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.
Download the latest MetaHQ database and configure the CLI:
$ metahq setup
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
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