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Customization of https://github.com/biocodellc/ontology-data-pipeline to work with the FuTRES Ontology for Vertebrate Traits
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README.md

fovt-data-pipeline

This repository contains the configuration directives to run the ontology-data-pipeline for the FuTRES project using the FuTRES Ontology for Vertebrate Traits (FOVT).

Getting Started

Install docker and then clone this repository. Once that is done, you can enter the following:

./run_test.sh 

The above script first checks for the latest docker image. This may take awhile to install the ontology-data-pipeline image on the first run. After the test runs, you should see output that ends with:

...
INFO:root:b'    writing /process/test_data/vertnet/output/output_reasoned_csv/data_1.ttl.csv\n'
INFO:root:reasoned_csv output at test_data/vertnet/output/output_reasoned_csv/data_1.ttl.csv

Once you have verified things work using the test procedure above, you can then run data through the pipeline using:

./run.sh {INPUT_DATAFILE} {OUTPUT_DIRECTORY}

An example of running the above command would look like:

./run.sh data/ray/ray_data_full.csv data/ray/output

This looks for a data file called "ray_data_full.csv" and writes output to data/ray/output

This repository contains all of the configuration files needed to process data. If you want to modify configuration settings, refer to ontology-data-pipeline for instructions.

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