Notes form today's call:

Tasks for Ben
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A. Metacat search system and search serialization, address scalability
	SEARCH:
	-create semantic query schema (semQuery.xsd) based on pathQuery and ecogrid query
	-create schema for semantic query results (semQueryResults.xsd)
		-include original query issued
		-include annotation matches (aEML)
		-include data package matches (EML)	
	-create parser for semQuery - compatible with SMS API query mechanism currently used in Morpho
	-include Metacat action for semQuery
	
	PERFORMANCE:
	-Metacat stores Annotation for EML (aEML?)
	-aEML documents are loaded when Metacat initialized and when subsequent CRUD actions occur. This is similar to how the spatial search feature operates.
	-By pre-processing the aEML documents into a persistent DB rather than the current transitory Derby DB, we won't have to perform the processing each time metacat is restarted.
	-queries that use large term expansion sets may need to be optimized for DB query performance.



F. Ability to store ontologies in Metacat or other repository
-Add ontology registration/search features
	-Upload Ontology file
		-metadata file to describe the ontology (EML pointing to OWL resource)?
	-Search concepts/labels/descriptions of ontologies - basic keyword/xpath searching (no reasoning)
	-Search across ontologies for equivalence/mapping (?)
	-Retrieve ontologies 
		-ontology retrieval by logical uri (action=getOntology, URI=?)
		-provide listing of all versions of a given ontology (action=getOntologyVersions, URI=?)
		-provide listing of all ontologies w/ logical-physical map (action=getOntologies)
	-view ontologies
		-semtools skin to include ontology rendering (XSLT for showing the contents of the owl)
		-visualization?
	-edit ontologies (webProtege, collaborative protege)?

-survey for others technologies, see:
	http://mmisw.org/orr/ - odd use of URIs for classnames (no # delimiter)
	http://bioportal.bioontology.org/
	http://www.bioontology.org/wiki/index.php/NCBO_REST_services
	http://protegewiki.stanford.edu/wiki/WebProtege - still no support for Protege 4 or OWL 2 - but on their road map

    

C. Web interface for searching (semtools skin)
	-search form mimics Morpho plugin search form:
		-Entity/Characteristic/Protocol/Standard -or- Measurement =/!= <ontologyClass>
		-Grouping (any/all)
		-Nested groups
		-Same Observation option
	-search form allows ontology browsing with simple searching within ontologies to find the correct concept
		-Morpho has this with the plugin using a tree/table hybrid to visualize the ontology.
		-Google's GWT has a good tree widget that I was able to make display our ontology - probably pursue that approach with GWT support added to Metacat as a bonus.
	-create stylesheets for displaying:
		-aEML - should pull in information from the data package that it annotates
		-semQueryResults - shows information from the annotation match as well as the EML that is annotated.
	

Milestone 1: Release metacat and morpho

B. Materialized view of data and ontology and annotation for data queries

Milestone 2: Release with new data query feature


Other tasks to be considered for later
--------------------------------------

K. Address how to version and maintain ontologies and their terms

D. Sensible summarization

E. Refining/improving annotation UI in Morpho

H. Develop approach to automate some aspects of annotation
  -- e.g., lots of data sets that have same schema, need minor tweaks to apply to similar data sets
  -- Link measurement types to existing data sets (e.g., rough annotation based on attribute units, names, descriptions?)

I. Semantic metadata (choose keywords and other metadata fields, e.g., taxonomic names, from ontologies)

J. Add ability to annotate based on geographic/temporal coverage and other structured info from EML


Other tasks
-----------
M. Need at least medium sized corpus of annotated data sets crossing disciplines for testing
  -- see list of data sets to be annotated (https://semtools.ecoinformatics.org/notes/corpus/target-data-sets/)
     -- goal to generate the list of data sets to be annotated
  -- Margaret for SBC data
  -- Mark for plant traits

N. Develop additional ontologies (cover rest of SBC cases, expand to other sites?)