XMDR Prototype Progress Report

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XMDR Prototype Progress Report

• John McCarthy and Kevin D. Keck
• XMDR Project Quarterly Meeting
• 15 March, 2005
• UC Berkeley Faculty Club

2
Purposes of XMDR Prototype for ISO/IEC 11179
Registry Standard

• Extend semantics management capabilities
• Explore uses of terminologies and ontologies
• Systematize representation of relationships
• Adapt test emerging semantic technologies
• Help resolve registration harmonization issues
  for different metadata standards
• Propose revisions to 11179 Parts 2 3 (Ver. 3)
• Show how proposed revisions to metadata registry
  standards can be implemented
• Demonstrate Reference Implementation (RI)

3
XMDR Prototype Architecture Initial Implemented
Modules
Subversion
Java
Jena, Xerces
Lucene
Jena, OWI KS
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XML files for each metadata object were extracted
from EDR via scripts
Extract Script - works on underlying html -
follows each link - gets html file for each
linked object
Conversion Script - works on html files - creates
xml file for each
First stepall xx items linked from Countries of
the World Next step bulk load all metadata item
instances from EDR
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Html to xml file conversion example

• Show html file and then its xml transform

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XMDR Prototype contains an xml file for each
metadata item instance

• Administered Items
• Classification Schemes
• Conceptual Domains
• Contexts (for Administered Items)
• Data Elements
• Data Element Concepts
• Object Classes
• Properties
• Representation Classes
• Value Domains

Other Items Relationships What else?
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XMDR Prototype example dual purpose rdf/xml
file DC-Country_Label (extract)

• ltDataElement rdfabout""
• xmlnsmdr"http//hpcrd.lbl.gov/SDM/XMDR/ont/i
  so11179-3v2.owl"
• xmlnsrdf"http//www.w3.org/1999/02/22-rdf-sy
  ntax-ns"
• mdrmeaning"DC-Country_Label.xml"
• mdrregistrationAuthority"http//oaspub.epa.g
  ov/edr"gt
• ltidentifiergt
• ltregistrationAuthorityIdentifiergt
• ltinternationalCodeDesignatorgten-USlt/internat
  ionalCodeDesignatorgt
• ltorganizationIdentifiergtEPAlt/organizationIde
  ntifiergt
• lt/registrationAuthorityIdentifiergt
• lt/identifiergt
• ltadministrationRecordgt
• ltregistrationStatusgtStandardlt/registrationStat
  usgt
• ltadministrativeStatusgtFinallt/administrativeSta
  tusgt
• ltcreationDategt????lt/creationDategt
• lt/administrationRecordgt
• ltsteward mdrorganization"ORG-1044"
• mdrcontact"CON-20068"/gt

ltterminologicalEntry mdrentryContext"CXT-St
andard"gt ltcomponentgt ltsectionLanguagegt
ltlanguagegtenglt/languagegt ltcountryIdentifiergtUSAlt/
countryIdentifiergt lt/sectionLanguagegt
ltdesignationgt ltnamegtCountry Namelt/namegt
lt/designationgt ltdefinitiongt lttextgtThe name
that represents a primary geopolitical unit of
the world.lt/textgt lt/definitiongt
lt/componentgt lt/terminologicalEntrygt ltterminologi
calEntry mdrentryContext"CXT-XML_Tag_Final"
gt ltcomponentgt ltsectionLanguagegt ltlangua
gegtenglt/languagegt ltcountryIdentifiergtUSAlt/country
Identifiergt lt/sectionLanguagegt
ltdesignationgt ltnamegtCountryNamelt/namegt
lt/designationgt lt/componentgt
lt/terminologicalEntrygt lt/DataElementgt
boil down contents and add annotations
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XMDR files serve dual purposexml and
OWL-compatible rdf

• Well-formed XML
• XML serialization of RDF
• Conforms with 11179 OWL ontology
• Base tag includes rdfabout attribute
• Literals encoded as element content
• URIs encoded as attribute values
• striped resource, property, resource, use
  abbreviated form for anonymous nodes

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Xml schema specifies constraints

• Relax NG schema to make xml files
• Enforces constraints for 11179 OWL

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Relationships are implemented as LINKS to other
xml files
ltentity-typegtDataElement lt/entity-typegt
ltnamegtCountry of Birthlt/namegt ltconceptual
domaingtCountry lt/conceptual domaingt ltvalue
domaingtCountries of the World lt/value domaingt
Metadata schema includes relationships that
specify which attributes can or must link to
other entity-types
ltentity-typegtConceptualDomainlt/entity-typegt
ltnamegtCountrylt/namegt
ltentity-typegtValueDomainlt/entity-typegt ltnamegt
Countries of the World lt/namegt
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How can terminologies and ontologies help manage
metadata?

• At the level of metadata instances in a registry,
  connect metadata entities via shared terms
• via automatic indexing of metadata words
• via text values from specific metadata elements
• At the level of the 11179 (or other) metamodel,
  ontologies can help specify formal relationships
• is-a and part-of hierarchies, etc.
• Inheritance, aggregation,
• for automatic searching of sub-classes inverses
• to specify semantic pathways for indexing

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Protégé Editor was used to create OWL ontology
for 11179 metamodel

• insert screenshot from Protégé

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Protégé OWLViz Plug-in Displays OWL Class
Hierarchy for 11179
Built on top of GraphViz
14
Class hierarchy includes simple and union
is-arelationships
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Is-a and union hierarchies can nest to arbitrary
depth in OWL
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ISO/IEC 11179 fragment is expressed as an OWL
ontology using RDF syntax
lt?xml version"1.0" encoding"ISO-8859-1"?gt ltrdfR
DF xmlnsrdf"http//www.w3.org/1999/02/22-rdf
-syntax-ns" xmlnsrdfs"http//www.w3.org/200
0/01/rdf-schema" xmlnsowl"http//www.w3.org
/2002/07/owl" xmlns"http//www.owl-ontologie
s.com/unnamed.owl" xmlbase"http//www.owl-ont
ologies.com/unnamed.owl"gt ltowlOntology
rdfabout""/gt ltowlClass rdfID"Registrar"gt
ltrdfssubClassOf rdfresource"http//www.w3.org
/2002/07/owlThing"/gt ltrdfssubClassOfgt
ltowlRestrictiongt ltowlcardinality
rdfdatatype"http//www.w3.org/2001/XMLSchemaint
" gt1lt/owlcardinalitygt
ltowlonPropertygt ltowlObjectProperty
rdfID"contact"/gt lt/owlonPropertygt
lt/owlRestrictiongt lt/rdfssubClassOfgt
ltrdfssubClassOfgt ltowlRestrictiongt
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Lucene facilitates text indexing to search on
words phrases
Word Index birth country world
Name Index birth country
Other Indexes
Phrase searches done on results
ltentity-typegtTerminologylt/entity-typegt
ltnamegtUnited Nations XXXXlt/namegt
ltentity-typegtValueDomainlt/entity-typegt ltnamegt
Countries of the World lt/namegt
ltentity-typegtConceptualDomainlt/entity-typegt
ltnamegtCountrylt/namegt
ltentity-typegtDataElement lt/entity-typegt
ltnamegtCountry of Birthlt/namegt ltconceptual
domaingtCountry lt/conceptual domaingt ltvalue
domaingtCountries of the World lt/value domaingt
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Lucene text search capabilities, with examples

• Simple word search
• Wild-card word search
• Fuzzy or stem search ()
• Search specified field
• Search for links
• Distance (in words)
• Phrases
• Boolean operators

country
coun
country
namecoun
linkhttp)
country world4
countries of the world
AND, "", OR, NOT, "-"
http//lucene.apache.org/java/docs/queryparsersynt
ax.html
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More text search capabilities

• Range search
• Boosting a term
• Grouping
• Field grouping
• Escape special characters

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Advanced search interface can automatically
generate syntax
Field/Column
Operator
Value
Conjunctions
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show Text Queries here

• show Text Query examples here
• Queries and results

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Distinguish text vs rdf queries

• What text queries do
• What rdf queries do
• What are the major differences?

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Reasoners use OWL ontologies to augment RDF
graph queries
RDF Query (rdql/ndql)
Reasoner Jena or Racer (memory)
result set includes subclasses, inverses, etc.
OWL 11179 Ontology
OWL built-in rules
11179 metadata (xml/rdf files)
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Uses of RDF queries

• Expand queries to other classes in a hierarchy
• E.g., all data elements that have to do with
  infectious diseases
• E.g. what attributes are there for images of
  carcinomas vs basil cell
• Go from concepts back to des even if only have
  concepts in des (do index)

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RDF Queries are very different from text search
or SQL!
QUERY SELECT ?t WHERE (lthttp//erdos.lbl.gov/xmdr/
data/VDALL.1.15147.1.xmlgt rdftype ?t) USING
mdr FOR lthttp//hpcrd.lbl.gov/SDM/XMDR/ont/iso1117
9-3v2.owlgt RESULT ?t lthttp//hpcrd.lbl.gov/SDM/X
MDR/ont/iso11179-3v2.owlEnumeratedValueDomaingt lth
ttp//hpcrd.lbl.gov/SDM/XMDR/ont/iso11179-3v2.owl
ValueDomaingt lthttp//hpcrd.lbl.gov/SDM/XMDR/ont/is
o11179-3v2.owlAdministeredItemgt ltowlThinggt ltrdfs
Resourcegt search includes sub-classes and
inverses
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Registering/Loading Metadata

• Browse and upload file(s)
• Form interface

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Lessons Learned to Date

• XML-RDF files can serve dual purpose (may be
  first time this has been done?)
• Independent modules facilitate testing many
  possible new toolsBUT
• take more time to implement maintain
• State of art for open-source OWL reasoners not
  very advanced (none yet for OWL-DL)

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Unresolved Issues

• Performance using files for objects
• Relationship representation
• XML objects display browsing
• User-friendly interface for RDF queries
• external data sources, ontologies, terminologies
  (maybe via indexing?)
• Harmonization with MMR
• Others??

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Next Steps

• Load data from EDR other sources
• Implement advanced text search UI
• Use style sheets to display xml as html
• Add validation and mapping modules
• Connect terminology/ontology to items