ArticleDatabase : the journal of biological databases and curation2010
An advanced web query interface for biological databases.
Article in Database : the journal of biological databases and curation, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- Proteomic profiling of zinc homeostasis mechanisms in Pseudomonas aeruginosa through data-dependent and data-independent acquisition mass spectrometry.Metallomics : integrated biometal science · 2025Article
- Proteomic profiling of zinc homeostasis mechanisms inbioRxiv : the preprint server for biology · 2025Article
- MinOmics, an Integrative and Immersive Tool for Multi-Omics Analysis.Journal of integrative bioinformatics · 2018Article
- ArthropodaCyc: a CycADS powered collection of BioCyc databases to analyse and compare metabolism of arthropods.Database : the journal of biological databases and curation · 2016Article
- Explorative search of distributed bio-data to answer complex biomedical questions.BMC bioinformatics · 2014Article
- MetaPathways: a modular pipeline for constructing pathway/genome databases from environmental sequence information.BMC bioinformatics · 2013Article
- Groups: knowledge spreadsheets for symbolic biocomputing.Database : the journal of biological databases and curation · 2013Article
- The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases.Nucleic acids research · 2012Article
- A survey of metabolic databases emphasizing the MetaCyc family.Archives of toxicology · 2011Review
- EcoCyc: a comprehensive database of Escherichia coli biology.Nucleic acids research · 2011Article
Corrections and comments
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Authors and funding
2 authors.
Funding
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. The SAQP is part of the Pathway Tools software and is available as part of several bioinformatics web sites powered by Pathway Tools, including the BioCyc.org site that contains more than 500 Pathway/Genome DBs.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.