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SMS Breakout Nov 2004

Difference between version 42 and version 2:

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- !! Topics for SMS Breakout, AHM Nov 3rd, 2004
+ !! Topics for SMS Breakout at SEEK AHM
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- Wednesday, November 3, 1:30 -- 5:00 (Walnut, 6th)
+ ! ''Wednesday, November 3, 1:30 -- 5:00 (Walnut, 6th)''
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- The Plan:
+ ! ''Moderator: Bertram Ludaescher''
Removed lines 7-25
- * Overview and Updates from those attending
- ** Presentations from SMS group members
- * Concrete Use Cases
- **
- * Discuss concrete use cases (Matt, Mark)
- * Kepler Status: Ontology-based browsing and searching (Shawn, Chad)
- ** Actors
- ** Data
- * Pipeline integration tasks
- ** Actor-actor integration
- ** Data-actor integration
- ** Utilizing Jenny Wang's schema matching tool
- * From-scratch design of a semantics-driven UI
- ** what would we build in a world free of contraints
-
-
- * Topic 1
- ** Subtopic 1a
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-
+ * Updates: Overview and Progress
+ ** Semantic Typing
+ * General Discussion
+ ** Current issues
+ ** New ideas
+ ** Priorities
+ ** Goals (Short-term, 6-month, 1 year)
+
+
+ ! Notes
+
+ * Bertram (overview)
+ ** requirements:
+ *** semantic (in addition to structural) annotation of:
+ **** services (actor) and
+ **** datasets
+ *** for ... discovery, WF design, ...
+ *** prerequisites: what does this annotation langauge have?
+ ** structural types
+ *** array of float; list of record of (int, float, string); etc.
+ *** e.g., relational schema type, ptolemy type
+ *** applies both to data and "functions" (actors)
+ *** essentially, useful for plumbing -- the level of the programmer, or data provider
+ ** semantic type
+ *** formal expression referencing concepts in an ontology
+ *** to provide a high-level, conceptual of data and services
+ ** data(set)
+ *** informal descriptions: eml style metadata, keywords, controlled vocabularly
+ *** formal description
+ **** dataset ~ concept
+ **** attribute (column) ~ concept
+ **** fine-grained:
+ ***** query(X1, X2, ..., Xn) ~ concept expression(X1, ..., Xn)
+ ***** Xi are "tags" or variables point to substructure
+ ** actors (services)
+ *** overall function
+ *** input/output signature (-> reuse framework from dataset annotation)
+ ** Questions
+ *** How do you require that certain things must be registered, e.g., that a lat lon point has an x and y coord
+ *** How do you handle null values in a table ... e.g., a row doesn't have an x value
+ *** What is the difference between an annotation langauge and a description logic
+ * Shawn (details of semantic registration language)
+ ** simplified Antweb example
+ *** abundance datasets
+ *** d1,d2 have similar structure (geo-referenced data)
+ *** d3 is differently structured (co-occurence based)
+ *** d4 lists host/parasite relationships (inquilinism)
+ ** Measurement, parasitism ontology (from SWDB'04 paper)
+ *** [Presentation|http://cvs.ecoinformatics.org/cvs/cvsweb.cgi/~checkout~/seek/projects/kr-sms/presentations/bowers_beam_sept_04.ppt]
+ *** observation, TaxonID, Parasite, Host
+ *** Example: annotating d1 ...
+ ----
+ d1(Ge,Sp,Co,Lt,Ln) ~ \\
+ Observation(O), value(O,Co), context(O,S), location(S,P), LatLonPoint(P),
+ latDeg(P,Lt), lonDeg(P,Ln), item(O,A), Abundance(A), property(A,N), SciName(N),
+ genus(N,Ge), species(N,Se).
+ ----
+ *** Who is creating these mappings?
+ *** Shawn: use of a tool
+
+ * Discussion about interface ...
+ ** Can we use growl browser to do the semantic annotation mappings graphically
+ *** similar in style to xml mapping tools
+ *** what is missing:
+ **** multiple selection of nodes
+ **** difficult to get relevant stuff when you expand nodes ... many nodes you don't care about up the inheritence tree
+ **** just want subclass and derived properties
+ **** graph query language ... to filter ... decouple what you show and select
+ ***** e.g., i am only interested in isa links, so you might want to have a power user language, to subset what you are currently showing
+ ***** would generalize; think it would be a useful extension to these visual editors, ... "+ isa; - any"
+ ***** expression language for power use to turn on and off certain things; incremental search that start from results
+ **** graphic frame logic
+ ***** a fundamental problem with visualization formulas as opposed to logical _consequent_ of the formulas
+
+ * Jessie: ProFormaVis -- based on Angiosperm ontology
+ ** structures, attributes-values
+ ** reads in ontology; divides the gui into structure hierarchy, selected structure description details
+ ** the ontology doesn't try to define what a plant is, but gives the set of things you might want to say about plants
+ ** trying to describe a specimen, e.g., leaf, with attribute veination pattern, and anastomosing and arcuate...
+ *** the veination patther is anastomosing and arcuate
+ ** the end to end application: the scientist refines the set of things and properties (attribute values) that are useful for a collection; a form is generated / configured based on those filters; for others to classify items to
+ ** Bob Morris, et al., allows general description of things -- Structure of Descriptive Data -- TADWIG
+ ** Commercial program called Lucid 3
+
+ * Nico on Taxon / SMS
+ ** partial overlaps
+ ** give me the ants of south america ... give all concepts of ants (may be thousands) ...
+ ** Deana: in biodiversity use case; want to group by function, which is similar to form
+ *** Several international ones that are comprehensive in traits and functions
+ *** Weren't sure the relevance to north america plants
+ *** in KNB now, can do exactly the same search (via ITIS) ... through markup via EML
+ ** rich: given two identifiers how are they similar
+
+ * follow-up list
+ ** growl extension selective viewing / filtered views based on some keywords / or in general queries / or just let user select nodes in the neighborhoods in the tree
+ ** schema mapping language ... what is taxon doing versus what is sms doing (for annotations) and how can each be informed by each other
+ *** for taxon, mapping into exchange schema ... trying to determine how concepts are represented within a database
+ *** for sms, mapping into ontology
+ ** more examples for annotation
+ *** deana possible small kr/sms working group to identify useful items to annotation (workflow and data) and map to Rich's ontologies
+ ** interface for annotation ... filtering Rich's ontology ... to form-style interface for annotation (Laura, Jessie, and Deana)
+ ** graph-based ontology queries for filtering and selecting ontology (Serguei, GrOWL)
+ ** SMS/Taxon link-up points
+ *** compare mapping languages
+ *** data discovery queries w/ taxon
+ *** similarity between ids
+ *** operations that sms needs ... taxon ops that sms needs
+ *** how does sms know when to call a taxon service? e.g., via which concepts in the rich's ontology?
+ ** sparrow to owl; owl to sparrow
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+ * Next steps (...)

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