written by Attila Csordas with edits from Juan Antonio Vizcaino, Tobias Ternent, Gerhard Mayer and Deepti Jaiswal Kundu Version 0.9.2 (10 Dec 2018)
This document describes the steps regularly happening during the process of generally valid submissions. As such it serves the purpose of providing the basics for new PRIDE curators. For irregularities, common issues and their resolutions please see the other Google Document shared with curators called “Common PRIDE Submission Issues”.
I. External Documentation II. Important locations on the EBI filesystem and technical info III. Google Spreadsheets used for curation work IV. Software tools V. Basic concepts VI. Submission Overview VII. RT ticket tracking system VIII. Validation IX. Submission X. Submission annotation: dataset tags and country of origin XI. Post-submission jobs XII. Publication/reference XIII. Common submission issues XIV. Dataset resubmission XV. Command Line Utilities: FTP and Aspera XVI: How to create a new ticket XVIl. Updating px.xml on PC
:I. External Documentation
ProteomeXchange Submit data page: http://www.proteomexchange.org/submission
Submission Tutorial: http://www.proteomexchange.org/sites/proteomexchange.org/files/documents/px_submission_tutorial.pdf
Submission Guidelines: www.ebi.ac.uk/pride/help/archive/submission
FAQ: www.ebi.ac.uk/pride/help/archive/faq
PRIDE tools and libraries: http://www.ebi.ac.uk/pride/help/tools
Dataset tags: http://www.ebi.ac.uk/pride/help/archive/tags
II. Important locations on the EBI filesystem and technical info
Pipeline script directory: /nfs/pride/work/archive/filtering_px_submission_pipeline - Main directory where all the submission pipeline scripts are saved and run.
Submission queue directory: /nfs/pride/web/archive_submission_queue - Directory where all the incoming submission tickets are stored. Basically it generates to user automatically after the submission. A single ticket basically contains the path for the dropbox folder where data are stored immediately after the submission. User’s data will be taken from here for further submission process in PRIDE.