Semantic eScience Class Fall 2011

Instructors: Professor Deborah McGuinness with lectures from Professor Joanne Luciano, Professor Peter Fox, and grad student Jim McCusker.
TA: Weijing Chen - Office Hours:Wednesday afternoons 5:00 pm - 8:00 pm in Winslow 2128
suggested auxiliary meetings: Tetherless Education Wednesday Evenings (TWed):
Meeting times: Monday afternoons 1:00 pm - 3:50; Winslow 1140
NOTICE - IRENE changed the first class to August 31 at 5:15pm!
Office Hours: By appointment and walk-in in Winslow 2104 (Professor McGuinness) and Winslow 2143 (Professor Luciano)

phone: 276-4404 (Professor McGuinness) and 276-4939 (Professor Luciano)
Class Listing: SEMANTIC E-SCIENCE CLASS WILL MEET IN WINSLOW BUILDING from 1:00 pm - 3:50 pm - except for the first class due to Hurricane Irene which is being rescheduled to August 31 at 5:15pm.

  • CSCI 6962 - 01, 86933
  • CSCI 4969 - 01, 87927
  • ITWS 6960 - 01, 87198
  • ITWS 4969 - 01, 87928


Table of Contents


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.


Goals: 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.


Topics for Semantic e-Science/ Foundations:

  • Semantic Methodologies
  • Knowledge Representation for e-Science
  • Ontology Engineering and Re-Use for e-Science
  • Knowledge Integration for e-Science
  • Semantic Data Integration
  • Semantic Web Languages, Tools and Services
  • Semantic Infrastructure and Architecture for e-Science
  • Semantic Grid Middleware
  • Ontology Evolution for e-Science
  • Knowledge Management for e-Science
  • e-Science Workflow Management
  • Data life-cycle for e-Science
  • Data Mining and Knowledge Discovery

Semantic Web Applications and Ontologies for:

  • Semantic Web for Health Care and Life Science
  • Semantic Web for Bio-Med-informatics
  • Semantic Web for System and Integrated Biology
  • Semantic Web for Sun, Earth, Environment and Climate
  • Semantic Web for Chemistry, Physics and Astronomy
  • Semantic Web for Engineering
  • Semantic Web and Digital Libraries and Scientific Publications

Semantic e-Science Project options

  • Configuration and Deployment of Semantic Virtual Observatories
    • Oceanography, astronomy, geology
  • Ontology Merging and Validation Test-bed
  • Semantic Language and Tool Use and Evaluation
  • Semantic eScience Implementation Evaluation
  • Semantic Collaboration Case Studies
  • Semantic Application Development and Demonstration

Course Calendar

  • Class 1: Monday, August 29 UPDATED due to Hurricane Irene to Wednesday August 31 at 5:15
  • NO CLASS on Labor Day September 5
  • Class 2: Monday, September 12
  • Class 3: Monday, September 19
  • Class 4: Monday, September 26
  • Class 5: Monday, October 3
  • Class 6: TUESDAY, October 11
  • Class 7: Monday, October 17
  • Class 8: Monday, October 24
  • Class 9: Monday, October 31
  • Class 10: Monday November 7
  • Class 11: Monday, November 14
  • Class 12: Monday November 21
  • Class 13: Monday November 28
  • Class 14: Monday December 5

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 in the campus if you have the problem.

readings: Ontologies 101, Semantic Web, e-Science, RDFS, OWL Guide.
assignments and powerpoints are in process of being updated from the 2010 version
Assignment 0 - Semantic eScience 2011 Assignment 0 [Download]
Summary - Turn in a ONE PAGE description of the reading you liked best, two main points, and why you thought the points were interesting and useful.
Class Notes: Semantic eScience 2011 Class Notes for August 31st [Download]
reading: Semantic Web for the Working Ontologist (first few chapters). Alternate reading - OWL Pizza Tutorial.
Assignment 1 - Semantic eScience 2011 Assignment 1 - 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.
Class Notes:Semantic eScience 2011 Class Notes for September 12th [Download]
Link to last year's assignment 1 Understanding and Extending the Virtual Solar Terrestrial Observatory Ontology

This week's class will be taught by Jim McCusker -

SemantAqua - Semantic Water Quality Portal example:

reading: Use Cases
Use Case Template - Semantic eScience Use Case Template 2011 [Download]
Video Lecture Part 1, Part 2
Class Notes:Semantic eScience 2011 Class Notes for September 19th [Download]
Partial use case example 1
Partial use case example 2

This week's class is taught by Professor Peter Fox

reading: Ontology Tool Summary, Pellet, OWL-S, SAWSDL, Wine Agent
Assignment 2 - Semantic eScience 2011 Assignment 2 - Use-case Driven Knowledge Enoding [Download]
Summary - Document a semantic eScience use case and prepare a presentation.
Class Notes:Semantic eScience 2011 Class Notes for September 26th [Download]
reading: Ontology Evolution - see below under reference list for full citation
PopSciGrid demo - on tobacco prevalence and potential data that may impact people's smoking habits -
OWL-S editor tutorial


OWL-S and WSDL references
CMAP download
  • Class 6: Class Presentation I: TUESDAY October 11, 2011 Use Cases - Part II of Assignment 2

Individual Student Use Case Homeworks - Each student should upload their presentation and use case submission
For Mushroom Project:
Here are the links recommended by Nathan Wilson:
His Masters Thesis: Important reference for creating an an initial macroscopic fungal ontology
Nathan's Presentation PDF:Semantic eScience 2011 Nathan's PPT [Download]
Mushroom OWL: Semantic eScience 2011 Mushroom Ontology [Download]
Use Case Document:Semantic eScience 2011 Mushroom Use Case [Download]
Readme: Semantic eScience 2011 Mushroom Readme [Download]
The new link for Materials:

reading: review ontology evolution reading.
reading: Semantic Water Quality project papers and demonstration.
Turn in one page on highlights of evolution reading and water quality reading. Focus on what aspects of ontology evolution and the water quality portal project you might reuse in your project. One page of highlights is due by Monday October 24, 2011 at 12 noon.
assignment 3: Semantic eScience 2011 Ontology Project DOC [Download]
Semantic eScience 2011 Ontology Project PDF [Download] November 14, 2011 Ontology Projects
Class Notes: Semantic eScience 2011 Class Notes for October 17th
  • Class 8: October 24, 2011 Class exercise II: Foundations IV: Ontology Evolution and Knowledge Management
    Jim McCuster will give the lecture


  • Reading assignment: Provenance papers and exemplar eScience papers. See reading class 8 below. PML, Inference Web, IAAI VSTO, Semantic eScience Web Services, Computers and Geosciences.
Enabling Incremental Enhancement of Provenance Records via User Annotation [Download] - James Michaelis, presented by Deborah McGuinness
reading: Evaluation
additional material: Summative versus Formative evaluation


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


additional materials Orchard Irrigation and Diabetic Exchange
Optional Readings: CALO
reading: none - presentations next week
reading: semantic integration

Extra Slides November 28, 2011

Enabling Incremental Enhancement of Provenance Records via User Annotation [Download] - James Michaelis, presented by Deborah McGuinness
reading: Provenance/ PML
  • Class 13: Class Presentation III: Term assignment - Project Outcome, November 28, 2011
  • Class 14: Post project evaluation: Individual evaluations of team experience, individual contributions, and extra credit for additional suggestions for ways to leverage and use provenance. December 5, 2011
    Semantic eScience 2011 Final Assignment [Download]


Course 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

Suggested Prerequisites

  • Knowledge such as that gained in a Semantic Web class (e.g., CSCI-6961)
  • Knowledge such as that gained in a Web Science class (e.g., CSCI-xx)
  • or permission of the instructors

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 -

  • 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


Class 6: Reading Assignment:

Class 7: Reading Assignment:
Review Ontology Evolution reading from week 5.
Turn in one page on highlights of evolution reading and water quality reading. Focus on what aspects of ontology evolution and the water quality portal project you might reuse in your project. One page of highlights is due by Monday October 24, 2011 at 12 noon.
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.

Course: Semantic eScience

Date: to