refactor: scanner_coordinate_system -> local_coordinate_system

src/biodata_schema/components/subjects.py

@@ -5,6 +5,7 @@
 from enum import Enum
 from typing import Annotated, List, Optional
 
+from biodata_models.cell_line import CellLineModel
 from biodata_models.organizations import Organization
 from biodata_models.pid_names import PIDName
 from biodata_models.species import Species, Strain
@@ -195,3 +196,18 @@ class CalibrationObject(DataModel):
     objects: Optional[list[Device]] = Field(
         default=None, title="Objects", description="For calibration objects that are built up from one or more devices."
     )
+
+
+class CellLine(DataModel):
+    """Description of a cultured cell line"""
+
+    cell_line_name: str = Field(..., title="Cell line name")
+    cell_line_type: CellLineModel = Field(
+        ..., title="Cell line type", description="Use CellLineLookup.get_by_name/search_by_name to populate"
+    )
+    species: Species.ONE_OF = Field(..., title="Species")
+    protein: PIDName = Field(..., title="Protein labeled", description="Protein uses UniProt registry")
+    gene: PIDName = Field(..., title="Gene targeted", description="Gene uses NCBI taxonomy")
+    cell_structure: str = Field(..., title="Cell structure protein found in")
+    fluorescent_protein: PIDName = Field(..., title="Fluorescent protein", description="Uses FPbase")
+    clone_number: Optional[int] = Field(default=None, title="Clone number")

src/biodata_schema/core/subject.py

@@ -1,11 +1,17 @@
-"""schema for mostly mouse metadata"""
+"""schema for subject metadata"""
 
 from typing import Annotated, Literal, Optional
 
 from pydantic import Field, SkipValidation
 
 from biodata_schema.base import DataCoreModel, Discriminated, DraftRequirement
-from biodata_schema.components.subjects import CalibrationObject, HumanSubject, MouseSubject, NonHumanPrimateSubject
+from biodata_schema.components.subjects import (
+    CalibrationObject,
+    CellLine,
+    HumanSubject,
+    MouseSubject,
+    NonHumanPrimateSubject,
+)
 
 
 class Subject(DataCoreModel):
@@ -20,8 +26,8 @@ class Subject(DataCoreModel):
         title="Subject ID",
     )
 
-    subject_details: Discriminated[MouseSubject | HumanSubject | NonHumanPrimateSubject | CalibrationObject] = Field(
-        ..., title="Subject Details"
-    )
+    subject_details: Discriminated[
+        MouseSubject | HumanSubject | NonHumanPrimateSubject | CellLine | CalibrationObject
+    ] = Field(..., title="Subject Details")
 
     notes: Optional[str] = Field(default=None, title="Notes")

tests/test_subjects.py

@@ -3,6 +3,7 @@
 from datetime import datetime
 
 import pytest
+from biodata_models.cell_line import CellLineModel
 from biodata_models.organizations import Organization
 from biodata_models.pid_names import PIDName
 from biodata_models.registries import Registry
@@ -11,6 +12,7 @@
 from biodata_schema.components.subjects import (
     BreedingInfo,
     CalibrationObject,
+    CellLine,
     Housing,
     HumanSubject,
     LightCycle,
@@ -230,3 +232,42 @@ def test_breeding_info(self):
         assert breeding_info.maternal_genotype == "wt/wt"
         assert breeding_info.paternal_id == "P001"
         assert breeding_info.paternal_genotype == "wt/wt"
+
+
+class TestCellLine:
+    """Test the Cell Line model"""
+
+    def test_cellline(self):
+        """Test of cell line"""
+
+        subject = CellLine(
+            cell_line_name="AICS-0005",
+            cell_line_type=CellLineModel(
+                name="Human induced pluripotent stem cell line cell",
+                registry=Registry.CLO,
+                registry_identifier="CLO:0037308",
+            ),
+            species=Species.HUMAN,
+            protein=PIDName(
+                name="paxilin",
+                registry=Registry.UNIPROT,
+                registry_identifier="P49023",
+            ),
+            gene=PIDName(
+                name="paxilin",
+                abbreviation="PXN",
+                registry=Registry.NCBI,
+                registry_identifier="NM_0028593",
+            ),
+            cell_structure="cytoskeleton",
+            fluorescent_protein=PIDName(
+                name="enhanced GFP",
+                abbreviation="EGFP",
+                registry=Registry.FPbase,
+                registry_identifier="R9NL8",
+            ),
+            clone_number=1,
+        )
+
+        assert subject.cell_structure == "cytoskeleton"
+        assert subject.species == Species.HUMAN