Taxonomically Informed Metabolite Annotation

The initial work is available at https://doi.org/10.3389/fpls.2019.01329, and many improvements have been made since then. The workflow is illustrated in Figure 1.

This repository contains everything needed to perform Taxonomically Informed Metabolite Annotation.

It is provided with an example from well-known pharmacopoeia plants.

Here is what you minimally need:

• A feature list with or without candidate annotations, if you are using GNPS, it can be your GNPS job ID.
• The source organism of the extract you are annotating, if you are associating metadata within GNPS, it can be your GNPS job ID.
• An edge list, if you are using GNPS, it can be your GNPS job ID.

Optionally, you may want to add:

• An in-house structure-organism pairs library (we provide LOTUS as starting point for each user)
• Your own manual or automated annotations (we currently support annotations coming from ISDB and SIRIUS)

Repo preparation

shell git clone git@github.com:taxonomicallyinformedannotation/tima-python.git cd tima-python

Windows Notice

If you are using Windows, you will need to install Choco.

Then run:

shell choco install curl choco install gzip choco install unzip choco install wget

Please also follow the procedure described here to ensure files will be proberly encoded.

To run in docker:

shell docker build -t tima-python . # optional docker run -it --rm -v $PWD:/app tima-python

To run locally:

shell conda env create -f environment.yml && conda activate tima-python

Copy initial parameters

```shell

copy the default params to adapat to your data later on

cp -R config/default config/params ```

Structure-organism pairs library

```shell bash src/getlotus.sh && python src/preparelotus.py &&

python prepare_closed.py && # only if you have access to it

python src/preparelibrary.py && python src/prepareadducts.py && ```

Annotations

Get MS2 annotations

```shell

normally it would be 'python src/process_spectra.py' but for now we have to think about it.

instead we provide an example file coming from the new ISDB.

It also works with annotations coming from GNPS (see next steps)

bash src/getexampleisdb.sh ```

Format MS2 annotations

```shell

depending on the annotation tool you used

python src/preparegnps.py && # optional python src/prepareisdb.py ```

Complement MS2 annotations (with spectral clusters and chemical taxonomy of annotations)

shell python src/prepare_edges.py && python src/prepare_features_components.py && python src/prepare_features_classification.py

Get biological taxonomy information

shell bash src/get_gnverifier.sh && python src/prepare_taxa.py

And finally the graal!

NOT READY YET

```shell

python process_annotations.py

```

NOTE: you can use --help or -h argument for all .py steps to get more info