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The Rat Genome Database Curators: Who, What, Where, Why

Mary Shimoyama, G. Thomas Hayman, Stanley J. F. Laulederkind, Rajni Nigam, Timothy F. Lowry, Victoria Petri, Jennifer R. Smith, Shur-Jen Wang, Diane H. Munzenmaier, Melinda R. Dwinell, Simon N. Twigger, Howard J. Jacob (+1 others)
2009 PLoS Computational Biology  
Citation: Shimoyama M, Hayman GT, Laulederkind SJF, Nigam R, Lowry TF, et al. (2009) The Rat Genome Database Curators: Who, What, Where, Why.  ...  One database where such curation work takes place is the Rat Genome Database (RGD; [4] .  ... 
doi:10.1371/journal.pcbi.1000582 pmid:19956751 pmcid:PMC2775909 fatcat:3uyifumxofel3axr3fcbhlop4m

OUP accepted manuscript

2019 Database: The Journal of Biological Databases and Curation  
The Rat Genome Database (RGD) PhenoMiner tool has provided the first step in this effort by standardizing and integrating data from individual studies as well as NBRP and PhysGen. iii Methods Our work  ...  Current resources such as NBRP and PhysGen provided some preliminary work in rat phenotype databases.  ...  Genome Database and PhenoMiner The Rat Genome Database (rgd. mcw. edu) is the most comprehensive data repository and informatics platform for the laboratory rat (27) .  ... 
doi:10.1093/database/baz037 fatcat:ifj26ad6grh2vcqvbtnxoevdwq

Non-curated distributed databases for experimental data and models in neuroscience

R C Cannon, F W Howell, N H Goddard, E De Schutter
2002 Network  
Such a scheme has advantages in the ease of database creation and in the equitable assignment of perceived intellectual property by keeping the control of data in the hands of the experts who collected  ...  One axis on which they may be distinguished is the degree of top-down control, or curation, involved in data entry.  ...  Acknowledgements This work is funded through the United Kingdom Medical Research Council, a visiting postdoctoral fellowship to Robert Cannon from the FWO, Belgium, and through EC grants QLG3-1999-00763  ... 
doi:10.1088/0954-898x_13_3_310 pmid:12222822 fatcat:rf7yvnluprbjjdbws5sdfu42ei

Text Mining to Support Gene Ontology Curation and Vice Versa [chapter]

Patrick Ruch
2016 Msphere  
Databases workfl ows must start recording explicitly all the data they curate and ideally also some of the data they do not curate.  ...  In this chapter, we explain how text mining can support the curation of molecular biology databases dealing with protein functions.  ...  While most of these systems seem exploratory studies, some seem deeply integrated in the curation workfl ow, as shown by the OntoMate tool designed by the Rat Genome Database [ 17 ] , the STRING DB for  ... 
doi:10.1007/978-1-4939-3743-1_6 pmid:27812936 fatcat:qegtjj5flvbqpj4evpe3zttb24

MAPanalyzer: a novel online tool for analyzing microtubule-associated proteins

Yuan Zhou, Shiping Yang, Tonglin Mao, Ziding Zhang
2015 Database: The Journal of Biological Databases and Curation  
Benchmarks on the curated testing dataset and the Arabidopsis thaliana whole genome dataset have shown that the proposed predictor outperforms not only its own components (i.e. the machine learning classifiers  ...  In the database, a core MAP dataset, which is fully manually curated from the literature, is further enriched by MAP information collected via automated pipeline.  ...  Lei Zhu at China Agricultural University for her advices about data curation. Conflict of interest. None declared.  ... 
doi:10.1093/database/bav108 pmid:26568329 pmcid:PMC4644220 fatcat:tlsj36s3dncgzoeotd4o6qc4xu

AnnotCompute: annotation-based exploration and meta-analysis of genomics experiments

J. Zheng, J. Stoyanovich, E. Manduchi, J. Liu, C. J. Stoeckert
2011 Database: The Journal of Biological Databases and Curation  
Our system leverages semantic annotations of functional genomics experiments with controlled vocabulary and ontology terms, such as those from the MGED Ontology, to compute conceptual dissimilarities between  ...  The ever-increasing scale of biological data sets, particularly those arising in the context of high-throughput technologies, requires the development of rich data exploration tools.  ...  Acknowledgements We thank the external evaluators who participated in our user study for helping assess the effectiveness of AnnotCompute.  ... 
doi:10.1093/database/bar045 pmid:22190598 pmcid:PMC3244265 fatcat:5ylxvysbjjhglalbycnfws3f4e

Automation of gene function prediction through modeling human curators' decisions in GO phylogenetic annotation project [article]

Haiming Tang, Paul D Thomas, Huaiyu Mi
2018 arXiv   pre-print
Here we present an automated pipeline for phylogenetic annotation and inference, which simulates the standard annotation procedures of curators and models the curators' decisions during the manual curation  ...  The Gene Ontology Consortium launched the GO-PAINT project (Phylogenetic Annotation and INference Tool) 9 years ago and is currently being used in the GO Reference Genome Annotation Project to support  ...  It may seem trivial to PAINT curators who are experiences biologists, but algorithms have no biological knowledge.  ... 
arXiv:1802.07204v1 fatcat:q62otjeidbc5zoxlghkqlmlvi4

Challenges of Connecting Chemistry to Pharmacology: Perspectives from Curating the IUPHAR/BPS Guide to PHARMACOLOGY

Christopher Southan, Joanna L. Sharman, Elena Faccenda, Adam J. Pawson, Simon D. Harding, Jamie A. Davies
2018 ACS Omega  
This has been achieved by populating our database with expert-curated relationships between documents, assays, quantitative results, chemical structures, their locations within the documents, and the protein  ...  Connecting chemistry to pharmacology has been an objective of Guide to PHARMACOLOGY (GtoPdb) and its precursor the International Union of Basic and Clinical Pharmacology Database (IUPHAR-DB) since 2003  ...  The information in the paper was consistent with the proposed INN: list 104 WHO drug information, Vol. 24, No. 4, 2010, where alvelestat was first declared as n2s, as shown in Figure 7 .  ... 
doi:10.1021/acsomega.8b00884 pmid:30087946 pmcid:PMC6070956 fatcat:47x2hqwgmbaqbgkkuou2425bte

Accessing Expert-Curated Pharmacological Data in the IUPHAR/BPS Guide to PHARMACOLOGY

Joanna L. Sharman, Simon D. Harding, Christopher Southan, Elena Faccenda, Adam J. Pawson, Jamie A. Davies
2018 Current Protocols in Bioinformatics  
The IUPHAR/BPS Guide to PHARMACOLOGY is an expert-curated, openaccess database of information on drug targets and the substances that act on them.  ...  The database includes concise overviews of the properties of 1,700 data-supported human drug targets and related proteins, divided into families, and 9,000 small molecule and peptide experimental ligands  ...  This work was supported by IUPHAR and the BPS.  ... 
doi:10.1002/cpbi.46 pmid:30040201 fatcat:nnzrqfhpjramdcaibug3zfxihu

A crowdsourcing workflow for extracting chemical-induced disease relations from free text

Tong Shu Li, Àlex Bravo, Laura I. Furlong, Benjamin M. Good, Andrew I. Su
2016 Database: The Journal of Biological Databases and Curation  
Although expert manual curation is the standard method for extracting these relations from the literature, it is expensive and impractical to apply to large numbers of documents, and therefore alternative  ...  All code and results are publicly available at crowd_cid_relex Database URL: V C The Author(s)  ...  Acknowledgements We would like to thank Dr Zhiyong Lu for sending us the evaluation dataset and for allowing us to participate in the BioCreative Database, Vol. 2016, Article ID baw051 challenge.  ... 
doi:10.1093/database/baw051 pmid:27087308 pmcid:PMC4834205 fatcat:cwibv4vsofapxfqi6qufnm6ep4

Critical Assessment of Protein Intrinsic Disorder Prediction [article]

Marco Necci, Damiano Piovesan, Silvio C E Tosatto, CAID Predictors, DisProt Curators
2020 bioRxiv   pre-print
Intriguingly, some of the top performing methods are also among the fastest.  ...  The Critical Assessment of protein Intrinsic Disorder prediction (CAID) experiment was established as a community-based blind test to determine the state of the art in predicting intrinsically disordered  ...  ZD acknowledges funding from ELTE Thematic Excellence Programme (ED-18-1-2019-0030) supported by the Hungarian Ministry for Innovation and Technology and the "Lendület" grant from the Hungarian Academy  ... 
doi:10.1101/2020.08.11.245852 fatcat:tzys2dxya5fibghjjglpmt7p2i

When humans are the exception: Cross-species databases at the interface of biological and clinical research

Sabina Leonelli
2012 Social Studies of Science  
This paper identifies and discusses four key problems encountered by database curators when integrating human and non-human data within the same database: (1) picking criteria for what counts as reliable  ...  By considering database development through the eyes of curators, this study casts new light on the complex conjunctions of biological and clinical practice, model organisms and human subjects, and material  ...  Acknowledgments This research was funded by the ESRC as part of the ESRC Centre for Genomics in Society.  ... 
doi:10.1177/0306312711436265 pmid:22848998 fatcat:qpazntpt4negbda4ev2t4qswbq

In silico tools for signal transduction research

J. M. Lindvall
2003 Briefings in Bioinformatics  
The databases considered here can provide a well-structured overview on the subject and a basis for advanced bioinformatics analysis to interpret the function of genomic sequences or to analyse signalling  ...  , ie making sense of the molecular interactions in a context-dependent way. (c) Where are the signalling events taking place?, eg when a resting cell becomes activated.  ...  Acknowledgment The authors would like to thank Dr Tahmina C.  ... 
doi:10.1093/bib/4.4.315 pmid:14725344 fatcat:6jinsfbdpfcdvd4lcouhfoqfyy

In the beginning there was babble…

Daniel J Klionsky, Elspeth A. Bruford, J. Michael Cherry, Jonathan Hodgkin, Stanley J.F. Laulederkind, Amy G. Singer
2012 Autophagy  
Similarly, the HUGO Gene Nomenclature Committee (HGNC), the International Committee on Standardized Genetic Nomenclature for Mice, curators at the Rat Genome Database, and the Zebrafish Nomenclature Committee  ...  to ask who makes the decision about which name is the standard one, and/or who is in charge of maintaining the established nomenclature?  ... 
doi:10.4161/auto.20665 pmid:22836666 pmcid:PMC3625114 fatcat:o55l5zlsqzadhaxijybfc5iada

Facets and measures of gene ontology annotation quality in model organism databases

W. John MacMullen
2007 Proceedings of the American Society for Information Science and Technology  
quality of annotations made by one or more human database curators.  ...  degrees variation of GO annotations made by one or more human database curators.  ...  musculus RGD, the Rat Genome Database, for Rattus norvegicus SGD, the Saccaromyces Genome Database, for Saccharomyces cerevisiae (yeast) TAIR, the Arabidopsis Information Resource, for Arabidopsis thaliana  ... 
doi:10.1002/meet.14504301260 fatcat:orynl5czgjbuvcvceap7tqywwa
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