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/