Table 1

Granularity Schemes used in Ontologies of Anatomy.

Levels of Granularity [ordered from fine < coarse]

Domain/Application

Parent Class Affiliation

Ontology/Controlled Vocabulary

Version


'macromolecular complex' < 'organelle part' < 'organelle' < 'cell part' < 'cell';

additional types: "envelope', 'extracellular region', 'extracellular region part', 'membrane-enclosed lumen', 'symplast', 'synapse', 'synapse part', 'virion', 'virion part'

genomic and proteomic

'cellular component'

Gene Ontology (GO)

1.689


units of structural organization: 'Biological macromolecule' < 'Cell' < 'Portion of tissue' < 'Organ' < 'Organ system' < 'Cardinal body part' < 'Body';

subdivisions/cardinal parts of units: 'Cardinal cell part', 'Cardinal tissue part', 'Cardinal organ part', 'Organ system subdivision', 'Subdivision of cardinal body part';

'cross-granular' types, spanning over several levels of granularity: 'Acellular anatomical structure', 'Anatomical cluster', 'Gestational structure', 'Vestigial embryonic structure'

human anatomy - to a limited degree also vertebrate anatomy

'Anatomical structure'

Foundational Model of Anatomy (FMA)

3.0


MicroscopicStructure, in no clear order: 'Cell', 'CellularStructure', 'Cilium', 'Liposome', 'MicroOrganism'

OrganicSolidStructure: 'Cell' < 'Body structure' < 'Organism'

medical coding and classification, medical terminologies,

'MicroscopicStructure'; 'OrganicSolidStructure'

Galen

1.1


'Microanatomic Structure' [i.e.: 'Macromolecular Structure' < 'Cell'] < 'Tissue' < 'Organ' < 'Organ System' < 'Body Part' - 'Body Region';

additional types: 'Body Cavity', 'Body Fluid or Substance', 'Embryologic Structure or System',

medical coding for clinical care, translational and basic research, and public information and administrative activities

'Anatomical Structure, System, or Substance'

NCI Thesaurus

09.07


No clear order: 'Body organ structure', 'Body region structure', 'Body space structure', 'Body system structure', 'Body tissue structure', 'Body wall structure', 'Cell structure', 'Developmental body structure', 'Entire anatomical structure', 'Human body structure', 'Intercellular anatomical structure', 'Non-human body structure', 'Sex structure', 'Structure of bilateral paired structures', 'Structure of multiple topographic sites', 'Structure of product of conception', 'Transplant'

clinical terms

'Anatomical structure'

SNOMED-CT

2009_01_31


'cell' < 'portion of tissue' < 'multi-tissue structure' < 'compound organ' < 'organism subdivision' < 'whole organism'

Zebrafish anatomy and development

'anatomical structure'

Zebrafish anatomy and development

1.22



Xenopus anatomy and development

Xenopus anatomy and development

1.19


'cell' < 'portion of tissue' < 'multi-tissue structure' < 'compound organ' < 'organism subdivision' < 'body'

multispecies fish anatomy

'anatomical structure'

Teleost anatomy and development

1.120


'Biological small molecule' < 'Biological Macromolecule' < 'Cell part' < 'Cell' < 'gross anat structure' < 'Organism';

with 'gross anat structure' comprising: 'Organ part' < 'Organ' < 'Body part subdivision' < 'Body part' < 'Body'

vertebrate anatomy; derived mainly from FMA

'Biological object''

Basic Vertebrate Anatomy

1.1


No clear order: 'anatomic region', 'body fluid or substance', 'organ system'

anatomical dictionary for the adult mouse

'adult mouse'

Mouse adult gross anatomy

1.195


No clear order: 'adipose tissue phenotype', 'cardiovascular system phenotype', 'cellular phenotype', 'craniofacial phenotype', 'digestive/alimentary phenotype', etc.

standard terms for annotating mammalian phenotypic data

'mammalian phenotype'

Mammalian phenotype

1.298


No clear order: 'anatomical system', 'embryonic structure', 'larval structure', 'tissue'

a structured controlled vocabulary of the anatomy of Amphibians

-

Amphibian gross anatomy

1.8


'Anatomy', 'Cell', 'Nucleus';

with 'Anatomy' comprising: 'axis', 'body region', 'extracellular component', 'organ', 'organism'

anatomy of C. elegans

'C. elegans Cell and Anatomy Ontology'

C. elegans gross anatomy

1.31


'cell component' < 'multi-cell-component structure' < 'cell' < 'portion of tissue' < 'multi-tissue structure' < 'organ system subdivision' < 'organ system' < 'organism subdivision' < 'organism';

additional types: 'acellular anatomical structure', 'anatomical structure with acellular and cellular components', developing anatomical structure', 'endocrine organ', 'cell cluster organ', 'compound cell cluster organ', 'sense organ'

anatomy of Drosophila melanogaster

'anatomical structure'

Drosophila gross anatomy

1.30


'cell component' < 'cells' < 'portion of tissue' < 'multi-tissue structure' < 'compound organ' < 'organism subdivision' < 'multi-cellular organism'

additional types: 'acellular anatomical structure', 'anatomical group', 'egg', 'extraembryonic structure',

a structured controlled vocabulary of the anatomy of mosquitoes.

'anatomical structure'

Mosquito gross anatomy

1.10


'acellular anatomical structure', 'portion of organism substance', 'whole organism';

remarkably with 'organ system' as a subtype of 'whole organism'

an ontology for spider comparative biology including anatomical parts, behavior, and products

'anatomical entity'

Spider Ontology

1.17


'cell component' < 'cell' < 'portion of tissue' < 'multi-tissue structure' < 'compound organ' < 'organism subdivision' < 'multi-cellular organism'

additional types: 'acellular anatomical structure', 'anatomical group', 'bar', 'carina', 'extraembryonic structure', 'inflection', 'ruga', 'sculpture', 'sense organ', 'sulcus'

anatomy of Hymenoptera

'anatomical structure'

Hymenoptera Anatomy Ontology

SVN Revision 2804


'cell component' < 'cell' < 'portion of tissue' < 'multi-tissue structure' < 'compound organ' < 'organism subdivision' < 'multi-cellular organism'

additional types: 'acellular anatomical structure', 'anatomical group', 'embryonic structure', extraembryonic structure',

anatomy of Bilateria

'anatomical structure'

Bilateria anatomy

-


'plant cell' < 'tissue' < 'organ' < 'whole plant'

additional types: 'gametophyte', 'in vitro cultured cell, tissue and organ', 'sporophyte'

botanical anatomy & morphology

'plant structure'

Plant structure

1.64


No clear order: 'composite structure', 'fruitbody', 'hypha', 'mycelium', 'pseudohypha', 'sporophore', 'unicellular structure'

a structured controlled vocabulary for the anatomy of fungi.

'microbial structure ontology'

Fungal gross anatomy

1.3


fiat object part: 'Regional Part Of Cell Component' < 'Regional Part Of Cell'

object: 'Molecule' < 'Cellular Component' < 'Cell' - 'Extracellular Structure'

object aggregate: 'Aggregate Object' < 'Population'

biomedical structures from macromolecules to supracellular level

'fiat object part', 'object', 'object aggregate'

Subcellular Anatomy Ontology (SAO)

1.2.5


'cell component' < 'cell' < 'portion of tissue' < 'multi-tissue structure' < 'compound organ' < 'organism subdivision' < 'multi-cellular organism'

additional types: 'acellular anatomical structure', 'anatomical group', 'extraembryonic structure',

cross-species anatomy: platform for integrating different species-specific anatomy ontologies

'anatomical structure'

Common Anatomy Reference Ontology (CARO)

1.3


No clear order: 'acellular anatomical structure', 'anatomical group', 'anepisternum', (...), 'cell', 'cell part', 'cerebellum lobule vi', etc.

multi-species anatomy, generated from union of existing species-specific anatomy ontologies

'anatomical structure'

Uber anatomy ontology (UBERON)

1.72


No clear order: 'appendage', 'body part', 'cardiovascular system', 'craniofacial tissue', 'developmental tissue - animal', 'digestive system', 'fat tissue', etc.

Minimal set of terms for anatomy

'animal component'

Minimal anatomical terminology (MAT)

1.1


'subatomic particle' < 'atom' < 'molecular entity' < 'poly molecular composite Entity' [i.e. 'molecular complex' < 'structured nonbiological entity'/'structured biological entity' [i.e. 'cellular component' < 'cell' < 'organism part' < 'organism']]

biomedicine

'material entity'

BioTop

-


Various ontologies and their partly implicit, partly explicit levels of granularity of anatomical structures (from [50]).

Vogt BMC Bioinformatics 2010 11:289   doi:10.1186/1471-2105-11-289

Open Data