What is ontology?

December 19th, 2013

The topic of a blog in my mind, after five days at the American Geophysical Union 2013 Fall Meeting discussing Earth and space science informatics, is to give an introduction of ontology to researchers in Earth and environmental sciences and beyond.

To attract your interest, I would say that ontology is the invisible hand behind anything. (It took me a few minutes to think about whether I should add an ‘an’ before the ‘ontology’ here. For reasons see below.)

First let’s see the etymology of the word ‘ontology’. According to Wiktionary (http://en.wiktionary.org/wiki/ontology), ontology is ‘originally Latin ontologia (1606, Ogdoas Scholastica, by Jacob Lorhard (Lorhardus)), from Ancient Greek ὤν (ōn, “on”), present participle of εἰμί (eimi, “being, existing, essence”) + λόγος (logos, “account”).’

Second let’s see the definition of the word. It is also interesting to see that Wiktionary claims that in philosophy the word ‘ontology’ can be either uncountable or countable. For the former, ontology is defined by Wiktionary as ‘The branch of metaphysics that addresses the nature or essential characteristics of being and of things that exist; the study of being.’ This definition is more or less the same as another one done by the Oxford English Dictionary, ‘The science or study of being; that branch of metaphysics concerned with the nature or essence of being or existence.’ That Oxford definition was used in my PhD defense (http://www.slideshare.net/MarshallXMa/ontology-spectrum-for-geological-data-interoperability-phddefence). For the countable ‘ontology’, Wiktionary defines it as ‘The theory of a particular philosopher or school of thought concerning the fundamental types of entity in the universe.’ I had not done any work relevant to that definition yet but I just found Oxford also has a similar definition ‘As a count noun: a theory or conception relating to the nature of being.’

The word metaphysics is mentioned in the definition of ontology as an unaccountable noun. In now days when people talk about metaphysics they often refer to Aristotle (384 – 322 BCE). If you (especially those who are working for a Doctor of PHILOSOPHY ;-)) are interested in his study you can read the two most famous books 1) Politics: A Treatise on Government and 2) The Ethics of Aristotle by him on the Gutenberg website (http://www.gutenberg.org/ebooks/author/2747). The story does not stop here. In a famous Chinese book, I Ching (or the Book of Changes, c. 450 – 250 BCE), there are also topics about metaphysics, such as a sentence which is my personal favorite: ‘What is above form is called Tao; what is within form is called tool.’

The philosophical meaning of the word ontology is the background and for most cases in the domain of Earth and space science informatics we care more about another meaning of the word: ontology as a countable noun in computer science. Before discussing definition of ontology as a computer science word, let’s first see how hot this word is in recent years. I did a few searches with the topic ‘ontology’ in isiknowledge.com (on Dec 19, 2013), which showed that there are about 44884 publications for all years, and publication numbers for separate periods are 1470/1945–1995, 1498/1995–2000, ~7901/2000–2005, ~24528/2005–2010, and ~16891/2010–2013. If I refined the results by limiting to the research area ‘Computer Science’, the results are: ~22251/all years, 114/1945–1995, 673/1995–2000, ~5095/2000–2005, ~14316/2005–2010, and ~5971/2010–2013. And there are a big number of publications that applied informatics and were filtered out by the keyword ‘Computer Science’. From those results we can see many meanings, one is that works with the computer science ‘ontology’ has been increasing significantly since 2000.

For the definition of the computer science word ‘ontology’, many people have cited the publications of T.R. Gruber (1993, 1995, see: http://dx.doi.org/10.1006/knac.1993.1008 and http://dx.doi.org/10.1006/ijhc.1995.1081): ‘An ontology is an explicit specification of a conceptualization’. Middle 1990s is the golden age for discussing the definition of ontology. N. Guarino (1997, see: http://dx.doi.org/10.1006/ijhc.1996.0091) made a nice review of the definition of ‘ontology’, in which I think one key point he discussed was the ‘shared conceptualization’ feature of an ontology. So in my PhD dissertation (Ma, 2011, see: http://www.itc.nl/library/papers_2011/phd/ma.pdf) I tried to re-address the definition of the computer science ‘ontology’: ‘Ontologies in computer science are defined as shared conceptualizations of domain knowledge (Gruber, 1995; Guarino, 1997b)…’

Third, after seeing the definition of ontology, let’s focus on how to put a computer science ‘ontology’ into practice, especially in the domain of Earth and space science informatics. Early 2000s is the golden age for that work. McGuinness (2003, see: http://www-ksl.stanford.edu/people/dlm/papers/ontologies-come-of-age-mit-press-%28with-citation%29.htm) made a wonderful discussion of the ontology spectrum. McGuinness also made a footnote to that spectrum figure: ‘This spectrum arose out of a conversation in preparation for an ontology panel at AAAI ’99. The panelists (Gruninger, Lehman, McGuinness, Ushold, and Welty), chosen because of their years of experience in ontologies found that they encountered many forms of specifications that different people termed ontologies. McGuinness refined the picture to the one included here.’ When I was doing my PhD I read this note and I tried to find a few other publications by people in the panelists listed by McGuinness, and I did find a few that also discussed the ontology spectrum, for example:
Welty, C., 2002. Ontology-driven conceptual modeling. In: Pidduck, A.B., Mylopoulos, J., Woo, C.C., Ozsu, M.T. (Eds.), Advanced Information Systems Engineering, Lecture Notes in Computer Science, vol. 2348. Springer-Verlag, Berlin & Heidelberg, Germany, pp. 3-3. Lecture slides available at: http://www.cs.toronto.edu/caise02/cwelty.pdf
Obrst, L., 2003. Ontologies for semantically interoperable systems. In: Proceedings of the Twelfth International Conference on Information and Knowledge Management, New Orleans, LA, USA, 366-369.
Uschold, M., Gruninger, M., 2004. Ontologies and semantics for seamless connectivity. SIGMOD Record 33 (4), 58–64.
Borgo, S., Guarino, N., Vieu, L., 2005. Formal ontology for semanticists. In: Lecture notes of the 17th European Summer School in Logic, Language and Information (ESSLLI 2005), Edinburgh, Scotland, 12pp. http://www.loa-cnr.it/Tutorials/ESSLLI1.pdf

OS1
An ontology spectrum (from McGuinness 2003)

To help myself understand the ontology spectrum better, I redrew the diagram (see below) in my PhD dissertation. Very recently (Dec 03, 2013) Jim McGusker, a PhD student with McGuinness, made a thorough explanation of the spectrum in his blog (see: http://info.5amsolutions.com/blog/bid/154967/6-Points-Along-the-Ontology-Spectrum).

OS2
Ontology spectrum (adapted from Borgo et al., 2005; McGuinness, 2003; Obrst, 2003; Uschold and Gruninger, 2004; Welty, 2002). Texts in italics explain a typical relationship in each ontology type (from Ma 2011)

Finally, I would like to share a few examples for different types of ontologies following the spectrum:

Catalog/Glossary:
Neuendorf, K.K.E., Mehl, J.J.P., Jackson, J.A., 2005. Glossary of Geology, 5th edition. American Geological Institute: Alexandria, VA, USA, p. 800. See latest version at: http://www.agiweb.org/pubs/glossary/

Taxonomy:
BGS Rock Classification Scheme, see: https://www.bgs.ac.uk/bgsrcs/

Thesaurus:
AQSIQ, 1988. GB/T 9649-1988 The Terminology Classification Codes of Geology and Mineral Resources. General Administration of Quality Supervision, Inspection and Quarantine of P.R. China (AQSIQ). Standards Press of China, Beijing, China. 1937 pp.

Conceptual Schema:
NADM Steering Committee, 2004. NADM Conceptual Model 1.0—A conceptual model for geologic map information: U.S. Geological Survey Open-File Report 2004-1334, North American Geologic Map Data Model (NADM) Steering Committee, Reston, VA, USA, 58 pp. See: http://pubs.usgs.gov/of/2004/1334

Ontologies encoded in RDF format:
Semantic Web for Earth and Environmental Terminology (SWEET). See: http://sweet.jpl.nasa.gov/

Now a short wrap up about what is ontology:
For fun: the invisible hand behind anything;
In philosophy: (uncountable) the science or study of being; that branch of metaphysics concerned with the nature or essence of being or existence; (countable) a theory or conception relating to the nature of being;
In computer science: shared conceptualization of domain knowledge.

To put ontologies (computer science) into practice, keep in mind an ontology spectrum with enriching meanings: catalog/glossary -> taxonomy -> thesaurus -> conceptual schema -> formal constraints.

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