1. The cell ontology covers multiple taxonomic contexts OntologyContext# of links to cl MAadult mouse1 FMAadult human658 XAOfrog63 AAOamphibian ZFAzebrafish391 TAObony fish385 FBbtfruitfly53 POplants* CLall cells-

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

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 (Danio rerio) Annotations: ‘obo foundry unique label’ ‘zebrafish amacrine 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 ‘zebrafish amacrine cell’

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

5. Adding taxonomic knowledge to multi- species ontologies Kusnierczyk JBI 2008 – Taxonomy-based partitioning of the Gene Ontology Deegan BMC Bioinformatics 2010 – Added the following links to GO: only_in_taxon : part_of only never_in_taxon : part_of only not – Can be used in any multi-species ontology Phenoscape – Annotating variability across taxa