Service Composition for Biomedical Applications

doctoral programme in informatics engineering

october 1st, 2012

supervisor

José Luís Guimarães Oliveirauniversidade de aveiro

jury

Artur Manuel Soares da Silvauniversidade de aveiro

Víctor Maojo Garcíauniversidade politécnica de madrid

Rui Pedro Sanches de Castro Lopesescola superior de tecnologia e gestão

do instituto politécnico de bragança

Francisco José Moreira Coutouniversidade de lisboa

Carlos Manuel Azevedo Costauniversidade de aveiro

Pedro Lopes

[email protected]

FOR BIOMEDICAL APPLICATIONS

SERVICE COMPOSITION

mailto:[email protected]



bioinformatics & computational biology

software engineering

SERVICE COMPOSITION

DECREASED DISEASE RISK

ELEVATED DISEASE RISK

DATA EVOLUTION

0

250

500

750

1000

1250

1500

2004 2005 2006 2007 2008 2009 2010 2011 2012

548

719

858968

10781170

12301330 1380

162 171 139 110 110 95 58 96 92

New Total

NAR database list evolution, from 2004 to 2012

DATA EVOLUTION

bioinformatics requirements

computer science

developments

more data

more tools

innovation

more data

innovation

DATA EVOLUTION

new software and hardware

bioinformatics requirements

more tools

more data

innovation

more tools

DATA EVOLUTION

DATA EVOLUTION

more data

more tools

innovation

NEW STRATEGIES TO IMPROVE AND ADD VALUE TO SERVICE COMPOSITION SCENARIOS

more datamore tools

innovation

workflow-based strategies for service composition

resource integration approaches for service composition

enhancing service composition with the semantic web and rad


SCIENTIFIC WORKFLOWS

SCIENTIFIC WORKFLOWS

data outresult analysisknowledge exchange

data inintegration perspective

distributed composition control

INTEROPERABILITY CHALLENGE

scientific workflowsworkflow & service interoperabilityparallelization, security, integration

previous workdynamicflowtaverna is the de facto workbench for scientific workflows

data sharingknowledge exchange semanticscollaborative and reproducible research

activity executioncombine and evaluate multiple independent activities

deliver service & workflow execution in real-time web-based environment

deploy a scalable architecture to enable service composition between multiple data & services providers ?

WORKFLOW COMPOSITION ARCHITECTURE

5CLIENT APPLICATIONS

4APPLICATION ENGINE

3DATA MANAGEMENT

2WORKFLOW ENGINE

1WORKFLOWS

DataCombination

Engine

WEBSERVICE

WEBSERVICE

WEBSERVICE

WorkflowExecutionEngine

Taverna

Hibernate

API

interaction xsdxml schema for service compositionnormalize service input and outputenable autonomous data exchanges

workflow enginenew java-based taverna workflow wrapperenable distributed service orchestration

open knowledge provider hub

WORKFLOW COMPOSITION ARCHITECTURE


4APPLICATION ENGINE

3DATA MANAGEMENT

2WORKFLOW ENGINE

1WORKFLOWS

DataCombination

Engine

WEBSERVICE

WEBSERVICE

WEBSERVICE

WorkflowExecutionEngine

Taverna

Hibernate

API

HIGHLIGHTS

web-based workspacealways-available collaborative environment

custom on-demand data analysis

a new strategy for advanced service composition that enables collaborative & distributed research !

new interoperability standardcommunication language to enable automated data exchanges from multiple providers

ease the creation of distributed service composition workflows

distributed scientific workflowscomplex interactions between heterogeneous services

distributed signal substantiation tasks

workflow execution enginewrap taverna execution online

real-time activity processing

RESULTSEU-ADR WEB PLATFORMhttp://bioinformatics.ua.pt/euadr

http://bioinformatics.ua.pt/euadr


RESULTSEU-ADR WEB PLATFORMhttp://bioinformatics.ua.pt/euadr

automatic filtering and substantiation of drug safety signals A Bauher-Mehren, EM van Mulligen, P Avillach, MC Carrascosa, B Singh, R Garcia-Serna, Pedro Lopes, José Luís Oliveira, G Diallo, J Mestres, E Ahlberg Helgee, S Boyer, F Sanz, JA Kors, LI Furlong

plos computational biologymarch 2012

the eu-adr web platform: delivering advanced pharmacovigilance toolsJosé Luís Oliveira, Pedro Lopes, Tiago Nunes, David Campos, S Boyer, E Ahlberg, EM Van Mulligen, JA Kors, B Singh, LI Furlong, F Sanz, A Bauer-Mehren, MC Carrascosa, J Mestres, P Avillach, G Diallo, C Diaz, J Van der Lei

pharmacoepidemiology and drug safety [second revision]october 2012

a bioinformatics hub for pharmacovigilance knowledge providersPedro Lopes, David Campos, Tiago Nunes, José Luís Oliveira

acm transactions on management information systems [ongoing]november 2012



INTEGRATION CHALLENGE

previous workscientific workflows ideal for service-service interactionsservice composition for resource integration

design a service composition strategy to enable agile integration of enriched human variome knowledge ?

genetic dataset aggregationextract data from distributed lsdbs

genotype-to-phenotype integrationenrich human variome data with connections to multiple data types

content accreditationpromote correct authorship, ownership and attribution

UNDERSTAND CHANGES IN OUR GENETIC SEQUENCE

INTEGRATION STRATEGY

LOVD

GENE LIST

LSDB LIST

APPLICATION ENGINE

UMD IDB Other

ARABELLAFEED READER

API

external datamiscellaneous heterogeneous sources

from gene ontology to protein databases

distributed lsdbscustom variant readers and web crawling

multiple non-standardized formats

deliver knowledgeweb application

variome api

INTEGRATION ARCHITECTURE

API

CSV XML SQL REST


4APPLICATION ENGINE

3BUILD ENGINE

2INTEGRATION MIDDLEWARE

1CONFIGURATION

BUILD ENGINE

apirest api for external, enables service composition scenarios

extensible data modelcore (gene + variant) plus extensionslightweight link-based connections

advanced integration engineservice composition for intelligent lsdb data extractionvariation dataset enrichment

data gathering wrappersconfigurable resources

load data from csv, xml, sql and rest sources

flexible configurationsingle resource setup file

innovative service composition description schema

API

CSV XML SQL REST


4APPLICATION ENGINE

3BUILD ENGINE

2INTEGRATION MIDDLEWARE

1CONFIGURATION

BUILD ENGINE

INTEGRATION ARCHITECTURE

HIGHLIGHTS

innovative uigene mesh and liveviewcontent accreditation

new service composition methods allow understanding, exploring and connecting human variome knowledge !

variation integrationservice composition approach to gather genetics dataset from multiple external resources

extensible modelsimplified description and addition of new external service composition actors

interoperabilityunique service composition variome apiaccess to curated collection of genetic variants

RESULTSWAVE: WEB ANALYSIS OF THE VARIOMEhttp://bioinformatics.ua.pt/wave



RESULTSWAVE: WEB ANALYSIS OF THE VARIOMEhttp://bioinformatics.ua.pt/wave

a holistic approach for integrating genomic variation informationPedro Lopes and José Luís Oliveira

10th spanish symposium on bioinformaticsmalaga, spain, october 2010

an extensible platform for variome data integration Pedro Lopes and José Luís Oliveira

10th ieee international conference on information technology and applications in biomedicinecorfu, greece, november 2010

wave: web analysis of the variome Pedro Lopes, Raymond Dalgleish and José Luís Oliveira

human mutationmarch 2011



NEXT-GENERATION BIOMEDICAL APPLICATIONS

the semantic web paradigmthe perfect solution for life sciences natural complexity

previous worknew service composition strategies for interoperability using scientific workflowsnew service composition strategies for resource integration

life sciencescomplex mesh of data and servicesmodern demands keep pushing computer science forward

rapid application developmenteasily-configurable service composition implementation environment

build the next generation of service composition applications faster

enhanced rapid application developmentstraightforward service composition setup process

design a new semantic web framework to streamline the creation of next generation biomedical applications ?

advanced data integration enginerich service composition description, flexible integration from heterogeneous resources

state-of-the-art interoperabilityapis enable service composition for everything and everyone

semantic knowledge managementinvolve semantic web technologies at all service composition layers

knowledge federationenable distributed access to knowledge

empower ecosystemsdelivery network for custom cross-platform and cross-device applications

NEXT-GENERATION BIOMEDICAL APPLICATIONS

FRAMEWORK MODEL

API

DATA INTEGRATION CONNECTORS

dc:title rdfs:labelowl:imports

KNOWLEDGE BASE

CSV XML SQL SPARQL

REST JAVA LDATA SPARQL

foaf:name

SINGLE INSTANCE

interoperabilitydata out

integrationdata in

KNOWLEDGE FEDERATION LAYER

API


KNOWLEDGE BASE

CSV XML SQL SPARQL


API


KNOWLEDGE BASE

CSV XML SQL SPARQL


API


dc:title rdfs:labelowl:imports

KNOWLEDGE BASE

CSV XML SQL SPARQL


foaf:name

FEDERATION

FRAMEWORK MODEL

FRAMEWORK ARCHITECTURE

JavaRESTpubby

LinkedData

JosekiSPARQL

ABSTRACTION ENGINE


5API

4APPLICATION ENGINE

3KNOWLEDGE BASE

2INTEGRATION ENGINE

1EXTERNAL SOURCES

CSV SQLXML SPARQL

JavaRESTpubby

LinkedData

JosekiSPARQL

ABSTRACTION ENGINE


5API

4APPLICATION ENGINE

3KNOWLEDGE BASE

2INTEGRATION ENGINE

1EXTERNAL SOURCES

CSV SQLXML SPARQL

future-proof interoperabilityrest services

sparql endpoint + linkeddata interfaces available by default

java + javascript libraries

streamlined application engine“semantic web in a box”

straightforward backend deployment with tomcat

semantic knowledge managementmysql-based triplestorejena-supported methods

advanced integration enginesemantic web translationnew extract-transform-load strategy

flexible service composition configurationcomprehensive connectors & selectorsload data from csv, xml, sql and sparql sources

modern client-side developmentready for any ui framework

FRAMEWORK ARCHITECTURE

rapid application developmentquickly build a new service composition application ecosystem

HIGHLIGHTS

a framework to empower the creation of next-generation service composition-based semantic software !

semantic data integration platformflexible acquisition and translation of data from heterogeneous resources

semantic web and linkeddata interoperabilityfuture-proof interoperability with the most innovative application paradigmsemantic reasoning and inference

federationrest, sparql and linkeddata apis

one query, multiple knowledge bases

RESULTSCOEUShttp://bioinformatics.ua.pt/coeus



RESULTSCOEUShttp://bioinformatics.ua.pt/coeus

towards knowledge federation in biomedical applications Pedro Lopes and José Luís Oliveira

7th international conference on semantic systemsgraz, austria, october 2011

a semantic web application framework for health systems interoperabilityPedro Lopes and José Luís Oliveira

international workshop on managing interoperability and complexity in health systemsglasgow, scotland, november 2011

coeus: “semantic web in a box” for biomedical applicationsPedro Lopes and José Luís Oliveira

journal of biomedical semantics [second revision]october 2012

coeus: a semantic web application framework Pedro Lopes and José Luís Oliveira

4th international semantic web applications & tools for life sciences workshoplondon, united kingdom, december 2012







coeus evaluation

LEGACY DISEASECARD

LEGACY DISEASECARD

evaluationperfect benchmark for a new coeus instance

primitive engineeringstatic integration/navigation protocolconstrained data model

rare diseases research portalcollection of pointers to disease pages

used for academia and clinical research

evolutionimperative to update scientific dataset

new features for users and developers

CREATING A NEW COEUS INSTANCE

deliver knowledgeuse apis to create advanced user interfacesuse apis to access data

configure service compositiondefine resource descriptions for connectorsspecify data selectors

setup new application modelre-use existing ontologies

improve omim basic model

build triplestoreautonomous process

pull data from configured resources into semantic knowledge base

# locus entity:entity_Locus :isEntityOf :concept_Ensembl, :concept_EntrezGene, :concept_GeneCards, :concept_HGNC, :concept_MapView, :concept_UCSC; :isIncludedIn :seed_Diseasecard4; dc:description "Collects Locus entity knowledge."^^xsd:string; dc:title "Locus"^^xsd:string; a :Entity, owl:NamedIndividual; rdfs:label "entity_Locus"^^xsd:string;

# hgnc concept:concept_HGNC :hasEntity :entity_Locus; :hasResource :resource_HGNC; :isExtendedBy :resource_ClinicalTrials, :resource_ENZYME, :resource_Ensembl, :resource_HGNC, :resource_KEGG, :resource_MedlinePlus, :resource_UniProt; dc:description "Concept relating HGNC data."^^xsd:string; dc:title "HGNC"^^xsd:string; a :Concept, owl:NamedIndividual; rdfs:label "concept_hgnc"^^xsd:string;








# hgnc connector:resource_HGNC :endpoint "http://www.genenames.org/cgi-bin/hgnc_downloads.cgi?title=HGNC+output+data&col=gd_hgnc_id&col=gd_app_sym&col=gd_app_name&col=gd_pub_chrom_map&status=Approved&status_opt=1&level=pri&where=gd_app_sym+like+%27#replace#%27&order_by=gd_app_sym_sort&limit=&format=text&submit=submit&.cgifields=&.cgifields=level&.cgifields=chr&.cgifields=status&.cgifields=hgnc_dbtag"^^xsd:string; :extends :concept_HGNC; :extension "rdfs:label"^^xsd:string; :hasKey :csv_HGNC_id; :isResourceOf :concept_HGNC; :loadsFrom :csv_HGNC_id, :csv_HGNC_name; :method "complete"^^xsd:string; :order 3 ; dc:description "Resource connecting gene HGNC information."^^xsd:string; dc:publisher "csv"^^xsd:string; dc:title "HGNC"^^xsd:string; a :Resource, owl:NamedIndividual; rdfs:label "resource_hgnc"^^xsd:string;

# hgnc identifier selector:csv_HGNC_id :isKeyOf :resource_HGNC; :loadsFor :resource_HGNC; :property "dc:source|dc:identifier"^^xsd:string; :query "0"^^xsd:string; dc:description "Information for HGNC CSV resource loading: loads HGNC id."^^xsd:string; dc:title "HGNC_id"^^xsd:string; a :CSV, owl:NamedIndividual; rdfs:label "csv_hgnc_id"^^xsd:string;

# hgnc name selector :csv_HGNC_name :loadsFor :resource_HGNC; :property "rdfs:comment|dc:description"^^xsd:string; :query "2"^^xsd:string; dc:description "Information for HGNC CSV resource loading: loads HGNC name."^^xsd:string; dc:title "HGNC_name"^^xsd:string; a :CSV, owl:NamedIndividual; rdfs:label "csv_hgnc_name"^^xsd:string;

http://pedrolopes.net

















0

GENE

HGNCOMIM

DISEASE

GENE

EntrezUniProt

PROTEIN

HPO

ONTOLOGY

DRUG

DrugBank

PDB

InterPro

PROTEIN

MeSH

ONTOLOGY

GENE

EnsemblProsite

PROTEIN

UMLS

ONTOLOGY

PharmGKB

DRUG

Pubmed

LITERATURE

3

2

1








# javapt.ua.bioinformatics.API.getTriple(“coeus:hgnc_BRCA2”, ”p”, ”o”, “xml”);

# resthttp://bioinformatics.ua.pt/coeus/api/triple/coeus:hgnc_BRCA2/p/o/csv

# sparql federationPREFIX dc: <http://purl.org/dc/elements/1.1/>PREFIX diseasome: <http://www4.wiwiss.fu-berlin.de/diseasome/resource/diseasome/>PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>PREFIX coeus: <http://bioinformatics.ua.pt/coeus/>SELECT ?pdb ?meshWHERE {{ SERVICE <http://www4.wiwiss.fu-berlin.de/diseasome/sparql> { <http://www4.wiwiss.fu-berlin.de/diseasome/resource/genes/BRCA2> rdfs:label ?label } }{ SERVICE <http://bioinformatics.ua.pt/coeus/sparql> { _:gene dc:title ?label . _:gene coeus:isAssociatedTo ?uniprot } }{ SERVICE <http://bioinformatics.ua.pt/coeus/sparql> { ?uniprot coeus:isAssociatedTo ?pdb . ?pdb coeus:hasConcept coeus:concept_PDB } }{ SERVICE <http://bioinformatics.ua.pt/coeus/sparql> { ?uniprot coeus:isAssociatedTo ?mesh . ?mesh coeus:hasConcept coeus:concept_MeSH } }}

http://bioinformatics.ua.pt/coeus/api/triple/coeus:hgnc_BRCA2/p/o/csv

http://bioinformatics.ua.pt/coeus/api/triple/coeus:hgnc_BRCA2/p/o/csv

http://purl.org/dc/elements/1.1/

http://purl.org/dc/elements/1.1/

http://www4.wiwiss.fu-berlin.de/diseasome/resource/diseasome/

http://www4.wiwiss.fu-berlin.de/diseasome/resource/diseasome/

http://www.w3.org/2000/01/rdf-schema#

http://www.w3.org/2000/01/rdf-schema#

http://bioinformatics.ua.pt/coeus/

http://bioinformatics.ua.pt/coeus/

http://www4.wiwiss.fu-berlin.de/diseasome/sparql

http://www4.wiwiss.fu-berlin.de/diseasome/sparql

http://www4.wiwiss.fu-berlin.de/diseasome/resource/genes/BRCA2

http://www4.wiwiss.fu-berlin.de/diseasome/resource/genes/BRCA2

http://bioinformatics.ua.pt/coeus/sparql






RESULTSTHE NEW DISEASECARDhttp://bioinformatics.ua.pt/dc4



RESULTSTHE NEW DISEASECARDhttp://bioinformatics.ua.pt/dc4

improved availabilityavailable to researchers through web applicationavailable to developers through default apis

easy setupsimplified resource integrationstraightforward client-side application creation

efficient developmentrapid application development at its best

reduced implementation effort compared to similar systems



service compositionpioneering framework for enhanced semantic web-based service composition

next-generation strategies for integration and interoperability

interoperabilitynew strategies for workflow-based service composition

advanced methods to deliver knowledge

integrationinnovative integrative approach to describe service composition

flexible integration engine to compose heterogeneous resources

1

2

3


CONCLUSIONS

future perspectives


FUTURE PERSPECTIVES

beyond service compositionsoftware-as-a-service use is increasing

streamlined and lightweight interactions are everywhere

linkeddata and the semantic websemantic web as the foundation for new software engineering strategies

linkeddata is a growing knowledge network

modern software platformsgrowing relevance of efficient content deliveryone knowledge base, multiple cross-platform & cross-device clients

worldwide knowledge networksmore sophisticated knowledge expression technologies

richer, meaningful data are more connected

business valueresearch and enterprise are intertwinedcoeus use goes beyond science

THANK YOU

doctoral programme in informatics engineering

october 1st, 2012

supervisor

José Luís Guimarães Oliveirauniversidade de aveiro

jury

Artur Manuel Soares da Silvauniversidade de aveiro

Víctor Maojo Garcíauniversidade politécnica de madrid

Rui Pedro Sanches de Castro Lopesescola superior de tecnologia e gestão

do instituto politécnico de bragança

Francisco José Moreira Coutouniversidade de lisboa

Carlos Manuel Azevedo Costauniversidade de aveiro

Pedro Lopes

[email protected]


SERVICE COMPOSITION



Service Composition for Biomedical Applications

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