Add explanation doc on binary enums vs booleans

Add documentation explaining why binary enums are often preferred
over boolean types, drawing from the tidyverse design principles.
Covers extensibility, clarity, self-documenting code, and the
"name the scale" pattern. Includes LinkML-specific examples.

Reference: https://design.tidyverse.org/boolean-strategies.html

Author: claude

docs/explanations/binary-enums-vs-booleans.md

@@ -0,0 +1,168 @@
+# Prefer Binary Enums Over Booleans
+
+When modeling data that has two possible states, it may be tempting to use a boolean type (`true`/`false`). However, in many cases, a two-element enumeration (binary enum) is the better choice. This document explains why and when to prefer binary enums over booleans in your LinkML schemas.
+
+## The Case for Binary Enums
+
+The [Tidy Design Principles](https://design.tidyverse.org/boolean-strategies.html) from the tidyverse project articulate several compelling reasons to prefer enums even when there are only two choices.
+
+### 1. Extensibility
+
+If you later discover a third (or fourth, or fifth) option, you'll need to change the interface. With an enum, adding new values is straightforward. With a boolean, you face a breaking change.
+
+**Example:** Consider a data submission status. You might initially think "submitted" or "not submitted" covers it:
+
+```yaml
+# Boolean approach - seems simple at first
+slots:
+  is_submitted:
+    range: boolean
+```
+
+But what about "pending review", "rejected", or "withdrawn"? With a boolean, you're stuck. With an enum, you simply add new values:
+
+```yaml
+# Enum approach - extensible
+enums:
+  SubmissionStatus:
+    permissible_values:
+      SUBMITTED:
+      NOT_SUBMITTED:
+      PENDING_REVIEW:   # Easy to add later
+      REJECTED:         # Easy to add later
+```
+
+### 2. Clarity of Intent
+
+Boolean values often have asymmetric clarity. `something = TRUE` tells you what *will* happen, but `something = FALSE` only tells you what *won't* happen, not what will happen instead.
+
+**Example from tidyverse:** The `sort()` function uses `decreasing = TRUE/FALSE`. Reading `decreasing = FALSE` leaves ambiguity:
+- Does it mean "sort in increasing order"?
+- Or does it mean "don't sort at all"?
+
+Compare this with `vctrs::vec_sort()` which uses `direction = "asc"` or `direction = "desc"`. Both options are explicit and self-documenting.
+
+### 3. Avoiding Cryptic Negations
+
+Boolean parameters often require mental gymnastics to interpret, especially with negated names.
+
+**Example from tidyverse:** The `cut()` function has a `right` parameter:
+- `right = TRUE`: right-closed, left-open intervals `(a, b]`
+- `right = FALSE`: right-open, left-closed intervals `[a, b)`
+
+A clearer design would be `open_side = c("right", "left")` or `bounds = c("[)", "(]")`.
+
+### 4. Self-Documenting Code
+
+Enums make data and code more readable without needing to consult documentation.
+
+```yaml
+# What does this mean? Need to check docs.
+sample:
+  is_control: false
+
+# Self-explanatory
+sample:
+  sample_type: EXPERIMENTAL
+```
+
+### 5. The "Name the Scale" Pattern
+
+When converting booleans to enums, consider naming the scale with values that represent points on it. This signals that intermediate values could be added.
+
+**Example:** Instead of `verbose = TRUE/FALSE`, use:
+
+```yaml
+enums:
+  VerbosityLevel:
+    permissible_values:
+      NONE:
+        description: No output
+      MINIMAL:
+        description: Errors only
+      NORMAL:
+        description: Standard output
+      VERBOSE:
+        description: Detailed output
+      DEBUG:
+        description: All available information
+```
+
+## When Booleans Are Acceptable
+
+Booleans remain appropriate in certain cases:
+
+1. **Truly binary states**: The states are fundamentally and permanently binary (e.g., physical properties like "alive/dead" in certain contexts)
+
+2. **Well-named parameters**: The parameter name makes both states crystal clear (e.g., `include_header` where `false` clearly means "exclude header")
+
+3. **Toggle operations**: When the operation is clearly about enabling/disabling something (`enabled = true/false`)
+
+## LinkML Examples
+
+### Binary Enum Pattern
+
+```yaml
+enums:
+  SortDirection:
+    permissible_values:
+      ASCENDING:
+        description: Sort from lowest to highest
+        meaning: SIO:001395  # ascending order
+      DESCENDING:
+        description: Sort from highest to lowest
+        meaning: SIO:001396  # descending order
+
+  StrandOrientation:
+    permissible_values:
+      FORWARD:
+        description: Forward/plus strand
+        meaning: SO:0000853  # forward_strand
+      REVERSE:
+        description: Reverse/minus strand
+        meaning: SO:0000854  # reverse_strand
+
+  PresenceStatus:
+    permissible_values:
+      PRESENT:
+        description: The entity is present
+      ABSENT:
+        description: The entity is absent
+      NOT_DETERMINED:
+        description: Presence could not be determined
+```
+
+### Applying to Slots
+
+```yaml
+slots:
+  sort_direction:
+    range: SortDirection
+    description: Direction for sorting results
+
+  strand:
+    range: StrandOrientation
+    description: DNA strand orientation
+
+  presence:
+    range: PresenceStatus
+    description: Whether the feature was detected
+```
+
+## Summary
+
+| Aspect | Boolean | Binary Enum |
+|--------|---------|-------------|
+| Extensibility | Poor - breaking change to add states | Good - add new values easily |
+| Clarity | Often asymmetric | Both values explicit |
+| Documentation | Requires external docs | Self-documenting |
+| Ontology mapping | Not possible | Supports `meaning` annotations |
+| Future-proofing | Risky | Safe |
+
+When in doubt, prefer a two-element enum. The small additional effort pays dividends in clarity, maintainability, and extensibility.
+
+## References
+
+- [Tidy Design Principles: Prefer an enum, even if only two choices](https://design.tidyverse.org/boolean-strategies.html)
+- [Tidy Design Principles: Explicit Strategies](https://design.tidyverse.org/explicit-strategies.html)
+- [Tidy Design Principles: Extract strategies into objects](https://design.tidyverse.org/strategy-objects.html)

docs/index.md

@@ -10,6 +10,10 @@ A collection of commonly used value sets
 - [Agentic IDE Support](how-to-guides/agentic-ide-support.md)
 - [Sync UniProt Species](how-to-guides/sync-uniprot-species.md)
 
+## Explanations
+
+- [Prefer Binary Enums Over Booleans](explanations/binary-enums-vs-booleans.md) - Why two-element enums are often better than boolean types
+
 Note: this schema consists ONLY of enums, so it is normal
 that classes and slots are empty.