SSSOM now specifies an algorithm for hashing records (i.e., rows in a SSSOM TSV file) to support interoperability across implementations and make semantic mappings more FAIR
π https://mapping-commons.github.io/sssom/spec-support-hashing
Implementations are already available in SSSOM-Java and sssom-pydantic
huge thanks to @dgouttegattat for leading the development of this part of the SSSOM spec!
i wrote about some of the challenges with semantic mappings πΊοΈ
https://cthoyt.com/2026/01/20/semantic-mapping-challenges.html
#ontology #owl #rdf #sssom #semanticweb #knowledgegraphs #skos
There are many challenges associated with the curation, publication, acquisition, and usage of semantic mappings. This post examines their philosophical, technical, and practical implications, highlights existing solutions, and describes opportunities for next steps for the community of curators, semantic engineers, software developers, and data scientists who make and use semantic mappings.
every wanted to put semantic mappings in SSSOM into @wikidata
now you can
At the 4th Ontologies4Chem Workshop in Limburg an der Lahn, I proposed an initial crosswalk between the Simple Standard for Sharing Ontological Mappings (SSSOM) and the Wikidata semantic mapping data model. This post describes the motivation for this proposal and the concrete implementation Iβve developed in sssom-pydantic.
biomappings is a project for predicting and curating semantic mappings between biomedical vocabularies in SSSOM
i'm working in @NFDI with researchers from other disciplines, so I recently did a full refactor of the underlying code into a new project, SSSOM Curator (https://github.com/cthoyt/sssom-curator) to make it more accessible outside of biomedicine
Here's a screen cast describing how it works:
The EBI has recently published a preprint describing OxO2, the second major version of their ontology mapping service, now based on SSSOM: https://arxiv.org/abs/2506.04286
nice to see citation of SeMRA and reuse of the comprehensive SSSOM semantic mapping datasets we produced and archived on Zenodo: https://zenodo.org/communities/biopragmatics/records?q&f=subject%3ASemantic%20Mappings
EMBL-EBI created OxO to enable users to map between datasets that are annotated with different ontologies. Mappings identified by the first version of OxO were not necessarily logically sound, lacked important provenance information such as author and reviewer, and could timeout or crash for certain requests. In this paper we introduce OxO2 to address these concerns. Provenance is addressed by implementing SSSOM, a mapping standard that defines provenance for mappings. SSSOM defines the conditions under which logical sound mappings can be derived and is implemented in OxO2 using Nemo, a Datalog rule engine. To ensure reasoning is performant and memory efficient, Nemo implements a number of strategies that ensures OxO2 will be stable for all requests. Due to these changes, OxO2 users will be able to integrate between disparate datasets with greater confidence.
I'm currently generating cross-lingual mappings for educational resources and found a fun non-trivial negative mapping:
kim.lp:0000122 (Gymnasium) and mesh:D020446 (Fitness Centers) aren't related, because Gymnasium is one of the types of German high school
SSSOM is the perfect place to store this (curated via Biomappings: https://github.com/biopragmatics/biomappings/pull/204)
Maybe I should suggest to the #SSSOM folks that we should start charging people for the SSSOM specification? π€
If we apply the βIEEE rateβ of $58 for 2 pages of meaningful content, we could charge at least $300 just for the part about the SSSOM/TSV format (~10 pages)! π€ π€ π€
Hey, the IEEE gets away with that, why not us?
If you are working with #SSSOM and are wondering about how you were supposed to pronounce the acronym, Iβve got you covered: incenp.org/notes/2025/sssom-prβ¦
(Sorry to all those who had never heard about #SSSOM until now; most likely you can safely continue to ignore it, unless you happen to be working on semantic mappings, in which case I hope it might interest you.)
At the ChEBI 2.0 workshop, Muhammad Arsalan is presenting how ChEBI is using the Bioregistry to standardize its cross-references, generate URLs on their front-end, and more
I couldn't image but in one week the #TS4NFDI hands on workshop in Hannover will be already over.
I'm looking forward to discuss #ontology #mapping approaches including #SSSOM with @cthoyt , @nichtich and Nick Juty from https://fair-impact.eu/ and @bioschemas in Hannover.
There are still a handful free places. If you want to join us at the @tibhannover feel free to register via: https://www.nfdi4chem.de/event/ts4nfdi-community-hands-on-workshop/
FAIR-IMPACT identifies practices, policies, tools and technical specifications to guide researchers, repository managers, research performing organisations, policy makers and citizen scientists towards a FAIR data management cycle. The focus is on persistent identifiers (PIDs), metadata, ontologies, metrics, certification and interoperability, starting with real-life use cases on social sciences and humanities, the photon and neutron sciences, life sciences and agri-food and environmental sciences.
Charles Tapley Hoyt
Damien Goutte-Gattat
Bioregistry
Roman Baum