Quick Start

Every installation of the MetaHQ CLI requires the setup command to be run. This will download the MetaHQ database from Zenodo and configure the package.

Setup

If you haven't already, download the latest MetaHQ database and configure the CLI by running the following:

metahq setup

Retrieve

Query the database for curated, biological context annotations. Below is an example of a query for expert-curated tissue annotations from human RNA-Seq samples:

metahq retrieve tissues --terms "UBERON:0000948,UBERON:0000955" \
    --level sample --filters "species=human,tech=rnaseq,ecode=expert" \
    --metadata "sample,series,description" --fmt tsv --output annotations.tsv

This command outputs a tabular dataset with columns [sample, series, description, sources, UBERON:0000948, UBERON:0000955]. An additional file is also created called CITATION__<date>.txt providing citation information for the original sources of annotations returned in your query. Please cite the original sources of any annotations that you use along with MetaHQ.

Some annotations in MetaHQ come from sources with non-commercial licenses (e.g., CC BY-NC). You can filter for annotations with permissive licenses using the --license argument:

metahq retrieve tissues --terms "UBERON:0000948,UBERON:0000955" \
    --level sample --filters "species=human,tech=rnaseq,ecode=expert" \
    --license permissive

See the retrieve documentation for more details.

Tissue and disease queries require standardized ontology term ID inputs. The following command will identify the top five most similar MONDO disease ontology term IDs to "heart attack".

metahq search --query "heart attack" --type disease --ontology MONDO -k 5

The EBI Ontology Lookup Service is also an excellent way to find term IDs. See the links below:

UBERON/CL (tissues/celltypes):
https://www.ebi.ac.uk/ols4/ontologies/uberon

MONDO (diseases):
https://www.ebi.ac.uk/ols4/ontologies/mondo