feat: CellLine

docs/source/biodata_models/external.md

@@ -4,15 +4,23 @@ External registries act as an application programming interfaces (API). They all
 
 ## Model definitions
 
-### MouseAnatomyModel
+### AnatomyModel
+
+Shared Pydantic model for species-specific anatomy terms. Fields typed as `AnatomyModel` can use a lookup subclass such as `MouseAnatomyLookup` or `HumanAnatomyLookup`, which provides ontology-specific lookup behavior.
+
+| Name | Registry | Registry Identifier |
+|------|-------|--------|
+| `heart` | `Registry.EMAPA` | `EMAPA:16105` |
+
+### MouseAnatomyLookup
 
 [EMAPA](https://www.ebi.ac.uk/ols4/ontologies/emapa)
 
-Base model for mouse anatomy. Some examples:
+Lookup model for mouse anatomy terms. Use `search_by_name` to find terms and `get_by_name` for an exact label match.
 
 | Name | Registry | Registry Identifier |
 |------|-------|--------|
-| `heart` | `Registry.EMAPA` |  `16105`  |
+| `heart` | `Registry.EMAPA` | `EMAPA:16105` |
 
 ### Gene
 

docs/source/components/configs.md

@@ -24,7 +24,7 @@ Configuration of a catheter
 
 | Field | Type | Title (Description) |
 |-------|------|-------------|
-| `targeted_structure` | [MouseAnatomyModel](../biodata_models/external.md#mouseanatomymodel) | Targeted blood vessel (Use options from MouseBloodVessels) |
+| `targeted_structure` | [AnatomyModel](../biodata_models/external.md#anatomymodel) | Targeted blood vessel (For common mouse blood-vessel targets, use MouseBloodVessels with MouseAnatomyLookup.get_by_name.) |
 | `device_name` | `str` | Device name (Must match a device defined in the instrument.json) |
 
 

docs/source/components/coordinates.md

@@ -23,7 +23,7 @@ Definition an atlas
 | `size_unit` | [SizeUnit](../biodata_models/units.md#sizeunit) | Size unit  |
 | `resolution` | `List[float]` | Resolution  |
 | `resolution_unit` | [SizeUnit](../biodata_models/units.md#sizeunit) | Resolution unit  |
-| `origin` | [MouseAnatomyModel](../biodata_models/external.md#mouseanatomymodel) | Origin (Defines the position of (0,0,0) in the coordinate system) |
+| `origin` | ONE OF: [Origin](../biodata_models/coordinates.md#origin), [AnatomyModel](../biodata_models/external.md#anatomymodel) | Origin (Defines the position of (0,0,0) in the coordinate system) |
 | `axes` | List[[Axis](#axis)] | Axis names (Axis names and directions) |
 | `axis_unit` | [SizeUnit](../biodata_models/units.md#sizeunit) | Size unit  |
 | `handedness` | Optional[[Handedness](#handedness)] | Handedness (Whether the coordinate system is right-handed or left-handed) |
@@ -57,7 +57,7 @@ Definition of a coordinate system
 | Field | Type | Title (Description) |
 |-------|------|-------------|
 | `name` | `str` | Name (Convention is to use <Origin>_<POS_X_DIR><POS_Y_DIR><POS_Z_DIR> etc) |
-| `origin` | [MouseAnatomyModel](../biodata_models/external.md#mouseanatomymodel) | Origin (Defines the position of (0,0,0) in the coordinate system) |
+| `origin` | ONE OF: [Origin](../biodata_models/coordinates.md#origin), [AnatomyModel](../biodata_models/external.md#anatomymodel) | Origin (Defines the position of (0,0,0) in the coordinate system) |
 | `axes` | List[[Axis](#axis)] | Axis names (Axis names and directions) |
 | `axis_unit` | [SizeUnit](../biodata_models/units.md#sizeunit) | Size unit  |
 | `handedness` | Optional[[Handedness](#handedness)] | Handedness (Whether the coordinate system is right-handed or left-handed) |

docs/source/components/devices.md

@@ -676,9 +676,9 @@ Description of a contact on a myomatrix thread
 
 | Field | Type | Title (Description) |
 |-------|------|-------------|
-| `body_part` | [MouseAnatomyModel](../biodata_models/external.md#mouseanatomymodel) | Body part of contact insertion (Use MouseBodyParts) |
+| `body_part` | [AnatomyModel](../biodata_models/external.md#anatomymodel) | Body part of contact insertion (For common mouse body parts, use MouseBodyParts with MouseAnatomyLookup.get_by_name.) |
 | `relative_position` | [AnatomicalRelative](../biodata_models/coordinates.md#anatomicalrelative) | Relative position (Position relative to procedures coordinate system) |
-| `muscle` | [MouseAnatomyModel](../biodata_models/external.md#mouseanatomymodel) | Muscle of contact insertion (Use MouseEmgMuscles) |
+| `muscle` | [AnatomyModel](../biodata_models/external.md#anatomymodel) | Muscle of contact insertion (For common mouse EMG muscles, use MouseEmgMuscles with MouseAnatomyLookup.get_by_name.) |
 | `in_muscle` | `bool` | In muscle  |
 
 
@@ -688,7 +688,7 @@ Description of a thread of a myomatrix array
 
 | Field | Type | Title (Description) |
 |-------|------|-------------|
-| `ground_electrode_location` | [MouseAnatomyModel](../biodata_models/external.md#mouseanatomymodel) | Location of ground electrode (Use GroundWireLocations) |
+| `ground_electrode_location` | [AnatomyModel](../biodata_models/external.md#anatomymodel) | Location of ground electrode (For common mouse ground-wire locations, use MouseGroundWireLocations with MouseAnatomyLookup.get_by_name.) |
 | `contacts` | List[[MyomatrixContact](#myomatrixcontact)] | Contacts  |
 
 

docs/source/components/injection_procedures.md

@@ -4,12 +4,15 @@
 
 ### Injection
 
-Description of an injection procedure
+Description of an injection procedure.
+
+For common mouse injection targets, use MouseInjectionTargets with
+MouseAnatomyLookup.get_by_name(...).
 
 | Field | Type | Title (Description) |
 |-------|------|-------------|
 | `injection_materials` | List[[ViralMaterial](#viralmaterial) or [NonViralMaterial](#nonviralmaterial)] | Injection material  |
-| `targeted_structure` | Optional[[MouseAnatomyModel](../biodata_models/external.md#mouseanatomymodel)] | Injection target (Use InjectionTargets) |
+| `targeted_structure` | Optional[[AnatomyModel](../biodata_models/external.md#anatomymodel)] | Injection target (Species-specific anatomy term; use the appropriate lookup (e.g., MouseAnatomyLookup or HumanAnatomyLookup).) |
 | `relative_position` | Optional[List[[AnatomicalRelative](../biodata_models/coordinates.md#anatomicalrelative)]] | Relative position  |
 | `dynamics` | List[[InjectionDynamics](#injectiondynamics)] | Injection dynamics (List of injection events, one per location/depth) |
 | `protocol_id` | `Optional[str]` | Protocol ID (DOI for protocols.io) |

docs/source/components/surgery_procedures.md

@@ -100,7 +100,7 @@ Ground wire implant procedure
 
 | Field | Type | Title (Description) |
 |-------|------|-------------|
-| `ground_electrode_location` | [MouseAnatomyModel](../biodata_models/external.md#mouseanatomymodel) | Location of ground electrode  |
+| `ground_electrode_location` | [AnatomyModel](../biodata_models/external.md#anatomymodel) | Location of ground electrode (For common mouse ground-wire locations, use MouseGroundWireLocations with MouseAnatomyLookup.get_by_name.) |
 | `ground_wire_hole` | `Optional[int]` | Ground wire hole (For SHIELD implants, the hole number for the ground wire) |
 | `ground_wire_material` | Optional[[GroundWireMaterial](#groundwirematerial)] | Ground wire material  |
 | `ground_wire_diameter` | `Optional[float]` | Ground wire diameter  |

docs/source/inheritance.md

@@ -33,7 +33,7 @@ For assets created during analysis that aggregate across multiple acquisitions o
 from datetime import datetime, timezone
 
 from biodata_schema.core.metadata import Metadata
-from biodata_schema.core.processing import DataProcess, Processing, ProcessName, ProcessStage
+from biodata_schema.core.processing import DataProcess, Processing, ProcessStage
 from biodata_schema.core.quality_control import QCMetric, QCStatus, QualityControl, Stage, Status
 from biodata_schema.components.identifiers import Code
 from biodata_models.modalities import Modality
@@ -45,7 +45,7 @@ source = Metadata.model_validate_json(open("metadata.nd.json").read())
 new_processing = Processing.create_with_sequential_process_graph(
     data_processes=[
         DataProcess(
-            process_type=ProcessName.IMAGE_TILE_FUSING,
+            process_type="Image tile fusing",
             name="Tile fusing",
             experimenters=["Dr. Dan"],
             stage=ProcessStage.PROCESSING,

docs/source/model.md

@@ -35,7 +35,7 @@ Description of model evaluation
 
 | Field | Type | Title (Description) |
 |-------|------|-------------|
-| `process_type` | [ProcessName](biodata_models/process_names.md#processname) |   |
+| `process_type` | `str` |   |
 | `performance` | List[[PerformanceMetric](model.md#performancemetric)] | Evaluation performance  |
 | `name` | `str` | Name (Unique name of the processing step. If not provided, the type will be used as the name.) |
 | `stage` | [ProcessStage](processing.md#processstage) | Processing stage  |
@@ -65,7 +65,7 @@ Description of model training
 
 | Field | Type | Title (Description) |
 |-------|------|-------------|
-| `process_type` | [ProcessName](biodata_models/process_names.md#processname) |   |
+| `process_type` | `str` |   |
 | `train_performance` | List[[PerformanceMetric](model.md#performancemetric)] | Training performance (Performance on training set) |
 | `test_performance` | Optional[List[[PerformanceMetric](model.md#performancemetric)]] | Test performance (Performance on test data, evaluated during training) |
 | `test_evaluation_method` | `Optional[str]` | Test evaluation method (Approach to cross-validation or Train/test splitting) |

docs/source/processing.md

@@ -35,7 +35,7 @@ Description of a single processing step
 
 | Field | Type | Title (Description) |
 |-------|------|-------------|
-| `process_type` | [ProcessName](biodata_models/process_names.md#processname) | Process type  |
+| `process_type` | `str` | Process type  |
 | `name` | `str` | Name (Unique name of the processing step. If not provided, the type will be used as the name.) |
 | `stage` | [ProcessStage](processing.md#processstage) | Processing stage  |
 | `code` | [Code](components/identifiers.md#code) | Code (Code used for processing) |

docs/source/registries.rst

@@ -19,7 +19,6 @@ Registries are models that are linked to an external definition, like the NCBI s
    biodata_models/modalities
    biodata_models/organizations
    biodata_models/pid_names
-   biodata_models/process_names
    biodata_models/reagent
    biodata_models/registries
    biodata_models/species

examples/processing.py

@@ -10,7 +10,6 @@
 from biodata_schema.core.processing import (
     DataProcess,
     Processing,
-    ProcessName,
     ProcessStage,
     ResourceTimestamped,
     ResourceUsage,
@@ -62,7 +61,7 @@
     ],
     data_processes=[
         DataProcess(
-            process_type=ProcessName.IMAGE_TILE_FUSING,
+            process_type="Image tile fusing",
             experimenters=["Dr. Dan"],
             stage=ProcessStage.PROCESSING,
             start_date_time=t,
@@ -90,7 +89,7 @@
             ),
         ),
         DataProcess(
-            process_type=ProcessName.FILE_FORMAT_CONVERSION,
+            process_type="File format conversion",
             pipeline_name="Imaging processing pipeline",
             experimenters=["Dr. Dan"],
             stage=ProcessStage.PROCESSING,
@@ -104,7 +103,7 @@
             ),
         ),
         DataProcess(
-            process_type=ProcessName.IMAGE_DESTRIPING,
+            process_type="Image destriping",
             pipeline_name="Imaging processing pipeline",
             experimenters=["Dr. Dan"],
             stage=ProcessStage.PROCESSING,
@@ -121,7 +120,7 @@
             name="Analysis 1",
             stage=ProcessStage.ANALYSIS,
             experimenters=["Some Analyzer"],
-            process_type=ProcessName.ANALYSIS,
+            process_type="Analysis",
             start_date_time=t,
             end_date_time=t,
             output_path="path/to/outputs",
@@ -135,7 +134,7 @@
             name="Analysis 2",
             stage=ProcessStage.ANALYSIS,
             experimenters=["Some Analyzer"],
-            process_type=ProcessName.ANALYSIS,
+            process_type="Analysis",
             start_date_time=t,
             end_date_time=t,
             output_path="path/to/outputs",

pyproject.toml

@@ -14,7 +14,7 @@ readme = "README.md"
 dynamic = ["version"]
 
 dependencies = [
-    'biodata-models>=1.0.1,<2',
+    'biodata-models>=2.0.2,<3',
     'pydantic>=2.7, <3',
     'pydantic-extra-types',
     'tzdata',
@@ -30,7 +30,7 @@ dev = [
     'pytest>=8.3',
     'pytest-cov>=6',
     'ruff>=0.11',
-    'semver',
+    'semver>=3.0.0',
 ]
 
 docs = [
@@ -70,7 +70,6 @@ ignore-words-list = 'nd,DeviceC'
 testpaths = ["tests"]
 strict_config = true
 strict_markers = true
-markers = ["online: tests requiring external services"]
 
 [tool.ruff]
 line-length = 120

schemas/metadata_schema.json

@@ -9102,8 +9102,8 @@
                "type": "string"
             },
             "process_type": {
-               "$ref": "#/$defs/ProcessName",
-               "title": "Process type"
+               "title": "Process type",
+               "type": "string"
             },
             "name": {
                "default": "",
@@ -26888,8 +26888,9 @@
                "type": "string"
             },
             "process_type": {
-               "$ref": "#/$defs/ProcessName",
-               "default": "Model evaluation"
+               "default": "Model evaluation",
+               "title": "Process Type",
+               "type": "string"
             },
             "name": {
                "default": "",
@@ -27047,8 +27048,9 @@
                "type": "string"
             },
             "process_type": {
-               "$ref": "#/$defs/ProcessName",
-               "default": "Model training"
+               "default": "Model training",
+               "title": "Process Type",
+               "type": "string"
             },
             "name": {
                "default": "",
@@ -37433,60 +37435,6 @@
          "title": "Procedures",
          "type": "object"
       },
-      "ProcessName": {
-         "description": "Process names",
-         "enum": [
-            "Analysis",
-            "Compression",
-            "Denoising",
-            "Ephys curation",
-            "Ephys postprocessing",
-            "Ephys preprocessing",
-            "Ephys visualization",
-            "Fiducial segmentation",
-            "File format conversion",
-            "Fix color range",
-            "Fluorescence event detection",
-            "Image atlas alignment",
-            "Image background subtraction",
-            "Image cell classification",
-            "Image cell quantification",
-            "Image cell segmentation",
-            "Image cross-image alignment",
-            "Image destriping",
-            "Image flat-field correction",
-            "Image importing",
-            "Image mip visualization",
-            "Image multiscaling",
-            "Image radial correction",
-            "Image spot detection",
-            "Image spot spectral unmixing",
-            "Image thresholding",
-            "Image tile alignment",
-            "Image tile fusing",
-            "Image tile projection",
-            "Manual curation",
-            "Model evaluation",
-            "Model training",
-            "Neuron skeleton processing",
-            "Neuropil subtraction",
-            "Other",
-            "Pipeline",
-            "Simulation",
-            "Skull stripping",
-            "Spatial timeseries demixing",
-            "Spike sorting",
-            "Video ROI classification",
-            "Video ROI cross session matching",
-            "Video ROI segmentation",
-            "Video ROI timeseries extraction",
-            "Video motion correction",
-            "Video plane decrosstalk",
-            "dF/F estimation"
-         ],
-         "title": "ProcessName",
-         "type": "string"
-      },
       "ProcessStage": {
          "description": "Stages of processing",
          "enum": [