Charles Tapley HoytJan 20

i wrote about some of the challenges with semantic mappings 🗺️

https://cthoyt.com/2026/01/20/semantic-mapping-challenges.html

#ontology #owl #rdf #sssom #semanticweb #knowledgegraphs #skos

Challenges with Semantic Mappings

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.

Biopragmatics
Charles Tapley HoytJan 8

every wanted to put semantic mappings in SSSOM into @wikidata

now you can

https://cthoyt.com/2026/01/08/sssom-to-wikidata.html

#semanticweb #semanticmapping #sssom #ontologies

Mapping from SSSOM to Wikidata

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 I’ve developed in sssom-pydantic.

Biopragmatics
Charles Tapley HoytNov 24

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:

📺 https://www.youtube.com/watch?v=FkXkOhT8gdc

#sssom #semanticmapping #semanticweb

GitHub - cthoyt/sssom-curator: Prediction and curation of semantic mappings in SSSOM

Prediction and curation of semantic mappings in SSSOM - cthoyt/sssom-curator

GitHub
Charles Tapley HoytNov 4

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

#sssom #semanticmapping #semanticweb

OxO2 -- A SSSOM mapping browser for logically sound crosswalks

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.

arXiv.org
Charles Tapley HoytAug 27, 2025

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)

#mapping #sssom #semanticmapping #skos #owl

Map between educational resources by cthoyt · Pull Request #204 · biopragmatics/biomappings

This PR covers generates mappings between resources related to education level, disciplines, and modeling of educational resources.

GitHub
Show threadDamien Goutte-GattatApr 16, 2025

Maybe I should suggest to the #SSSOM folks that we should start charging people for the SSSOM specification? 🤔

If we apply the “IEEE rate” 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)! 🤑 🤑 🤑

Hey, the IEEE gets away with that, why not us?

Damien Goutte-GattatApr 8, 2025

If you are working with #SSSOM and are wondering about how you were supposed to pronounce the acronym, I’ve got you covered: incenp.org/notes/2025/sssom-pr…

(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.)

SSSOM Pronunciation Alignment Chart

BioregistryNov 19, 2024

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

#chembl #ebi #chebi #sssom #cheminformatics

Show threadRoman BaumApr 2, 2024

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/

#base4nfdi #nfdirocks #nfdi #fairimpact #bioschemas

FAIR-IMPACT

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.

Damien Goutte-GattatAug 22, 2023

Be efficient: drop Python!

https://social.incenp.org/display/6e391d55-5464-e51c-f52b-e72488845887

Be efficient: drop Python!

(Yes, this is a troll.) Extracting #mappings from an #ontology to a #SSSOM file, using the #OntologyAccessKit in #Python: $ time runoak -i sqlite:uberon.db...