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The pathway ontology – updates and applications

Victoria Petri, Pushkala Jayaraman, Marek Tutaj, G Hayman, Jennifer R Smith, Jeff De Pons, Stanley JF Laulederkind, Timothy F Lowry, Rajni Nigam, Shur-Jen Wang, Mary Shimoyama, Melinda R Dwinell (+3 others)
2014 Journal of Biomedical Semantics  
The ontology allows for the standardized annotation of rat, and of human and mouse genes to pathway terms.  ...  The Pathway Ontology (PW) developed at the Rat Genome Database (RGD), covers all types of biological pathways, including altered and disease pathways and captures the relationships between them within  ...  Acknowledgements RGD is funded by grant HL64541 from the National Heart, Lung and Blood Institute on behalf of the National Institutes of Health.  ... 
doi:10.1186/2041-1480-5-7 pmid:24499703 pmcid:PMC3922094 fatcat:ljtud6bsx5dnhpn76pzpy6u5fq

The Rat Genome Database 2009: variation, ontologies and pathways

M. R. Dwinell, E. A. Worthey, M. Shimoyama, B. Bakir-Gungor, J. DePons, S. Laulederkind, T. Lowry, R. Nigram, V. Petri, J. Smith, A. Stoddard, S. N. Twigger (+1 others)
2009 Nucleic Acids Research  
access to the data in a variety of formats including linear genome viewers, pathway diagrams and biological ontologies.  ...  The Rat Genome Database (RGD, http://rgd.mcw. edu) was developed to provide a core resource for rat researchers combining genetic, genomic, pathway, phenotype and strain information with a focus on disease  ...  ACKNOWLEDGEMENTS In addition to the listed authors, we wish to thank the following group of committed people: Kent Brodie, Diane Munzenmaier, Andrew Patzer, and Stacy Zacher.  ... 
doi:10.1093/nar/gkn842 pmid:18996890 pmcid:PMC2686558 fatcat:nz5sci74qfegtnyvq2zzsfbiu4

INOH: ontology-based highly structured database of signal transduction pathways

S. Yamamoto, N. Sakai, H. Nakamura, H. Fukagawa, K. Fukuda, T. Takagi
2011 Database: The Journal of Biological Databases and Curation  
INOH applications INOH Ontology Viewer INOH Ontology Viewer (http://www.inoh.org/ontologyviewer) is a web application, which allows user to browse and search ontology by names, synonyms and IDs of INOH  ...  Due to the small-scale, manual curation, the newly curated and updated data is released once or twice a year. We update the released data, especially black-box events.  ... 
doi:10.1093/database/bar052 pmid:22120663 pmcid:PMC3225078 fatcat:bdc3krkuefhurcgb7y5qnp72dy

Bioinformatics: Basics, Development, and Future [chapter]

Ibrokhim Y. Abdurakhmonov
2016 Bioinformatics - Updated Features and Applications  
Bioinformatics research and application include the analysis of molecular sequence and genomics data; genome annotation, gene/protein prediction, and expression profiling; molecular folding, modeling,  ...  The emergence and advances of the bioinformatics field, however, are tightly associated with the computerized programming and software developments needed for the handling and structural and functional  ...  , and epigenetics elements into the bioinformatics annotation and ontology tools and software [120] .  ... 
doi:10.5772/63817 fatcat:otwfgrcmgfdglibb5afk2oktce

GO-Elite: a flexible solution for pathway and ontology over-representation

Alexander C. Zambon, Stan Gaj, Isaac Ho, Kristina Hanspers, Karen Vranizan, Chris T. Evelo, Bruce R. Conklin, Alexander R. Pico, Nathan Salomonis
2012 Computer applications in the biosciences : CABIOS  
We introduce GO-Elite, a flexible and powerful pathway analysis tool for a wide array of species, identifiers (IDs), pathways, ontologies and gene sets.  ...  In addition to the Gene Ontology (GO), GO-Elite allows the user to perform over-representation analysis on any structured ontology annotations, pathway database or biological IDs (e.g. gene, protein or  ...  Huang and Dr John H. Morris for their assistance in establishing the GO-Elite web service.  ... 
doi:10.1093/bioinformatics/bts366 pmid:22743224 pmcid:PMC3413395 fatcat:dayn6pkilrb4pctr77bo457g5e

Establishing a consensus for the hallmarks of cancer based on gene ontology and pathway annotations

Yi Chen, Fons. J. Verbeek, Katherine Wolstencroft
2021 BMC Bioinformatics  
Results Here we present the results of a comparative analysis of cancer hallmark mapping strategies, based on Gene Ontology and biological pathway annotation, from different studies.  ...  Background The hallmarks of cancer provide a highly cited and well-used conceptual framework for describing the processes involved in cancer cell development and tumourigenesis.  ...  Acknowledgements We would like thank the authors of Uhlen et al, and Sunjae Lee in particular, for his helpful advice and quick responses to queries about the reuse of their data.  ... 
doi:10.1186/s12859-021-04105-8 pmid:33823788 fatcat:vokdvxoqyjbgvfgchq37e7yj5u

Variation benchmark datasets: update, criteria, quality and applications [article]

Anasua Sarkar, Yang Yang, Mauno Vihinen
2019 bioRxiv   pre-print
The updated VariBench facilitates development and testing of new methods and comparison of obtained performance to previously published methods.  ...  Then there are several datasets for molecule-specific and disease-specific applications, as well as one dataset for variation phenotype effects.  ...  The latter has a link due to its huge size, the others since they are databases and as such easy to use directly and updated by third parties.  ... 
doi:10.1101/634766 fatcat:ldyqezaj5nbefow72db32zd7hu

Variation benchmark datasets: update, criteria, quality and applications

2019 Database: The Journal of Biological Databases and Curation  
The updated VariBench facilitates development and testing of new methods and comparison of obtained performances to previously published methods.  ...  Then there are several datasets for molecule-specific and disease-specific applications, as well as one dataset for variation phenotype effects.  ...  Funding The financial support from Vetenskapsrådet (VR 2015-02510), Swedish Cancer Society (CAN 2017/699) and National Natural Science Foundation of China (61602332) is gratefully acknowledged.  ... 
doi:10.1093/database/baz117 pmid:32016318 pmcid:PMC6997940 fatcat:f2pr6okwkfcezl64pjwphzl2ui

ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks

Gabriela Bindea, Bernhard Mlecnik, Hubert Hackl, Pornpimol Charoentong, Marie Tosolini, Amos Kirilovsky, Wolf-Herman Fridman, Franck Pagès, Zlatko Trajanoski, Jérôme Galon
2009 Computer applications in the biosciences : CABIOS  
ClueGO integrates Gene Ontology (GO) terms as well as KEGG/BioCarta pathways and creates a functionally organized GO/pathway term network.  ...  A one-click update option allows ClueGO to automatically download the most recent GO/KEGG release at any time.  ...  ACKNOWLEDGEMENTS We thank A Van Cortenbosch for the name of the tool. Conflict of Interest: none declared.  ... 
doi:10.1093/bioinformatics/btp101 pmid:19237447 pmcid:PMC2666812 fatcat:6q3lnfp7fbgk5dkuj5h2tn7tim

Application of Bioinformatics Methodologies in the Fields of Skin Biology and Dermatology [chapter]

Sidra Younis, Valeriia Shnayder, Miroslav Blumenberg
2016 Bioinformatics - Updated Features and Applications  
The psoriatic patients Application of Bioinformatics Methodologies in the Fields of Skin Biology and Dermatology  ...  Microarrays empower us to see both the "forest and the trees."  ...  Starting with the uploaded list, DAVID make available "tables" containing details known about the genes, "charts" which contain over-represented pathways, ontological categories, etc., as well as "clusters  ... 
doi:10.5772/63799 fatcat:lq7mbyal6bcedacklqvdp24byq

Bioinformatics for RNA‐Seq Data Analysis [chapter]

Shanrong Zhao, Baohong Zhang, Ying Zhang, William Gordon, Sarah Du, Theresa Paradis, Michael Vincent, David von Schack
2016 Bioinformatics - Updated Features and Applications  
Bioinformatics -Updated Features and Applications Bioinformatics for RNA-Seq Data Analysis http://dx.doi.org/10.5772/63267 Bioinformatics for RNA-Seq Data Analysis http://dx.  ...  technologies such as Illumina and the corresponding data analysis workflow is summarized in Figure 1 .  ...  Functional enrichment analyses rely upon annotation databases such as Gene Ontology (GO) [67] , Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways [68] , DAVID [69] , and other commercial knowledge  ... 
doi:10.5772/63267 fatcat:vud46vhdijalflsj3ktawkvhse

An ontology-driven semantic mashup of gene and biological pathway information: Application to the domain of nicotine dependence

Satya S. Sahoo, Olivier Bodenreider, Joni L. Rutter, Karen J. Skinner, Amit P. Sheth
2008 Journal of Biomedical Informatics  
We created the Entrez Knowledge Model (EKoM), an information model in OWL for the gene resources, and integrated it with the extant BioPAX ontology designed for pathway resources.  ...  Methods: We use an ontology-driven approach to integrate two gene resources (Entrez Gene and Homol-oGene) and three pathway resources (KEGG, Reactome and BioCyc), for five organisms, including humans.  ...  The authors want to thank Lee Peters who created the RDF store in Oracle and helped craft and run the SPARQL queries and Jonathan Pollock for valuable input on model organism databases.  ... 
doi:10.1016/j.jbi.2008.02.006 pmid:18395495 pmcid:PMC2766186 fatcat:2pyc76cacvfl5npklwhksksb7a

Updating annotations with the distributed annotation system and the automated sequence annotation pipeline

William Speier, Michael F. Ochs
2012 Computer applications in the biosciences : CABIOS  
integrates annotations from multiple array platforms and provides unified annotations in an R environment; and the third wraps the UniProt database for integration with the SPICE DAS client.  ...  The integration between BioDAS ProServer and Automated Sequence Annotation Pipeline (ASAP) provides an interface for querying diverse annotation sources, chaining and linking results, and standardizing  ...  In this example, the Gene Ontology and pathway annotations are linked across platforms and the output is combined into an R environment object.  ... 
doi:10.1093/bioinformatics/bts530 pmid:22945787 pmcid:PMC3476339 fatcat:kjyc6smgavc2xfcwaqxr77lp2a

Update of gene expression/methylation and MiRNA profiling in colorectal cancer; application in diagnosis, prognosis, and targeted therapy

Amir Mehrgou, Shahram Teimourian, Eduardo Andrés-León
2022 PLoS ONE  
Utilizing R packages (DOSE, Enrichplot, and clusterProfiler) and DAVID database, the Functional Enrichment analysis and the detection of KEGG pathways were performed.  ...  Conclusion In addition to diagnostic- and prognostic-applicability, the discerned profiles can assist in targeted therapy and current therapeutic strategies.  ...  Protein-protein interactions and determination of hub genes As shown in Functional enrichment analysis and KEGG pathways The gene-ontology analysis of vDEGs produced three terms in the context of biological  ... 
doi:10.1371/journal.pone.0265527 pmid:35333898 pmcid:PMC8956198 fatcat:3dcis2lh25bdxeuiqjqbf4t45e

Use of a modular ontology and a semantic annotation tool to describe the care pathway of patients with amyotrophic lateral sclerosis in a coordination network

Sonia Cardoso, Pierre Meneton, Xavier Aimé, Vincent Meininger, David Grabli, Gilles Guezennec, Jean Charlet
2021 PLoS ONE  
We also created a semantic annotation tool specific to the French language and the specificities of our corpus, the Ontology-Based Semantic Annotation Module (OnBaSAM), using the OntoPaRON ontology as  ...  The objective of this study was to describe the care pathway of patients with amyotrophic lateral sclerosis (ALS) based on real-life textual data from a regional coordination network, the Ile-de-France  ...  Alzheimer's disease, Parkinson's disease), facilitation of the updating and handling of knowledge by taking the evolution of systems into account (social assistance system, medical advances), and the promotion  ... 
doi:10.1371/journal.pone.0244604 pmid:33406098 pmcid:PMC7787442 fatcat:lonk2qqffzazji33dczxxd57t4
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