AbXtract/AIRR File to Orion Dataset - AbXtract

Category Paths

Follow one of these paths in the Orion user interface, to find the floe.

  • Solution-based/Biologics/Antibody Design

  • Role-based/Bioinformatician

  • Role-based/Biologist

  • Product-based/AbXtract

Description

Upload an AbXtract (Excel, TSV, CSV) processed dataset into Orion. Some important considerations:

  1. These are typically only files that have been processed by the NGS Pipeline - AbXtract Floe already, downloaded as a CSV file and modified.

  2. Datasets must contain select column headers that correspond to the AbXtract fields.

  3. They may also upload AIRR-compatible files. Special fields can be added here, including off_rate, on_rate, and KD, which can be added to the downstream dataset to look at on-rate, off-rate and affinity in context of sequences in the interactive Analyze tool.

Lastly, one can use Orion’s standard upload to load CSV (only CSV allowed), which can take on different headers, but just be cautious about using these in additional AbXtract floes, particularly if they contain fields the platform does not recognize.

Parameter title in user interface (promoted name)

  • Failed Dataset Output Name (data_out) type: dataset_out: Contains failed records from both upstream and downstream processes.
    Default: problematic.upload_processed_abxtract

Parameter title in user interface (promoted name)

  • Uploaded file is in AIRR-compatible format (is_airr) type: boolean: File has AIRR-compatible headers rather than being an AbXtract-produced file. AbXtract-relevant fields will be extracted and converted to AbXtract-compatible fields.
    Default: False

Parameter title in user interface (promoted name)

  • Output Name of the Uploaded Dataset (data_out) type: dataset_out: This is the name of the uploaded process record within the Orion environment.