Putting an ontology of the atoms in order


I’ve come to the end of one thread of my playing with an ontology of the Periodic table of the Elements – thanks to an excellent third year project by Ionica Durchi. I’ve already written about an ontology of the atoms, where each atom is described according to its electronic configuration; then the atom families are also defined according to common electronic configuration. It is this electronic configuration that defines the physicochemical properties of the atom, the substances it forms and the families we observe in the Periodic table. An OWLViz view of this ontology can be seen below.



This ontology lacks the explicative power of the standard view of the Periodic Table. As we move left to right in the table, we have increasing atomic mass; we also observe periodicity in the physicochemical properties of the elements. As this periodicity or regularity happens, we group similar elements together. So, lithium, sodium, potassium, cesium and so on are all light, soft, highly reactive, combine with halides in the ratio one to one, and so on. This gives us the standard view of the Periodic table below with the alkali metals described above on the far left-hand-side (though note that the tabular form is a visual artefact of putting it on a two-dimensional medium – it’s really a spiral).


Source: http://www.bpc.edu/mathscience/chemistry/images/periodic_table_of_elements.jpg


My ontology has all the information (or proxies for it) for the standard view of the Periodic table, but it doesn’t show off this periodicity. So, the problem I set for Ionica was to implement an algorithm and some visualisation that would bridge this gap. The rules of engagement were couched as the two questions that could be asked of the ontology:


  1. What is the next atom;
  2. To what family does the atom belong



These two questions encapsulate the two dimensions along which the Periodic Table is arranged – the increasing atom mass and the periodically occurring physicochemical families to which tey belong. The aim was to be able to render the ontology as the periodic table looks, putting in gaps where appropriate. Just as Mendeleev left in gaps where he thought elements should be present (though not yet discovered), the algorithm for rendering the ontology, using the two questions above, should put the atoms in order of increasing atomic mass, but also order them in a second dimension by physicochemical famly.




Ionica’s algorithm for doing this is outlined in the decision tree below. It takes the next element in increasing atomic number and then it checks its membership against any of the already displayed elements. Depending on the result, it goes either on the ‘Yes’ branch and it that case it only sticks the element beneath the one with the same superClass or if the results is ‘No’ it creates a new column for the newly ‘discovered’ element and shuffles all the elements above accordingly. After executing any of the branches, it goes to the top, extracting the next element and repeating the process until space has been allocated for all elements.








The pictures below show the programme working with various ranges of atomic number (as a proxy for atomic mass) and/or their year of discovery. The algorithm can be seen working, adding in gaps into the table as necessary. The application looks like this (below) and can filter by discovery year and do specified ranges of atomic numbers.




For atomic numbers 3 to 20 we just get three rows of elements up until the element prior to the first transition element; the algorithm checks each atom in turn to see if it’s a member of a current groups – on reaching sodium the answer is, for the first time, yes, and a new period is started.


On reaching scandium, we find it is not a member of the boron family or any other family, so a gap for a new family should be started.




This carries on adding “gaps” until all the transition elements are done. Then we get the rest of the Periodic Table as we’d expect to see.



If we start with element 2 (helium) we end up with the noble gases on the left hand side:




This looks strange, but is conceptually OK, as the “table” is continuous, so having the noble gases at the left or right doesn’t really matter. However, we do prefer to have the non-metals together on the right hand side – so there’s a little tweek to the algorithm to deal with hydrogen and helium. A future piece of work may render the thing as a rotatable spiral…



The algorithm also leaves gaps appropriately for “undiscovered” elements:


Drawing the Periodic table from year 0 to 1891 (above) has only those elements that Mendeleev knew.



The ontology has all the information about the periodicity of the physicochemical properties of the elements (or that which accounts for it), but doesn’t make this explicit. It is only the layout that makes this periodicity with increasing atomic mass explicit. A simple observation it may be, but espite the ontology having the knowledge, it is how that knowledge is presented that often matters.


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