An advanced web query interface for biological databases.

Database : the Journal of Biological Databases and Curation
Mario Latendresse, Peter D Karp

Abstract

Although most web-based biological databases (DBs) offer some type of web-based form to allow users to author DB queries, these query forms are quite restricted in the complexity of DB queries that they can formulate. They can typically query only one DB, and can query only a single type of object at a time (e.g. genes) with no possible interaction between the objects--that is, in SQL parlance, no joins are allowed between DB objects. Writing precise queries against biological DBs is usually left to a programmer skillful enough in complex DB query languages like SQL. We present a web interface for building precise queries for biological DBs that can construct much more precise queries than most web-based query forms, yet that is user friendly enough to be used by biologists. It supports queries containing multiple conditions, and connecting multiple object types without using the join concept, which is unintuitive to biologists. This interactive web interface is called the Structured Advanced Query Page (SAQP). Users interactively build up a wide range of query constructs. Interactive documentation within the SAQP describes the schema of the queried DBs. The SAQP is based on BioVelo, a query language based on list comprehension...Continue Reading

References

Feb 17, 2006·BMC Bioinformatics·Aaron Birkland, Golan Yona
Jan 27, 2007·BMC Bioinformatics·Tony HåndstadPål Saetrom
Mar 9, 2007·Bioinformatics·Sarah Cohen-BoulakiaChristine Froidevaux
Jan 16, 2009·BMC Genomics·Damian SmedleyArek Kasprzyk
Aug 18, 2009·Genome Biology·Alexei V EvsikovCarol J Bult

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Citations

Apr 28, 2011·Archives of Toxicology·Peter D Karp, Ron Caspi
Sep 17, 2013·Database : the Journal of Biological Databases and Curation·Michael TraversPeter D Karp
Nov 26, 2010·Nucleic Acids Research·Ingrid M KeselerPeter D Karp
Jul 7, 2011·Journal of Medical Economics·Andrés SternMaría Rull
Oct 21, 2011·Disability and Rehabilitation·Amy M DennettKevin Mulrain
Apr 14, 2011·The World Journal of Biological Psychiatry : the Official Journal of the World Federation of Societies of Biological Psychiatry·Michael SoykaUNKNOWN WFSBP Task Force on Treatment, Guidelines for Substance Use Disorders
Mar 10, 2016·Thyroid : Official Journal of the American Thyroid Association·Tristan Mirko StrujaPhilipp Schuetz
Oct 11, 2014·The Journal of Maternal-fetal & Neonatal Medicine : the Official Journal of the European Association of Perinatal Medicine, the Federation of Asia and Oceania Perinatal Societies, the International Society of Perinatal Obstetricians·Ricardo F Sousa-SantosJoão F M A L Bernardes
Dec 30, 2014·Endocrine Practice : Official Journal of the American College of Endocrinology and the American Association of Clinical Endocrinologists·Susan P DemarestRobert A Adler
Jun 1, 2016·Database : the Journal of Biological Databases and Curation·Patrice Baa-PuyouletStefano Colella
Jun 22, 2018·Journal of Integrative Bioinformatics·Alexandre MaesMarc Baaden
Sep 29, 2015·Thyroid : Official Journal of the American Thyroid Association·Danilo VillagelinLaura S Ward
Feb 26, 2014·BMC Bioinformatics·Marco MasseroliStefano Ceri
Oct 12, 2013·Journal of Physics. Condensed Matter : an Institute of Physics Journal·K O E HenrikssonK Nordlund

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Datasets Mentioned

BETA
GM75742

Methods Mentioned

BETA
Y2H

Software Mentioned

FlyMine
Entrez
SQL
Internet Explorer ( IE )
Safari
Perl
QBE
EcoCyc
Internet Explorer
BioMart

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