Title: XMDR Prototype Progress Report
1XMDR Prototype Progress Report
- John McCarthy and Karlo Berket
- XMDR Project Quarterly Meeting
- 19 July, 2006
- UC Berkeley Faculty Club
2Progress 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
3Created XMDR Prototype Download Web Site
Demo http//xmdr.lbl.gov/software/
4Ontologies 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
5Refined mapping of caDSR metadata into XMDR
prototype
- Demonstrate active outline at xmdr.lbl.gov/caDSR-x
mdr-mapping/
6Loaded 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
7Demo 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
8Used 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
9Experimented 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
10Experimented with MITs Longwell User Interface
for Faceted Metadata
11Solbrig Tools
12Next 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
13END, 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
14Other Topics? Extra Slides
15Longer 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
16Tools
- 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.
17XMDR Prototype Architecture Initial Implemented
Modules
External Interface
RegistryStore (possibly remote)
Registry
Java
RetrievalIndex
LogicBasedIndex
FullTextIndex
11179 Metamodel as OWL Ontology
Jena RDFS,etc.
Lucene