I am discussing with the ontology communities OBO-relations, OBO, RO, GO, FMA about the relations that are used in the biology ontology. In RO, OBO there exists around 12 kinds of relations which are well defined under meronymy, class and spatial inclusion relations. With regard to the spatial inclusion relation I think that a few more relations needs to be introduced for connecting material spatial objects with materials. Because the relationships are require to create connections between a material with another material in relation to the manner in which they co-exist (nucleus enclosed_by nuclear membrane) and between a material and a material with respect to their arrangements (Histones wound_around DNA). With the existing set of spatial relations such as—located_in; contained_in; adjacent_to we cannot apply to the concepts such as nucleus and nuclear membrane; or mitochondria and double membrane. Inorder to connect these propositions, I propose the following:
nucleus enveloped_by/covered_by/enclosed_by/surrounded_by nuclear membrane
mitochondria enveloped_by/covered_by/enclosed_by/surrounded_by double membrane
However, which of the above is valid needs to be worked out by defining these relations. Well the community has invited proposals for such relations along with definitions.
Here is my proposal for such relationships:
encloses / enclosed_by
envelopes / enveloped_by
surrounds / surrounded_by
covers / covered_by
attaches / attached_to
connects / connected_to (RCC)
I am working on defining some of the above relations. I shall post later once the definitions are circulated in the community.