lsids and rdf kevin richards tdwg 2006. introduction kevin richards (landcare research nz)...
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LSIDs and RDFKevin Richards
TDWG 2006
Introduction
• Kevin Richards (Landcare Research NZ)– Landcare Informatics group– GUID Subgroup– LSID .NET code port
• Disclaimer / intended audience
• Overview of tutorial
Requirements
• Files on network– ftp://cissus.mobot.org/incoming/tdwg/Tutorial/– Username: garfile Password: garden2003
• Internet connection
• Text editor (or xml editor)
RDF
• What is RDF– Resource Description Framework– w3C– Describes resources on the web– Putting data on the web– Intended for machine processing– Has a defined xml syntax– Semantic relationships of data objects– Aimed at distributed data with varying types
RDF Triples
• English language equivalent – “http://www.example.org/index.html has a creator whose value is John Smith”
• Uses GUIDs (Web based GUIDs – URIs, etc)– Eg GUID1 has creator GUID2
• Subject : Predicate : Object format– Subject (the object being described)
• GUID or blank (infinite set)
– Predicate (the relationship/property type)• GUID to a property type, eg the ID of the property “creator”
– Object (the value assigned to the subject object)• GUID of another object, blank, or literal
• Build up map/graph of object relationships
RDF Graphs• The basis of RDF• Useful analysis and equivalence calculation tool• Eg
– example.org/index.html page created by staffid 85740– example.org/index.html page language is english (en)
• Equivalent Triples– <http://www.example.org/index.html> <http://purl.org/dc/elements/1.1/creator>
<http://www.example.org/staffid/85740> .
<http://www.example.org/index.html> <http://www.example.org/terms/creation-date> "August 16, 1999" . <http://www.example.org/index.html> <http://purl.org/dc/elements/1.1/language> "en"
RDF formats
• Statement - “http://www.example.org/index.html has a creator whose value is John Smith”
• N3 notation – :http://www.example.org/index.html dc:creator “John Smith”.
• Xml – <rdf:Description rdf:about="http://www.example.org/index.html">
<dc:creator>John Smith</dc:creator>
</rdf:Description>
Basic RDF<?xml version="1.0"?><rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/">
<rdf:Description rdf:about="http://www.example.org/index.html"><dc:language>en</dc:language>
</rdf:Description>
</rdf:RDF>
• rdf:Description – basic description xml node• Every xml node must be namespaced and the namespace must be
resolvable• DublinCore – handy set of basic descriptive elements, such as title,
creator, language, etc
rdf:resourceEg
<?xml version="1.0"?><rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/">
<rdf:Description rdf:about="http://www.example.org/index.html"><dc:language>en</dc:language><dc:creator rdf:resource="http://www.ldodds.com/foaf/foaf-
a-matic/JohnSmith" /></rdf:Description>
</rdf:RDF>
RDF Types
• Define data types• Improves control of input data ranges• Eg birthDate of a person
<person:birthDate rdf:dataType= "http://www.w3.org/2001/XMLSchema#date“>1940-6-19</person:birthDate>
• Eg example.com employee Jane Smith is of type Person(n3 notation)
_:jane exterms:mailbox <mailto:[email protected]> . _:jane rdf:type exterms:Person . _:jane exterms:name "Jane Smith" . _:jane exterms:empID "23748"
RDF Example FOAF
• Go to FOAF-a-matic web site – http://www.ldodds.com/foaf/foaf-a-matic
• Create Profile, Generate RDF
• Copy RDF
• Go to W3C RDF Validator– http://www.w3.org/RDF/Validator/– Validate RDF – displays triples
Inference
FOAF Person A
FOAF Person B
Rdf triple – A knows B
FOAF Person C
Rdf triple – B knows C
Inferred triple - A is one degree separated from C
RDF Exercise 1• Create some RDF instance xml for a specimen
– Make up an namespace for the elements– Make up elements for:
• Specimen Catalog Number (eg SP1)• Specimen Collected By • Specimen Locality
– Validate using RDF validator on the web
• Eg RDF<?xml version="1.0"?><rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/">
<rdf:Description rdf:about="http://www.example.org/index.html"><dc:language>en</dc:language>
</rdf:Description>
</rdf:RDF>
Example Solution<?xml version="1.0"?><rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:spec="http://specimen.org/specimens/">
<rdf:Description rdf:about=“SP1"><spec:catalogNumber>SP1</spec:catalogNumber><spec:collectedBy>Fred Smith</spec:collectedBy><spec:locality>George St</spec:locality>
<spec:collectedDate rdf:dataType=“http://www.w3.org/2001/XMLSchema#date”>2006-10-18</spec:collectedDate>
</rdf:Description>
</rdf:RDF>
RDF Schema
• Similar to xml schema
• Define RDF classes, types and properties
• Namespace - http://www.w3.org/2000/01/rdf-schema#
RDF Schema• Example Schema – TCS-RDF<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:dcterms="http://purl.org/dc/terms/"xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:tn="http://tdwg.org/2006/03/12/TaxonNames/">
<rdfs:Class rdf:about="http://tdwg.org/2006/03/12/TaxonNames/TaxonName"><rdfs:label xml:lang="en">Taxon Name</rdfs:label><rdfs:subClassOf rdf:resource="http://www.w3.org/2000/01/rdf-
schema#Resource"/></rdfs:Class>
<rdf:Property rdf:about="http://tdwg.org/2006/03/12/TaxonNames/nameComplete"><rdfs:label xml:lang="en">Name Complete</rdfs:label><rdfs:domain
rdf:resource="http://tdwg.org/2006/03/12/TaxonNames/TaxonName"/><rdfs:range rdf:resource="http://www.w3.org/2000/01/rdf-
schema#Literal"/></rdf:Property>
</rdf:RDF>
RDF Exercise 2
• Collection RDF Schema– Write an RDF schema to describe our
collection.org example LSIDs– Write an instance of this schema using
rdf:Description tag or typed tag– Validate using RDF validator on the web
RDF
• RDF Triple Stores– What are they– Problems
• size• speed of lookup• distribution/duplication
Ontologies
• Defined using RDFS or OWL (Web Ontology Language) & others
• Dublin Core – eg http://purl.org/dc/elements/1.1/creator – Eg http://www.example.org/index.html has a creator whose
value is John Smith = • Subject = http://www.example.org/index.html • Predicate = http://purl.org/dc/elements/1.1/creator • Object = http://www.example.org/staffid/85740 (John’s Id)
• FOAF (Friend Of A Friend)• TDWG ontologies?
RDF Tools
• RDF Tools/Software– Protégé– Altova SemanticWorks– Oracle triple stores– W3c Validator
RDF References
• RDF Primer – http://www.w3.org/TR/rdf-primer/• RDF Syntax -
http://www.w3.org/TR/rdf-syntax-grammar/• RDF Schema -
http://www.w3.org/TR/rdf-schema/• Another Primer -
http://notabug.com/2002/rdfprimer/• w3c RDF Tutorial -
http://www.w3schools.com/rdf/default.asp• Dublin Core RDF - http://dublincore.org/
PART 2 - LSIDs
LSIDs
• Overview
• Requirements:– Files on network
• ftp://cissus.mobot.org/incoming/tdwg/Tutorial/• Username: garfile Password: garden2003
– Web server (IIS)– Text editor
LSIDs
• Background on GUIDs– What is a GUID?
• Globally Unique IDentifier• Persistent• Opaque & transparent• Resolvable?• Examples: UUID, DOI, Handle, LSID, PURL
LSIDs
– What is an LSID?• Life Science IDentifier• Developed by OMG & W3C• Implemented by the team at IBM• Structure –
urn:lsid:authority:namespace:object:revisionEg urn:lsid:indexfungorum.org:names:213649
• Used for – data objects, databases, images, files etc?
• Versioning• Whos using them
GUID subgroup
• Subgroup decisions:– To use LSIDs for identifying biodiversity data, but not
exclude use of other GUIDs– Reuse GUIDs where they already exist, eg some
DOIs for literature (assuming no commercial restrictions)
– Use RDF for metadata of objects identified by LSIDs– Implement as a minimum the HTTP GET metadata
service for each LSID server/resolver– See GUID Report -
http://wiki.gbif.org/guidwiki/wikka.php?wakka=GUID2Report&show_comments=1
Pros and Cons of LSIDs Tied to physical addresses Inspection required to determine
identical contents Brittle (broken links)
URL
LSID Same Id = same content Location independent Enables transparent caching Formalized, rich metadata
Requires specialised software to resolve an LSID (not built in to most software)
Cons
LSID Tools and Services
• IBM LSID Launchpad• Firefox LSID Browser• LSID Tester (Rod Page)• Web based resolver – http://lsid.biopathways.org/resolver/
• Example LSID servers:– Bio Pathways –
http://lsid.biopathways.org/resolver/urn:lsid:gene.ucl.ac.uk.lsid.biopathways.org:hugo:MVP (doesn’t work with Launchpad)
– Index Fungorum - urn:lsid:indexfungorum.org:names:213649 – IPNI – urn:lsid:ipni.org:names:30000959-2:1.1.2.1– uBio - urn:lsid:ubio.org:namebank:11815
LSID Code
• Current Code Stacks– Open Source (sourceforge.net)– Java, C++, Perl (IBM)– Microsoft .NET (Myself)
An LSID is resolved using a three-part resolution
1 – Resolve LSID
Authority
1 – Resolve LSID
Authority
2 – Get AvailableServices
2 – Get AvailableServices
DataStore
DataStore
Meta DataStore
Meta DataStore
3 – RetrieveData
ClientClient
DNS + HTTP
Query Authority
WSDL
Data via
SOAP, HTTP,FTP, NFS, AFS,DFS
DNS Lookup
• Example• Go to command prompt• > nslookup• > set type=srv• > _lsid._tcp.indexfungorum.org • Results in :
lsid.indexfungorum.org (194.203.77.68)-> used as authority location for resolving
indexfungorum.org LSIDs
Questions before hands on tutorial?
Really Simple LSID
• A basic LSID setup– LSID server with only one service for returning
metadata for LSIDs using HTTP GET– IIS + PHP
• Specimen collection example– urn:lsid:collection.org:specimens:[id]– Specimen text files to load metadata from– No data
LSID Authority Setup
IIS
LSID HTTP Request
PHPscripts
Default is to return wsdl of php authority location
LSID Metadata Request
Return metadata
Load metadata from file
Step 1 IIS authority
• Add ‘authority’ folder to c:\inetpub\wwwroot
• Copy authority files to authority directory
• Start IIS:– Configure authority as a web application
• Explain files
Step 2 PHP
• Copy PHP files to c:\php
• Configure IIS to run PHP files (add php5isapi.dll to the mappings for authority)
• Add index.php to default docs
• Set security permissions on php files/dir?
Step 3 Configure LSID Launchpad
• Add local host authority for collection.org
• Add application for text editor• Test, eg
lsidres:urn:lsid:indexfungorum.org:names:213649
Step 4 Test authority
• Test authority– Browse to http://localhost/authority/
• Test metadata– Browse to http://localhost/authority/metadata.php– Browse to http://localhost/authority/metadata.php?
lsid=urn:lsid:collection.org:specimens:1
• Test using LSID Launchpad– lsidres:urn:lsid:collection.org:specimens:1– Cant read/display it as it is text, not rdf
Use RDF for metadata
• Use the RDF collection schema (created in the RDF section) in our LSID authority
• Build an RDF instance for the schema
• Test the LSID metadata using LSID Launchpad– Eg lsidres:urn:lsid:collection.org:specimens:4
Linking to other data
• Add link for the person• Eg
– Change collectedBy property<rdf:Property rdf:about="&coll;collectedBy">
<rdfs:label xml:lang="en">Collected By</rdfs:label><rdfs:isDefinedBy rdf:resource="&coll;"/><rdfs:domain rdf:resource="&coll;Specimen"/><rdfs:range
rdf:resource="http://collection.org/specimens/Person"/></rdf:Property>
to the rdf schema– Add
<coll:collectedBy rdf:resource="urn:lsid:collection.org:people:1"/>
To the instance
Linking to other data
• See lsidres:urn:lsid:collection.org:specimens:6
• Highlights of the LSID Java Stack– Simple APIs, synchronous and asynchronous– Support for HTTP, SOAP and FTP– WSDL, Data and Metadata Cache– Highly configurable
• Cache location/policy, host-mappings, metadata handling
– Leverages many Java technologies• Xerces, Xalan, Axis, wsdl4J, and Castor
Java LSID Code
Java LSID Web Application
LSID Server
LSID Server
Services Configuration FileServices Configuration FileStartup
Load services
Service RegistryService Registry
LSID Request Lookup Service for LSID authority
Create registry
Response
LSID Authority ClassesLSID Authority ClassesCall appropriate authority class function
HTTP Req
HTTP Resp
Internet
LSID Resolution code (Client)• Given an LSID in String format, we can easily open an InputStream
to the data or metadata. (listing1)
LSID lsid = new LSID(“urn:lsid…”);LSIDResolver resolver = new LSIDResolver(lsid);InputStream data = resolver.getData();
• If we care about which protocol or location to use, we can choose from those available in the WSDL returned from getAvailableServices.
LSIDWSDLWrapper wsdl = resolver.getWSDLWrapper();LSIDDataPort port = wsdl.getPortForProtocol(WSDLConstants.SOAP);InputStream in = resolver.getData(port);
LSID References• LSID Source Forge - http://lsid.sourceforge.net/• LSID .NET Source Forge -
http://sourceforge.net/projects/lsid-dotnet• LSID Tutorial -
http://www-128.ibm.com/developerworks/opensource/library/os-lsid/
• LSID Specification - http://www.omg.org/cgi-bin/doc?dtc/04-05-01• LSID Tester - http://linnaeus.zoology.gla.ac.uk/~rpage/lsid/tester/• LSID Launchpad -
http://www-124.ibm.com/developerworks/downloads/detail.php?group_id=124&what=rele&id=553
• GUID Subgroup - http://www.tdwg.org/TDWG_GUID.htm• GUID Subgroup Reports
– http://wiki.gbif.org/guidwiki/wikka.php?wakka=GUID2Report&show_comments=1
– http://wiki.tdwg.org/twiki/pub/TIP/TipDocuments/GUID1Report.pdf
• Firefox LSID developer site - http://lsid.mozdev.org/
Thanks to• Ricardo Pereira • Roger Hyam • Rod Page• Lee Belbin• The team at Landcare Research:
• Jerry Cooper• Nick Spencer• Aaron Wilton• Michael Cochrane