MSID: 101918 Version: 1 DOI: 10.1101/2023.02.28.530247

fred-atherden commented 2 weeks ago

MSID: 101918

Version: 1

Preprint DOI: https://doi.org/10.1101/2023.02.28.530247

Step 1. Awaiting reviews

Editorial to post reviews via hypothesis

Useful links:

DocMap: https://data-hub-api.elifesciences.org/enhanced-preprints/docmaps/v2/by-publisher/elife/get-by-manuscript-id?manuscript_id=101918
New model tracking: https://docs.google.com/spreadsheets/d/1_fHaoOy7hjyocptKtVJRijeNpUY4hBS7Ck_aVmx6ZJk/
Reviews on sciety: https://sciety.org/articles/activity/10.1101/2023.02.28.530247

For trouble shooting (e.g. no Docmaps available):

DocMap issue addressing: https://miro.com/app/board/uXjVNCwK6EI=/
Explore DataHub DocMaps API: https://lookerstudio.google.com/reporting/4c2f0368-babb-4beb-b5b3-497e7e7b0f08/page/ejphD
Unmatched submissions and preprints: https://lookerstudio.google.com/u/0/reporting/9f86204f-3bf7-477c-9b18-5c5ef141bf69/page/p_gxi57ha93c
Unmatched manuscripts spreadsheet: https://docs.google.com/spreadsheets/d/15QcK8w-ssB7109RQEDtFpJPZ0J5HTGxoHa_2TtpMBbg/edit#gid=1336081641

Step 2. Preview reviewed preprint

Production QC content ahead of publication

Instructions:

QC preview: https://prod--epp.elifesciences.org/previews/101918v1
Update ticket with any problems (add blocked label)
When QC OK, add QC OK label to ticket and add publication date and time to https://docs.google.com/spreadsheets/d/1amAlKvdLcaDp5W8Z8g77NmkwbMF5n_u89ArSqPMO8jg
Move card to next column
(At end of the day post link in #enhanced-preprint and ask for PDF to be generated)

Useful links:

Preprint DOI : https://doi.org/10.1101/2023.02.28.530247
Confirm reviews returned by EPP: https://prod--epp.elifesciences.org/api/reviewed-preprints/101918/v1/reviews
To update the MECA path in the docmap: https://docs.google.com/spreadsheets/d/1mctCQuNFBjSn97Lihy7_vBO6z7-N-oqyLv4clyi6zHg

Step 3: Awaiting search reindex

This step adds the reviewed preprint to the homepage: https://elifesciences.org

The search reindex is triggered once an hour. We need the reviewed preprint to be indexed as the search application serves the journal homepage.

Useful links:

Jenkins pipeline to reindex search can be triggered sooner or monitored here: https://alfred.elifesciences.org/job/process/job/process-reindex-reviewed-preprints/

Step 4: Published! PDF requested

Waiting for PDF to be generated

Useful links:

PDF tracking: https://docs.google.com/spreadsheets/d/106_XeDjmuBae7gexOTNzg60lapeqjl2aRn9DzupGyS8/

Step 5: Introduce PDF to data folder and git repo

Upload PDF to relevent folder in git repo https://github.com/elifesciences/enhanced-preprints-data/

Step 6: Done!

[ ] Kettle is on!

elife-bot commented 1 week ago

- error: [aff-multiple-ids] Affiliation contains more than one institution-id element: https://ror.org/03taz7m60; https://ror.org/058zz0t50; https://ror.org/0444fnd49 in 10 https://ror.org/03taz7m60 https://ror.org/058zz0t50 https://ror.org/0444fnd49 Department of Integrative Anatomical Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
! warning: [aff-no-wrap] Affiliation doesn't have an institution-wrap element (the container for institution name and id). Is that correct?
! warning: [aff-no-wrap] Affiliation doesn't have an institution-wrap element (the container for institution name and id). Is that correct?
! warning: [aff-no-wrap] Affiliation doesn't have an institution-wrap element (the container for institution name and id). Is that correct?
! warning: [aff-no-wrap] Affiliation doesn't have an institution-wrap element (the container for institution name and id). Is that correct?
! warning: [aff-no-wrap] Affiliation doesn't have an institution-wrap element (the container for institution name and id). Is that correct?
! warning: [aff-no-wrap] Affiliation doesn't have an institution-wrap element (the container for institution name and id). Is that correct?
! warning: [aff-no-wrap] Affiliation doesn't have an institution-wrap element (the container for institution name and id). Is that correct?
! warning: [aff-no-wrap] Affiliation doesn't have an institution-wrap element (the container for institution name and id). Is that correct?
! warning: [aff-multiple-institution] Affiliation contains more than one institution element: Department of Development; Keck School of Medicine, University of Southern California in 9Department of Development, Stem Cell, and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
! warning: [aff-no-wrap] Affiliation doesn't have an institution-wrap element (the container for institution name and id). Is that correct?
! warning: [aff-no-wrap] Affiliation doesn't have an institution-wrap element (the container for institution name and id). Is that correct?
! warning: [mixed-citation-other-publication-flag] mixed-citation in reference (id=c64) has a publication-type='other'. Is that correct?
! warning: [p-all-bold] Content of p element is entirely in bold - 'Table S1: Differentially expressed genes for low resolution rod clusters (LR / ER)'. Is this correct?
! warning: [p-all-bold] Content of p element is entirely in bold - 'Table S2: Differentially expressed genes for low resolution cone clusters (S / LM)'. Is this correct?
! warning: [p-all-bold] Content of p element is entirely in bold - 'Table S3: Differentially expressed genes for late vs early maturing L/M cone populations'. Is this correct?
! warning: [p-all-bold] Content of p element is entirely in bold - 'Table S4: SCENIC RSS scores for low resolution clusters'. Is this correct?
! warning: [p-all-bold] Content of p element is entirely in bold - 'Table S5: SCENIC RSS scores for high resolution clusters'. Is this correct?
! warning: [p-all-bold] Content of p element is entirely in bold - 'Table S6: Pseudotime-correlated genes and gene modules'. Is this correct?
! warning: [p-all-bold] Content of p element is entirely in bold - 'Table S7: Differentially expressed genes for low resolution early rod and L/M cone clusters (ER / LM)'. Is this correct?
+ info: [article-version-flag] This is preprint version 1.2.
+ info: [permissions-info] This article is licensed under a CC BY 4.0 license. https://creativecommons.org/licenses/by/4.0/ https://elifeproduction.slab.com/posts/licensing-and-copyright-rqdavyty#permissions-info

ameenanaji commented 1 week ago

Hi @fred-atherden , the authors have provided a provisional author response, and I am asking Ed Office to add this now

fred-atherden commented 1 week ago

OK thanks Ameena

ameenanaji commented 1 week ago

@fred-atherden the provisional author response has been added

elife-bot commented 1 week ago

- error: [aff-multiple-ids] Affiliation contains more than one institution-id element: https://ror.org/00412ts95; https://ror.org/03pjgt842 in 1 https://ror.org/00412ts95 https://ror.org/03pjgt842 The Vision Center, Department of Surgery, and Saban Research Institute, Children’s Hospital Los Angeles, Los Angeles, CA, USA
- error: [aff-multiple-ids] Affiliation contains more than one institution-id element: https://ror.org/03taz7m60; https://ror.org/058zz0t50; https://ror.org/046rm7j60 in 4 https://ror.org/03taz7m60 https://ror.org/058zz0t50 https://ror.org/046rm7j60 Department of Biochemistry & Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- error: [aff-multiple-ids] Affiliation contains more than one institution-id element: https://ror.org/03taz7m60; https://ror.org/058zz0t50; https://ror.org/046rm7j60 in 6 https://ror.org/03taz7m60 https://ror.org/058zz0t50 https://ror.org/046rm7j60 Maternal-Fetal Medicine Division of the Department of Obstetrics and Gynecology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- error: [aff-multiple-ids] Affiliation contains more than one institution-id element: https://ror.org/03taz7m60; https://ror.org/058zz0t50; https://ror.org/0444fnd49 in 8 https://ror.org/03taz7m60 https://ror.org/058zz0t50 https://ror.org/0444fnd49 Department of Radiology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- error: [aff-multiple-ids] Affiliation contains more than one institution-id element: https://ror.org/03taz7m60; https://ror.org/058zz0t50; https://ror.org/0444fnd49 in 9 https://ror.org/03taz7m60 https://ror.org/058zz0t50 https://ror.org/0444fnd49 Department of Development, Stem Cell, and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
! warning: [aff-no-wrap] Affiliation doesn't have an institution-wrap element (the container for institution name and id). Is that correct?
! warning: [aff-no-wrap] Affiliation doesn't have an institution-wrap element (the container for institution name and id). Is that correct?
! warning: [aff-no-wrap] Affiliation doesn't have an institution-wrap element (the container for institution name and id). Is that correct?
! warning: [aff-no-wrap] Affiliation doesn't have an institution-wrap element (the container for institution name and id). Is that correct?
! warning: [aff-multiple-institution] Affiliation contains more than one institution element: Department of Development; Keck School of Medicine, University of Southern California in 9 https://ror.org/03taz7m60 https://ror.org/058zz0t50 https://ror.org/0444fnd49 Department of Development, Stem Cell, and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
! warning: [aff-no-wrap] Affiliation doesn't have an institution-wrap element (the container for institution name and id). Is that correct?
! warning: [aff-no-wrap] Affiliation doesn't have an institution-wrap element (the container for institution name and id). Is that correct?
! warning: [mixed-citation-other-publication-flag] mixed-citation in reference (id=c64) has a publication-type='other'. Is that correct?
! warning: [p-all-bold] Content of p element is entirely in bold - 'Table S1: Differentially expressed genes for low resolution rod clusters (LR / ER)'. Is this correct?
! warning: [p-all-bold] Content of p element is entirely in bold - 'Table S2: Differentially expressed genes for low resolution cone clusters (S / LM)'. Is this correct?
! warning: [p-all-bold] Content of p element is entirely in bold - 'Table S3: Differentially expressed genes for late vs early maturing L/M cone populations'. Is this correct?
! warning: [p-all-bold] Content of p element is entirely in bold - 'Table S4: SCENIC RSS scores for low resolution clusters'. Is this correct?
! warning: [p-all-bold] Content of p element is entirely in bold - 'Table S5: SCENIC RSS scores for high resolution clusters'. Is this correct?
! warning: [p-all-bold] Content of p element is entirely in bold - 'Table S6: Pseudotime-correlated genes and gene modules'. Is this correct?
! warning: [p-all-bold] Content of p element is entirely in bold - 'Table S7: Differentially expressed genes for low resolution early rod and L/M cone clusters (ER / LM)'. Is this correct?
+ info: [article-version-flag] This is preprint version 1.2.
+ info: [permissions-info] This article is licensed under a CC BY 4.0 license. https://creativecommons.org/licenses/by/4.0/ https://elifeproduction.slab.com/posts/licensing-and-copyright-rqdavyty#permissions-info

JGilbert-eLife commented 1 week ago

@fred-atherden We've published the wrong version of this RP; should have been the bioRxiv v3 -- eJP has a mismatch between version number and URL.

Can you pull over https://www.biorxiv.org/content/10.1101/2023.02.28.530247v3 so we can update this?

Thanks!

James

fred-atherden commented 5 days ago

@JGilbert-eLife thanks - done!

@gnott, please could you redeposit the crossref metadata for this one?

Query w/ Dave about updating search here

gnott commented 4 days ago

Hi @fred-atherden, sounds good. I scheduled the Crossref deposit only using elife-bot,

PYTHONPATH=. python starter/starter_ScheduleCrossrefPreprint.py -e live -a 101918 -v 1

fred-atherden commented 4 days ago

Ace - thanks!

elifesciences / publish-reviewed-preprints-issues