OrthoDB
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OrthoDB

Release: 11, Nov 2022

This version:
http://purl.orthodb.org/
Latest version:
http://purl.orthodb.org/
Revision:
V11.0
See also:
http://www.orthodb.org/
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9825584/
mailto:support@orthodb.org
Download serialization:
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License:
http://insertlicenseURIhere.example.org
Visualization:
Visualize with WebVowl
Evaluation:
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Cite as:
Revision: V11.0.
Ontology Specification Draft

Abstract

The hierarchical catalog of orthologs that maps genomics to functional data

Introduction back to ToC

OrthoDB provides evolutionary and functional annotations of genes in a diverse sampling of eukaryotes, prokaryotes, and viruses. Genomics continues to accelerate our exploration of gene diversity and orthology is the most precise way of bridging gene functional knowledge with the rapidly expanding universe of genomic sequences. OrthoDB samples the most diverse organisms with the best quality genomics data to provide the leading coverage of species diversity. This update of the underlying data to over 18 000 prokaryotes and almost 2000 eukaryotes with over 100 million genes propels the coverage to another level. This achievement also demonstrates the scalability of the underlying OrthoLoger software for delineation of orthologs, freely available from https://orthologer.ezlab.org. In addition to the ab-initio computations of gene orthology used for the OrthoDB release, the OrthoLoger software allows mapping of novel gene sets to precomputed orthologs and thereby links to their annotations. The LEMMI-style benchmarking of OrthoLoger ensures its state-of-the-art performance and is available from https://lemortho.ezlab.org. The OrthoDB web interface has been further developed to include a pairwise orthology view from any gene to any other sampled species. OrthoDB-computed evolutionary annotations as well as extensively collated functional annotations can be accessed via REST API or SPARQL/RDF, downloaded or browsed online from https://www.orthodb.org.

Namespace declarations

Table 1: Namespaces used in the document
NCBIgenome<https://www.ncbi.nlm.nih.gov/genome/?term=>
[Ontology NS Prefix]<http://purl.orthodb.org/>
annotation<http://purl.uniprot.org/annotation/>
bibo<http://purl.org/ontology/bibo/>
dcterms<http://purl.org/dc/terms/>
disease<http://purl.uniprot.org/diseases/>
ensembl<http://rdf.ebi.ac.uk/resource/ensembl/>
ensemblgenomes<http://ensemblgenomes.org/id/>
entrez<http://www.ncbi.nlm.nih.gov/gene/>
enzyme<http://purl.uniprot.org/enzyme/>
foaf<http://xmlns.com/foaf/0.1/>
interpro<http://www.ebi.ac.uk/interpro/entry/>
isoform<http://purl.uniprot.org/isoforms/>
keyword<http://purl.uniprot.org/keywords/>
location<http://purl.uniprot.org/locations/>
obo<http://purl.obolibrary.org/obo/>
odbgene<http://purl.orthodb.org/odbgene/>
odbgroup<http://purl.orthodb.org/odbgroup/>
odborganism<http://purl.orthodb.org/odborganism/>
orth<http://purl.org/net/orth#>
owl<http://www.w3.org/2002/07/owl#>
position<http://purl.uniprot.org/position/>
pubmed<http://purl.uniprot.org/pubmed/>
range<http://purl.uniprot.org/range/>
rdf<http://www.w3.org/1999/02/22-rdf-syntax-ns#>
rdfs<http://www.w3.org/2000/01/rdf-schema#>
skos<http://www.w3.org/2004/02/skos/core#>
spin<http://spinrdf.org/spin#>
taxon<http://purl.uniprot.org/taxonomy/>
tissue<http://purl.uniprot.org/tissues/>
uniprot<http://purl.uniprot.org/uniprot/>
up<http://purl.uniprot.org/core/>
xml<http://www.w3.org/XML/1998/namespace>
xsd<http://www.w3.org/2001/XMLSchema#>

The hierarchical catalog of orthologs: Overview back to ToC

This ontology has the following classes and properties.

Classes

Object Properties

Data Properties

Annotation Properties

The hierarchical catalog of orthologs: Description back to ToC

OrthoDB partial dump. Data by E.Zdobnov Computational Evolutionary Genomics Group. Converted to RDF by Dmitry Kuznetsov, Swiss Institute of Bioinformatics.

Cross-reference for The hierarchical catalog of orthologs classes, object properties and data properties back to ToC

This section provides details for each class and property defined by The hierarchical catalog of orthologs.

Classes

Cladec back to ToC or Class ToC

IRI: http://purl.orthodb.org/Clade

Clade (or level) is a level in NCBI taxonomy choosen to build orthologous groups for underneath species' genes
has super-classes
Taxon c
is in range of
og Built At op

Ensemblc back to ToC or Class ToC

IRI: http://purl.orthodb.org/Ensembl

Ensembl gene or protein URIs, i.e. those with classical ENS* prefix
has super-classes
Xref c

Ensemblgenomesc back to ToC or Class ToC

IRI: http://purl.orthodb.org/Ensemblgenomes

Ensembl Genomes xrefs, i.e. those ids who do not start with classical ENS* prefix
has super-classes
Xref c

Entrezc back to ToC or Class ToC

IRI: http://purl.orthodb.org/Entrez

NCBI Entrez gene (aka gid) xrefs
has super-classes
Xref c

Geneontologyc back to ToC or Class ToC

IRI: http://purl.orthodb.org/Geneontology

Gene Ontology xrefs. IDs are transformed by replacement of GO: prefix with GO_ to conform with RDF Turtle format
has super-classes
Xref c

Interproc back to ToC or Class ToC

IRI: http://purl.orthodb.org/Interpro

Interpro domain xrefs
has super-classes
Xref c

N C I T C14250c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C14250

is equivalent to
Organism c

NCBI taxonomy rootc back to ToC or Class ToC

IRI: http://purl.uniprot.org/taxonomy/_1

The root node in NCBI taxonomy; a fictive taxon with no direct biological meaning, to maintain data integrity.
has super-classes
Thing c

ODBgenec back to ToC or Class ToC

IRI: http://purl.orthodb.org/Gene

Gene in OrthoDB.
has super-classes
Thing c
is in domain of
aa Sequence dp, description dp, gene Nb Exons dp, gene Translated Length dp, member Of op, name dp, organism op, xref op
is in range of
has Member op

Organismc back to ToC or Class ToC

IRI: http://purl.org/net/orth#Organism

is equivalent to
Organism c

Organismc back to ToC or Class ToC

IRI: http://purl.orthodb.org/Organism

A living being, such as an animal, a plant, a bacterium, or a fungus., Any individual living (or previously living) being. Example: animal, human being. An organim is associated to a taxon such as "Homo Sapiens", NCBI taxonomy identifier: 9606.
is in domain of
genome I D op
is in range of
organism op

OrthoGroupSiblingc back to ToC or Class ToC

IRI: http://purl.orthodb.org/OrthoGroupSibling

Orthologous group siblings; defined by the fraction of InterPro domains shared with other groups of orthologs.
has super-classes
Thing c
is in domain of
sibling O G op, sibling Similarity dp, tax Tree Distance dp, xref Resource op
is in range of
sibling op

Orthologs Clusterc back to ToC or Class ToC

IRI: http://purl.org/net/orth#OrthologsCluster

is equivalent to
ODBgroup c

S O 0005855c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0005855

is equivalent to
ODBgroup c

Sequence Unitc back to ToC or Class ToC

IRI: http://purl.org/net/orth#SequenceUnit

is equivalent to
ODBgene c

Speciesc back to ToC or Class ToC

IRI: http://purl.orthodb.org/Species

Leaf of the OrthoDB taxonomy, usually has rank species in NCBI taxonomy;
has super-classes
Taxon c

Taxonc back to ToC or Class ToC

IRI: http://purl.uniprot.org/core/Taxon

Class containing organism ids according to NCBI taxonomy, as well as other info; imported from and is compatible with Uniprot RDF data.
is equivalent to
NCBI taxonomy root c
has super-classes
Class c
has sub-classes
Clade c, Species c
is in domain of
common Name ap, host op, other Name op, rank op, reference Proteome op, scientific name op, strain op
is in range of
host op

Uniprotc back to ToC or Class ToC

IRI: http://purl.orthodb.org/Uniprot

Uniprot proteins URIs, e.g. http://purl.uniprot.org/uniprot/P12345
has super-classes
Xref c

Xrefc back to ToC or Class ToC

IRI: http://purl.orthodb.org/Xref

Class containing external references for OrthoDB genes; instances are blank nodes with collections of real URLs and eventual supplementary data.
has super-classes
Thing c
has sub-classes
Ensembl c, Ensemblgenomes c, Entrez c, Geneontology c, Interpro c, Uniprot c
is in domain of
description dp, name dp, xref D B op, xref Resource op
is in range of
xref op

Object Properties

ancestral O Gop back to ToC or Object Property ToC

IRI: http://purl.orthodb.org/ancestralOG

Hierarchical relation between the current group and its ancestral group built on an upper [closer to the root] taxonomic level
has domain
ODBgroup c
has range
ODBgroup c

genome I Dop back to ToC or Object Property ToC

IRI: http://purl.orthodb.org/genomeID

has domain
Organism c
is also defined as
data property

has Memberop back to ToC or Object Property ToC

IRI: http://purl.orthodb.org/hasMember

Orthogroup has a member gene
has domain
ODBgroup c
has range
ODBgene c
is inverse of
member Of op

hostop back to ToC or Object Property ToC

IRI: http://purl.uniprot.org/core/host

has domain
Taxon c
has range
Taxon c

member Ofop back to ToC or Object Property ToC

IRI: http://purl.orthodb.org/memberOf

Gene is a member of orthogroup
has domain
ODBgene c
has range
ODBgroup c
is inverse of
has Member op

og Built Atop back to ToC or Object Property ToC

IRI: http://purl.orthodb.org/ogBuiltAt

Points to the clade (level) at which the orthogroup is built

has characteristics: functional

has domain
ODBgroup c
has range
Clade c

organismop back to ToC or Object Property ToC

IRI: http://purl.uniprot.org/core/organism

has domain
ODBgene c
has range
Organism c
is also defined as
data property

other Nameop back to ToC or Object Property ToC

IRI: http://purl.uniprot.org/core/otherName

has characteristics: functional

has domain
Taxon c
is also defined as
data property

rankop back to ToC or Object Property ToC

IRI: http://purl.uniprot.org/core/rank

has domain
Taxon c
is also defined as
data property

reference Proteomeop back to ToC or Object Property ToC

IRI: http://purl.uniprot.org/core/referenceProteome

has domain
Taxon c
is also defined as
data property

scientific nameop back to ToC or Object Property ToC

IRI: http://purl.uniprot.org/core/scientificName

has characteristics: functional

has super-properties
name op
has domain
Taxon c
is also defined as
data property

siblingop back to ToC or Object Property ToC

IRI: http://purl.orthodb.org/sibling

has domain
ODBgroup c
has range
OrthoGroupSibling c

sibling O Gop back to ToC or Object Property ToC

IRI: http://purl.orthodb.org/siblingOG

has domain
OrthoGroupSibling c
has range
ODBgroup c

strainop back to ToC or Object Property ToC

IRI: http://purl.uniprot.org/core/strain

has domain
Taxon c
is also defined as
data property

xrefop back to ToC or Object Property ToC

IRI: http://purl.orthodb.org/xref

link to blank node serving as a container for external reference detailed data
has domain
ODBgene c
ODBgroup c
has range
Xref c

xref D Bop back to ToC or Object Property ToC

IRI: http://purl.orthodb.org/xrefDB

URL pointing to the external resource
has domain
Xref c

xref Resourceop back to ToC or Object Property ToC

IRI: http://purl.orthodb.org/xrefResource

External reference URL
has domain
OrthoGroupSibling c
Xref c

Data Properties

aa Sequencedp back to ToC or Data Property ToC

IRI: http://purl.orthodb.org/aaSequence

protein sequence representing gene in OrthoDB
has domain
ODBgene c
has range
string

clade Total Species Countdp back to ToC or Data Property ToC

IRI: http://purl.orthodb.org/cladeTotalSpeciesCount

Count of species in the clade where OG is built
has domain
ODBgroup c
has range
integer

countdp back to ToC or Data Property ToC

IRI: http://purl.orthodb.org/count

count of something
has range
integer

descriptiondp back to ToC or Data Property ToC

IRI: http://purl.orthodb.org/description

Description of the term referenced
has domain
ODBgene c
ODBgroup c
Xref c
has range
string

gene Nb Exonsdp back to ToC or Data Property ToC

IRI: http://purl.orthodb.org/geneNbExons

Number of exons of the protein representing the gene in OrthoDB
has domain
ODBgene c
has range
int

gene Translated Lengthdp back to ToC or Data Property ToC

IRI: http://purl.orthodb.org/geneTranslatedLength

Length of the protein representing the gene in OrthoDB
has domain
ODBgene c
has range
int

genome I Dop back to ToC or Data Property ToC

IRI: http://purl.orthodb.org/genomeID

has range
string
is also defined as
object property

match Positiondp back to ToC or Data Property ToC

IRI: http://purl.orthodb.org/matchPosition

start..stop on sequence where signature matches
has range
string

namedp back to ToC or Data Property ToC

IRI: http://purl.orthodb.org/name

Name of the term referenced
has domain
ODBgene c
Xref c
has range
string

og Evol Ratedp back to ToC or Data Property ToC

IRI: http://purl.orthodb.org/ogEvolRate

Evolutionary rate over all OG genes
has domain
ODBgroup c
has range
float

og Functional Categorydp back to ToC or Data Property ToC

IRI: http://purl.orthodb.org/ogFunctionalCategory

Functional category COG
has domain
ODBgroup c
has range
string

og In Species Countdp back to ToC or Data Property ToC

IRI: http://purl.orthodb.org/ogInSpeciesCount

Count of species actually present in OG
has domain
ODBgroup c
has range
integer

og Median Exons Countdp back to ToC or Data Property ToC

IRI: http://purl.orthodb.org/ogMedianExonsCount

Median of exon counts over all OG proteins
has domain
ODBgroup c
has range
float

og Median Protein Lengthdp back to ToC or Data Property ToC

IRI: http://purl.orthodb.org/ogMedianProteinLength

Median of protein sequence lengths over all OG
has domain
ODBgroup c
has range
float

og Multi Copy Genes Countdp back to ToC or Data Property ToC

IRI: http://purl.orthodb.org/ogMultiCopyGenesCount

Count of multi-copy genes over all OG genes
has domain
ODBgroup c
has range
integer

og Percent In Speciesdp back to ToC or Data Property ToC

IRI: http://purl.orthodb.org/ogPercentInSpecies

Percentage of species actually present in OG vs. all species in the clade where the OG is built at.
has domain
ODBgroup c
has range
integer

og Percent Single Copydp back to ToC or Data Property ToC

IRI: http://purl.orthodb.org/ogPercentSingleCopy

Percentage of species having single-copy gene vs. all species in the OG
has domain
ODBgroup c
has range
integer

og Single Copy Genes Countdp back to ToC or Data Property ToC

IRI: http://purl.orthodb.org/ogSingleCopyGenesCount

Count of single-copy genes over all OG genes
has domain
ODBgroup c
has range
integer

og Stddev Exons Countdp back to ToC or Data Property ToC

IRI: http://purl.orthodb.org/ogStddevExonsCount

Standard deviation of exon counts over all OG proteins
has domain
ODBgroup c
has range
float

og Stddev Protein Lengthdp back to ToC or Data Property ToC

IRI: http://purl.orthodb.org/ogStddevProteinLength

Standard deviation of protein sequence lengths over all OG
has domain
ODBgroup c
has range
float

og Total Genes Countdp back to ToC or Data Property ToC

IRI: http://purl.orthodb.org/ogTotalGenesCount

Count of genes over entire OG
has domain
ODBgroup c
has range
integer

other Nameop back to ToC or Data Property ToC

IRI: http://purl.uniprot.org/core/otherName

has characteristics: functional

has range
string
is also defined as
object property

rankop back to ToC or Data Property ToC

IRI: http://purl.uniprot.org/core/rank

has range
string
is also defined as
object property

reference Proteomeop back to ToC or Data Property ToC

IRI: http://purl.uniprot.org/core/referenceProteome

has range
boolean
is also defined as
object property

scientific nameop back to ToC or Data Property ToC

IRI: http://purl.uniprot.org/core/scientificName

has characteristics: functional

has range
string
is also defined as
object property

sibling Similaritydp back to ToC or Data Property ToC

IRI: http://purl.orthodb.org/siblingSimilarity

Similarity between two sibling orthologous groups expressed in percent
has domain
OrthoGroupSibling c
has range
integer

strainop back to ToC or Data Property ToC

IRI: http://purl.uniprot.org/core/strain

has range
string
is also defined as
object property

tax Tree Distancedp back to ToC or Data Property ToC

IRI: http://purl.orthodb.org/taxTreeDistance

number of hops from the top of OrthoDB-selected NCBI taxonomy, e.g. Bacteria has 0 hops
has domain
OrthoGroupSibling c
has range
integer

Annotation Properties

common Nameap back to ToC or Annotation Property ToC

IRI: http://purl.uniprot.org/core/commonName

has domain
Taxon c

Legend back to ToC

c: Classes
op: Object Properties
dp: Data Properties

Acknowledgments back to ToC

The authors would like to thank Silvio Peroni for developing LODE, a Live OWL Documentation Environment, which is used for representing the Cross Referencing Section of this document and Daniel Garijo for developing Widoco, the program used to create the template used in this documentation.