Advanced querying interface for biochemical network databases

Brendan Elliott; Stephen Mayes; Ali Cakmak; Gultekin Ozsoyoglu; Z. Meral Ozsoyoglu

doi:10.1145/1774088.1774417

Advanced querying interface for biochemical network databases

Brendan Elliott^*, Stephen Mayes, Ali Cakmak, Gultekin Ozsoyoglu, Z. Meral Ozsoyoglu

^*Corresponding author for this work

Case Western Reserve University

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

2 Citations (Scopus)

Abstract

Querying biochemical networks in flexible ways over the web is important to facilitate ongoing biological research. In this paper, we present a querying interface for biological networks, more specifically, metabolic networks. The interface allows for the specification of a large class of containment, path, and neighborhood queries with ease from a web browser. The query specification process is user-friendly, employs hierarchically arranged relationships among biological entities, and uses autocomplete features. The interface is provided as part of PathCase, a system to store, query, visualize and analyze metabolic pathways at different levels of detail.

Original language	English
Title of host publication	APPLIED COMPUTING 2010 - The 25th Annual ACM Symposium on Applied Computing
Pages	1526-1533
Number of pages	8
DOIs	https://doi.org/10.1145/1774088.1774417
Publication status	Published - 2010
Externally published	Yes
Event	25th Annual ACM Symposium on Applied Computing, SAC 2010 - Sierre, Switzerland Duration: 22 Mar 2010 → 26 Mar 2010

Publication series

Name	Proceedings of the ACM Symposium on Applied Computing

Conference

Conference	25th Annual ACM Symposium on Applied Computing, SAC 2010
Country/Territory	Switzerland
City	Sierre
Period	22/03/10 → 26/03/10

Keywords

H.2.8 [Database applications]: Scientific Databases - query language, visualization, biological networks

Access to Document

10.1145/1774088.1774417

Cite this

@inproceedings{bb00eabfdaa94609a5aa0bb3544adce1,

title = "Advanced querying interface for biochemical network databases",

abstract = "Querying biochemical networks in flexible ways over the web is important to facilitate ongoing biological research. In this paper, we present a querying interface for biological networks, more specifically, metabolic networks. The interface allows for the specification of a large class of containment, path, and neighborhood queries with ease from a web browser. The query specification process is user-friendly, employs hierarchically arranged relationships among biological entities, and uses autocomplete features. The interface is provided as part of PathCase, a system to store, query, visualize and analyze metabolic pathways at different levels of detail.",

keywords = "H.2.8 [Database applications]: Scientific Databases - query language, visualization, biological networks",

author = "Brendan Elliott and Stephen Mayes and Ali Cakmak and Gultekin Ozsoyoglu and Ozsoyoglu, {Z. Meral}",

year = "2010",

doi = "10.1145/1774088.1774417",

language = "English",

isbn = "9781605586380",

series = "Proceedings of the ACM Symposium on Applied Computing",

pages = "1526--1533",

booktitle = "APPLIED COMPUTING 2010 - The 25th Annual ACM Symposium on Applied Computing",

note = "25th Annual ACM Symposium on Applied Computing, SAC 2010 ; Conference date: 22-03-2010 Through 26-03-2010",

}

Elliott, B, Mayes, S, Cakmak, A, Ozsoyoglu, G & Ozsoyoglu, ZM 2010, Advanced querying interface for biochemical network databases. in APPLIED COMPUTING 2010 - The 25th Annual ACM Symposium on Applied Computing. Proceedings of the ACM Symposium on Applied Computing, pp. 1526-1533, 25th Annual ACM Symposium on Applied Computing, SAC 2010, Sierre, Switzerland, 22/03/10. https://doi.org/10.1145/1774088.1774417

Advanced querying interface for biochemical network databases. / Elliott, Brendan; Mayes, Stephen; Cakmak, Ali et al.
APPLIED COMPUTING 2010 - The 25th Annual ACM Symposium on Applied Computing. 2010. p. 1526-1533 (Proceedings of the ACM Symposium on Applied Computing).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

TY - GEN

T1 - Advanced querying interface for biochemical network databases

AU - Elliott, Brendan

AU - Mayes, Stephen

AU - Cakmak, Ali

AU - Ozsoyoglu, Gultekin

AU - Ozsoyoglu, Z. Meral

PY - 2010

Y1 - 2010

N2 - Querying biochemical networks in flexible ways over the web is important to facilitate ongoing biological research. In this paper, we present a querying interface for biological networks, more specifically, metabolic networks. The interface allows for the specification of a large class of containment, path, and neighborhood queries with ease from a web browser. The query specification process is user-friendly, employs hierarchically arranged relationships among biological entities, and uses autocomplete features. The interface is provided as part of PathCase, a system to store, query, visualize and analyze metabolic pathways at different levels of detail.

AB - Querying biochemical networks in flexible ways over the web is important to facilitate ongoing biological research. In this paper, we present a querying interface for biological networks, more specifically, metabolic networks. The interface allows for the specification of a large class of containment, path, and neighborhood queries with ease from a web browser. The query specification process is user-friendly, employs hierarchically arranged relationships among biological entities, and uses autocomplete features. The interface is provided as part of PathCase, a system to store, query, visualize and analyze metabolic pathways at different levels of detail.

KW - H.2.8 [Database applications]: Scientific Databases - query language, visualization, biological networks

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U2 - 10.1145/1774088.1774417

DO - 10.1145/1774088.1774417

M3 - Conference contribution

AN - SCOPUS:77954691060

SN - 9781605586380

T3 - Proceedings of the ACM Symposium on Applied Computing

SP - 1526

EP - 1533

BT - APPLIED COMPUTING 2010 - The 25th Annual ACM Symposium on Applied Computing

T2 - 25th Annual ACM Symposium on Applied Computing, SAC 2010

Y2 - 22 March 2010 through 26 March 2010

ER -

Advanced querying interface for biochemical network databases

Abstract

Publication series

Conference

Keywords

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