This repo contains data models generated using LinkML for BICAN knowledgebase. LinkML is a linked data modeling language that supports YAML, RDF, and JSON.
In /linkml-schema, there are linkML yaml schema files that adhere to the linkML version of 1.5.0.
- The Library Generation Model is designed to represent types and relationships of samples and digital data assets generated during processes that generate multimodal genomic data.
- The Genome Annotation Model is designed to represent types and relationships of an organism's annotated genome i.e. gene annotations, genome annotations, genome assemblies, organisms.
- The Anatomical Strucutre Model is designed to represent types and relationships of anatomical brain structures.
- The existing models such as Biolink and CCN are imported.
In /json-schema and /models_py, there are json and py files generated using linkML schema for e.g.:
gen-json-schema linkml-schema/genome_annotation.yaml > json-schema/genome_annotation.jsongen-pydantic linkml-schema/genome_annotation.yaml > models_py/genome_annotation.py
In /data-examples, there are source data files:
figure1exampledata.yamlis representing relational data in figure 1 ofA high-resolution transcriptomic and spatial atlas of cell types in the whole mouse brain- https://www.biorxiv.org/content/10.1101/2023.03.06.531121v1.full.pdf
Notes: Initialize the packages using:
python -m pip install .python -m pip install .[test]
Run pytest to run all tests in /tests
Here are the BICAN LinkML knowledgebase schemas and their statuses.
| Model | Version | Release | Status |
|---|---|---|---|
| Assertion Evidence Model | [] | [] | under development |
| Library Generation Model | [] | [] | under development |
| Anatomical Structure Model | [] | [] | under development |
| Genome Annotation Model | [] | [] | under development |
| BICAN BioLink | [] | [] | under development |
| CCN2 | [] | [] | deprecated |
| Figure1 | [] | [] | deprecated |
Satra Ghosh (PI -- MIT)
Lydia Ng (PI -- Allen Institute for Brain Science)
Puja Trivedi (MIT)
Dorota Jarecki (MIT)
Prajal Bishkawarma (Allen Institute for Brain Science)
Tim Fliss (Allen Insitute for Brain Science)
Pamela Baker (Allen Institute for Brain Science)
Patrick Ray (Allen Institute for Brain Science)
These materials are provided under the Attribution International 4.0 (CC-BY-4.0) license, which is available at https://creativecommons.org/licenses/by/4.0/
An extensible brain knowledge base and toolset spanning modalities for multi-species data-driven cell types BICAN Knowledgebase National Institute of Mental Health Award # 1U24MH130918-01