A package to interact with the HuBMAP Human Reference Atlas Ontology. The package can be used to perform ontology queries programmatically or through a command-line interface.
Clone the repository:
git clone https://github.com/ccb-hms/HuBMAPy.git
Install package using pip on the cloned repository folder:
pip3 install .
hubmapy -q QUERY [-o OUTPUT] [-n NAME]
To display a help message with descriptions of tool arguments do:
hubmapy -h or hubmapy --help
-q QUERY Input query file containing a single SPARQL query.
-o OUTPUT Path to output folder for the query results files.
-n NAME Name of the query, to be included in the generated query results file.
Import the HuBMAPy library:
import hubmapy
Then use as follows:
hubmap = hubmapy.HuBMAPy()
From here various built-in queries can be performed, for example:
df = hubmap.biomarkers_for_all_cell_types()
where df is a data frame containing the query results.
Additionally, it is possible to perform arbitrary queries specified by users:
df = hubmap.do_query_from_file(query_file_path='...')
where query_file_path is an absolute path to a SPARQL query file. Or:
df = hubmap.do_query(query='...', query_name='...')
where query is a string containing a SPARQL query.
The package supports the following built-in queries:
- biomarkers_for_all_cell_types()
- biomarkers_for_all_cell_types_in_anatomical_structure(anatomical_structure=
obo:UBERON_0002371) # bone marrow - biomarkers_for_cell_type_in_anatomical_structure(cell_type=
obo:CL_0000787, anatomical_structure=obo:UBERON_0002371) # memory B cell, bone marrow - tissue_blocks_in_anatomical_structure(anatomical_structure=
obo:UBERON_0002048) - tissue_block_count_for_all_anatomical_structures()
- anatomical_structures_in_tissue_block(tissue_block='...')
- locations_of_all_cell_types()
- evidence_for_specific_cell_type(cell_type=
obo:CL_0002394) # i.e., publication DOIs - evidence_for_all_cell_types()
- cell_types_from_biomarkers(biomarkers=
[hgnc:633,hgnc:800])
- ROBOT v1.8.3 (https://github.com/ontodev/robot)
- CCF Ontology v2.0.0-alpha.18 (https://github.com/hubmapconsortium/ccf-ontology)