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Evaluating the predictive accuracy of curated biological pathways in a public knowledgebase

Adam J Wright, Marija Orlic-Milacic, Karen Rothfels, Joel Weiser, Quang M Trinh, Bijay Jassal, Robin A Haw, Lincoln D Stein
2022 Database: The Journal of Biological Databases and Curation  
Abstract Reactome is a database of human biological pathways manually curated from the primary literature and peer-reviewed by experts.  ...  Out of the 847 test cases, curators' predictions agreed with the experimental evidence in 670 and disagreed in 177 cases, resulting in ∼81% overall accuracy.  ...  Reactome team members, in particular Dr Guanming Wu, Dr Peter D'Eustachio and Dr Lisa Matthews for helpful discussions of the topic and data presented in this manuscript.  ... 
doi:10.1093/database/baac009 pmid:35348650 pmcid:PMC9216552 fatcat:bqwvge623zb3xf54hjlzn7dm74

FunSecKB: the Fungal Secretome KnowledgeBase

G. Lum, X. J. Min
2011 Database: The Journal of Biological Databases and Curation  
The entries were mapped to the UniProt database and any annotations of subcellular locations that were either manually curated or computationally predicted were included in FunSecKB.  ...  The Fungal Secretome KnowledgeBase (FunSecKB) provides a resource of secreted fungal proteins, i.e. secretomes, identified from all available fungal protein data in the NCBI RefSeq database.  ...  Acknowledgements We thank Gary Walker at YSU and the anonymous reviewers for providing helpful comments on improving the article. Conflict of interest. None Declared.  ... 
doi:10.1093/database/bar001 pmid:21300622 pmcid:PMC3263735 fatcat:lrvnbcp26belff5z7d363npxna

Systems biology model repository for macrophage pathway simulation

M. Nagasaki, A. Saito, A. Fujita, G. Tremmel, K. Ueno, E. Ikeda, E. Jeong, S. Miyano
2011 Bioinformatics  
The Macrophage Pathway Knowledgebase (MACPAK) is a computational system that allows biomedical researchers to query and study the dynamic behaviors of macrophage molecular pathways.  ...  It integrates the knowledge of 230 reviews that were carefully checked by specialists for their accuracy and then converted to 230 dynamic mathematical pathway models.  ...  Since MACPAK is manually curated (by four researchers that built, checked and double-checked the CSML models), the quotations from the original publication can be used as a benchmark to test and evaluate  ... 
doi:10.1093/bioinformatics/btr173 pmid:21505034 fatcat:vxxnphdk5zcutam4f2sv6dwpou

PlantSecKB: the Plant Secretome and Subcellular Proteome KnowledgeBase

Gengkon Lum, John Meinken, Jessica Orr, Stephanie Frazier, Xiang Min
2014 Computational Molecular Biology  
The database contains information collected from three sources: (1) subcellular locations that were curated or computationally predicted in the UniProtKB; (2) subcellular locations and features predicted  ...  We developed the Plant Secretome and Subcellular Proteome KnowledgeBase (PlantSecKB) for the plant research community to access and curate plant protein subcellular locations, with a focus on secreted  ...  We have evaluated the prediction accuracy of the methods we used in this study and compared it with the accuracies of other methods (Table 1) (Min, 2010; Meinken and Min, 2012) .  ... 
doi:10.5376/cmb.2014.04.0001 fatcat:y2ag2yovf5cwljf3rpkl3evahm

Exploring soybean metabolic pathways based on probabilistic graphical model and knowledge-based methods

Jie Hou, Gary Stacey, Jianlin Cheng
2015 EURASIP Journal on Bioinformatics and Systems Biology  
The completion of soybean genome sequence led to a number of transcriptomic studies (RNA-seq), which provide a resource for gene discovery and functional analysis.  ...  The results show that this method can predict new relationships between genes, improving on traditional reference pathway maps.  ...  Acknowledgements The work was partially supported by a NSF grant (IOS1025752), a grant from the US Department of Energy (DE-SC0004898), an NSF CAREER award (DBI1149224), and an NIH grant (R01GM093123).  ... 
doi:10.1186/s13637-015-0026-5 pmid:28194174 pmcid:PMC5270328 fatcat:z47anngrk5ewtlygzsmmek6jba

Computational Systems Biology Approach for the Study of Rheumatoid Arthritis: From a Molecular Map to a Dynamical Model

Vidisha Singh, Marek Ostaszewski, George D Kalliolias, Gilles Chiocchia, Robert Olaso, Elisabeth Petit-Teixeira, Tomáš Helikar, Anna Niarakis
2017 Genomics and Computational Biology  
In this work we present a systematic effort to summarize current biological pathway knowledge concerning Rheumatoid Arthritis (RA).  ...  We are constructing a detailed molecular map based on exhaustive literature scanning, strict curation criteria, re-evaluation of previously published attempts and most importantly experts' advice.  ...  The assembly of a molecular map comprising biological pathways of interest and integrating information from literature and public databases could serve as the first step.  ... 
doi:10.18547/gcb.2018.vol4.iss1.e100050 pmid:29951575 pmcid:PMC6016388 fatcat:h3437qmtfrbtpnguopynly5teq

MetazSecKB: the human and animal secretome and subcellular proteome knowledgebase

John Meinken, Gary Walker, Chester R. Cooper, Xiang Jia Min
2015 Database: The Journal of Biological Databases and Curation  
The subcellular location of a protein is a key factor in determining the molecular function of the protein in an organism.  ...  MetazSecKB is a secretome and subcellular proteome knowledgebase specifically designed for metazoan, i.e. human and animals.  ...  Feng Yu for his assistance in maintaining the server. Conflict of interest. None declared.  ... 
doi:10.1093/database/bav077 pmid:26255309 pmcid:PMC4529745 fatcat:l2lolknaqjeqdlmfv66b5fq72e

FunSecKB2: a fungal protein subcellular location knowledgebase

John Meinken, David K. Asch, Kofi A. Neizer-Ashun, Guang-Hwa Chang, Chester R.Cooper JR, Xiang Jia Min
2014 Computational Molecular Biology  
The assignments of protein subcellular locations were based on curated information and prediction using seven computational tools.  ...  A primary analysis revealed that the secretome size of a fungal species is one of the determining factors to its lifestyle.  ...  Feng Yu for their assistance in maintaining the server and Jessica Orr and Stephanie Frazier for manually curating secreted proteins.  ... 
doi:10.5376/cmb.2014.04.0007 fatcat:rojts6icynaz5gfzpxvyi3hiwy

Literature-based predictions of treatments for genetic disease pathology [article]

Cole A Deisseroth, Won-Seok Lee, Ji-Yoen Kim, Hyun-Hwan Jeong, Julia Wang, Huda Yahya Zoghbi, Zhandong Liu
2022 bioRxiv   pre-print
We compare PARMESAN's drug-gene hypotheses to all of the drug-gene relationships displayed by DrugBank, and see a strong correlation between the prediction score and the predictive accuracy such that predictions  ...  This publicly available tool provides an automated way to prioritize drug screens to target the most-promising drugs to test, thereby saving time and resources in the development of therapeutics for genetic  ...  Acknowledgements: We thank Roopashri Holehonnur, Nigel Lee, Dongxue Mao, Sasidhar Pasupuleti, Ying-Wooi Wan, Shinya Yamamoto, Megan Mair, Tarik Onur, Juan Botas, and the members of the labs of Huda Zoghbi  ... 
doi:10.1101/2022.09.08.506253 fatcat:twga7bpfizaipfti5qgqsztnne

Collaborative, Multidisciplinary Evaluation of Cancer Variants Through Virtual Molecular Tumor Boards Informs Local Clinical Practices

Shruti Rao, Beth Pitel, Alex H. Wagner, Simina M. Boca, Matthew McCoy, Ian King, Samir Gupta, Ben Ho Park, Jeremy L. Warner, James Chen, Peter K. Rogan, Debyani Chakravarty (+3 others)
2020 JCO Clinical Cancer Informatics  
METHODS In this review, we evaluate and summarize the landscape of available tools, resources, and evidence used in the evaluation of somatic and germline tumor variants within the context of molecular  ...  CONCLUSION Advances in cancer genomics interpretation aid in better patient and disease classification, more streamlined identification of relevant literature, and a more thorough review of available treatments  ...  of early-stage oncology drugs or biologics and 91% of late-stage drugs from pharmaceutical companies involved the use of biomarker tests. 3 In addition, over a third of drug approvals in 2019 included  ... 
doi:10.1200/cci.19.00169 pmid:32644817 pmcid:PMC7397775 fatcat:6hwpu2yivfacnfj2fthnp7akwu

Expert curation for building network-based dynamical models: a case study on atherosclerotic plaque formation

Amel Bekkar, Anne Estreicher, Anne Niknejad, Cristina Casals-Casas, Alan Bridge, Ioannis Xenarios, Julien Dorier, Isaac Crespo
2018 Database: The Journal of Biological Databases and Curation  
Abstract Knowledgebases play an increasingly important role in scientific research, where the expert curation of biological knowledge in forms that are amenable to computational analysis (using ontologies  ...  In this work, we demonstrate how expert curation can also play a more direct role in research, by supporting the use of network-based dynamical models to study a specific biological process.  ...  Examples of such curated knowledgebases are UniProtKB/Swiss-Prot (12) and IMEx (13) .  ... 
doi:10.1093/database/bay031 pmid:29688381 pmcid:PMC5887269 fatcat:cqjzklxwlvbe5ls4td4642rxne

Genome-Scale Metabolic Modeling Enables In-Depth Understanding of Big Data

Anurag Passi, Juan D. Tibocha-Bonilla, Manish Kumar, Diego Tec-Campos, Karsten Zengler, Cristal Zuniga
2021 Metabolites  
Finally, we provide a perspective in emerging areas, such as annotation, data managing, and machine learning, in which GEMs will play a key role in the further utilization of Big Data.  ...  In addition to the up-to-date review of GEMs currently available, we assessed a plethora of tools for developing new GEMs that include macromolecular expression and dynamic resolution.  ...  Recently, machine learning (ML) has been applied to improve the accuracy of GEMs by combining the knowledgebase of the biological system with the predictive power of ML [106] .  ... 
doi:10.3390/metabo12010014 pmid:35050136 pmcid:PMC8778254 fatcat:5fmdx5rjj5aqnbdm3f2i635mwy

The Gene Ontology Annotation (GOA) Database: sharing knowledge in Uniprot with Gene Ontology

E. Camon
2004 Nucleic Acids Research  
The GOA project is grateful for the support of Grants QRLT-2001-00015 and QLRI-2000-00981 of the European Commission and a supplementary NIH grant, 1R01HGO2273-01.  ...  ACKNOWLEDGEMENTS We especially thank all colleagues worldwide who have contributed to the information content of the GOA data set and to the development of annotation and retrieval tools.  ...  This was facilitated with the help of UniProt curation, which led to the successful mapping to GO from existing references, resources and publications.  ... 
doi:10.1093/nar/gkh021 pmid:14681408 pmcid:PMC308756 fatcat:aqclkomfwrgdfeeaq6ik2tqabe

Reconstruction of metabolic pathways by combining probabilistic graphical model-based and knowledge-based methods

Qi Qi, Jilong Li, Jianlin Cheng
2014 BMC Proceedings  
In contrast, ab initio metabolic network construction methods can predict novel reactions and interactions, but its accuracy tends to be low leading to a lot of false positives.  ...  Using individual reactions and interactions extracted from different pathways of many organisms to guide pathway construction is new and improves both the coverage and accuracy of metabolic pathway construction  ...  Declarations The publication charges for this article were funded by the University of Missouri, Columbia. This article has been published as part of BMC Proceedings  ... 
doi:10.1186/1753-6561-8-s6-s5 pmid:25374614 pmcid:PMC4202177 fatcat:rsjbpl63kvfghbxeijiraocela

Expansion of the Gene Ontology knowledgebase and resources

2016 Nucleic Acids Research  
In this update, we summarize the current contents of the GO knowledgebase, and present several new features and improvements that have been made to the ontology, the annotations and the tools.  ...  The Gene Ontology (GO) is a comprehensive resource of computable knowledge regarding the functions of genes and gene products.  ...  ACKNOWLEDGEMENTS We want to acknowledge the broad community of scientists who have contributed to the GO knowledgebase, as biocurators and software developers (see http://geneontology. org/page/acknowledgments-contributors  ... 
doi:10.1093/nar/gkw1108 pmid:27899567 pmcid:PMC5210579 fatcat:h7hb33vstnffpbjaxsfnxflcyy
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