Merge branch 'master' into add-support-for-extension-slots

CHANGELOG.md

@@ -4,6 +4,7 @@
 
 - Add the concept of "propagatable slots".
 - Add the concept of "extension slots".
+- Add the entity reference `sssom:NoTermFound` to express the concept of an "unmapped entity" ([issue](https://github.com/mapping-commons/sssom/issues/28))
 - Replace `semantic_similarity_score` with `similarity_score` and `semantic_similarity_measure` with `similarity_measure` in the data model ([issue](https://github.com/mapping-commons/sssom/issues/385))
 
 ## SSSOM version 0.15.1

examples/schema/no_term_found.sssom.tsv

@@ -0,0 +1,16 @@
+#curie_map:
+#  HP: http://purl.obolibrary.org/obo/HP_
+#  MP: http://purl.obolibrary.org/obo/MP_
+#  obo: http://purl.obolibrary.org/obo/
+#  orcid: https://orcid.org/
+#mapping_set_id: https://w3id.org/sssom/commons/examples/no_term_found.sssom.tsv
+#creator_id:
+#  - orcid:0000-0002-7356-1779
+#subject_source: obo:hp
+#object_source: obo:mp
+#license: "https://creativecommons.org/publicdomain/zero/1.0/"
+#mapping_provider: "https://w3id.org/sssom/core_team"
+#comment: This is an example file for the SSSOM for illustration only. Its contents are entirely fabricated.
+subject_id	predicate_id	object_id	mapping_justification
+HP:0009124	skos:exactMatch	MP:0000003	semapv:ManualMappingCuration
+HP:0000411	skos:exactMatch	sssom:NoTermFound	semapv:ManualMappingCuration

src/docs/create-mapping-commons.md

@@ -1,17 +1,20 @@
-# Getting started
+## Getting started
 
 - First, create a virtual environment of your choice (anaconda, venv, pyenv, poetry etc.). If you need assistance with virtual environments, [here's a guide](https://berkeleybop.github.io/best_practice/python_environments) to help you setup pyenv and use poetry with it.
 - Install the [cruft](https://github.com/cruft/cruft) package. Cruft enables keeping projects up-to-date with future updates made to this original template.
 
     ```
     pip install cruft
     ```
+
 - Create a project using the [mapping-commons-cookiecutter](https://github.com/mapping-commons/mapping-commons-cookiecutter) template.
+
     ```
     cruft create https://github.com/mapping-commons/mapping-commons-cookiecutter
     ```
 
 This kickstarts an interactive session where you declare the following:
+
 - `project_name`: Name of the project. [defaults to: my-commons-name]
 - `github_org`: Name of the github org the project belongs to. [defaults to: my-org]
 - `project_description`: Description of the project [defaults to: 'This is the project description.']
@@ -20,13 +23,14 @@ This kickstarts an interactive session where you declare the following:
 - `yo`: Choose from [1]: Yes, [2]: No [**TEST OPTION FOR NOW**]
 - `license`: Choose from [1]: Yes, [2]: No [**TEST OPTION FOR NOW**]
 
-# What does this do?
+## What does this do?
 
 The following files and directories are autogenerated in the project:
-# TODO
 
-# Version control
-## GitHub
+### TODO
+
+## Version control
+### GitHub
 
 1. Go to [https://github.com/new] and follow the instructions, being sure to
    NOT add a README or .gitignore file (this cookiecutter template will take
@@ -40,27 +44,31 @@ The following files and directories are autogenerated in the project:
    git push -u origin main
    ```
 
-## GitLab
+### GitLab
 
-### TODO
+#### TODO
 
-# Future updates to the project's boilerplate code
+## Future updates to the project's boilerplate code
 
 In order to be up-to-date with the template, first check if there is a mismatch between the project's boilerplate code and the template by running:
+
 ```
 cruft check
 ```
 
 This indicates if there is a difference between the current project's boilerplate code and the latest version of the project template. If the project is up-to-date with the template:
+
 ```
 SUCCESS: Good work! Project's cruft is up to date and as clean as possible :).
 ```
 
 Otherwise, it will indicate that the project's boilerplate code is not up-to-date by the following:
+
 ```
 FAILURE: Project's cruft is out of date! Run `cruft update` to clean this mess up.
 ```
 
+
 For viewing the difference, run `cruft diff`. This shows the difference between the project's boilerplate code and the template's latest version.
 
-After running `cruft update`, the project's boilerplate code will be updated to the latest version of the template.
+After running `cruft update`, the project's boilerplate code will be updated to the latest version of the template.

src/docs/presentations.md

@@ -1,5 +1,11 @@
 # Presentations
 
+## A Simple Standard for Ontological Mappings 2024: The case for prioritising 5-Star mappings (Every Cure, internal seminar) 
+
+- August 1<sup>st</sup>, 2024, virtual
+- Talk to [Every Cure](https://everycure.org/) technical team (Knowledge Sharing Series) to make the case for prioritising the collection of mapping provenance.
+- [Slides](https://docs.google.com/presentation/d/1_KkSeZcKyzsQVlZe8qkl7iEvii3HX0QKR58uvbirTDM/edit)
+
 ## Workshop on Prefixes, CURIEs, and IRIs 2023
 
 - November 27<sup>th</sup>, 2023, virtual

src/docs/related-documentation.md

@@ -1,8 +1,8 @@
 ## Related documentation
 
-- [SSSOM Toolkit](https://mapping-commons.github.io/sssom-py/index.html#)
-- [SSSOM Java](https://incenp.org/dvlpt/sssom-java/)
-- Semantic Mapping Vocabulary (SEMAPV): "https://mapping-commons.github.io/semantic-mapping-vocabulary/"
-- LinkML: "https://linkml.io/linkml/"
-- OBO Academy: "https://oboacademy.github.io/obook/"
-- Monarch Initiative: "https://monarch-initiative.github.io/monarch-documentation/"
+- [SSSOM Toolkit](https://mapping-commons.github.io/sssom-py/index.html#): A toolkit and library for processing SSSOM files in Python
+- [SSSOM Java](https://incenp.org/dvlpt/sssom-java/): A toolkit and library for processing SSSOM files in Java
+- [Semantic Mapping Vocabulary (SEMAPV)](https://mapping-commons.github.io/semantic-mapping-vocabulary/): The mapping vocabulary used for mapping justifications and specialised mapping predicates
+- [LinkML](https://linkml.io/linkml/): The modelling framework used by SSSOM
+- [OBO Academy](https://oboacademy.github.io/obook/): Ontology and mapping related training materials
+- [Monarch Initiative](https://monarch-initiative.github.io/monarch-documentation/): Knowledge Graph related products supported by the Monarch Initiatives, including many tools using and producing SSSOM

src/docs/spec-model.md

@@ -82,6 +82,22 @@ In addition, predicates from the following sources MAY also be encouraged:
 * any relation from the [Relation Ontology (RO)](https://obofoundry.org/ontology/ro.html);
 * any relation under [skos:mappingRelation](http://www.w3.org/2004/02/skos/core#mappingRelation) in the [Semantic Mapping Vocabulary](https://mapping-commons.github.io/semantic-mapping-vocabulary/).
 
+
+## Representing unmapped entities
+
+The special value `sssom:NoTermFound` MAY be used as the `object_id` of a mapping to explicitly state that the subject of said mapping cannot be mapped to any entity in the domain represented by the `object_source` slot.
+
+Likewise, the `sssom:NoTermFound` value MAY be used as the `subject_id` of a mapping to state that the object of said mapping cannot be mapped to any entity in the domain represented by the `subject_source` slot.
+
+When that special value is used as the `subject_id` (respectively `object_id`), the `subject_source` (respectively `object_source`) slot SHOULD be defined.
+
+The `sssom:NoTermFound` value MUST NOT be used in any other slot than `subject_id` or `object_id`.
+
+The meaning of the NOT predicate modifier in a mapping that refers to `sssom:NoTermFound` is unspecified.
+
+When computing cardinality values (to fill the `mapping_cardinality` slot), mappings that refer to `sssom:NoTermFound` MUST be ignored.
+
+
 ## Non-standard slots
 
 <a id="non-standard-slots"></a>

src/sssom_schema/schema/sssom_schema.yaml

@@ -186,19 +186,7 @@ slots:
     range: EntityReference
     required: true
     slot_uri: owl:annotatedProperty
-    examples:
-      - value: skos:exactMatch
-  predicate_modifier:
-    description: A modifier for negating the prediate. See https://github.com/mapping-commons/sssom/issues/40 for discussion
-    range: predicate_modifier_enum
-    see_also:
-      - https://github.com/mapping-commons/sssom/issues/107
-    examples:
-      - value: Not
-        description: Negates the predicate, see documentation of predicate_modifier_enum
-  predicate_label:
-    description: The label of the predicate/relation of the mapping
-    range: string
+
     examples:
       - value: owl:sameAs
         description: The subject and the object are instances (owl individuals), and the two instances are the same.
@@ -224,6 +212,20 @@ slots:
         description: Two terms are related in some way. The meaning is frequently consistent across a single set of mappings. Note this property is often overloaded even where the terms are of a different nature (e.g. interpro2go)
       - value: rdfs:seeAlso
         description: The subject and the object are associated in some unspecified way. The object IRI often resolves to a resource on the web that provides additional information.
+  predicate_modifier:
+    description: A modifier for negating the predicate. See https://github.com/mapping-commons/sssom/issues/40 for discussion
+    range: predicate_modifier_enum
+    see_also:
+      - https://github.com/mapping-commons/sssom/issues/107
+    examples:
+      - value: Not
+        description: Negates the predicate, see documentation of predicate_modifier_enum
+  predicate_label:
+    description: The label of the predicate/relation of the mapping
+    range: string
+    examples:
+      - value: has cross-reference
+        description: The label of the oboInOwl:hasDbXref property to represent cross-references.
   predicate_type:
     description: The type of entity that is being mapped.
     range: entity_type_enum
@@ -806,3 +808,12 @@ classes:
         description: Indicates whether a slot can be propagated from a mapping
           down to individual mappings.
         range: boolean
+  NoTermFound:
+    class_uri: sssom:NoTermFound
+    description: sssom:NoTermFound can be used in place of a subject_id or object_id
+      when the corresponding entity could not be found. It SHOULD be used in conjuction with
+      a corresponding subject_source or object_source to signify where the term was not found.
+    see_also:
+      - https://github.com/mapping-commons/sssom/issues/28
+      - https://github.com/mapping-commons/sssom/blob/master/examples/schema/no_term_found.sssom.tsv
+