Help: Quest for Orthologs - Challenge 6

Inputs Outputs Method References



Quest for Orthologs (QfO) Benchmark pipeline with Nextflow and Docker. The workflow takes as input the ortholog predictions of a method in either tab-delimited format that lists pairs of orthologs or an orthoxml file. The predictions must be done on the QfO reference proteomes, either on the dataset of 2011 or 2018. For how to retrieve the reference proteomes, please consider the instructions on the current benchmark service. The workflow is structured as the standard OpenEBench benchmarking workflows in three main steps:

  1. Validation and preprocessing: validate the input predictions and convert them into an internal format.
  2. Compute the benchmark metrics for various benchmarks (e.g. Gene Ontology Conservation Test - Number of Orthologs relations / Avg. Schlicker similarity).
  3. Benchmark consolidation: generate the aggregation datasets with all the computed metrics and the consolidated results file ready to be pushed to the official OpenEBench Benchmarking Registry.

    drawing

If you want to learn more about the Quest for Orthologs benchmarking pipeline, clone this repository, and read the instructions in the README file.