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