BIRDQL

BIRDQL Biological Query Language

BIRDQL in few words

This query language is conceived by Hoan Nguyen[1].

The heterogeneous data integrated in integrator system or BIRD System are represented by several relational tables. The exploitation of these data by SQL queries is not obvious except for developers or computer scientist experts.

Building queries with SQL in this context is not easy with because that requires to use joins (terme technique) to select data in multiple tables. This complexity must be hidden by HTML forms but a lot of queries can not be setup with HTML forms.

We proposes own query language (BIRDQL), there is new standard biological query language allowing the biologist or clinician to create data retrieval protocols without exhaustive knowledge of the data sources and their architecture. BIRD System is driven with a high level query engine: BIRDQL, which makes it possible for biologists to express easily queries and to extract knowledge by classical constraints and scientific functions (StructuralDistance,SequencePattern,AssociationRule...).

BIRDQL in not a mathematically complete language but indeed an idiom adpated to the GUI, human readable enough to be modified by hand. The construction of this BIRDQL query engine was used some main idea from SaadaQL [2]. SaadaQL query language was developed in the framework of my PhD ( Astrophysics & Virtual Observatory ,2002-2005) at university of Strasbourg.

Data can be selected with BIRD Data Access Protocol

BIRDQL Grammar

ID <list of id/ac/query_id > DB <bank names>

WH <Field> Contains <(kw1 & kw2) | kw_n>

WH PATTERN <function SequencePattern() >

WH PATTERN <function DiagonalMolecule()>

WH PATTERN <function InteractionProtein()>

WH PATTERN <function AssociationRule()>

WH SQLNative select from ...

FD <Field out1,Field out2,... / GET_COUNT/GET_DR(bankname)>

OF <OFFSET, Default OF=0>

LM <number of maximum display>

FM <Fasta/Flat/Xml/CSV/Simple/Object/OID>

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BIRDQL example

Data can be selected with BIRD Data Access Protocol

Two other examples below also show how to use the BIRD-QL syntax.

Example 1: simple query, search and fasta format generation

ID * DB UNIPROT

WH TEXT contains "synthetase" & "tyrosyl" & not ("homo sapiens" & "human")

FD AC, ID,DE,OX,SQ

LM 100

FM FASTA

Result

>Q92PK5 | SYY_RHIME | Tyrosyl-tRNA synthetase (EC 6.1.1.1) (Tyrosine--tRNA ligase) (TyrRS). | 382 MSEFKSDFLHTLSERGFIHQTSDDAGLDQLFRTETVTAYIGFDPTAASLHAGGLIQIMMLHWLQATGHRPISLMGGGTGMVGDPSFKDEARQLMTPETI...

Example 2: FullText query with operator: & , not (TEXT=definition, organism scientific organism common, dbref,..)

ID * DB REFSEQ

WH TEXT Contains "Tyrosyl-tRNA synthetase" & "Homo sapiens"

LM 100

FM FASTA

//

ID * DB UNIPROT

WH TEXT contains "histone" & not "homo sapiens"

FD AC,DE,OS

LM 3

FM FLAT

//

ID * DB UNIPROT

WH TEXT contains not "homo sapiens"

FD AC,DE,OS

LM 3

Example 2: complex query, GBFULL=EST+ WGS +Release +New

ID * DB GBFULL

WH OC Contains "Eukaryote"

WH DR Contains "GO"

WH GENE contains "GF100027"

FM FASTA

The query above allow to search in Genbank full, the Eucaryotic sequences containing the GF100027 gene with a cross reference in GeneOntology.

Example 3: mining in GENBANK EST

ID * DB GBEST

WH TISSUE_TYPE contains "retina"

WH DEV_STAGE contains "adult"

LM 100

FD AC,DE,OX,OC,tissue_type,dev_stage,chr

FM FLAT

Example 4: Mining in GENBANK EST

ID CJ133635,CJ133593,CJ133659 DB GBEST

WH DE contains "AMINOTRANSFERASE"

WH OC contains "Eukaryota" & not "Metazoa"

WH TISSUE_TYPE contains "retina"

FD AC,DE,OX,OC,tissue_type,dev_stage,chr

FM FLAT

Example 5: Mining in EST

ID * DB GBEST

WH TISSUE_TYPE contains "colon"

WH DEV_STAGE contains "adult"

LM 100

FD AC,DE,OX,OC,tissue_type,dev_stage,chr,os

FM FLAT

Example 6: Mining In PDB

ID * DB PDB

WH TEXT contains "DMD" & "ERYTHRINA CORALLODENDRON"

LM 10

FM FASTA

//

ID * DB PDB

WH TEXT contains "METAL BINDING PROTEIN" & "LACTOFERRIN"

WH FUNCTION Diagnonal3D()>125

FUZZY 100

LM 100

FM FASTA

//

ID * DB PDB

WH TEXT "METAL BINDING PROTEIN" & "LACTOFERRIN"

WH FUNCTION Diagnonal3D()>125

FUZZY 100

LM 100

FM SIMPLE

//

ID * DB PDB

WH CL contains "METAL BINDING PROTEIN"

WH DE contains "LACTOFERRIN"

WH FUNCTION Diagnonal3D()>125

LM 10

FM FLAT

//

ID * DB PDB

WH CL contains "METAL BINDING PROTEIN"

WH DE contains "LACTOFERRIN"

WH FUNCTION Diagnonal3D()>125

FD GET_COUNT

FM FLAT

Example 7: Get GENE ONTOLOGY or DBREF

ID Q32437 DB UNIPROT

FD AC,DR(GO)

//

ID Q34215 DB UNIPROT FD AC,DR(InterPro)

>>Result:

   AC   Q32437;
   DR   GO; GO:0009507; C:chloroplast; IEA:InterPro.
   DR   GO; GO:0016021; C:integral to membrane; IEA:UniProtKB-KW.
   ......
   //
   AC   Q34215;
   DR   Pfam; PF00033; Cytochrom_B_N; 1.

Example 9: DBSNP

Example 9.1: get DBSNP with XML format ID 268 DB DBSNP

Example 9.2: find snp by position

ID * DB DBSNP

WH SQLNative select id from dbsnp_ds_ch3.fulltext where XMLEXISTS('$i/Rs/Assembly/Component/MapLoc[@physMapInt=30466018] ' passing text as "i")

LM 1000

FM FLAT

Example 9.2: find snp by position

ID * DB DBSNP WH SQLNative select id from dbsnp_ds_ch18.fulltext where XMLEXISTS('$i/Rs/Assembly/Component/MapLoc[@physMapInt>=30466000 and @physMapInt<=30466200 ] ' passing text as "i") FM FLAT //

Example 9.3: find snp by position and reference sequence (GRCh37.p2)

ID * DB DBSNP WH SQLNative Select ID from dbsnp_ds_ch8.fulltext where XMLEXISTS('$i/Rs/Assembly/Component/MapLoc[@physMapInt=19817621 and ../../@groupLabel="GRCh37.p2"] ' passing text as "i") FM FLAT //