1. Developing anatomy ontologies in the context of others Melissa Haendel, Chris Mungall, Carlo Torniai, Matt Yoder

2. lung respiratory gaseous exchange lobular organ parenchymatous organ solid organ pleural sac thoracic cavity organ thoracic cavity multicellular organismal process abnormal lung morphology abnormal respiratory system morphology GO MPO MA FMA abnormal pulmonary acinus morphology abnormal pulmonary alveolus morphology lung alveolus respiratory system process organ system respiratory system Lower respiratory tract alveolar sac pulmonary acinus organ system respiratory system EHDAA2 lung lung bud respiratory primordium pharyngeal region develops_from part_of is_a (SubClassOf) surrounded_by The problem: Data Silos

3. Differences in bone and bone tissue representation Ontology alignment

4. How to synchronize anatomy ontologies  “mapping”  Xref strategy  imports/MIREOT Three approaches:

5. There are issues with mappings Class AClass BIn Bioportal?Useful? FMA extensor retinaculum of wrist MA retinaYesNo FMA portion of bloodMA bloodNoYes ZFA MaculaMA maculaYesNo ZFA aortic archMA arch of aortaYesDubious ZFA hypophysisMA pitiuitaryNoYes FMA tibiaFBbt tibiaYesNo FMA colonGAZ Colón, PanamaYesNo PATO maleChebi maleate 2(-)YesNo

6. Zebrafish terms are is_a subtypes of teleost terms is_a Zebrafish Anatomy Teleost Anatomy Ontology Reconciliation and linking between TAO and ZFA Logic implemented via Xrefs- difficult to keep synchronized

7. Xref Semantics across ontologies treat-xrefs-as-equivalent: CARO treat-xrefs-as-equivalent: GO treat-xrefs-as-equivalent: VSAO treat-xrefs-as-is_a: VHOG treat-xrefs-as-reverse-genus-differentia: MA part_of NCBITaxon:10088 These are some assertions in UBERON, and relate the Xrefs in Uberon to classes in other ontologies using specified semantics. This allows merging of ontologies in taxonomically appropriate ways

8. Zebrafish terms are is_a subtypes of teleost terms is_a Zebrafish Anatomy Teleost Anatomy Ontology Reconciliation and linking between TAO and ZFA Logic implemented via Xrefs- difficult to keep synchronized X

9. Using Uberon for alignment facilitates identification of missing classes Ontology alignment

10. anatomical structure endoderm of forgut lung bud lung respiration organ organ foregut alveolus alveolus of lung organ part FMA:lung MA:lung endoderm GO: respiratory gaseous exchange MA:lung alveolus FMA: pulmonary alveolus is_a (taxon equivalent) develops_from part_of is_a (SubClassOf) capable_of NCBITaxon: Mammalia EHDAA: lung bud only_in_taxon pulmonary acinus alveolar sac lung primordium swim bladder respiratory primordium NCBITaxon: Actinopterygii Uberon classes connect to other ontologies via a variety of relations Uberon classes

11. Synchronization by reuse from external ontologies One can import a whole ontology or just portions of another ontology MIREOT: Minimum information to reference an external ontology term CARO VSAO TAOModularized ontology

12. To get the imports working well To have distributed social responsibility assigned Design patterns to ensure we are all doing the same thing To check for consistency and errors across multiple ontologies using reasoners to get correct results for all users -These ontologies are supposed to be orthogonal but aren’t always Visualization tools that can aid non-ontology experts in identifying errors across multiple ontologies Modularizing ontologies – We need:

13. Modularizing ontologies  Identify key points of integration between ontologies  Invest energy in understanding what is out there, i.e. seek to import and reuse, rather than “aligning” later  Modularize based on domain or taxon  Let the reasoner help do the work  Work together to distribute work

14. More about using ontologies together RO/BFO HAO RO/BFO

15. Ontologies can help reconcile annotations