The Experts below are selected from a list of 177 Experts worldwide ranked by ideXlab platform
Jennifer A Byrne - One of the best experts on this subject based on the ideXlab platform.
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semi automated fact checking of Nucleotide Sequence reagents in biomedical research publications the seek blastn tool
PLOS ONE, 2019Co-Authors: Cyril Labbé, Natalie Grima, Thierry Gautier, Bertrand Favier, Jennifer A ByrneAbstract:Nucleotide Sequence reagents are verifiable experimental reagents in biomedical publications, because their Sequence identities can be independently verified and compared with associated text descriptors. We have previously reported that incorrectly identified Nucleotide Sequence reagents are characteristic of highly similar human gene knockdown studies, some of which have been retracted from the literature on account of possible research fraud. Because of the throughput limitations of manual verification of Nucleotide Sequences, we developed a semi-automated fact checking tool, Seek & Blastn, to verify the targeting or non-targeting status of published Nucleotide Sequence reagents. From previously described and unknown corpora of 48 and 155 publications, respectively, Seek & Blastn correctly extracted 304/342 (88.9%) and 1066/1522 (70.0%) Nucleotide Sequences and a predicted targeting/ non-targeting status. Seek & Blastn correctly predicted the targeting/ non-targeting status of 293/304 (96.4%) and 988/1066 (92.7%) of the correctly extracted Nucleotide Sequences. A total of 38/39 (97.4%) or 31/79 (39.2%) Seek & Blastn predictions of incorrect Nucleotide Sequence reagent use were correct in the two literature corpora. Combined Seek & Blastn and manual analyses identified a list of 91 misidentified Nucleotide Sequence reagents, which could be built upon through future studies. In summary, incorrect Nucleotide Sequence reagents represent an under-recognized source of error within the biomedical literature, and fact checking tools such as Seek & Blastn may help to identify papers and manuscripts affected by these errors.
Guy Cochrane - One of the best experts on this subject based on the ideXlab platform.
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The international Nucleotide Sequence database collaboration.
Nucleic acids research, 2020Co-Authors: Masanori Arita, Ilene Karsch-mizrachi, Guy CochraneAbstract:The International Nucleotide Sequence Database Collaboration (INSDC; http://www.insdc.org/) has been the core infrastructure for collecting and providing Nucleotide Sequence data and metadata for >30 years. Three partner organizations, the DNA Data Bank of Japan (DDBJ) at the National Institute of Genetics in Mishima, Japan; the European Nucleotide Archive (ENA) at the European Molecular Biology Laboratory's European Bioinformatics Institute (EMBL-EBI) in Hinxton, UK; and GenBank at National Center for Biotechnology Information (NCBI), National Library of Medicine, National Institutes of Health in Bethesda, Maryland, USA have been collaboratively maintaining the INSDC for the benefit of not only science but all types of community worldwide.
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The international Nucleotide Sequence database collaboration.
Nucleic acids research, 2017Co-Authors: Ilene Karsch-mizrachi, Toshihisa Takagi, Guy CochraneAbstract:For more than 30 years, the International Nucleotide Sequence Database Collaboration (INSDC; http://www.insdc.org/) has been committed to capturing, preserving and providing access to comprehensive public domain Nucleotide Sequence and associated metadata which enables discovery in biomedicine, biodiversity and biological sciences. Since 1987, the DNA Data Bank of Japan (DDBJ) at the National Institute for Genetics in Mishima, Japan; the European Nucleotide Archive (ENA) at the European Molecular Biology Laboratory's European Bioinformatics Institute (EMBL-EBI) in Hinxton, UK; and GenBank at National Center for Biotechnology Information (NCBI), National Library of Medicine, National Institutes of Health in Bethesda, Maryland, USA have worked collaboratively to enable access to Nucleotide Sequence data in standardized formats for the worldwide scientific community. In this article, we reiterate the principles of the INSDC collaboration and briefly summarize the trends of the archival content.
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The International Nucleotide Sequence Database Collaboration.
Nucleic acids research, 2015Co-Authors: Guy Cochrane, Ilene Karsch-mizrachi, Toshihisa TakagiAbstract:The International Nucleotide Sequence Database Collaboration (INSDC; http://www.insdc.org) comprises three global partners committed to capturing, preserving and providing comprehensive public-domain Nucleotide Sequence information. The INSDC establishes standards, formats and protocols for data and metadata to make it easier for individuals and organisations to submit their Nucleotide data reliably to public archives. This work enables the continuous, global exchange of information about living things. Here we present an update of the INSDC in 2015, including data growth and diversification, new standards and requirements by publishers for authors to submit their data to the public archives. The INSDC serves as a model for data sharing in the life sciences.
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The International Nucleotide Sequence Database Collaboration.
Nucleic acids research, 2012Co-Authors: Yasukazu Nakamura, Guy Cochrane, Ilene Karsch-mizrachiAbstract:The International Nucleotide Sequence Database Collaboration (INSDC; http://www.insdc.org), one of the longest-standing global alliances of biological data archives, captures, preserves and provides comprehensive public domain Nucleotide Sequence information. Three partners of the INSDC work in cooperation to establish formats for data and metadata and protocols that facilitate reliable data submission to their databases and support continual data exchange around the world. In this article, the INSDC current status and update for the year of 2012 are presented. Among discussed items of international collaboration meeting in 2012, BioSample database and changes in submission are described as topics.
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The International Nucleotide Sequence Database Collaboration.
Nucleic acids research, 2011Co-Authors: Ilene Karsch-mizrachi, Yasukazu Nakamura, Guy CochraneAbstract:The members of the International Nucleotide Sequence Database Collaboration (INSDC; http://www.insdc.org) set out to capture, preserve and present globally comprehensive public domain Nucleotide Sequence information. The work of the long-standing collaboration includes the provision of data formats, annotation conventions and routine global data exchange. Among the many developments to INSDC resources in 2011 are the newly launched BioProject database and improved handling of assembly information. In this article, we outline INSDC services and update the reader on developments in 2011.
Cyril Labbé - One of the best experts on this subject based on the ideXlab platform.
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Semi-automated fact-checking of Nucleotide Sequence reagents in biomedical research publications: The Seek & Blastn tool
PLoS ONE, 2019Co-Authors: Cyril Labbé, Natalie Grima, Thierry Gautier, Bertrand Favier, Jennifer ByrneAbstract:Nucleotide Sequence reagents are verifiable experimental reagents in biomedical publications , because their Sequence identities can be independently verified and compared with associated text descriptors. We have previously reported that incorrectly identified Nucleotide Sequence reagents are characteristic of highly similar human gene knockdown studies, some of which have been retracted from the literature on account of possible research fraud. Because of the throughput limitations of manual verification of Nucleotide Sequences, we developed a semi-automated fact checking tool, Seek & Blastn, to verify the targeting or non-targeting status of published Nucleotide Sequence reagents. From previously described and unknown corpora of 48 and 155 publications, respectively, Seek & Blastn correctly extracted 304/342 (88.9%) and 1066/1522 (70.0%) Nucleotide Sequences and a predicted targeting/ non-targeting status. Seek & Blastn correctly predicted the targeting/ non-targeting status of 293/304 (96.4%) and 988/1066 (92.7%) of the correctly extracted Nucleotide Sequences. A total of 38/39 (97.4%) or 31/79 (39.2%) Seek & Blastn predictions of incorrect Nucleotide Sequence reagent use were correct in the two literature corpora. Combined Seek & Blastn and manual analyses identified a list of 91 misidentified Nucleotide Sequence reagents, which could be built upon through future studies. In summary, incorrect Nucleotide Sequence reagents represent an under-recognized source of error within the biomedical literature , and fact checking tools such as Seek & Blastn may help to identify papers and manuscripts affected by these errors.
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semi automated fact checking of Nucleotide Sequence reagents in biomedical research publications the seek blastn tool
PLOS ONE, 2019Co-Authors: Cyril Labbé, Natalie Grima, Thierry Gautier, Bertrand Favier, Jennifer A ByrneAbstract:Nucleotide Sequence reagents are verifiable experimental reagents in biomedical publications, because their Sequence identities can be independently verified and compared with associated text descriptors. We have previously reported that incorrectly identified Nucleotide Sequence reagents are characteristic of highly similar human gene knockdown studies, some of which have been retracted from the literature on account of possible research fraud. Because of the throughput limitations of manual verification of Nucleotide Sequences, we developed a semi-automated fact checking tool, Seek & Blastn, to verify the targeting or non-targeting status of published Nucleotide Sequence reagents. From previously described and unknown corpora of 48 and 155 publications, respectively, Seek & Blastn correctly extracted 304/342 (88.9%) and 1066/1522 (70.0%) Nucleotide Sequences and a predicted targeting/ non-targeting status. Seek & Blastn correctly predicted the targeting/ non-targeting status of 293/304 (96.4%) and 988/1066 (92.7%) of the correctly extracted Nucleotide Sequences. A total of 38/39 (97.4%) or 31/79 (39.2%) Seek & Blastn predictions of incorrect Nucleotide Sequence reagent use were correct in the two literature corpora. Combined Seek & Blastn and manual analyses identified a list of 91 misidentified Nucleotide Sequence reagents, which could be built upon through future studies. In summary, incorrect Nucleotide Sequence reagents represent an under-recognized source of error within the biomedical literature, and fact checking tools such as Seek & Blastn may help to identify papers and manuscripts affected by these errors.
Jennifer Byrne - One of the best experts on this subject based on the ideXlab platform.
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Semi-automated fact-checking of Nucleotide Sequence reagents in biomedical research publications: The Seek & Blastn tool
PLoS ONE, 2019Co-Authors: Cyril Labbé, Natalie Grima, Thierry Gautier, Bertrand Favier, Jennifer ByrneAbstract:Nucleotide Sequence reagents are verifiable experimental reagents in biomedical publications , because their Sequence identities can be independently verified and compared with associated text descriptors. We have previously reported that incorrectly identified Nucleotide Sequence reagents are characteristic of highly similar human gene knockdown studies, some of which have been retracted from the literature on account of possible research fraud. Because of the throughput limitations of manual verification of Nucleotide Sequences, we developed a semi-automated fact checking tool, Seek & Blastn, to verify the targeting or non-targeting status of published Nucleotide Sequence reagents. From previously described and unknown corpora of 48 and 155 publications, respectively, Seek & Blastn correctly extracted 304/342 (88.9%) and 1066/1522 (70.0%) Nucleotide Sequences and a predicted targeting/ non-targeting status. Seek & Blastn correctly predicted the targeting/ non-targeting status of 293/304 (96.4%) and 988/1066 (92.7%) of the correctly extracted Nucleotide Sequences. A total of 38/39 (97.4%) or 31/79 (39.2%) Seek & Blastn predictions of incorrect Nucleotide Sequence reagent use were correct in the two literature corpora. Combined Seek & Blastn and manual analyses identified a list of 91 misidentified Nucleotide Sequence reagents, which could be built upon through future studies. In summary, incorrect Nucleotide Sequence reagents represent an under-recognized source of error within the biomedical literature , and fact checking tools such as Seek & Blastn may help to identify papers and manuscripts affected by these errors.
Thierry Gautier - One of the best experts on this subject based on the ideXlab platform.
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Semi-automated fact-checking of Nucleotide Sequence reagents in biomedical research publications: The Seek & Blastn tool
PLoS ONE, 2019Co-Authors: Cyril Labbé, Natalie Grima, Thierry Gautier, Bertrand Favier, Jennifer ByrneAbstract:Nucleotide Sequence reagents are verifiable experimental reagents in biomedical publications , because their Sequence identities can be independently verified and compared with associated text descriptors. We have previously reported that incorrectly identified Nucleotide Sequence reagents are characteristic of highly similar human gene knockdown studies, some of which have been retracted from the literature on account of possible research fraud. Because of the throughput limitations of manual verification of Nucleotide Sequences, we developed a semi-automated fact checking tool, Seek & Blastn, to verify the targeting or non-targeting status of published Nucleotide Sequence reagents. From previously described and unknown corpora of 48 and 155 publications, respectively, Seek & Blastn correctly extracted 304/342 (88.9%) and 1066/1522 (70.0%) Nucleotide Sequences and a predicted targeting/ non-targeting status. Seek & Blastn correctly predicted the targeting/ non-targeting status of 293/304 (96.4%) and 988/1066 (92.7%) of the correctly extracted Nucleotide Sequences. A total of 38/39 (97.4%) or 31/79 (39.2%) Seek & Blastn predictions of incorrect Nucleotide Sequence reagent use were correct in the two literature corpora. Combined Seek & Blastn and manual analyses identified a list of 91 misidentified Nucleotide Sequence reagents, which could be built upon through future studies. In summary, incorrect Nucleotide Sequence reagents represent an under-recognized source of error within the biomedical literature , and fact checking tools such as Seek & Blastn may help to identify papers and manuscripts affected by these errors.
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semi automated fact checking of Nucleotide Sequence reagents in biomedical research publications the seek blastn tool
PLOS ONE, 2019Co-Authors: Cyril Labbé, Natalie Grima, Thierry Gautier, Bertrand Favier, Jennifer A ByrneAbstract:Nucleotide Sequence reagents are verifiable experimental reagents in biomedical publications, because their Sequence identities can be independently verified and compared with associated text descriptors. We have previously reported that incorrectly identified Nucleotide Sequence reagents are characteristic of highly similar human gene knockdown studies, some of which have been retracted from the literature on account of possible research fraud. Because of the throughput limitations of manual verification of Nucleotide Sequences, we developed a semi-automated fact checking tool, Seek & Blastn, to verify the targeting or non-targeting status of published Nucleotide Sequence reagents. From previously described and unknown corpora of 48 and 155 publications, respectively, Seek & Blastn correctly extracted 304/342 (88.9%) and 1066/1522 (70.0%) Nucleotide Sequences and a predicted targeting/ non-targeting status. Seek & Blastn correctly predicted the targeting/ non-targeting status of 293/304 (96.4%) and 988/1066 (92.7%) of the correctly extracted Nucleotide Sequences. A total of 38/39 (97.4%) or 31/79 (39.2%) Seek & Blastn predictions of incorrect Nucleotide Sequence reagent use were correct in the two literature corpora. Combined Seek & Blastn and manual analyses identified a list of 91 misidentified Nucleotide Sequence reagents, which could be built upon through future studies. In summary, incorrect Nucleotide Sequence reagents represent an under-recognized source of error within the biomedical literature, and fact checking tools such as Seek & Blastn may help to identify papers and manuscripts affected by these errors.
