diff --git a/src/docs/index.md b/src/docs/index.md index eda57981..3d967114 100644 --- a/src/docs/index.md +++ b/src/docs/index.md @@ -2,26 +2,27 @@ ![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: +The Simple Standard for Sharing Ontological Mappings (SSSOM) is a community-driven standard designed to facilitate the exchange and integration of semantic entity mappings. +As data interoperability becomes increasingly crucial across various domains, SSSOM provides a standardized format to share mappings, enabling researchers and developers to more easily connect and utilize diverse datasets. +By establishing a common framework, SSSOM enhances the consistency, quality, and discoverability of mappings, thereby supporting more effective data integration and analysis. -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. +- **Standardization**: SSSOM provides a unified format for representing semantic, or ontological, mappings, making it easier for different systems and organizations to exchange mapping data consistently. +- **Interoperability**: By using SSSOM, data from diverse sources can be integrated more seamlessly, allowing for improved data analysis and research across various fields, including biology, healthcare, and information technology. -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. +Beyond defining the standard itself, the **SSSOM Core Team** and the SSSOM community also develop reference tools and software libraries for working with the standard. -## SSSOM at a glance +## SSSOM at a glance: Model and Exchange Format -### Basic concepts +### Basic model 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: +A **SSSOM mapping** is a statement that there is a correspondence between two semantic entities. It comprises two components: 1. The **core mapping** (or **raw mapping**), which is a triple `` 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). +2. **Metadata** that provide supplementary pieces of information about the core mapping. This notably includes information about the *provenance* of the statement (for example, who authored the statement), the *confidence* with which the mappings holds, and its *justification* (a reason that supports the fidelity of the mapping between the subject and the object, such as _expert review_, or _exact lexical matching_ on the entities' primary names). -A **SSSOM mapping set** is a collection of SSSOM mappings, with its own metadata. +A **SSSOM mapping set** is a collection of SSSOM mappings. Mapping sets can also be associated with metadata, such as license statements, or a description. ### The SSSOM/TSV format @@ -60,7 +61,8 @@ KF_FOOD:F004 braeburn skos:broadMatch FOODON:00002473 apple (whole) semapv:Manua **Related software** -- [SSSOM Toolkit](https://mapping-commons.github.io/sssom-py/) (reference implementation of the standard, in Python) +- [sssom-py](https://mapping-commons.github.io/sssom-py/) (reference implementation of the standard, a toolkit and API for processing mappings, written in Python) +- [SSSOM-Java](https://incenp.org/dvlpt/sssom-java/) (an implementation of the SSSOM standard for the Java language) ## The SSSOM Core Team @@ -72,21 +74,32 @@ You can find any of the members of the SSSOM core team [on GitHub](https://githu You can also reach us in the [OBO Foundry Slack](https://obo-communitygroup.slack.com/archives/C01DP18L5GW), in the `#sssom` channel. +### Steering committee + +The Steering committee is a self-appointed group of SSSOM contributors, whose aim is to drive the evolution of the standard and coordinate community contributions. + +* [Nicolas Matentzoglu](https://orcid.org/0000-0002-7356-1779) (Semanticly, Independent Consultant; [@matentzn](https://github.com/matentzn)) +* [Damien Goutte-Gattat](https://orcid.org/0000-0002-6095-8718) (Flybase) +* [Harshad Hegde](https://orcid.org/0000-0002-2411-565X) (LBNL) +* [Chris Mungall](https://orcid.org/0000-0002-6601-2165) (LBNL) +* [Melissa Haendel](https://orcid.org/0000-0001-9114-8737) (UNC) + ### 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) +* [Anita Caron](https://orcid.org/0000-0002-6523-4866) (EMBL-EBI) +* [Charlie Hoyt](https://orcid.org/0000-0003-4423-4370) (Harvard Medical School; [@cthoyt](https://github.com/cthoyt)) * [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) +* [Emily Hartley](https://orcid.org/0000-0001-5839-2535) (Critical Path Institute) +* [Ernesto Jimenez-Ruiz](https://orcid.org/0000-0002-9083-4599) (City, University of London) +* [Harry Caufield](https://orcid.org/0000-0001-5705-7831) (LBNL) * [Henriette Harmse](https://orcid.org/0000-0001-7251-9504) (EMBL-EBI) +* [James McLaughlin](https://orcid.org/0000-0002-8361-2795) (EMBL-EBI) +* [John Graybeal](https://orcid.org/0000-0001-6875-5360) (Independent Consultant) +* [Sierra Moxon](https://orcid.org/0000-0002-8719-7760) (LBNL) +* [Simon Jupp](https://orcid.org/0000-0002-0643-3144) (SciBite) +* [Thomas Liener](https://orcid.org/0000-0003-3257-9937) (Independent Consultant) * [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) +* [William Duncan](https://orcid.org/0000-0001-9625-1899) (University of Florida) ### Contributors @@ -97,6 +110,8 @@ You can also reach us in the [OBO Foundry Slack](https://obo-communitygroup.slac * [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) +* [Cassia Trojahn](https://orcid.org/0000-0002-0096-2766) +* [Clement Jonquet](https://orcid.org/0000-0002-2404-1582) * [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) @@ -104,10 +119,12 @@ You can also reach us in the [OBO Foundry Slack](https://obo-communitygroup.slac * [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) +* [Ian Braun](https://orcid.org/0000-0002-2389-9288) * [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) +* [Javier Millán Acosta](https://orcid.org/0000-0002-4166-7093) * [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) @@ -123,9 +140,12 @@ You can also reach us in the [OBO Foundry Slack](https://obo-communitygroup.slac * [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) +* [Sophie Aubin](https://orcid.org/0000-0003-4805-8220) * [Sue Bello](https://orcid.org/0000-0003-4606-0597) +* [Sujay Patil](https://orcid.org/0000-0001-6142-1106) +* [Sven Hertling](https://orcid.org/0000-0003-0333-5888) * [Tim Putman](https://orcid.org/0000-0002-4291-0737) +* [Vinicius de Souza](https://orcid.org/0000-0002-4971-0439) ## Acknowledgements