Explore a MODO and access its data

There are multiple ways to use a MODO and interact with it’s elements.

Explore a MODO and it’s elements

MODO metadata can be easily accessed via CLI or using the python api:

python

from modos.api import MODO

# Create modo object (see Create and modify MODO)
modo = MODO(path = "data/ex")

# Show metadata as dictionary
modo.show_contents()
# {'ex': {'@type': 'MODO', 'creation_date': '2024-02-19T00:00:00', 'description': ..}

cli

modos show "data/ex"

The objects structure can be visualized by displaying the internal hierarchy:

python

modo.list_arrays()
#/
# ├── assay
# │   └── assay1
# ├── data
# │   └── demo1
# ├── reference
# │   └── reference1
# └── sample
#     └── sample1

cli

modos show --zarr "data/ex"
#/
# ├── assay
# │   └── assay1
# ├── data
# │   └── demo1
# ├── reference
# │   └── reference1
# └── sample
#     └── sample1

Note

MODOS internally uses zarr’s hierarchy groups. Each sub-directory represents a new hierarchy group. Any array-like data can directly be stored within these hierarchy groups, while other file formats are stored separately.

All files part of a MODO can be listed:

python

[fi for fi in modo.list_files()]
# [PosixPath('data/ex/reference1.fa'), PosixPath('data/ex/demo1.cram')]

cli

modos show --files "data/ex"
# data/ex/reference1.fa
# data/ex/demo1.cram

Publish a MODO as linked data

A semantic artifact can be created from the digital object and published as linked data. In this process JSON metadata are converted to RDF and all relative paths are converted to URI’s.

python

modo.knowledge_graph(uri_prefix="http://demo-data")
# <Graph identifier=N1aa0d4f1f3d9428b9c01e703096c5c96 (<class 'rdflib.graph.Graph'>)>

cli

modos publish --base-uri "http://demo-data" "data/ex"
# @prefix EDAM: <http://edamontology.org/> .
# @prefix NCIT: <http://purl.obolibrary.org/obo/NCIT_> .
# @prefix modos: <https://w3id.org/sdsc-ordes/modos-schema/> .
# @prefix schema1: <http://schema.org/> .
# @prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
#
# <http://demo-data/assay/assay1> a modos:Assay ;
#     schema1:description "Dummy assay for tests." ;
#     schema1:name "Assay 1" ;
#     modos:has_data <http://demo-data/demo1> ;
#     modos:has_sample <http://demo-data/sample1> ;
#     modos:omics_type NCIT:C84343 .
#
#     ...

Enrich metadata

Genomic files such as cram files store relevant metadata, e.g. their reference sequences, in their header. These information can be automatically extracted and included into a MODO.

# Enrich modo
modo.enrich_metadata()

# Check the added elements
modo.list_arrays()