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README.md

IDR studies

Published screens Published experiments

All metadata associated with published studies in IDR is managed in this repository.

Study name

After acceptance, IDR studies must be named as idr<NNNN>-<name>-<description> where idr<NNNN> is the accession number of the study using an incremental four digits integer, <name> is the name of one of the authors associated with the publication, usually the first author, and <description> is a short description of the study or the name of the project/consortium. The study name should be lowercase.

Study repository

For each new study, a repository must be created on GitHub under the IDR organization using the study name as defined above. When ready for publication in the IDR, the study repository must be registered in the top-level idr-metadata repository as a submodule.

A study repository contains all original and curated metadata files associated with a study. The idr0000-lastname-example repository contains the templates that should be used by submitters when sending original metadata files for screen or experiment studies. The structure of each study repository should use the following layout:

.travis.yml                                  # Travis CI configuration file, used for validation (mandatory)
bulk.yml                                     # Import configuration file for multi-experiment or multi-screen studies (optional)
experimentA/                                 # Curated metadata for experimentA (if applicable)
    idrNNNN-experimentA-annotation.csv       # Curated annotation file (mandatory)
    idrNNNN-experimentA-assays.txt           # Original annotation file (recommended)
    idrNNNN-experimentA-bulk.yml             # Configuration file for import (mandatory)
    idrNNNN-experimentA-bulkmap-config.yml   # Configuration file for annotation (mandatory)
    idrNNNN-experimentA-filePaths.tsv        # Files/folder to be imported (mandatory)
experimentB/                                 # Curated metadata for experimentB (if applicable)
   ...
idrNNNN-study.txt                            # Top-level metadata file describing the study (mandatory)
screenA/                                     # Curated metadata for screenA if applicable
    idrNNNN-screenA-annotation.csv           # Curated annotation file (mandatory)
    idrNNNN-screenA-bulk.yml                 # Configuration file for import (mandatory)
    idrNNNN-screenA-bulkmap-config.yml       # Configuration file for annotation (mandatory)
    idrNNNN-screenA-library.txt              # Original annotation file (recommended)
    idrNNNN-screenA-plates.tsv               # Plates to be imported (mandatory)
screenB/                                     # Curated metadata for screenB if applicable
   ...
scripts/                                     # Folder containing custom scripts associated with the study (optional)
README.md                                    # Optional top-level readme (optional)
requirements.txt                             # Python dependencies used for Travis or scripts (recommended)