72010 SemWebTech lecture 8: SWT for HCLS background and data integration

After the ontology languages and general aspects of ontology engineering, we now will delve into one specific application area: SWT for health care and life sciences. Its frontrunners in bioinformatics were adopters of some of the Semantic Web ideas even before Berners-Lee, Hendler, and Lassila wrote their Scientific American paper in 2001, even though they did not formulate their needs and intentions in the same terminology: they did want to have shared, controlled vocabularies with the same syntax, to facilitate data integration—or at least interoperability—across Web-accessible databases, have a common space for identifiers, it needing to be a dynamic, changing system, to organize and query incomplete biological knowledge, and, albeit not stated explicitly, it all still needed to be highly scalable [1].

Bioinformaticians and domain experts in genomics already organized themselves together in the Gene Ontology Consortium, which was set up officially in 1998 to realize a solution for these requirements. The results exceeded anyone’s expectations in its success for a range of reasons. Many tools for the Gene Ontology (GO) and its common KR format, .obo, have been developed, and other research groups adopted the approach to develop controlled vocabularies either by extending the GO, e.g., rice traits, or adding their own subject domain, such as zebrafish anatomy and mouse developmental stages. This proliferation, as well as the OWL development and standardization process that was going on at about the same time, pushed the goal posts further: new expectations were put on the GO and its siblings and on their tools, and the proliferation had become a bit too wieldy to keep a good overview what was going on and how those ontologies would be put together. Put differently, some people noticed the inferencing possibilities that can be obtained from moving from obo to OWL and others thought that some coordination among all those obo bio-ontologies would be advantageous given that post-hoc integration of ontologies of related and overlapping subject domains is not easy. Thus came into being the OBO Foundry to solve such issues, proposing a methodology for coordinated evolution of ontologies to support biomedical data integration [2].

People in related disciplines, such as ecology, have taken on board experiences of these very early adopters, and instead decided to jump on board after the OWL standardization. They, however, were not only motivated by data(base) integration. Referring to Madin et al’s paper [3] again, I highlight three points they made: “terminological ambiguity slows scientific progress, leads to redundant research efforts, and ultimately impedes advances towards a unified foundation for ecological science”, i.e., identification of some serious problems they have in ecological research; “Formal ontologies provide a mechanism to address the drawbacks of terminological ambiguity in ecology”, i.e., what they expect that ontologies will solve for them (disambiguation); and “and fill an important gap in the management of ecological data by facilitating powerful data discovery based on rigorously defined, scientifically meaningful terms”, i.e., for what purpose they want to use ontologies and any associated computation (discovery). That is, ontologies not as a—one of many possible—tool in the engineering/infrastructure means, but as a required part of a method in the scientific investigation that aims to discover new information and knowledge about nature (i.e., in answering the who, what, where, when, and how things are the way they are in nature).

What has all this to do with actual Semantic Web technologies? On the one hand, there are multiple data integration approaches and tools that have been, and are being, tried out by the domain experts, bioinformaticians, and interdisciplinary-minded computer scientists [4], and, on the other hand, there are the W3C Semantic Web standards XML, RDF(S), SPARQL, and OWL. Some use these standards to achieve data integration, some do not. Since this is a Semantic Web course, we shall take a look at two efforts who (try to) do, which came forth from the activities of the W3C’s Health Care and Life Sciences Interest Group. More precisely, we take a closer look at a paper written about 3 years ago [5] that reports on a case study to try to get those Semantic Web Technologies to work for them in order to achieve data integration and a range of other things. There is also a more recent paper from the HCLS IG [6], where they aimed at not only linking of data but also querying of distributed data, using a mixture of RDF triple stores and SKOS. Both papers reveal their understanding of the purposes of SWT, and, moreover, what their goals are, their experimentation with various technologies to achieve them, and where there is still some work to do. There are notable achievements described in these, and related, papers, but the sought-after “killer app” is yet to be announced.

The lecture will cover a ‘historical’ overview and what more recent ontology-adopters focus on, the very basics of data integration approaches that motivated the development of ontologies, and we shall analyse some technological issues and challenges mentioned in [5] concerning Semantic Web (or not) technologies.

References:

[1] The Gene Ontology Consortium. Gene ontology: tool for the unification of biology. Nature Genetics, May 2000;25(1):25-9.

[2] Barry Smith, Michael Ashburner, Cornelius Rosse, Jonathan Bard, William Bug, Werner Ceusters, Louis J. Goldberg, Karen Eilbeck, Amelia Ireland, Christopher J Mungall, The OBI Consortium, Neocles Leontis, Philippe Rocca-Serra, Alan Ruttenberg, Susanna-Assunta Sansone, Richard H Scheuermann, Nigam Shah, Patricia L. Whetzel, Suzanna Lewis. The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nature Biotechnology 25, 1251-1255 (2007).

[3] Joshua S. Madin, Shawn Bowers, Mark P. Schildhauer and Matthew B. Jones. (2008). Advancing ecological research with ontologies. Trends in Ecology & Evolution, 23(3): 159-168.

[4] Erhard Rahm. Data Integration in Bioinformatics and Life Sciences. EDBT Summer School, Bolzano, Sep. 2007.

[5] Ruttenberg A, Clark T, Bug W, Samwald M, Bodenreider O, Chen H, Doherty D, Forsberg K, Gao Y, Kashyap V, Kinoshita J, Luciano J, Scott Marshall M, Ogbuji C, Rees J, Stephens S, Wong GT, Elizabeth Wu, Zaccagnini D, Hongsermeier T, Neumann E, Herman I, Cheung KH. Advancing translational research with the Semantic Web, BMC Bioinformatics, 8, 2007.

[6] Kei-Hoi Cheung, H Robert Frost, M Scott Marshall, Eric Prud’hommeaux, Matthias Samwald, Jun Zhao, and Adrian Paschke. A journey to Semantic Web query federation in the life sciences. BMC Bioinformatics 2009, 10(Suppl 10):S10

Note: references 1, 2, and (5 or 6) are mandatory reading, and 3 and 4 are recommended to read.

Lecture notes: lecture 8 – SWLS background and data integration

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