mapping-commons · matentzn · Aug 2, 2024 · Jul 31, 2024 · Jul 31, 2024 · Jul 31, 2024
diff --git a/mkdocs.yml b/mkdocs.yml
@@ -31,38 +31,36 @@ nav:
     - Introduction: spec-intro.md
     - Data model:
       - Introduction: spec-model.md
+      - Applying Chaining Rules: chaining-rules.md
       - LinkML documentation: linkml-index.md
+      - SSSOM profiles: sssom-profiles.md
     - Serialisations:
       - Introduction: spec-formats.md
       - SSSOM/TSV serialisation: spec-formats-tsv.md
       - OWL/RDF serialisation: spec-formats-owl.md
       - JSON serialisation: spec-formats-json.md
-  - FAQ: faq.md
   - Resources for contributors: contributing.md
   - Resources for users:
-    - Use cases: 
-      - Overview: usecases.md
+    - FAQ: faq.md
+    - Community:
+      - Use Cases: usecases.md
+      - Workshops: workshops.md
+      - Presentations: presentations.md
+    - Training materials:
+      - Overview: training.md
+      - Basic Tutorial: tutorial.md
+    - How to:
+      - Mapping Justifications: mapping-justifications.md
+      - How to use mapping predicates: mapping-predicates.md
+      - Set up a mapping registry/commons: mapping-commons.md
+      - A basic guide for the SSSOM toolkit: toolkit.md
+      - 5-Star Entity Mappings - Cheatsheet: 5star-mappings.md
+      - Matching tool implementation guide: matching-tool-implementation-guide.md
       - How to gradually enrich OMOP mappings with SSSOM: tutorials/omop-mappings.md
-    - Workshops: workshops.md
-    - Presentations: presentations.md
-    - Basic Tutorial: tutorial.md
-    - Mapping Justifications: mapping-justifications.md
-    - How to use mapping predicates: mapping-predicates.md
-    - Set up a mapping registry/commons: mapping-commons.md
-    - Overview of Chaining Rules: chaining_rules.md
-    - A basic guide for the SSSOM toolkit: toolkit.md
-    - 5-Star Entity Mappings - Cheatsheet: 5star-mappings.md
-    - Update schema/context and release: update.md
-    - Matching tool implementation guide: matching-tool-implementation-guide.md
-    - SSSOM profiles: sssom-profiles.md
-    - Glossary: glossary.md
-  - 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/"
+    - Reference:
+      - Glossary: glossary.md
+  - Related documentation: related-documentation.md
+  - Funding: funding.md
 
 site_url: https://mapping-commons.github.io/sssom/
 repo_url: https://github.com/mapping-commons/sssom/

diff --git a/src/docs/chaining_rules.md → src/docs/chaining-rules.md b/src/docs/chaining_rules.md → src/docs/chaining-rules.md
diff --git a/src/docs/funding.md b/src/docs/funding.md
@@ -0,0 +1,51 @@
+## Funding
+
+The Simple Standard for Sharing Ontological Mappings (SSSOM) is a community-driven project which has received support from many different sources.
+We list the most important ones in the following.
+
+### Volunteering efforts
+
+A huge fraction of the work on SSSOM has been done by volunteers without dedicated grant support.
+We hereby acknowledge their contributions as being absolutely essential. A selection of amazing contributions (by no means exhaustive):
+
+- The development of [SSSOM Java](https://incenp.org/dvlpt/sssom-java/)
+- Hundreds of careful contributions to discussions on the [SSSOM issue tracker](https://github.com/mapping-commons/sssom/issues)
+- The first draft of the [Mapping Registry Cookiecutter](https://github.com/mapping-commons/mapping-commons-cookiecutter)
+- We try to keep track of other [Community efforts here](https://github.com/mapping-commons/sssom/discussions/318)
+
+### Phenomics First (NIH / NHGRI #1RM1HG010860-01)
+
+A lot of the groundwork of SSSOM was done to support a disease mapping project as part of the [Mondo Disease Ontology](https://github.com/monarch-initiative/mondo),
+which included, but was not limited to:
+
+- Creation of a basic metadata model
+- Implementation of validation and parsing methods in [sssom-py](https://github.com/mapping-commons/sssom-py)
+- Generating [training materials](../training.md)
+- Organising [workshops](../workshops.md)
+- Outreach activties to clinical communities such as [OHDSI](https://www.ohdsi.org/)
+
+The grant was awared to members of the Monarch Initiative.
+
+### Monarch (NIH / OD #5R24OD011883)
+
+To support development of cross-species mappings and knowledge graph integration for the [Monarch Knowledge Graph](https://monarchinitiative.org/),
+a few new features had to be supported:
+
+- Groundwork for the [Semantic Mapping Vocabulary](https://github.com/mapping-commons/semantic-mapping-vocabulary) which contains, for example, cross-species mapping properties.
+- The advancement of the concepts and tools behind the "Mapping Commons", including supporting the development of the [Mapping Registry Cookiecutter](https://github.com/mapping-commons/mapping-commons-cookiecutter)
+- Various improvements to the SSSOM metadata model, including the introduction of curation rules.
+- The [OxO2 SSSOM mapping browser](https://github.com/EBISPOT/oxo2)
+
+The grant was awared to members of the Monarch Initiative.
+
+### Bosch Gift to LBNL
+
+A lot of the work on tooling was supported by a Bosch Gift to the Lawrence Berkely National Laboratory (Chris Mungall group). We thank Bosch for their generous support which helped us with the following:
+
+- Implementation of conversion and testing methods in [sssom-py](https://github.com/mapping-commons/sssom-py)
+- The development of training materials
+- The development of specialised matching tools such as [OAK lexmatch](https://incatools.github.io/ontology-access-kit/guide/mappings.html) which provided the first implementation of the SSSOM standard in a matching tool.
+
+### DARPA: Young Faculty Award W911NF2010255
+
+A huge amount of refactoring of [sssom-py](https://github.com/mapping-commons/sssom-py) and development best practices, as well as training materials, was provided through this grant (awared to Benjamin M. Gyori). Other contributions include work on the [Semantic mapping reasoner and assembler](https://github.com/biopragmatics/semra)
diff --git a/src/docs/index.md b/src/docs/index.md
@@ -129,28 +129,5 @@ You can also reach us in the [OBO Foundry Slack](https://obo-communitygroup.slac
 
 ## Acknowledgements
 
-### Funding
-
-#### Phenomics First
-
-Parts of this work were funded by Phenomics First (NIH / NHGRI #1RM1HG010860-01):
-
-- design of the specification;
-- integration of `sssom-py` into Mondo;
-- development of the `sssom-py` command-line interface.
-
-#### Bosch Gift to LBNL
-
-Parts of this work were funded by a gift from [Bosch](https://www.bosch.com/) to the Lawrence Berkely National Laboratories (LBNL):
-
-- `sssom-py`:
-    - IO functionality,
-    - file format converters,
-    - testing framework,
-    - deployment on the [Python Package Index](https://pypi.org/);
-- SSSOM documentation (this document).
-
-### Significant contributions
-
-- The [Link Model Language (LinkML) project](https://github.com/linkml) (used to define the data model).
-- Harvard Medical School (through significant contributions of Charlie Hoyt, including refactoring of sssom-py, release and quality control infrastructure).
+- See [Funding](funding.md) for details on direct contributions.
+- We thank the [Link Model Language (LinkML) project](https://github.com/linkml) and team for their great framework and the LinkML team for their support developing the schema.
diff --git a/src/docs/related-documentation.md b/src/docs/related-documentation.md
@@ -0,0 +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/"
diff --git a/src/docs/training.md b/src/docs/training.md
@@ -0,0 +1,27 @@
+## SSSOM Training materials
+
+- [Elevator pitch](#elevator)
+- [Tutorials and Guides](#guides)
+- [Related tutorials](#related)
+
+<a id="elevator"></a>
+
+### Elevator pitch
+
+<iframe width="560" height="315" src="https://www.youtube.com/embed/T-YP-Lv9k2s?si=tN9lHUFcovkyvm6z" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" referrerpolicy="strict-origin-when-cross-origin" allowfullscreen></iframe>
+
+<a id="guides"></a>
+
+### Tutorials and Guides
+
+- [Mapping curation with SSSOM](https://oboacademy.github.io/obook/tutorial/sssom-tutorial/)
+- [Are these two entities the same? A guide.](https://oboacademy.github.io/obook/howto/are-two-entities-the-same/). An important tutorial that explains that it is not directly possible to determine if two things are the same across ontologies, but its still worth doing when explicitly recording the rationale.
+- [Linking across vocabularies: Semantic Entity Matching](https://oboacademy.github.io/obook/lesson/entity-matching/): Entity matching is the process of establishing a link between an identifier in one semantic space to an identifier in another. There are many cultures of thought around entity matching, including Ontology Matching, Entity Resolution and Entity Linking.
+
+<a id="related"></a>
+
+### Related tutorials
+
+- [Introduction to processing mappings with SSSOM and sssom-py CLI](https://oboacademy.github.io/obook/tutorial/sssom-toolkit/)
+- [Introduction to matching with OAK lexmatch](https://oboacademy.github.io/obook/tutorial/lexmatch-tutorial/)
+- [Curating Semantic Mappings with Biomappings](https://oboacademy.github.io/obook/tutorial/biomappings/)
diff --git a/src/docs/update.md b/src/docs/update.md