The document summarizes integrating genome and proteome data from Francisella tularensis in RDF. It discusses integrating data from multiple sources, including genome annotations, proteomics experiments, and transcriptomics data. Semantic data integration across "omes" data silos is demonstrated using RDF and the open source Sesame framework. Reifying biological statements, such as identified peptides and abundances, allows more complex queries across the integrated data.

1. Semantic Web Applications and Tools for Life Sciences
November 2008
Genome and Proteome data integration in RDF
Nadia Anwar, Ela Hunt, Walter Kolch and Andy Pitt
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Data Discovery

2. Outline
• Data Integration in Bioinformatics.
• Semantic data integration
• Francisella
• Integrating genome annotations with experimental proteomics data in RDF
• Further work

3. Data Integration is not a solved problem

4. Information discovery is not Integrated
High TP Microarray Proteomics
Computational Computational
Sequencing experiments experiments
analysis analysis Systems Biology
Synthetic Networks/
Genomics Proteomics Pathways
Sequence Peptide Profiles Predictions
Gene Expression
ORF Prediction Transcript Profile Peptide Abundance
Genome Transcript Protein Identification
Comparisons Abundance Protein Interactions
PT-Modifications Metabolomics
LIMS LIMS LIMS LIMS
Genome Regulatory Networks Metabolic Pathways
Translational
Medicine

5. Semantic Data Integration across omes data silos
Data Genes Transcripts Peptides Metabolites Genotype Information
Data Discovery

6. Proof of concept
Francisella tularensis
ulceroglandular
tularaemia
respiratory oculoglandular
tularaemia tularaemia

7. Bioterrorism
• Francisella tularensis is a very successful intracellular pathogen that causes
severe disease (respiratory tulareamia is the most acute form of the disease)
• low infectious dose (10-50 bacterium compared to anthrax which requires
8,000-15,000 spores)
• weaponisation fears

8. Data sources
Genome

9. RDF
http://img.jgi.doe.gov/cgi-bin/pub/main.cgi?section=TaxonDetail&page=taxonDetail&taxon_oid=639633024#export
229976
+
(3)IMG_S:genomic_location_strand
229107
TPR
(3)IMG_S:genomic_location_end
(2)RDFS:comment (3)IMG_S:genomic_location_start
(1)RDF:type (4)IMG:gene_oid=639752258 (3)IMG_S:locus_tag FTN_0209
RDF:description

10. Data sources
Genome annotations
http://supfam.cs.bris.ac.uk/
RDF#type RDF:description
http://purl.uniprot.org/core/Protein_Family
SUPERFAMILY:cgi-bin/model.cgi?model=0040419
SUPERFAMILY:Assignment_Region 155-367
SUPERFAMILY:Score 5.1e-39
SUPERFAMILY:SCOP_ID SUPERFAMILY:cgi-bin/scop.cgi?sunid=52540
http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protein&id=118496616 SUPERFAMILY:SCOP_Fold
P-loop containing nucleoside triphosphate hydrolases
SUPERFAMILY:Family_ID
SUPERFAMILY:Evalue 81269
7.33e-06
SUPERFAMILY:Family_Description
Extended AAA-ATPase domain
SUPERFAMILY:Similar_Structure
1l8q A:77-289
Francisella SuperFamily Data

11. Data sources
Genome annotations - KEGG
http://www.genome.jp/dbget-bin/www_bget?pathway+ftn00010
http://img.jgi.doe.gov/schema#gene
http://www.genome.jp/dbget-bin/www_bget?ftn:FTN_0298
http://img.jgi.doe.gov/schema#gene_name rdfs:comment rdfs:seeAlso rdfs:seeAlso
glpX fructose http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EC:3.1.3.11] http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[SP:A0Q4N9_FRATN]
http://www.genome.jp/dbget-bin/www_bfind?F.tularensis_U112
Genome annotations - NCBI protein
http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protein&id=118496616
RDF:type RDF:idsymbol RDFS:#seeAlso http://purl.uniprot.org/Annotation/
RDF:description YP_897666.1 http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?[refseqp-SeqVersion:YP_897666.1]+-e chromosomal
http://www.ncbi.nlm.nih.gov/sites/gquery?term=Francisella+tularensis+novicida

12. Data sources
Genome annotations - GO
RDF:type RDF:description
mgla:GO_Annotation#ID http://amigo.geneontology.org/cgi-bin/amigo/go.cgi?view=details&query=0006749
mgla:GO_Annotation#Term glutathione
http://www.genome.jp/dbget-bin/www_bget?ftn:FTN_0277
mgla:GO_Annotation#Ontology biological_process
mgla:GO_Annotation#Level
7
http://www.compbio.dundee.ac.uk/Software/GOtcha/iscore
0.879989490261963
http://www.compbio.dundee.ac.uk/Software/GOtcha/cscore
5.7273821328517
Poson annotations - Cogs
http://www.ncbi.nlm.nih.gov/sites/entrez?db=cdd&cmd=search&term=COG0508
mgla:cogNumber
mgla:cogDomain AceF
https://tools.nwrce.org/cgi-bin/fnu112/poson.cgi?poson=PSN082435 mgla:cogDescription
mgla:cogCategory Pyruvate/2-oxoglutarate
dihydrolipoamide

13. Data sources - experiments
Transcriptomics

14. Data sources - experiments
Proteomics

15. Proteomics WT vs Mgla Mutant

16. Francisella tularensis novicida U112
WildType MglA mutant
Whole Cell Soluble Membrane Whole Cell Soluble Membrane
(3) (3) (3) (3) (3) (3)
(4) (4) (4) (4) (4) (4)
Sequest DRAGON Sequest DRAGON Sequest DRAGON
Sequest DRAGON Sequest DRAGON Sequest DRAGON
Identification Relative Abundance
P val <0.01
Two-sided t-test

18. RDF - excel conversion
Pval
Genome
Pval-1
analysis
Identified Peptide mgla:poson
abundance mgla:experiment PSN rdfs:seeAlso
PSNV2 rdfs:seeAlso
PSNV3 rdfs:seeAlso
FTN
rdfs:seeAlso
DDBID
Peptide
sequence
predicate GO SP EC
subject
object

19. Data integration
Reconciled Identifiers
(WashU-B) PSN.V1
(COGs) COGID (WashU-B) PSN.V2
(NCBI) PROTEINID (WashU-B) PSN.V3 (IMG) GENEID (WashU-P) DDB
(Fn ORF ID) FTN (Refseq) ACNo
(Gene Ontology) GOID (ENZYME) E.C.No (Uniprot) ACNo

20. Data Integration
Adding new experiments
Experiment Public
2
Experiment domain data
1
PSN rdfs:seeAlso
PSNV2 rdfs:seeAlso
PSNV3 rdfs:seeAlso
FTN
rdfs:seeAlso
Experiment
3 DDBID
Experiment
4
GO AC No. EC

21. Data integration
Sesame
NadiaAnwar:~ nadia$ openrdf-sesame-2.1/bin/console.sh
Connected to default data directory
Commands end with '.' at the end of a line
Type 'help.' for help
> connect http://127.0.0.1:8080/openrdf-sesame/.
Disconnecting from default data directory
Connected to http://127.0.0.1:8080/openrdf-sesame/
> show r.
+----------
|SYSTEM ("System configuration repository")
|ftnRepoNative ("Francisella Test")
|FrancisellaNative ("FrancisellaTestStore")
|FrancisellaReified ("Native store with RDF Schema inferencing")
|FrancisellaReified_index2 ("Native store with RDF Schema inferencing")
|Francisella ("Native store with RDF Schema inferencing")
+----------
> open FrancisellaReified_index2.
Opened repository 'FrancisellaReified_index2'

22. Sesame
Data load (ftnRepoNative) - native (spoc,posc)
Data File time (s) triples
francisella_locus_tag.nt 8.93 1,767
interact-prot.nt 88.51 20,682
interact-prot-peptides.nt 248,647
mgla search db.fasta.blastp4 ypURL.n3 9.7 1,719
NC_008601.nt 43.14 12,781
Ft_novicidaU112go.nt 359.14 2,548
francisella.rdf2.nt 43.41 10,434
francisellaSUPERFAMILY.nt 57.88 16,110
francisellaPROTEIN.fasta.nt 13.63 5,160
Soluble.nt 588.87 336,761
WholeCell.nt 469.02 112,625
Membranes.nt 1003.19 298,771

23. Data Integration
Mgla data (ftnRepoNative)
analysis
Identified Peptide mgla:poson
abundance PSN rdfs:seeAlso
PSNV2 rdfs:seeAlso
PSNV3 rdfs:seeAlso
FTN
rdfs:seeAlso
Experiment
DDBID
Peptide
sequence
SELECT psn, ftn, ec FROM
{ftn} rdfs:seeAlso {ec},
GO SP EC
{psn} rdfs:seeAlso {ftn},
{analysis} mgla:poson {psn}
WHERE ec LIKE “*[EC:*”
USING NAMESPACE
mgla =<http://www.francisella.org/novicida/schema/fnu112/experiments/mgla/>

24. Data Integration
Mgla data (ftnRepoNative)
analysis
rdf:about
Identified Peptide mgla:poson
mgla:sequence
mgla:experiment
abundance PSN rdfs:seeAlso
PSNV2 rdfs:seeAlso
PSNV3 rdfs:seeAlso
FTN
Peptide
sequence rdfs:seeAlso
DDBID
SELECT abundance, psn, ec, ftn FROM
{ftn} rdfs:seeAlso {ec},
{psn} rdfs:seeAlso {ftn}, GO SP EC
{analysis} mgla:poson {psn},
{analysis} mgla:experiment {abundance},
WHERE ec LIKE “*[EC:*”
USING NAMESPACE
mgla =<http://www.francisella.org/novicida/schema/fnu112/experiments/mgla/>

25. Really easy, But....
• Simple excel to RDF conversion does not enable all queries
• Not a simple conversion - Data needs to be “modelled”
analysis
rdf:about
Identified Peptide mgla:poson
mgla:sequence
mgla:experiment
abundance PSN
identifiedIn Experiment
Peptide Peptide Sequence
Replicate
{
sequence
hasAbundance
abundance

26. Data Integration
Reified statements
rdf:type
analysis Identified Peptide
Peptide
sequence
mgla:poson
PSN rdfs:seeAlso
PSNV2 rdfs:seeAlso
PSNV3 rdfs:seeAlso
FTN
Experiment
Replicate
rdfs:seeAlso
t
jec
rd f:ob DDBID
analysis data
rdf:type rdf:Statement
rd
rdf:s
f:
pr
ubje
ct GO SP EC
ed
analysis data
ica
mgla:PeptideAbundance
te
InExperimentReplicate
abundance

27. Sesame
Reified Data load - native-RDFS (spoc,posc,posc)
Data File time (s) time(mins) triples
FnU112Version3.nt 383.44 6.3 58,474
PosonMappings.nt 84.56 1.4 13,760
francisella_locus_tag.nt 16.73 0.3 1,767
ConstructHasGeneID.nt 23.00 0.4 1,719
interact-prot.nt 124.95 2.1 20,682
interact-prot-pepteides.nt 1127.97 18.7 248,647
interact-protSeeAlsoisbURL.nt 10.67 0.2 1,528
goAnnotation_URLID.nt 74.14 1.2 20,501
NC_008601.nt 75.84 1.3 12,781
Membranes_CogNumberURL.nt 8.60 0.1 2,548
Ft_novicida_U112_go.nt 561.38 9.3 2,548
francisella.rdf2.nt 46.19 0.8 10,602
francisellaSUPERFAMILY.nt 66.67 1.1 16,110
francisellaPROTEIN.fasta.nt 15.27 0.3 5,160
SolubleReifeid_3.rdf 1392.98 23.2 580,873
WholeCellReified_3.rdf 941.16 15.6 184,221
Membranes_3.rdf 1026.66 17.111 416,086
fnU112_draftRDFschemaV4.nt 215010.98 3,583.5 501

28. Queries
which posons have the most highly abundant peptides
select ftn , psn, exp, abundance from
{psn} rdfs:seeAlso {psnv2},
{psnv2} rdfs:seeAlso {psnv3},
{psnv3} rdfs:seeAlso {ftn},
{analysis} fnu112:poson {psn},
{analysis} rdf:type {rdf:Statement},
{analysis} rdf:object {exp},
{analysis} mgla:PeptideAbundance {abundance}
where xsd:integer(abundance) > 100000
and ftn LIKE "*FTN*"
using namespace
mgla=<http://www.francisella.org/novicida/schema/fnu112/experiments/mgla/>,
fnu112=<http://www.francisella.org/novicida/fnu112/schema/fnu112/experiments/
mgla#>

29. Queries
which posons have the most highly abundant peptides

30. Queries
which experiments have the most highly abundant peptides

31. Reified statements
• Reified mgla data are much bigger (4 more statements/abundance)
• The really interesting queries return Java out of memory error (-Xms-1024M -
Xmx 1536M)
identifiedIn Experiment
Peptide Sequence
Replicate
{
• Haven’t yet tested shortcut path expression
hasAbundance
{ {reifSubj} reifPred {reifObj} } pred {obj}
abundance
{ {seq} identifiedIn {ExpRep} } hasAbundance {abd}
<#WholeCell_Lvl7_02.12> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/1999/02/22-rdf-syntax-ns#Statement>.
<#WholeCell_Lvl7_02.12> <http://www.w3.org/1999/02/22-rdf-syntax-ns#subject> <http:/www.francisella.org/novicida/schema/fnu112/experiments/mgla/WholeCell_Lvl7_02.1>.
<#WholeCell_Lvl7_02.12> <http://www.w3.org/1999/02/22-rdf-syntax-ns#predicate> <http:/www.francisella.org/novicida/schema/fnu112/experiments/mgla/InExperimentReplicate>.
<#WholeCell_Lvl7_02.12> <http://www.w3.org/1999/02/22-rdf-syntax-ns#object> <http:/www.francisella.org/novicida/schema/fnu112/experiments/mgla/wildtype/01_wc_01>.
<#WholeCell_Lvl7_02.12> <http:/www.francisella.org/novicida/schema/fnu112/experiments/mgla/PeptideAbundance> "2594".

32. Comparison of integrated experimental data
Distinct and overlapping posons identified within each biological fraction (>20000)
171 146
185
mem sol
mem MINUS sol sol MINUS mem
select distinct psn from select distinct psn from
{x} fns:poson {psn}, {x} fns:poson {psn},
{x} fn:InExperimentReplicate {experiment}, {x} fn:InExperimentReplicate {experiment},
{analysis} rdf:subject {x}, {analysis} rdf:subject {x},
{analysis} rdf:object {exp}, INTERSECT {analysis} rdf:object {exp},
{analysis} fn:PeptideAbundance {abundance} {analysis} fn:PeptideAbundance {abundance}
select distinct psn from
where xsd:integer(abundance) > 20000 where xsd:integer(abundance) > 20000
{x} fns:poson {psn},
and experiment LIKE "*mem*" and experiment LIKE "*sol*"
{x} fn:InExperimentReplicate {experiment},
MINUS MINUS
{analysis} rdf:subject {x},
select distinct psn from select distinct psn from
{analysis} rdf:object {exp},
{x} fns:poson {psn}, {x} fns:poson {psn},
{analysis} fn:PeptideAbundance {abundance}
{x} fn:InExperimentReplicate {experiment}, {x} fn:InExperimentReplicate {experiment},
where xsd:integer(abundance) > 20000
{analysis} rdf:subject {x}, {analysis} rdf:subject {x},
and experiment LIKE "*sol*"
{analysis} rdf:object {exp}, {analysis} rdf:object {exp},
INTERSECT
{analysis} fn:PeptideAbundance {abundance} {analysis} fn:PeptideAbundance {abundance}
select distinct psn from
where xsd:integer(abundance) > 20000 where xsd:integer(abundance) > 20000
{x} fns:poson {psn},
and experiment LIKE "*sol*" and experiment LIKE "*mem*"
{x} fn:InExperimentReplicate {experiment},
using namespace using namespace
{analysis} rdf:subject {x},
{analysis} rdf:object {exp},
{analysis} fn:PeptideAbundance {abundance}
where xsd:integer(abundance) > 20000
and experiment LIKE "*mem*"
using namespace

33. Comparison of integrated experimental data
Distinct and overlapping posons identified within each biological fraction (<5000)
219 125
245
mem sol
mem MINUS sol sol MINUS mem
select distinct psn from select distinct psn from
{x} fns:poson {psn}, {x} fns:poson {psn},
{x} fn:InExperimentReplicate {experiment}, {x} fn:InExperimentReplicate {experiment},
{analysis} rdf:subject {x}, {analysis} rdf:subject {x},
{analysis} rdf:object {exp}, INTERSECT {analysis} rdf:object {exp},
{analysis} fn:PeptideAbundance {abundance} {analysis} fn:PeptideAbundance {abundance}
select distinct psn from
where xsd:integer(abundance) < 5000 where xsd:integer(abundance) < 5000
{x} fns:poson {psn},
and experiment LIKE "*mem*" and experiment LIKE "*sol*"
{x} fn:InExperimentReplicate {experiment},
MINUS MINUS
{analysis} rdf:subject {x},
select distinct psn from select distinct psn from
{analysis} rdf:object {exp},
{x} fns:poson {psn}, {x} fns:poson {psn},
{analysis} fn:PeptideAbundance {abundance}
{x} fn:InExperimentReplicate {experiment}, {x} fn:InExperimentReplicate {experiment},
where xsd:integer(abundance) < 5000
{analysis} rdf:subject {x}, {analysis} rdf:subject {x},
and experiment LIKE "*sol*"
{analysis} rdf:object {exp}, {analysis} rdf:object {exp},
INTERSECT
{analysis} fn:PeptideAbundance {abundance} {analysis} fn:PeptideAbundance {abundance}
select distinct psn from
where xsd:integer(abundance) < 5000 where xsd:integer(abundance) < 5000
{x} fns:poson {psn},
and experiment LIKE "*sol*" and experiment LIKE "*mem*"
{x} fn:InExperimentReplicate {experiment},
using namespace using namespace
{analysis} rdf:subject {x},
{analysis} rdf:object {exp},
{analysis} fn:PeptideAbundance {abundance}
where xsd:integer(abundance) < 5000
and experiment LIKE "*mem*"
using namespace

34. Further work
• Queries are slow in the native repository, database repositories are probably
faster.
• Adding transcriptomic experiment:
Wt Vs mglA mutant
GEO AC GSE5468
• RDF-S inferencing?

35. Acknowledgements
• Funding: BBSRC -Radical Solutions for Researching the Proteome
• University of Glasgow, Glasgow
• Prof. Walter Kolch
• Dr Andy Pitt
• University of Strathclyde, Glasgow
• Dr Ela Hunt (Scientific Advisor)
• University of Washington, Seattle
• Prof. Dave Goodlett (Scientific Advisor)
• Dr Mitch Brittnacher, Mathew Radey, Laurence Rohmer
• Dr Tina Guina (MglA experiment)

36. Abundance thresholds....
• SeRQL aggregate functions would be nice to have
• Queries to find low and high abundance values:
• WHERE abundance BETWEEN MEDIAN(abundance) AND
MAX(abundance)
• WHERE abundance BETWEEN MIN(abundance) and MEDIAN(abundance)