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Table 1 Summary of existing anatomical ontologies and comparison with Uberon

From: Uberon, an integrative multi-species anatomy ontology

Ontology

Domain and applicability

Class count

Relations count

Relationship count

Text definitions

Computable definitions

Uberon

Animalia

6,546

IPD, 49

18,569

68%

35%

FMA

Homo sapiens (A)

80,467

IP, 15

124,392

1%

None

EHDAA2

Homo sapiens (AE)

2,397

IPD, 7

10,517

4%

None

MA

Mus (A)

2,982

IP, 2

3,775

None

None

EMAPA

Mus (E)

5,087

IP, 4

13,862

None

None

ZFA

Danio rerio (zebrafish) (AE)

2,656

IPD, 5

10,295

64%

None

TAO

Teleosti (bony fishes) (AE)

3,036

IPD, 5

4,828

49%

None

XAO

Xenopus (frog) (AE)

1,014

IPD, 6

2,238

72%

None

AAO

Amphibia (A)

1,601

IPD, 11

2,673

60%

None

FBbt

Drosophila (fruitfly) (AE)

7,110

IPD, 23

15,676

44%

24%

WBbt

C. elegans (nematode) (AE)

6,712

IPD, 6

12,187

70%

None

NCIt

Cancer-primarily Mammalia (AE)

3,506

IP, 3

5,913

67%

Yes

NIF [14]

Neuroscience-primarily Mammalia (A)

1,608

IP, 6

2,420

38%

Yes

BTO

All (AE)

630

IPD, 4

885

85%

None

EFO

Experimental factors all (AE)

1,004

IP, 5

1,127

55%

None

MESH

Indexing all (AE)

1,426

I

1,795

84%

None

BILA

Bilateria (AE)

114

IPD

132

44%

None

CARO

Metazoa (AE)

50

IP

49

100%

Nonea

PO

Viridiplantae (plant) (AE)

1,329

IPD, 7

2,180

100%

None

CL

Cells all (A)

1,925

IPD, 17

5,082

80%

48%

  1. The first column states the ontology (full names and descriptions of these ontologies are given in the text). The second column states the domain: A, adult/post-embryonic structures; E, embryonic/developing structures. The third column shows the number of classes. The fourth column shows which of the three core relations are used (I, is_a/subclass; P, part_of; D, develops_ from) together with the number of relations used. The fifth column shows the number of logical relationships in the ontology. The sixth and seventh columns show the percentage of the ontology that has definitions (textual and computable, respectively). In cases where the scope of an ontology extends beyond anatomy, we list only the anatomical subset. aThe beta OWL version of CARO includes computable definitions. AAO, Amphibian Anatomy Ontology; BILA, Bilaterian Ontology; BTO, Brenda Tissue Ontology; CARO, Common Anatomy Reference Ontology; CL, Cell Type Ontology; EFO, Experimental Factor Ontology; EHDAA/EHDAA2, Edinburgh Human Developmental Anatomy, abstract version/abstract version 2; EMAP/EMAPA, Edinburgh Mouse Atlas Project, EMAPA is the abstraction from all stages; FBbt, FlyBase Anatomy Ontology; FMA, Foundational Model of Anatomy; MA, Mouse Anatomy Ontology; MESH, Medical Subject Headings; NCIt, National Cancer Institute thesurus; NIF, Neuroscience Information Framework; PO, Plant structure Ontology; TAO, Teleost Anatomy Ontology; WBbt, Worm Anatomy Ontology; XAO, Xenopus Anatomy Ontology; ZFA, Zebrafish Anatomy Ontology.