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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.