User and Developer Interaction with Editable and Readable Ontologies

The process of building ontologies is a difficult task that involves collaboration between ontology developers and domain experts and requires an ongoing interaction between them. This collaboration is made more difficult, because they tend to use different tool sets, which can hamper this interaction. In this paper, we propose to decrease this distance between domain experts and ontology developers by creating more readable forms of ontologies, and further to enable editing in normal office environments. Building on a programmatic ontology development environment, such as Tawny-OWL, we are now able to generate these readable/editable from the raw ontological source and its embedded comments. We have this translation to HTML for reading; this environment provides rich hyperlinking as well as active features such as hiding the source code in favour of comments. We are now working on translation to a Word document that also enables editing. Taken together this should provide a significant new route for collaboration between the ontologist and domain specialist.Comment: 5 pages, 5 figures, accepted at ICBO 2017, License update

A document-centric approach for developing the tolAPC ontology

Abstract Background There are many challenges associated with ontology building, as the process often touches on many different subject areas; it needs knowledge of the problem domain, an understanding of the ontology formalism, software in use and, sometimes, an understanding of the philosophical background. In practice, it is very rare that an ontology can be completed by a single person, as they are unlikely to combine all of these skills. So people with these skills must collaborate. One solution to this is to use face-to-face meetings, but these can be expensive and time-consuming for teams that are not co-located. Remote collaboration is possible, of course, but one difficulty here is that domain specialists use a wide-variety of different “formalisms” to represent and share their data – by the far most common, however, is the “office file” either in the form of a word-processor document or a spreadsheet. Here we describe the development of an ontology of immunological cell types; this was initially developed by domain specialists using an Excel spreadsheet for collaboration. We have transformed this spreadsheet into an ontology using highly-programmatic and pattern-driven ontology development. Critically, the spreadsheet remains part of the source for the ontology; the domain specialists are free to update it, and changes will percolate to the end ontology. Results We have developed a new ontology describing immunological cell lines built by instantiating ontology design patterns written programmatically, using values from a spreadsheet catalogue. Conclusions This method employs a spreadsheet that was developed by domain experts. The spreadsheet is unconstrained in its usage and can be freely updated resulting in a new ontology. This provides a general methodology for ontology development using data generated by domain specialists