uPub Status Definitions
- Not Started: Models have not begun reconciliation. These models have a gene model page on Notion, but may or may not have a reconciler yet.
- Currently Reconciling: Models that have been claimed by a reconciler and are currently in-process for reconciliation.
- Finished Reconciliation: Models that have completed reconciliation (reconciled in Apollo, passed in Gene Model Checker and reconciled files are uploaded to Box) and the uPub for the gene model is being drafted.
- Awaiting Summary(y/ies): Models that have a nearly complete uPub document, aside from adding gene summaries and/or species summaries. Everything except the summaries should be finished in the document, so that when the missing summary is added, it can be swiftly sent for approval.
- Sent for Approval: Models where the uPub has been sent for approval via DocuSign and are awaiting both faculty and student co-author response.
- Sent for Re-Approval: Models that have been retrofitted re-sent to only faculty members via DocuSign and are awaiting their response.
- Coauthor Edits: Models that have received feedback from faculty/student co-authors via DocuSign and suggested changes need to be made in the document before co-authors approve.
- Approved: All faculty/student co-authors have approved of the uPub document.
- Pre-Submission: Model is under review by other team members to ensure gene model and uPub document is complete. During this time, the blastp results and synteny figure will be checked by OCR Validation and the gene model will be submitted to NCBI for Third Party Annotation. [This is currently where we are keeping the models that have undergone the 2024 round of retrofitting].
- Ready for Publication: Gene model and uPub document is ready to be submitted to the microPublication Biology journal.
- In Portal: Models that had been previously submitted to microPublication Biology, rejected for minor text issues and are now updated per the journal’s request and re-submitted.
- Sent for Publication: uPub document has been submitted and under review by the journal.
- Review Received: Reviewers from the journal have responded with suggested changes for the uPub document. The review will need to be addressed, adjustments will need to be made, and a response should be written back to the reviewers before the model is resubmitted to the journal.
- Reviews Responded – Ready to Resubmit: Changes suggested by the journal to the document are made and a response to the review is completed.
- Resubmitted to Journal: uPub document has been resubmitted to the journal.
- Published: Gene model and uPub is published by microPublication Biology journal.
- Page Last Updated: September 12, 2024