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With Registered Reports Towards Large Scale Data Curation [article]

Steffen Herbold
2020 arXiv   pre-print
Within this paper, we propose the use of registered reports to scale the curation of manually validated data.  ...  The scale of manually validated data is currently limited by the effort that small groups of researchers can invest for the curation of such data.  ...  Registered Reports The Center for Open Science states that with a registered report "you're simply specifying to your plan in advance, before you gather data." 1 The pre-registration of the report defines  ... 
arXiv:2001.01972v1 fatcat:ppjm266rx5gftptcpitrnnxnja

ECDL 2008 Conference Report

José H. Canós, Pablo de la Fuente
2008 D-Lib Magazine  
However, increasingly domains, especially related to e-science, are being found where large-scale workflows are built by assembling other workflows and/or services and later (re)used to produce data on  ...  Thus, having well-curated workflows is becoming a necessity in large e-science environments. Prof.  ... 
doi:10.1045/november2008-canos fatcat:3hh7wbfxa5hyfdzvgdhxyufwia

A framework for organizing cancer-related variations from existing databases, publications and NGS data using a High-performance Integrated Virtual Environment (HIVE)

Tsung-Jung Wu, Amirhossein Shamsaddini, Yang Pan, Krista Smith, Daniel J. Crichton, Vahan Simonyan, Raja Mazumder
2014 Database: The Journal of Biological Databases and Curation  
Currently, BioMuta has 26 cancer types with 13 896 small-scale and 308 986 large-scale study-derived variations.  ...  Because of the petabytes of data and information present in NGS primary repositories, a platform HIVE (High-performance Integrated Virtual Environment) for storing, analyzing, computing and curating NGS  ...  Yu for help with database and interface development, S. Kelly for EDRN data integration and Dr V.  ... 
doi:10.1093/database/bau022 pmid:24667251 pmcid:PMC3965850 fatcat:cob43ptnp5hgnfmouec26ozvp4

Fluxdata.org: Publication and Curation of Shared Scientific Climate and Earth Sciences Data

Marty Humphrey, Deb Agarwal, Catharine van Ingen
2009 2009 Fifth IEEE International Conference on e-Science  
creation of such synthesis datasets curation infrastructure to support management of large- that continue to grow and evolve with new data, data scale shared scientific data such as synthesis  ...  Large- contributor of the raw data and wants the data to be used scale virtual organizations such as CASA/LEAD [1], to advance science (but with proper attribution).  ... 
doi:10.1109/e-science.2009.25 dblp:conf/eScience/HumphreyAI09 fatcat:xzgx6i5wvvdt7mqfmm2tpldu64

Gene Variant Databases and Sharing: Creating a Global Genomic Variant Database for Personalized Medicine

Lora J.H. Bean, Madhuri R. Hegde
2016 Human Mutation  
Large-scale sequencing done in both research and diagnostic laboratories has linked many new genes to rare diseases, but has also generated a number of variants that we cannot interpret today.  ...  users with different goals.  ...  of resources that could otherwise be directed towards a single streamlined effort with a uniform format for data collection and reporting.  ... 
doi:10.1002/humu.22982 pmid:26931283 pmcid:PMC4846518 fatcat:5m4n7x57ivafrhprxuwt6mkgz4

FINDbase: a relational database recording frequencies of genetic defects leading to inherited disorders worldwide

Sjozef van Baal, Polynikis Kaimakis, Manyphong Phommarinh, Daphne Koumbi, Harry Cuppens, Francesca Riccardino, Milan Macek, Charles R. Scriver, George P. Patrinos
2006 Nucleic Acids Research  
Registered users from three different groups, namely administrator, national coordinator and curator, are responsible for database curation and/or data entry/correction online via a password-protected  ...  disorder name and the related gene, accompanied by links to any corresponding locus-specific mutation database, to the respective Online Mendelian Inheritance in Man entries and the mutation together with  ...  The data entry page can be found in the 'Curators' section. Once logged in, the registered user connects with Publication data editor, for further guidance through the data entry procedure.  ... 
doi:10.1093/nar/gkl934 pmid:17135191 pmcid:PMC1747180 fatcat:laovpgryerbhhnaz23itzvwt3e

Guidelines for Data Acquisition, Quality & Curation for Observational Research Designs (DAQCORD)

Ari Ercole, Vibeke Brinck, Jilske Huijben, Pradeep George, Ramona Hicks, Michael Jarrett, Mary Vassar, Lindsay Wilson, the DAQCORD collaborators
2020 Journal of Clinical and Translational Science  
, either alone or in combination with other data sets.  ...  We aimed to develop a framework for the design, documentation and reporting of data curation methods in order to advance the scientific rigour, reproducibility and analysis of the data.  ...  We formed a Steering Committee consisting of seven individuals with professional backgrounds in informatics and data management and/or experience in data curation/data set design in large-scale observational  ... 
doi:10.1017/cts.2020.24 pmid:33244417 pmcid:PMC7681114 fatcat:syctyr6m3zekhauij6a2osmnh4

Big Data Curation [chapter]

André Freitas, Edward Curry
2016 New Horizons for a Data-Driven Economy  
large-scale data curation.  ...  registered member with curation rights, directly curate the data or remove erroneous data.  ... 
doi:10.1007/978-3-319-21569-3_6 fatcat:v4lm3qb75fde5jrd6afdrll2ea

Data Curation through Catalogs: A Repository-Independent Model for Data Discovery

Helenmary Sheridan, Anthony J. Dellureficio, Melissa A. Ratajeski, Sara Mannheimer, Terrie R. Wheeler
2021 Journal of eScience Librarianship  
Institutional data repositories are the acknowledged gold standard for data curation platforms in academic libraries.  ...  The article also reports on the development of a community of practice for data catalogs and data discovery initiatives.  ...  Acknowledgements The authors would like to thank Ian Lamb for writing the software code for the original data catalog that was used by the Data Catalog Collaboration Project (DCCP) which became the DDC  ... 
doi:10.7191/jeslib.2021.1203 fatcat:ak7ztu72lbby5lh3a4whmqkd4a

The Digital Index of North American Archaeology: networking government data to navigate an uncertain future for the past

Eric C. Kansa, Sarah W. Kansa, Josh J. Wells, Stephen J. Yerka, Kelsey N. Myers, Robert C. DeMuth, Thaddeus G. Bissett, David G. Anderson
2018 Antiquity  
millennia and at a continental scale.  ...  It also aids in the preservation of those data and makes efforts to archive these research results more resilient to political turmoil.  ...  Archaeological linked data and DINAA The DINAA project is not alone in developing information systems to integrate large-scale cultural heritage data.  ... 
doi:10.15184/aqy.2018.32 fatcat:uuhpkmb3djhhllxb6q5wwfx65a

CrisisTracker: Crowdsourced social media curation for disaster awareness

J. Rogstadius, M. Vukovic, C. A. Teixeira, V. Kostakos, E. Karapanos, J. A. Laredo
2013 IBM Journal of Research and Development  
Victims, volunteers, and relief organizations are increasingly using social media to report and act on large-scale events, as witnessed in the extensive coverage of the 2010-2012 Arab Spring uprisings  ...  We present CrisisTracker, an online system that in real time efficiently captures distributed situation awareness reports based on social media activity during large-scale events, such as natural disasters  ...  We thank Rebecca Curzon and Vicki Kraeling for promoting the study with disaster practitioners. Finally, we thank Ko-Hsun Huang for key guidance in gathering, analysis, and interpretation of data.  ... 
doi:10.1147/jrd.2013.2260692 fatcat:qd77wruhofe5vpfv65bt6x626m

Preliminary Study on the Impact of Literature Curation in a Model Organism Database on Article Citation Rates

Tanya Berardini, Ron Daniel, Amanda Clare, Michael Lauruhn, Leonore Reiser
2016 D-Lib Magazine  
scale studies not captured by TAIR's literature curation pipeline.  ...  Generally it is the authors of those articles that contribute annotations to TAIR although any registered community member is welcome to submit data.  ... 
doi:10.1045/september2016-berardini fatcat:udzvw2d3pneoddv2vkhtveiv2q

Magnitude of Blood Pressure Change and Clinical Outcomes after Thrombectomy in Stroke Caused by Large Artery Occlusion

Mohammad Anadani, Marius Matusevicius, Georgios Tsivgoulis, André Peeters, Ana Paiva Nunes, Michelangelo Mancuso, Christine Roffe, Adam de Havenon, Niaz Ahmed
2021 European Journal of Neurology  
SBP increase after thrombectomy in large artery occlusion stroke is associated with poor functional outcome.  ...  We analyzed thrombectomy treated patients registered in the SITS International Stroke Thrombectomy Registry from 01-01-2014 to 03-09-2019.  ...  In order to maintain high data quality, we only included data from centers which registered at least 10 patients and had 3-month follow-up data on at least 70% of patients.  ... 
doi:10.1111/ene.14807 pmid:33682232 fatcat:xdsbsd3xbbdlveijkm3mxvz2rm

2DSpotDB: A Database for the Annotated Two-dimensional Polyacrylamide Gel Electrophoresis of Pathogen Proteins

Dae-Won Kim, Won-Gi Yoo, Myoung-Ro Lee, Yu-Jung Kim, Shin-Hyeong Cho, Won-Ja Lee, Jung-Won Ju
2011 Genomics & Informatics  
We here present a web-based integrated database, called 2DSpotDB, for the management of proteome data derived from several pathogens.  ...  The biological interpretation of two-dimensional (2D) gel electrophoresis experiments is a key step toward understanding the functions of biological systems.  ...  With the rapid growth in proteomic raw data in pathogen laboratories, a current challenge is the meaningful management of the results of such large-scale studies, including spot identification and annotation  ... 
doi:10.5808/gi.2011.9.4.197 fatcat:umfsuiezendk7i6rd5h6r5pmb4

ClinGen Allele Registry links information about genetic variants

Piotr Pawliczek, Ronak Y. Patel, Lillian R. Ashmore, Andrew R. Jackson, Chris Bizon, Tristan Nelson, Bradford Powell, Robert R. Freimuth, Natasha Strande, Neethu Shah, Sameer Paithankar, Matt W. Wright (+7 others)
2018 Human Mutation  
More than 650 million distinct variants are currently registered, including those from gno-mAD, ExAC, dbSNP, and ClinVar, including a small number of variants registered by Registry users.  ...  The ClinGen Allele Registry addresses this problem by providing (1) globally unique "canonical" variant identifiers (CAids) on demand, either individually or in large batches; (2) access to variant-identifying  ...  Continuous development in coordination with key stakeholders are in process toward overcoming these limitations.  ... 
doi:10.1002/humu.23637 pmid:30311374 fatcat:judlwmbwzbhp7gn76ocnuexkne
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