Ontologies in the Fish Tank: Using the Zebrafish Anatomy Ontology with other OBO Ontologies to Annotate

Expression and Phenotype

Yvonne Bradford*, Ceri Van Slyke

Outline

1. Use of Modular Ontologies to generate post composed entities2. How does ZFA synchronize with the CL?

ZFIN has successfully used modular ontologies to generate post composed

entities for expression curation and E+Q(+E) statements for phenotype curation

For expression ZFIN utilizes the ZFA by itself or in conjunction with ZFA, GO-CC, and Spatial Ontologies for post composed entities

For Phenotype curation ZFIN utilizes the ZFA, GO-MF, GO-BP ontologies that can be post composed with the ZFA, GO-CC, GO-MF, Spatial, or

MPATH ontologies to create post composed Entities

Built in restrictions for valid use of Entity + Quality terms

Selecting relational quality terms automatically opens the E2 field to allow for annotation of related Entity

Outline

1. Use of Modular Ontologies to generate post composed entities2. How does ZFA synchronize with the CL?

• What is the best way to sync ZFA and CL?• Should ZFA be MIREOTing CL?• Which format is better for syncing? OBO vs. OWL• What tools are available to sync? – We would like tools that allow for:

1. automatic syncing2. that identify when a cycle will be created in outside ontologies3. create logical defs for those terms that are added 4. the ability for editors to accept or reject terms that are added5. the ability to revert ontology after changes are made

• When syncing – what about multiple paths to root?

ZFA erythroblast is_a TAO erythroblast, is_a CL erythroblast and TAO erythroblast is_a CL erythroblast

1. How are multiple paths to root dealt with in syncing and do tools identify this?2. How do leaf node ontologies make sure changes in higher ontologies do not cause

problems in the structure of the leaf node ontology?

Effectively Synchronizing is a Challenge