diff --git a/mkdocs.yml b/mkdocs.yml index 90d6f29e..ed017174 100644 --- 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 b/src/docs/chaining-rules.md similarity index 100% rename from src/docs/chaining_rules.md rename to src/docs/chaining-rules.md diff --git a/src/docs/funding.md b/src/docs/funding.md new file mode 100644 index 00000000..8cbc69c9 --- /dev/null +++ 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 index 63c8b0d4..eda57981 100644 --- 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 new file mode 100644 index 00000000..3c78e2c4 --- /dev/null +++ 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 new file mode 100644 index 00000000..3ed15dd0 --- /dev/null +++ b/src/docs/training.md @@ -0,0 +1,27 @@ +## SSSOM Training materials + +- [Elevator pitch](#elevator) +- [Tutorials and Guides](#guides) +- [Related tutorials](#related) + + + +### Elevator pitch + + + + + +### 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. + + + +### 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/) \ No newline at end of file diff --git a/src/docs/update.md b/src/docs/update.md deleted file mode 100644 index 36402bab..00000000 --- a/src/docs/update.md +++ /dev/null @@ -1,10 +0,0 @@ -## Final process - -1. Finish your edits and merge them into master -2. Rebuild the LinkML model using the [“build” action](https://github.com/mapping-commons/sssom/blob/master/.github/workflows/build.yml) -3. Create a [GitHub release](https://github.com/mapping-commons/sssom/releases) - - This will automatically trigger a PyPI release using [this action](https://github.com/mapping-commons/sssom/blob/master/.github/workflows/pypi-publish.yaml), of the sssom_schema module - - The context file is packaged and delivered to projects that depend on `sssom-schema`. -4. Updating sssom-py - 1. After the pypi release is completed, update sssom-schema dependency using `poetry update sssom-schema`. The new context is available and accessible via `pkg_resources`. - 1. Release `sssom-py` using the same method as `sssom-schema` above. \ No newline at end of file