[ENH] BEP032: Require anatomical_reference_point when stereotaxic coordinates are given

src/appendices/microelectrode-surgical-coordinates.md

@@ -14,7 +14,7 @@ There are two major anatomical markers on the dorsal surface of the brain that a
 
 **Lambda**: the meeting point of the sagittal suture (between left and right parietal bones) and the lambdoid suture (between parietal and occipital bones).
 
-Both points serve as standard reference points for stereotaxic coordinates in neuroscience research. `(0,0,0)` is assumed to be Bregma when working with rodents. It may optionally be defined differently using `anatomical_reference_point`, and MUST be defined for other species.
+Both points serve as standard reference points for stereotaxic coordinates in neuroscience research. The point that `(0,0,0)` refers to MUST be stated in the `anatomical_reference_point` column of `*_probes.tsv` whenever stereotaxic coordinates are given, for every species. Bregma is the usual choice for rodents, but it is not assumed.
 
 ## Stereotaxic Coordinate System Conventions
 

src/modality-specific-files/microelectrode-electrophysiology.md

@@ -373,10 +373,10 @@ probe02	tetrode	-1.2	-2.1	-3.5	0	10	45	R	Neuralynx	TT-12345	4	n/a	n/a	n/a	tip	Br
 **Intracellular electrophysiology example:**
 
 ```tsv
-probe_name	type	AP	ML	DV	AP_angle	ML_angle	rotation_angle	hemisphere	manufacturer	electrode_count	coordinate_reference_point	associated_brain_region	associated_brain_region_id	reference_atlas
-pipette01	patch-pipette	-1.8	0.5	-2.2	30	0	0	L	Sutter	1	tip	Visual Cortex Layer 2/3	VISp2/3	AllenCCFv3
-pipette02	patch-pipette	-1.8	-0.5	-2.2	30	0	0	R	Sutter	1	tip	Visual Cortex Layer 2/3	VISp2/3	AllenCCFv3
-pipette03	sharp-electrode	-3.2	1.2	-3.8	20	5	0	L	WPI	1	tip	Prefrontal Cortex Layer 5	PL5	Franklin-Paxinos
+probe_name	type	AP	ML	DV	AP_angle	ML_angle	rotation_angle	hemisphere	manufacturer	electrode_count	coordinate_reference_point	anatomical_reference_point	associated_brain_region	associated_brain_region_id	reference_atlas
+pipette01	patch-pipette	-1.8	0.5	-2.2	30	0	0	L	Sutter	1	tip	Bregma	Visual Cortex Layer 2/3	VISp2/3	AllenCCFv3
+pipette02	patch-pipette	-1.8	-0.5	-2.2	30	0	0	R	Sutter	1	tip	Bregma	Visual Cortex Layer 2/3	VISp2/3	AllenCCFv3
+pipette03	sharp-electrode	-3.2	1.2	-3.8	20	5	0	L	WPI	1	tip	Bregma	Prefrontal Cortex Layer 5	PL5	Franklin-Paxinos
 ```
 
 For details on the surgical coordinate system used to describe probe placement during surgery (AP, ML, DV, angles, and

src/schema/objects/columns.yaml

@@ -152,9 +152,10 @@ anatomical_reference_point:
   name: anatomical_reference_point
   display_name: Anatomical reference point
   description: |
-    Anatomical reference point for stereotaxic coordinates (for example, `Bregma`, `Lambda`).
-    If not specified, `Bregma` is assumed for rodents.
-    MUST be defined for species other than rodents.
+    Anatomical reference point from which the stereotaxic coordinates of the probe are
+    measured (for example, `Bregma`, `Lambda`).
+    This column MUST be defined whenever any of the `AP`, `ML`, or `DV` columns are present,
+    for every species, since those coordinates cannot be interpreted without it.
   type: string
 depth__probes:
   name: depth

src/schema/rules/checks/microephys.yaml

@@ -16,3 +16,21 @@ MicroephysRequiredCoordsystemWithSpace:
     - '"space" in entities'
   checks:
     - associations.coordsystem != null
+
+# Stereotaxic coordinates cannot be interpreted without knowing the point they are
+# measured from, so requiring the reference point is conditioned on their presence.
+MicroephysRequiredAnatomicalReferencePoint:
+  issue:
+    code: MICROEPHYS_ANATOMICAL_REFERENCE_POINT_REQUIRED
+    message: |
+      The `anatomical_reference_point` column MUST be defined in `*_probes.tsv` when
+      stereotaxic coordinates are given, that is, when any of the `AP`, `ML`, or `DV`
+      columns are present.
+    level: error
+  selectors:
+    - intersects([datatype], ["ecephys", "icephys"])
+    - suffix == "probes"
+    - extension == ".tsv"
+    - columns.AP != null || columns.ML != null || columns.DV != null
+  checks:
+    - columns.anatomical_reference_point != null

src/schema/rules/tabular_data/microephys.yaml

@@ -29,7 +29,9 @@ microephysProbes:
     depth__probes: optional
     rotation_angle: recommended
     coordinate_reference_point: recommended
-    anatomical_reference_point: optional
+    anatomical_reference_point:
+      level: optional
+      level_addendum: required if `AP`, `ML`, or `DV` are present
     hemisphere__probes: recommended
     associated_brain_region: recommended
     associated_brain_region_id: recommended