Semantic eScience 2012

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Instructor: Professor Deborah McGuinness - dlm at cs dot rpi dot edu
TA: Katie Chastain - chastk at rpi dot edu
Meeting times: Monday afternoon 1:00 pm - 3:50 pm.
Office Hours: By appt in Winslow 2104
phone: 518-276-4404a
TA Office Hours: Wednesdays, 5-6:30pm, in the Winslow common area
Class Listing: Semantic eScience
CSCI 6962 - 01, 26868 , CSCI 4969 - 01, 27716
ITWS 6960 - 01, 27640 , ITWS 4969 - 01, 27717

Class Location Winslow 1140

Science has fully entered a new mode of operation. E-science, defined as a combination of science, informatics, computer science, cyberinfrastructure and information technology is changing the way all of these disciplines do both their individual and collaborative work.

Scientists are facing global problems of a magnitude, complexity and interdisciplinary nature that progress is limited by a trained and agile workforce.

At present, there is a lack formal training in the key cognitive and skill areas that would enable graduates to become key participants in e-science collaborations. The purpose is to teach methodologies, and provide application experience and skill-sets in an inter-disciplinary forum to students and interested participants.

As semantic technologies have been gaining momentum in various e-Science areas (for example, W3C's new interest group for semantic web health care and life science), it is important to offer semantic-based methodologies, tools, middleware to facilitate scientific knowledge modeling, logical-based hypothesis checking, semantic data integration and application composition, integrated knowledge discovery and data analyzing for different e-Science applications.

Partially influenced by the Artificial Intelligence community, the Semantic Web researchers have largely focused on formal aspects of semantic representation languages or general-purpose semantic application development, with inadequate consideration of requirements from specific science areas. On the other hand, general science researchers are growing ever more dependent on the web, but they have no coherent agenda for exploring the emerging trends on the semantic web technologies. It urgently requires the development of a multi-disciplinary field to foster the growth and development of e-Science applications based on the semantic technologies and related knowledge-based approaches.
To fill the gaps that are currently present in the integrative nature of informatics for the translation of science into requirements for the underlying and largely syntactic e-infrastructure.
To fill the gaps that are currently present in the integrative nature of informatics for the translation of science into requirements for the underlying and largely syntactic e-infrastructure.
Learning Objective:
  • Ontology Development, Merging and Validation
  • Semantic Language and Tool Use and Evaluation
  • Use Case Development and Elaboration
  • Semantic eScience Implementation and Evaluation via Use Cases
  • Semantic Application Development and Demonstration
  • Group Project and Team Development, Use Case Implementation and Evaluation
  • TBC
Assessment Criteria:
  • Via written assignments with specific percentage of grade allocation provided with each assignment
  • Via oral presentations with specific percentage of grade allocation provided
  • Via group presentations
  • Via participation in class (not to exceed 10% of total)
  • Late submission policy: first time with valid reason – no penalty, otherwise 20% of score deducted each late day
Academic Integrity:
Student-teacher relationships are built on trust. For example, students must trust that teachers have made appropriate decisions about the structure and content of the courses they teach, and teachers must trust that the assignments that students turn in are their own. Acts, which violate this trust, undermine the educational process. The Rensselaer Handbook of Student Rights and Responsibilities defines various forms of Academic Dishonesty and you should make yourself familiar with these. In this class, all assignments that are turned in for a grade must represent the student’s own work. In cases where help was received, or teamwork was allowed, a notation on the assignment should indicate your collaboration. Submission of any assignment that is in violation of this policy will result in a penalty.

If found in violation of the academic dishonesty policy, students may be subject to two types of penalties. The instructor administers an academic (grade) penalty, and the student may also enter the Institute judicial process and be subject to such additional sanctions as: warning, probation, suspension, expulsion, and alternative actions as defined in the current Handbook of Student Rights and Responsibilities. If you have any question concerning this policy before submitting an assignment, please ask for clarification.

Course Calendar

Refer to Reading/ Assignment/ Reference list for each week (see below). Note that the schedule and the reading list may evolve depending upon some outside speaker availability. Also, last year's class page has some additional useful content -

  • CLASS 1: Monday, August 27
  • NO CLASS on Labor Day September 3
  • CLASS 2: Monday, September 10
  • CLASS 3: Monday, September 17 (Jim McCusker will present)
  • CLASS 4: Monday, September 24
  • CLASS 5: Monday, October 1
  • CLASS 6: TUESDAY, October 8
  • CLASS 7: Monday, October 15
  • CLASS 8: Monday, October 22
  • CLASS 9: Monday, October 29
  • CLASS 10: Monday November 6
  • CLASS 11: Monday, November 12
  • CLASS 12: Monday November 19
  • CLASS 13: Monday November 26
  • CLASS 14: Monday December 3

Course Syllabus

For complete reading citation with link(s) to papers, see reference list below.

NOTICE: Part of readings may be inaccessible when downloaded off the campus. You could download them on campus or via vpn if you have the problem.

NOTICE: remember to check back as the schedule may change as the term progresses

  • CLASS 1- August 27, 2012: Introduction to eScience and the Semantic Web - Semantic eScience 2012 Lecture 1 [Download]
  • readings: Ontologies 101, Semantic Web, e-Science, RDFS, OWL Guide.
    assignments and powerpoints are in process of being updated from the 2011 version
    Assignment 1 - Semantic eScience 2012 Assignment 1 [Download]
    Summary - Turn in a maximum 2 PAGE description of the reading you liked best, two main points, and why you thought the points were interesting and useful. Also, include one idea for a use case that you might be interested in proposing for a class.
    Class Notes: Semantic eScience 2012 Class Notes for August 27 [Download]
  • CLASS 2 - September, 10, 2012: Semantic eScience 2012 Lecture 2 [Download]
    In-class guest presentations:
    Jim Myers' SEAD slideshow [Download] & SEAD use case example [Download]
    Patrice Seyed's Hydro-Eco presentation [Download]

    Use Cases

  • reading: Semantic Web for the Working Ontologist (first few chapters). Alternate reading - OWL Pizza Tutorial. Also read the use case template and partial use cases below.
    Assignment 2 - Semantic eScience 2012 Assignment 2 - Designing a Use Case [Download]

    Use Case Template - Semantic eScience Use Case Template 2012 [Download]

    Direct link
    SemantAqua - Semantic Water Quality Portal example:

    Partial use case example 1
    Partial use case example 2

    Class Notes:Semantic eScience 2012 Class Notes for September 10th [Download]

  • CLASS 3 - September 17, 2012 : Foundations II: Ontology Engineering [Download] September 17, 2012
  • This week's class will be taught by Jim McCusker -

    Assignment 3 - Semantic eScience 2012 Assignment 3 - Representing Knowledge and Understanding Representations - Understanding and Extending an Ontology [Download]
    Summary - Review and ontology, make some simple extensions, and answer a few questions using those extensions.

    Link to previous year's assignment on extending an ontology Understanding and Extending the Virtual Solar Terrestrial Observatory Ontology
    Video Lectures from 2011 Part 1, Part 2
    Class Notes: Semantic eScience 2012 Class Notes for September 17th [Download]
    Notes from Amar's 9/21 workshop [Download]

  • CLASS 4 - September 24, 2012: Use Case Presentations: Use Case development [Download],
    reading: Ontology Tool Summary, Pellet, OWL-S, SAWSDL, Wine Agent
    Assignment 4 - Semantic eScience 2012 Assignment 4 - Use-cases revisited. [Download]
    Summary - Read the community science paper and create another abbreviated use case.
    Class Notes:Semantic eScience 2012 Class Notes for September 24th [Download]
  • CLASS 5 - October 1, 2012: Project determination: Semantic eScience 2011 Lecture 5 [Download] .
    Anticipated external use case presentation
    ClassNotes:Semantic eScience 2012 ClassNotes5 [Download]

  • PopSciGrid demo - on tobacco prevalence and potential data that may impact people's smoking habits -
    Semantic Water Quality Portal papers: review static demo and read at least the eScience 2012 paper. is the main project page. The static demo is available from and the publications list is at:
    The most recent paper is available at:
    Wang, P., Fu, L., Patton, E.W., McGuinness, D.L., Dein, J., and Bristol, S. 2012. Towards Semantically-enabled Exploration and Analysis of Environmental Ecosystems. In Proceedings of 8th IEEE International Conference on eScience (October 8-12 2012, Chicago, IL).

    Turn in one page on highlights water quality and popscigrid reading. Focus on what aspects the water quality portal project and the PopSciGrid project you might reuse in your project. One page of highlights is due by Tuesday October 9, 2012 at 12 noon.

    OWL-S editor tutorial

    OWL-S and WSDL references
    CMAP download
  • CLASS 6: TUESDAY October 8, 2012 Semantic Applications: SemantAqua, PopSciGrid, and Use-Case driven ontology design and Class Project discussion
  • Forthcoming will be materials about this year's projects. The link for last year's materials is up at

    reading: Ontology Evolution - see below under reference list for full citation
    assignment 5: Semantic eScience 2012 Ontology Project DOC [Download]
    Semantic eScience 2012 Ontology Project PDF [Download]
    Class Notes: Semantic eScience 2012 Class Notes for October 9th
  • CLASS 7 - October 15: Ontology Evolution Ontology Evolution
  • Class Notes: Semantic eScience Notes Oct 15 [Download]

    reading: Review the SemantAqua papers - aimed at reviewing how one might write up a project like yours.
  • CLASS 8 - October 22: Group Project Presentations Round 1:
  • reading: PML and Inference web papers along with VSTO paper
    Begin to populate your project page
    Please confirm that you can write to your pages. If for some reason you can not write to your class web pages, then create your web page somewhere and move it over to the tw website in the next week. The class will begin by looking at your course project web pages.
  • CLASS 9 - October 29: Foundations: Languages, Provenance, Tools (and possible external use case presentation)
    Hurricane Sandy modification
  • reading: none other than reading for your project.
    assignment 7: Semantic eScience 2012 Ontology Project Round 2 DOC [Download]
    Semantic eScience 2012 Ontology Project PDF [Download]

  • CLASS 10 - November 5: Project Presentation Round 2 and Semantic Modeling Languages and Provenance
    Lecture Notes: Semantic eScience Lecture Notes Nov5 [Download]
    Class Notes: Semantic eScience Class Notes Nov5 [Download]
  • reading: Evaluation readings
  • CLASS 11 - November 12: Using Tools
  • reading: Integration papers
  • CLASS 12 - November 19: Evaluation
  • Lecture Powerpoint: Semantic eScience Evaluation Lecture [Download]
    Guest presentation from Chris Welty from the IBM Watson Team - The use of semantics in Watson.
    Semantic eScience 2012 Final Project Iteration [Download]

  • CLASS 13 - November 26: Class Presentation III: Final Term assignment presentations
  • Final project evaluation: Semantic eScience Final Individual Evaluation homework [Download]

  • CLASS 14 - December 3: Project evaluation: Individual evaluations of team experience, individual contributions, and extra credit for additional suggestions for ways to leverage and use provenance. Final update reports. December 3, 2012

    Reference List

    Class 1 Reading Assignment:

    • Semantic Web:
    T Berners-Lee, J Hendler, O Lassila. The Semantic Web. Scientific American, 2001. alternative link -

    Grigoris Antoniou and Frank van Harmelen. Semantic Web Primer
    • [OWL Guide] Michael K. Smith, Chris Welty, and Deborah L. McGuinness. OWL Web Ontology Language Guide. World Wide Web Consortium (W3C) Recommendation. February 10, 2004.


    Class 2: Reading Assignment:

    Alternate reading for the working ontologist book -

    • Alan Rector, Nick Drummond, Matthew Horridge, Jeremy Rogers, Holger Knublauch, Robert Stevens, Hai Wang, Chris Wroe. OWL Pizzas: Practical Experience of Teaching OWL-DL: Common Errors & Common Patterns. EKAW 2004.

    Optional reading -

    Class 3: Reading Assignment:

    • Use Cases:



    Class 4: Reading Assignment:

    • Wine Agent:

    Class 5: Reading Assignment:

    • [Ontology Evolution] Deborah L. McGuinness, Richard Fikes, James Rice, and Steve Wilder.

    An Environment for Merging and Testing Large Ontologies. In Proceedings of the 7th International Conference on Principles of Knowledge Representation and Reasoning (KR2000), Breckenridge, Colorado, USA 12-15 April 2000


  • OWL-S editor tutorial
  • OWL-S and WSDL references
  • CMAP download
  • Class 6: Reading Assignment:

    Class 7: Reading Assignment:
    Review Semantic Water Quality Portal papers. Look particularly at the static web page demonstration. You will need to generate a static demonstration page and this is one example.
    Begin an outline for your static web page demo and turn in the outline. One outline is due for each group and it should be turned in by noon on Monday October 22.
    This is worth 5 points of the overall class score.

    Water Quality papers:

    Wang, P., Zheng, J., Fu, L., Patton, E., Lebo, T., Ding, L., Liu, Q., Luciano, J.S., and McGuinness, D.L. 2011. A Semantic Portal for Next Generation Monitoring Systems. In Proceedings of 10th International Semantic Web Conference (October 23-27 2011, Bonn, Germany).

    Zheng, J., Wang, P., Patton, E., Lebo, T., Luciano, J.S., and McGuinness, D.L. 2011. A Semantically-Enabled Provenance-Aware Water Quality Portal. In Proceedings of EIM 2011 (September 28-29 2011, Santa Barbara, CA, USA).

    Review static demo:

    Class 8: Reading Assignment:

    • Inference Web - McGuinness and Pinheiro da Silva. Explaining Answers from the Semantic Web: The Inference Web Approach. Web Semantics: Science, Services and Agents on the World Wide Web Special issue: International Semantic Web Conference 2003 - Edited by K.Sycara and J.Mylopoulis. Volume 1, Issue 4. Journal published Fall, 2004
    • McGuinness, D.L.; Zeng, H.; Pinheiro da Silva, P.; Ding, L.; Narayanan, D.; Bhaowal, M. Investigations into Trust for Collaborative Information Repositories: A Wikipedia Case Study. The Workshop on the Models of Trust for the Web (MTW'06), Edinburgh, Scotland, May 22, 2006. 2006.

    Class 9: Reading Assignment:

    additional material: Summative versus Formative evaluation

    additional material: Example of evaluation
    additional material: Template example for Evaluation

    Class 10: Reading Assignment:
    Optional Readings: Alyssa Glass, Deborah L. McGuinness, Paulo Pinheiro da Silva, and Michael Wolverton. Trustable Task Processing Systems. In Roth-Berghofer, T., and Richter, M.M., editors, KI Journal, Special Issue on Explanation, Kunstliche Intelligenz, 2008.
    Andrew. J. Cowell, Deborah L. McGuinness, Carrie F. Varley, and David A. Thurman. Knowledge-Worker Requirements for Next Generation Query Answering and Explanation Systems. In the Proceedings of the Workshop on Intelligent User Interfaces for Intelligence Analysis, International Conference on Intelligent User Interfaces (IUI 2006), Sydney, Australia

    Class 11: Reading Assignment:

    • Integration:
    • Fox, P.; McGuinness, D.L.; Raskin, R.; Sinha, K. A Volcano Erupts: Semantically Mediated Integration of Heterogeneous Volcanic and Atmospheric Data. Proceedings of the First Workshop on Cyberinfrastructure: Information Management in eScience, co-located with the ACM Conference on Information and Knowledge Management, Lisbon, Portugal, November 9, 2007.
    • Boyan Brodaric and Florian Probst. Enabling Cross-Disciplinary e-Science by Integrating Geoscience Ontologies with DOLCE. Under Review. 2008.
    • Yolanda Gil, Ewa Deelman, Mark Ellisman, Thomas Fahringer, Geoffrey Fox, Dennis Gannon, Carole Goble, Miron Livny, Luc Moreau, Jim Myers, "Examining the Challenges of Scientific Workflows," Computer , vol. 40, no. 12, pp. 24-32, December, 2007.

    Class 12: Reading Assignment:

    Class 13: Reading Assignment: None.

    Attendance Policy

    Enrolled students may miss at most one class without permission of the instructor. Once one class has been missed (with or without permission) no additional classes may be missed without permission.