the record for the pre-print:
https://pubmed.ncbi.nlm.nih.gov/34845452/

And here is the publication:
https://pubmed.ncbi.nlm.nih.gov/35164548/

I downloaded the XML for the published version. It does include the PMID of the pre-print but not in a very obvious way. It's in this section:

      <CommentsCorrectionsList>
        <CommentsCorrections RefType="UpdateOf">
          <RefSource>bioRxiv. 2021 Dec 14;:</RefSource>
          <PMID Version="1">34845452</PMID>
        </CommentsCorrections>
      </CommentsCorrectionsList>

So far there aren't that many pombe pre-prints in PubMed so maybe an automated system for updating the PMIDs isn't worth it yet.