Post ABS activities

The ontology workshop preceding ABS (August 7-8) was quite successful and the three other organizers and I should soon be planning the next meeting, which will be the four of us meeting with other ontology types from the OBO community.  The poster at ABS wasn’t a huge success, but several people came by and most seemed to understand what I was trying to do, even if they hadn’t heard of NBO previously.  The take home for me was that having a relatively strong anatomy ontology helped overcome some of the annotation problems that NBO’s (lack of) coverage for spider related behaviors.

So what have I been up to since ABS.  Most of my arachnolinuga focus has been on attempting to properly support participant expressions, especially to be able to represent individuals properly.  There are numerous challenges here.  For example, how to represent a set (one or more) of legs that are part_of an individual spider.  ‘Some leg part_of Spider001’ doesn’t seem to fly, at least when I try to construct it in Protege, so I’m leery that even if the OWLAPI lets me create such an expression, other tools and reasoners will either ignore it or choke on it.  For the moment I am punting on this issue – specify an individual leg; if there are others explicitly mentioned, they can be specified as additional individuals, otherwise saying one leg was involved in an act is a failure of omission, which seems to be the lessor evil.

For the moment, this support is focusing on the arachadmin database and editor.  I will worry about OWL generation once the representation is stable in the database, which will, in turn, depend on what is required to sensibly build statements in the editor.

 

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One thought on “Post ABS activities

  1. Of course, I spoke in error in the second paragraph – you can define a class of legs that are part_of value Spider001. I knew that value restrictions existed, but Protege seems to provide less support for their expression than other types (some, cardinality, etc.) of class restrictions. So we are left with somewhat better specification – legs that are part_of male make contact with legs that are part_of female. Perhaps that is all we can extract in this case – not necessarily one-to-one contact relationship or even equal numbers of legs in involved or the full set of legs for each spider (probably wrong in any case).

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