my presentation at the annual research meet

February 18, 2010

as part of annual research meet in HBCSE, I presented the current work of my ph.d.  It was mainly focussing on “to determine a fixed set of relation names to represent secondary school level cell biology”. The abstract can be read from here.  there were useful inputs and comments on the work.

the presentation depicted the number of concepts at 8,9,11 standards and the number of relation names required to link these concepts.


minimal set of relation names in RCM

June 30, 2009

as part of my ph.d. work in the area of refined concept map (RCM) in biology education, i am working on analyzing the school textbooks of 8, 9, 11 standards on the domain of cell biology. i mapped the domain of each 3 standards using the RCM method i.e. using a fixed and a minimal set of relation names for mapping the concepts.  the hypothesis of the study was that even if the complexity in the domain increases with an increase in the number of concepts, but the relation names that provide meaning to these concepts would be a fixed and a minimal set. the following is a brief summary of the results:

std.          no. of concepts             no. of relation names

8                             75                                        11

9                           195                                        16

11                         500                                        15

the most widely used relation names are: consists of, includes, comprised of, surrounded by, located in, has function, has attribute.

i am also analyzing the other components involved, such as the frequency of relation names, the no. of concepts connected to specific relation names, etc.  across all the 3 standards.

it is really an interesting and exciting exercise which i enjoy working on.

negation of relation names

June 25, 2009

In the relations ontology we express:
eukaryotes consists of nucleus  ==> consists_of(eukaryotes, nucleus)
eurkaryotic cell enveloped by cell membrane ==> enveloped_by(cell, cell membrane)

as I am representing the school textbook, I find a few sentences to be of the form of negation. These are:

prokaryotes does not consist of nucleus ==> ~consists_of(prokaryotes, nucleus)
prokaryotes not enveloped by membrane  ==> ~enveloped_by(prokaryotes, membrane)

Such negations are useful for students to understand the difference between eukaryotes and prokaryotes and cannot be avoided during representation.

so my query is: can we include the negations of relation names in the relations ontology. how can we represent such negation relation names.

since ~consists_of, ~enveloped_by are negation of consists_of, enveloped_by respectively, does the relation names ~consists_of, ~enveloped_by still fall under the meronymic inclusion and spatial inclusion  respectively.

I think so.  In the above assertions, we know in reality that prokaryotes donot consists of nucleus, but this is equally important for representation. In cases such as something may cease to exist at a particular time t then we still have to represent such assertions even though these would be in negation forms.

But the question that is grappling my mind is the following:

ontology is the representation of types. it represents what exists in reality. now something that does not exist in reality, and yet if we want to represent it then would we still be creating ontology of non-existent entities. and if yes, then would it still be  ontology.

Perhaps, philosophers can  provide a convincing argument for my question.

relations and functions in biology

May 27, 2009

As we know that functions (1 to 1) are different from relations (1 to many). All functions are relations, but not all relations are functions. In the case of creating an ontology for biology, we use relations. But, in biology, is it possible to apply the functions as well. Can there be any such relation which is a function in the case of biomedical ontology. For example, part-of, composed-of, located-in, surrounded-by, etc. are all relations in the context of biomedical ontology. Or do we have to always understand biology ontology in terms of relations only and not functions.

Prof. Barry Smith (University of Buffalo) clarifies the distinction between ontology of relations and the way relations and functions are treated in a set theory. Further he emphasizes on the functional associations (in mathematical sense) can occur in process relations. For example, process-a regulates process-b.

Now this sounds interesting. In this case, I think, some of the process relations can be functional. Such process relations are : regulates, transforms into, derives from, develops into, preceded by, results into, etc.

Let me illustrate with a few assertions:
Larva transforms into pupa
zygote develops into foetus
blastula transforms into gastrula

What I am trying to point out is that the domain and range for these process relations will always be of  1 to 1 mapping. So, these process relations can be of functional type.

But the structural relations such as part of, surrounded by can not be of functional type as a domain can have many ranges in such relations.

P.S. This post is based on my discussion on relations and functions in biology on the OBO mailing list.