A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
Filters
AN EVIDENCE ONTOLOGY FOR USE IN PATHWAY/GENOME DATABASES
2003
Biocomputing 2004
Preserved Fulltext
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
2004
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2018; you can also visit the original URL.
The file type is application/pdf.
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
2011
Nucleic Acids Research
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2018; you can also visit the original URL.
The file type is application/pdf.
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
2005
Nucleic Acids Research
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
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
2012
Database: The Journal of Biological Databases and Curation
Preserved Fulltext
The Internet Archive has a preservation copy of this work in our general collections.
The file type is application/pdf.
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
2007
Nucleic Acids Research
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
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
2009
Nucleic Acids Research
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2018; you can also visit the original URL.
The file type is application/pdf.
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
2004
Bioinformatics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2018; you can also visit the original URL.
The file type is application/pdf.
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
2013
Nucleic Acids Research
Preserved Fulltext
The Internet Archive has a preservation copy of this work in our general collections.
The file type is application/pdf.
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]
2020
arXiv
pre-print
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
Other Versions
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
2022
Frontiers in Bioinformatics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2022; you can also visit the original URL.
The file type is application/pdf.
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
2015
Human Molecular Genetics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
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
2009
Briefings in Bioinformatics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
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
2014
EcoSal Plus
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
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]
2017
Msphere
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
, 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
« Previous
Showing results 1 — 15 out of 263 results