a primer for constructing and analyzing conceptual structures

May 20, 2011

Refined concept mapping, a development over the regular concept mapping is an approach towards introducing rigor and parsimony in representing knowledge. The method proposed suggests substitution of the ambiguous relation names with well-defined relation names to concepts consistently while mapping a domain. We suggest the use of
this method for introducing rigor in concept mapping and position it among other models of knowledge representation in an inverse semantic spectrum. This paper was presented at the 18th ICCS 2010 conference.

Now in continuation, we have proposed to develop a primer (guide, tutorial) that can be used to apply RCM as a methodology for representing knowledge. This has been accepted at the CSLTA 2011 workshop to be held in conjunction with the 19th ICCS 2011 conference.

In this paper, a rationale and proposal for developing a primer for teaching-learning of conceptual structures is presented. The skills required and developed by an engagement of constructing and analyzing conceptual structures are richer and easier to be dealt with in school education. The teaching-learning context of CS is fundamental and important enough to introduce the topics from logic, philosophy, computer science and linguistics. A proposal is made for the formation of a special interest group for the primer. More about the paper.

The framework of the primer comprises of Units (lesson plans) with specific Learning Objectives. We suggest that the primer can serve as a guide to areas such as knowledge representation, conceptual structures, etc.


introducing rigor in concept maps

August 9, 2010

i have been working in the area of refined concept maps for science education. so far we have communicated our research in conferences on science education, concept mapping, etc.

recently, our work got published in Springer’s LNAI  book.  the paper ‘introducing rigor in concept maps’ was presented in the 18th international conference on conceptual structures 2010 at kuching, malaysia. the paper talks about applying rigor by focusing on relation names, the re-representation of sentences to propositions in RDF triples format, and how the refined concept mapping methodology can act as a bridge between informal and formal models of knowledge bases.

Meena Kharatmal & Nagarjuna G.: Introducing rigor in concept maps. In M. Croitoru, S. Ferre, and D. Lukose (Eds.), ICCS 2010, LNAI 6208, pp. 199-202, Springer Verlag 2010.

I acknowledge:

  • HBCSE for providing with funding support for the conference
  • ICCS 2010 for providing sponsorship for tutorials and workshops

citations to our work on refined concept mapping

June 16, 2010

being a phd student and getting to know that my research work is being cited by peers is good news!

google scholar shows it all.

cheers to peers!

check out papers on refined concept mapping from the publications page of my blog.


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.


concept mapping – article in indian journal

November 24, 2009

I have been always thinking to publish our research work for an Indian audience. Atleast in India, the community of educationists, teachers, etc., get to know what we are working on. With this objective, I had
submitted some preliminary findings of my Ph.D. work to an Indian Journal. The following research paper has been published in the Indian Educational Review (a journal published by NCERT).

Kharatmal M. (2009): Concept Mapping for Eliciting Students’ Understanding of Science. Indian Educational
Review. 45(2), pp.31-43.

The article is on display in our library. I have also uploaded the article which can be downloaded from the publications page of my blog


change in the names of scientific terms in marathi textbooks

September 12, 2009

Today, discussion over lunch made me curious to find out who decides the changes in the scientific terms that are used in the textbook.

We were discussing about the Marathi Vishwakosh Project that HBCSE is involved in. In the early years of HBCSE, V G Kulkarni (Founder Director, HBCSE)  instigated the project on language in science. Since then, there are a few members who are working in this area.

Deshmukh explained the volumes of work that the project is coming up with. It has been decided to bring a separate volume for biology subject and produce it in three parts. Related to the scientific terminology, he mentioned that a few scientific terminology in marathi textbook has been changed and hence the members have to pay heed to the latest usage of the term. He gave two instances of such change: the marathi term for auricle has been changed from karnika to alind; for ventricle it has been changed from javanika to nilay;  the other instance of marathi term for skull has been changed from kavati to karkara. I was anxious to know why the name of the terms got changed, who decides that such change is required in textbook, what is the rationale behind it. May be the textbook bureau decides about these changes. Jayashree too agreed, and she added that it could be that they want to give a more specific word for a very specialized part.

But i am not yet convinced. Can a name of a scientific term change over a period of time. Well of course, if the meaning that is implied to it changes. But in this case, atleast the meanings of auricle, ventricle, skull  are not yet changed, and their english names of terms are still the same. So what makes the marathi language textbook bureau to change it. Then we thought we should check the bodies/organizations who possibly could be involved in this work. We all headed to the library, and referred a few books related to Vishwakosh, Paribhasha Granth, etc. We could find atleast two bodies who have been involved in this work since the 1970s: Bhasha Sanchalanalay (Directorate of Language); and Maharashtra Rajya Sahitya-Sanskriti Mandal (Maharashtra State Board of Literature and Culture). Perhaps one can write/meet these people and find out more.

As i am also interested in the language of science, all this discussion has made me more curious, and i am into finding out as to who decides the changes in the scientific terms and what is the rationale behind it.


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.


what is so different about GNOWSYS

April 7, 2009

Gnowsys can be used to represent structural knowledge, process modelling, as far as scientific knowledge is concerned. But then there also exists several other modelling tools such as—OBO-edit, Protege, OPM, KEGG, Virtual Cel, Cell Designer, Reactome, GO, etc. which can as well represent knowledge. So then, an obvious query that comes to my mind is  what is so different about Gnowsys? Isn’t it just an addition to the existing modelling tools. Nagarjuna explained that the differences are in the form mentioned below:

One of them is the architecture of Gnowsys itself being different with the other tools. As per the gnowsys architecture, everything that goes in is a node for e.g. concept, concept type, instance, relation, relation type, attributes, attribute type, are all stored as nodes, but in the form of networked nodes. A node cannot have meaning on its own. Its meaning is established only by its neighborhood. For instance, X is related to Y, and it can have many such simple relations.  This is in accordance, with the theory that knowledge exists in a network. If we want to understand what is force, then its understanding can be acquired depending on what relations does the concept force shares with other concepts like, mass, inertia, acceleration, etc.

Gnowsys can create versions even if there is a single (simple) change to a node. This change can be in the form of either adding a node, editing a node, adding a relation, editing a relation, deleting a relation. From this list even if there is change in just one kind, then also it can create versions and record the history. This kind of change is accordance with the degrees of conceptual change that Paul Thagard explains in his book Conceptual Revolutions. According to Thagard,  conceptual change can occure when there is addition of concepts, addition of relations. With this model of versioning, gnowsys can record the changes that ocurs in people’s conceptual framework, thus enabling to trace the conceptual changes.

Another difference is that gnowsys does not store knowledge in any kind of file system. It is on the web, in another way to put it, gnowsys does not ask in which file format should it save the knowledge created. But at the same time, it can possibly exchange to various formats that of OWL.

The other difference is that gnowsys can store multiple ontologies. Using just one application of Gnowsys, it would be possible to store structural knowledge, process, metabolic pathways, etc. It will be interesting to see the multiple ontologies by importing a few of the existing ontologies (can be cell division, gene ontology, metabolic pathways, environment ontology,  etc.)  from the public domain and from several different places and allow these ontologies to store in gnowsys.

It would be useful to know, if there are other differences.

This excerpt is based on discussion over tea.


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