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AN EVIDENCE ONTOLOGY FOR USE IN PATHWAY/GENOME DATABASES

P.D. KARP, S. PALEY, C.J. KRIEGER, P. ZHANG
2003 Biocomputing 2004  
We also describe an implementation of the ontology within the Pathway Tools software environment, which is used to query and update Pathway/Genome DBs such as EcoCyc, MetaCyc, and HumanCyc.  ...  An important emerging need in Model Organism Databases (MODs) and other bioinformatics databases (DBs) is that of capturing the scientific evidence that supports the information within a DB.  ...  Acknowledgments Julio Collado-Vides contributed to development of evidence codes related to transcriptional regulation.  ... 
doi:10.1142/9789812704856_0019 fatcat:g5zo2izjg5hepgen7h44hw6viq

An evidence ontology for use in pathway/genome databases

P D Karp, S Paley, C J Krieger, P Zhang
2004 Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing  
We also describe an implementation of the ontology within the Pathway Tools software environment, which is used to query and update Pathway/Genome DBs such as EcoCyc, MetaCyc, and HumanCyc.  ...  An important emerging need in Model Organism Databases (MODs) and other bioinformatics databases (DBs) is that of capturing the scientific evidence that supports the information within a DB.  ...  Acknowledgments Julio Collado-Vides contributed to development of evidence codes related to transcriptional regulation.  ... 
pmid:14992503 fatcat:jrwhlmnn65d65eaayhvbxgyuca

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases

R. Caspi, T. Altman, K. Dreher, C. A. Fulcher, P. Subhraveti, I. M. Keseler, A. Kothari, M. Krummenacker, M. Latendresse, L. A. Mueller, Q. Ong, S. Paley (+6 others)
2011 Nucleic Acids Research  
The MetaCyc database (http://metacyc.org/) provides a comprehensive and freely accessible resource for metabolic pathways and enzymes from all domains of life.  ...  Most reactions in MetaCyc pathways are linked to one or more well-characterized enzymes, and both pathways and enzymes are annotated with reviews, evidence codes and literature citations.  ...  ACKNOWLEDGEMENTS This article was prepared as an account of work sponsored by an agency of the US Government.  ... 
doi:10.1093/nar/gkr1014 pmid:22102576 pmcid:PMC3245006 fatcat:zclxsx4caze4zc3sg7zsjxhhau

Expansion of the BioCyc collection of pathway/genome databases to 160 genomes

P. D. Karp
2005 Nucleic Acids Research  
The BioCyc database collection is a set of 160 pathway/genome databases (PGDBs) for most eukaryotic and prokaryotic species whose genomes have been completely sequenced to date.  ...  In addition, each bacterial PGDB includes predicted operons for the corresponding species.  ...  This financial support does not constitute an endorsement of the views expressed herein. Funding to pay the Open Access publication charges for this article was provided by NIH grant GM70065.  ... 
doi:10.1093/nar/gki892 pmid:16246909 pmcid:PMC1266070 fatcat:ttfs5gffgvgebfj5fvozjybg2m

Enhancing a Pathway-Genome Database (PGDB) to capture subcellular localization of metabolites and enzymes: the nucleotide-sugar biosynthetic pathways of Populus trichocarpa

Ambarish Nag, Tatiana V. Karpinets, Christopher H. Chang, Maor Bar-Peled
2012 Database: The Journal of Biological Databases and Curation  
Pathway-Genome Databases (PGDBs) of the SRI Pathway Tools software that drives much biochemical knowledge representation on the internet.  ...  In this report, we provide an informal mechanism using the existing Pathway Tools framework to integrate protein and metabolite sub-cellular localization data with the existing representation of the nucleotide-sugar  ...  The central object for organism-level representation is a pathway-genome database (PGDB), which through automated methods can be generated from annotated genomes.  ... 
doi:10.1093/database/bas013 pmid:22465851 pmcid:PMC3316911 fatcat:z5gs64plvfbm3asmiltl74kyxq

The MetaCyc Database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases

R. Caspi, H. Foerster, C. A. Fulcher, P. Kaipa, M. Krummenacker, M. Latendresse, S. Paley, S. Y. Rhee, A. G. Shearer, C. Tissier, T. C. Walk, P. Zhang (+1 others)
2007 Nucleic Acids Research  
BioCyc (BioCyc.org) is a collection of more than 350 organism-specific Pathway/ Genome Databases (PGDBs).  ...  The BioCyc PGDBs generated by SRI are offered for adoption by any interested party for the ongoing integration of metabolic and genome-related information about an organism.  ...  P.Z. and S.Y.R. were supported in part by NSF grant DBI-0417062, and C.T. was supported in part by a gift from Pioneer Hi-Bred.  ... 
doi:10.1093/nar/gkm900 pmid:17965431 pmcid:PMC2238876 fatcat:dz3ilfbpwbhdljbqnqvpezmoma

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases

Ron Caspi, Tomer Altman, Joseph M. Dale, Kate Dreher, Carol A. Fulcher, Fred Gilham, Pallavi Kaipa, Athikkattuvalasu S. Karthikeyan, Anamika Kothari, Markus Krummenacker, Mario Latendresse, Lukas A. Mueller (+6 others)
2009 Nucleic Acids Research  
BioCyc (BioCyc.org) is a collection of more than 500 organism-specific Pathway/Genome Databases (PGDBs). Each BioCyc PGDB contains the full genome and predicted metabolic network of one organism.  ...  The BioCyc PGDBs generated by SRI are offered for adoption by any party interested in curation of metabolic, regulatory, and genomerelated information about an organism.  ...  ACKNOWLEDGEMENTS We thank Dr Carol Bult and Dr Alexei Evsikov from the Jackson Laboratory for their contribution of pathways from the MouseCyc database.  ... 
doi:10.1093/nar/gkp875 pmid:19850718 pmcid:PMC2808959 fatcat:3mdlecp47rbszcro7wmgktztqi

Using functional and organizational information to improve genome-wide computational prediction of transcription units on pathway-genome databases

P. R. Romero, P. D. Karp
2004 Bioinformatics  
Pathway-genome databases (PGDBs) add metabolic and other organizational (i.e. protein complexes) information to the annotated genome, and are able to capture TU organization information.  ...  This was due in part to missing information in BsubCyc, which prevented full use of the predictor's features.  ...  Suzanne Paley provided helpful suggestions for the development of our predictor.  ... 
doi:10.1093/bioinformatics/btg471 pmid:14751985 fatcat:osapibjcjvf3hmhdmvc6bzyvje

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases

Ron Caspi, Tomer Altman, Richard Billington, Kate Dreher, Hartmut Foerster, Carol A. Fulcher, Timothy A. Holland, Ingrid M. Keseler, Anamika Kothari, Aya Kubo, Markus Krummenacker, Mario Latendresse (+8 others)
2013 Nucleic Acids Research  
BioCyc (BioCyc.org) is a collection of >3000 organism-specific Pathway/Genome Databases (PGDBs), each containing the full genome and predicted metabolic network of one organism, including metabolites,  ...  The MetaCyc database (MetaCyc.org) is a comprehensive and freely accessible database describing metabolic pathways and enzymes from all domains of life.  ...  During this automated process, a predicted metabolic network is created in the form of a Pathway/Genome Database (PGDB).  ... 
doi:10.1093/nar/gkt1103 pmid:24225315 pmcid:PMC3964957 fatcat:mfa4okdnxvhwrgf27kguvrss2q

Pathway Tools version 24.0: Integrated Software for Pathway/Genome Informatics and Systems Biology [article]

Peter D. Karp, Suzanne M. Paley, Peter E. Midford, Markus Krummenacker, Richard Billington, Anamika Kothari, Wai Kit Ong, Pallavi Subhraveti, Ingrid M. Keseler, Ron Caspi
2020 arXiv   pre-print
The software creates and manages a type of organism-specific database called a Pathway/Genome Database (PGDB), which the software enables database curators to interactively edit.  ...  Scientists around the world have created more than 9,800 PGDBs by using Pathway Tools, many of which are curated databases for important model organisms.  ...  Christos Ouzounis was a co-developer of the original metabolic pathway prediction algorithm, contributed an early version of the import/export system, and has been a source of much sound advice.  ... 
arXiv:1510.03964v4 fatcat:3plt5gcqmvg33pi6vd2mhufsda

Pathway Tools Management of Pathway/Genome Data for Microbial Communities

Peter D. Karp, Suzanne Paley, Markus Krummenacker, Anamika Kothari, Michael J. Wannemuehler, Gregory J. Phillips
2022 Frontiers in Bioinformatics  
The Pathway Tools (PTools) software provides a suite of capabilities for storing and analyzing integrated collections of genomic and metabolic information in the form of organism-specific Pathway/Genome  ...  PTools also provides a tool for searching for metabolic transformation routes across an organism community.  ...  ACKNOWLEDGMENTS We thank Lawrance Chandra for his contributions.  ... 
doi:10.3389/fbinf.2022.869150 fatcat:ruvtrod7s5aclictns32grlbpy

Integrative pathway genomics of lung function and airflow obstruction

Sina A. Gharib, Daan W. Loth, María Soler Artigas, Timothy P. Birkland, Jemma B. Wilk, Louise V. Wain, Jennifer A. Brody, Ma'en Obeidat, Dana B. Hancock, Wenbo Tang, Rajesh Rawal, H. Marike Boezen (+37 others)
2015 Human Molecular Genetics  
We used a knockout mouse model to functionally validate MMP10's role in influencing lung's susceptibility to cigarette smoke-induced emphysema.  ...  By integrating pathway analysis with population-based genomics, we unraveled biologic processes underlying pulmonary function traits and identified a candidate gene for obstructive lung disease.  ...  We used the default z-statistic for enrichment and second-best SNP to randomly associated signals in GSA-SNP. We queried Gene Ontology and KEGG databases for gene sets.  ... 
doi:10.1093/hmg/ddv378 pmid:26395457 pmcid:PMC4643644 fatcat:o2bd6xjskrgerpeiawkqxknr5a

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

P. D. Karp, S. M. Paley, M. Krummenacker, M. Latendresse, J. M. Dale, T. J. Lee, P. Kaipa, F. Gilham, A. Spaulding, L. Popescu, T. Altman, I. Paulsen (+2 others)
2009 Briefings in Bioinformatics  
Pathway Tools is a production-quality software environment for creating a type of model-organism database called a Pathway/Genome Database (PGDB).  ...  More than 800 PGDBs have been created using Pathway Tools by scientists around the world, many of which are curated DBs for important model organisms.  ...  Christos Ouzounis was a co-developer of the original metabolic pathway prediction algorithm, contributed an early version of the import/export system, and has been a source of much sound advice.  ... 
doi:10.1093/bib/bbp043 pmid:19955237 pmcid:PMC2810111 fatcat:efngfucyp5dgpjjrggtcgrss2e

The EcoCyc Database

Peter D. Karp, Daniel Weaver, Suzanne Paley, Carol Fulcher, Aya Kubo, Anamika Kothari, Markus Krummenacker, Pallavi Subhraveti, Deepika Weerasinghe, Socorro Gama-Castro, Araceli M. Huerta, Luis Muñiz-Rascado (+10 others)
2014 EcoSal Plus  
EcoCyc is an electronic reference source for E. coli biologists, and for biologists who work with related microorganisms.  ...  The web site and downloadable software contain tools for analysis of high-throughput datasets. In addition, a steady-state metabolic flux model is generated from each new version of EcoCyc.  ...  Acknowledgments Monica Riley led the curation of EcoCyc for many years, from its inception. Her efforts created the content for the first organism-scale metabolic database.  ... 
doi:10.1128/ecosalplus.esp-0009-2013 pmid:26442933 pmcid:PMC4243172 fatcat:7pymd2qgnfaw3bauwad5hox5l4

Protein Bioinformatics Databases and Resources [chapter]

Chuming Chen, Hongzhan Huang, Cathy H. Wu
2017 Msphere  
, PTM databases, ontologies, specialized protein databases, and other (miscellaneous) databases.  ...  For each category of databases listed in Table 1 , we select some representatives and describe them briefly in section 2.  ...  The 2015 release of BioCyc includes 7,667 Pathway/Genome Databases.  ... 
doi:10.1007/978-1-4939-6783-4_1 pmid:28150231 pmcid:PMC5506686 fatcat:rrclcq47p5hqrlffz2v2xexjoy
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