CRAVE: a database, middleware and visualization system for phenotype ontologies

Georgios V Gkoutos; Eain C. J. Green; Simon Greenaway; Andrew Blake; Ann-Marie Mallon; John M Hancock

doi:10.1093/bioinformatics/bti147

CRAVE: a database, middleware and visualization system for phenotype ontologies

Georgios V Gkoutos, Eain C. J. Green, Simon Greenaway, Andrew Blake, Ann-Marie Mallon, John M Hancock

Adran Cyfrifiadureg

Allbwn ymchwil: Cyfraniad at gyfnodolyn › Erthygl › adolygiad gan gymheiriaid

9 Dyfyniadau (Scopus)

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Motivation:
A major challenge in modern biology is to link genome sequence information to organismal function. In many organisms this is being done by characterizing phenotypes resulting from mutations. Efficiently expressing phenotypic information requires combinatorial use of ontologies. However tools are not currently available to visualize combinations of ontologies. Here we describe CRAVE (Concept Relation Assay Value Explorer), a package allowing storage, active updating and visualization of multiple ontologies.

Results:
CRAVE is a web-accessible JAVA application that accesses an underlying MySQL database of ontologies via a JAVA persistent middleware layer (Chameleon). This maps the database tables into discrete JAVA classes and creates memory resident, interlinked objects corresponding to the ontology data. These JAVA objects are accessed via calls through the middleware's application programming interface. CRAVE allows simultaneous display and linking of multiple ontologies and searching using Boolean and advanced searches.

Iaith wreiddiol	Saesneg
Tudalennau (o-i)	1257-1262
Nifer y tudalennau	6
Cyfnodolyn	Bioinformatics
Cyfrol	21
Rhif cyhoeddi	7
Dynodwyr Gwrthrych Digidol (DOIs)	https://doi.org/10.1093/bioinformatics/bti147
Statws	Cyhoeddwyd - 01 Ebr 2005

Mynediad at Ddogfen

10.1093/bioinformatics/bti147

Cysylltiad parhaol

Dolen barhaus

Ffeiliau eraill a chysylltiadau

http://hdl.handle.net/2160/12076

Dyfynnu hyn

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title = "CRAVE: a database, middleware and visualization system for phenotype ontologies",

abstract = "Motivation: A major challenge in modern biology is to link genome sequence information to organismal function. In many organisms this is being done by characterizing phenotypes resulting from mutations. Efficiently expressing phenotypic information requires combinatorial use of ontologies. However tools are not currently available to visualize combinations of ontologies. Here we describe CRAVE (Concept Relation Assay Value Explorer), a package allowing storage, active updating and visualization of multiple ontologies.Results: CRAVE is a web-accessible JAVA application that accesses an underlying MySQL database of ontologies via a JAVA persistent middleware layer (Chameleon). This maps the database tables into discrete JAVA classes and creates memory resident, interlinked objects corresponding to the ontology data. These JAVA objects are accessed via calls through the middleware's application programming interface. CRAVE allows simultaneous display and linking of multiple ontologies and searching using Boolean and advanced searches. ",

author = "Gkoutos, {Georgios V} and Green, {Eain C. J.} and Simon Greenaway and Andrew Blake and Ann-Marie Mallon and Hancock, {John M}",

year = "2005",

month = apr,

day = "1",

doi = "10.1093/bioinformatics/bti147",

language = "English",

volume = "21",

pages = "1257--1262",

journal = "Bioinformatics",

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TY - JOUR

T1 - CRAVE: a database, middleware and visualization system for phenotype ontologies

AU - Gkoutos, Georgios V

AU - Green, Eain C. J.

AU - Greenaway, Simon

AU - Blake, Andrew

AU - Mallon, Ann-Marie

AU - Hancock, John M

PY - 2005/4/1

Y1 - 2005/4/1

N2 - Motivation: A major challenge in modern biology is to link genome sequence information to organismal function. In many organisms this is being done by characterizing phenotypes resulting from mutations. Efficiently expressing phenotypic information requires combinatorial use of ontologies. However tools are not currently available to visualize combinations of ontologies. Here we describe CRAVE (Concept Relation Assay Value Explorer), a package allowing storage, active updating and visualization of multiple ontologies.Results: CRAVE is a web-accessible JAVA application that accesses an underlying MySQL database of ontologies via a JAVA persistent middleware layer (Chameleon). This maps the database tables into discrete JAVA classes and creates memory resident, interlinked objects corresponding to the ontology data. These JAVA objects are accessed via calls through the middleware's application programming interface. CRAVE allows simultaneous display and linking of multiple ontologies and searching using Boolean and advanced searches.

AB - Motivation: A major challenge in modern biology is to link genome sequence information to organismal function. In many organisms this is being done by characterizing phenotypes resulting from mutations. Efficiently expressing phenotypic information requires combinatorial use of ontologies. However tools are not currently available to visualize combinations of ontologies. Here we describe CRAVE (Concept Relation Assay Value Explorer), a package allowing storage, active updating and visualization of multiple ontologies.Results: CRAVE is a web-accessible JAVA application that accesses an underlying MySQL database of ontologies via a JAVA persistent middleware layer (Chameleon). This maps the database tables into discrete JAVA classes and creates memory resident, interlinked objects corresponding to the ontology data. These JAVA objects are accessed via calls through the middleware's application programming interface. CRAVE allows simultaneous display and linking of multiple ontologies and searching using Boolean and advanced searches.

UR - http://hdl.handle.net/2160/12076

U2 - 10.1093/bioinformatics/bti147

DO - 10.1093/bioinformatics/bti147

M3 - Article

C2 - 15550481

SN - 1367-4803

VL - 21

SP - 1257

EP - 1262

JO - Bioinformatics

JF - Bioinformatics

IS - 7

ER -

CRAVE: a database, middleware and visualization system for phenotype ontologies

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