Atlas Metadata

Aggregated information about the Expression Atlas dataset. Get the dataset here.

Introduction

Based on a curated selection of tissue groupings - organs, and anatomical systems - produce mapping files based on OLS:

UBERON_0000020  sense organ UBERON_0000966  retina

Use metadata from Expression Atlas experiments to find terms without mappings to aid further curation.

Dependencies:

• Snakemake (tested with 6.6.1) via Conda.
• Container quay.io/ebigxa/atlas-metadata-base:1.0.1

Run

git clone https://github.com/gxa/atlas-metadata
conda activate snakemake@6.6.1 # this depends on the name where snakemake env is available
cd atlas-metadata
snakemake --use-conda --conda-frontend mamba \
        --profile $CLUSTER_PROFILE \
        $CONDA_PREFIX_LINE \
        $DRY_RUN_LINE \
        --latency-wait 150 \
        --keep-going \
        --config \
        atlas_exps=<path-to-atlas-exps-for-bulk> \
        --restart-times $RESTART_TIMES \
        -j $NPROC --use-singularity -s

Expression Atlas per-release workflow

• Run the associated CI job according to internal SOP and follow up from there.

Curation workflow

The files to curate are curated/anatomical_systems/ids.tsv and curated/organs/ids.tsv . We strive to not have any unmapped tissues show up in the UI while keeping the lists manageable for the users.

1. Change the mapping as needed
2. Run make to regenerate files
3. Run git diff to look at consequences of the change
4. git commit your change

Anatomical systems

The systems we use are children of UBERON_0000467 - "anatomical system" in OLS - that are being trimmed down manually. Laura suggested the following rules of curating this list:

1. If one anatomical system only contains another system as children term -> just import the children term. Example: instead of importing entire sense organ system, import sensory system.
2. If one anatomical system is the children of others just import the parent term Example: instead of importing lacrimal apparatus just import its parent sensory system.
3. If one anatomical system contains no children, don’t import the anatomical system. Example: don’t import dermatological-muscosal system
4. If one anatomical system is not applicable to human, don’t import it. Example: don’t import water vascular system

Organs

Children of organ in UBERON are abstract kinds of organs e.g. cavitated compound organ. We have instead chosen concrete and recognisable leaves in the ontology e.g. kidney.

Curation notes

Gustatory System: For now in Atlas we just have tongue mapped to gustatory system. Tongue is also mapped to digestive system and sensory system. We kept it out but if we have more experiments for gustatory system tissues we shall include it back.