[kepler-dev] Semantics

Matthew Jones jones at nceas.ucsb.edu
Thu Jun 12 10:16:57 PDT 2008


In addition to Shawn's excellent summary, I wanted to add that there is 
one other overview paper from SSDBM of the semantic features that did 
make it into Kepler:

Berkley C, Bowers S, Jones MB, Ludaescher B, Schildhauer M, Tao J. 2005. 
Incorporating Semantics in Scientific Workflow Authoring. 17th 
International Conference on Scientific and Statistical Database 
Management.  IEEE Computer Society.

http://users.sdsc.edu/~ludaesch/Paper/sms-ssdbm05.pdf

Matt

Shawn Bowers wrote:
> Hi Maliha:
> 
> Here are some answers to your questions below.
> 
>> where can i read more information about the Semantic Mediation System(SMS)
>> implemented in Kepler.
> 
> The "semantic mediation system" is an umbrella term used primarily in
> the SEEK project to denote ontology-based approaches for describing
> and integrating data, and somewhat less prominantly, actors and
> workflows.
> 
> Within Kepler, there were a number of prototypes developed to test out
> certain semantic functionality, and some of these are part of the
> current system.  Some of these (but not all) are described in the
> Kepler 1.0 User Manual
> (http://www.kepler-project.org/Wiki.jsp?page=Documentation).  We've
> written a few papers on the ideas as well (see below).
> 
>> WHich brings me to my next qeustion. Is it
>> implemented in kepler or is it a 'work in progress' because I downloaded
>> kepler and tried the "Semantic type annotation" thingy but as there are no
>> underlying ontologies ( im saying there are none becuase i dont see any...
>> just a few custom made deifinitions are visible).
> 
> The ability to semantically annotate actors is implemented within
> Kepler as well as to a lesser degree, the ability to search for actors
> via these annotations. There are two types of annotations that are
> possible. One is an annotation of the actor as a whole (basically
> tagging the actor with one or more ontology classes), and another is
> the ability to annotate actor I/O ports.
> 
> The former is used to build the actor library in Kepler 1.0.  In
> particular, the library (component part of the left panel) is built
> from four different, small ontologies (this is the classified view).
> These are each OWL-DL ontologies that are stored within Kepler. When
> searching for actors, the ontology is also being used to "expand"
> keyword searches. There are other "prototype" ontologies w/in Kepler
> that were created to demonstrate other types of annotations, which can
> also be used to annotate the ports of some actors. These are displayed
> when using the port-annotation part of the annotation dialog.  Actors
> can be annotated via the annotation widgets and then saved back to the
> library (where the annotations become part of the actor metadata and
> are then searchable).
> 
> When building Kepler, it is possible to add (and remove) OWL-DL
> ontologies to Kepler via a config file. However, Kepler 1.0 does not
> provide an easy mechanism to add these ontologies via the UI.
> 
> We have used this ability when configuring different distributions of
> Kepler (e.g., Kepler/CIPRES and Kepler/pPOD which is available from
> http://daks.ucdavis.edu/kepler-ppod). In particular, these
> distributions have a custom set of actors that are annotated to a
> domain-specific actor ontology.
> 
> As far as I am aware, no actors in the current 1.0 distribution have
> port-level annotations. (This may change in newer releases of Kepler,
> but there are no concrete plans for this now.) If actors are annotated
> at this level, there are some simple tools available that leverage
> these annotations. One is "in-place" searching of actors. In
> particular, right-clicking on an actor, you can search for
> "compatible" actors (which searches for input or output types
> depending on the type of search performed). Also, there is a
> type-checking widget that can be started by right-clicking on the
> design canvas. This tool checks both semantic and structural (data)
> types of actor connections in a workflow, and displays different
> levels of "matching" and highlights type errors on the workflow
> itself.
> 
> Ptolemy (which Kepler is built from) also provides a unit system for
> annotating ports with units, which provides similar types of behavior
> but specialized for unit checking, etc.
> 
>> Are there any good papers/writeups etc out there to see how kepler does
>> resource discovery etc. I found a good presentation "Semantic Mediation in
>> SEEK/Kepler: Exploiting Semantic Annotation for Discovery, Analysis, and
>> Integration of Scientific Data and Workflows" By Shawn Bowers and Bertram
>> Ludäscher but Im not sure what they talk about in their presentation is
>> actually implemented or they are still working on it.
> 
> All of the tools discussed in the presentation are implemented and are
> in Kepler now.
> 
> There are some additional tools and approaches that haven't made their
> way into Kepler, but have been implemented as prototypes.
> 
> Here is a list of some papers related to this work:
> 
> - S Bowers, B Ludäscher: A Calculus for Propagating Semantic
> Annotations Through Scientific Workflow Queries. In QLQP, EDBT
> Workshops 2006: 712-723. URL:
> http://daks.ucdavis.edu/~sbowers/Bowers_et_al_QLQP06.pdf
> 
> This paper discussed an algorithms and approaches for automatically
> generating semantic annotations of ports and intermediate and derived
> data based on partial annotations (e.g., annotations on input data).
> The algorithms have been implemented, but are not part of Kepler
> today.
> 
> - S Bowers and B Ludaescher. Actor-Oriented Design of Scientific
> Workflows. In International Conference on Conceptual Modeling
> (ER'2005), LNCS, volume 3716, 2005. URL:
> http://daks.ucdavis.edu/~sbowers/bowers_SWF_er05.pdf
> 
> This paper generally talks about ideas related to semantic annotation
> of workflows.
> 
> - S Bowers and B Ludaescher. An Ontology-Driven Framework for Data
> Transformation in Scientific Workflows. In International Workshop on
> Data Integration in the Life Sciences (DILS'04), LNCS, volume 2994,
> 2004.URL: http://daks.ucdavis.edu/~sbowers/bowers_ONTOTRANS_dils04.pdf
> 
> This paper talks about some early ideas and an algorithm for
> performing automatic transformation of data (i.e., automatically
> generating a type of "shim" or "adapter) between annotated actors
> passing XML data (e.g., wsdl web services).
> 
> Please let me know if you have more questions.
> 
> Thanks,
> Shwan
> 
>>
>> Thanks
>>
>> Maliha Aziz
>>
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-- 
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Matthew B. Jones
Director of Informatics Research and Development
National Center for Ecological Analysis and Synthesis (NCEAS)
UC Santa Barbara
jones at nceas.ucsb.edu                       Ph: 1-907-523-1960
http://www.nceas.ucsb.edu/ecoinfo
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