Alan Ruttenberg School of Dental Medicine Vision, History, Communities Alan Ruttenberg Oral Diagnostic Sciences Clinical and Translational Data Exchange

Alan Ruttenberg School of Dental Medicine “Nothing like the Web has ever happened in all of human history. The scale of its impact and the rate of its adoption are unparalleled. This is a great opportunity as well as an obligation. If we are to ensure the Web benefits the human race we must first do our best to understand it. The Web is the largest human information construct in history. The Web is transforming society. In order to understand what the Web is, engineer its future and ensure its social benefit we need a new interdisciplinary field that we call Web Science.” Statement of purpose at the Web Science TrustWeb Science Trust ( ) 2

Alan Ruttenberg School of Dental Medicine “The Web was designed as an information space, with the goal that it should be useful not only for human-human communication, but also that machines would be able to participate and help. One of the major obstacles to this has been the fact that most information on the Web is designed for human consumption, and even if it was derived from a database with well defined meanings (in at least some terms) for its columns, that the structure of the data is not evident to a robot browsing the web. Leaving aside the artificial intelligence problem of training machines to behave like people, the Semantic Web approach instead develops languages for expressing information in a machine processable form.” Tim Berners Lee ( 3

Alan Ruttenberg School of Dental Medicine Goals of this section Discuss motivations for the semantic web Discuss predecessors of the semantic web Give an idea of the timeline and some key contributors Discuss several schools of thought around use of the semantic web Give pointers to some centers of activity 4

Alan Ruttenberg School of Dental Medicine Why a semantic web? Why a web? What of the web (of documents) does well What fails? Motivation: Integration Motivation: Reducing barriers to information Motivation: Substrate for intelligent agents Motivation: Efficiency/Network effect Community specific goals (more below) 5

Alan Ruttenberg School of Dental Medicine Predecessors The Web Artificial Intelligence – The AI winter – Berners-Lee explicitly disavows AI in Remote procedure calls (COM, CORBA) Relational Databases, SQL 6

Alan Ruttenberg School of Dental Medicine Schools of thought Standards community – W3C Information modelers – RDF centric Ontology(science) driven Linked data community Computer science research communities Data preservationists Political activists 7

Alan Ruttenberg School of Dental Medicine Standards, W3C International organization: World Wide Web Consortium Funded by membership of industry and academic group Many activities related to HTML-related standards Good process for reaching consensus Highly diverse in goals and vision Example: HCLS, PROV, OWL, RDF, SPARQL 8

Alan Ruttenberg School of Dental Medicine Information Modelers Goals is to design flexible and efficient data modeling language Subject of study tends to be data, not what it is about Comes from tradition of research in technologies such as data structures, relational databases, XML, AI knowledge representation languages Tend to be naïve regarding, or consider irrelevant more careful use of ontology. Use RDF as a syntax 9

Alan Ruttenberg School of Dental Medicine Ontology(science) Most familiar to me: OBO Foundry Goal is to provide a non-redundant, modular and interconnected set of ontologies for recording results of scientific study of biology and medicine Semantic web is a means to an end – Goals: Discovery, recording and analysis of experiments, access to literature and other knowledge support for researchers – Query and gather data about different species and kinds of experimental evidence = integration – Considers careful ontology as necessary to achieve this – A set of domain-specific communities who attempt to share principles and tools for ontology development – Reproducible science 10

Alan Ruttenberg School of Dental Medicine Data preservationists The problem: How to make sure data is available for future uses such as research Confounded by number or/changing data format standards, storage standards, difficulty collecting and making usable documention Web access is appealing as meeting the goal providing availability. RDF/OWL accepted (sometimes grudgingly) as potential solution to generation and obsolescence of data formats Example communities: Museum and cultural history, Biodiversity, Government records 11

Alan Ruttenberg School of Dental Medicine Political Activists Believe more transparent access to all government related information will lead to a more participatory society. From a research perspective focuses on processes that might be enabled by web that do/may transform society Interaction with law around copyright and licensing Web Science Trust: 12

Alan Ruttenberg School of Dental Medicine Computer science researchers Define formal semantics (e.g. model theory) Look at problems of implementation – Reasoning – Query – Scaling A subset of applications – Search – Information content – Data analysis – Ontology alignment – Network analysis 13

Alan Ruttenberg School of Dental Medicine Linked data Populist movement to publicize and encourage deployment of data on the semantic web Strong connection to web of documents – for human browsing in addition to automated query Larger vision than only semantic web “Five star” scale for linked data ( – make your stuff available on the Web (whatever format) under an open license – make it available as structured data (e.g., Excel instead of image scan of a table) – use non-proprietary formats (e.g., CSV instead of Excel) – use URIs to denote things, so that people can point at your stuff – link your data to other data to provide context “linking data” tends to take priority over correctly linking data. Popular technologies: Ontology matching, Recognition of same entities. 14

Alan Ruttenberg School of Dental Medicine Selected US Centers W3C (Berners-Lee, Semantic Web Activity) Stanford Bioportal (Dumontier) Buffalo (Ruttenberg) Wright State (Sheth, Hitzler) UCSD (Martone) RPI/Data.gov (Hendler) Harvard (Clark, Cicaresse) OHSU (Haendel, Torniai) 15

Alan Ruttenberg School of Dental Medicine Select international centers Manchester University (Parsia, Sattler, Stevens) European Bioinformatics Institute EBI (UK) Oxford University (Horrocks, UK) DERI (Decker, Ireland) Free University of Bozen · Bolzano (Italy) Institute of Applied Informatics and Formal Description (Germany) Vrije Universiteit (van Harmelen, Netherlands) RIKEN (Japan) 16

Alan Ruttenberg School of Dental Medicine Possible discussions What are pitfalls of associated with this vision Can these various interests actually coordinate? Is the success of the semantic web dependent on them doing so? What other technologies might compete? Can the (semantic) web really transform society? Is ontology engineering necessary? 17

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