Week 4 - February 15, 2011: Journal Club (1)

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This week is like a journal club. This is where we all read a paper and one person presents the paper to the group and we discuss it in detail. Those who are not presenting read the paper so that there can be an intelligent and informed discussion about the paper. Those who are not presenting, bring their questions and their interpretation to the discussion.

titanpad for today

This is Assignment 2, it is due Week 4:

This assignment will be updated to reflect today's class decision. The Translational Medicine Ontology Paper is tmo_r1.pdf [Download] (tmo_r1.01)

Note: This assignment is due in 2 parts: Part I: Due Thursday February 10!:

  • Choose a topic of interest, identify a question to pursue, search for relevant papers, and propose up to 3 to be considered for presentation and discussion in class. Please order your choices so we know your order of preference for presentation. THE PROPOSED PAPER TITLES (and links) must be posted to this web page WITHIN 2 DAYS of week 3 CLASS (so by THURSDAY February 10 at 7 PM eastern time). Professors will choose one paper for each of you to present by Friday morning February 11.

Part II: Due Tuesday (in 1 week):

  • For Scott and Ping, read and present the TMO paper.
  • For Peter, give response to Tim's questions about what we can do based on the PCAST report (Chapter X).
  • For other students, read Papers that are assigned in Part One.
    • If the papers assigned contains one that you proposed, then you will be presenting in the next class.
    • If your paper was not chosen, you will be asking questions and constructively critiquing the presentation. Prepare two questions to ask about the paper.

Reading Assignment for Week 4 Journal Club (1):

Written Assignment for next class:

  • As above: If you are not presenting, prepare questions and submit them to the professors prior to class.

Presentation Assignment for next class:

  • As above: If you are presenting a paper, prepare a 20-minute presentation. Include:
  • An overview of the major sections of the paper starting with the research question.

Student 10 minute presentation sign-up sheet

Presenter Time Outline by Author - ex. Patton's outline Presentation - include link to presentation Outline of Paper Notes / Questions
Eric 1. The Ontology Design section (pp. 9-10) mentions the manual mapping of 201 target classes from 40 ontologies to classes in TMO. Did the group consider any ontology alignment techniques to automate this process and support future scalability and adaptability?
2. The Translational Medicine Knowledge Base section (pp. 13-14) says that the TMO, dataset, and mapping files (i.e., the TMKB) are loaded available via a SPARQL endpoint powered by OpenLink Virtuoso 6. Are there any other thoughts on how the TMO will enable a distributed TMKB, with federated querying, or will the research focus remain on a single knowledge base?
Jin Question 1: "Semantic Web technologies enable the integration of heterogeneous data using explicit semantics, the expression of rich and well-defined models for data aggregation, and the application of logic to gain new knowledge from the raw data [9]. Also, semantic technologies may be used to encode metadata such as provenance, i.e. where the data came from and how it was generated [10] [11]. In the paper, it mentions these main benefits of using semantic web technologies." So my question is does TMO brings all these benefits to the domain application, if so, can you give some example of how can we use TMO to enable health data aggregation and health services/application to gain new knowledge from the raw data? Question 2: Throughout the paper, I see a lot EHRs been mentioned, pages 2, 3, 20, 21, etc. and I see a term call "Linking Open Drug Data" on page 5. I have skim through LODD paper, and believe they published all sorts of data, such as data about drugs, traditional Chinese medicine, clinical trials, diseases, and pharmaceutical companies. So my second question is how does TMO provides a foundation for types declared in both Linking Open Drug Data and EHRs?
Peter 5:30 Development of Federated EHR Through Metadata Tagged Data Elements [Download]
Scott and Ping 6:00 Presentation of Translational Medicine Ontology and Knowledge Base [Download]

Paper Presentation For Next Week:

Presenter Paper
Jin Semantic Web Portal: A Platform for Better Browsing and Visualizing Semantic Data
Eric Process Specification Language (PSL): Theories and Applications

Other papers of interest:

Presenter Paper
Eric Bringing Semantics to Web Services With OWL-S
Eric SAWSDL: Semantic Annotations for WSDL and XML Schema
Jin AI for the Web — ontology based community Web portals
Jin SEAL: a framework for developing SEmantic portALS
Jin Semantic web portals: state-of-the-art survey
Jin An evaluation of Semantic Web portals

Some journals relevant to this class: