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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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Semantic Web Resolutions: 2011

January 3rd, 2011

Have attempted to elucidate at least part of my research agenda for the coming year — blogged at: http://blogs.nature.com/jhendler/2011/01/03/semantic-web-new-years-resolutions

-Jim Hendler

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Fall 2010 TWC Undergraduate Research Summary

December 20th, 2010

The Fall 2010 semester marked the beginning of the Tetherless World Constellation’s undergraduate research program at Rensselaer Polytechnic Institute (RPI). Although TWC has enjoyed significant contributions from RPI undergrads since its inception, this term we stepped up our game by more “formally” incorporating a group of undergrads into TWC’s research programs, established regular meetings for the group, and with input from the students began outfitting their own space in RPI’s Winslow Building.

Patrick West, my fellow TWC undergrad research coordinator and I asked the students to blog about their work throughout the semester; with the end of term, we asked them to post summary descriptions of their work and their thoughts about the fledgling TWC undergrad research program itself. We’ve provided short summaries and links to those blogs below…

  • Cameron Helm began the term coming up to speed on SPARQL and RDF, experimented with several of the public TWC endpoints, and then worked with Phillip on basic visualizations. He then slashed his way through the tutorials on TWC’s LOGD Portal, eventually creating impressive visualizations such as this earthquake map. Cameron is very interested in the subject of data visualization and looks to do more work in this area in the future.
  • After a short TWC learning period, Dan Souza began helping doctoral candidate Evan Patton create an Android version of the Mobile Wine Agent application, with all the amazing visualization and data integration required, including Twitter and Facebook integration. Mid-semester Dan also responded to the call to help with the crash” development of the Android/iPhone TalkTracker app, in time for ISWC 2010 in early November. Dan continues to work with Evan and others for early 2011 releases of Android, iPhone/iPad Touch and iPad versions of the Mobile Wine Agent.
  • David Molik reports that he learned web coding skills, ontology creation, server installation and administration. David contributed to the development and operation of a test site for the new, semantic web savvy website for the Biological and Chemical Oceanography Data Management Office BCO-DMO of the Woods Hole Oceanographic Institute.
  • Jay Chamberlin spent much of his time working on the OPeNDAP Project, an open source server to distribute scientific data that is stored in various formats. His involvement included everything from learning his way around the OPeNAP server, to working with infrastructure such as TWC’s LDAP services, to helping migrate documentation from the previous Wiki to the new Drupal site, to actually implementing required changes to the OPeNDAP code base.
  • Phillip Ng worked on a wide variety of projects this fall, starting with basic visualizations, helping with ISWC applications, and including iPad development for the Mobile Wine Agent. Phillip’s blog is fascinating to read as he works his way through the challenges of creating applications, including his multi-part series on implementing the social media features.
  • Alexei Bulazel began working with Dominic DiFranzo on a health-related mashup using Data.gov datasets and is now working on a research paper with David on “human flesh search engine” techniques, a topic that top thinkers including Tetherless World Senior Constellation Professor Jim Hendler have explored in recent talks. Note: For more background on this phenomena, see e.g. China’s Cyberposse, NY Times (03 Mar 2010)

Many of these students will be continuing on with these or other projects at TWC in 2011; we also expect several new students to be joining the group. The entire team at the Tetherless World Constellation thanks them for their efforts and many important contributions this fall, and looks forward to being amazed by their continued great work in the coming year!

John S. Erickson, Ph.D.

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Linked Data and the Semantic Web (Nature Blog)

June 3rd, 2010

I have written a blog about the Linked Open Government Project:

(intro)
This entry is a backgrounder, rather than a technical piece – the goal is to introduce some new work that my RPI laboratory has been doing aimed at using Semantic Web technologies to help the US government in their data sharing efforts at the Data.gov site. Since similar work is going on on the British Data.gov.uk website, led by my colleagues Tim Berners-Lee and Nigel Shadbolt, (with some “friendly rivalry” between the two), I thought it might be worth providing some background, and pointers to this work.

(update – DOH!  Here is the link:

http://blogs.nature.com/jhendler/2010/06/01/linked-open-government-data-and-the-semantic-web

)

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Web Accessibility in an Educational Context

October 25th, 2009

I’m currently at the annual meeting for the Human Factors and Ergonomics Society and a few hours ago I was attending a set of presentations by the Internet TG on Input and Output on the Web. One of the talks that caught my attention was by Wayne Shebilske of Wright State University on the use of screen readers to help impaired students complete tasks within educational programs such as WebCT, student status management software, and the like. There seem to be many problems with such tools as Dr. Shebilske pointed out based on his study. I think this could be a prime candidate for SW technologies to step in to improve the end user experience. I foresee using such tools along with technologies like RDFa to give the user a better representation of the content being displayed and improving the overall quality of life for these individuals.

Evan

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