| Removed lines 10-20 |
| - * Concrete Use Cases |
| - ** Matt on Ecological Niche Model and examples of integration/mediation needs |
| - ** Mark on Biodiversity examples |
| - * Kepler Issues |
| - ** Unique Identifiers (use of LSIDs ...) |
| - ** New Ontology-based browsing and searching |
| - ** Semantic types for (relational) datasets and actor ports |
| - ** Pipeline integration tasks |
| - *** Actor-actor integration |
| - *** Data-actor integration |
| - *** Utilizing Jenny Wang's schema matching tool |
| Removed line 27 |
| - ! Participants |
| Removed lines 29-30 |
| - * ... |
| - |
| Line 33 was replaced by lines 19-118 |
| - * ... |
| + * 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 |
| + |
| + * Next steps (...) |
