Add a method slot to Feature for the annotation method behind a hit

.linkmllint.yaml

@@ -0,0 +1,11 @@
+# Configuration for `just lint` (linkml-lint reads this file from the repository root).
+extends: recommended
+rules:
+  standard_naming:
+    # StrandEnum in ber_feature_model.yaml uses the GFF3 column 7 symbols as its values, so a
+    # strand written in a GFF3 file reads back unchanged.
+    exclude:
+      - "+"
+      - "-"
+      - "."
+      - "?"

src/ber_central_schema/schema/attributes.yaml

@@ -0,0 +1,67 @@
+id: https://w3id.org/ber-data/attributes
+name: attributes
+title: Reusable attributes (draft)
+version: 0.1.0
+description: >-
+  String-valued attributes for metadata, annotations, and source-reported evidence, with an
+  optional CURIE for the key and an optional number for the value.
+license: https://creativecommons.org/publicdomain/zero/1.0/
+prefixes:
+  linkml: https://w3id.org/linkml/
+  battr: https://w3id.org/ber-data/attributes/
+  kb_cdm: http://kbase.github.io/cdm-schema/linkml/
+  nmdc: https://w3id.org/nmdc/
+default_prefix: battr
+default_range: string
+imports:
+  - linkml:types
+classes:
+  Attribute:
+    title: Attribute
+    class_uri: battr:Attribute
+    description: One named value attached to a record by a consuming model.
+    notes:
+      - GFF column 9 is a minimal use case, alongside tabular annotations and metadata.
+        This module has no dependency on GFF, Feature, Contig, or a genomic coordinate system.
+      - A key is not an identifier; repeated keys can remain separate entries in an ordered list.
+        Consuming models choose attachment and cardinality. Keys are source names, not a controlled vocabulary.
+      - Each value of a multivalued source attribute is its own Attribute entry, with the same key,
+        in source order; one entry never holds a joined list.
+      - attribute_cv_id and numeric_value follow the NMDC AttributeValue pattern that BERtron and the
+        KBase CDM use (an optional attribute CURIE plus the raw string, with a typed value), which
+        this pair can be projected onto later. key and value keep the source's text.
+    attributes:
+      key:
+        title: Key
+        slot_uri: battr:key
+        range: string
+        required: true
+        description: Source-reported attribute name, unnormalized (for example a GFF tag or metadata key).
+      value:
+        title: Value
+        slot_uri: battr:value
+        range: string
+        required: true
+        description: >-
+          The source's text for one value, as a string: not typed or normalized, with any escaping
+          the source format defines decoded (a GFF3 %2C is stored as a comma).
+      attribute_cv_id:
+        title: Attribute CV ID
+        slot_uri: battr:attribute_cv_id
+        range: uriorcurie
+        description: >-
+          A CURIE for what the key means, from an ontology or controlled vocabulary, for example
+          EDAM:data_1667 (E-value) for both e-value and
+          evalue. key keeps the source spelling either way.
+        exact_mappings:
+          - kb_cdm:attribute_cv_id
+      numeric_value:
+        title: Numeric value
+        slot_uri: battr:numeric_value
+        range: float
+        description: >-
+          value read as a number, only for keys known to be numeric. value
+          keeps the source text, so 3.4e-28 and 3.40E-28 stay distinguishable.
+        exact_mappings:
+          - kb_cdm:numeric_value
+          - nmdc:numeric_value

src/ber_central_schema/schema/ber_central_schema.yaml

@@ -5,7 +5,7 @@ title: BRIDGE Central Schema
 description: >-
   The central BRIDGE schema for harmonized cross-BER data access. Defines
   shared base elements and composes domain modules (currently:
-  measurements.yaml).
+  measurements.yaml and ber_feature_model.yaml).
 license: Apache-2.0
 see_also:
   - https://github.com/ber-data/bridge-central-schema
@@ -14,13 +14,19 @@ see_also:
 prefixes:
   bridge_central_schema: https://w3id.org/ber-data/bridge-central-schema/
   linkml: https://w3id.org/linkml/
+  # Also declared here: the generated Python leaves out prefixes that only an imported module
+  # declares when enum meanings use them (the feature model's ContigCollectionTypeEnum and
+  # ScoreTypeEnum).
+  MIXS: https://w3id.org/mixs/
+  EDAM_DATA: http://edamontology.org/data_
   schema: http://schema.org/
 default_prefix: bridge_central_schema
 default_range: string
 
 imports:
   - linkml:types
   - measurements
+  - ber_feature_model
 
 classes: