# Presentation: 859524

## XMDR Prototype Overview

**XMDR Prototype Overview**

**John McCarthy and Karlo Berket**
**International Ecoinformatics Technical Collaboration**
**October, 2006**
**Faculty Club**
**University of California**
**Berkeley**

- 1

**Notes:**
Karlo Berket joined LBL’s XMDR Project group as a part time programmer in January 2006
He comes to us from the Cybersecurity and Network :& Distributed Systems Research Group at LBNL,
which continues to occupy and pay for the other half of his working hours

## XML Prototype Overview Outline

**Review XMDR Prototype motivation & goals **
**Describe architecture & modular implementation**
**Summarize content loaded to date & planned**
**Demonstrate current XMDR Prototype (v.1 & 2) **
**Text Search and Inference queries & results **
**XMDR portal for software, data & documentation**
**Discuss next steps & major challenges**

- 2

**Notes:**
Prepared this with Larry in mind as the architype for primary audience

Tell story about painful upgrade from T23 to T43
Analogy to upgrading 11179 to include more formal semantic information
We’ve been hearing about inference from Frank for a number of years (Prolog, etc.)

Problem that had a silver lining
Karlo machine crashed, so he had to re-install—did it on xmdr server and revised recipe

## Goals of the open source XMDR prototype implementation testbed

**Demonstrate *****feasibility***** & *****utility***** of proposed revisions to ISO/IEC 11179**
**Provide open-source reference implementation with XMDR capabilities**
**Determine the necessary features to leverage semantic interoperability between ‘concept’ systems and ‘data elements’ **
**e.g., for ontology lifecycle management & harmonization**
**Explore benefits of representing XMDR content using**** ****emerging semantic technologies (e.g., RDF, OWL, CL, ...)**
**integrate open source tools to create, maintain, deploy XMDR standards**
**test capabilities and performance of candidate tools**
**Assemble semantic metadata with different structures from diverse sources to test various semantic technologies**
**terminologies, thesauri, ontologies, ...**
**From health, environment, geography, ...**
**Help identify ways to resolve registration & harmonization issues for different metadata standards, including ODM & MMF**

- 10

## How does the XMDR prototype seek to overcome 11179-ed2 limitations?

**Add more rigorous & formal specification for**
**Concepts and concept systems (ontologies)**
**Relationships between metamodel components**
**Continuing evolution toward increasing granularity & details**
**Use concepts to unify different types of metadata**
**and axioms for conceptual & structural relationships **
**Support more powerful software tools**
**for richer text searching beyond relational technology**
**for inference queries based on structural metadata**
**Build interfaces to aid searching & navigation**
**hide complexities of inference queries**
**combine text searching and inference**
**Bridge the realms of concepts & data artifacts**
**More explicit connections to & use of other metadata standards**

- 6

## How does XMDR Prototype differ from current 11179 technology?

**Evolutionary aspects**
**Finer-grained, more formal metadata**
**e.g., distinct attributes for measurement units **
**rather than just part of textual description**
**Machine inference complements text searching**
**Revolutionary aspects**
**Use of formal ontologies, logic, and inference**
**to specify 11179 metamodel**
**to store, search, retrieve and display metadata**
**Logic engines & machine reasoning**
**Now implementing 2****nd**** generation prototype**
**after past year’s experience with version 1**
**reloading and adding to example contents**

- 12

**Notes:**
Many years ago, I remember Frank Olken asserting how we needed 
to store complete and detailed schema information in
graph databases so we could use logic programming to do 
Automatic inferencing in order to search and navigate
Large and complex universes of metadata.

At the time, it seemed pretty esoteric, academic, and impractical.
But in the meantime logic programming and inference technology 
Has matured, computing capabilities have grown substantially,
and our metadata challenges have grown as well.

And now I’m finally beginning to understand Frank’s prophetic vision
As something we can now implement in practical ways in order
To dramatically improve the capabilities and potential of metadata registries.

## XMDR Prototype Architecture: Initial Implemented Modules

**Ontology Editor**

**Protege**

**11179 OWL Ontology**

**XMDR Prototype Architecture: Initial Implemented Modules**

**Authentication Service (defer)**

**MappingEngine (defer)**

**Registry**

**External**
**Interface**

**MetadataValidator**

**XML Schema (for XML)**
**Jena (for RDF)**
**Protégé & Swoop (for OWL)**

**Java**

**RetrievalIndex**

**FullTextIndex**

**Lucene**

**LogicBasedIndex**

**Jena, [Sesame?]**

**RegistryStore**

**WritableRegistryStore**

**Subversion**

- 11

**Notes:**
Tools in smaller different font &
Lines around boxes for print version
Black print on pastel blocks

Show Protégé creating ontology used to define storage

Evaluated OWI KS and Racer but they had performance and other issues (see data in prior presentation)

Paid version of Saxon may be able to do schema-driven transformations

Karlo says mapping between concept systems could be done by loading additional OWL files
Mapping happens at 2 levels: between different instances of same OWL class; and between dif instances within a class (e.g., Data Elements)

## As XMDR uses UML for 11179 metamodel, XMDR adds XML (schema), RDF & OWL

**As XMDR uses UML for 11179 metamodel,**** ****XMDR adds XML (schema), RDF & OWL**

**OWL XMDR Ontology & annotations ****Types & Cardinalities**

**RDF Spec ****Triples: binary labeled relationships**

**XMDR XML Schema**
**What things go in own files? Which property direction stored? Sequential ordering of properties**

**XMDR XML Objects ****Files**

- 16

***Dotted lines indicate steps that are done by hand (i.e., not automated)***

**11179 UML Specification**** ****(proposed ed3)** **(Poseidon xmi file)**

- Scripts (plus some hand editing (may use commercial tools in the future)

**Notes:**
In the future, XML schema may be able to enforce most of the constraints from OWL, RDF, and XML automatically

Can create regular XML Schema from Relax-NG specs using TRANG

## Used UML to generate OWL statements

**Current automation tools did not work**
**tools use UML2, but current 11179 spec is UML1.x**
**but even UML 2 from Poseidon did not work**
**tried TopBraid (Knublauch), Sandpiper**
**Created script(s) for converting UML to OWL**
**Tested with XMI output from Poseidon 3.2.1-0**
**Quicker updating of prototype from 11179 draft spec**
**Current version of scripts do not**
**Translate datatypes**
**Separate packages into separate namespaces**
**Create owl:disjointWith properties**
**Translate OCL rules/restrictions**
**(e.g., registered is either an administered item or an attached item)**

- [new]

**Notes:**
UML 2 from Poseidon may have failed either due to Poseidon or to non-compliant XMDR specs

## Different ontologies help support XMDR prototype at different levels

**Different ontologies help support XMDR prototype at different levels**

- 11179 classes, properties & relations

- SWEET
- & Other Ontologies

_**Metamodel Level**_

_**11179 Registry Level**_

_**Application Software Level**_

- Concepts & Terms

- Database A

**Data** **Element** 1

**Data Element 2**

**Data Element 3**

- 15

- Data Element Metadata

**Notes:**
$$ Might want to invert the order and put Application Software Level at the top

## *Diverse XMDR example content being re-loaded via lexgrid, scripts, and XSLT

- Original Source A

- Lexgrid Source A

- XSLT
- script

- Harold Solbrig
- (Mayo,Apelon)

***Diverse XMDR example content being ****re-loaded via lexgrid, scripts, and XSLT**

- Concept System A

- A Concepts

- A Relationships

- 17

**XSLT scripts updated to work with new XMDR specification**

**Notes:**
KARLO: the loaded content will need to be modified (depends on version using for demo) 

## Example concept system content is being reloaded into XMDR Prototype

***via Lexgrid***
**NBII_2002-2003  biodiversity **
**NCI_Thesaurus_06.02d health**
**GEMET_2001.0 Multilingual Environmental Thesaurus **
**ISO4217_1981 currency codes**
**ISO3166_V-10 country codes**
**Mouse_1.32  anatomy**
**DTIC_1.0 Department of Defense**
***via special purpose scripts***
**Omega ontology**
**NASA SWEET-earthrealm extract**
**caDSR (released data elements from “web site” file)**

- 18

## Additional Metadata Content planned for XMDR Prototype

**Current 11179 Data Element Registries**
**EDR (EPA Environmental Data Registry)**
**caDSR (full NCI Cancer Data Standards Registry)**
**Possible Candidate Concept Systems and Ontologies**
**IETF RFC 3066 Language Codes**
**USGS Geographic Names Information System**
**Getty Thesaurus of Geographic Names**
**I.T.I.S. - Integrated Taxonomic Information System**
**Adult Mouse Anatomy**
**Foundational Model of Anatomy **
**NASA SWEET (Semantic Web Earth & Environmental Terminologies)**
**EPA Chemical Substance Registry **
**GO (Gene Ontology), ....Agrovoc,  ...and possibly others**

- 19

- 2005-07-27

**Notes:**
Main criteria are 
   wide range of substantive fields of interest
   different types of data structures, complexity, and other types of challenges

## caDSR illustrates mapping of metadata into XMDR prototype

**See active outline at **_**[http://xmdr.lbl.gov/mappings/cde-xmdr](http://xmdr.lbl.gov/mappings/cde-xmdr)**_**-mapping/ **
**Both it and the above are from earlier mappings, but show how it is done**

- 20

## Extract from draft 11179 ed 3 metamodel UML diagram

## Omega Ontology illustrates challenges of how to load complex new content

**Omega is a “terminological ontology” **
**reorganization & synthesis of WordNet & Mikrokosmos**
**adds higher level ontology to organize multiple ontologies**
**somewhat mysterious files (o4, wnvfrm, d, efrm, pfrm, tfrm)**
**Initial loading of Omega was as follows:**
**Entity relationships conform to Concept_System figure **
**Entity ->Attribute conforms to Classification_Scheme figure**
**Omega Attributes map to 11179 ed3 Facets**
**with two extensions to current draft 11179 ed3 proposal**
**Each facet may have a datatype and description**
**There may be multiple instances of a facet type**
**This initial mapping needs further discussion!**

- 21

**Notes:**
Karlo may want to edit this

## *XMDR prototype contains an XML file for each 11179 Identified Item

**           ****3 Concept Systems *****e.g., NBII, NCI Thesaurus (3)***
**         ****51 Classification Schemes *****e.g., CDISC Codelists (51)***
**         ****86 Conceptual Domains *****e.g., Countries of the World (86)***
**    ****2,244 Characteristics *****e.g., Examined, Analyzed (2244)***
**    ****1,735 Object Classes *****e.g., Participant, Finding (1735)***** **
**    ****4,417 Data Element Concepts *****e.g., Country Label (4417)***
**    ****5,987 Data Elements *****e.g., Country Name (5987)***
**    ****3,118 Value Domains *****e.g., countries of the world (3118)***

**  ****87,907 Concepts *****e.g., River outflow***
**         ****96 Relations *****e.g., broader, Allele_Has_Activity***
**128,377 Links**
**           ****0 Organizations *****e.g., EPA***
**         ****14 Units of Measure *****e.g., %, ml/min, seconds***

- 22

**Notes:**
KARLO SAYS it will take a day to write a script to get the numbers automatically from the prototype
(competing priority with loading data and text search)
We will only put numbers where we have at least one of that type of item

NOTE: our intention is to have at least one example item for each type of Identified Item in the new 11179 metamodel
-- includes classes, associations, and relations

## Each 11179 Identified Item in XMDR (e.g., object, concept, data element)  is

**Logically stored as a separate XMDR file/document**
**In Subversion code management system**
**with files stored in Subversion’s database**
**in order to help support versioning and access control**
**Compliant with three complementary standards:**
**XML (document constraints)**
**RDF (graph constraints)**
**OWL ontology (11179 draft ed3 constraints)**
***...******and will in the future be***
**Validated against a 11179 XMDR XML Schema**
**generated mostly automatically from 11179 UML2 specs**
**to automatically enforce XML, RDF, and OWL constraints  **

- 24

- 2005-07-27

## What happens to xmdr files before they can be used for text searching or inference?

**What happens to xmdr files before they can be used for text searching or inference?**

- Lucene

- Lucene indexes

_**xmdr **_
_**files**_

- Jena

- Model A
- Model B
- XMDR Ontology...etc

**Text queries (Lucene)**

**Inference queries (Jena)**

- Search/Query results are sets of tuples with URIs for xmdr files pictured above or substructures within files

**& ****other**** sources**

- [all xmdr files]

- [each system (A,B,...etc) loaded individually]

- Union of all models

- Concept System A

- A Relations

- A Relations

- Registry B

- B Data Elements

- B Relations

- A Concepts

- A Concepts

**NCI Thesaurus**

**EPA Data Registry**

- 23

**Notes:**
In the future, we may want to invert the vertical ordering of objects in this slide

## XMDR XML schema can add several important benefits... 

**Schema specifies what is **_***required***_** as well as what is **_***legal***_
**Divides metadata into files conforming to XML schema**
**Normalizes data (ala’ relational “one fact in one place”)**
**Facilitates XSLT transformations by reducing degrees of freedom to a canonical encoding within the RDF standard**
**Relax NG can be used to create XMDR prototype schema**
**RNG validator can enforce many OWL ontology constraints**
**TRang can automatically translate into XML schema syntax**

- 25

**Notes:**
KARLO: - none of this actually exists as far as I know; if leave should talk about in abstract 

## RDF provides complementary benefits on top of XML

**All the advantages of XML **_***plus***_** ...**
**RDF provides more explicit semantics than XML**
**Users can employ a growing set of RDF tools**
**e.g., SPARQL query language, SWRL rule language, Jena inference**
**More powerful retrieval capabilities**
**Using many different RDF graph query tools**
**RDF’s graph data model supports inference**
**e.g., inclusion of subsumed sub-classes **
**Results can be either **
**tuples (ala relational tables)**
**XML/RDF graphs (being developed for W3C’s SPARQL)**
**Facilitates integrated use and management of multiple related concepts within different concept systems**

- 26

## OWL ontology specification adds richer semantics atop RDF & XML

**All the advantages of XML & RDF **_***plus***_**...**
**RNG validator enforces many OWL ontology constraints**
**Classes and subclasses (is-a relationships)**
**Union classes**
**Inverses**
**Same-as, same-property-as, same-class-as**
**Restriction classes (restrict range, cardinality, etc. of property based on type of subject)**
**...****and tools for creation, editing, visualization, and management (Protégé & plug-ins)**

- 27

## *XMDR Prototype example: dual purpose rdf/xml file (extract) for one GEMET term

***XMDR Prototype example: dual purpose rdf/xml file (extract) for one GEMET term**

**<Reference_Concept xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"**
**                   ****xmlns="http://hpcrd.lbl.gov/SDM/XMDR/ont/iso11179-3e3draft_r1_7.owl#"**
**                   ****xml:base="http://xmdr.lbl.gov/xmdr2/data/OMEGA-4/R-C/50010/1451.xml"**
**                   ****rdf:about="">**
**   ****<Identified_Item.data_identifier rdf:datatype="http://www.w3.org/2001/XMLSchema#string">OMEGA-4/R-C/50010/1451.xml</Identified_Item.data_identifier>**
**   ****<Identified_Item.version rdf:datatype="http://www.w3.org/2001/XMLSchema#string">4</Identified_Item.version>**
**   ****<Identified_Item.identification_source rdf:resource="http://xmdr.lbl.gov/xmdr2/data/OMEGA-4/N/5001.xml"/>**
**   ****<Designatable_Item.designation rdf:parseType="Resource">**
**      ****<Designation.sign rdf:datatype="http://www.w3.org/2001/XMLSchema#string">table tennis</Designation.sign>**
**      ****<Designation.designation_context_relevant_designation rdf:parseType="Resource">**
**         ****<Designation_Context.scope rdf:resource="http://xmdr.lbl.gov/xmdr2/data/OMEGA-4/C-1.xml"/>**
**      ****</Designation.designation_context_relevant_designation>**
**   ****</Designatable_Item.designation>**
** ****<Concept.container rdf:resource="http://xmdr.lbl.gov/xmdr2/data/OMEGA-4/CS.xml"/>**
**</Reference_Concept>**

**Karlo show new version**
**Annotate parts that **
**illustrate RDF & OWL**

- 28

**Notes:**
HIDE for Huntsville; Karlo hopes to have replacement ready by Ecoterm the next week

KARLO suggests we try showing more compact representation of triples (using N3 or similar tool)
Perhaps in addition to the full blown XMDR RDF/XML format such as above 

Concept is shorthand in xmdr name
Property is RDF type subject

Subject property object
Xml serialization 
Class name for tag is shorthand for property

## *XMDR RDF graph query facilities complement text query capabilities

**Underlying SPARQL has SQL-like structured queries**
*e.g., **SELECT ?x  WHERE (?x rdf:type xmdr:Concept_System)*** **
**Can span items that are only indirectly connected**
*e.g., data elements associated with a conceptual domain*
*inferred inverses (e.g., xmdr:Relation.member/xmdr:Link.relation)*
*Some depend on relations in concept system*
**Expand queries to subsumed classes in hierarchy**
*e.g., all cities within state and states within countries*
**Transitivity**
*e.g., all subclasses subsumed by a higher order class*
*e.g., all superclasses (ancestors) of a particular class*
*Others depend on SPARQL capabilities*
**Least common ancestor ***(minimal generalization)*
*e.g., closest subsuming concept for 2 concepts*
**Siblings**
*e.g., other airport codes comparable to “SFO”*

- 29

**Notes:**
KARLO: not sure if it can do all of that (maybe we should mention SPARQL instead) -- this is something Frank would probably know better 

## Reasoners use OWL ontologies to augment RDF graph queries

**RDF Query**
- (rdql/nrdql/_SPARQL_)

**Reasoners**
- Jena
- (knows RDF & OWL)
- (main memory)

**result set**
*Includes tuples*
*with subclasses,*
*inverses, etc.*

_**Jena**_** is**
** ****a Java framework for building Semantic Web applications;**
** ****a rule-based inference engine;**
** ****a programmatic environment for RDF, RDFS & OWL; **
** ****open source – originally from HP Labs Semantic Web Programme.**
** ****available at http://jena.sourceforge.net/**

- 11179 metadata (xml/rdf/owl files)

- OWL built-in rules

- OWL 11179 Metamodel Ontology

- Several choices

- 30

## *XMDR Advanced text search interface(not yet in new version of prototype)

***XMDR Advanced text search interface****(not yet in new version of prototype)**

- More Results>>

- XMDR Web Interface 0.4, LBNL

*Search for* "any:(+country +(code name))"

**xmdr.lbl.gov/xmdr/**

- 31

**Notes:**
This one is for the old version if you are demoing it.

## *Web interface for inference queries http://xmdr.lbl.gov/xmdr2/

- 32

- Reference_Concept

- NBII

**Notes:**
KARLO: yes, replace (if showing new version) 

## *Inference query results 

- 33

**Notes:**
XML link shows the XML representation of the data item (shown back in slide 15)
INFO link shows detailed information about the item (including inferred info -- shown on next slide)

## *Info shows details about items (including inferred info)

- 38

**Notes:**
KARLO: REPLACE

## *Info about incoming links as well

- 34

**Notes:**
KARLO: yes, replace (if showing new version) 

## Extract from draft 11179 ed 3 metamodel UML diagram

## *Demo & Discuss XMDR

**List of 3 Concept_System items now in the prototype: ****	**
_**[http://xmdr.lbl.gov/xmdr2/mixed/results.jsp?itemtype=Concept_System&linktype=&linkdirection=to&link=&field=any&anonymous=true&inftype=NO_INF&all=&exact=&any=&not=&frag=&maxresults=0](http://xmdr.lbl.gov/xmdr2/mixed/results.jsp?itemtype=Concept_System&linktype=&linkdirection=to&link=&field=any&anonymous=true&inftype=NO_INF&all=&exact=&any=&not=&frag=&maxresults=0)**_
**“****River outflow” Reference_Concept from NBII:**
- _[http://](http://erdos.lbl.gov/xmdr/display.jsp?item=https://xmdr.lbl.gov/svn/private/content/trunk/NBII-2002-2003/R-C/7502.xml)__[erdos.lbl.gov/xmdr/display.jsp?item](http://erdos.lbl.gov/xmdr/display.jsp?item=https://xmdr.lbl.gov/svn/private/content/trunk/NBII-2002-2003/R-C/7502.xml)__[=https://xmdr.lbl.gov/svn/private/content/trunk/NBII-2002-2003/R-C/7502.xml](http://erdos.lbl.gov/xmdr/display.jsp?item=https://xmdr.lbl.gov/svn/private/content/trunk/NBII-2002-2003/R-C/7502.xml)__ _
**“****useFor” Relation_Role from NBII:**
- _[http://xmdr.lbl.gov/xmdr2/mixed/display_new.jsp?item=http://xmdr.lbl.gov/xmdr2/data/NBII-2002-2003/R-R/useFor.xml](http://xmdr.lbl.gov/xmdr2/mixed/display_new.jsp?item=http://xmdr.lbl.gov/xmdr2/data/NBII-2002-2003/R-R/useFor.xml)__ _

- 37

**Notes:**
KARLO: REPLACE IF SHOWING NEW VERSION

## Notable features of XMDR Advanced Inference Search

**You don’t have to know SPARQL**
**but you can see the generated SPARQL query**
**Each search component has pop-up help screen **
**Choice of reasoners **
***None, Jena OWL micro, Jena RDFS default***
**Can restrict search to target object type**
***e.g., concept system, data element, concept, value domain, etc. ***
**Can restrict search by object attributes or links**
***e.g., administrativeStatus, designation, etc.***
**Combines some elements of XMDR text search**
***phrases, words (all, at least one, without), strings***
**Simple output summary & control**
***Result count, specify number displayed per screen***
***Show results as web addresses, literals, or both***

- 35

**Notes:**
KARLO has updated object type and attribute names to current specification 

## XMDR Prototype Web Site has downloadable code & content

**Demo http://xmdr.lbl.gov/software/**

- 40

**Notes:**
KARLO: MAY NEED NEW SCREENSHOT

## Next priorities for XMDR Prototypeare currently under discussion

**Update XMDR metamodel & data to reflect 11179 revisions**
**revised UML model, figures & text submitted to editor Ray Gates**
**Karlo revising prototype model & XML schema to reflect revisions**
**Prototype experience is helping inform model revisions**
**explore more general ways to handle evolving model revisions**
**e.g., generate schemas from axiomitized ontologies**
**Add more metadata  **
**especially for example 11179 registries, i.e. EPA-EDR, caDSR**
**Other content that stretches the current model (e.g., Omega)**
**Improve tools & procedures for input data mapping/loading**
**reduce need for a new script for each new dataset**
**Extend XMDR System Features**
**experiment more with Longwell for faceted metadata**
**references to externally maintained independent metadata**
**explore possibilities for multiple & distributed registry databases**
**selective transitive closure queries for (1) exact match;(2) nodes above or below current node; or(3) within specified number of arcs**
**Ontology Lifecycle Management**** – versions & semantic drift**
**Integrate management of semantics, data, and content **

- 41

**Notes:**
Will improve appearance on XMDR

## MIT’s Longwell Project may be a good user interface for faceted metadata

- 39

**Notes:**
KARLO: nothing new to report here (make note last experimented in July) 

## Technical Challenges and Issues for XMDR Implementation Testbed

**Complexity**
**Representation of relations**
**XML + RDF + OWL is a lot**
**Omega ontology raised a number of issues**
**how to provide extensibility for unknown future complexities?**
**Scalability & performance**
**Currently includes [number] objects & [number] RDF triples**
**maybe indexing and/or distributed registries will help?**
**Model Evolution**
**may be able to generate directly from UML?**
**RDF Issues**
**RDF queries yield tuples, not RDF objects (W3C addressing this)**
**RDF tools won’t create XMDR files (add wrapper constraints?)**
**External metadata sources, ontologies, terminologies**
**Harmonize with ODM, MMF, Common Logic, Web Services **

- 45

**Notes:**
NEED NUMBERS ABOVE

## Thanks & Acknowledgements

**Bruce Bargmeyer, Principal Investigator**
**Kevin Keck, Initial Designer & Implementor**
**Frank Olken, Theory & Model Development**
**Harold Solbrig, Lexgrid, Model Development, etc!**
**L8 and SC 32/WG 2 Standards Committees**
**Major XMDR Project Sponsors and Collaborators**
**U.S. Environmental Protection Agency**
**Department of Defense**
**National Cancer Institute**
**U.S. Geological Survey**
**And others!**

## Introduction to the XMDR Project: selected overview documents

_**[www.xmdr.org/](http://www.xmdr.org/)**_** **
_**[hpcrd.lbl.gov/SDM/XMDR/overview.html](http://hpcrd.lbl.gov/SDM/XMDR/overview.html)**_** (link from xmdr.org)**
_**[hpcrd.lbl.gov/SDM/XMDR/presentations/XMDR_Elevator](http://hpcrd.lbl.gov/SDM/XMDR/presentations/XMDR_Elevator_Summary_rough_draft.ppt)**__**[_ ](http://hpcrd.lbl.gov/SDM/XMDR/presentations/XMDR_Elevator_Summary_rough_draft.ppt)**__**[Summary_rough_draft.ppt](http://hpcrd.lbl.gov/SDM/XMDR/presentations/XMDR_Elevator_Summary_rough_draft.ppt)**_**  (overview) **
**xmdr.lbl.gov/xmdr/    (prototype system) **
_**[hpcrd.lbl.gov/SDM/XMDR/arch/index.html](http://hpcrd.lbl.gov/SDM/XMDR/arch/index.html)**_**   (architecture) **
_**[erdos.lbl.gov/mediawiki/index.php/Main_Page](http://erdos.lbl.gov/mediawiki/index.php/Main_Page)**_** (project wiki)**
_**[hpcrd.lbl.gov](http://hpcrd.lbl.gov/SDM/XMDR/presentations/)**__**[/SDM/XMDR/presentations/](http://hpcrd.lbl.gov/SDM/XMDR/presentations/)**_**   (esp recent ones) **
_**[hpcrd.lbl.gov/SDM/XMDR/presentations/XMDR-Prototype-Status-Oct-2005.ppt](http://hpcrd.lbl.gov/SDM/XMDR/presentations/XMDR-Prototype-Status-Oct-2005.ppt)**_**   (status report) **

- 51

## Other Topics? Extra Slides below here

**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**

- 47

## Review: why do we need metadata registries and how are they used?

**Design *****(design time)***
**Databases, XML Schemas & related applications**
**Data engineering & documentation**
**Concepts, Terminologies, Taxonomies, Ontologies**
**Data Integration & Administration *****(design + run time)***
**Combine information from diverse sources**
**Discover ****hidden relationships**** between data**
**Link concepts and data**
**Support interactive uses *****(run time)***
**Data entry forms, output explanation**
**Data navigation & warehousing, federated queries**
**Semantic Services & Computing *****(design + run time)***
**MDR metadata interchange & semantic grids**
**Ground concepts found in RDF statements & ontologies **

- 3

- 2005-07-27

**Notes:**
Cait says this is lot of info to put in simple pictures!

## Evolution of metadata technology

**From unstructured natural language text metadata to structured metadata**
**multi-faceted classification schemes**
**explicit modeling and characterization of relationships **
**graph based metamodels to aid comprehension and searching **
**formal ontologies (description logic et al.) **
**support for inference**
**AND from human consumption to machine processing for**
**detailed query/search**
**inference (e.g., transitive search, subsumption testing, etc.),**
**units conversion, **
**query processing in federated database systems **
**Two new key technologies **
**Graph databases (e.g., RDF) facilitate visualization & machine processing **
**Description logic (e.g., OWL) for more precise semantics & machine reasoning**
**which carry out graph searches according to stored formal rules **

- 7

## What are major limitations of current registry technology and standards?

**Natural language descriptions are too limited**
**imprecise and fuzzy, even for human users**
**computer software cannot process unambiguously**
**does not help identify what is known and not known**
**require too much intervention by expensive humans**
**Weak integration of concepts with data artifacts**
**relationships not well-specified**
**Lack of scalability **
**for multiple terminologies & myriad databases **
**Limited relationships with other standards**
**e.g., terminologies, ontologies, OMG, etc.**
**formal axioms to specify relationships, etc. **

- 5

## What are the primary functional goals of the XMDR Prototype system?

**Enhance capabilities**** to capture and retrieve **_***semantics***_**       of information artifacts (e.g., data elements and value domains) in metadata registries using terminologies, taxonomies, ontologies, etc. ...**
**Improve representation of relationships**** between data (e.g., objects, data elements & domains) and concept structures (ontologies, taxonomies, thesauri, terminologies, ...)**** **
**Register complex semantic metadata**** (concept structures, terminologies) in more formal, systematic ways (e.g., description logic) to facilitate machine processing for**
**creating and managing names, definitions, terms, etc.**
**linking together data elements, etc. across multiple systems**
**discovering relationships among data elements & terms**

- 8

## Advanced 11179 E3 Use Scenario

**A User is concerned about a specific type of cancer**
**Wants to discover any documents on the web (reliable and unreliable sources) about the disease, causes, treatment, victims, and researchers**
**Wants to link concepts and individuals found in text to metadata and data in databases (where metadata/data relate to the concepts/individuals)**
**Wants to find relevant information where the terms used for the concepts vary: by regions, disciplines, scientific nomenclature, vernacular usage, language, and names of individuals.**
**Want to find information that is related through generalization and specialization and other relationships.**
**Note: No assumption of federation or central control over data and text generation. However, well managed concept systems and metadata (e.g., data definitions) help.**

- 9

## Role of terminologies and ontologies in metadata registries

**Sources for concepts, concept definitions, object classes, properties, value meanings, external references**
**Terminologies as classification schemes (e.g., taxonomies)**
**Ontologies to specify semantic relationships**
**is-a, part-of, instance-of, ...**
**inheritance permits more compact definitions**
**semantic pathways for indexing**
**facilitates searching subclasses & inverses**
**Frameworks for integration of multiple schemas ...**
**Help connect metadata entities via shared terms**
**via automatic indexing of metadata words**
**via text values from specific metadata elements**

- 14

## 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.**

- 49

## XMDR helps manage concepts in conjuntion with data elements

**In general, we want to register any concept based graph structure comprised of nodes, relationships, and possibly axioms**
**possibly including millions of concepts, millions of terms, and millions of relationships (maybe billions).**
** **
**We want to link the concepts (e.g., research organization w, person x, disease y, location z) to data and text, even when we may only have a probabilistic notion of w, x, y, and z.**

- 50

## Definition

## RDF Example