feat: cell line

docs/source/components/subjects.md

@@ -25,6 +25,37 @@ Description of a calibration object
 | `objects` | Optional[List[[Device](devices.md#device)]] | Objects (For calibration objects that are built up from one or more devices.) |
 
 
+### CellLine
+
+Description of a cultured cell line
+
+| Field | Type | Title (Description) |
+|-------|------|-------------|
+| `cell_line_name` | `str` | Cell line name  |
+| `cell_line_id` | `Optional[str]` | Cell line ID  |
+| `source` | [Organization](../biodata_models/organizations.md#organization) | Source (Where the subject was acquired from.) |
+| `cell_line_type` | `biodata_models.cell_line.CellLineModel` | Cell line type  |
+| `species` | [Species](../biodata_models/species.md#species) | Species  |
+| `clone_number` | `Optional[int]` | Clone number  |
+
+
+### FluorescentCellLine
+
+Description of a cultured cell line with fluorescent label
+
+| Field | Type | Title (Description) |
+|-------|------|-------------|
+| `protein` | [PIDName](../biodata_models/pid_names.md#pidname) | Protein labeled (Protein uses UniProt registry) |
+| `cell_structure` | `str` | Cell structure the protein is found in  |
+| `fluorescent_protein` | [PIDName](../biodata_models/pid_names.md#pidname) | Fluorescent protein (Uses FPbase) |
+| `cell_line_name` | `str` | Cell line name  |
+| `cell_line_id` | `Optional[str]` | Cell line ID  |
+| `source` | [Organization](../biodata_models/organizations.md#organization) | Source (Where the subject was acquired from.) |
+| `cell_line_type` | `biodata_models.cell_line.CellLineModel` | Cell line type  |
+| `species` | [Species](../biodata_models/species.md#species) | Species  |
+| `clone_number` | `Optional[int]` | Clone number  |
+
+
 ### HomeCageEnrichment
 
 Materials provided in animal home cage

docs/source/subject.md

@@ -21,5 +21,5 @@ Description of a subject of data collection
 | Field | Type | Title (Description) |
 |-------|------|-------------|
 | `subject_name` | `str` | Subject name (Unique name for the subject of data acquisition) |
-| `subject_details` | [MouseSubject](components/subjects.md#mousesubject) or [HumanSubject](components/subjects.md#humansubject) or [NonHumanPrimateSubject](components/subjects.md#nonhumanprimatesubject) or [CalibrationObject](components/subjects.md#calibrationobject) | Subject Details  |
+| `subject_details` | [MouseSubject](components/subjects.md#mousesubject) or [HumanSubject](components/subjects.md#humansubject) or [NonHumanPrimateSubject](components/subjects.md#nonhumanprimatesubject) or [CellLine](components/subjects.md#cellline) or [FluorescentCellLine](components/subjects.md#fluorescentcellline) or [CalibrationObject](components/subjects.md#calibrationobject) | Subject Details  |
 | `notes` | `Optional[str]` | Notes  |

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 +196,26 @@ 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_id: Optional[str] = Field(default=None, title="Cell line ID")
+    source: Organization.ONE_OF = Field(
+        ...,
+        description="Where the subject was acquired from.",
+        title="Source",
+    )
+    cell_line_type: CellLineModel = Field(..., title="Cell line type")
+    species: Species.ONE_OF = Field(..., title="Species")
+    clone_number: Optional[int] = Field(default=None, title="Clone number")
+
+
+class FluorescentCellLine(CellLine):
+    """Description of a cultured cell line with fluorescent label"""
+
+    protein: PIDName = Field(..., title="Protein labeled", description="Protein uses UniProt registry")
+    cell_structure: str = Field(..., title="Cell structure the protein is found in")  # TODO: ontology/enum in model
+    fluorescent_protein: PIDName = Field(..., title="Fluorescent protein", description="Uses FPbase")

src/biodata_schema/core/subject.py

@@ -1,11 +1,18 @@
-"""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,
+    FluorescentCellLine,
+    HumanSubject,
+    MouseSubject,
+    NonHumanPrimateSubject,
+)
 
 
 class Subject(DataCoreModel):
@@ -20,8 +27,8 @@ class Subject(DataCoreModel):
         title="Subject name",
     )
 
-    subject_details: Discriminated[MouseSubject | HumanSubject | NonHumanPrimateSubject | CalibrationObject] = Field(
-        ..., title="Subject Details"
-    )
+    subject_details: Discriminated[
+        MouseSubject | HumanSubject | NonHumanPrimateSubject | CellLine | FluorescentCellLine | 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,
+    FluorescentCellLine,
     Housing,
     HumanSubject,
     LightCycle,
@@ -230,3 +232,38 @@ def test_breeding_info(self):
         assert breeding_info.maternal_genotype == "wt/wt"
         assert breeding_info.paternal_name == "P001"
         assert breeding_info.paternal_genotype == "wt/wt"
+
+
+class TestCellLine:
+    """Test the Cell Line model"""
+
+    def test_cellline(self):
+        """Test of cell line"""
+
+        subject = FluorescentCellLine(
+            cell_line_name="AICS-0005",
+            cell_line_id="AICS-0005",
+            cell_line_type=CellLineModel(
+                name="Human induced pluripotent stem cell line cell",
+                registry=Registry.CLO,
+                registry_identifier="CLO:0037308",
+            ),
+            source=Organization.AI,
+            species=Species.HUMAN,
+            protein=PIDName(
+                name="paxilin",
+                registry=Registry.UNIPROT,
+                registry_identifier="P49023",
+            ),
+            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