1. LSIDs and RDF Kevin Richards TDWG 2006

2. Introduction Kevin Richards (Landcare Research NZ) –Landcare Informatics group –GUID Subgroup –LSID.NET code port Disclaimer / intended audience Overview of tutorial

3. Requirements Files on network –ftp://cissus.mobot.org/incoming/tdwg/Tutorial/ftp://cissus.mobot.org/incoming/tdwg/Tutorial/ –Username: garfile Password: garden2003 Internet connection Text editor (or xml editor)

4. 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

5. 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

6. 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 –. "August 16, 1999". "en"

7. 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 – John Smith

8. Basic RDF <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/"> en 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

9. rdf:resource Eg <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/"> en

10. RDF Types Define data types Improves control of input data ranges Eg birthDate of a person 1940-6-19 Eg example.com employee Jane Smith is of type Person (n3 notation) _:jane exterms:mailbox. _:jane rdf:type exterms:Person. _:jane exterms:name "Jane Smith". _:jane exterms:empID "23748"

11. RDF Example FOAF Go to FOAF-a-matic web site –http://www.ldodds.com/foaf/foaf-a-matichttp://www.ldodds.com/foaf/foaf-a-matic Create Profile, Generate RDF Copy RDF Go to W3C RDF Validator –http://www.w3.org/RDF/Validator/http://www.w3.org/RDF/Validator/ –Validate RDF – displays triples

12. 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

13. 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 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/"> en

14. Example Solution <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:spec="http://specimen.org/specimens/"> SP1 Fred Smith George St 2006- 10-18 http://www.w3.org/2001/XMLSchema#date

15. RDF Schema Similar to xml schema Define RDF classes, types and properties Namespace - http://www.w3.org/2000/01/rdf-schema#

16. 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/"> Taxon Name Name Complete

17. 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

18. RDF RDF Triple Stores –What are they –Problems size speed of lookup distribution/duplication

19. 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?

20. RDF Tools RDF Tools/Software –Protégé –Altova SemanticWorks –Oracle triple stores –W3c Validator

21. RDF References RDF Primer – http://www.w3.org/TR/rdf-primer/http://www.w3.org/TR/rdf-primer/ RDF Syntax - http://www.w3.org/TR/rdf-syntax- grammar/http://www.w3.org/TR/rdf-syntax- grammar/ RDF Schema - http://www.w3.org/TR/rdf- schema/http://www.w3.org/TR/rdf- schema/ Another Primer - http://notabug.com/2002/rdfprimer/ http://notabug.com/2002/rdfprimer/ w3c RDF Tutorial - http://www.w3schools.com/rdf/default.asp http://www.w3schools.com/rdf/default.asp Dublin Core RDF - http://dublincore.org/http://dublincore.org/

22. PART 2 - LSIDs

23. LSIDs Overview Requirements: –Files on network ftp://cissus.mobot.org/incoming/tdwg/Tutorial/ Username: garfile Password: garden2003 –Web server (IIS) –Text editor

24. LSIDs Background on GUIDs –What is a GUID? Globally Unique IDentifier Persistent Opaque & transparent Resolvable? Examples: UUID, DOI, Handle, LSID, PURL

25. LSIDs –What is an LSID? Life Science IDentifier Developed by OMG & W3C Implemented by the team at IBM Structure – urn:lsid:authority:namespace:object:revision Eg urn:lsid:indexfungorum.org:names:213649 Used for – data objects, databases, images, files etc? Versioning Whos using them

26. 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 http://wiki.gbif.org/guidwiki/wikka.php?wakka=GUID2Report&show_comments=1

27. 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

28. LSID Tools and Services IBM LSID Launchpad Firefox LSID Browser LSID Tester (Rod Page) Web based resolver – http://lsid.biopathways.org/resolver/ http://lsid.biopathways.org/resolver/ Example LSID servers: –Bio Pathways – http://lsid.biopathways.org/resolver/urn:lsid:gene.ucl.ac.uk.lsid.biopathw ays.org:hugo:MVP (doesn’t work with Launchpad) http://lsid.biopathways.org/resolver/urn:lsid:gene.ucl.ac.uk.lsid.biopathw ays.org:hugo:MVP –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

29. LSID Code Current Code Stacks –Open Source (sourceforge.net) –Java, C++, Perl (IBM) –Microsoft.NET (Myself)

30. An LSID is resolved using a three- part resolution 1 – Resolve LSID Authority 1 – Resolve LSID Authority 2 – Get Available Services 2 – Get Available Services Data Store Data Store Meta Data Store Meta Data Store 3 – Retrieve Data Client DNS + HTTP Query Authority WSDL Data via SOAP, HTTP, FTP, NFS, AFS, DFS

31. 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

32. Questions before hands on tutorial?

33. 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

34. LSID Authority Setup IIS LSID HTTP Request PHP scripts Default is to return wsdl of php authority location LSID Metadata Request Return metadata Load metadata from file

35. 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

36. 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?

37. 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

38. Step 4 Test authority Test authority –Browse to http://localhost/authority/http://localhost/authority/ Test metadata –Browse to http://localhost/authority/metadata.phphttp://localhost/authority/metadata.php –Browse to http://localhost/authority/metadata.php?lsid=urn:lsid:c ollection.org:specimens:1 http://localhost/authority/metadata.php?lsid=urn:lsid:c ollection.org:specimens:1 Test using LSID Launchpad –lsidres:urn:lsid:collection.org:specimens:1 –Cant read/display it as it is text, not rdf

39. 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

40. Linking to other data Add link for the person Eg –Change collectedBy property Collected By to the rdf schema –Add To the instance

41. Linking to other data See lsidres:urn:lsid:collection.org:specimens:6

42. 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

43. Java LSID Web Application LSID Server LSID Server Services Configuration File Startup Load services Service Registry LSID Request Lookup Service for LSID authority Create registry Response LSID Authority Classes Call appropriate authority class function HTTP Req HTTP Resp Internet

44. 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);

45. LSID References LSID Source Forge - http://lsid.sourceforge.net/http://lsid.sourceforge.net/ LSID.NET Source Forge - http://sourceforge.net/projects/lsid- dotnethttp://sourceforge.net/projects/lsid- dotnet LSID Tutorial - http://www- 128.ibm.com/developerworks/opensource/library/os-lsid/http://www- 128.ibm.com/developerworks/opensource/library/os-lsid/ LSID Specification - http://www.omg.org/cgi-bin/doc?dtc/04-05-01http://www.omg.org/cgi-bin/doc?dtc/04-05-01 LSID Tester - http://linnaeus.zoology.gla.ac.uk/~rpage/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=553http://www- 124.ibm.com/developerworks/downloads/detail.php?group_id=124 &what=rele&id=553 GUID Subgroup - http://www.tdwg.org/TDWG_GUID.htmhttp://www.tdwg.org/TDWG_GUID.htm GUID Subgroup Reports –http://wiki.gbif.org/guidwiki/wikka.php?wakka=GUID2Report&show_c omments=1http://wiki.gbif.org/guidwiki/wikka.php?wakka=GUID2Report&show_c omments=1 –http://wiki.tdwg.org/twiki/pub/TIP/TipDocuments/GUID1Report.pdfhttp://wiki.tdwg.org/twiki/pub/TIP/TipDocuments/GUID1Report.pdf Firefox LSID developer site - http://lsid.mozdev.org/http://lsid.mozdev.org/

46. Thanks to Ricardo Pereira Roger Hyam Rod Page Lee Belbin The team at Landcare Research: Jerry Cooper Nick Spencer Aaron Wilton Michael Cochrane