From 4e5d54150febb3511164d70816fd04f63177c219 Mon Sep 17 00:00:00 2001
From: Charles Tapley Hoyt <cthoyt@gmail.com>
Date: Sun, 24 May 2026 14:48:30 +0200
Subject: [PATCH 01/29] Add `derived_from` field

---
 CHANGELOG.md                              |  1 +
 examples/schema/derived_from.sssom.tsv    | 20 +++++++++++
 mkdocs.yml                                |  1 +
 src/docs/inference.md                     | 43 +++++++++++++++++++++++
 src/sssom_schema/schema/sssom_schema.yaml | 38 ++++++++++++++++++++
 5 files changed, 103 insertions(+)
 create mode 100644 examples/schema/derived_from.sssom.tsv
 create mode 100644 src/docs/inference.md

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 27513e0e..cf5f1e95 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -21,6 +21,7 @@
 - Add `reviewer_agreement` slot ([issue](https://github.com/mapping-commons/sssom/issues/510))
 - Allow encoding pipe characters in multi-valued slots in SSSOM/TSV format ([issue](https://github.com/mapping-commons/sssom/issues/429)).
 - Specify a standard SSSOM hashing function ([issue](https://github.com/mapping-commons/sssom/issues/436)).
+- Add `derived_from` slot ([issue](https://github.com/mapping-commons/sssom/issues/537))
 
 ## SSSOM version 1.0.0
 
diff --git a/examples/schema/derived_from.sssom.tsv b/examples/schema/derived_from.sssom.tsv
new file mode 100644
index 00000000..d896d1a1
--- /dev/null
+++ b/examples/schema/derived_from.sssom.tsv
@@ -0,0 +1,20 @@
+# curie_map:
+#   cas: https://commonchemistry.cas.org/detail?cas_rn=
+#   CHEBI: http://purl.obolibrary.org/obo/CHEBI_
+#   mesh: http://id.nlm.nih.gov/mesh/
+#   orcid: https://orcid.org/
+#   semapv: https://w3id.org/semapv/vocab/
+#   skos: http://www.w3.org/2004/02/skos/core#
+#   mapping: http://www.w3.org/2004/02/skos/core#
+# license: https://creativecommons.org/publicdomain/zero/1.0/
+# mapping_set_id: https://github.com/mapping-commons/sssom/blob/master/examples/schema/derived_from.sssom.tsv
+# creator_id:
+#  - orcid:0000-0003-4423-4370
+# see_also:
+#  - https://github.com/mapping-commons/sssom/issues/537
+# sssom_version: 1.1
+subject_id	subject_label	predicate_id	object_id	object_label	mapping_justification	derived_from	comment
+mesh:C000089	ammeline	skos:exactMatch	CHEBI:28646	ammeline	semapv:ManualMappingCuration
+CHEBI:28646	ammeline	skos:exactMatch	cas:645-92-1	Ammeline	semapv:ManualMappingCuration
+mesh:C000089	ammeline	skos:exactMatch	cas:645-92-1	Ammeline	 semapv:MappingChaining	mapping:36a1f9244ea7641a90987c82f33c25c0c13712ee8f48207b2a0825f8a4e4e26a|mapping:bb768f0b1e1643298f4df1a381001f6ed68fcc8fff49b371f0235b51dbab9e1e	this example needs to refer to both the mappings on row 18 and 19 by mapping sameness identifier
+CHEBI:28646	ammeline	skos:exactMatch	mesh:C000089	Ammeline	 semapv:MappingInversion	mapping:36a1f9244ea7641a90987c82f33c25c0c13712ee8f48207b2a0825f8a4e4e26a	this example just needs to refer to the mapping on row 18 by the mapping sameness identifier
diff --git a/mkdocs.yml b/mkdocs.yml
index daadd1a5..def153a5 100644
--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -54,6 +54,7 @@ nav:
           - Introduction: spec-support.md
           - Hashing mapping records: spec-support-hashing.md
           - Applying Chaining Rules: chaining-rules.md
+          - Inference: inference.md
   - Resources for contributors: contributing.md
   - Resources for users:
       - FAQ: faq.md
diff --git a/src/docs/inference.md b/src/docs/inference.md
new file mode 100644
index 00000000..0c97b2be
--- /dev/null
+++ b/src/docs/inference.md
@@ -0,0 +1,43 @@
+# Inference
+
+There are several mechanisms for inference:
+
+- Inference via chaining (see [chaining rules](chaining-rules.md)), which should
+  be tagged with `semapv:MappingChaining` as a justification
+- Inference via mapping inversion, which should be tagged with
+  `semapv:MappingInversion` as a justification
+- Inference via prior knowledge, which should be tagged with
+  `semapv:BackgroundKnowledgeBasedMatching` as a justification
+
+## Referring to Evidence
+
+The `derived_from` field was introduced in
+[#537](https://github.com/mapping-commons/sssom/issues/537) in order to
+reference the original subject-predicate-object triple from which new mappings
+are inferred/derived.
+
+The following table demonstrates how the mapping sameness identifier (MSI) can
+be referenced in the `derived_from` field when doing both mapping chaining
+(i.e., using multiple mappings to infer a new one) and mapping inversion.
+
+```
+# curie_map:
+#   cas:  	https://commonchemistry.cas.org/detail?cas_rn=
+#   CHEBI: http://purl.obolibrary.org/obo/CHEBI_
+#   mesh: http://id.nlm.nih.gov/mesh/
+#   orcid: https://orcid.org/
+#   semapv: https://w3id.org/semapv/vocab/
+#   skos: http://www.w3.org/2004/02/skos/core#
+#   mapping: http://w3id.org/mapping/
+# license: https://creativecommons.org/publicdomain/zero/1.0/
+# mapping_set_id: https://github.com/mapping-commons/sssom/blob/master/examples/schema/derived_from.sssom.tsv
+# creator_id:
+#  - orcid:0000-0003-4423-4370
+```
+
+| subject_id   | subject_label | predicate_id    | object_id    | object_label | mapping_justification        | derived_from                                                                                                                                       | comment                                                                                               |
+| ------------ | ------------- | --------------- | ------------ | ------------ | ---------------------------- | -------------------------------------------------------------------------------------------------------------------------------------------------- | ----------------------------------------------------------------------------------------------------- |
+| mesh:C000089 | ammeline      | skos:exactMatch | CHEBI:28646  | ammeline     | semapv:ManualMappingCuration |                                                                                                                                                    |                                                                                                       |
+| CHEBI:28646  | ammeline      | skos:exactMatch | cas:645-92-1 | Ammeline     | semapv:ManualMappingCuration |                                                                                                                                                    |                                                                                                       |
+| mesh:C000089 | ammeline      | skos:exactMatch | cas:645-92-1 | Ammeline     | semapv:MappingChaining       | mapping:36a1f9244ea7641a90987c82f33c25c0c13712ee8f48207b2a0825f8a4e4e26a\|mapping:bb768f0b1e1643298f4df1a381001f6ed68fcc8fff49b371f0235b51dbab9e1e | this example needs to refer to the firs two mappings in this table by mapping sameness identifier     |
+| CHEBI:28646  | ammeline      | skos:exactMatch | mesh:C000089 | Ammeline     | semapv:MappingInversion      | mapping:36a1f9244ea7641a90987c82f33c25c0c13712ee8f48207b2a0825f8a4e4e26a                                                                           | this example just needs to refer to the first mappingin this table by the mapping sameness identifier |
diff --git a/src/sssom_schema/schema/sssom_schema.yaml b/src/sssom_schema/schema/sssom_schema.yaml
index f2421f06..77fbb1e3 100644
--- a/src/sssom_schema/schema/sssom_schema.yaml
+++ b/src/sssom_schema/schema/sssom_schema.yaml
@@ -1144,6 +1144,43 @@ slots:
       - https://github.com/mapping-commons/sssom/issues/78
       - https://github.com/mapping-commons/sssom/pull/259
       - https://github.com/mapping-commons/sssom/blob/master/examples/schema/issue_tracker.sssom.tsv
+  derived_from:
+    description:
+      A set of [mapping sameness identifiers
+      (MSIs)](https://github.com/ts4nfdi/mapping-sameness-identifier) for
+      mappings that were used to derive this mapping, e.g., through mapping
+      chaining or inversion, represented as CURIEs. It's left to the curator to
+      decide on the appropriate CURIE/URI prefix for encoding MSIs as CURIEs,
+      but suggested at minimum to use `mapping` as the CURIE prefix (as in the
+      examples)
+    range: EntityReference
+    multivalued: true
+    slot_uri: prov:wasDerivedFrom
+    instantiates:
+      - sssom:Versionable
+    annotations:
+      added_in: "1.1"
+    see_also:
+      - https://github.com/mapping-commons/sssom/issues/537
+      - https://github.com/mapping-commons/sssom/pull/548
+      - https://github.com/mapping-commons/sssom/blob/master/examples/schema/derived_from.sssom.tsv
+    examples:
+      - value: mapping:36a1f9244ea7641a90987c82f33c25c0c13712ee8f48207b2a0825f8a4e4e26a
+        description:
+          A single value can be used when inverting the mapping
+          mesh:C000089-skos:exactMatch-CHEBI:28646, whose mapping sameness
+          identifier is
+          36a1f9244ea7641a90987c82f33c25c0c13712ee8f48207b2a0825f8a4e4e26a, to
+          get mapping CHEBI:28646-skos:exactMatch-mesh:C000089
+      - value: mapping:36a1f9244ea7641a90987c82f33c25c0c13712ee8f48207b2a0825f8a4e4e26a|mapping:bb768f0b1e1643298f4df1a381001f6ed68fcc8fff49b371f0235b51dbab9e1e
+        description:
+          The mappings mesh:C000089-skos:exactMatch-CHEBI:28646 and
+          CHEBI:28646-skos:exactMatch-cas:645-92-1 (whose mapping sameness
+          identifiers are respectively
+          mapping:36a1f9244ea7641a90987c82f33c25c0c13712ee8f48207b2a0825f8a4e4e26a
+          and
+          mapping:bb768f0b1e1643298f4df1a381001f6ed68fcc8fff49b371f0235b51dbab9e1e)
+          can be used to infer mesh:C000089-skos:exactMatch-cas:645-92-1.
   see_also:
     description:
       A URL specific for the mapping instance. E.g. for kboom we have a
@@ -1320,6 +1357,7 @@ classes:
       - similarity_measure
       - see_also
       - issue_tracker_item
+      - derived_from
       - other
       - comment
     class_uri: owl:Axiom

From fcbf0569696ad3fce72d3fc73836d31826ebe644 Mon Sep 17 00:00:00 2001
From: Charles Tapley Hoyt <cthoyt@gmail.com>
Date: Sun, 24 May 2026 14:52:20 +0200
Subject: [PATCH 02/29] Fix descriptions of mappings

---
 examples/schema/derived_from.sssom.tsv | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/examples/schema/derived_from.sssom.tsv b/examples/schema/derived_from.sssom.tsv
index d896d1a1..78c89930 100644
--- a/examples/schema/derived_from.sssom.tsv
+++ b/examples/schema/derived_from.sssom.tsv
@@ -16,5 +16,5 @@
 subject_id	subject_label	predicate_id	object_id	object_label	mapping_justification	derived_from	comment
 mesh:C000089	ammeline	skos:exactMatch	CHEBI:28646	ammeline	semapv:ManualMappingCuration
 CHEBI:28646	ammeline	skos:exactMatch	cas:645-92-1	Ammeline	semapv:ManualMappingCuration
-mesh:C000089	ammeline	skos:exactMatch	cas:645-92-1	Ammeline	 semapv:MappingChaining	mapping:36a1f9244ea7641a90987c82f33c25c0c13712ee8f48207b2a0825f8a4e4e26a|mapping:bb768f0b1e1643298f4df1a381001f6ed68fcc8fff49b371f0235b51dbab9e1e	this example needs to refer to both the mappings on row 18 and 19 by mapping sameness identifier
-CHEBI:28646	ammeline	skos:exactMatch	mesh:C000089	Ammeline	 semapv:MappingInversion	mapping:36a1f9244ea7641a90987c82f33c25c0c13712ee8f48207b2a0825f8a4e4e26a	this example just needs to refer to the mapping on row 18 by the mapping sameness identifier
+mesh:C000089	ammeline	skos:exactMatch	cas:645-92-1	Ammeline	 semapv:MappingChaining	mapping:36a1f9244ea7641a90987c82f33c25c0c13712ee8f48207b2a0825f8a4e4e26a|mapping:bb768f0b1e1643298f4df1a381001f6ed68fcc8fff49b371f0235b51dbab9e1e	this example needs to refer to the first two mappings in this document by mapping sameness identifier
+CHEBI:28646	ammeline	skos:exactMatch	mesh:C000089	Ammeline	 semapv:MappingInversion	mapping:36a1f9244ea7641a90987c82f33c25c0c13712ee8f48207b2a0825f8a4e4e26a	this example just needs to refer to the first mapping in this document by the mapping sameness identifier

From d93e27c06a2cb918a7b3f4c9bd45497a304e508e Mon Sep 17 00:00:00 2001
From: Charles Tapley Hoyt <cthoyt@gmail.com>
Date: Sun, 24 May 2026 14:53:25 +0200
Subject: [PATCH 03/29] Fix spurious whitespace

---
 examples/schema/derived_from.sssom.tsv | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/examples/schema/derived_from.sssom.tsv b/examples/schema/derived_from.sssom.tsv
index 78c89930..12a3bffb 100644
--- a/examples/schema/derived_from.sssom.tsv
+++ b/examples/schema/derived_from.sssom.tsv
@@ -16,5 +16,5 @@
 subject_id	subject_label	predicate_id	object_id	object_label	mapping_justification	derived_from	comment
 mesh:C000089	ammeline	skos:exactMatch	CHEBI:28646	ammeline	semapv:ManualMappingCuration
 CHEBI:28646	ammeline	skos:exactMatch	cas:645-92-1	Ammeline	semapv:ManualMappingCuration
-mesh:C000089	ammeline	skos:exactMatch	cas:645-92-1	Ammeline	 semapv:MappingChaining	mapping:36a1f9244ea7641a90987c82f33c25c0c13712ee8f48207b2a0825f8a4e4e26a|mapping:bb768f0b1e1643298f4df1a381001f6ed68fcc8fff49b371f0235b51dbab9e1e	this example needs to refer to the first two mappings in this document by mapping sameness identifier
-CHEBI:28646	ammeline	skos:exactMatch	mesh:C000089	Ammeline	 semapv:MappingInversion	mapping:36a1f9244ea7641a90987c82f33c25c0c13712ee8f48207b2a0825f8a4e4e26a	this example just needs to refer to the first mapping in this document by the mapping sameness identifier
+mesh:C000089	ammeline	skos:exactMatch	cas:645-92-1	Ammeline	semapv:MappingChaining	mapping:36a1f9244ea7641a90987c82f33c25c0c13712ee8f48207b2a0825f8a4e4e26a|mapping:bb768f0b1e1643298f4df1a381001f6ed68fcc8fff49b371f0235b51dbab9e1e	this example needs to refer to the first two mappings in this document by mapping sameness identifier
+CHEBI:28646	ammeline	skos:exactMatch	mesh:C000089	Ammeline	semapv:MappingInversion	mapping:36a1f9244ea7641a90987c82f33c25c0c13712ee8f48207b2a0825f8a4e4e26a	this example just needs to refer to the first mapping in this document by the mapping sameness identifier

From 77007f7566dee9e10968eecbe8bbee437836a3a7 Mon Sep 17 00:00:00 2001
From: Charles Tapley Hoyt <cthoyt@gmail.com>
Date: Sun, 24 May 2026 14:57:02 +0200
Subject: [PATCH 04/29] Update derived_from.sssom.tsv

---
 examples/schema/derived_from.sssom.tsv | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/examples/schema/derived_from.sssom.tsv b/examples/schema/derived_from.sssom.tsv
index 12a3bffb..f5284ed4 100644
--- a/examples/schema/derived_from.sssom.tsv
+++ b/examples/schema/derived_from.sssom.tsv
@@ -5,7 +5,7 @@
 #   orcid: https://orcid.org/
 #   semapv: https://w3id.org/semapv/vocab/
 #   skos: http://www.w3.org/2004/02/skos/core#
-#   mapping: http://www.w3.org/2004/02/skos/core#
+#   mapping: http://w3id.org/mapping/
 # license: https://creativecommons.org/publicdomain/zero/1.0/
 # mapping_set_id: https://github.com/mapping-commons/sssom/blob/master/examples/schema/derived_from.sssom.tsv
 # creator_id:

From 701d28e3874fb530a2c99f4b224bbd9aeb98f76d Mon Sep 17 00:00:00 2001
From: Charles Tapley Hoyt <cthoyt@gmail.com>
Date: Sun, 24 May 2026 15:00:49 +0200
Subject: [PATCH 05/29] Remove text about how to encode CURIE/URI prefix

---
 src/sssom_schema/schema/sssom_schema.yaml | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/src/sssom_schema/schema/sssom_schema.yaml b/src/sssom_schema/schema/sssom_schema.yaml
index 77fbb1e3..e25bca79 100644
--- a/src/sssom_schema/schema/sssom_schema.yaml
+++ b/src/sssom_schema/schema/sssom_schema.yaml
@@ -1149,10 +1149,7 @@ slots:
       A set of [mapping sameness identifiers
       (MSIs)](https://github.com/ts4nfdi/mapping-sameness-identifier) for
       mappings that were used to derive this mapping, e.g., through mapping
-      chaining or inversion, represented as CURIEs. It's left to the curator to
-      decide on the appropriate CURIE/URI prefix for encoding MSIs as CURIEs,
-      but suggested at minimum to use `mapping` as the CURIE prefix (as in the
-      examples)
+      chaining or inversion, represented as CURIEs.
     range: EntityReference
     multivalued: true
     slot_uri: prov:wasDerivedFrom

From 31f7cbbc8aab782bf5085a74123e626d76db2466 Mon Sep 17 00:00:00 2001
From: Charles Tapley Hoyt <cthoyt@gmail.com>
Date: Sun, 24 May 2026 15:06:16 +0200
Subject: [PATCH 06/29] Remove recommendation to use MSI in description

---
 src/sssom_schema/schema/sssom_schema.yaml | 22 ++++++++++++----------
 1 file changed, 12 insertions(+), 10 deletions(-)

diff --git a/src/sssom_schema/schema/sssom_schema.yaml b/src/sssom_schema/schema/sssom_schema.yaml
index e25bca79..4b42cc65 100644
--- a/src/sssom_schema/schema/sssom_schema.yaml
+++ b/src/sssom_schema/schema/sssom_schema.yaml
@@ -1146,9 +1146,8 @@ slots:
       - https://github.com/mapping-commons/sssom/blob/master/examples/schema/issue_tracker.sssom.tsv
   derived_from:
     description:
-      A set of [mapping sameness identifiers
-      (MSIs)](https://github.com/ts4nfdi/mapping-sameness-identifier) for
-      mappings that were used to derive this mapping, e.g., through mapping
+      A set of CURIEs referring to mappings (i.e., subject-predicate-object
+      triples) that were used to derive this mapping, e.g., through mapping
       chaining or inversion, represented as CURIEs.
     range: EntityReference
     multivalued: true
@@ -1165,18 +1164,21 @@ slots:
       - value: mapping:36a1f9244ea7641a90987c82f33c25c0c13712ee8f48207b2a0825f8a4e4e26a
         description:
           A single value can be used when inverting the mapping
-          mesh:C000089-skos:exactMatch-CHEBI:28646, whose mapping sameness
-          identifier is
-          36a1f9244ea7641a90987c82f33c25c0c13712ee8f48207b2a0825f8a4e4e26a, to
+          mesh:C000089-skos:exactMatch-CHEBI:28646, represented with the
+          [mapping sameness identifier
+          (MSI)](https://github.com/ts4nfdi/mapping-sameness-identifier) for is
+          `36a1f9244ea7641a90987c82f33c25c0c13712ee8f48207b2a0825f8a4e4e26a`, to
           get mapping CHEBI:28646-skos:exactMatch-mesh:C000089
       - value: mapping:36a1f9244ea7641a90987c82f33c25c0c13712ee8f48207b2a0825f8a4e4e26a|mapping:bb768f0b1e1643298f4df1a381001f6ed68fcc8fff49b371f0235b51dbab9e1e
         description:
           The mappings mesh:C000089-skos:exactMatch-CHEBI:28646 and
-          CHEBI:28646-skos:exactMatch-cas:645-92-1 (whose mapping sameness
-          identifiers are respectively
-          mapping:36a1f9244ea7641a90987c82f33c25c0c13712ee8f48207b2a0825f8a4e4e26a
+          CHEBI:28646-skos:exactMatch-cas:645-92-1, whose [mapping sameness
+          identifiers
+          (MSIs)](https://github.com/ts4nfdi/mapping-sameness-identifier) are
+          respectively
+          `mapping:36a1f9244ea7641a90987c82f33c25c0c13712ee8f48207b2a0825f8a4e4e26a`
           and
-          mapping:bb768f0b1e1643298f4df1a381001f6ed68fcc8fff49b371f0235b51dbab9e1e)
+          `mapping:bb768f0b1e1643298f4df1a381001f6ed68fcc8fff49b371f0235b51dbab9e1e`,
           can be used to infer mesh:C000089-skos:exactMatch-cas:645-92-1.
   see_also:
     description:

From 0b7adbf0958a057dd212183d8ebbf6275979aabf Mon Sep 17 00:00:00 2001
From: Charles Tapley Hoyt <cthoyt@gmail.com>
Date: Sun, 24 May 2026 15:09:18 +0200
Subject: [PATCH 07/29] Update sssom_schema.yaml

---
 src/sssom_schema/schema/sssom_schema.yaml | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/src/sssom_schema/schema/sssom_schema.yaml b/src/sssom_schema/schema/sssom_schema.yaml
index 4b42cc65..481da9b8 100644
--- a/src/sssom_schema/schema/sssom_schema.yaml
+++ b/src/sssom_schema/schema/sssom_schema.yaml
@@ -1146,9 +1146,10 @@ slots:
       - https://github.com/mapping-commons/sssom/blob/master/examples/schema/issue_tracker.sssom.tsv
   derived_from:
     description:
-      A set of CURIEs referring to mappings (i.e., subject-predicate-object
-      triples) that were used to derive this mapping, e.g., through mapping
-      chaining or inversion, represented as CURIEs.
+      A set of CURIEs referring to mappings (i.e.,
+      subject-predicate-object-predicate-modifier quadruple) that were used to
+      derive this mapping, e.g., through mapping chaining or inversion,
+      represented as CURIEs.
     range: EntityReference
     multivalued: true
     slot_uri: prov:wasDerivedFrom

From 33795caa95cf5877f9c6b648713724827682f95f Mon Sep 17 00:00:00 2001
From: Charles Tapley Hoyt <cthoyt@gmail.com>
Date: Sun, 24 May 2026 15:10:18 +0200
Subject: [PATCH 08/29] Update inference.md

---
 src/docs/inference.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/docs/inference.md b/src/docs/inference.md
index 0c97b2be..3f184b10 100644
--- a/src/docs/inference.md
+++ b/src/docs/inference.md
@@ -36,8 +36,8 @@ be referenced in the `derived_from` field when doing both mapping chaining
 ```
 
 | subject_id   | subject_label | predicate_id    | object_id    | object_label | mapping_justification        | derived_from                                                                                                                                       | comment                                                                                               |
-| ------------ | ------------- | --------------- | ------------ | ------------ | ---------------------------- | -------------------------------------------------------------------------------------------------------------------------------------------------- | ----------------------------------------------------------------------------------------------------- |
+| ------------ | ------------- | --------------- | ------------ | ------------ | ---------------------------- | -------------------------------------------------------------------------------------------------------------------------------------------------- |-------------------------------------------------------------------------------------------------------|
 | mesh:C000089 | ammeline      | skos:exactMatch | CHEBI:28646  | ammeline     | semapv:ManualMappingCuration |                                                                                                                                                    |                                                                                                       |
 | CHEBI:28646  | ammeline      | skos:exactMatch | cas:645-92-1 | Ammeline     | semapv:ManualMappingCuration |                                                                                                                                                    |                                                                                                       |
-| mesh:C000089 | ammeline      | skos:exactMatch | cas:645-92-1 | Ammeline     | semapv:MappingChaining       | mapping:36a1f9244ea7641a90987c82f33c25c0c13712ee8f48207b2a0825f8a4e4e26a\|mapping:bb768f0b1e1643298f4df1a381001f6ed68fcc8fff49b371f0235b51dbab9e1e | this example needs to refer to the firs two mappings in this table by mapping sameness identifier     |
+| mesh:C000089 | ammeline      | skos:exactMatch | cas:645-92-1 | Ammeline     | semapv:MappingChaining       | mapping:36a1f9244ea7641a90987c82f33c25c0c13712ee8f48207b2a0825f8a4e4e26a\|mapping:bb768f0b1e1643298f4df1a381001f6ed68fcc8fff49b371f0235b51dbab9e1e | this example needs to refer to the first two mappings in this table by mapping sameness identifier    |
 | CHEBI:28646  | ammeline      | skos:exactMatch | mesh:C000089 | Ammeline     | semapv:MappingInversion      | mapping:36a1f9244ea7641a90987c82f33c25c0c13712ee8f48207b2a0825f8a4e4e26a                                                                           | this example just needs to refer to the first mappingin this table by the mapping sameness identifier |

From cb34aeb7c2523b139de2091aea219795eb3b9f31 Mon Sep 17 00:00:00 2001
From: Charles Tapley Hoyt <cthoyt@gmail.com>
Date: Sun, 24 May 2026 15:12:31 +0200
Subject: [PATCH 09/29] Use example.org dummy URI

---
 examples/schema/derived_from.sssom.tsv | 2 +-
 src/docs/inference.md                  | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/examples/schema/derived_from.sssom.tsv b/examples/schema/derived_from.sssom.tsv
index f5284ed4..e45610c8 100644
--- a/examples/schema/derived_from.sssom.tsv
+++ b/examples/schema/derived_from.sssom.tsv
@@ -5,7 +5,7 @@
 #   orcid: https://orcid.org/
 #   semapv: https://w3id.org/semapv/vocab/
 #   skos: http://www.w3.org/2004/02/skos/core#
-#   mapping: http://w3id.org/mapping/
+#   mapping: https://example.com/mapping/
 # license: https://creativecommons.org/publicdomain/zero/1.0/
 # mapping_set_id: https://github.com/mapping-commons/sssom/blob/master/examples/schema/derived_from.sssom.tsv
 # creator_id:
diff --git a/src/docs/inference.md b/src/docs/inference.md
index 3f184b10..ac374fce 100644
--- a/src/docs/inference.md
+++ b/src/docs/inference.md
@@ -28,7 +28,7 @@ be referenced in the `derived_from` field when doing both mapping chaining
 #   orcid: https://orcid.org/
 #   semapv: https://w3id.org/semapv/vocab/
 #   skos: http://www.w3.org/2004/02/skos/core#
-#   mapping: http://w3id.org/mapping/
+#   mapping: https://example.com/mapping/
 # license: https://creativecommons.org/publicdomain/zero/1.0/
 # mapping_set_id: https://github.com/mapping-commons/sssom/blob/master/examples/schema/derived_from.sssom.tsv
 # creator_id:

From 9fb8dcbd308ba8d5fb67a998c80561f54325d1df Mon Sep 17 00:00:00 2001
From: Charles Tapley Hoyt <cthoyt@gmail.com>
Date: Sun, 24 May 2026 15:15:54 +0200
Subject: [PATCH 10/29] Update inference.md

---
 src/docs/inference.md | 16 ++++++++++------
 1 file changed, 10 insertions(+), 6 deletions(-)

diff --git a/src/docs/inference.md b/src/docs/inference.md
index ac374fce..fd5a499b 100644
--- a/src/docs/inference.md
+++ b/src/docs/inference.md
@@ -13,12 +13,16 @@ There are several mechanisms for inference:
 
 The `derived_from` field was introduced in
 [#537](https://github.com/mapping-commons/sssom/issues/537) in order to
-reference the original subject-predicate-object triple from which new mappings
-are inferred/derived.
+reference the original subject-predicate-object-predicate modifier quadruple
+from which new mappings are inferred/derived.
 
-The following table demonstrates how the mapping sameness identifier (MSI) can
-be referenced in the `derived_from` field when doing both mapping chaining
-(i.e., using multiple mappings to infer a new one) and mapping inversion.
+The following example demonstrates how the `derived_from` field when doing both
+mapping chaining (i.e., using multiple mappings to infer a new one) and mapping
+inversion. The local unique identifiers used for mappings in this example are
+related to the proposal in
+https://github.com/ts4nfdi/mapping-sameness-identifier (which currently is under
+finalization). For now, the SSSOM specification isn't currently prescribing how
+to assign CURIEs to mapping quads.
 
 ```
 # curie_map:
@@ -36,7 +40,7 @@ be referenced in the `derived_from` field when doing both mapping chaining
 ```
 
 | subject_id   | subject_label | predicate_id    | object_id    | object_label | mapping_justification        | derived_from                                                                                                                                       | comment                                                                                               |
-| ------------ | ------------- | --------------- | ------------ | ------------ | ---------------------------- | -------------------------------------------------------------------------------------------------------------------------------------------------- |-------------------------------------------------------------------------------------------------------|
+| ------------ | ------------- | --------------- | ------------ | ------------ | ---------------------------- | -------------------------------------------------------------------------------------------------------------------------------------------------- | ----------------------------------------------------------------------------------------------------- |
 | mesh:C000089 | ammeline      | skos:exactMatch | CHEBI:28646  | ammeline     | semapv:ManualMappingCuration |                                                                                                                                                    |                                                                                                       |
 | CHEBI:28646  | ammeline      | skos:exactMatch | cas:645-92-1 | Ammeline     | semapv:ManualMappingCuration |                                                                                                                                                    |                                                                                                       |
 | mesh:C000089 | ammeline      | skos:exactMatch | cas:645-92-1 | Ammeline     | semapv:MappingChaining       | mapping:36a1f9244ea7641a90987c82f33c25c0c13712ee8f48207b2a0825f8a4e4e26a\|mapping:bb768f0b1e1643298f4df1a381001f6ed68fcc8fff49b371f0235b51dbab9e1e | this example needs to refer to the first two mappings in this table by mapping sameness identifier    |

From 5ef24ecb9dedc0c54af7087bec5618826c40fd0c Mon Sep 17 00:00:00 2001
From: Charles Tapley Hoyt <cthoyt@gmail.com>
Date: Mon, 25 May 2026 00:10:22 +0200
Subject: [PATCH 11/29] Update sssom_schema.yaml

---
 src/sssom_schema/schema/sssom_schema.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/sssom_schema/schema/sssom_schema.yaml b/src/sssom_schema/schema/sssom_schema.yaml
index 481da9b8..53adc31c 100644
--- a/src/sssom_schema/schema/sssom_schema.yaml
+++ b/src/sssom_schema/schema/sssom_schema.yaml
@@ -1146,7 +1146,7 @@ slots:
       - https://github.com/mapping-commons/sssom/blob/master/examples/schema/issue_tracker.sssom.tsv
   derived_from:
     description:
-      A set of CURIEs referring to mappings (i.e.,
+      A set of identifiers referring to mappings (i.e.,
       subject-predicate-object-predicate-modifier quadruple) that were used to
       derive this mapping, e.g., through mapping chaining or inversion,
       represented as CURIEs.

From 780e1061961047002e9bd7507dbf3048d998b8aa Mon Sep 17 00:00:00 2001
From: Charles Tapley Hoyt <cthoyt@gmail.com>
Date: Mon, 25 May 2026 19:29:40 +0200
Subject: [PATCH 12/29] Update src/docs/inference.md

Co-authored-by: Nico Matentzoglu <nicolas.matentzoglu@gmail.com>
---
 src/docs/inference.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/docs/inference.md b/src/docs/inference.md
index fd5a499b..b8a9cf7a 100644
--- a/src/docs/inference.md
+++ b/src/docs/inference.md
@@ -16,7 +16,7 @@ The `derived_from` field was introduced in
 reference the original subject-predicate-object-predicate modifier quadruple
 from which new mappings are inferred/derived.
 
-The following example demonstrates how the `derived_from` field when doing both
+The following example demonstrates how the `derived_from` field can be leveraged when doing both
 mapping chaining (i.e., using multiple mappings to infer a new one) and mapping
 inversion. The local unique identifiers used for mappings in this example are
 related to the proposal in

From c0130aed3d09162998808fe2cf6c6afb7a0146a9 Mon Sep 17 00:00:00 2001
From: Charles Tapley Hoyt <cthoyt@gmail.com>
Date: Mon, 25 May 2026 19:29:54 +0200
Subject: [PATCH 13/29] Update src/docs/inference.md

Co-authored-by: Nico Matentzoglu <nicolas.matentzoglu@gmail.com>
---
 src/docs/inference.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/docs/inference.md b/src/docs/inference.md
index b8a9cf7a..f0283e16 100644
--- a/src/docs/inference.md
+++ b/src/docs/inference.md
@@ -44,4 +44,4 @@ to assign CURIEs to mapping quads.
 | mesh:C000089 | ammeline      | skos:exactMatch | CHEBI:28646  | ammeline     | semapv:ManualMappingCuration |                                                                                                                                                    |                                                                                                       |
 | CHEBI:28646  | ammeline      | skos:exactMatch | cas:645-92-1 | Ammeline     | semapv:ManualMappingCuration |                                                                                                                                                    |                                                                                                       |
 | mesh:C000089 | ammeline      | skos:exactMatch | cas:645-92-1 | Ammeline     | semapv:MappingChaining       | mapping:36a1f9244ea7641a90987c82f33c25c0c13712ee8f48207b2a0825f8a4e4e26a\|mapping:bb768f0b1e1643298f4df1a381001f6ed68fcc8fff49b371f0235b51dbab9e1e | this example needs to refer to the first two mappings in this table by mapping sameness identifier    |
-| CHEBI:28646  | ammeline      | skos:exactMatch | mesh:C000089 | Ammeline     | semapv:MappingInversion      | mapping:36a1f9244ea7641a90987c82f33c25c0c13712ee8f48207b2a0825f8a4e4e26a                                                                           | this example just needs to refer to the first mappingin this table by the mapping sameness identifier |
+| CHEBI:28646  | ammeline      | skos:exactMatch | mesh:C000089 | Ammeline     | semapv:MappingInversion      | mapping:36a1f9244ea7641a90987c82f33c25c0c13712ee8f48207b2a0825f8a4e4e26a                                                                           | this example just needs to refer to the first mapping in this table by the mapping sameness identifier |

From c9337bf14f2d610bb29e47ed7a862db6f8510467 Mon Sep 17 00:00:00 2001
From: Charles Tapley Hoyt <cthoyt@gmail.com>
Date: Mon, 25 May 2026 19:30:07 +0200
Subject: [PATCH 14/29] Update src/sssom_schema/schema/sssom_schema.yaml

Co-authored-by: Nico Matentzoglu <nicolas.matentzoglu@gmail.com>
---
 src/sssom_schema/schema/sssom_schema.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/sssom_schema/schema/sssom_schema.yaml b/src/sssom_schema/schema/sssom_schema.yaml
index 53adc31c..4b23372c 100644
--- a/src/sssom_schema/schema/sssom_schema.yaml
+++ b/src/sssom_schema/schema/sssom_schema.yaml
@@ -1167,7 +1167,7 @@ slots:
           A single value can be used when inverting the mapping
           mesh:C000089-skos:exactMatch-CHEBI:28646, represented with the
           [mapping sameness identifier
-          (MSI)](https://github.com/ts4nfdi/mapping-sameness-identifier) for is
+          (MSI)](https://github.com/ts4nfdi/mapping-sameness-identifier)
           `36a1f9244ea7641a90987c82f33c25c0c13712ee8f48207b2a0825f8a4e4e26a`, to
           get mapping CHEBI:28646-skos:exactMatch-mesh:C000089
       - value: mapping:36a1f9244ea7641a90987c82f33c25c0c13712ee8f48207b2a0825f8a4e4e26a|mapping:bb768f0b1e1643298f4df1a381001f6ed68fcc8fff49b371f0235b51dbab9e1e

From 632a43595cd621de5ae730948f417404f435cc3e Mon Sep 17 00:00:00 2001
From: Charles Tapley Hoyt <cthoyt@gmail.com>
Date: Mon, 25 May 2026 19:30:17 +0200
Subject: [PATCH 15/29] Update src/docs/inference.md

Co-authored-by: Nico Matentzoglu <nicolas.matentzoglu@gmail.com>
---
 src/docs/inference.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/docs/inference.md b/src/docs/inference.md
index f0283e16..e423df40 100644
--- a/src/docs/inference.md
+++ b/src/docs/inference.md
@@ -21,7 +21,7 @@ mapping chaining (i.e., using multiple mappings to infer a new one) and mapping
 inversion. The local unique identifiers used for mappings in this example are
 related to the proposal in
 https://github.com/ts4nfdi/mapping-sameness-identifier (which currently is under
-finalization). For now, the SSSOM specification isn't currently prescribing how
+review). For now, the SSSOM specification isn't currently prescribing how
 to assign CURIEs to mapping quads.
 
 ```

From 0d86489e894fc46760d0fc0b419dd70a050f80a0 Mon Sep 17 00:00:00 2001
From: Charles Tapley Hoyt <cthoyt@gmail.com>
Date: Tue, 26 May 2026 10:40:35 +0200
Subject: [PATCH 16/29] Update inference.md

---
 src/docs/inference.md | 112 +++++++++++++++++++++++++++++++++++++-----
 1 file changed, 100 insertions(+), 12 deletions(-)

diff --git a/src/docs/inference.md b/src/docs/inference.md
index e423df40..80183924 100644
--- a/src/docs/inference.md
+++ b/src/docs/inference.md
@@ -9,6 +9,29 @@ There are several mechanisms for inference:
 - Inference via prior knowledge, which should be tagged with
   `semapv:BackgroundKnowledgeBasedMatching` as a justification
 
+## Background on Mapping Triples, Quadruples, and Records
+
+This section provides a brief background on different ways of referencing a
+mapping appearing in SSSOM.
+
+A mapping triple has a subject, predicate, and object as in (`mesh:C000089`,
+`skos:exactMatch`, `CHEBI:28646`). A mapping triple does not clarify the
+judgment on whether a triple is true or false, nor how the mapping was created.
+
+A mapping quadruple has a subject, predicate, object, and predicate modifier.
+The addition of the predicate modifier allows a mapping quadruple to explicitly
+denote the judgment on whether a triple is true or false. For example,
+(`mesh:C000089`, `skos:exactMatch`, `CHEBI:28646`, True) explicitly represents
+that the above subject, predicate, object triple is true, while (`CHEBI:10057`,
+`skos:exactMatch`, `mesh:C002563`, False) is false because `CHEBI:10057` refers
+to 9H-xanthene, a small molecule, and `mesh:C002563` refers to xanthan gum, a
+polysaccharide.
+
+A mapping record refers to the subject, predicate, object, predicate modifier,
+and all other fields in the SSSOM data model (except where otherwise stated in
+["Hashing a SSSOM mapping record"](spec-support-hashing.md), such as the
+`record_id`).
+
 ## Referring to Evidence
 
 The `derived_from` field was introduced in
@@ -16,13 +39,20 @@ The `derived_from` field was introduced in
 reference the original subject-predicate-object-predicate modifier quadruple
 from which new mappings are inferred/derived.
 
-The following example demonstrates how the `derived_from` field can be leveraged when doing both
-mapping chaining (i.e., using multiple mappings to infer a new one) and mapping
-inversion. The local unique identifiers used for mappings in this example are
-related to the proposal in
-https://github.com/ts4nfdi/mapping-sameness-identifier (which currently is under
-review). For now, the SSSOM specification isn't currently prescribing how
-to assign CURIEs to mapping quads.
+The following example demonstrates how the `derived_from` field can be leveraged
+in two scenarios:
+
+1. mapping chaining. the table contains a SKOS exact match from `mesh:C000089`
+   to `CHEBI:28646` and from `CHEBI:28646` to `cas:645-92-1`. The third row of
+   the table contains a SKOS exact match from `mesh:C000089` to `cas:645-92-1`
+   produced through mapping chaining. The `derived_from` column in this row
+   contains CURIEs referring to the
+   `mesh:C000089`-`skos:exactMatch`-`CHEBI:28646` and
+   `CHEBI:28646`-`skos:exactMatch`-`cas:645-92-1` concatenated with a pipe
+2. mapping inversion. the fourth row of the table contains a SKOS exact match
+   from `CHEBI:28646` to `mesh:C000089` produced through mapping inversion of
+   the first row of the table. The `derived_from` column in this row contains
+   the CURIE referring to the `mesh:C000089`-`skos:exactMatch`-`CHEBI:28646`
 
 ```
 # curie_map:
@@ -39,9 +69,67 @@ to assign CURIEs to mapping quads.
 #  - orcid:0000-0003-4423-4370
 ```
 
-| subject_id   | subject_label | predicate_id    | object_id    | object_label | mapping_justification        | derived_from                                                                                                                                       | comment                                                                                               |
-| ------------ | ------------- | --------------- | ------------ | ------------ | ---------------------------- | -------------------------------------------------------------------------------------------------------------------------------------------------- | ----------------------------------------------------------------------------------------------------- |
-| mesh:C000089 | ammeline      | skos:exactMatch | CHEBI:28646  | ammeline     | semapv:ManualMappingCuration |                                                                                                                                                    |                                                                                                       |
-| CHEBI:28646  | ammeline      | skos:exactMatch | cas:645-92-1 | Ammeline     | semapv:ManualMappingCuration |                                                                                                                                                    |                                                                                                       |
-| mesh:C000089 | ammeline      | skos:exactMatch | cas:645-92-1 | Ammeline     | semapv:MappingChaining       | mapping:36a1f9244ea7641a90987c82f33c25c0c13712ee8f48207b2a0825f8a4e4e26a\|mapping:bb768f0b1e1643298f4df1a381001f6ed68fcc8fff49b371f0235b51dbab9e1e | this example needs to refer to the first two mappings in this table by mapping sameness identifier    |
+| subject_id   | subject_label | predicate_id    | object_id    | object_label | mapping_justification        | derived_from                                                                                                                                       | comment                                                                                                |
+| ------------ | ------------- | --------------- | ------------ | ------------ | ---------------------------- | -------------------------------------------------------------------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------ |
+| mesh:C000089 | ammeline      | skos:exactMatch | CHEBI:28646  | ammeline     | semapv:ManualMappingCuration |                                                                                                                                                    |                                                                                                        |
+| CHEBI:28646  | ammeline      | skos:exactMatch | cas:645-92-1 | Ammeline     | semapv:ManualMappingCuration |                                                                                                                                                    |                                                                                                        |
+| mesh:C000089 | ammeline      | skos:exactMatch | cas:645-92-1 | Ammeline     | semapv:MappingChaining       | mapping:36a1f9244ea7641a90987c82f33c25c0c13712ee8f48207b2a0825f8a4e4e26a\|mapping:bb768f0b1e1643298f4df1a381001f6ed68fcc8fff49b371f0235b51dbab9e1e | this example needs to refer to the first two mappings in this table by mapping sameness identifier     |
 | CHEBI:28646  | ammeline      | skos:exactMatch | mesh:C000089 | Ammeline     | semapv:MappingInversion      | mapping:36a1f9244ea7641a90987c82f33c25c0c13712ee8f48207b2a0825f8a4e4e26a                                                                           | this example just needs to refer to the first mapping in this table by the mapping sameness identifier |
+
+For the purposes of inference, the mapping quadruple should be used:
+
+1. Mapping triples are insufficient: without the judgment of whether a mapping
+   is true or false, then an algorithm could accidentally conclude from
+   `A skos:exactMatch B` and `B (not) skos:exactMatch C` that
+   `A skos:exactMatch C`. This is why mapping triples are insufficient
+2. Full mapping records are inflexible: the SSSOM data should be flexible so if
+   additional evidence (i.e., records) for a given mapping quadruple are found,
+   then the confidence in the inferred/derived mapping (e.g., chained or
+   inverted)can be adjusted accordingly. This is possible because most chaining
+   and inversion algorithms logically operate on mapping quadruples, and not on
+   records.
+
+Note: the local unique identifiers used for mappings in this example are related
+to the proposal in https://github.com/ts4nfdi/mapping-sameness-identifier (which
+currently is under review). For now, the SSSOM specification isn't currently
+prescribing how to assign CURIEs to mapping quads.
+
+### Example with Negative Mappings
+
+The following example uses mapping chaining combine with negated mappings to
+infer a non-trivial negative mapping. This illustrates why mapping quadruples
+(i.e., subject-predicate-modifier-object) are required over mapping triples
+(i.e., subject-predicate-object).
+
+```
+# curie_map:
+#   cas:  	https://commonchemistry.cas.org/detail?cas_rn=
+#   CHEBI: http://purl.obolibrary.org/obo/CHEBI_
+#   mesh: http://id.nlm.nih.gov/mesh/
+#   orcid: https://orcid.org/
+#   semapv: https://w3id.org/semapv/vocab/
+#   skos: http://www.w3.org/2004/02/skos/core#
+#   mapping: https://example.com/mapping/
+# license: https://creativecommons.org/publicdomain/zero/1.0/
+# creator_id:
+#  - orcid:0000-0003-4423-4370
+```
+
+| subject_id | subject_label | predicate_id | predicate_modifier | object_id |
+object_label | mapping_justification | derived_from | comment | | ----------- |
+------------- | --------------- | ------------------ | ------------ |
+------------ | ---------------------------- |
+------------------------------------------------------------------------- |
+------------------------------------------------------------------------ |
+
+---
+
+| | CHEBI:10057 | 9H-xanthene | skos:exactMatch | Not | mesh:C002563 | xanthan
+gum | semapv:ManualMappingCuration | | | | CAS:92-83-1 | Xanthene |
+skos:exactMatch | | CHEBI:10057 | 9H-xanthene | semapv:ManualMappingCuration | |
+| | CAS:92-83-1 | Xanthene | skos:exactMatch | Not | mesh:C002563 | xanthan gum
+| semapv:MappingChaining | mapping:
+58f24ccfaf71431276da873c9e7b77ea61a2425e4e8b283b943542290deb292b~ | mapping:
+bb1162fb2afb1c519c0aa8be98c352061720af220e2d052c571a1fecabff9800 | this example
+uses the first two mappings in the table, imporantly, incorporating the negative
+modifier in the identifiers |

From 4a2fa7829b6f42034fe88383788f0a7ba7ed0f25 Mon Sep 17 00:00:00 2001
From: Charles Tapley Hoyt <cthoyt@gmail.com>
Date: Tue, 26 May 2026 10:42:15 +0200
Subject: [PATCH 17/29] Update sssom_schema.yaml

---
 src/sssom_schema/schema/sssom_schema.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/sssom_schema/schema/sssom_schema.yaml b/src/sssom_schema/schema/sssom_schema.yaml
index 4b23372c..fe49f9c2 100644
--- a/src/sssom_schema/schema/sssom_schema.yaml
+++ b/src/sssom_schema/schema/sssom_schema.yaml
@@ -1147,7 +1147,7 @@ slots:
   derived_from:
     description:
       A set of identifiers referring to mappings (i.e.,
-      subject-predicate-object-predicate-modifier quadruple) that were used to
+      subject-predicate-object-predicate modifier quadruple) that were used to
       derive this mapping, e.g., through mapping chaining or inversion,
       represented as CURIEs.
     range: EntityReference

From f039c5099c5f4716747dcd1bae51ff01d0d6db09 Mon Sep 17 00:00:00 2001
From: Charles Tapley Hoyt <cthoyt@gmail.com>
Date: Tue, 26 May 2026 10:47:01 +0200
Subject: [PATCH 18/29] Update inference.md

---
 src/docs/inference.md | 25 ++++++-------------------
 1 file changed, 6 insertions(+), 19 deletions(-)

diff --git a/src/docs/inference.md b/src/docs/inference.md
index 80183924..ef66ba44 100644
--- a/src/docs/inference.md
+++ b/src/docs/inference.md
@@ -70,7 +70,7 @@ in two scenarios:
 ```
 
 | subject_id   | subject_label | predicate_id    | object_id    | object_label | mapping_justification        | derived_from                                                                                                                                       | comment                                                                                                |
-| ------------ | ------------- | --------------- | ------------ | ------------ | ---------------------------- | -------------------------------------------------------------------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------ |
+|--------------|---------------|-----------------|--------------|--------------|------------------------------|----------------------------------------------------------------------------------------------------------------------------------------------------|--------------------------------------------------------------------------------------------------------|
 | mesh:C000089 | ammeline      | skos:exactMatch | CHEBI:28646  | ammeline     | semapv:ManualMappingCuration |                                                                                                                                                    |                                                                                                        |
 | CHEBI:28646  | ammeline      | skos:exactMatch | cas:645-92-1 | Ammeline     | semapv:ManualMappingCuration |                                                                                                                                                    |                                                                                                        |
 | mesh:C000089 | ammeline      | skos:exactMatch | cas:645-92-1 | Ammeline     | semapv:MappingChaining       | mapping:36a1f9244ea7641a90987c82f33c25c0c13712ee8f48207b2a0825f8a4e4e26a\|mapping:bb768f0b1e1643298f4df1a381001f6ed68fcc8fff49b371f0235b51dbab9e1e | this example needs to refer to the first two mappings in this table by mapping sameness identifier     |
@@ -115,21 +115,8 @@ infer a non-trivial negative mapping. This illustrates why mapping quadruples
 #  - orcid:0000-0003-4423-4370
 ```
 
-| subject_id | subject_label | predicate_id | predicate_modifier | object_id |
-object_label | mapping_justification | derived_from | comment | | ----------- |
-------------- | --------------- | ------------------ | ------------ |
------------- | ---------------------------- |
-------------------------------------------------------------------------- |
------------------------------------------------------------------------- |
-
----
-
-| | CHEBI:10057 | 9H-xanthene | skos:exactMatch | Not | mesh:C002563 | xanthan
-gum | semapv:ManualMappingCuration | | | | CAS:92-83-1 | Xanthene |
-skos:exactMatch | | CHEBI:10057 | 9H-xanthene | semapv:ManualMappingCuration | |
-| | CAS:92-83-1 | Xanthene | skos:exactMatch | Not | mesh:C002563 | xanthan gum
-| semapv:MappingChaining | mapping:
-58f24ccfaf71431276da873c9e7b77ea61a2425e4e8b283b943542290deb292b~ | mapping:
-bb1162fb2afb1c519c0aa8be98c352061720af220e2d052c571a1fecabff9800 | this example
-uses the first two mappings in the table, imporantly, incorporating the negative
-modifier in the identifiers |
+| subject_id  | subject_label | predicate_id    | predicate_modifier | object_id    | object_label | mapping_justification        | derived_from                                                                                                                                        | comment                                                                                                                   |
+|-------------|---------------|-----------------|--------------------|--------------|--------------|------------------------------|-----------------------------------------------------------------------------------------------------------------------------------------------------|---------------------------------------------------------------------------------------------------------------------------|
+| CHEBI:10057 | 9H-xanthene   | skos:exactMatch | Not                | mesh:C002563 | xanthan gum  | semapv:ManualMappingCuration |                                                                                                                                                     |                                                                                                                           |
+| CAS:92-83-1 | Xanthane      | skos:exactMatch |                    | CHEBI:10057  | 9H-xanthene  | semapv:ManualMappingCuration |                                                                                                                                                     |                                                                                                                           |
+| CAS:92-83-1 | Xanthene      | skos:exactMatch | Not                | mesh:C002563 | xanthan gum  | semapv:MappingChaining       | mapping:58f24ccfaf71431276da873c9e7b77ea61a2425e4e8b283b943542290deb292b~\|mapping:bb1162fb2afb1c519c0aa8be98c352061720af220e2d052c571a1fecabff9800 | this example uses the first two mappings in the table, imporantly, incorporating the negative modifier in the identifiers |

From 7093151843e693c3c88e4268792701b84ff65b91 Mon Sep 17 00:00:00 2001
From: Charles Tapley Hoyt <cthoyt@gmail.com>
Date: Tue, 26 May 2026 10:47:09 +0200
Subject: [PATCH 19/29] Update inference.md

---
 src/docs/inference.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/docs/inference.md b/src/docs/inference.md
index ef66ba44..d80a05ed 100644
--- a/src/docs/inference.md
+++ b/src/docs/inference.md
@@ -70,7 +70,7 @@ in two scenarios:
 ```
 
 | subject_id   | subject_label | predicate_id    | object_id    | object_label | mapping_justification        | derived_from                                                                                                                                       | comment                                                                                                |
-|--------------|---------------|-----------------|--------------|--------------|------------------------------|----------------------------------------------------------------------------------------------------------------------------------------------------|--------------------------------------------------------------------------------------------------------|
+| ------------ | ------------- | --------------- | ------------ | ------------ | ---------------------------- | -------------------------------------------------------------------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------ |
 | mesh:C000089 | ammeline      | skos:exactMatch | CHEBI:28646  | ammeline     | semapv:ManualMappingCuration |                                                                                                                                                    |                                                                                                        |
 | CHEBI:28646  | ammeline      | skos:exactMatch | cas:645-92-1 | Ammeline     | semapv:ManualMappingCuration |                                                                                                                                                    |                                                                                                        |
 | mesh:C000089 | ammeline      | skos:exactMatch | cas:645-92-1 | Ammeline     | semapv:MappingChaining       | mapping:36a1f9244ea7641a90987c82f33c25c0c13712ee8f48207b2a0825f8a4e4e26a\|mapping:bb768f0b1e1643298f4df1a381001f6ed68fcc8fff49b371f0235b51dbab9e1e | this example needs to refer to the first two mappings in this table by mapping sameness identifier     |
@@ -116,7 +116,7 @@ infer a non-trivial negative mapping. This illustrates why mapping quadruples
 ```
 
 | subject_id  | subject_label | predicate_id    | predicate_modifier | object_id    | object_label | mapping_justification        | derived_from                                                                                                                                        | comment                                                                                                                   |
-|-------------|---------------|-----------------|--------------------|--------------|--------------|------------------------------|-----------------------------------------------------------------------------------------------------------------------------------------------------|---------------------------------------------------------------------------------------------------------------------------|
+| ----------- | ------------- | --------------- | ------------------ | ------------ | ------------ | ---------------------------- | --------------------------------------------------------------------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------- |
 | CHEBI:10057 | 9H-xanthene   | skos:exactMatch | Not                | mesh:C002563 | xanthan gum  | semapv:ManualMappingCuration |                                                                                                                                                     |                                                                                                                           |
 | CAS:92-83-1 | Xanthane      | skos:exactMatch |                    | CHEBI:10057  | 9H-xanthene  | semapv:ManualMappingCuration |                                                                                                                                                     |                                                                                                                           |
 | CAS:92-83-1 | Xanthene      | skos:exactMatch | Not                | mesh:C002563 | xanthan gum  | semapv:MappingChaining       | mapping:58f24ccfaf71431276da873c9e7b77ea61a2425e4e8b283b943542290deb292b~\|mapping:bb1162fb2afb1c519c0aa8be98c352061720af220e2d052c571a1fecabff9800 | this example uses the first two mappings in the table, imporantly, incorporating the negative modifier in the identifiers |

From 91402478de935041a756cf134365e9783f182e4d Mon Sep 17 00:00:00 2001
From: Charles Tapley Hoyt <cthoyt@gmail.com>
Date: Tue, 26 May 2026 10:49:44 +0200
Subject: [PATCH 20/29] Update inference.md

---
 src/docs/inference.md | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/src/docs/inference.md b/src/docs/inference.md
index d80a05ed..b56dd079 100644
--- a/src/docs/inference.md
+++ b/src/docs/inference.md
@@ -115,8 +115,8 @@ infer a non-trivial negative mapping. This illustrates why mapping quadruples
 #  - orcid:0000-0003-4423-4370
 ```
 
-| subject_id  | subject_label | predicate_id    | predicate_modifier | object_id    | object_label | mapping_justification        | derived_from                                                                                                                                        | comment                                                                                                                   |
-| ----------- | ------------- | --------------- | ------------------ | ------------ | ------------ | ---------------------------- | --------------------------------------------------------------------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------- |
-| CHEBI:10057 | 9H-xanthene   | skos:exactMatch | Not                | mesh:C002563 | xanthan gum  | semapv:ManualMappingCuration |                                                                                                                                                     |                                                                                                                           |
-| CAS:92-83-1 | Xanthane      | skos:exactMatch |                    | CHEBI:10057  | 9H-xanthene  | semapv:ManualMappingCuration |                                                                                                                                                     |                                                                                                                           |
-| CAS:92-83-1 | Xanthene      | skos:exactMatch | Not                | mesh:C002563 | xanthan gum  | semapv:MappingChaining       | mapping:58f24ccfaf71431276da873c9e7b77ea61a2425e4e8b283b943542290deb292b~\|mapping:bb1162fb2afb1c519c0aa8be98c352061720af220e2d052c571a1fecabff9800 | this example uses the first two mappings in the table, imporantly, incorporating the negative modifier in the identifiers |
+| subject_id  | subject_label | predicate_id    | predicate_modifier | object_id    | object_label | mapping_justification        | derived_from                                                                                                                                        | comment                                                                                                                    |
+| ----------- | ------------- | --------------- | ------------------ | ------------ | ------------ | ---------------------------- | --------------------------------------------------------------------------------------------------------------------------------------------------- | -------------------------------------------------------------------------------------------------------------------------- |
+| CHEBI:10057 | 9H-xanthene   | skos:exactMatch | Not                | mesh:C002563 | xanthan gum  | semapv:ManualMappingCuration |                                                                                                                                                     |                                                                                                                            |
+| CAS:92-83-1 | Xanthane      | skos:exactMatch |                    | CHEBI:10057  | 9H-xanthene  | semapv:ManualMappingCuration |                                                                                                                                                     |                                                                                                                            |
+| CAS:92-83-1 | Xanthene      | skos:exactMatch | Not                | mesh:C002563 | xanthan gum  | semapv:MappingChaining       | mapping:58f24ccfaf71431276da873c9e7b77ea61a2425e4e8b283b943542290deb292b~\|mapping:bb1162fb2afb1c519c0aa8be98c352061720af220e2d052c571a1fecabff9800 | this example uses the first two mappings in the table, importantly, incorporating the negative modifier in the identifiers |

From b91b8ec8756c9a1c8570657d4833f170fed7692e Mon Sep 17 00:00:00 2001
From: Charles Tapley Hoyt <cthoyt@gmail.com>
Date: Tue, 26 May 2026 11:06:19 +0200
Subject: [PATCH 21/29] Update inference.md

---
 src/docs/inference.md | 11 +++++++----
 1 file changed, 7 insertions(+), 4 deletions(-)

diff --git a/src/docs/inference.md b/src/docs/inference.md
index b56dd079..9e76d801 100644
--- a/src/docs/inference.md
+++ b/src/docs/inference.md
@@ -25,7 +25,8 @@ denote the judgment on whether a triple is true or false. For example,
 that the above subject, predicate, object triple is true, while (`CHEBI:10057`,
 `skos:exactMatch`, `mesh:C002563`, False) is false because `CHEBI:10057` refers
 to 9H-xanthene, a small molecule, and `mesh:C002563` refers to xanthan gum, a
-polysaccharide.
+polysaccharide. By convention, mapping triples are implicitly considered to
+refer to the "true" mapping quadruple.
 
 A mapping record refers to the subject, predicate, object, predicate modifier,
 and all other fields in the SSSOM data model (except where otherwise stated in
@@ -47,12 +48,14 @@ in two scenarios:
    the table contains a SKOS exact match from `mesh:C000089` to `cas:645-92-1`
    produced through mapping chaining. The `derived_from` column in this row
    contains CURIEs referring to the
-   `mesh:C000089`-`skos:exactMatch`-`CHEBI:28646` and
-   `CHEBI:28646`-`skos:exactMatch`-`cas:645-92-1` concatenated with a pipe
+   `mesh:C000089`-`skos:exactMatch`-`CHEBI:28646`-True and
+   `CHEBI:28646`-`skos:exactMatch`-`cas:645-92-1`-True mapping quadruples,
+   concatenated with a pipe
 2. mapping inversion. the fourth row of the table contains a SKOS exact match
    from `CHEBI:28646` to `mesh:C000089` produced through mapping inversion of
    the first row of the table. The `derived_from` column in this row contains
-   the CURIE referring to the `mesh:C000089`-`skos:exactMatch`-`CHEBI:28646`
+   the CURIE referring to the
+   `mesh:C000089`-`skos:exactMatch`-`CHEBI:28646`-True quad.
 
 ```
 # curie_map:

From ece15356575b351a8a3d75864f50c4be0a6386bb Mon Sep 17 00:00:00 2001
From: Charles Tapley Hoyt <cthoyt@gmail.com>
Date: Tue, 26 May 2026 11:53:41 +0200
Subject: [PATCH 22/29] Updates based on Damien's comments

---
 src/docs/inference.md                     | 4 ++--
 src/sssom_schema/schema/sssom_schema.yaml | 3 +--
 2 files changed, 3 insertions(+), 4 deletions(-)

diff --git a/src/docs/inference.md b/src/docs/inference.md
index 9e76d801..83e97f74 100644
--- a/src/docs/inference.md
+++ b/src/docs/inference.md
@@ -94,8 +94,8 @@ For the purposes of inference, the mapping quadruple should be used:
 
 Note: the local unique identifiers used for mappings in this example are related
 to the proposal in https://github.com/ts4nfdi/mapping-sameness-identifier (which
-currently is under review). For now, the SSSOM specification isn't currently
-prescribing how to assign CURIEs to mapping quads.
+currently is under review). For now, the SSSOM specification isn't prescribing
+how to assign identifiers to mapping quadruples.
 
 ### Example with Negative Mappings
 
diff --git a/src/sssom_schema/schema/sssom_schema.yaml b/src/sssom_schema/schema/sssom_schema.yaml
index fe49f9c2..d1949e37 100644
--- a/src/sssom_schema/schema/sssom_schema.yaml
+++ b/src/sssom_schema/schema/sssom_schema.yaml
@@ -1148,8 +1148,7 @@ slots:
     description:
       A set of identifiers referring to mappings (i.e.,
       subject-predicate-object-predicate modifier quadruple) that were used to
-      derive this mapping, e.g., through mapping chaining or inversion,
-      represented as CURIEs.
+      derive this mapping, e.g., through mapping chaining or inversion.
     range: EntityReference
     multivalued: true
     slot_uri: prov:wasDerivedFrom

From 2d9a45f1761f901dd2aa70946e1d466c8405dac4 Mon Sep 17 00:00:00 2001
From: Charles Tapley Hoyt <cthoyt@gmail.com>
Date: Tue, 26 May 2026 15:12:32 +0200
Subject: [PATCH 23/29] Update src/docs/inference.md

Co-authored-by: Nico Matentzoglu <nicolas.matentzoglu@gmail.com>
---
 src/docs/inference.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/docs/inference.md b/src/docs/inference.md
index 83e97f74..60e7cc3a 100644
--- a/src/docs/inference.md
+++ b/src/docs/inference.md
@@ -101,7 +101,7 @@ how to assign identifiers to mapping quadruples.
 
 The following example uses mapping chaining combine with negated mappings to
 infer a non-trivial negative mapping. This illustrates why mapping quadruples
-(i.e., subject-predicate-modifier-object) are required over mapping triples
+(i.e., subject-predicate-object-predicate modifier) are required over mapping triples
 (i.e., subject-predicate-object).
 
 ```

From a28d899d8f0076eb58b8d845700ecee8c4068e20 Mon Sep 17 00:00:00 2001
From: Charles Tapley Hoyt <cthoyt@gmail.com>
Date: Tue, 26 May 2026 15:12:46 +0200
Subject: [PATCH 24/29] Update src/docs/inference.md

Co-authored-by: Nico Matentzoglu <nicolas.matentzoglu@gmail.com>
---
 src/docs/inference.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/docs/inference.md b/src/docs/inference.md
index 60e7cc3a..733106c0 100644
--- a/src/docs/inference.md
+++ b/src/docs/inference.md
@@ -51,7 +51,7 @@ in two scenarios:
    `mesh:C000089`-`skos:exactMatch`-`CHEBI:28646`-True and
    `CHEBI:28646`-`skos:exactMatch`-`cas:645-92-1`-True mapping quadruples,
    concatenated with a pipe
-2. mapping inversion. the fourth row of the table contains a SKOS exact match
+2. mapping inversion. The fourth row of the table contains a SKOS exact match
    from `CHEBI:28646` to `mesh:C000089` produced through mapping inversion of
    the first row of the table. The `derived_from` column in this row contains
    the CURIE referring to the

From 082a97465a48c926b8874840e59325261bdf5368 Mon Sep 17 00:00:00 2001
From: Charles Tapley Hoyt <cthoyt@gmail.com>
Date: Tue, 26 May 2026 15:12:57 +0200
Subject: [PATCH 25/29] Update src/docs/inference.md

Co-authored-by: Nico Matentzoglu <nicolas.matentzoglu@gmail.com>
---
 src/docs/inference.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/docs/inference.md b/src/docs/inference.md
index 733106c0..456a798a 100644
--- a/src/docs/inference.md
+++ b/src/docs/inference.md
@@ -43,7 +43,7 @@ from which new mappings are inferred/derived.
 The following example demonstrates how the `derived_from` field can be leveraged
 in two scenarios:
 
-1. mapping chaining. the table contains a SKOS exact match from `mesh:C000089`
+1. mapping chaining. The table contains a SKOS exact match from `mesh:C000089`
    to `CHEBI:28646` and from `CHEBI:28646` to `cas:645-92-1`. The third row of
    the table contains a SKOS exact match from `mesh:C000089` to `cas:645-92-1`
    produced through mapping chaining. The `derived_from` column in this row

From 788319d3b6d3d73232c0a03da7ab96f57e27ea72 Mon Sep 17 00:00:00 2001
From: Charles Tapley Hoyt <cthoyt@gmail.com>
Date: Tue, 26 May 2026 15:13:40 +0200
Subject: [PATCH 26/29] Update src/docs/inference.md

Co-authored-by: Nico Matentzoglu <nicolas.matentzoglu@gmail.com>
---
 src/docs/inference.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/docs/inference.md b/src/docs/inference.md
index 456a798a..69dab404 100644
--- a/src/docs/inference.md
+++ b/src/docs/inference.md
@@ -88,7 +88,7 @@ For the purposes of inference, the mapping quadruple should be used:
 2. Full mapping records are inflexible: the SSSOM data should be flexible so if
    additional evidence (i.e., records) for a given mapping quadruple are found,
    then the confidence in the inferred/derived mapping (e.g., chained or
-   inverted)can be adjusted accordingly. This is possible because most chaining
+   inverted) can be adjusted accordingly. This is possible because most chaining
    and inversion algorithms logically operate on mapping quadruples, and not on
    records.
 

From c55565250733cdb9b284529b5e7f504ac04ed7f7 Mon Sep 17 00:00:00 2001
From: Charles Tapley Hoyt <cthoyt@gmail.com>
Date: Tue, 26 May 2026 15:14:37 +0200
Subject: [PATCH 27/29] Update cas CURIEs and labels

---
 src/docs/inference.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/docs/inference.md b/src/docs/inference.md
index 69dab404..becef2c1 100644
--- a/src/docs/inference.md
+++ b/src/docs/inference.md
@@ -121,5 +121,5 @@ infer a non-trivial negative mapping. This illustrates why mapping quadruples
 | subject_id  | subject_label | predicate_id    | predicate_modifier | object_id    | object_label | mapping_justification        | derived_from                                                                                                                                        | comment                                                                                                                    |
 | ----------- | ------------- | --------------- | ------------------ | ------------ | ------------ | ---------------------------- | --------------------------------------------------------------------------------------------------------------------------------------------------- | -------------------------------------------------------------------------------------------------------------------------- |
 | CHEBI:10057 | 9H-xanthene   | skos:exactMatch | Not                | mesh:C002563 | xanthan gum  | semapv:ManualMappingCuration |                                                                                                                                                     |                                                                                                                            |
-| CAS:92-83-1 | Xanthane      | skos:exactMatch |                    | CHEBI:10057  | 9H-xanthene  | semapv:ManualMappingCuration |                                                                                                                                                     |                                                                                                                            |
-| CAS:92-83-1 | Xanthene      | skos:exactMatch | Not                | mesh:C002563 | xanthan gum  | semapv:MappingChaining       | mapping:58f24ccfaf71431276da873c9e7b77ea61a2425e4e8b283b943542290deb292b~\|mapping:bb1162fb2afb1c519c0aa8be98c352061720af220e2d052c571a1fecabff9800 | this example uses the first two mappings in the table, importantly, incorporating the negative modifier in the identifiers |
+| cas:92-83-1 | Xanthene      | skos:exactMatch |                    | CHEBI:10057  | 9H-xanthene  | semapv:ManualMappingCuration |                                                                                                                                                     |                                                                                                                            |
+| cas:92-83-1 | Xanthene      | skos:exactMatch | Not                | mesh:C002563 | xanthan gum  | semapv:MappingChaining       | mapping:58f24ccfaf71431276da873c9e7b77ea61a2425e4e8b283b943542290deb292b~\|mapping:bb1162fb2afb1c519c0aa8be98c352061720af220e2d052c571a1fecabff9800 | this example uses the first two mappings in the table, importantly, incorporating the negative modifier in the identifiers |

From 78cd6c2a214c4c37329189cd2b30c068f7ca093d Mon Sep 17 00:00:00 2001
From: Charles Tapley Hoyt <cthoyt@gmail.com>
Date: Tue, 26 May 2026 15:14:41 +0200
Subject: [PATCH 28/29] Reformat

---
 src/docs/inference.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/docs/inference.md b/src/docs/inference.md
index becef2c1..babc5633 100644
--- a/src/docs/inference.md
+++ b/src/docs/inference.md
@@ -101,8 +101,8 @@ how to assign identifiers to mapping quadruples.
 
 The following example uses mapping chaining combine with negated mappings to
 infer a non-trivial negative mapping. This illustrates why mapping quadruples
-(i.e., subject-predicate-object-predicate modifier) are required over mapping triples
-(i.e., subject-predicate-object).
+(i.e., subject-predicate-object-predicate modifier) are required over mapping
+triples (i.e., subject-predicate-object).
 
 ```
 # curie_map:

From df417498266827e34da8aca0a89e9b0c3a70e92a Mon Sep 17 00:00:00 2001
From: Charles Tapley Hoyt <cthoyt@gmail.com>
Date: Tue, 26 May 2026 15:15:57 +0200
Subject: [PATCH 29/29] Update src/docs/inference.md

Co-authored-by: Nico Matentzoglu <nicolas.matentzoglu@gmail.com>
---
 src/docs/inference.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/docs/inference.md b/src/docs/inference.md
index babc5633..bd40d43e 100644
--- a/src/docs/inference.md
+++ b/src/docs/inference.md
@@ -99,7 +99,7 @@ how to assign identifiers to mapping quadruples.
 
 ### Example with Negative Mappings
 
-The following example uses mapping chaining combine with negated mappings to
+The following example uses mapping chaining combined with negated mappings to
 infer a non-trivial negative mapping. This illustrates why mapping quadruples
 (i.e., subject-predicate-object-predicate modifier) are required over mapping
 triples (i.e., subject-predicate-object).