Adding Meaning To Your Data

Making your data more meaningful Using BioMOBY and my Grid Taverna services as examples Duncan Hull University of Manchester BioSapiens Network of Excellence 2007-12-04

Outline
Semantic Web redux
Semantic web stack,
There are lots of TLAs (three letter acronyms) in this talk, unavoidable
XML, URI, Namespaces, Unicode,
RDF, RDFS OWL
In this talk when I say “data” I usually mean Web Services…
Example: InterProScan
BioMOBY http://www.biomoby.org
myGrid Taverna http://www.mygrid.org.uk
myExperiment http://www.myexperiment.org
Conclusions
What did we learn?

The semantic web “knows what you mean” thanks to added meaning
According to Tim Berners-Lee, Ora Lassila and Jim Hendler http://scholar.google.com/scholar?q=semantic+web
… and Mark Butler from HP labs http://www.flickr.com/photos/dullhunk/303503677/
Vague, audacious, “visionary”, controversial and/or doomed (depending on who you ask)
in practice this means…

Semantic Web “stack”
A suite of technology and standards* for adding meaning to data
Taken from “Semantic Web Architecture: Stack or Two Towers?” by Ian Horrocks et al see http://dx.doi.org/10.1007/11552222_4 and http://www.flickr.com/photos/dullhunk/415645490/

… But first, InterProScan…
InterProScan: Protein domains identifier @ EBI http://view.ncbi.nlm.nih.gov/pubmed/15980438
http://www.ebi.ac.uk/Tools/webservices/rest/submit?tool=iprscan&sequence=uniprot:slpi_human&seqtype=P&email=homer@simpsons.com
That horrendously long URI submits a job to InterProScan with 4 parameters
?tool=iprscan “use the InterProScan tool”
&sequence=uniprot:slpi_human “…with the sequence secretory leukocyte proteinase inhibitor (SLPI) in UniProt format”
&seqtype=P “sequence type is protein (e.g. not DNA)”
&email:homer@simpsons.com “email results to Homer Simpson”
Returns a job identifier e.g. iprscan-20071203-18053660
http://www. ebi .ac. uk/cgi-bin/iprscan/iprscan ? tool=iprscan &jobid= iprscan-20071203-18053660

Back to the Stack

URI, Unicode, XML and Namespaces
Bottom of semantic web stack:
Namespaces http://www.w3.org/TR/xml-names/
eXtensible Markup Language (XML) http://www.w3.org/TR/xml
Uniform Resource Identifiers (URI) http://www.ietf.org/rfc/rfc3986
Unicode http://www.unicode.org/charts

URI: Uniform Resource IDENTIFIER
URIs include Uniform Resource Locators (URLs) most people are familiar with for locating things, usually just called them “links”…
E.g. http://www.biosapiens.info locator for the biosapiens website
E.g. http://view.ncbi.nlm.nih.gov/pubmed/16015280 locates a biosapiens publication
Not persistent, sometimes unstable and break e.g. “404 not found”
Not guaranteed to be unique
URIs include Uniform Resource Names (URNs) for naming things that are less familiar like ISBN, Digital Object Identifiers (DOI) and Life Science Identifiers (LSID) etc
E.g. urn:doi:10.1038/sj.ejhg.5201470 names a publication using DOI
E.g. urn:isbn:0387484361 names a book using ISBN
E.g. urn:lsid:ncbi.nlm.nih.gov.lsid.biopathways.org:genbank:bx247883 names a biological sequence using LSID
Unlike URLs, URNs are UNIQUE and PERSISTENT
URIs can be names , identifiers or locators (sometimes all three)
See URI Generic syntax http://www.ietf.org/rfc/rfc3986 and URN syntax http://www.ietf.org/rfc/rfc2141 from the Internet Engineering Task Force (IETF)

Unicode: Boring but important
Unicode provides a unique number for every character
no matter what the platform (Windows, Unix, iPhone, toaster etc)
no matter what the program (protein database, email client etc)
no matter what the language (English, Chinese, Swahili… you name it)
E.g. U+0041 is the number for “LATIN CAPITAL A”
E.g. U+0F03 is the number for “TIBETAN MARK GTER YIG MGO -UM GTER TSHEG MA”
E.g. U+221E Is the number for “INFINITY”
http://www. unicode . org/standard/WhatIsUnicode .html http://www. tbray .org/ongoing/When/200x/2003/04/06/Unicode

XML: eXtensible Markup Language, boring but incredibly useful
Data marked using tags as “trees”
<operation name="InterProScan" method="get">
<request>
<parameter name="sequence" type="xsd:string" required="true"/>
</request>
<response>
<representation mediaType="text/xml" element="yn:ResultSet">
<parameter name="totalResults"
type="xsd:nonNegativeInteger"
</response>
</operation>

Namespaces
“ XML namespaces provide a simple method for qualifying element and attribute names used in XML by associating them with namespaces identified by URI references.”
<?xml version="1.0" standalone="yes"?>
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xmlns:xsd= http ://www.w3.org/2001/XMLSchema …
What this means is that
<xsi:fred> and <xsd:fred>
Are different because they belong in different namespaces, “ xsi:fred ” is shorthand for http://www.w3.org/2001/XMLSchema-instance:fred Allows us to have lots of different things called “fred”

Describing Web Services
This (xml, uri, namespaces + xml) gives us enough to describe Web Services
There are two styles of services on the Web: “RESTful” and “RESTless”
“ RESTful” (usually no SOAP): described with (Web Application Description Language) WADL https://wadl.dev.java.net/
“ RESTless” (uses SOAP and WSDL): described with Web Services Description Language (WSDL) http://www.w3.org/TR/wsdl
Most services you’ll come across in bioinformatics are the latter… but that might change

WSDL, WuzzDuLL, MiserabuL…
WSDL http://www.ebi.ac.uk/Tools/webservices/wsdl/WSInterProScan.wsdl
Describes Inputs and Outputs, tells us how to interact with service
Registries of Web Services, like myGrid and BioMOBY use these WSDLs to build their index
But, its really difficult to find services based on information in their WSDL
Poor metadata e.g. input “ string ” name “ in0 ”, “ in1 ”, “ out1 ” etc
Often auto-generated by tools, not humans
No constraints on what can be said
Machine readable but not very human readable

RDF and OWL: Adding metadata and semantics
Web Ontology Language (OWL) http://www.w3.org/TR/owl-features/
Resource Description Framework (RDF) http://www.w3.org/TR/rdf-primer/ (M&S stands for model and syntax)
RDF Schema (RDFS) http://www.w3.org/TR/rdf-schema/

RDF and RDF schema
RDF is just triples of (subject, verb , object ) we can say things about services like
InterproScan isA service
InterProScan isA protein_domains_identifier
InterProScan hasInput protein_sequence
InterProScan hasOutput InterProScan_report
The idea is simple …
… but unfortunately the specifications are syntax are horrible to read and write
But see http://notabug.com/2002/rdfprimer/ by Aaron Swartz
RDF Schema gives us “templates” for RDF

BioMOBY.org
A registry of annotated Web Services:
BioMOBY has three ontologies
Namespace e.g. genbank
Object e.g. protein_sequence (inputs and outputs)
Services (tasks e.g. alignment )
And an API too, which lets users add terms to ontology when they register services
Everything in BioMOBY is annotated (unlike myGrid and myExperiment)
Ontologies and Services are available from:
http://biomoby.org/cgi-bin/serviceList
http://biomoby.org/RESOURCES/MOBY-S/Namespaces
http://biomoby.org/RESOURCES/MOBY-S/Objects
http://biomoby.org/RESOURCES/MOBY-S/Services

myGrid Taverna
myGrid has a registry of services
Many aren’t annotated
… but arbitrary services can be added, not just BioMOBY
Lovingly curated by Franck Tanoh and Katy Wolstencroft
Using a single ontology http://www.mygrid.org.uk/ontology
Accessible from Taverna workflow engine
myGrid makes a bit more use of OWL but not much

Web Ontology Language (OWL)
RDF and RDFS provide limited capabilities for reasoning
All men are mortal
Socrates is a man
--------------------------------------
Therefore Socrates is mortal
Do this using deductive reasoners like FaCT++, Pellet, KAON2 etc
Ulrike Sattlers list of reasoners
http://www.cs.man.ac.uk/~sattler/reasoners.html
http://flickr.com/photos/dullhunk/337473755/ socrates picture

What can a reasoner do?
Subsumption check knowledge is correct, e.g. all protein_sequences are biological_sequences
Equivalence check knowledge is minimally redundant e.g. SLPI and WAP4 are synonyms for “Secretory leukocyte protease inhibitor”
Consistency check that knowledge is meaningful, no contradictions are made SLP1 can’t be both a DNA_sequence and a protein_sequence because these are disjoint classes
Instantiation check if an individual is an instance of a class is myProtein and instance of SLPI ?
Used Protégé, you have used a reasoner

Semantic Web Services in a nutshell User driven Bit of an afterthought Lots of user generated metadata Metadata yes Kind of Yes Yes Yes! Community participation possibly? A bit No no no! Reasoning / semantics Maybe? no yes API? Taverna 2 / myExperiment myGrid BioMOBY

www.myExperiment.org
Getting large quantities or high-quality metadata about services is time-consuming and expensive…
Many new web applications rely on users to provide metadata for them
E.g. flickr, myspace, facebook, delicious etc
People annotate services by uploading collections of services, workflows
Can “tag” them

Conclusions
We really need standard metadata to describe and find services
Standards are boring but important
You’re unlikely to win a Nobel prize for creating or using one…
But science can’t work without them
Especially “data-driven” rather than “hypothesis-driven” Science
We’ve looked at semantic web standards for describing Web Services, using InterProScan as an example
And myGrid, BioMOBY and myExperiment too
But didn’t talk about DAS / BioDAS
Thanks for listening

Acknowledgements and References
Thanks to everyone I robbed stuff off :
Carole Goble, Homer Simpson, David De Roure, Tim Bray, Mark Butler, Stian Soiland, Katy Wolstencroft, Franck Tanoh, Rod Page, Mark Wilkinson, myGrid team, myExperiment team, Ian Horrocks, Ulrike Sattler, Tim Berners-Lee, Ora Lassila, Jim Hendler, Steve Pettifer, Douglas Kell, IETF, W3C etc
These slides are also available at http://www.slideshare.net/dullhunk/slideshows
See Also:
This talk mostly about semantics rather than web services: see also “Web of Science - REST or SOAP?” at http://www.slideshare.net/dullhunk/web-of-science-rest-or-soap/
BioMOBY http://view.ncbi.nlm.nih.gov/pubmed/12511062
myGrid Ontology http://view.ncbi.nlm.nih.gov/pubmed/18048194
Taverna workflow http://view.ncbi.nlm.nih.gov/pubmed/16845108
myExperiment: social networking for workflow-using e-scientists (Goble and DeRoure) http://portal.acm.org/citation.cfm?doid=1273360.1273361
Questions?

Adding Meaning To Your Data

by Duncan Hull on Dec 04, 2007

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