This week saw the addition of 28 new records, update of 80 records, and addition of one new collection to the Semantic Farm and the Bioregistry, many motivated by the WikiPathways project and contributed by Javier Millán Acosta.

New Records

Of the 28 new records were added, several were follow-ups to last week’s updates on the Ontologies4Chem conference, including the addition of 17 records for components of PubChem’s RDF. The Semantic Farm/Bioregistry also received three external contributions:

  1. the Cleavage Atlas by Rens de Groot
  2. Digital Identity Optimization and Ontology of Digital Identity Reference Vocabulary by Daniel Beránek
  3. ChEMBL Assay by Javier Millán Acosta.

The Clinical Metadata Exploration Ontology (CMEO) was accepted in the OBO Foundry and was automatically added by the weekly update workflow.

Prefix Name
chembl.assay ChEMBL assay
cleavageatlas Cleavage Atlas
CMEO Clinical Metadata Exploration Ontology
dio-odi Digital Identity Optimization and Ontology of Digital Identity Reference Vocabulary
formats File Formats
iochem ioChem-BD Schema
math Math Vocabulary
ofbo Organic Flow Battery Ontology
ontoiochem OntoIochem Core Ontology
pubchem.anatomy PubChem anatomy
pubchem.author PubChem author
pubchem.conserveddomain PubChem conserved domain
pubchem.cooccurrence PubChem co-occurrence
pubchem.descriptor PubChem descriptor
pubchem.disease PubChem disease
pubchem.endpoint PubChem endpoint
pubchem.grant PubChem grant
pubchem.journal PubChem journal
pubchem.measuregroup PubChem measure group
pubchem.nbr PubChem neighbor
pubchem.organization PubChem organization
pubchem.pathway PubChem pathway
pubchem.protein PubChem protein
pubchem.reference PubChem reference
pubchem.source PubChem source
pubchem.synonym PubChem synonym
sabdab Structural Antibody Database
stat POSIX Statistics Operations

Updated Records

This week, 80 records were updated as a combination of manual contributions and alignment with 30+ external registries.

A key highlight was the 11 improvements submitted by Javier Millán Acosta on behalf of the WikiPathways project that added additional providers to several resources for chemicals, reactions, proteins, and cells relevant for annotating pathways in WikiPathways that appear in its RDF and can be queried by SPARQL.

Of these, several included the addition of RDF URI format strings, which encode how a local unique identifier from a resource should be encoded as a URI in RDF, versus a regular URI format string, which is used for resolution to a human-readable webpage. Some of these additions were providers, which are third party URIs which can be used to get information about an entity. For example, Javier added the RDF URI format in PubChem for NCBI Taxonomy (ncbitaxon).

Prefix Name
asmo Atomistic Simulation Methods Ontology
atc Anatomical Therapeutic Chemical Classification System
bcio The Behaviour Change Intervention Ontology
building Building Ontology
cdco Crystallographic Defect Core Ontology
CHEBI Chemical Entities of Biological Interest
chembl.cell ChEMBL database of bioactive drug-like small molecules - Cell lines section
chemspider ChemSpider
CHMO Chemical Methods Ontology
CHR Chromosome Ontology
CiTO Citation Typing Ontology
climoo.plastico ClimOO - Plastic Ontology
climoo.sdc2 ClimOO - Sustainable Development and Climate Ontology
dbpedia.property DBPedia Property
EC Enzyme Nomenclature
edam EDAM Ontology
edm.fibo Financial Industry Business Ontology
EFO Experimental Factor Ontology
emmo Elementary Multiperspective Material Ontology
EMRO Emotion Response Ontology
ENVO Environment Ontology
fabio The FRBR-aligned Bibliographic Ontology
FLOPO Flora Phenotype Ontology
geosparql GeoSPARQL
geosparql.function GeoSPARQL Function
geosparql.rule GeoSPARQL Rule
google.patent Google Patents
inchikey InChIKey
iofcore Industrial Ontology Foundry (IOF) Core Ontology
kpio Key Performance Indicator ontology
lipidmaps LIPID MAPS
m4i Metadata4Ing
mathmoddb MathModDB Ontology and Knowledge Graph for Mathematical Models
mirbase.mature miRBase mature miRNA
MMO Measurement method ontology
MOD PSI-MOD Protein Modifications Ontology
MOLSIM Molecular Simulation Ontology
MS Mass spectrometry ontology
ncbibook NCBI Bookshelf
NCBIGene NCBI Gene
NCBITaxon NCBI Taxonomy
oboe The Extensible Observation Ontology
OEO Open Energy Ontology
PATO Phenotype And Trait Ontology
physh Physics Subject Headings
pmdco Platform Material Digital Core Ontology
pride Proteomics Identification Database Ontology
prima Provenance Information for Materials Science Ontology
pubchem.bioassay PubChem bioassay
pubchem.cell PubChem cell line
pubchem.classification PubChem classification
pubchem.element PubChem element
pubchem.substance PubChem substance
pubchem.vocabulary PubChem Vocabulary
pubmed PubMed
rfam RNA family database
rhea Rhea reaction
RXNO Name Reaction Ontology
scretf ScerTF
SIO Semanticscience Integrated Ontology
SLM SwissLipid
sre.cpo Chemical Process Ontology
sre.hlo Higher Level Ontology
tib.io Information Objects Ontology
tib.lis Industrial Data Ontology
tib.mat Material properties ontology
tib.mdo Materials Design Ontology
tib.mt Mobility Theme
time Time Ontology in OWL
TTO Teleost taxonomy ontology
UBERON Uber Anatomy Ontology
uniprot UniProt Protein
uniref UniRef
UO Units of measurement ontology
UPA Unipathway
vcard Virtual Contact File
voc4cat A vocabulary for the catalysis disciplines
VT Vertebrate trait ontology
XAO Xenopus Anatomy Ontology
ZP Zebrafish Phenotype Ontology

New Collections

Finally, I implemented a workflow for constructing a Semantic Farm/Bioregistry collection from a SPARQL endpoint that encodes its prefix definitions using SHACL in #2205. I used this to construct a collection for WikiPathways (0000048) which reflects many of the additions and updates from this week. Javier also suggested I could apply this same workflow to Rhea, AOP Wiki, and other resources that make SPARQL endpoints available.