Overview of deliverables
------------------------
DROPPED 1.  Develop and ratify a community-driven core ontology for representing observational data.
DROPPED 2.  Develop an open-source reference implementation for the core observation ontology (i.e., a concrete OWL
representation and associated software services) to facilitate its use in informatics projects and frameworks (including
those of the Observation Ontology Workshop). 
3.  Revise and extend the structure of EML so that it is capable of storing
semantic annotations that ref-erence the core observation ontology, as part
of the reference implementation.
4.  Demonstrate new capabilities enabled by the reference implementation by
extending existing software already in use by the ecological community: the
EML storage system, Metacat, to provide annotation storage and ontology
reasoning services; and the metadata editor, Morpho, for semantic annotation
and a range of semantically enhanced services (e.g., searching, summarizing,
visualization, etc.).
5.  Engage the community through workshops to solicit use cases to drive
research and development, and to evaluate the effectiveness of the semantic
extensions to Morpho, Metacat, and EML.

Prioritized deliverables
------------------------
* Metacat semantic extensions
    Open-source and generic services to support the core observation
    ontology reference implementation:

    Phase I: emphasis on dataset-level annotations and results
    a. Build advanced search that can navigate the observation structure and produce a structured query; then
       reapply the UI to building an annotation; emphasis on usability and understandability of the UI
    b. Use existing structured search mechanism as a way to drill down through the ontologies to
       create an annotation, that gets tagged to the overall data set instead of being bound
       directly to the attributes (updaide: constrains annotation appropriately; allows structured search;
       downside: limits searches to annotation/ontology, can't use data in search because it is not bound 
       to the annotation)

    c. Extensions to Metacat fo ontology storage and access (assume this is here, except IDs and versions)
    d. Extensions to Metacat for annotation storage and access (assume this is here, except IDs and versions)

    e. Hierarchical browsing and navigation of Metacat collections
    f. Visualize/display annotations over data (extend eml attribute display with semantics)
    g. Simple web-based interface for tagging EML document with ontology term (not so useful)

    Phase II: focus on matching annotations to attribute structure
      -- allows data-driven queries
      -- enables sensible summarization features

* EML/Annotation language integration
    a. Develop new EML modules that support semantic annotation to the core
    observation ontology that reduces the redundancies between existing EML
    descriptions and those captured formally within the core ontology (such
    as those currently existing between EML and OBOE). Provide tools and
    guidelines for migrating legacy EML metadata to this new EML approach.

* Morpho annotation extensions
    a. Design and implement graphical user interfaces within Morpho for
    annotation of ecological data, and integrate these facilities with
    existing metadata generation within Morpho to streamline the data
    publishing process.  Develop mechanisms to automate the annotation
    process, as well as mechanisms to create, apply, and edit annotation
    templates.

* Sensible summarization
    a. Design and implement a concept browser in Morpho for selecting
    relevant concepts from one or more ontologies for data browsing and
    summarization.  Link this browser to the existing data view in Morpho so
    that the data view adjusts as concepts are selected, calculating
    aggregated statistics based on user preferences as needed by particular
    semantic views of the data.  Design and implement these data
    summarization algorithms in an efficient system building on existing
    capabilities in relational and multi-dimensional database systems.
    Incorporate graphical data exploration tools into Morpho. 

* Morpho semantic search
    a. Design and implement graphical user interfaces within Morpho for
    semantic searching, and allow a user to refine their intended semantic
    search concepts based on textual search terms.  Integrate these semantic
    search extensions with the existing text-based searches in Morpho.
    b. New Morpho interfaces for searching and browsing Metacat and local 
    collections, which will leverage many of the Metacat extensions.



TODO
----
* Ben: create canonical repository for OBOE, delete others, update web to point there
* Ben: agree on namespace for OBOE and versioning approach for ontology and annotations, update owl files
* Ben: develop scenarios that describe the emain ways in which the metacat advanced structure search/annotaiton tool would
be used
* Ben: develop proposal for how IDs and namespaces for ontologies and annotations will be handled
* Mark: Examine the Morpho term browser with the NBII vocabulary