This week saw the addition of the Library of Congress Class Schemes registry, an overhaul of the alignment workflow with the Zazuko registry, the addition of 18 new records, and finally the update of 222 records in the Semantic Farm and the Bioregistry.

External Alignment

The Semantic Farm/Bioregistry ingests content from 36 external resources both to reduce curation burden but also to increase its coverage of resources across a variety of domains and disciplines.

Adding Library of Congress Classification Schemes

The United States Library of Congress (LOC) Classification Schemes covers various classification systems across the natural sciences, humanities, and library sciences, such as the Medical Subject Headings (MeSH), Iconclass, and Dewey Decimal Classification (DDC). I implemented an alignment workflow that ingests its entries and semi-automatically maps them to Semantic Farm/Bioregistry records based on lexical matching of prefixes in biopragmatics/bioregistry#2156.

Compared to other external registries, LOC Classification Schemes is information poor - it only contains prefixes and names for its records, whereas external registries like Identifiers.org have higher minimum metadata standards. A comparison of metadata standards across all 36 external registries is available here and is automatically updated when new ones (like LOC) are added!

Updating Zazuko

Zazuko is a company that builds semantic web technologies and solutions. It develops several of its own controlled vocabularies and ontologies to support its work, and importantly hosts https://prefix.zazuko.com, a unique frontend to many key semantic web controlled vocabularies and ontologies.

I recently found that they host metadata about the resources they index that isn’t available through its API, but rather through RDF files in N-tuples format on their GitHub repository (e.g., for Cube schema). Therefore, I updated the alignment workflow in biopragmatics/bioregistry#2144 to parse key metadata such as names and descriptions. Given this new context, I was motivated to curate the remaining information for dozens of these resources in order to meet the Semantic Farm/Bioregistry’s minimum metadata standards for new records.

There are countless opportunities for ingesting new records from external records, which are perfect for new curators who are interested to get involved. If that sounds like you, have a look at this curation guide.

New Records

The Semantic Farm/Bioregistry enables the community to submit new records to best cover their resources and resources they use. This week had two external contributions that were accepted (with several under review):

I contributed XHTML Datatypes (xh11d), then curated mappings from the LinkML core metamodel types to xh11d in linkml/linkml-model#289, giving LinkML a better grounding to previously established semantic web standards.

Universal Decimal Classification (UDC) was added in biopragmatics/bioregistry#2153 in order to complete the mapping from Dublin Core Terms encoding schemes to corresponding records in the Semantic Farm/Bioregistry. The other eight schemes listed already had corresponding records.

The remaining new records were all ingested from Zazuko and appropriately enriched to meet minimum metadata requirements for the Semantic Farm/Bioregistry in biopragmatics/bioregistry#2144.

Prefix Name
b59 barnard59
cube.meta Cube Schema meta data extension
cube.relation Cube Schema relation vocabulary
cube.schema Cube schema
duv Dataset Usage Vocabulary
fairmap FAIR Mappings Schema
qudt.constant QUDT VOCAB Physical Constants Release 3.1.10
qudt.currency QUDT VOCAB Currency Units Release 3.0.0
qudt.dimensionvector QUDT VOCAB Dimension Vectors Release 3.1.10
qudt.discipline QUDT Disciplines Ontology
qudt.prefix QUDT VOCAB Decimal Prefixes
qudt.quantitykind QUDT Quantity Kind Vocabulary
qudt.sou QUDT VOCAB Systems of Units Release 3.1.10
qudt.unit QUDT VOCAB Units of Measure
rr R2RML vocabulary
seipid Scholarly Entity International Persistent Identifier Infrastructure
udc Universal Decimal Classification
xh11d XHTML Datatypes

Updated Records

There were 238 updates, which came from a combination of alignment to LOC Class Schemes, enrichment from metadata from Zazuko, and other updates ingested from external registries.

Of those updates, only one was done as a stand-alone contribution. I updated the record for the Gainesville Core Ontology record in biopragmatics/bioregistry#2152 to ensure that it links to a downloadable OWL file in preparation for the Ontologies4Chem conference next week.

Updated Prefix Name
ac Activity Streams
acl Basic Access Control ontology
afo Allotrope Merged Ontology Suite
agricola Agricultural Online Access
ahol Animal Health Ontology for Livestock
aio The Artificial Intelligence Ontology
APO Ascomycete phenotype ontology
APOLLO_SV Apollo Structured Vocabulary
atc Anatomical Therapeutic Chemical Classification System
atol Animal Trait Ontology for Livestock
bao BioAssay Ontology
bcio The Behaviour Change Intervention Ontology
BERVO Biological and Environmental Research Variable Ontology
bibo The Bibliographic Ontology
biodivthes Biodiversity Thesaurus
biolink BioLink Model
biomodels.teddy Terminology for Description of Dynamics
biotop BioTop
birnlex Biomedical Informatics Research Network Lexicon
bko SBGN Bricks data and ontology
cc Creative Commons Rights Expression Language
ccf Human Reference Atlas Common Coordinate Framework Ontology
cco Cell Cycle Ontology
ccon Cerrado Concepts Ontology
cellosaurus Cellosaurus
cert The Cert Ontology
CHEBI Chemical Entities of Biological Interest
chemfont.chemical ChemFOnt chemical
ChEMROF Chemical Entity Materials and Reactions Ontological Framework
CHMO Chemical Methods Ontology
CHR Chromosome Ontology
cidoc.crm CIDOC Conceptual Reference Model
CL Cell Ontology
cmc.umg Cell Model Catalogue Göttingen
cmpo Cellular Microscopy Phenotype Ontology
cnt Representing Content in RDF
covid19 SARS-CoV-2
cryoem Cryo Electron Microscopy ontology
csp Computer Retrieval of Information on Science Projects Thesaurus
csvw CSV on the Web Vocabulary
ctcae Common Terminology Criteria for Adverse Events
DataCite DataCite Ontology
dbo DBPedia Ontology
dc Dublin Core Elements (1.1)
dcam Dublin Core Metadata Initiative Abstract Model
dcat Data Catalog
dcmitype DCMI Type Vocabulary
dcterms Dublin Core Metadata Initiative Terms
ddc Dewey Decimal Classification
ddi Data Documentation Initiative Vocabulary
dermo Human Dermatological Disease Ontology
dicom Digital Imaging and Communications in Medicine ontology
doap Description of a Project
DOID Human Disease Ontology
DPO Drosophila Phenotype Ontology
dqv Data Quality Vocabulary
DRON The Drug Ontology
dsw Darwin Semantic Web Ontology
earl Evaluation and Report Language
ecg Electrocardiogram Ontology
ECOCORE An ontology of core ecological entities
ecso The Ecosystem Ontology
ECTO Environmental conditions, treatments and exposures ontology
edda EDDA Study Designs Taxonomy
EFO Experimental Factor Ontology
ENVO Environment Ontology
envthes Thesaurus for long-term ecological research, monitoring, experiments
eol Environment Ontology for Livestock
epso Epilepsy and Seizure Ontology
evorao EVORA Ontology
exif Exif data description vocabulary
fabio The FRBR-aligned Bibliographic Ontology
faldo Feature Annotation Location Description Ontology
FBbt Drosophila gross anatomy
FBcv FlyBase Controlled Vocabulary
FBdv Drosophila development
FBSP Fly taxonomy
FLOPO Flora Phenotype Ontology
FMA Foundational Model of Anatomy
foaf Friend of a Friend
FOODON The Food Ontology
fplx FamPlex
FRBR Functional Requirements for Bibliographic Records
FYPO Fission Yeast Phenotype Ontology
gainesville.core Gainesville Core Ontology
galen GALEN
geonames.ontology GeoNames Ontology
geosparql GeoSPARQL
geosparql.function GeoSPARQL Function
geosparql.rule GeoSPARQL Rule
gexo Gene Expression Ontology
gfo General Formal Ontology
gist gist ontology
GO Gene Ontology
gpml WikiPathways GPML Vocabulary
gr GoodRelations
GRO Gramene Growth Stage Ontology
grddl Gleaning Resource Descriptions from Dialects of Languages
gs1 GS1 Web Vocabulary
hcpcs Healthcare Common Procedure Coding System
hgnc HUGO Gene Nomenclature Committee
hl7 HL7 External Code System
hoip Homeostasis imbalance process ontology
HP Human Phenotype Ontology
hydra The Hydra Core Vocabulary
icaltzd iCalendar with Time Zone
icd10cm International Classification of Diseases, 10th Revision, Clinical Modification
icd10pcs International Classification of Diseases, 10th Revision, Procedure Coding System
icd9 International Classification of Diseases, 9th Revision
icd9cm International Classification of Diseases, 9th Revision, Clinical Modification
icf International Classification of Functioning, Disability and Health
iconclass Iconclass Classification
idocovid19 The COVID-19 Infectious Disease Ontology
idoden Dengue Fever Ontology
inbio Invasion Biology Ontology
inchi International Chemical Identifier
interlex InterLex
iobc Interlinking Ontology for Biological Concepts
ito Intelligence Task Ontology
jcrb Japanese Collection of Research Bioresources Cell Bank
lbo Livestock Breed Ontology
ldp Linked Data Platform Vocabulary
legacy.capcldb Prostate Cancer Cell Line Database
lexvo.ontology Lexvo Ontology
loc.classschemes Library of Congress Classification Schemes
locn ISA Programme Location Core Vocabulary
log SWAP Logic Ontology
loinc Logical Observation Identifiers Names and Codes
lpt Livestock Product Trait Ontology
m4i Metadata4Ing
medlineplus MedlinePlus
mesh Medical Subject Headings
metabobank MetaboBank
METPO Microbial Ecophysiological Trait and Phenotype Ontology
MIXS Minimum Information about any (x) Sequence
MOD PSI-MOD Protein Modifications Ontology
modsci Modern Science Ontology
MOLSIM Molecular Simulation Ontology
mosaic MOSAiC Ontology
MRO MHC Restriction Ontology
msc Mathematics Subject Classification
mwo NFDI MatWerk Ontology
nando Nanbyo Disease Ontology
nemo2 Neural ElectroMagnetic Ontology
nexus NeXus Ontology
NIF_CELL NIF Cell
nlm National Library of Medicine Catalog
npo NanoParticle Ontology
oa Web Annotation Ontology
OBA Ontology of Biological Attributes
OBI Ontology for Biomedical Investigations
og Open Graph protocol
ogc.sf Open Geospatial Consortium Simple Features Vocabulary
OHD Oral Health and Disease Ontology
oidc Solid OpenID Connect vocabulary
om Ontology of units of Measure
omim Online Mendelian Inheritance in Man
OMO OBO Metadata Ontology
OMRSE Ontology for Modeling and Representation of Social Entities
OOSTT Ontology of Organizational Structures of Trauma centers and Trauma systems
opb Ontology of Physics for Biology
org Core organization ontology
orphanet.ordo Orphanet Rare Disease Ontology
orth Orthology Ontology
owl Web Ontology Language
panet Photon and Neutron Experimental Techniques Ontology
PATO Phenotype And Trait Ontology
phenx PhenX Toolkit
PHIPO Pathogen Host Interaction Phenotype Ontology
plos PLOS Thesaurus
PREFER Precision Fermentation Ontology
prov PROV Namespace
qb The data cube vocabulary
qudt Quantities, Units, Dimensions, and Types Ontology
radlex RSNA Informatics RadLex
rcb RIKEN Bioresource Center Cell Bank
rdf Resource Description Framework
rdfa RDFa Vocabulary for Term and Prefix Assignment, and for Processor Graph Reporting
rdfs RDF Schema
reproduceme REPRODUCE-ME Ontology
reto Regulation of Transcription Ontology
rexo Regulation of Gene Expression Ontology
RO Relation Ontology
RoleO Role Ontology
ror Research Organization Registry
rrid Research Resource Identification
rxnorm RxNorm
salmon Salmon Ontology
saref.ehaw SAREF4EHAW: an extension of SAREF for eHealth Ageing Well domain
sasap The State of Alaska’s Salmon and People Ontology
schema Schema.org
sd SPARQL 1.1 Service Description
sdmx SDMX-RDF vocabulary
sh Shapes Constraint Language
shex Shape Expression Vocabulary
shsh SHACL in SHACL
sioc.core Semantically-Interlinked Online Communities Core Ontology
skos Simple Knowledge Organization System
skosxl Simple Knowledge Organization System eXtension for Labels
smiles Simplified molecular-input line-entry system
solid Solid Terms
sosa Sensor, Observation, Sample, and Actuator Ontology
ssn Semantic Sensor Network Ontology
sstim Sensory Stimulation Ontology
stemmcellbank CReM iPSC Catalog
sty UMLS Semantic Types Ontology
suzhou.cell Suzhou Research Institute Cell Bank
SYMP Symptom Ontology
tib.bk Basic Classification
time Time Ontology in OWL
ubigene UbiGene
uniprot UniProt Protein
uniprot.core Uniprot Core Ontology
UO Units of measurement ontology
UPHENO Unified Phenotype Ontology
valuesets Value Sets
vandf Veterans Administration National Drug File
vann A vocabulary for annotating vocabulary descriptions
vcard Virtual Contact File
vido Virus Infectious Disease Ontology
vivo VIVO Ontology
vmh.gene Virtual Metabolic Human gene
vmh.metabolite Virtual Metabolic Human metabolite
vmh.reaction Virtual Metabolic Human reaction
VO Vaccine Ontology
void Vocabulary of Interlinked Datasets
vs SemWeb Vocab Status ontology
vso Vital Sign Ontology
VT Vertebrate trait ontology
WBPhenotype C. elegans phenotype
wdrs Protocol for Web Description Resources (POWDER): POWDER-S Vocabulary
wgs84 WGS84 Geo Positioning
XCO Experimental condition ontology
xhv XHTML Vocabulary
xkos An SKOS extension for representing statistical classifications
xsd XML Schema Definition
ZFA Zebrafish anatomy and development ontology
ZFS Zebrafish developmental stages ontology