XMDR Prototype Progress Report

1
XMDR Prototype Progress Report

• John McCarthy and Karlo Berket
• XMDR Project Quarterly Meeting
• 19 July, 2006
• UC Berkeley Faculty Club

2
Progress Report Outline

• Created XMDR Prototype download web site
• http//xmdr.lbl.gov/software/ includes open
  source licensing
• Added more ontology/terminology metadata to
  prototype
• NBII biodiversity ontology NCI metathesaurus,
  GEMET data
• Loaded 11179-ed 2 registry metadata into XMDR
  prototype
• refined specifications for mappings from caDSR
  into XMDR prototype
• loaded selected caDSR metadata into prototype
• used xquery in Oracle to retrieve selected
  metadata from EPA Environmental Data Registry
  database into XML data structures
• map load EDR metadata after new XMDR prototype
  schema in July
• Installed faceted Longwell User Interface (from
  MIT Simile)
• Next steps major challenges

3
Created XMDR Prototype Download Web Site
Demo http//xmdr.lbl.gov/software/
4
Ontologies currently included in XMDR
Prototype ( are new)

• NASA sweet-earthrealm
• GEMET_2001.0 Multilingual Environmental
  Thesaurus
• ISO4217_1981 currency codes
• ISO3166_V-10 country codes
• NBII_2002-2003 biodiversity
• Mouse_1.32 anatomy
• DTIC_1.0 Department of Defense
• NCI_Thesaurus_05.03f health
• caDSR-sample-070706 11179 registry
• EPA_121504 small extract
• EDR_2005-03-23 small extract

5
Refined mapping of caDSR metadata into XMDR
prototype

• Demonstrate active outline at xmdr.lbl.gov/caDSR-x
  mdr-mapping/

6
Loaded caDSR registry metadata into XMDR
Prototype

• Tabular specification of mapping from caDSR to
  XMDR
• For high level, understandable description/documen
  tation
• caDSR web interface can get selected 11179
  metadata
• but not full set of objects and attributes
• xml download blows up after xxx objects
• XSL-T scripts to do mappings from caDSR and EDR
• oXygen software/eclipse plug-in facilitates this
  process
• caDSR API can access full 11179 registry metadata
• maybe later because this will take longer to
  implement

7
Demo Discuss caDSR in XMDR

• List of 11 Ontology items now in the prototype
  http//xmdr.lbl.gov/xmdr/mixed/results.jsp?itemty
  peOntologylinktypelinkdirectiontolinkfield
  anyanonymoustrueinftypeNO_INFallexactany
  notfragmaxresults0
• Ontology created for caDSR data
• http//xmdr.lbl.gov/xmdr/display.jsp?urldata/CS-c
  aDSR-sample-070706.xml
• DataElement items created for caDSR data
• http//xmdr.lbl.gov/xmdr/mixed/results.jsp?itemtyp
  eDataElementlinktypecontainerlinkdirectionto
  linkhttp3A2F2Fxmdr.lbl.gov2Fxmdr2Fdata2FCS-
  caDSR-sample-070706.xmlfieldanyanonymoustruei
  nftype NO_INFallexactanynotfragmaxresu
  lts0

8
Used Oracle Xquery facility with EPA
Environmental Data Registry database

• Created small example
• Specified XML structure in Oracles Xquery
  language
• Next steps will be to draft mappings load data
• ala mappings for caDSR
• more challenging because EDR is not in XML
• awaits new XMDR prototype schema
• Maybe use oXygen to download direct from Oracle

9
Experimented with MITs Longwell User Interface
for Faceted Metadata

• Longwell built and installed using
• Fresnel
• Presentation of semantic web data using lenses
• OpenRDF tools
• Default configuration
• loads RDF data
• creates faceted views
• Loading issues
• Only recognizes data inside rdfRDF blocks of XML
• Had to write XSLT to transform our data to
  acceptable format

10
Experimented with MITs Longwell User Interface
for Faceted Metadata
11
Solbrig Tools

• Machine-readable specs

12
Next priorities for XMDR Prototype-- more
discussion Thurs-Fri

• Update XMDR metamodel data to reflect 11179
  revisions
• revised UML model, figures text submitted to
  editor Ray Gates
• for working draft 1, which will become
  committee draft 1 for part 3
• Kevin revising prototype model XML schema to
  reflect revisions
• explore more general ways to handle evolving
  model revisions
• Add more metadata
• especially for example 11179 registries, i.e.
  EPA-EDR, caDSR
• Omega Ontology
• Improve tools procedures for input data
  mapping/loading
• Move wiki web download site to xmdr.lbl.gov
• Use Subversion to store xmdr data (rather than
  unix files)
• connect subversion to interface compare
  performance vs files
• Further enhancements to XMDR User Interface
• selective transitive closure queries for i.
  exact match ii. all nodes above or below
  current node iii. all nodes within specified
  number of arcs

13
END, Thanks, Acknowledgements

• This is the end of the presentation
• Slides following this one can be
• folded back into the mainline presentation,
• Held in reserve if questions arise they can help
• Dropped altogether

14
Other Topics? Extra Slides
15
Longer term challenges future goals for XMDR
prototype system

• Additional prototype features
• Extensions to 11179 metamodel
• Acquire develop complementary tools
• Analysis and evaluation of component modules
• Expand relationships with other organizations

16
Tools

• User-friendly interface for RDF inference queries
• Something like EDR UI with link labels inverse
  references
• RDF normalizer into XMDR format (to work with RDF
  tools)
• -----------
• Form interface for registration uploading
  metadata?
• Registry access services, query facilities, etc.
• Handling multiple registries within single
  registry server
• Extraction, Translation Loading (ETL) metadata
• aggregation operators for derived tables
  (statistical/OLAP)
• XBRL support for tables, etc.

17
XMDR Prototype Architecture Initial Implemented
Modules
External Interface
RegistryStore (possibly remote)
Registry
Java
RetrievalIndex
LogicBasedIndex
FullTextIndex
11179 Metamodel as OWL Ontology
Jena RDFS,etc.
Lucene