Semantic Technology Curriculum

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Curriculum

Workshop: Semantics 101 for Pharma

Workshop at EU CSS 2016, June 21

The workshop is offered at EU CSS 2016: "Semantics 101 for Pharma", see Semantics_101_for_Pharma_workshop_at_EU_CSS_2016,_June_21

Past: workshop at CSS 2016, March 13

A new workshop was offered at CSS 2016: "Semantics 101 for Pharma"

PhUSE CSS Conference in Silver Spring, MD
Sunday, March 13 7:30-9pm

Instructors:

  • Marc Andersen (StatGroup ApS)
  • Tim Williams:(UCB)

The fundamentals of Linked Data and the Resource Description Framework (RDF) will be presented using using practical examples based on CDISC standards and sample analysis results from clinical trials. Learn how to create RDF using R or SAS, explore local and remote Linked Data sources using SPARQL, and how to present Linked Data as HTML tables and interactive visualizations.

Through this course you will obtain a working knowledge using tools common to our industry that you may then apply to your own linked data projects. The workshop provides a foundation for participating in one of the many PhUSE Semantic Technology work groups.

No previous experience is assumed.

Workshop Materials

Attendees may optionally wish to install a SPARQL server on their local laptop to either follow along or to try out the concepts at a later time. Download the .ZIP file to obtain installation files for Apache Jena Fuseki and example files used during the workshop. NOTE: To obtain the file: 1. Click on the link below. 2. Click on .ZIP file on the resulting page to download to your local machine. You may need to choose "Save file as...".

Workshop slides from the Previous sessions are below. Note three parts.

File:Semantics101-PhUSE-CSS16-Pt1.pdf

File:Semantics101-PhUSE-CSS16-Pt2.pdf

File:Semantics101-PhUSE-CSS16-Pt3.pdf

PhUSE Annual Conference: October 2016 [Instructors: Marc Andersen, Tim Williams]
Slides from the 10-Oct-2016 are below (note 7 parts)

File:PhUSE Annual-Conference-2016 SemanticTech101 Workshop-part1.pdf


File:PhUSE Annual-Conference-2016 SemanticTech101 Workshop-part2.pdf


File:PhUSE Annual-Conference-2016 SemanticTech101 Workshop-part3.pdf


File:PhUSE Annual-Conference-2016 SemanticTech101 Workshop-part4.pdf


File:PhUSE Annual-Conference-2016 SemanticTech101 Workshop-part5.pdf


File:PhUSE Annual-Conference-2016 SemanticTech101 Workshop-part6.pdf


File:PhUSE Annual-Conference-2016 SemanticTech101 Workshop-part7.pdf


NEW! 10Oct2016 Take home exercises from the Semantics Workshop at PhUSE 2016

File:Semantics-Workshop-TakeHomeExercises.pdf

Also download this zip file to have the content needed for the exercises:

File:PhUSECSS-Semantics101-AttendeeFiles.zip


Future Offerings

To be decided.

Reading Material

- Semantic Web for the Working Ontologist. Second Edition. Morgan Kaufmann, 2011 by Dean Allemang and Jim Hendler
This is an excellent book, well-written, specifically on the modeling aspects of RDF, RDFS, OWL, and SKOS. If you are going to read one book on the subject, this is the one.

- Agency and the Semantic Web. Oxford University Press, 2007. by Christopher Walton
This book gives a broad outlook on knowledge systems and the semantic web, including more academic background on the computational aspects of the subject.

- Model Driven Engineering and Ontology Management. Second Edition. Springer, 2009. by Dragan Gasevic, Dragan Djuric, and Vladan Devedzic.
This book provides valuable insight on knowledge engineering in general and the relationship between the different modeling spaces.

Websites

The NCBO is an excellent resource for biomedical ontologies and related technologies. It provides a repository and federated search across a large number of biomedical ontologies.
Excellent resource for people just starting out.
A good example of why and how you should develop an ontology for a domain. Includes a case study and example development files for Protege
  • The Ontology for Clinical Research (OCRe)
The Ontology of Clinical Research (OCRe) is a formal ontology for describing human studies that provides methods for binding to external information standards (e.g. BRIDG) and clinical terminologies (e.g. SNOMED CT). Has links with the Human Studies Database. Is in active development
  • Semantic Web Technologies Course (OpenHPI)
This was a course I did earlier this year (available online). The course content is still available online for self-study at Semantic Web Technologies (Archive), which includes the videos, readings and tests.
  • A real great in depth course can be found on www.euclid-project.eu. An EU sponsored project aimed at spreading knowledge of linked data. Free ebooks, webinars, exercises, etc.


Ontology Editors

  • Protégé is a well-known free open source ontology editior developed at the Stanford Center for Biomedical Informatics Research.

http://protege.stanford.edu/

  • TopBraid is a commercial semantic modeling workbench developed by the company TopQuadrant. If you are familiar with Eclipse based environments, then you can get a head start using TopBraid.

http://topquadrant.com/
http://topquadrant.com/products/TB_install.php

  • Ontotext is known for its RDF database OWLIM.

http://www.ontotext.com/

  • Wikipedia has a good write up of Ontology Editors.

How to pick an Ontology Editor

There was a good suggestion that we shouldn't try and enforce an editor, instead allow people to choose their own. However, for conservation of energy I think we should define a core set of capabilities that whatever tool you use, you can be assured that your experience is the best it can be. These are proposals, and this is a wiki; if you don't agree then update the table. Additionally, if you've had a positive experience with an editor, add a column and mark it off.

Criterion Top Braid Composer Protege
Operating System Support
MS Windows
Linux
Mac OS X

Yes
Yes
Yes

Yes
Yes
Yes
Source Control
SVN
Git

Yes (built-in)
Yes (Install eGit)

No
No
RDF(s) Support Yes Patchy (Protege 4.X - OWL based editor)
TBC (Protege 3.X)
OWL Support Yes (1.0 and 2.0) Yes (2.0) (Protege 4.X)
Yes (1.0) (Protege 3.X)
SPARQL Support Yes (1.0 and 1.1) Yes (Protege 3.X)
Yes (Protege 4.X - 1.0 and 1.1 - uses OpenRDF)
File support input/output
RDF-XML
TTL
N3

Yes
Yes
Yes

Yes
Yes
Yes

Other Resources


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