Metadata-Version: 2.5
Name: biocognia-markers
Version: 0.1.0
Summary: The marker graph SCIMAP Pro, Plexora and other BioCognia products share: markers, cell families and the relations between them, each backed by evidence a machine checks
Author-email: Ajit Johnson Nirmal <ajitjohnson.n@gmail.com>
License-Expression: LicenseRef-Proprietary
Classifier: Intended Audience :: Science/Research
Classifier: Programming Language :: Python :: 3
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.12
Requires-Dist: numpy>=1.26
Requires-Dist: platformdirs>=4
Requires-Dist: scipy>=1.11
Description-Content-Type: text/markdown

# biocognia-markers

The marker graph that SCIMAP Pro, Plexora and other BioCognia products share.

- **Nodes:** markers and cell families.
- **Edges:** what is known about them: exceptions, exclusions, subsets, carriers and co-expression.
- **Evidence:** the evidence behind each node and edge.
- **Verification:** an item counts as verified only when a machine has found every part of it in
  its source (`biocognia-markers verify`).

```python
import biocognia_markers as bm

graph = bm.load()                       # the shipped graph, with the user's overlay laid over it
graph.resolve(["CD3e", "PD-1"])
graph.edges_of("m:pd1")
```

To add to the graph, an agent follows the skill `biocognia-marker-graph`
(`src/biocognia_markers/skills/marker-graph/SKILL.md`). `tools/migrate.py` built the first graph
from SCIMAP Pro's rule library and Plexora's vocabulary. Where those two sources disagree is
listed in `MIGRATION_REPORT.md`.
