MSID: 94658 Version: 2 DOI: 10.1101/2023.11.16.567478

[fred-atherden]

MSID: 94658

Version: 2

Preprint DOI: https://doi.org/10.1101/2023.11.16.567478

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=94658
• New model tracking: https://docs.google.com/spreadsheets/d/1_fHaoOy7hjyocptKtVJRijeNpUY4hBS7Ck_aVmx6ZJk/
• Reviews on sciety: https://sciety.org/articles/activity/10.1101/2023.11.16.567478

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/94658v2
• 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/10.1101/2023.11.16.567478
• Confirm reviews returned by EPP: https://prod--epp.elifesciences.org/api/reviewed-preprints/94658/v2/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]

error: [junk-character-presence-3] p element contains a junk character '□' which should be replaced or deleted.
warning: [ref-year-value-2] Ref with id c25 has a year element which does not contain a digit. Is it correct? (it's acceptable for this element to contain 'no date' or equivalent non-numerical information relating to year of publication)
warning: [ref-year-value-2] Ref with id c26 has a year element which does not contain a digit. Is it correct? (it's acceptable for this element to contain 'no date' or equivalent non-numerical information relating to year of publication)
warning: [ref-year-value-2] Ref with id c27 has a year element which does not contain a digit. Is it correct? (it's acceptable for this element to contain 'no date' or equivalent non-numerical information relating to year of publication)
warning: [ref-year-value-2] Ref with id c28 has a year element which does not contain a digit. Is it correct? (it's acceptable for this element to contain 'no date' or equivalent non-numerical information relating to year of publication)
warning: [ref-year-value-2] Ref with id c37 has a year element which does not contain a digit. Is it correct? (it's acceptable for this element to contain 'no date' or equivalent non-numerical information relating to year of publication)
warning: [ref-year-value-2] Ref with id c43 has a year element which does not contain a digit. Is it correct? (it's acceptable for this element to contain 'no date' or equivalent non-numerical information relating to year of publication)
warning: [ref-year-value-2] Ref with id c45 has a year element which does not contain a digit. Is it correct? (it's acceptable for this element to contain 'no date' or equivalent non-numerical information relating to year of publication)
warning: [mixed-citation-other-publication-flag] mixed-citation in reference (id=c7) has a publication-type='other'. Is that correct?
warning: [mixed-citation-person-group-flag-2] mixed-citation in reference (id=c25) does not have an author person-group. Is that correct?
warning: [mixed-citation-person-group-flag-2] mixed-citation in reference (id=c26) does not have an author person-group. Is that correct?
warning: [mixed-citation-person-group-flag-2] mixed-citation in reference (id=c27) does not have an author person-group. Is that correct?
warning: [mixed-citation-person-group-flag-2] mixed-citation in reference (id=c28) does not have an author person-group. Is that correct?
warning: [mixed-citation-person-group-flag-2] mixed-citation in reference (id=c43) does not have an author person-group. Is that correct?
warning: [mixed-citation-person-group-flag-2] mixed-citation in reference (id=c45) does not have an author person-group. Is that correct?
warning: [title-upper-case] Content of <title> element is entirely in upper case: Is that correct? 'REFERENCES'
warning: [p-all-bold] Content of p element is entirely in bold - 'Supplementary Figure 1. Dataset construction workflow.'. Is this correct?
warning: [p-all-bold] Content of p element is entirely in bold - 'Supplementary Figure 3. Rarefaction between MSI and MSS samples'. Is this correct?
warning: [p-all-bold] Content of p element is entirely in bold - 'Supplementary Figure 4. Association between TIL TCRβ profiles and patients’ characteristics.'. Is this correct?
warning: [p-all-bold] Content of p element is entirely in bold - 'Supplementary Figure 5. The performance of three machine learning models with three different algorithms is evaluated using receiver operating characteristic (ROC) curves.'. Is this correct?
warning: [p-all-bold] Content of p element is entirely in bold - 'Supplementary Figure 6. The rank coverage score of the combined model compared to NetMHCpan.'. Is this correct?
warning: [p-all-bold] Content of p element is entirely in bold - 'Supplementary Table 1. Clinical Characteristics of 28 CRC patients'. Is this correct?
warning: [p-all-bold] Content of p element is entirely in bold - 'Supplementary Table 2. Comparison of HLA calling accuracy between Acras-HLA and Optitype.'. Is this correct?
warning: [p-all-bold] Content of p element is entirely in bold - 'Supplementary Table 4. Percentage of unique and expanded TCR clones from 28 CRC patients'. Is this correct?
warning: [p-all-bold] Content of p element is entirely in bold - 'Supplementary Table 5. List of immunogenic peptides and non-immunogenic peptides from public databases'. Is this correct?
warning: [p-all-bold] Content of p element is entirely in bold - 'Supplementary Table 6. Performance of combined model in an independent dataset.'. Is this correct?
info: [article-version-flag] This is preprint version 1.2.