NETTAB 2005, Naples

Retrieving factual data and documents using IMGT-ML in the

IMGT information system ®

Denys Chaume, CNRS/IGH

NETTAB 2005, Naples

Table of Contents

• The IMGT information system®• IMGT-ONTOLOGY• IMGT-ML• IMGT-ML a query language• Use examples :

– Database queries (LIGM-DB)– Tool queries (Junction Analysis)– Document queries (SEFID)

• Conclusion

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Part 1 summary

• IMGT, the international ImMunoGeneTics information system®

• Relations between subsystems • IMGT-ONTOLOGY• IMGT-ML Schemas• IMGT-ML : seqData• IMGT-ML Architecture

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IMGT, the international ImMunoGeneTics information system®

• A high quality integrated knowledge resource specialized in the immunoglobulins, T cell receptors, major histocompatibilty complex and related proteins of the immune system of human and other vertebrates.

• Created in 1989 by M.-P. Lefranc (CNRS/UM II),• On the WEB since 1995, • 90.000 sequences, 110 species• The international reference for immunogenetics

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IMGT information system®IMGT/LIGM-DB

IMGT/GENE-DB

IMGT/PRIMER-DB

IMGT/PROTEIN-DB

IMGT/3Dstructure-DB

6 databases 10 processing tools

IMGT/MHC-DB

IMGT Scientific ChartIMGT RepertoireIMGT IndexIMGT Bloc-notes

~8000 HTML documents

IMGT/V-QUEST

IMGT/JunctionAnalysis

IMGT/GeneView

IMGT/GeneSearch

IMGT/LocusView

IMGT/Allele-Align

IMGT/PhyloGene

IMGT/StructuralQuery

IMGT/GeneFrequency

IMGT/GeneInfo

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Relations between subsystems

IMGT/LIGM-DB

IMGT/GENE-DB

IMGT/PRIMER-DB

IMGT/PROTEIN-DB

IMGT/3Dstructure-DB

IMGT/V-QUEST IMGT/JunctionAnalysis

IMGT/GeneView

IMGT/GeneSearchIMGT/LocusView

IMGT/Allele-Align

IMGT/PhyloGene IMGT/StructuralQuery

IMGT/GeneFrequency

prim

er/se

quen

ces

gene

s/re

fere

nce

sequ

ence

s

sequence

s/mutatio

ns

mutation/genes

genes/phylogeny

genes/3D structures

3D st

ruct

ures

que

ry

prot

ein/

3D st

ruct

ures

nucleotidic/protein sequences

gene localizatio

n

gene localization

sequences/specificity

gene and allele identification

analyse of junction

gene

and

alle

le id

entif

icat

ion

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IMGT-ONTOLOGY

Identification

Description

Classification

Obtention

Numerotation

Characteristics

Annotation

Genome

Origin, methodology

IMGT unique numbering

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domain

IMGT-ML Schemas

IMGTOntology

Identification

imgt

Numerotation

Obtention

Classification

IMGTData

knowledge

seqDataDescription

(biological & structural)

External schemas

IMGTQuery

querySeqData

queryKnowledge

IMGTData defines elements using types

defined by IMGTOntology schemas

IMGTOntology defines simpleTypes and

complexTypes

responseTemplate

IMGTQuery defines complementary elements

to formulate queries

Namespace : http://www.imgt.org/IMGT-ML

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IMGT-ML : seqData

Numerotation

catalogue simpleCatalogEntry

classification

identification

annotation

sequence

seqData

•

?

?

?

•

opt@moddate

req@credate

req@id

opt@name

req@numacc

req@id

references extRef

opt@refid

req@reltype

opt@secid

req@reftype

req@dbid? +

req@seqid

opt@complement

req@seqlen

Literature

Numerotationkeywords

?

?

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IMGT-ML Architecture

XML Schema(simpleTypes &complexTypes)

IMGT-ONTOLOGY

Documentation

Biologicalexpertize

Data Modeling

Controlled vocabulary

(nomenclature)

Distributionformat

Data consistency

Web serviceinteractions

XSLT

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Part 2 summary

• IMGT-ML : a database query language– Why it works

• IMGTQuery package• Examples

– IMGT/LIGM-DB query– Junction Analysis tool

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A very simple database

>1970printable charactersstarts with a uppercase character

intvarchar 255 char 10

1997IMGT, the internat…. Chaume

yeartitleauthor

Data are vectors : (author, title, year)

primitive types

user types

actual data

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Data definition domainsPrimitive domain

User domain (rules)

Actual domain (data)

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Actual data XML representation

<litRefList> <litRef> <author name="Chaume" /> <title>IMGT, the internat…. </title> <date year="1997" /> </litRef> …</litRefList>

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XML schema <xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" > <xs:element name="litRefList"> <xs:complexType> <xs:sequence> <xs:element ref="litRef" maxOccurs="unbounded"/> </xs:sequence> </xs:complexType> </xs:element> <xs:element name="litRef"> <xs:complexType> <xs:sequence> <xs:element ref="author" /> <xs:element ref="title" /> <xs:element ref="date" /> </xs:sequence> </xs:complexType> </xs:element> .....

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XML schema 1..... <xs:element name="author"> <xs:complexType> <xs:attribute name="name" type="xs:string"/> </xs:complexType></xs:element> <xs:element name="title" type="xs:string" /><xs:element name="date"> <xs:complexType> <xs:attribute name="year" type="xs:integer"/> </xs:complexType></xs:element>.....

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Schema 1 definition domainSchema1 domain

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XML schema 2..... <xs:element name="author"> <xs:complexType> <xs:attribute name="name" > <xs:simpleType> <xs:restriction base="xs:string"> <xs:maxLength value="10" /> <xs:pattern value="^[A-Z][a-z]+"/> </xs:restriction> </xs:simpleType> </xs:attribute> </xs:complexType></xs:element> <xs:element name="title"> <xs:simpleType> <xs:restriction base="xs:string"> <xs:maxLength value="255" /> </xs:restriction> </xs:simpleType></xs:element>

<xs:element name="date"> <xs:complexType> <xs:attribute name="year" > <xs:simpleType> <xs:restriction base="xs:string"> <xs:minInclusive value="1970"/> <xs:maxExclusive value="10000"/> </xs:restriction> </xs:simpleType> </xs:attribute> </xs:complexType></xs:element>.....

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Schema 2 definition domainsSchema 2 domain

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XML instanceand instance

domain

<litRefList> <litRef> <author name="Chaume" /> </litRef></litRefList>

..... <xs:element name="author"> <xs:complexType> <xs:attribute name="name"> <xs:simpleType> <xs:restriction base="xs:string"> <xs:enumeration value="Chaume" /> </xs:restriction> </xs:simpleType> </xs:attribute> </xs:complexType></xs:element> <xs:element name="title" type="xs:string" /><xs:element name="date"> <xs:complexType> <xs:attribute name="year" type="xs:integer"/> </xs:complexType></xs:element>.....

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Instance and query result domainsThe result of the query is the intersection of the "instance domain" and the "actual domain"

Instance domain

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IMGTQuery package

querySeqDataqueryKnowledge

domain

@data :labelListkeywordListfunctionalityListchainTypeListspecificityListmoleculeTypeListconfigurationList

seqData (+)

enumeration

minInclusive

maxInclusive

pattern

minExclusive

maxExclusive

responseTemplate

seqData

In any seqData sub-element

@complement (boolean)@of : @xxxx text()

Namespace : http://www.imgt.org/IMGT-ML/IMGTQuery

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Part 3 summary

• Example of IMGT/LIGM-DB queries• Request from Identification concept• AND operator (request)• AND operator (result)• OR operator• Request with domain restriction• Result control

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Example of IMGT/LIGM-DB queries

<q:querySeqData> <seqData>

<simpleCatalogEntry numacc="M26678"

/> </seqData></q:querySeqData>

<seqDataList> <seqData> <catalogEntry id="M26678" > <simpleCatalogEntry numacc="M26678" name="MMIGKZZZ"/> </catalogEntry> <identification> <partIdent moleculeType="DNA" configuration="rearranged"> <taxon taxonName="Mus musculus"/> </partIdent> </identification> <classification> <group name="IGKV"> <subgroup name="IGKV8"/> </group> </classification> …. </seqData></seqDataList>

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Request from Identification concept<q:querySeqData> <seqData> <partIdent chainType="Ig-Light"> <taxon taxonName="Homo sapiens"/> </partIdent> </seqData></q:querySeqData>

<seqDataList> <seqData id="AF001788" > <catalogue > ….

</catalogue> <identification>

<partIdent chainType="Ig-Light"> <taxon taxonName="Homo sapiens"/>

</partIdent> ….

</identification> </seqData> <seqData id="AF001799" > <catalogue > …. </seqData></seqDataList>

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AND operator (request)<q:querySeqData> <seqData> <annotation> <entity name="C-GENE"/> <region name="D-REGION"/> </annotation></seqData></q:querySeqData>

AND=intersection

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AND operator (result)

…. <entity name="C-GENE" partial="true"> <start location="4334"/> …. <end location="5440"/> </entity> <end location="5440"/> </cluster></annotation> ….

<seqDataList> <seqData id="U97590" > <catalogue> …. </catalogue> <identification> …. </identification> <annotation> <cluster name="D-J-C-CLUSTER"> <start location="1"/> <entity name="D-GENE"> <start location="1"/> <region name="D-REGION"> <start location="464"/> <end location="475"/> </region> <end location="600"/> </entity> ….

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OR operator<request> <seqData> <partIdent chainType="Ig-Light-Kappa" functionality="pseudogene"> <taxon taxonName="Homo sapiens"/> </partIdent> </seqData> <seqData> <partIdent chainType="Ig-Light-Lambda" functionality="pseudogene"> <taxon taxonName="Homo sapiens"/> </partIdent> </seqData></request>

<response> <seqData> <catalogEntry id="A25907" > …. </seqData> <seqData> <catalogEntry id="AF026482" > …. </seqData> <seqData> <catalogEntry id="AF026483" > …. </seqData> <seqData> <catalogEntry id="AF026484" > …. </seqData>

…</response>

OU=union

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<q:querySeqData> <seqData> <sequence>

<q:domain of="@length"> <q:maxInclusive value="400"/> <q:minInclusive value="100"/>

</q:restriction> </sequence> </seqData></q:querySeqData>

<q:querySeqData> <seqData> <sequence length="300"/> </seqData></q:querySeqData>

Request with domain restriction

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Result control<q:querySeqData> <seqData> <partIdent chainType="Ig" moleculeType="cDNA" configuration="rearranged"

specificity="anti-thyroid peroxidase (TPO)" > <taxon taxonName="Homo sapiens" /> </partIdent>

</seqData></q:querySeqData>

<q:responseTemplate><seqData> <classification><gene/></classification></seqData></q:responseTemplate>

Expected result :

<seqDataList nb="27"> <seqData id="AF306350"> <classification>

<gene name="IGHV1-69"/> <gene name="IGHD3-10"/>

<gene name="IGHJ6"/> </classification> </seqData> <seqData id="AF306376"> <classification>

<gene name="IGHV1-3"/> <gene name="IGHD4-4"/>

<gene name="IGHJ4"/> </classification> </seqData> .. ..

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Tools : Junction Analysis• Input : a sequence list, each sequence has a V gene and

a J gene.• Output : each sequence is annotated with locations of V,

D, J genes and N and P regions and sequences are aligned

seqDataList

seqDataclassification

seqDataList

seqData

annotation

alignement

proSequence

IMGTjcta

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Literature document queries (ORIEL project)

• Authors do not use this vocabulary• GO terms are too poor to describe

genes involved in immunoglobulin and T receptor synthesis

• Existing search engines do not index text with this vocabulary

How use IMGT-ONTOLOGY vocabulary to index literature documents ?

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SEFID Prototype search engine pipeline

IMGT-MLquery

IMGT/LIGM-DB SOAP server at EBI

Doc2Loc

Location (NCBI, INIST, SUDOC…)

Text analysis (LT-POS, …)

Statistics analysisOriel server

General purpose search engine

(E-BioSci, Collexis, … Full text publications

Doc2Loc

Literature ref.

E-BioSci

Accession #s Medline #s Abstract locations

AbstractsUseful wordsWord signatures

IMGT SOAP server

EBI SOAP serverCan be IMGT or DDBJ SOAP

server as well

E-BioSci Doc2Loc SOAP server

E-BioSci SOAP server

Oriel SOAP server implementing LT-Chunk from LTG (Edinburgh)

(home development)

Oriel SOAP server Word frequencies

(fingerprint)(home development)

E-BioSci SOAP serverOr any other search engine

(google)

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Conclusion

• IMGT-ML, very close to IMGT-ONTOLOGY, is compliant with Biology

• Using the same IMGT-ML format as input and output of modules (Web services) allows their chaining

• This makes easier the development of IMGT-CHOREOGRAPHY which is our near futur development.

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People• Kora Combres (CNRS/IGH, ORIEL project)

• Véronique Giudicelli (CNRS/IGH, IMGT-ONTOLOGY),

• Professeur Marie-Paule Lefranc (UM II, CNRS/IGH, IMGT project)

• Denys Chaume (CNRS/IGH, IMGT, ORIEL)