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The cell ontology covers multiple taxonomic contexts

The cell ontology covers multiple taxonomic contexts. Shared terms. cross-ontology link (sample). caro / uberon /all. cell. tissue. import. metazoa. skeleton. nervous system. gut. gonad. appendage. circulatory system. gland. mesoderm. respiratory airway. larva. muscle tissue.

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The cell ontology covers multiple taxonomic contexts

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  1. The cell ontology covers multiple taxonomic contexts

  2. Shared terms cross-ontology link (sample) caro /uberon/all cell tissue import metazoa skeleton nervous system gut gonad appendage circulatory system gland mesoderm respiratory airway larva muscle tissue skeletal tissue mollusca arthropoda vertebrata trachea bone mantle mushroom body limb fin vertebra tibia shell cuticle vertebral column foot antenna mesonephros parietal bone cephalopod drosophila teleost mammalia amphibia tentacle neuron types XYZ weberianossicle mammary gland tibiafibula brachial lobe mouse human zebrafish NO pons

  3. Xref macros: an easy way to formally connect to broader taxa treat-xrefs-as-genus-differentia: CL part_of NCBITaxon:7955 … [Term] id: ZFA:0009255 name: amacrine cell xref: CL:0000561 is_a: ZFA:0009051 ! interneuron relationship: part_of ZFA:0000119 ! retinal inner nuclear layer  Class: ZFA_0009051 (amacrine cell) EquivalentTo: CL_0000561 (amacrine cell) and BFO_0000050 (part of) some NCBITaxon_7955 (Daniorerio) Annotations: ‘obo foundry unique label’ ‘zebrafishamacrine cell’ … ZFA:amacrine cell is the taxonomic equivalent of CL:amacrine cell in zebrafish In the context of ZFA, it is called simple ‘amacrine cell’; In the context of the entire OBO Foundry, it is called ‘zebrafishamacrine cell’

  4. Synchronization through reasoning • Example • HAO:pleurite = INSECT:pleurite and part_of some Hymenopteran • HAO:pleurite = INSECT:pleurite and part_of some Hymenopteran • INSECT:pleuriteSubClassOfINSECT:sclerite •  • HAO:pleuriteSubClassOfHAO:sclerite • Approach is enhanced by • Logical definitions and other logical axioms in source ontologies • Taxonomic knowledge

  5. Adding taxonomic knowledge to multi-species ontologies • KusnierczykJBI 2008 • Taxonomy-based partitioning of the Gene Ontology • DeeganBMC Bioinformatics 2010 • Added the following links to GO: • only_in_taxon : part_of only <T> • never_in_taxon : part_of only not <T> • Can be used in any multi-species ontology • Phenoscape • Annotating variability across taxa

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