The process of building ontologies is a difficult task that involves collaboration between ontology developers and domain experts and requires an ongoing interaction between then. 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.
Ontologies are wide-spread in the field of biology and biomedicine,
as they facilitate the management of knowledge and the integration
of information, as in the Semantic Web
However, building an ontology is a challenging task due to the
use of languages with a sophisticated formalism (such as OWL),
especially when combined with a complex domain such as biology
or medicine. Normally ontologies are built as a collaboration
between domain specialists who have the knowledge of the domain
and ontology developers who know how to structure and represent
the knowledge; they have to work together to construct a robust
and accurate ontology. Often, community involvement during the
process of building ontologies using meetings, focus groups and the
like is very important
Biologists represent, manipulate and share their data in a widevariety of tools such as Microsoft Excel spreadsheets and Word documents. Unfortunately, these environments are far removed from the formal structured representation of the ontology development environments with which the ontologists work to build ontologies. As a result of this difference in tools it is unclear how we can bridge the gap between the the two groups; this would be useful to facilitate the interaction between domain specialists and ontologists and help to make more convenient for both sides to read and/or manipulate the ontology.
Ontology development environments are designed to produce
formal structured representation of any domain. Either using GUI
software such as Prote´ge´ 1 or a textual programmatic environment
such in Tawny-OWL
There are various tools for constructing and developing ontologies
with a variety of user interfaces and environments. The most popular
is Prote´ge´ which is an open-source tool that provides a user interface
to develop and construct ontologies of any domain. It has been
widely used for developing ontologies due to the variety of
plugins and frameworks
Conversely, Tawny-OWL is a textual interface for developing
ontologies in a fully programmatic manner
Recently, we have developed tolAPC ontology using a new
document-centric approach by including an Excel spreadsheet
directly in the development pipeline. The spreadsheet contains all
knowledge for the ontology which has been created and maintained
by a biologist. Meanwhile, we design the ontology patterns using
Tawny-OWL, then generate the axioms by extracting data from
the spreadsheet using Clojure. Thus, Tawny-OWL contains the
1 http://protege.stanford.edu/
spreadsheet as a part of the source code; which can be freely updated
and the ontology regenerated when needed. Hence, it remains as a
part of the ontology development process
In this approach, the Excel spreadsheet is totally developed by biologists; this has a significant advantage because it is a tool which they are familiar with and find convenient. However, we cannot ensure that the programmatic transformation of the values in the spreadsheet to the final ontology conforms with the domain specialists understanding, without the biologists reading and interacting with source code. Therefore, next we will discuss the probabilities of making this ontological source more readable by the specialists. 3
The first and most obvious mechanism for increasing ontology readability is to enable users to read and write the ontology using their native language. Internationalisation technologies are widespread and enable support for multiple languages for applications with a graphical user interface.
We next consider how we can enable support for multiple languages in textual user interface such as Tawny-OWL, giving the ontologist the ability to use their own native language for all parts of the development process.
The first option is using polyglot library. This part of the system mimics a fairly standard technique for internationalisation of programmatic code; the ontology is developed with a set of programmatic labels which are then referenced in a language, or locale bundle with an appropriate translation. In the case of TawnyOWL, this translation appears as rdfs:label annotations on the ontology entities (classes, properties etc). This overall process is shown in Figure 1, placing Italian and Arabic language translations onto the pizza ontology.
While this may enable internationalisation for users of
the ontology, it does not change the English-centric editing
environment. We would wish, instead, to internationalise the
entire source code of the ontology. This will make the entire
ontology more comprehensible and readable for all developers who
communicate in Italian and/or Arabic. This is fully supported with
a full conversion of the environment using the multilingual feature
of Tawny-OWL as in Figure 2, which shows the English, Italian
and Arabic version of the pizza ontology
These multilingual environments are advantageous for being readable and comprehensible by users when using their own language. This still leaves us in a programming environment, which is an environment unlikely to be familiar or comfortable to the most domain users. Moreover the ontology lacks a narrative structure, which means that it cannot be read in a literate fashion. We consider how to enable this in the next section. 4
The term literate programming was invented by
As Tawny-OWL is a fully programmatic environment, we can add comments freely, along with any additional mark-up that we wish. This enables us to produce different representation of the ontology.
We have previously discussed two examples of literate ontologies:
the first is the Amino Acid Ontology, taken from a previous
ICBO2015 tutorial about Tawny-OWL 2, while the second is a
version of the Karyotype ontology
Literate ontologies can be represented in different forms; using the various techniques for converting the markup text into different formalisms; webpages for example. Representing the ontology as an HTML webpage gives us the ability to navigate and browse the documentation either in order (section by section) or with a navigation facility (jumping between sections). It is also possible to hide or expose the “source” sections, leaving the reader to see just the documentation as appropriate. From the developer perspective, while the reader may still not be able to see the axiomatization in this way, the comments that they have checked are embedded directly next to the code which is an interpretation of them.
It is interesting to enable specialists to read and navigate through the ontology and its documentation. However, with HTML there are no editing facilities to modify and update the ontology. Therefore, rather than using HTML, we have also investigated the possibility to turn the whole ontology into a Word document, an environment which can also be modified, changed or updated. Now biologists and domain specialists are placed in an environment in which they can freely provide feedback on an existing ontology simply by interacting with Word documents. 5
In this paper, we have described our approach to the translation of ontologies into a form that domain users can interact with more naturally.
We have shown that it is possible to translate a textual environment like Tawny-OWL into another human language, or indeed a different script, including right-to-left text. To our knowledge, this is the first ontology editing environment with such textual and syntactic flexibility. Despite the fact that the multilingual ontologies approach is less relevant for scientific ontologies, it is already applied by some means in some cases of terminologies. For example, the use of some and only in Tawny-OWL rather than using universal and existential notations which implies the agreement for using alternative language for ontology development.
Further than this, however, we also translate the ontological source code into alternative visualisations such as HTML and Word documents which map directly back to the source, but which can differ from it: for instance, by enabling hyperlinks, adding section links and hide source code in favour of commentary. Especially with a Word document, this should enable a novel mechanism for interacting with an ontology: users can see and edit comments, with change tracking switched on, and use this as mechanism for feeding back to the ontology developer.
Using this approach, of course, only enables us to visualise
ontologies developed using Tawny-OWL. While a migration path
is provided
We still need to evaluate this kind of interaction rigorously. For this, we are proposing a focus group test which will be include specialists participants to read the document of the ontology and provide their opinion about it and whether they prefer to update any terminologies according to their expertise.
We are not proposing that Word documents will be directly used
by domain specialists for editing ontologies. We expect that an
ontologist will be involved with incorporating changes suggested
back to the domain user; in this sense, we are using a Word
document as an intermediate representation
Thanks to Newcastle university for supporting this research. Also, thanks to King Abdulaziz University, Jeddah, Saudi Arabia for funding and supporting the study.