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Literature DB >> 15961440

Querying and computing with BioCyc databases.

Markus Krummenacker¹, Suzanne Paley, Lukas Mueller, Thomas Yan, Peter D Karp.

Abstract

We describe multiple methods for accessing and querying the complex and integrated cellular data in the BioCyc family of databases: access through multiple file formats, access through Application Program Interfaces (APIs) for LISP, Perl and Java, and SQL access through the BioWarehouse relational database.

Mesh：

Year: 2005 PMID： 15961440 PMCID： PMC1450015 DOI： 10.1093/bioinformatics/bti546

Source DB: PubMed Journal: Bioinformatics ISSN： 1367-4803 Impact factor: 6.937

5 in total

1. An ontology for biological function based on molecular interactions.

Authors: P D Karp
Journal: Bioinformatics Date: 2000-03 Impact factor: 6.937

2. The MetaCyc Database.

Authors: Peter D Karp; Monica Riley; Suzanne M Paley; Alida Pellegrini-Toole
Journal: Nucleic Acids Res Date: 2002-01-01 Impact factor: 16.971

3. The EcoCyc Database.

Authors: Peter D Karp; Monica Riley; Milton Saier; Ian T Paulsen; Julio Collado-Vides; Suzanne M Paley; Alida Pellegrini-Toole; César Bonavides; Socorro Gama-Castro
Journal: Nucleic Acids Res Date: 2002-01-01 Impact factor: 16.971

4. The Pathway Tools software.

Authors: Peter D Karp; Suzanne Paley; Pedro Romero
Journal: Bioinformatics Date: 2002 Impact factor: 6.937

5. AraCyc: a biochemical pathway database for Arabidopsis.

Authors: Lukas A Mueller; Peifen Zhang; Seung Y Rhee
Journal: Plant Physiol Date: 2003-06 Impact factor: 8.340

5 in total

32 in total

1. Kinetic Modeling using BioPAX ontology.

Authors: Oliver Ruebenacker; Ion I Moraru; James C Schaff; Michael L Blinov
Journal: Proceedings (IEEE Int Conf Bioinformatics Biomed) Date: 2007-11-02

2. Pathway Tools version 19.0 update: software for pathway/genome informatics and systems biology.

Authors: Peter D Karp; Mario Latendresse; Suzanne M Paley; Markus Krummenacker; Quang D Ong; Richard Billington; Anamika Kothari; Daniel Weaver; Thomas Lee; Pallavi Subhraveti; Aaron Spaulding; Carol Fulcher; Ingrid M Keseler; Ron Caspi
Journal: Brief Bioinform Date: 2015-10-10 Impact factor: 11.622

Review 3. Network integration and graph analysis in mammalian molecular systems biology.

Authors: A Ma'ayan
Journal: IET Syst Biol Date: 2008-09 Impact factor: 1.615

Review 4. Database resources in metabolomics: an overview.

Authors: Eden P Go
Journal: J Neuroimmune Pharmacol Date: 2009-05-07 Impact factor: 4.147

5. Programming with models: modularity and abstraction provide powerful capabilities for systems biology.

Authors: Aneil Mallavarapu; Matthew Thomson; Benjamin Ullian; Jeremy Gunawardena
Journal: J R Soc Interface Date: 2009-03-06 Impact factor: 4.118

6. Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology.

Authors: Peter D Karp; Suzanne M Paley; Markus Krummenacker; Mario Latendresse; Joseph M Dale; Thomas J Lee; Pallavi Kaipa; Fred Gilham; Aaron Spaulding; Liviu Popescu; Tomer Altman; Ian Paulsen; Ingrid M Keseler; Ron Caspi
Journal: Brief Bioinform Date: 2009-12-02 Impact factor: 11.622

7. LeishCyc: a biochemical pathways database for Leishmania major.

Authors: Maria A Doyle; James I MacRae; David P De Souza; Eleanor C Saunders; Malcolm J McConville; Vladimir A Likić
Journal: BMC Syst Biol Date: 2009-06-05

8. PathwayAccess: CellDesigner plugins for pathway databases.

Authors: John L Van Hemert; Julie A Dickerson
Journal: Bioinformatics Date: 2010-07-20 Impact factor: 6.937

9. HMDB: a knowledgebase for the human metabolome.

Authors: David S Wishart; Craig Knox; An Chi Guo; Roman Eisner; Nelson Young; Bijaya Gautam; David D Hau; Nick Psychogios; Edison Dong; Souhaila Bouatra; Rupasri Mandal; Igor Sinelnikov; Jianguo Xia; Leslie Jia; Joseph A Cruz; Emilia Lim; Constance A Sobsey; Savita Shrivastava; Paul Huang; Philip Liu; Lydia Fang; Jun Peng; Ryan Fradette; Dean Cheng; Dan Tzur; Melisa Clements; Avalyn Lewis; Andrea De Souza; Azaret Zuniga; Margot Dawe; Yeping Xiong; Derrick Clive; Russ Greiner; Alsu Nazyrova; Rustem Shaykhutdinov; Liang Li; Hans J Vogel; Ian Forsythe
Journal: Nucleic Acids Res Date: 2008-10-25 Impact factor: 16.971

10. Annotation-based inference of transporter function.

Authors: Thomas J Lee; Ian Paulsen; Peter Karp
Journal: Bioinformatics Date: 2008-07-01 Impact factor: 6.937