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In the process of developing ERO in compliance with eagle-i project requirements, we have learned important lessons related to best practices for biomedical ontology development and interoperability with other ontology-based resource systems and community ontologies :

1. Reuse of existent ontologies

2. Use of layered import strategy

3. Best practices and Tools

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1. Reuse of existing ontologies

Using upper level ontologies such BFO and trying to reuse existing ontologies following the OBO Foundry orthogonality principles  has the advantage of guiding the development process and enabling the integration of other ontologies. However, when it comes to driving application UIs directly from an ontology, there is a need for implementation methods which exclude some upper level classes, specify or modify properties domain and range and deal with different modeling approaches (as not all the ontologies we have reused follow the same principles).

2. Use of layered import strategy

The strategy we used to separate the core and the application layer has shown its effectiveness as it has enabled parallel ontology development. The challenges it presents are related to keeping the annotations current and in preventing excessive proliferation of annotation properties as a quick way to simplify application development complexity. We have identified some common requirements in terms of annotations that are useful to drive a UI directly from an ontology and we will formalize them as design pattern.

3. Best practices and tools

For the development process, we have used Ontofox as a useful tool to MIREOT classes form other ontologies and generate our imports files. To drastically streamline this process, we developed scripts to automate the syncing of import files. To have the whole MIREOT roundtrip process integrated into an ontology editor such Protege would be ideal (i.e. selection of terms from an external ontology, updates to imported terms in the proper import files and checks of the ontology's consistency). We also identified the need to provide some community views or 'slims' with different content granularity and axiomatic complexity. Although at the present time there are some useful tools to facilitate this process (Ontodog)  to have these facilities integrated into an editing tool would be ideal.

Review process

Before the official release we have asked Jie Zheng and Melanie Courtot to review the ontology. The reviewers' comments and the actions taken are available in this Google doc. 

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