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Cell Name and Marker Validator Demo

Build Status

This project demonstrates how data about cell populations and gating strategies can be transformed into semantically rich linked data and validated, using ontologies such as the Protein Ontology and Cell Ontology. This validator is designed to implement the Cytometry Data Standard.

There are two ways to use this code:

  1. as a web application that validates a cell population name and gate definition against our proposed standard (under development), and compares them using information from the Protein Ontology and Cell Ontology
  2. as a script that processes an existing table of cell population names and gate definitions, used as a reference for developing the proposed standard

Usage

See the Makefile for software requirements and build tasks.

First, install requirements (optionally, use a virtual environment):

python3 -m pip install -r requirements.txt

Then, make all dependencies:

make all

The first time you run this, it must download the full Protein Ontology which can take some time. Subsequent builds with an existing build/ directory will be faster.

Web Service

Once dependencies are complete (see above), set the FLASK_APP variable, and start the server:

export FLASK_APP=src/run.py
flask run

Command Line Utility

The validation service can also be run over a file directly from the command line using src/validate.py:

python3 src/validate.py [CELL_NAMES] [CELL_LEVELS] [GATE_NAMES] [INPUT] > [OUTPUT_TSV]

The first three input files can be found in the build/ directory after building the dependencies:

  • CELL_NAMES (build/cell.tsv): Cell Ontology IDs & labels and/or synonyms (each distinct label or synonym has its own line, and IDs may be repeated)
  • CELL_LEVELS (build/cl-levels.tsv): Membrane parts for each Cell Ontology term (positive, negative, high, and low)
  • GATE_NAMES (build/marker.tsv): Protein Ontology IDs & labels and/or synonyms (each distinct label or synonym has its own line, and IDs may be repeated)

The input file should be the cell population & gates to validate. This file requires two columns:

  • Cell Population Name: The cell type from the Cell Ontology
  • Gating Definition: Comma-separated gates from the Protein Ontology