what is so different about GNOWSYS

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.


2 Responses to what is so different about GNOWSYS

  1. gnowgi says:

    Wish to add a significant point to the description above. Since we intend to bring all nodes in one network, no node should repeat. The network is a set of nodes, where the term ‘set’ is used in the technical sense of the term. Second, network is not a serial sequential form as textual representation is.

    Another point I made was: for storage as well as query we aggregate each node and its neighbourhood as the unit of network.

    In the third version of the concept paper that I am currently working on, I have addressed this question. Will upload the new version soon.

  2. Ya thanx Nagarjuna for your comments. Looking forward to the new version of the concept paper on gnowsys.

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