View Source Code of "Semantic eScience Class 2011"

<p><strong>Instructors</strong>: Professor Deborah McGuinness with lectures from Professor Joanne Luciano,  Professor Peter Fox, and grad student Jim McCusker.<br />
<strong> TA</strong>: Weijing Chen - chenw8@rpi.edu <strong>Office Hours</strong>:Wednesday afternoons 5:00 pm - 8:00 pm in Winslow 2128
<strong> suggested auxiliary meetings</strong>:  Tetherless Education Wednesday Evenings (TWed):  http://tw.rpi.edu/web/TWed
<strong>Meeting times</strong>: Monday afternoons 1:00 pm - 3:50; Winslow 1140<br />
<strong>  NOTICE - IRENE changed the first class to August 31 at 5:15pm!</strong>
<strong>Office Hours</strong>: By appointment and walk-in in Winslow 2104 (Professor McGuinness) and Winslow 2143 (Professor Luciano)<br />

<strong>phone</strong>: 276-4404 (Professor McGuinness) and 276-4939 (Professor Luciano)<br />
<strong>Class Listing</strong>: 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. 
<ul>
<li>CSCI 6962 - 01, 86933 </li>
<li> CSCI 4969 - 01, 87927 </li>
<li> ITWS 6960 - 01, 87198 </li>
<li> ITWS 4969 - 01, 87928 </li>
</ul>
</p>
 </p>
<h2>Table of Contents</h2>
<ul>
<li><a href="#description">Description</a></li>
<li><a href="#goal">Course Goals</a></li>
<li><a href="#topics">Topics</a></li>
<li><a href="#projects">Projects</a></li>
<li><a href="#calendar">Course Calendar</a></li>
<li><a href="#syllabus">Course Syllabus</a></li>
<li><a href="#objective">Course Learning Objective</a></li>
<li><a href="#criteria">Assessment Criteria</a></li>
<li><a href="#prereq">Suggested Prerequisites</a></li>
<li><a href="#ref">Reference List</a></li>
<li><a href="#attendance">Attendance Policy</a></li>
</ul>
<h2><a name="description"></a>Description</h2>

<p>Science has fully entered a new mode of operation. <a href="/web/Themes/web/theme/SemanticeScience">E-science</a>, 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.</p>
<p>Scientists are facing global problems of a magnitude, complexity and interdisciplinary nature that progress is limited by a trained and agile workforce.</p>
<p>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.</p>
<p>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.</p>
<p>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.</p>
<h2><a name="goal"></a>Goals</h2>
<p>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. </p>
<h2><a name="topics"></a>Topics</h2>

<p>Topics for Semantic e-Science/ Foundations:</p>
<ul>
<li> Semantic Methodologies</li>
<li> Knowledge Representation for e-Science</li>
<li> Ontology Engineering and Re-Use for e-Science</li>
<li> Knowledge Integration for e-Science</li>
<li> Semantic Data Integration</li>

<li> Semantic Web Languages, Tools and Services</li>
<li> Semantic Infrastructure and Architecture for e-Science</li>
<li> Semantic Grid Middleware</li>
<li> Ontology Evolution for e-Science</li>
<li> Knowledge Management for e-Science</li>
<li> e-Science Workflow Management</li>
<li>  Data life-cycle for e-Science</li>
<li> Data Mining and Knowledge Discovery </li>
</ul>
<p>Semantic Web Applications and Ontologies for:</p>
<ul>
<li> Semantic Web for Health Care and Life Science</li>
<li> Semantic Web for Bio-Med-informatics</li>
<li> Semantic Web for System and Integrated Biology</li>
<li> Semantic Web for Sun, Earth, Environment and Climate</li>
<li> Semantic Web for Chemistry, Physics and Astronomy</li>
<li> Semantic Web for Engineering</li>
<li> Semantic Web and Digital Libraries and Scientific Publications</li>
</ul>
<h2><a name="projects"></a>Semantic e-Science Project options</h2><ul>
<li> Configuration and Deployment of Semantic Virtual Observatories<ul>
<li> Oceanography, astronomy, geology </li></ul>
</li>
<li> Ontology Merging and Validation Test-bed</li>
<li> Semantic Language and Tool Use and Evaluation</li>
<li> Semantic eScience Implementation Evaluation</li>
<li> Semantic Collaboration Case Studies</li>

<li> Semantic Application Development and Demonstration</li>
</ul>
<h2><a name="calendar"></a>Course Calendar</h2>
<ul>
<li>  Class 1: Monday, August 29   UPDATED due to Hurricane Irene to Wednesday August 31 at 5:15</li>
<li> NO CLASS on Labor Day September 5</li>
<li> Class 2: Monday, September 12</li>
<li> Class 3: Monday, September 19</li>

<li> Class 4: Monday, September 26</li>
<li> Class 5: Monday, October 3</li>
<li> Class 6: TUESDAY, October 11</li>
<li> Class 7: Monday, October 17</li>
<li> Class 8: Monday, October 24</li>
<li> Class 9: Monday, October 31</li>

<li> Class 10: Monday November 7</li>
<li> Class 11: Monday, November 14</li>
<li> Class 12: Monday November 21</li>
<li> Class 13: Monday November 28</li>
<li> Class 14: Monday December 5 </li>
</ul>
<h2><a name="syllabus"></a>Course Syllabus</h2>

<p>For complete reading citation with link(s) to papers, see reference list below. </p>
<p>NOTICE: Part of readings may be inaccessible when downloaded off the campus. You could download them in the campus if you have the problem.</p>
<ul>
<li>Class 1:  Introduction to e-Science and Semantic Web August 31, 2011
</li>
<li>
Class 1 - <document href="SeS2011_week1Update.ppt" alt="Semantic eScience 2011 Lecture 1"/>
</li>
</ul>
<dl>
<dd>
<dl>
<dd>readings: Ontologies 101, Semantic Web, e-Science, RDFS, OWL Guide.<br />
</dd>
<dd>  assignments and powerpoints are in process of being updated from the 2010 version </dd>
<dd>
Assignment 0 - <document href="SeS2011Assignment00.pdf" alt="Semantic eScience 2011 Assignment 0"/>
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: <document href="SeS2011ClassNotes-2011-08-31.pdf" alt="Semantic eScience 2011 Class Notes for August 31st"/>
</dd>

</dl>
</dd>
</dl>
<ul>

<li>
Class 2 - <document href="SeS2011_week2Update.ppt" alt="Semantic eScience 2011 Lecture 2"/>
Foundations I: Methodologies, Knowledge Representation
</li>

</ul>
<dl>
<dd>
<dl>
<dd>reading: Semantic Web for the Working Ontologist (first few chapters).  Alternate reading - OWL Pizza Tutorial.<br />
</dd>

<dd>
Assignment 1 - <document href="SeS2011_HW.pdf" alt="Semantic eScience 2011 Assignment 1 - Representing Knowledge and Understanding Representations - Understanding and Extending an Ontology"/>
Summary - Review and ontology, make some simple extensions, and answer a few questions using those extensions.
Class Notes:<document href="SeS2011ClassNotes-2011-09-12.pdf" alt="Semantic eScience 2011 Class Notes for September 12th"/>
</dd>
<dd>Link to last year's assignment 1  <a href="/wiki.tw/images/e/ee/CSCI2010-6962-01_Assignment_1_VSTO.pdf" class="internal" title="CSCI2010-6962-01 Assignment 1 VSTO.pdf">  Understanding and Extending the Virtual Solar Terrestrial Observatory Ontology</a>
</dd>

</dl>
</dd>
</dl>
<ul>
<li>Class 3: Foundations II: <document href="SemanticeScience_ontology_engineering.ppt" alt="Ontology Engineering"/> September 19, 2011
</li>
This week's class will be taught by Jim McCusker - mccusj@rpi.edu
</ul>
<dl>

<dd>
<dl>
<dd>reading:  Use Cases<br />
</dd>
<dd>
Use Case Template - <document href="UseCase-Template_SeS" alt="Semantic eScience Use Case Template 2011 "/>
</dd>
http://tw.rpi.edu/media/latest/UseCase-Template_SeS
<dd>
Video Lecture <a href="http://tw.rpi.edu/videos/SemanticeScience2011-Class3-LecturePart1.MOV">Part 1</a>, <a href="http://tw.rpi.edu/videos/SemanticeScience2011-Class3-LecturePart2.MOV">Part 2</a>
Class Notes:<document href="SeS2011ClassNotes-2011-09-19.pdf" alt="Semantic eScience 2011 Class Notes for September 19th"/>
</dd>
SemantAqua - Semantic Water Quality Portal example:  http://tw.rpi.edu/web/project/SemantAQUA/UseCases
</dl>
</dd>
</dl>
<dl>
<dd>
<dl>
<dd><a href="/wiki.tw/images/a/ad/UseCase-SensorWeb-semantics_fox20080324.doc" class="internal" title="UseCase-SensorWeb-semantics fox20080324.doc"> Partial use case example 1</a>
</dd>
<dd><a href="/wiki.tw/images/0/03/UseCase-Volcano_Atmosphere_fox20080410.doc" class="internal" title="UseCase-Volcano Atmosphere fox20080410.doc"> Partial use case example 2</a><br />
</dd>
</dl>
</dd>
</dl>
<ul>
<li> Class 4: Class exercise I: <document href="SeS2011_usecases_week4.ppt" alt="Use Case development"/>, September 26, 2011
</li>
This week's class is taught by Professor Peter Fox pfox@cs.rpi.edu
</ul>

<dl>
<dd>
<dl>
<dd>reading:  Ontology Tool Summary, Pellet, OWL-S, SAWSDL, Wine Agent<br />
</dd>
</dl>
</dd>
</dl>
<dl>
<dd>
<dl>

<dd>
Assignment 2 - <document href="SeS2011_HW2.pdf" alt="Semantic eScience 2011 Assignment 2 - Use-case Driven Knowledge Enoding "/>
Summary - Document a semantic eScience use case and prepare a presentation.
Class Notes:<document href="SeS2011ClassNotes-2011-09-26.pdf" alt="Semantic eScience 2011 Class Notes for September 26th"/>
</dd>

</dl>
</dd>
</dl>
<ul>
<li>Class 5: Foundations III: <document href="SeS2011_week5.ppt" alt="Semantic eScience 2011 Lecture 5"/> Languages, Tools, and Services October 3, 2011
<document href="SeS2011_S_Healthcare.ppt" alt="Semantic eScience 2011 Scottish Healthcare Slides"/>
ClassNotes:<document href="SeS2011_ClassNotes5.pdf" alt="Semantic eScience 2011 ClassNotes5"/>
<ul>
</li>
</ul>

</li>
</ul>
<dl>
<dd>
<dl>
<dd>reading: Ontology Evolution - see below under reference list for full citation<br />
</dd>
<dd>
PopSciGrid demo - on tobacco prevalence and potential data that may impact people's smoking habits - http://tw.rpi.edu/web/project/PopSciGrid
</dl>
</dd>
</dl>
<dl>
<dd>
<dl>
<dd>OWL-S editor tutorial <a href="http://owlseditor.semwebcentral.org/documents/tutorial.pdf" class="external free" title="http://owlseditor.semwebcentral.org/documents/tutorial.pdf" rel="nofollow">http://owlseditor.semwebcentral.org/documents/tutorial.pdf</a><br />

</dd>
</dl>
</dd>
</dl>
<dl>
<dd>
<dl>
<dd>OWL-S and WSDL references <a href="http://www.daml.org/services/owl-s/1.1/owl-s-wsdl.html" class="external free" title="http://www.daml.org/services/owl-s/1.1/owl-s-wsdl.html" rel="nofollow">http://www.daml.org/services/owl-s/1.1/owl-s-wsdl.html</a><br />
</dd>
</dl>
</dd>
</dl>
<dl>
<dd>
<dl>

<dd>CMAP download <a href="http://cmapdownload.ihmc.us/coe/Web_InstallersV5.0/install.htm" class="external free" title="http://cmapdownload.ihmc.us/coe/Web_InstallersV5.0/install.htm" rel="nofollow">http://cmapdownload.ihmc.us/coe/Web_InstallersV5.0/install.htm</a><br />
</dd>
</dl>
</dd>
</dl>
<ul>
<li>Class 6: Class Presentation I: TUESDAY October 11, 2011  Use Cases - Part II of Assignment 2
</li>
</ul>
Individual Student Use Case Homeworks - Each student should upload their presentation and use case submission <here>http://tw.rpi.edu/web/Courses/SemanticeScience/Partof2Assignment2Submission
<b>For Mushroom Project</b>:
Here are the links recommended by Nathan Wilson:
http://eol.org
http://mushroomobserver.org
His Masters Thesis: http://collectivesource.com/taxy/thesis.html   Important reference for creating an an initial macroscopic fungal ontology
Nathan's Presentation PDF:<document href="SeS2011_Nathan.ppt" alt="Semantic eScience 2011 Nathan's PPT"/>
Mushroom OWL: <document href="SeS2011_mushroom.owl" alt="Semantic eScience 2011 Mushroom Ontology"/>
Use Case Document:<document href="SeS2011_mushroom.rtf" alt="Semantic eScience 2011 Mushroom Use Case"/>
Readme: <document href="SeS2011_mushroom_readme.rtf" alt="Semantic eScience 2011 Mushroom Readme"/>
<b>The new link for Materials: http://tw.rpi.edu/web/Courses/SemanticeScience/2011/FinalProjects</b>


<ul>
<li>Class 7: Use Case material continued and <a href="/wiki.tw/images/a/a0/SeS2010_week7_use_case_implementation.ppt" class="internal" title="SeS2010 week7 use case implementation.ppt"> Use Case Implementation</a> October 17, 2011

</li>
</ul>
<dl>
<dd>
<dl>
<dd>reading: review ontology evolution reading.   <br />
</dd>
<dd> 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. 
</dd>
<dd>assignment 3:  <document href="SeS2011_ontology_project.doc" alt="Semantic eScience 2011 Ontology Project DOC"/>
<document href="SeS2011_ontology_project.pdf" alt="Semantic eScience 2011 Ontology Project PDF"/> November 14, 2011 Ontology Projects
Class Notes: <a href="http://tw.rpi.edu/web/Courses/SemanticeScience/2011/ClassNotes_Oct_17_2011">Semantic eScience 2011 Class Notes for October 17th</a>
</dd>
</dl>
</dd>
</dl>
<ul>

<li>Class 8:    October 24, 2011  Class exercise II: Foundations IV: <a href="/wiki.tw/images/d/d5/SeS2010_week9_ont_evolutionUpdated.ppt" class="internal" title="SeS2010 week9 ont evolutionUpdated.ppt">Ontology Evolution and Knowledge Management</a>
<b>Jim McCuster will give the lecture</b>
<li> 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. <br />
</li>
</ul>
<ul>
<li>Class 9: Provenance and possible external use case presentation, <document href="SeS2011_Provenance.ppt" alt="Semantic eScience 2011 Oct 31 Provenance"/> Provenance for Semantic eScience</a> October 31, 2011
</li>
</ul>
<dl>
<dd>
<dl>

</dl>
</dd>
</dl>
<dl>
<dd>
<dl>
<dd><document href="ApplyingUserAnnotationsToProvenance.pdf" alt="Enabling Incremental Enhancement of Provenance Records via User Annotation"/> - James Michaelis, presented by Deborah McGuinness
</dd>
</dl>

</dd>
</dl>
<dl>
<dd>
<dl>
<dd>reading: Evaluation
<br />
</dd>
<dd>additional material: <a href="/wiki.tw/images/0/02/Summative_vs._Formative_Evaluation.pdf" class="internal" title="Summative vs. Formative Evaluation.pdf"> Summative versus Formative evaluation</a><br />

</dd>
</dl>
</dd>
</dl>
<dl>
<dd>
<dl>
<dd>additional material: <a href="/wiki.tw/images/3/34/Etc667_final_rubric_eval_example.pdf" class="internal" title="Etc667 final rubric eval example.pdf"> Example of evaluation</a>
</dd>
</dl>
</dd>
</dl>
<dl>
<dd>

<dl>
<dd>additional material: <a href="/wiki.tw/images/3/36/Formative_summative_eval_plan.doc" class="internal" title="Formative summative eval plan.doc"> Template example for Evaluation</a><br />
</dd>
</dl>
</dd>
</dl>
<dl>
<dd>
<dl>

</dl>
</dd>

</dl>
</dl>
</dd>
</dl>
<p>
</p>
<ul>
<li>Class 10: Evaluation : Application Project Evaluation <document href="SeS2011_evaluation.ppt" alt="Semantic eScience 2011 Project Evaluation "/>

Foundations V Architecture: <document href="SeS2011_evaluation.ppt" alt="Semantic eScience 2011 Project Evaluation "/> Evaluation, Infrastructure and Architecture, Middleware</a>  November 7, 2011
<li> Class exercise III: <a href="/wiki.tw/images/7/7e/SeS2010-week11_class_applic_proj_eval.ppt" class="internal" title="SeS2010-week11 class applic proj eval.ppt"> Application Project Evaluation</a> 
</li>

</li>
</ul>
<dl>
<dd>
<dl>
<dd>additional materials <a href="/wiki.tw/images/a/ad/OrchardIrrigation2008Presentation.ppt" class="internal" title="OrchardIrrigation2008Presentation.ppt"> Orchard Irrigation</a> and <a href="/wiki.tw/images/3/3d/DiabeticExchange2008Presentation.pdf" class="internal" title="DiabeticExchange2008Presentation.pdf"> Diabetic Exchange</a>
Optional Readings: <a href="http://ksl.stanford.edu/KSL_Abstracts/KSL-08-01.html" class="internal" title="Semantic2011CALO.pdf"> CALO</a>
<a href="http://ksl.stanford.edu/KSL_Abstracts/KSL-06-02.html" class="internal" title="Semantic2011NIMD.pdf"> NIMD</a>
</dd>
</dl>
</dd>
</dl>
<dd>reading: none - presentations next week<br />
</dd>
<ul>
<li>Class 11: Class Presentation II: Team Use Case Implementation
 November 14, 2011
</li>
<li>
<dd>Term assignment:  .DOC version<document href="SESTermAssignment.doc" alt="2011SeS_TermAssignment"/> Use Case: Iterating and Evolving, Lessons Learned</a>;  
PDF version<document href="SES_TermAssignment.pdf" alt="2011SeS_TermAssignment"/> Use Case: Iterating and Evolving, Lessons Learned</a>; 

</dd>
</li>
</ul>
<dd>reading: semantic integration<br />
</dd>
<li>Class 12: Foundations VI: <document href="SeS2011_Week12_.ppt" alt="Semantic eScience 2011 Nov 21 Lecture "/> Discovery, Access and Semantic Integration and Foundations VII: Data Mining and Knowledge Discovery</a> .  November 21, 2011.
</li>
</ul>
<p><a href="/wiki.tw/images/5/58/SeS2010_week13extra.ppt" class="internal" title="SeS2010 week13extra.ppt"> Extra Slides</a> November 28, 2011
</p>
<dd><document href="ApplyingUserAnnotationsToProvenance.pdf" alt="Enabling Incremental Enhancement of Provenance Records via User Annotation"/> - James Michaelis, presented by Deborah McGuinness
</dd>

<dl>
<dd>

<dl>
<dd>reading: Provenance/ PML<br />
</dd>
</dl>
</dd>
</dl>
<ul>
<li>Class 13:  Class Presentation III: Term assignment - Project Outcome, November 28, 2011
</li>
</ul>
<ul>
<li>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 
<document href="SeS2011FinalAssignment.doc" alt="Semantic eScience 2011 Final Assignment"/>

</li>
</ul>

<h2><a name="objective"></a>Course Learning Objective</h2>
<ul>
<li>  Ontology Development, Merging and Validation</li>

<li> Semantic Language and Tool Use and Evaluation</li>
<li> Use Case Development and Elaboration</li>
<li> Semantic eScience Implementation and Evaluation via Use Cases</li>
<li> Semantic Application Development and Demonstration</li>
<li> Group Project and Team Development, Use Case Implementation and Evaluation</li>
<li> TBC </li>

</ul>
<h2><a name="criteria"></a>Assessment Criteria</h2>
<ul>
<li> Via written assignments with specific percentage of grade allocation provided with each assignment</li>
<li> Via oral presentations with specific percentage of grade allocation provided</li>
<li> Via group presentations</li>
<li> Via participation in class (not to exceed 10% of total)</li>
<li> Late submission policy: first time with valid reason – no penalty, otherwise 20% of score deducted each late day </li>

</ul>
<h2><a name="prereq"></a>Suggested Prerequisites</h2>
<ul>
<li> Knowledge such as that gained in a Semantic Web class (e.g., CSCI-6961)</li>
<li> Knowledge such as that gained in a Web Science class (e.g., CSCI-xx)</li>
<li> or permission of the instructors </li>
</ul>
<h2><a name="ref"></a>Reference List</h2>
<p>Class 1 Reading Assignment:

</p>
<ul>
<li> [Ontologies 101]  Natalya F. Noy  and  Deborah L. McGuinness. <a href="http://ksl.stanford.edu/people/dlm/papers/ontology-tutorial-noy-mcguinness-abstract.html" class="external text" title="http://ksl.stanford.edu/people/dlm/papers/ontology-tutorial-noy-mcguinness-abstract.html" rel="nofollow">Ontology Development 101:  A Guide to Creating Your First Ontology</a>.   Stanford Knowledge Systems Laboratory Technical Report  KSL-01-05 and Stanford Medical Informatics Technical Report SMI-2001-0880, March 2001. 
</li>
</ul>
<ul>
<li>Semantic Web:
</li>
</ul>
<dl>
<dd>
<dl>
<dd>T Berners-Lee, J Hendler, O Lassila.  <a href="http://www.sciam.com/article.cfm?id=the-semantic-web" class="external text" title="http://www.sciam.com/article.cfm?id=the-semantic-web" rel="nofollow">The Semantic Web</a>. Scientific American, 2001.  alternative link - <a href="http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.115.9584&rep=rep1&type=pdf" class="external free" title="http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.115.9584&rep=rep1&type=pdf" rel="nofollow">http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.115.9584&rep=rep1&type=pdf</a><br />

</dd>
<dd> Grigoris Antoniou and Frank van Harmelen.  <a href="http://www.ics.forth.gr/isl/swprimer/" class="external text" title="http://www.ics.forth.gr/isl/swprimer/" rel="nofollow">Semantic Web Primer</a><br />
</dd>
</dl>
</dd>
</dl>
<ul>
<li>e-Science:  Hey, T., and Trefethen, A.  <a href="http://www.sciencemag.org/cgi/content/full/sci;308/5723/817" class="external text" title="http://www.sciencemag.org/cgi/content/full/sci;308/5723/817" rel="nofollow">Cyberinfrastructure for e-Science</a>.  Science 308, 5723 (2005), 817–821. 
</li>
<li>RDFS: <a href="http://www.w3.org/TR/rdf-schema/" class="external text" title="http://www.w3.org/TR/rdf-schema/" rel="nofollow">RDF Vocabulary Description Language 1.0: RDF Schema.</a>  World Wide Web Consortium (W3C) Recommendation.  February 10, 2004.

</li>
</ul>
<ul>
<li> [OWL Guide]  Michael K. Smith, Chris Welty, and  Deborah L. McGuinness.  <a href="http://www.w3.org/TR/owl-guide/" class="external text" title="http://www.w3.org/TR/owl-guide/" rel="nofollow">OWL Web Ontology Language Guide</a>. World Wide Web Consortium (W3C) Recommendation. February 10, 2004.
</li>
</ul>
<ul>
<li> "Sharing of Data Leads to Progress on Alzheimer’s," By GINA KOLATA, New York Times, August 12, 2010 <a href="http://www.nytimes.com/2010/08/13/health/research/13alzheimer.html?_r=1" class="external free" title="http://www.nytimes.com/2010/08/13/health/research/13alzheimer.html?_r=1" rel="nofollow">http://www.nytimes.com/2010/08/13/health/research/13alzheimer.html?_r=1</a>
</li>
</ul>
<p>Optional

</p>
<ul>
<li> Optional - OWL 2 Web Ontology Language Document Overview W3C Recommendation 27 October 2009. <a href="http://www.w3.org/TR/owl2-overview/" class="external free" title="http://www.w3.org/TR/owl2-overview/" rel="nofollow">http://www.w3.org/TR/owl2-overview/</a>
</li>
<li> Optional - Common Logic:  John Sowa, <a href="http://www.jfsowa.com/clce/clce07.htm" class="external text" title="http://www.jfsowa.com/clce/clce07.htm" rel="nofollow">Common Logic Controlled English</a>, March, 2007. (The previous link is an updated Section 7 of (the full) <a href="http://www.jfsowa.com/clce/specs.htm" class="external text" title="http://www.jfsowa.com/clce/specs.htm" rel="nofollow">Common Logic Controlled English</a> draft.)
</li>
</ul>
<p>Class 2: Reading Assignment:

</p>
<ul>
<li> Semantic Web for the Working Ontologist (Allemang and Henderl), first few chapters. The book is available at Amzaon.com, the RPI Library (check availability at library.rpi.edu),and an online preview is available Google Books: <a href="http://books.google.com/books?id=RnFjZTfPILcC&printsec=frontcover&cd=1&source=gbs_ViewAPI#v=onepage&q&f=false" class="external free" title="http://books.google.com/books?id=RnFjZTfPILcC&printsec=frontcover&cd=1&source=gbs_ViewAPI#v=onepage&q&f=false" rel="nofollow">http://books.google.com/books?id=RnFjZTfPILcC&printsec=frontcover&cd=1&source=gbs_ViewAPI#v=onepage&q&f=false</a>
</li>
</ul>
<p>Alternate reading -
</p>
<ul>
<li> 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. <a href="http://www.co-ode.org/resources/papers/ekaw2004.pdf" class="external free" title="http://www.co-ode.org/resources/papers/ekaw2004.pdf" rel="nofollow">http://www.co-ode.org/resources/papers/ekaw2004.pdf</a>

</li>
</ul>
<p>Optional reading -
</p>
<ul>
<li> Optional: McGuinness, D.L. "Ontologies come of age" <a href="http://www.ksl.stanford.edu/people/dlm/papers/ontologies-come-of-age-abstract.html" class="external free" title="http://www.ksl.stanford.edu/people/dlm/papers/ontologies-come-of-age-abstract.html" rel="nofollow">http://www.ksl.stanford.edu/people/dlm/papers/ontologies-come-of-age-abstract.html</a>
</li>
</ul>
<ul>
<li> Optional: Demir, et al., "The BioPAX community standard for pathway data sharing" Nature Biotechnology, Volume 28, Number 9, September 2010. <a href="http://www.nature.com/nbt/journal/v28/n9/pdf/nbt.1666.pdf" class="external free" title="http://www.nature.com/nbt/journal/v28/n9/pdf/nbt.1666.pdf" rel="nofollow">http://www.nature.com/nbt/journal/v28/n9/pdf/nbt.1666.pdf</a>
</li>

</ul>
<ul>
<li> Optional: Luciano, Joanne S. and Stevens, Robert D. OWL: PAX of mind or the AX? Experiences of Using OWL in the Development of BioPAX For the workshop OWL: Experiences and Directions, Gaithersburg, MD, USA, April 1-2, 2008. <a href="http://www.webont.org/owled/2008dc/papers/owled2008dc_paper_7.pdf" class="external free" title="http://www.webont.org/owled/2008dc/papers/owled2008dc_paper_7.pdf" rel="nofollow">http://www.webont.org/owled/2008dc/papers/owled2008dc_paper_7.pdf</a>
</li>
</ul>
<p>
Class 3: Reading Assignment:
</p>
<ul>
<li> Use Cases:
</li>
</ul>
<p>Required:

</p>
<ul>
<li> <a href="http://en.wikipedia.org/wiki/Use_case" class="external free" title="http://en.wikipedia.org/wiki/Use_case" rel="nofollow">http://en.wikipedia.org/wiki/Use_case</a>
</li>
<li> <a href="http://alistair.cockburn.us/index.php/Use_cases,_ten_years_later" class="external free" title="http://alistair.cockburn.us/index.php/Use_cases,_ten_years_later" rel="nofollow">http://alistair.cockburn.us/index.php/Use_cases,_ten_years_later</a>
</li>
</ul>
<p>Optional:
</p>
<ul>
<li><a href="http://members.aol.com/acockburn/papers/AltIntro.htm" class="external free" title="http://members.aol.com/acockburn/papers/AltIntro.htm" rel="nofollow">http://members.aol.com/acockburn/papers/AltIntro.htm</a>
</li>

</ul>
<p><a href="http://www.digilife.be/quickreferences/pt/functional%20requirements%20and%20use%20cases.pdf" class="external free" title="http://www.digilife.be/quickreferences/pt/functional%20requirements%20and%20use%20cases.pdf" rel="nofollow">http://www.digilife.be/quickreferences/pt/functional%20requirements%20and%20use%20cases.pdf</a></p>
<ul>
<li> <a href="http://alistair.cockburn.us/index.php/Resources_for_writing_use_cases" class="external free" title="http://alistair.cockburn.us/index.php/Resources_for_writing_use_cases" rel="nofollow">http://alistair.cockburn.us/index.php/Resources_for_writing_use_cases</a>
</li>
<li> <a href="http://alistair.cockburn.us/Usecasesintheoryandpractice180.ppt" class="external free" title="http://alistair.cockburn.us/Usecasesintheoryandpractice180.ppt" rel="nofollow">http://alistair.cockburn.us/Usecasesintheoryandpractice180.ppt</a>
</li>
<li> <a href="http://alistair.cockburn.us/Agileusecases1dy.ppt" class="external free" title="http://alistair.cockburn.us/Agileusecases1dy.ppt" rel="nofollow">http://alistair.cockburn.us/Agileusecases1dy.ppt</a>
</li>
<li> <a href="http://alistair.cockburn.us/index.php/Structuring_use_cases_with_goals" class="external free" title="http://alistair.cockburn.us/index.php/Structuring_use_cases_with_goals" rel="nofollow">http://alistair.cockburn.us/index.php/Structuring_use_cases_with_goals</a>

</li>
<li> <a href="http://www.foruse.com/publications/bibliographies/usecases.htm" class="external free" title="http://www.foruse.com/publications/bibliographies/usecases.htm" rel="nofollow">http://www.foruse.com/publications/bibliographies/usecases.htm</a>
</li>
<li> <a href="http://en.wikipedia.org/wiki/Use_case" class="external free" title="http://en.wikipedia.org/wiki/Use_case" rel="nofollow">http://en.wikipedia.org/wiki/Use_case</a>
</li>
<li> <a href="http://www.ddj.com/dept/architect/184414701" class="external free" title="http://www.ddj.com/dept/architect/184414701" rel="nofollow">http://www.ddj.com/dept/architect/184414701</a>
</li>
</ul>
<ul>
<li> RDFS:  <a href="http://www.w3.org/TR/rdf-schema/" class="external free" title="http://www.w3.org/TR/rdf-schema/" rel="nofollow">http://www.w3.org/TR/rdf-schema/</a>

</li>
</ul>
<p>Class 4: Reading Assignment:
</p>
<ul>
<li> Ontology Tool Summary:  Michael Denny. <a href="http://www.xml.com/pub/a/2004/07/14/onto.html" class="external text" title="http://www.xml.com/pub/a/2004/07/14/onto.html" rel="nofollow">Ontology Tools Survey</a>, Revisited. XML.com
</li>
<li> Pellet:  web page: <a href="http://pellet.owldl.com" class="external free" title="http://pellet.owldl.com" rel="nofollow">http://pellet.owldl.com</a>
</li>
<li> Pellet: Evren Sirin and Bijan Parsia and Bernardo Cuenca Grau and Aditya Kalyanpur and Yarden Katz, Pellet: a practical owl-dl reasoner.   Journal of Web Semantics. <a href="http://www.mindswap.org/papers/PelletJWS.pdf" class="external free" title="http://www.mindswap.org/papers/PelletJWS.pdf" rel="nofollow">http://www.mindswap.org/papers/PelletJWS.pdf</a>

</li>
<li> OWL-S:   David Martin, Mark Burstein, Drew McDermott, Deborah L. McGuinness, Sheila McIlraith, Massimo Paolucci,  Evren Sirin, Naveen Srinivasan, and Katia Sycara. <a href="http://springerlink.com/content/wp8q2133g5725340/" class="external text" title="http://springerlink.com/content/wp8q2133g5725340/" rel="nofollow">Bringing Semantics to Web Services with OWL-S</a>. World Wide Web Journal, Volume 10, Number 3, pp 243-277.  Also, <a href="http://www.ksl.stanford.edu/KSL_Abstracts/KSL-06-21.html" class="external text" title="http://www.ksl.stanford.edu/KSL_Abstracts/KSL-06-21.html" rel="nofollow">Stanford KSL Technical Report KSL-06-21</a>.
</li>
<li> SAWSDL: <a href="http://www.w3.org/TR/sawsdl/" class="external text" title="http://www.w3.org/TR/sawsdl/" rel="nofollow">Semantic Annotation of the Web Services Description Language</a>
</li>
</ul>
<ul>
<li>Wine Agent:
</li>

</ul>
<dl>
<dd>
<ul>
<li> Eric Hsu, and Deborah L. McGuinness. KSL Wine Agent: Semantic Web Testbed Application, Proceedings of the 2003 International Workshop on Description Logics (DL2003). Rome, Italy, September 5-7, 2003. <a href="ftp://ftp.ksl.stanford.edu/pub/KSL_Reports/KSL-03-17.pdf" class="external free" title="ftp://ftp.ksl.stanford.edu/pub/KSL_Reports/KSL-03-17.pdf" rel="nofollow">ftp://ftp.ksl.stanford.edu/pub/KSL_Reports/KSL-03-17.pdf</a>
</li>
<li> James Michaelis, Li Ding, Deborah McGuinness.  <a href="/wiki/The_TW_Wine_Agent:_A_Social_Semantic_Web_Demo" title=" A Social Semantic Web Demo"> The TW Wine Agent A Social Semantic Web Demo</a>.  ISWC 2008 Poster and Demo Track, 2008.  <a href="http://sunsite.informatik.rwth-aachen.de/Publications/CEUR-WS/Vol-401/iswc2008pd_submission_61.pdf" class="external free" title="http://sunsite.informatik.rwth-aachen.de/Publications/CEUR-WS/Vol-401/iswc2008pd_submission_61.pdf" rel="nofollow">http://sunsite.informatik.rwth-aachen.de/Publications/CEUR-WS/Vol-401/iswc2008pd_submission_61.pdf</a>
</li>

</ul>
</dd>
</dl>
<p>Class 5: Reading Assignment:
</p>
<ul>
<li> [Ontology Evolution] Deborah L. McGuinness, Richard Fikes, James Rice, and Steve Wilder.    
</li>
</ul>
<p><a href="http://www.ksl.stanford.edu/people/dlm/papers/kr00-abstract.html" class="external text" title="http://www.ksl.stanford.edu/people/dlm/papers/kr00-abstract.html" rel="nofollow">An Environment for Merging and Testing Large Ontologies</a>.  In Proceedings of the 7th International Conference on Principles of Knowledge Representation and Reasoning (KR2000), Breckenridge, Colorado, USA 12-15 April 2000<br />
[<a href="http://www.ksl.stanford.edu/people/dlm/papers/kr00-abstract.html" class="external free" title="http://www.ksl.stanford.edu/people/dlm/papers/kr00-abstract.html" rel="nofollow">http://www.ksl.stanford.edu/people/dlm/papers/kr00-abstract.html</a>
</p>
<ul>
<li> Prompt - <a href="http://protege.cim3.net/cgi-bin/wiki.pl?Prompt" class="external free" title="http://protege.cim3.net/cgi-bin/wiki.pl?Prompt" rel="nofollow">http://protege.cim3.net/cgi-bin/wiki.pl?Prompt</a>
</li>
</ul>

<p>optional:
</p>
<ul>
<li> Aseem Das, Wei Wu, and Deborah L. McGuinness. ``Industrial Strength Ontology Management. Stanford Knowledge Systems Laboratory Technical Report KSL-01-09 2001. In the   Proceedings of the International Semantic Web Working Symposium. Stanford, CA, July 2001.  Also published in In Isabel Cruz, Stefan Decker, Jerome Euzenat, and  Deborah L. McGuinness, eds. The Emerging Semantic Web.  (Book available from   <a href="http://www.inrialpes.fr/exmo/papers/emerging/" class="external free" title="http://www.inrialpes.fr/exmo/papers/emerging/" rel="nofollow">http://www.inrialpes.fr/exmo/papers/emerging/</a>). IOS Press, 2002.    Google Book version available at <a href="http://books.google.com/books?id=spmIS-CGxUAC&printsec=frontcover&dq=the+emerging+semantic+web+book&source=bl&ots=EoQSArw8Yf&sig=Eq4PFDc1QDSBASWavuKBG4DMdn4&hl=en&ei=Y0KqTKrEF5SOjAe7gtjsDA&sa=X&oi=book_result&ct=result&resnum=3&ved=0CCQQ6AEwAg#v=onepage&q&f=false" class="external free" title="http://books.google.com/books?id=spmIS-CGxUAC&printsec=frontcover&dq=the+emerging+semantic+web+book&source=bl&ots=EoQSArw8Yf&sig=Eq4PFDc1QDSBASWavuKBG4DMdn4&hl=en&ei=Y0KqTKrEF5SOjAe7gtjsDA&sa=X&oi=book_result&ct=result&resnum=3&ved=0CCQQ6AEwAg#v=onepage&q&f=false" rel="nofollow">http://books.google.com/books?id=spmIS-CGxUAC&printsec=frontcover&dq=the+emerging+semantic+web+book&source=bl&ots=EoQSArw8Yf&sig=Eq4PFDc1QDSBASWavuKBG4DMdn4&hl=en&ei=Y0KqTKrEF5SOjAe7gtjsDA&sa=X&oi=book_result&ct=result&resnum=3&ved=0CCQQ6AEwAg#v=onepage&q&f=false</a>

</li>
</ul>
<p><a href="http://www.ksl.stanford.edu/people/dlm/papers/ontologyBuilderVerticalNet-abstract.html" class="external free" title="http://www.ksl.stanford.edu/people/dlm/papers/ontologyBuilderVerticalNet-abstract.html" rel="nofollow">http://www.ksl.stanford.edu/people/dlm/papers/ontologyBuilderVerticalNet-abstract.html</a>
</p>

<li>   OWL-S editor tutorial http://owlseditor.semwebcentral.org/documents/tutorial.pdf
</li>
<li>  OWL-S and WSDL references http://www.daml.org/services/owl-s/1.1/owl-s-wsdl.html
</li>
<li>
        CMAP download http://cmapdownload.ihmc.us/coe/Web_InstallersV5.0/install.htm
</li>

<p>Class 6:  Reading Assignment:
</p>
<p>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).   http://tw.rpi.edu/web/doc/iswc2011_swqp 

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). 
http://tw.rpi.edu/web/doc/eim2011_swqp 

Review static demo:  http://inference-web.org/wiki/Semantic_Water_Quality_Portal 


</p>
<p>

Class 8: Reading Assignment:
</p>
<ul>
<li> PML -McGuinness, Ding, Pinheiro da Silva, Chang. PML 2: A Modular Explanation Interlingua. AAAI 2007 Workshop on Explanation-aware Computing, Vancouver, Can., 7/07. Stanford Tech report KSL-07-07. <a href="http://www.ksl.stanford.edu/KSL_Abstracts/KSL-07-07.html" class="external free" title="http://www.ksl.stanford.edu/KSL_Abstracts/KSL-07-07.html" rel="nofollow">http://www.ksl.stanford.edu/KSL_Abstracts/KSL-07-07.html</a>
</li>
</ul>
<ul>
<li> 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  <a href="http://www.ksl.stanford.edu/KSL_Abstracts/KSL-04-03.html" class="external free" title="http://www.ksl.stanford.edu/KSL_Abstracts/KSL-04-03.html" rel="nofollow">http://www.ksl.stanford.edu/KSL_Abstracts/KSL-04-03.html</a>
</li>
</ul>
<ul>

<li> 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. <a href="http://www.ksl.stanford.edu/KSL_Abstracts/KSL-06-05.html" class="external free" title="http://www.ksl.stanford.edu/KSL_Abstracts/KSL-06-05.html" rel="nofollow">http://www.ksl.stanford.edu/KSL_Abstracts/KSL-06-05.html</a>
</li>
</ul>
<ul>
<li> [IAAI VSTO] Deborah McGuinness, Peter Fox, Luca Cinquini, Patrick West, Jose Garcia, James L. Benedict, and Don Middleton. <a href="http://www.ksl.stanford.edu/KSL_Abstracts/KSL-07-01.html" class="external text" title="http://www.ksl.stanford.edu/KSL_Abstracts/KSL-07-01.html" rel="nofollow">The Virtual Solar-Terrestrial Observatory: A Deployed Semantic Web Application Case Study for Scientific Research</a>. In the Proceedings of the Nineteenth Conference on Innovative Applications of Artificial  Intelligence (IAAI-07). Vancouver, British Columbia, Canada, July 22-26, 2007. 
</li>
<li> [Semantic eScience  Web Services]  Peter Fox, Luca Cinquini, Deborah L. McGuinness, Patrick West, Jose Garcia, James L. Benedict and Stephan Zednik. <a href="http://vsto.hao.ucar.edu/presentations/FoxCinquiniMcGuinnessEtAlWebServiceMay15a.pdf" class="external text" title="http://vsto.hao.ucar.edu/presentations/FoxCinquiniMcGuinnessEtAlWebServiceMay15a.pdf" rel="nofollow">Semantic web services for interdisciplinary scientific data query and retrieval</a>. In the Proceedings of the Semantic eScience Workshop co-located with the Association for the Advancement of Artificial Intelligence Conference, Vancouver, CA., July 23, 2007.
</li>

<li> P. Fox, D. McGuinness, L. Cinquini, P. West, J. Garcia, and J. Benedict 2008, <a href="http://vsto.hao.ucar.edu/presentations/C_AND_G2007_final_figs.pdf" class="external text" title="http://vsto.hao.ucar.edu/presentations/C_AND_G2007_final_figs.pdf" rel="nofollow">Ontology-supported Scientific Data Frameworks: The Virtual Solar-Terrestrial Observatory Experience</a>, Computers and Geosciences, special issue on Geoscience Knowledge Representation for Cyberinfrastructure, in press.
</li>
</ul>
<p>Class 9: Reading Assignment:
</p>
<ul>
<li>Evaluation:  Twidale, M., Randall, D. and Bentley, R. 1994,<a href="/wiki.tw/images/5/5e/10.1.1.44.9125.pdf" class="internal" title="10.1.1.44.9125.pdf"> Situated evaluation for cooperative systems</a>,  Proceedings, Comp. Supp. Coop. Work 1994, Chapel Hill, NC, pp. 441-452.
</li>
</ul>
<dd>additional material: <a href="/wiki.tw/images/0/02/Summative_vs._Formative_Evaluation.pdf" class="internal" title="Summative vs. Formative Evaluation.pdf"> Summative versus Formative evaluation</a><br />

</dd>
</dl>
</dd>
</dl>
<dl>
<dd>
<dl>
<dd>additional material: <a href="/wiki.tw/images/3/34/Etc667_final_rubric_eval_example.pdf" class="internal" title="Etc667 final rubric eval example.pdf"> Example of evaluation</a>
</dd>
</dl>
</dd>
</dl>
<dl>
<dd>

<dl>
<dd>additional material: <a href="/wiki.tw/images/3/36/Formative_summative_eval_plan.doc" class="internal" title="Formative summative eval plan.doc"> Template example for Evaluation</a><br />
</dd>
</dl>
</dd>
</dl>
<p>
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. 
<a href="http://ksl.stanford.edu/KSL_Abstracts/KSL-08-01.html" class="internal" title="Semantic2011CALO.pdf"> CALO</a>
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
<a href="http://ksl.stanford.edu/KSL_Abstracts/KSL-06-02.html" class="internal" title="Semantic2011NIMD.pdf"> NIMD</a>
</p>
<p>Class 11: Reading Assignment:
</p>

<ul>
<li>Integration:
</li>
<li>  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.  <a href="ftp://ftp.ksl.stanford.edu/pub/KSL_Reports/KSL-07-09.pdf" class="external free" title="ftp://ftp.ksl.stanford.edu/pub/KSL_Reports/KSL-07-09.pdf" rel="nofollow">ftp://ftp.ksl.stanford.edu/pub/KSL_Reports/KSL-07-09.pdf</a>
</li>
</ul>
<ul>
<li>Sunil Movva, Rahul Ramachandran, Xiang Li, Phani Cherukuri, Sara Graves.  Noesis: A Semantic Search Engine and Resource Aggregator for Atmospheric Science.  NSTC2007.   <a href="http://esto.nasa.gov/conferences/nstc2007/papers/Ramachandran_Rahul_A3P4_NSTC-07-0084.pdf" class="external free" title="http://esto.nasa.gov/conferences/nstc2007/papers/Ramachandran_Rahul_A3P4_NSTC-07-0084.pdf" rel="nofollow">http://esto.nasa.gov/conferences/nstc2007/papers/Ramachandran_Rahul_A3P4_NSTC-07-0084.pdf</a>
</li>
</ul>
<ul>
<li>Boyan Brodaric and Florian Probst.  Enabling Cross-Disciplinary e-Science by Integrating Geoscience Ontologies with DOLCE.  Under Review. 2008.

</li>
</ul>
<ul>
<li>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. <a href="http://www.isi.edu/~gil/papers/computer-NSFworkflows07.pdf" class="external free" title="http://www.isi.edu/~gil/papers/computer-NSFworkflows07.pdf" rel="nofollow">http://www.isi.edu/~gil/papers/computer-NSFworkflows07.pdf</a> 
</li>
</ul>

<p>Class 12: Reading Assignment:
</p>
<p>
Class 13: Reading Assignment:  None.
</p>
<h2><a name="attendance"></a>Attendance Policy</h2>
<p>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.</p>
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