Advanced Semantic Technologies (Spring 2012)

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Instructor: Professor Deborah L. McGuinness - dlm at cs dot rpi dot edu
TA: Abigail Fuller - fullea6 at rpi dot edu (Office Hours: Thur 11:30-1:30 )
Meeting times: Tuesday 1:00 pm - 3:50 pm.

phone: 518-276-4464
Class Listing: CSCI 6965 - 01, 97543, CSCI 4967 - 01, 97014, ITWS 6962 - 01, 98113, ITWS 4963 - 01, 98438
Class Location Winslow 1140

Description

This course aims at showing the cutting edge research on semantic web and encouraging research capability for advanced students. Students attending this course should expect reading, presenting and evaluating important research papers on semantic web, identifying and surveying interesting semantic web research areas.

Schedule

  • Week 1: January 24, 2012
  • Week 2: January 31, 2012
  • Week 3: February 7, 2012
  • Week 4: February 14, 2012
  • Week 5: February 21, 2012
  • Week 6: February 28, 2012
  • Week 7: March 6, 2012
  • March 13 - Spring break
  • Week 8: March 20, 2012
  • Week 9: March 27, 2012
  • Week 10: April 3, 2012
  • Week 11: April 10, 2012
  • April 17 - no class - Grand Marshall Weed
  • Week 12: April 24, 2012
  • Week 13: May 1, 2012
  • Week 14: May 8, 2012

Weekly detail

Week 1 Jan 24, 2012

Class 1 - Advanced Semantic Technologies 2012 Lecture 1 [Download]
Notes - Jan-24 Titan Pad [Download]

  • Introduction to course

  • Outline of scope of Advanced Semantic Technologies
  • Journals we will examine
    • Journal of Web Semantics: http://www.elsevier.com/wps/find/journaldescription.cws_home/671322/description?navopenmenu=-2
    • Journal of AI Research: http://www.jair.org/
    • International Journal On Semantic Web and Information Systems: http://www.ijswis.org/
    • International Journal of Semantic Computin g (IJSC): http://www.worldscinet.com/ijsc/
    • International Journal of Metadata, Semantics and Ontologies (IJMSO): http://www.inderscience.com/browse/index.php?journalCODE=ijmso
    • Journal of Data Semantics: http://lbdwww.epfl.ch/e/Springer/
    • Journal of Semantics: http://jos.oxfordjournals.org/
  • Nature of articles - see the following conferences for additional topic/ subject areas
    • http://iswc2012.semanticweb.org/
    • http://www.eswc2012.org/
    • http://www.aaai.org/Conferences/
    • http://semtechbizsf2012.semanticweb.com/
  • this class will be most similar to the version of this class taught in 2010 -

http://tw.rpi.edu/portal/CSCI_6965_Emerging_Trends_in_Semantic_Technologies_%28Spring_2010%29

Week 2 - January 31, 2012

Notes - Jan-31 Titan Pad [Download]
Here are the Various Links from the Jan-31 Titan Pad:

  • Mushroom Identification: http://bit.ly/wJ2SGk
  • Water Quality Portal: http://tinyurl.com/6oxop3q
  • Elsevier Sciverse Collaboration: http://bit.ly/wWUWuq, http://www.hub.sciverse.com/action/home, http://www.applications.sciverse.com/action/gallery
  • Air Quality Portal: http://tw.rpi.edu/web/Courses/AdvancedSemanticTechnologies/2012 (Look for Linyun)
  • Linked Sensor Data: http://tw.rpi.edu/media/2012/01/31/ccd7/heiko-muller-slides.pdf
  • Water Quality Monitoring: http://www.kirkjalbert.com/about-me/, http://bit.ly/z3Kt61, http://www.watershed-mapping.rpi.edu
  • Linked Sensor Data and Data Quality: http://bit.ly/zQ8Ile, http://logd.tw.rpi.edu/demo/trends_in_smoking_prevalence_tobacco_policy_coverage_and_tobacco_prices
  • School of Ants: http://schoolofants.org/

Homework:
1 - turn in your written statement of your research interests following the instructions below.

  • Student 10 minute introduction - interests and experience

Instructions for written material

  • 1/2 - 3/4 page
  • should contain a clear statement of a research interest/ topic
  • should provide a few sentences on why this research is important, or its application
  • 3-5 keywords or phrases classifying the topic and if an index set or controlled vocabulary was used
  • should indicate what this research builds upon
  • should indicate (cite) related, or pre-cursor work
  • should present or discuss (short paragraph) some current (or proposed) work on the topic
  • should include citation references in a suitable format (i.e. indicating source)
  • this assignment has no grade associated with it but is required to be handed in

2. Read
From the Semantic Web to social machines: A research challenge for AI on the WWW by Hendler and Berners-Lee.
http://www.stanford.edu/class/cs227/Readings/hendler-berners-lee-semantic-web.pdf

Instructions for presentation and sign up

  • 10 mins, NO longer, some questions or comments should be anticipated
  • slides are optional, if you use them, please post them alongside your name in the table below
  • please sign up in 12 minute blocks starting at 1:20
  • enrolled students (top of the list below) will start
  • we will follow with others who wish to participate

Student 10 minute research interests presentation sign-up sheet

Presenter Time Topic Presentation Notes/Questions
Linyun Fu 1:20pm Semantic Air Quality Portal semantic-air-quality-portal.pptx [Download] Notes/Questions
Yu Chen Time Topic research-interest.ppt [Download] Notes/Questions
Qi Pan Time Topic personal-lib.ppt [Download] Notes/Questions
Heiko Muller Time Topic heiko-muller-slides.pdf [Download] Notes/Questions
Ping Wang Time Topic semantaqua.ppt [Download] Notes/Questions
Han Wang Time Topic mushroom.ppt [Download] Notes/Questions
Presenter Time Topic Presentation Notes/Questions

Week 3 - Feb 7, 2012

Notes - Feb-7 Titan Pad [Download]

Reading discussion and student presentations

Homework:
Write a short paragraph discussing how you would improve either Williams' or Subra's approach using semantic technologies. Email this to both Prof. McGuinness and Abigail before class next week. Please email no later than Feb 14, 12:30pm.

Please look at the water quality portal pages: http://tw.rpi.edu/web/project/SemantAQUA

1 - review the static demo at http://inference-web.org/wiki/Semantic_Water_Quality_Portal
2 - look at the live demo
3 - note the publication page - http://tw.rpi.edu/web/project/SemantAQUA/Publications
4 - read the International Semantic Web Conference 2011 paper
Wang, P., Zheng, J., Fu, L., Patton, E.W., 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).

and remembering the reading from the past classes - the social machines paper from the first week and the social papers from this past week,
write up a few pages on what it would take to take the current water quality portal and turn it into more of a community water portal.
1 - what kind of additional data would you be looking for?
2 - what kind of additional participation would you be looking for?
3 - what kind of additional technical challenges would you expect to encounter?
4 - what ideas do you have to overcome the technical challenges?

please be prepared to present a short discussion of your thoughts on these 4 questions in class.

Please turn in a write up of the answers to the 4 questions by 12:30 pm on Feb 14 to both abigail and deborah by email.

Week 4 February 14, 2012

Notes - Feb-14 Titan Pad [Download]

Reading for Next Week: Chinese Medicine [Download]

  • presentation by Sky Bristol from USGS - see titanpad for details.

extracted from the bottom of last week's titanpad:

for next week, review the four links
london air quality portal: http://www.londonair.org.uk/LondonAir/Default.aspx - yu present highlights to class
http://water.usgs.gov/nawqa/ - han will present to class
http://www.wlci.gov/ - amar will present to class
http://ecos.fws.gov/tat_services/ - linyun will present to class

for those not presenting - please send abigail and me a report for each of the 4 web sites above, what
1 - you found most interesting from the perspective of a potential semantic technology enabled project
2 - you found most confusing or most limiting in the current approach

also, abigail will upload a reading for the initial health information project. Please read that before class and submit a paragraph on highlights of the paper.

please submit your assignments by 12:30pm on Feb 21

Week 5 February 21, 2012

Titan Pad Link: http://twc.titanpad.com/266
Notes - Feb-21 Titan Pad [Download]

  • initial presentation from Anita de Waard on semantically integrating health information - topic area depression data.

Slides - Antidepressant Presentation [Download]

  • student highlights of readings.
  • breakout into project groups.

Homework-
Students should each post at most a 2 sentence description of an extension to the semantic water quality portal that brings in some notion of citizen science. This initial posting needs to be done by Friday Feb 24, 4pm. Everyone should read the other postings and then post at least one follow up question on another suggestion.

Forum Link - http://tw.rpi.edu/web/node/2193

Week 6 - Feb 28

Titan Pad Link: http://twc.titanpad.com/267
Notes - Feb-28 [Download]

Outside speaker or research presentations

Homework

1. Update the page Extensions to Water Quality Portal http://tw.rpi.edu/web/comment/reply/2193

 to add your Citizen Science Section (what you wrote in class is on the titanpad http://twc.titanpad.com/267? 

2. Add your name to one of two groups: (Linyun had received approval from Deborah to be in both groups).
Group 1: Aims to provide what a "Natural Resource Manager" needs to help them do their job. The natural resource manager needs
information from authoritative sources (datasets from USGS or related environmental monitoring sources) and through your project, encode
additional information (e.g. different names used in the different data sets, provenance information, etc.) that enable the natural resource
manager to make more informed decisions. Natural resource management professionals create, plan, monitor, direct and evaluate programs
that preserve the environment (source: http://bit.ly/yBs9Dq)
Ping propose an extension of SemantEco that's around the topic of animal feed operations at http://tw.rpi.edu/web/node/2193#comment-51, you can take a look if interested.
    *  This group might work more closely with USGS.
    * Possible Data Source (PDF; not ideal, but a possible starting point):  
    http://www.fws.gov/mountain-prairie/contaminants/papers/Hastings%20Pork%20CAFO%2000%20final%20report.pdf
        ** Linyun Fu
        ** Ping Wang
        ** Han Wang
        ** Weijing Chen
        ** Qi Pan
    [ADD YOUR NAME]

    • additional contact Sky Bristol

Group 2: Aims to choose one of the citizen science extensions discussed in class and here: http://tw.rpi.edu/web/comment/reply/2193.
WHER is an existing site for reporting wild life health event. You may take it as a site we can learn from.
http://www.whmn.org/wher/
http://www.wdin.org/documents/wher/WHER_FactSheet.pdf

        ** Linyun Fu
        ** Yue(Robin) Liu
        ** Bassem Makni
        ** Amar Viswanathan
        ** Yu Chen

 [ADD YOUR NAME]

    • additional contack Kirk Jalbert

Note: Both groups will work on the same platform, providing exentions in two different aspects.

3. By Sunday evening, March 4 you must have your name on one of the two lists, and have met with your classmates to vote on which extension your group will implement. You must post this decision by Monday noon, March 5.

4. Be prepared to present in class the answers to the following questions. Post the time of your presentation on the course website for the March 5, class.

 *1 - One question the resource manager or citizen scientist seeks to answer through your group's extension 
 *2 - One example of a successful answer to the question that would be hard to do without your group's extension 
 *3 - One or two data sources that provide the data the resource manager or citizen scientist will access through your extension in order to answer the question in number 1. 
 *4 - A starting point for initial tasks - what you will do first to implement the above. 
 *5 - Name two papers or projects done by others that the data manager or citizen scientst group should know about (that they have found by doing literature / web searches) 

Notes:
1. If you have not identified which group you will be in by posting to this page http://tw.rpi.edu/web/node/2193 by Saturday, with the group that you want to be in, then Deborah will assign you to either group 1 or group 2.

2. This demo site from Sky may provide you with some inspiration: http://my-beta.usgs.gov/websites/wlciIA/

Week 7 March 6

Titan Pad Link: http://twc.titanpad.com/268
Notes - Mar-6 Titan Pad [Download]

Small group presentations on initial project plans. See points 1-5 above

Presenter Time Topic Presentation Notes/Questions Citation
Presenter Time Topic natural resource manager Notes/Questions Citation
Presenter Time Topic citizen scientist [Download] Notes/Questions Citation

March 13 - Spring break =

Week 8 - March 20

Titan Pad Link: http://twc.titanpad.com/269
Notes - Mar-20 Titan Pad [Download]

Group presentations:

1. Each group will identify 2 related papers with the most relevance to your project. Then your group will present the papers to the class. Paper presentation should include
--highlights of the technical contributions of the paper
--impacts of this work for your project
2. Each group is responsible for a project status report presentation and writeup.
The status report should include:
--roles for members
--current focus areas
--current progress and challenges

Presenter Time Topic Presentation Notes/Questions Citation
Presenter Time Topic Presentation Notes/Questions Citation
Presenter Time Topic Presentation Notes/Questions Citation

Week 9 - March 27

Titan Pad Link: http://twc.titanpad.com/270
Notes - Mar-27 Titan Pad [Download]

Homework:
Begin your project web site.
Review
http://inference-web.org/wiki/Semantic_Water_Quality_Portal as background.
Also review the community science document that Deborah will send out.
1. You will need to turn in a paragraph about how your project might extend the notion of community science as presented in that proposal.

2. You will design your own version of a project demonstration web page.
It needs to include at least

  • Overview
  • Two example questions your project will allow people to answer or two example functions your project will support along with your anticipated approach to answering the questions
  • Provenance approach
  • The expected value of Semantic Technology in this project
  • The expected value of provenance in this project
  • Summary of enhancements to the semantic water quality portal page.

Project web site review and focus on semantic technology contribution.
Professor Luciano will lead the class today.

csv2rdf4lod presentation slides [Download]

Week 10 - April 3

Titan Pad Link: http://twc.titanpad.com/271
Notes - Apr-3 Titan Pad [Download]

Group presentations and class discussion.
Group presents:
1 - status report including progress, plans, and challenges
2 - 2 pieces of related work highlighting the relevance of the work to this work and distinguishing our projects from the related work. Please submit the titles and URLs of related work no later than 4 days prior to the presentation.
3 - outline of a writeup of this work that could go into a meeting such as IPAW or a workshop at ISWC. See Semantic Water portal papers for guidance.

Presenter Time Topic Presentation Notes/Questions Citation
Presenter Time Topic Presentation Notes/Questions Citation
Presenter Time Topic Presentation Notes/Questions Citation

We will make a plan to make progress on the final project.
The final submission will include
1 - a static web page hosted on a TWC machine to demonstrate the findings of the effort
2 - a project write up that is oriented to be submittable to a workshop with one revision round.

There will be one presentation of the almost final version and then another presentation of the final version.

Week 11 - April 10, 2012

Titan Pad Link: http://twc.titanpad.com/272
Notes - Apr-10 Titan Pad [Download]

  • Each team presents an overview of the project web page with

a - current content
b - planned content

  • each team member should speak to a portion of the web site.
  • Each team presents an outline for their final planned write up with names associated with leadership for each of the sections

  • each team presentation gets a total of 45 minutes for presentation. We anticipate 15 minutes of discussion directly related to the presentation.

Each web page must have at least the following sections:

  • Overview
  • Technical Foundations
  • Use Case
  • Demonstration - with static web page shots showing the results of asking a question and the results of your system. This week we can just have a textual description of what will be here
  • Discussion
    • The value of semantics in your demonstration
    • The value of provenance in your demonstration
  • Related Work
  • Data sources used
  • Future Work

Presenter Time Topic Presentation Notes/Questions Citation
Presenter Time Topic Presentation Notes/Questions Citation
Presenter Time Topic Presentation Notes/Questions Citation

Week 12 - April 17, 2012 no class - grand marshall week

Titan Pad Link: http://twc.titanpad.com/273
Notes - Apr-17 Titan Pad [Download]

Continue project work - please post updates to projects on your class project pages
Note that there will be a call with Josh and Sky from USGS at 1pm eastern for at least Deborah, Sky, Josh, Ping, Han. Others are welcome if they can make it.

Week 13 - April 24, 2012

Titan Pad Link: http://twc.titanpad.com/274
Notes - Apr-24 Titan Pad

Group presentations: Each member of the group will present one claim for either the advantage of semantics or provenance AND show an example in your application where you are showing value.
Note that these write ups need to be included in the project web page.
Please send your presentations to abigail and deborah.

the presentation should include
1 - the claim . e.g., encoding information in OWL allows us to do better semantic integration. Specifically encoding the meaning of polluted thing with the OWL definition that shows a thing that has a contaminant reading that is out of range allows us to automatically classify polluted things.
2 - the background semantic encoding or provenance encoding
3 - what would have been hard to do without using semantics or provenance encodings
4 - an example of the provenance usage or the owl definition in the setting of your example.
Show the OWL definition of a term if you are making claims about semantics.
Show the provenance encoding if you are making claims about provenance.
Show the result of the reasoner result for one query that proves your point
Show how you are exposing provenance in your interface if you are making claims about provenance

Since the groups did not go over the presentation web site last week, we will also need to do that this week.

Presenter Time Topic Presentation Notes/Questions Citation
Presenter Time Topic Presentation Notes/Questions Citation
Presenter Time Topic Presentation Notes/Questions Citation

Week 14 - May 1, 2012 Now moved to April 30 10am-12:50pm

Titan Pad Link: http://twc.titanpad.com/275
Notes - May-1 Titan Pad

Final project draft presentation. There will be an iteration on this presentation aimed at what it takes to make this publishable.

Draft presentation:

Each group has an hour to present total.
The presentation should include speaking slots for everyone on the team.
The project presentation needs to include:
1. Project overview
2. Use case
3. Architecture and technical approach making sure to include
a. Overview of the ontology
b. Provenance approach
4. Demonstration of the system in action. Make sure to include
a. Example using the ontology to answer a question in your use case
b. Example where you are using provenance to create some kind of provenance-aware service
c. a link to your outward facing project web site that also includes screen shots of your system in action as well as a link to the live demonstratoin
5. Related work
6. Discussion including
a. Learnings from the project
b. Claims about the need for and value of semantic technology in your project
c. Claims about the need for and value of provenance in your project
7. Future work
8. Roles and responsibilities for each of the team members

In the draft presentation if something is not completed for this week, let us know what will be done for next week.
The final project will include a final presentation and a walk through of your team outward facing web site. That web site needs to be on a Tetherless world machine (not just a student laptop) and is expected to stay up after the class ends.
The final web site needs to include both a static demonstration including screen grabs of your system in action as well as a link to the live system. We understand that the live system may not work after the class finishes (although we hope it continues to function) but the static demonstration should be available into the future.

Presenter Time Topic Presentation Notes/Questions Citation
Presenter Time Topic Presentation Notes/Questions Citation
Presenter Time Topic Presentation Notes/Questions Citation

Week 15 - May 8, 2012

Titan Pad Link: http://twc.titanpad.com/276
Notes - May-8 Titan Pad

Final assignment:

Final Assignment Advanced Semantic Technologies 2012

This assignment has two sections:
Section 1 is to completed as a team and is due on the last day of class – May 8 not later than 1pm.
Section 2 is completed individually and emailed to both Abigail and Deborah individually. This is due on May 10 at 10 am.

Section 1 – to be completed as a team.
1 – Finalize your outward facing project web site. The web site must be on a Tetherless world machine.
Your web site must have at least the following sections:
• Overview
• Technical Foundations . This section must include a description of the architecture and technical approach. It should include a subsection describing the ontology overview and the provenance approach.
• Use Case
• Demonstration - with static web page shots showing the results of asking a question and the results of your system.
• Discussion
o Learnings from your project
o Make sure to include claims you are making about your project showing
 The need for and value of semantics in your demonstration.
 The need for and value of provenance in your demonstration
o Make sure to support your claims with real examples showing what was difficult without your ontology definitions and the reasoner and/or without the provenance encoding and the provenance-aware services.
• Related Work - making sure to describe how your work leverages the related work and/or is different from it.
• Data sources used
• Future Work
• Bibliography (this can and most likely should include web sites)
Please also include an appendix that includes a description of the team members and what each team member contributed to the project.
You need to email a copy of the web page and your presentation to Abigail and Deborah by 12:59 pm on May 8.

Section 2.
This portion of the assignment must be done individually. This is to be submitted by email to Abigail and Deborah and is due no later than May 10 at 10 am eastern time.
A: Evaluation of you and your team members. In this section you are asked to evaluate your individual performance on the team and also of your team members. You only need to fill this in for yourself and team members. Please do make sure to fill it in on yourself.
For each person on your team starting with yourself and for each category below, please give a numerical rating from 1-10 with 10 being the best and then include one to four sentences on the reasoning for the rating.
Also, if someone other than a team member was particularly helpful to your project, please include comments about their contributions. You will be graded on your evaluation of yourself as well as your evaluation of you team members.
You do not need to do any evaluation of people NOT on your team but you must evaluate each member of your team separately including yourself.
Make sure to evaluate each team member in all categories.
The categories are:
1. Responsibilities: respond with a numerical value 1-10 with 10 being the highest AND include a short text description of responsibilities.
2. Challenges with working with this person: Respond with a number - 10 means no challenges, 1 means very many challenges. Describe challenges in text. You do not need to include challenges for yourself.
3. Accomplishments in the project: Include a numerical value between 1-10 with 10 being the highest. Include a textual description. (Note - it could be that someone accomplished something that was not part of their responsibilities which is why this is separate from point 1 above).
4. Work Effectiveness: numerical evaluation. 10 means very effective; 1 means very ineffective. Include a textual description.
5. Team Meeting Attendance: numerical evaluation. 10 means attended all meetings; 1 means missed many meetings. Include a textual description.
6. Communication skills: numerical evaluation. 10 means excellent communication. Include a textual description.
7. Teamwork: numerical evaluation. 10 means excellent teamwork. 1 means poor teamwork. Include a textual description.
8. Improvement Options: A description of each team member (including yourself ) could have improved individual performance as well as team performance.
9. Optional – comments

(renumbered after noticing that accomplishment did not have a number next to it)

B. Provide at least two clear statements of something that you learned in the class that would allow you to design or implement or write about a semantic technology project in the future. Give one example for each learning.

C. Leverage something that you learned in the class and/or did for the project to demonstrate the value of semantic technologies in your application. This could be considered input to the claims section in a paper you would submit for publication. Each claim should be able to fit into one sentence. You can support it with an example but make sure the claim can be articulated succinctly. This work should be done individually. When you defend the claim make a connection make a statement about something that you did on the project that enabled the team to make this claim. So for example you and other members of your team may make similar claims but each individual would have a different description of how their work supports this claim.

D. Leverage something that you learned in the class and/or did for the project to demonstrate the value of provenance in your application. This could be considered input to the claims section in a paper you would submit for publication. Each claim should be able to fit into one sentence. You should support it with an example but make sure the claim can be articulated succinctly. This work should be done individually. When you defend the claim make a connection make a statement about something that you did on the project that enabled the team to make this claim.

Note – if you have already been discussing your claims with team members as the result of previous work on the project, please include a statement about who you did what with.

Due date: May 10, 10 am

Presenter Time Topic Presentation Notes/Questions Citation
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Course evaluation worksheet

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. of an academic grade penalty or . If you have any question concerning this policy before submitting an assignment, please ask for clarification.

Attendance Policy

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

Grading Policy

Grades will be determined based on homework assignments along with class participation. Late assignments will drop 10% of the possible value of the assignment for each day late.