We added 80 new records, updated 54 records, and made a constellation of improvements and updates to the Semantic Farm and Bioregistry in the first two weeks of October 2026. This post gives more detail and links to external resources for further reading. For new readers, a brief reminder that the Semantic Farm is a domain-agnostic generalization on the Bioregistry to better serve other natural sciences, engineering sciences, and humanities and social sciences communities, especially within the context of the NFDI. ## Highlights 1. Records were added for ontologies from the World Avatar, which support multiscale modeling from the molecular level to municipal systems and weather patterns. I wrote about this in detail in my previous post 2. A record describing the European Synchrotron Radiation Facility (ESFR) Experimental Techniques Ontology (ESRFET) was added and members of DAPHNE4NFDI suggested several improvements to physics-related ontologies, including the NeXus Ontology (`nexus`) (also used DAPHNE4NFDI, FAIRmat, and NFDI-MatWerk) and the Photon and Neutron Experimental Techniques Ontology (`PaNET`)). This demonstrates the relatively low barrier for community involvement in the Semantic Farm and that NFDI consortia and their respective members can take initiative to maintain records describing both their first-party resources and third-party resources they use. 3. Improved workflow for ingesting and aligning records for ontologies in the Open Biological and Biomedical Ontology (OBO) Foundry. I wrote about this in detail here. 4. Implemented a draft workflow for calculating ontology reuse as part of NFDI Section Metadata Working Group for Ontology Harmonization and Mapping’s agenda for summarizing ontology usage across NFDI consortia. See the pull request and results. ## New Prefixes Aside from the 74 new records added for ontologies from the World Avatar project, six new records were added, five of which cover cell and cell line resources appearing in Cellosaurus cross-references. Added Prefix | Name ---|--- cmc.umg | Cell Model Catalogue Göttingen legacy.capcldb | Prostate Cancer Cell Line Database metabobank | MetaboBank stemmcellbank | CReM iPSC Catalog suzhou.cell | Suzhou Research Institute Cell Bank ubigene | UbiGene ## Updated Prefixes In total, 54 prefixes were updated Prefix | Name ---|--- addicto | Addiction Ontology afo | Allotrope Merged Ontology Suite agrovoc | AGROVOC APO | Ascomycete phenotype ontology CHEBI | Chemical Entities of Biological Interest chemfont.chemical | ChemFOnt chemical chemfont.ontology | ChemFOnt Ontology CMO | Clinical measurement ontology cmpo | Cellular Microscopy Phenotype Ontology coho | Cohort Ontology dicom | Digital Imaging and Communications in Medicine ontology DOID | Human Disease Ontology DPO | Drosophila Phenotype Ontology dsw | Darwin Semantic Web Ontology ECOCORE | An ontology of core ecological entities EMAPA | Mouse Developmental Anatomy Ontology fabio | The FRBR-aligned Bibliographic Ontology FBbt | Drosophila gross anatomy FBcv | FlyBase Controlled Vocabulary FBdv | Drosophila development FLOPO | Flora Phenotype Ontology frbrer | Functional Requirements for Bibliographic Records Entity-Relationship Model grddl | Gleaning Resource Descriptions from Dialects of Languages icd10 | International Classification of Diseases, 10th Revision icd9 | International Classification of Diseases, 9th Revision inchi | International Chemical Identifier iso.3166 | ISO 3166-1 Country Code jcrb | Japanese Collection of Research Bioresources Cell Bank loc.relator | Library of Congress Relator lpt | Livestock Product Trait Ontology MMO | Measurement method ontology MONDO | Mondo Disease Ontology MOP | Molecular Process Ontology nlm | National Library of Medicine Catalog OBA | Ontology of Biological Attributes OHD | Oral Health and Disease Ontology ontocape | Ontology for computer aided process engineering orphanet.ordo | Orphanet Rare Disease Ontology PAIN | The Pain Ontology PATO | Phenotype And Trait Ontology pfam | Pfam protein family rcb | RIKEN Bioresource Center Cell Bank smiles | Simplified molecular-input line-entry system uat | Unified Astronomy Thesaurus UBERON | Uber Anatomy Ontology vmh.gene | Virtual Metabolic Human gene vmh.metabolite | Virtual Metabolic Human metabolite vmh.reaction | Virtual Metabolic Human reaction voc4cat | A vocabulary for the catalysis disciplines VT | Vertebrate trait ontology worldavatar.compchem | WorldAvatar computational chemistry ontology worldavatar.kin | WorldAvatar ontology for chemical kinetic reaction mechanisms WormBase | WormBase ZP | Zebrafish Phenotype Ontology * * * The Semantic Farm is an open data resource, so if you want to see more detail about the everyday churn, have a look at recent pull requests to the GitHub repository

it appears that AberOWL has taken down its programmatic API and replaced it with just MCP - see docs at http://aber-owl.net/docs. I couldn't find any evidence of the old API, and the previous endpo...

I am currently supporting Philip Strömert and Noura Rayya in the efforts to modernize and revitalize the Chemical Methods Ontology (CHMO) to support annotation of instrumentation used to produce experimental data captured in the Chemotion electronic laboratory notebook as part of NFDIChem. This post is about the adoption of Simple Standard for Sharing Ontological Mappings (SSSOM) to support interoperability between CHMO and other resources, and the workflow I developed to compare overlapping manual curations from different researchers. Philip and Noura have already completed the important initial steps of assuming maintainership from the Royal Society of Chemistry, porting the ontology to use a standardized Ontology Development Kit (ODK) layout, and revising the definitions of many classes based on the IUPAC GoldBook. ## Landscape of Resources There are several other NFDI consortia including NFDI4Cat (catalysis), DAPHNE4NFDI (photon and neutron physics), and FAIRmat (materials science) that have similar goals to annotate instrumentation. While each reuse CHMO to some extent for this purpose, DAPHNE4NFDI additionally develops the Photon and Neutron Experimental Techniques (PANET) Ontology and FAIRmat develops the NeXus format and associated NeXus Ontology as part of the NOMAD materials science data management platform. Further, there are several other resources with similar goals including the Allotrope Foundation Ontology (AFO), the deprecated Physico-chemical Methods and Properties (FIX) ontology, the deprecated Physico-chemical process (REX) ontology, IUPAC GoldBook, and Wikidata. # Establishing Interoperability In order to establish interoperability between these many resources, we are using the Simple Standard for Sharing Ontological Mappings (SSSOM) to curate exact matches, narrow matches, and broad matches between CHMO terms and external ones in PANET, NeXuS (sort of), AFO, FIX, REX, IUPAC GoldBook, and Wikidata. First, Philip had Ambika, a student research assistant (_Hiwi_ , abbreviated in German), work for several months to manually curate mappings from CHMO to REX, FIX, AFO, and Wikidata (see this PR). In parallel, I took the opportunity to spin up a new instance of a SSSOM Curator repository within the NFDI Section Metadata Working Group for Ontology Harmonization and Mappings GitHub repository, run lexical prediction to generate candidate mappings from CHMO, and efficiently manually curate the results in this PR. and this PR over the course of about an hour. ## Need for Comparison The next challenge was to efficiently triage the similarities and differences between my curations and Ambika’s. Therefore, I implemented a workflow for comparing the manually curated mappings in two SSSOM documents in cthoyt/sssom-pydantic#141. This workflow creates a Markdown file describing similarities and differences. I chained together the following two CLI commands with `sssom_pydantic` to get the separate mapping files from Ambika’s branch in the NFDI4Chem fork of CHMO, merge them, then run the comparison against my own curations. Note that these won’t be reproducible after the branch is merged and deleted, and the actual results will change as more curation is done. $ sssom_pydantic merge \ --input https://github.com/NFDI4Chem/rsc-cmo/raw/refs/heads/Add-tsv-files/src/mappings/fix-mappings.sssom.tsv \ --input https://github.com/NFDI4Chem/rsc-cmo/raw/refs/heads/Add-tsv-files/src/mappings/afo-mappings.sssom.tsv \ --input https://github.com/NFDI4Chem/rsc-cmo/raw/refs/heads/Add-tsv-files/src/mappings/rex-mappings.sssom.tsv \ --input https://github.com/NFDI4Chem/rsc-cmo/raw/refs/heads/Add-tsv-files/src/mappings/wikidata-mappings.sssom.tsv \ --standardize \ --output ambika.sssom.tsv $ sssom_pydantic compare \ ambika.sssom.tsv \ https://github.com/nfdi-de/section-metadata-wg-onto/raw/refs/heads/main/sssom/data/positive.sssom.tsv \ --standardize \ --standardize-flip \ --left-label Ambika \ --right-label Charlie Since the comparison workflow outputs Markdown, its results can easily be embedded in GitHub issues or my blog, which is itself written in Markdown. ## Results I am happy with the first version of the comparison workflow. Luckily, there were only a small number of discrepancies which have obvious solutions. There were also a few interesting discrepancies which were novel to either my or Ambika’s curations, which can be reviewed by a third curator (sorry Philip, more work for you). ## Next Steps I think that it can be extended to identify and report on one-to-many, many-to-one, and many-to-many mappings which arise when jointly examining two mapping sets. After Philip and others interact with the results, I’m sure we will be able to extend it with other analyses. More generally, the implementation of the comparison workflow is part of a larger suite of workflows that I would like to describe in future posts including: 1. merging manually curated mappings 2. generating OWL ontology bridges 3. incorporating SSSOM into ODK builds, which I will support Damien Goutte-Gattat to document in the ODK repository and the OBOOK. 4. unify this analysis with my other idea for doing automated evaluation of predicted mappings, which I hope can be used to run future mapping challenges Without further ado, here’s the comparison, copied verbatim from the output of the previous command: # Comparison between Ambika and Charlie 1. CHMO to FIX 2. CHMO to REX ## CHMO to FIX ### Subject Comparison * 288 entities appear as subjects only in Ambika * 19 entities appear as subjects only in Charlie only * 138 entities appear as subjects in both The following 6 subjects (4.3%) appearing in both have conflicting objects: subject_id | subject_label | Ambika | both | Charlie ---|---|---|---|--- CHMO:0000141 | diffraction method | FIX:0000004 (crystallography) | FIX:0000217 (diffraction method) | CHMO:0000164 | electron scattering | FIX:0000666 (electron scattering spectroscopy) | FIX:0000401 (electron scattering) | CHMO:0000255 | flame atomic emission spectroscopy | FIX:0000935 (spark method) | FIX:0000928 (flame atomic emission spectroscopy) | CHMO:0000307 | X-ray emission spectroscopy | FIX:0000673 (X-ray fluorescence spectroscopy) | FIX:0000100 (X-ray emission spectroscopy) | CHMO:0000366 | electron energy loss spectroscopy | FIX:0000664 (electron impact spectroscopy) | FIX:0000663 (electron energy loss spectroscopy) | CHMO:0000570 | proton transfer reaction ion trap mass spectrometry | FIX:0000919 (proton transfer reaction ion trap mass spectrometry) | | FIX:0000918 (proton transfer reaction mass spectrometry) ### Object Comparison * 296 entities appear as objects only in Ambika * 19 entities appear as objects only in Charlie * 138 entities appear as objects in both The following 2 objects (1.4%) appearing in both have conflicting subjects: object_id | object_label | Ambika | both | Charlie ---|---|---|---|--- FIX:0000629 | pulsed field gel electrophoresis | CHMO:0002315 (pulsed-field electrophoresis) | | CHMO:0002316 (pulsed-field gel electrophoresis) FIX:0000816 | square-wave polarography | CHMO:0000040 (square-wave voltammetry) | CHMO:0000035 (square-wave polarography) | ### Subject-Object Pair Comparison * 301 subject-object pairs only appear in Ambika * 20 subject-object pairs only appear in Charlie * 137 subject-object pairs appear in both The following 1 subject-object pairs (0.7%) appearing in have conflicting predicates or predicate modifiers: subject_id | subject_label | object_id | object_label | warning | Ambika | Charlie ---|---|---|---|---|---|--- CHMO:0000164 | electron scattering | FIX:0000401 | electron scattering | different predicate | skos:narrowMatch | skos:exactMatch ## CHMO to REX ### Subject Comparison * 1 entities appear as subjects only in Ambika * 18 entities appear as subjects only in Charlie only * 0 entities appear as subjects in both ### Object Comparison * 1 entities appear as objects only in Ambika * 18 entities appear as objects only in Charlie * 0 entities appear as objects in both ### Subject-Object Pair Comparison * 1 subject-object pairs only appear in Ambika * 18 subject-object pairs only appear in Charlie * 0 subject-object pairs appear in both

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