mapping-commons · gouttegd · Jul 11, 2024 · Apr 3, 2024 · Apr 7, 2024 · Apr 14, 2024
diff --git a/Makefile b/Makefile
@@ -89,7 +89,7 @@ $(DOCDIR):
 
 gendoc: $(DOCDIR)
 	cp -rf $(SRC)/docs/* $(DOCDIR) ; \
-	$(RUN) gen-doc -d $(DOCDIR) $(SOURCE_SCHEMA_PATH) --template-directory $(TEMPLATE_DIR)
+	$(RUN) gen-doc -d $(DOCDIR) $(SOURCE_SCHEMA_PATH) --template-directory $(TEMPLATE_DIR) --index-name linkml-index
 
 testdoc: gendoc serve
 

diff --git a/mkdocs.yml b/mkdocs.yml
@@ -25,16 +25,20 @@ markdown_extensions:
       emoji_index: !!python/name:materialx.emoji.twemoji
       emoji_generator: !!python/name:materialx.emoji.to_svg
 nav:
-  - Home: home.md
-  - About SSSOM: about.md
-  - Specification: index.md
-  - Overview: spec.md
+  - Home: index.md
+  - Introduction: introduction.md
+  - Specification:
+    - Introduction: spec-intro.md
+    - Data model:
+      - Introduction: spec-model.md
+      - LinkML documentation: linkml-index.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
-  - Credits: credits.md
-  - Contact us: contact.md
-  - Resources for contributors:
-    - How to contribute?: contributing.md
-    - Code of Conduct: code_of_conduct.md
+  - Resources for contributors: contributing.md
   - Resources for users:
     - Use cases: 
       - Overview: usecases.md

diff --git a/poetry.lock b/poetry.lock
diff --git a/pyproject.toml b/pyproject.toml
@@ -10,11 +10,11 @@ authors = [
 license = "MIT"
 
 [tool.poetry.dependencies]
-python = "^3.8"
+python = "^3.8.1"
 linkml-runtime = "*"
 
 [tool.poetry.dev-dependencies]
-linkml = "^1.6.2"
+linkml = "^1.7.0"
 mkdocs-material = "^8.2.8"
 mkdocs-mermaid2-plugin = "^1.1.1"
 

diff --git a/src/docs/about.md b/src/docs/about.md
diff --git a/src/docs/code_of_conduct.md b/src/docs/code_of_conduct.md
diff --git a/src/docs/contact.md b/src/docs/contact.md
diff --git a/src/docs/contributing.md b/src/docs/contributing.md
@@ -1,4 +1,4 @@
 # Contributing to SSSOM
 
 - [Contribution guidelines](https://github.com/mapping-commons/sssom/blob/master/CONTRIBUTING.md)
-- [Code of Conduct](https://github.com/mapping-commons/sssom/blob/master/CODE_OF_CONDUCT.md)
+- [Code of Conduct](https://github.com/mapping-commons/sssom/blob/master/CODE_OF_CONDUCT.md)
diff --git a/src/docs/credits.md b/src/docs/credits.md
diff --git a/src/docs/home.md b/src/docs/home.md
diff --git a/src/docs/index.md b/src/docs/index.md
@@ -0,0 +1,151 @@
+# Simple Standard for Sharing Ontological Mappings (SSSOM)
+
+![SSSOM banner](images/sssom-banner.png)
+
+**SSSOM** is the Simple Standard for Sharing Ontological Mappings. It comprises three distinct components that are intended to be used together to facilitate the exchange of semantic mappings:
+
+1. a machine-readable and extensible vocabulary to describe metadata of mappings;
+2. a data model to represent mappings and their associated metadata;
+3. several file formats to represent sets of mappings on disk and on the network.
+
+Beyond defining the standard itself, the **SSSOM Core Team** also aims to implement open and community-driven collaborative workflows designed to evolve the standard continuously to address changing requirements and mapping practices, and to provide reference tools and software libraries for working with the standard.
+
+## SSSOM at a glance
+
+### Basic concepts
+
+The [data model](spec-model.md) of SSSOM is centered around two fundamental concepts: mappings and mapping sets.
+
+A **SSSOM mapping** is a statement that there is a correspondence of some sort between two semantic entities. It comprises two components:
+
+1. The **core mapping** (or **raw mapping**), which is a triple `<subject, predicate, object>` that represents the correspondence itself between a subject entity, for example a class in an ontology, and an object entity, for example an identifier in some database, via a semantic mapping predicate, for example `skos:exactMatch`.
+2. **Metadata** that provide supplementary pieces of information about the core mapping. This notably includes information pertaining to the *provenance* of the statement (for example, who emitted the statement, in other words who decided that the subject and the object should be mapped) and its *justification* (why should the subject and the object be mapped).
+
+A **SSSOM mapping set** is a collection of SSSOM mappings, with its own metadata.
+
+### The SSSOM/TSV format
+
+The main format proposed by the SSSOM standard to exchange mapping sets is the [SSSOM/TSV format](spec-formats-tsv.md). Here is a basic example of a file in that format:
+
+```
+#curie_map:
+#  HP: "http://purl.obolibrary.org/obo/HP_"
+#  MP: "http://purl.obolibrary.org/obo/MP_"
+#license: "https://creativecommons.org/publicdomain/zero/1.0/"
+#title: "Sample mapping set"
+subject_id	subject_label	predicate_id	object_id	object_label	mapping_justification
+HP:0008551	Microtia	skos:exactMatch	MP:0000018	small ears	semapv:LexicalMatching
+HP:0000411	Protruding ear	skos:exactMatch	MP:0000021	prominent ears	semapv:LexicalMatching
+```
+
+### Quick links
+
+**General**
+
+- [GitHub page](https://github.com/mapping-commons/sssom)
+- [Detailed description](introduction.md)
+- [Formal specification](spec-intro.md)
+
+**Publications**
+
+- [A Simple Standard for Sharing Ontological Mappings (SSSOM)](https://doi.org/10.1093/database/baac035) (initial publication in _Database_)
+- [A Simple Standard for Ontological Mappings 2022: Updates of data model and outlook](https://zenodo.org/record/7672104) (paper and presentation at the Ontology Matching Workshop 2022)
+- [A Simple Standard for Ontological Mappings 2023: Updates on data model, collaborations and tooling](https://zenodo.org/record/8202395) (paper and presentation at the Ontology Matching Workshop 2023)
+- [Other presentations](presentations.md)
+
+**Related software**
+
+- [SSSOM Toolkit](https://mapping-commons.github.io/sssom-py/) (reference implementation of the standard, in Python)
+
+## The SSSOM Core Team
+
+### Contact
+
+The preferred way to contact the SSSOM team is through the [issue tracker](https://github.com/mapping-commons/issues) (for problems with SSSOM) or the [GitHub discussion forums](https://github.com/mapping-commons/sssom/discussions) (for general questions).
+
+You can find any of the members of the SSSOM core team [on GitHub](https://github.com/orgs/mapping-commons/teams/sssom-core). Their GitHub profiles usually also provide email addresses.
+
+You can also reach us in the [OBO Foundry Slack](https://obo-communitygroup.slack.com/archives/C01DP18L5GW), in the `#sssom` channel.
+
+### Documentation/specification editors
+
+* [Nicolas Matentzoglu](https://orcid.org/0000-0002-7356-1779) (Semanticly Ltd; [@matentzn](https://github.com/matentzn))
+* [Chris Mungall](https://orcid.org/0000-0002-6601-2165) (LBL)
+* [Ernesto Jimenez-Ruiz](https://orcid.org/0000-0002-9083-4599) (City, University of London)
+* [John Graybeal](https://orcid.org/0000-0001-6875-5360) (Stanford)
+* [William Duncan](https://orcid.org/0000-0001-9625-1899) (LBL)
+* [David Osumi-Sutherland](https://orcid.org/0000-0002-7073-9172) (EMBL-EBI)
+* [Simon Jupp](https://orcid.org/0000-0002-0643-3144) (SciBite)
+* [James McLaughlin](https://orcid.org/0000-0002-8361-2795) (EMBL-EBI)
+* [Henriette Harmse](https://orcid.org/0000-0001-7251-9504) (EMBL-EBI)
+* [Tiffany Callahan](https://orcid.org/0000-0002-8169-9049) ([@callahantiff](https://github.com/callahantiff))
+* [Charlie Hoyt](https://orcid.org/0000-0003-4423-4370) (Harvard Medical School; [@cthoyt](https://github.com/cthoyt))
+* [Thomas Liener](https://orcid.org/0000-0003-3257-9937) (Pistoia Alliance)
+* [Harshad Hegde](https://orcid.org/0000-0002-2411-565X) (LBL)
+
+### Contributors
+
+* [Alasdair Gray](https://orcid.org/0000-0002-5711-4872)
+* [Alex Wagner](https://orcid.org/0000-0002-2502-8961)
+* [Amelia L. Hoyt](https://orcid.org/0000-0003-1307-2508)
+* [Andrew Williams](https://orcid.org/0000-0002-0692-412X)
+* [Anne Thessen](https://orcid.org/0000-0002-2908-3327)
+* [Benjamin M. Gyori](https://orcid.org/0000-0001-9439-5346)
+* [Bill Baumgartner](https://orcid.org/0000-0001-6717-5313)
+* [Christopher Chute](https://orcid.org/0000-0001-5437-2545)
+* [Chris T. Evelo](https://orcid.org/0000-0002-5301-3142)
+* [Damion Dooley](https://orcid.org/0000-0002-8844-9165)
+* [Davera Gabriel](https://orcid.org/0000-0001-9041-4597)
+* [Harold Solbrig](https://www.wikidata.org/wiki/Q44607574)
+* [HyeongSik Kim](https://orcid.org/0000-0002-3002-9838)
+* [Ian Harrow](https://orcid.org/0000-0003-0109-0522)
+* [James Malone](https://orcid.org/0000-0002-1615-2899)
+* [James Overton](https://orcid.org/0000-0001-5139-5557)
+* [James P. Balhoff](https://orcid.org/0000-0002-8688-6599)
+* [James Stevenson](https://orcid.org/0000-0002-2568-6163)
+* [Jiao Dahzi](https://orcid.org/0000-0001-5052-3836)
+* [Joe Flack](https://orcid.org/0000-0002-2906-7319)
+* [Jooho Lee](https://orcid.org/0000-0002-2955-3405)
+* [Julie McMurry](https://orcid.org/0000-0002-9353-5498)
+* [Kori Kuzma](https://orcid.org/0000-0002-9954-7449)
+* [Kristin Kostka](https://orcid.org/0000-0003-2595-8736)
+* [Lauren Chan](https://orcid.org/0000-0002-7463-6306)
+* [Melissa Haendel](https://orcid.org/0000-0001-9114-8737)
+* [Monica Munoz-Torres](https://orcid.org/0000-0001-8430-6039)
+* [Nicole Vasilevsky](https://orcid.org/0000-0001-5208-3432)
+* [Nomi Harris](https://orcid.org/0000-0001-6315-3707)
+* [Núria Queralt-Rosinach](https://orcid.org/0000-0003-0169-8159)
+* [Sabrina Toro](https://orcid.org/0000-0002-4142-7153)
+* [Sebastian Koehler](https://orcid.org/0000-0002-5316-1399)
+* [Shahim Essaid](https://orcid.org/0000-0003-2338-2550)
+* [Sierra Moxon](https://orcid.org/0000-0002-8719-7760)
+* [Sue Bello](https://orcid.org/0000-0003-4606-0597)
+* [Tim Putman](https://orcid.org/0000-0002-4291-0737)
+
+## 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).