lsids and rdf kevin richards tdwg 2006. introduction kevin richards (landcare research nz)...

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:jane@example.org> . _: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