data

Data directory

This directory contains existing data and references files to be added to the SRP analytics database. These data are not private in any way, but mainly serve as reference files for the broader repository.

Data file manifest

The data file manifest contains a link to all the other data files, including those referenced in this document. This file can be found here.

Data Schema and validaton

Incoming data requires a pre-defined schema so we can validate things BEFORE they are going to be processed by our pipeline. This schema also enables an easy way to check if a file CAN be processed before adding it to the list.

The data schema file can be found here.

To validate incoming data your file must be one of the following types:

1. morphology
2. behavior
3. zebrafishMapping
4. fses

You must download install the linkML tool using pip by following the instructions on the LinkML page.

To validate a single file you need the type of file and the path to the file.

linkml-validate fses/FSES_indoor_outdoor_study.csv -C fses -s srp_templates.yaml

This will validate the fses file.

Chemical reference information

Many of the build files are actual reference information.

Chemical id file

Chemical classification file

compTox file

Environmental sample information

Sample id file

Existing Zebrafish data