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The NCBI BioCollections Database

Shobha Sharma, Stacy Ciufo, Elena Starchenko, Dakshesh Darji, Larry Chlumsky, Ilene Karsch-Mizrachi, Conrad L Schoch
2018 Database: The Journal of Biological Databases and Curation  
The National Center for Biotechnology Information BioCollections Database was established to allow the association of specimen vouchers and related sequence records to their home institutions.  ...  This process also allows cross-linking from the home institution for quick identification of all records originating from each collection. Database URL: https://www.ncbi.nlm.nih.gov/biocollections  ...  Acknowledgements The authors would like to acknowledge Scott Federhen and dedicate this paper in his memory.  ... 
doi:10.1093/database/bay006 pmid:29688360 pmcid:PMC5824777 fatcat:yepa4drzlba6rdaku6fk5eisvy

Specimen Identifiers: Linking tissues, DNA samples, and sequence data to voucher specimens in publicly accessible databases

Daniel Mulcahy
2022 Biodiversity Information Science and Standards  
The NCBI BioCollections Database curators have resolved the duplicate institution codes problem, by adding the three-letter country code (or state code, within the same country).  ...  future aggregate database structures (e.g., GBIF, GGBN, NCBI, and the DES).  ...  The NCBI BioCollections Database curators have resolved the duplicate institution codes problem, by adding the three-letter country code (or state code, within the same country).  ... 
doi:10.3897/biss.6.94625 fatcat:qssrl257tnamxhskbhlddwgycy

ENA Source Attribute Helper: An Application Programming Interface to facilitate accurate reference to biological source data

Vikas Gupta, Joana Paupério, Josephine Burgin, Suran Jayathilaka, Guy Cochrane
2022 F1000Research  
for the institutions and collections holding the vouchers.  ...  The API does not however support the search of voucher specimen codes, as these need to be obtained directly from the voucher institutions.  ...  Acknowledgements We would like to thank Conrad Schoch, Shobba Sharma and the NCBI taxonomy team for providing information on the NCBI biocollections database and its ftp access.  ... 
doi:10.12688/f1000research.123934.1 fatcat:37ks2amzizaj5bkdofmhcaj76y

Using standard keywords in publications to facilitate updates of new fungal taxonomic names

Conrad L. Schoch, M. Catherine Aime, Wilhelm de Beer, Pedro W. Crous, Kevin D. Hyde, Lyubomir Penev, Keith A. Seifert, Marc Stadler, Ning Zhang, Andrew N. Miller
2017 IMA Fungus  
The combination of manual curation and the reliance on updates from submitters to the public sequence databases is currently inefficient and impedes the comprehensive and timely release of records with  ...  As a result, the potential for automated searches of publication aggregators are improved, as well as the accurate curation of taxonomic information.  ...  ACKNOWLEDGEMENTS We are grateful to Stacy Ciufo (NCBI) for her help in preparing the figure and table.  ... 
doi:10.1007/bf03449466 fatcat:sfpucaty2fesjcrpvbxpcsefai

GenBank

Eric W Sayers, Mark Cavanaugh, Karen Clark, Kim D Pruitt, Conrad L Schoch, Stephen T Sherry, Ilene Karsch-Mizrachi
2021 Nucleic Acids Research  
Recent updates include resources for data from the SARS-CoV-2 virus, including a SARS-CoV-2 landing page, NCBI Datasets, NCBI Virus and the Submission Portal.  ...  GenBank® (https://www.ncbi.nlm.nih.gov/genbank/) is a comprehensive, public database that contains 15.3 trillion base pairs from over 2.5 billion nucleotide sequences for 504 000 formally described species  ...  GenBank has long followed the standards of structuring vouchers using Darwin Core formats (9) that allows us to link to specimen pages at external biorepositories using URLs curated in the NCBI BioCollections  ... 
doi:10.1093/nar/gkab1135 pmid:34850943 pmcid:PMC8690257 fatcat:bgeuokddybcwnjh3mpy7rah6rm

Knowledge Extraction from Specimen-Derived Data from GenBank to Enrich Biodiversity Information

Takeru Nakazato
2021 Biodiversity Information Science and Standards  
NCBI (National Center for Biotechnology Information) publishes the BioCollections database (Sharma et al. 2019), and these data may be able to refine the description.  ...  In the future, I plan to map these extracted IDs to the collection IDs in the biodiversity information database.  ...  NCBI (National Center for Biotechnology Information) publishes the Bio Collections database ( Sharma et al. 2019), and these data may be able to refine the description.  ... 
doi:10.3897/biss.5.73787 fatcat:naqgiosz5zd6rm3zuksiuqfcau

Current situation of DNA Barcoding data in biodiversity and genomics databases and data integration for museomics

Takeru Nakazato
2019 Biodiversity Information Science and Standards  
Recently, NCBI launched a new database called BioCollections, including 7,930 culture collections, museums, herbaria, and other natural history collections.  ...  for Biotechnology Information (NCBI, US) under the International Nucleotide Sequence Database Collaboration (INSDC) for more than 30 years.  ...  from the NCBI FTP (file transfer protocol) site and extracted biodiversity features including specimen voucher IDs and BOLD IDs.  ... 
doi:10.3897/biss.3.35165 fatcat:5536wkg5jjgshazsj7xzu62uxa

GRSciColl: Registry of Scientific Collections maintained by the community for the community

Marie Grosjean, Morten Høfft, Marcos Gonzalez, Tim Robertson, Andrea Hahn
2021 Biodiversity Information Science and Standards  
the National Center for Biotechnology Information (NCBI) BioCollections database.  ...  In addition, we worked with the team at Integrated Digitized Biocollections (iDigBio) to import their collection information into GRSciColl.  ...  The GBIF Nodes and publishing community, Barbara Thiers and the Index Herbariorum staff, Cat Chapman and the iDigBio staff, David Schindel, The Society for the Preservation of Natural History Collections  ... 
doi:10.3897/biss.5.74354 fatcat:4dh7e2ltovftxg64m66wzm2hba

Institution Codes, Collection Codes, and Specimen Identifiers: linking voucher specimen to Tissues, DNA Samples, and Sequence Data

Daniel Mulcahy
2022 Zenodo  
The National Center for Biotechnology Information (NCBI), which hosts GenBank, has created a BioCollections Database to curate metadata for natural history collections and link sequence data to voucher  ...  and the Barcode of Life Database (BOLD).  ... 
doi:10.5281/zenodo.6593552 fatcat:o55ziqs5rregzf3bdynabzj5ku

NCBI Taxonomy: a comprehensive update on curation, resources and tools

Conrad L Schoch, Stacy Ciufo, Mikhail Domrachev, Carol L Hotton, Sivakumar Kannan, Rogneda Khovanskaya, Detlef Leipe, Richard Mcveigh, Kathleen O'Neill, Barbara Robbertse, Shobha Sharma, Vladimir Soussov (+4 others)
2020 Database: The Journal of Biological Databases and Curation  
The National Center for Biotechnology Information (NCBI) Taxonomy includes organism names and classifications for every sequence in the nucleotide and protein sequence databases of the International Nucleotide  ...  Most notable is the shift from a single SQL database to a series of linked databases tied to a framework of data called NameBank.  ...  In addition to acknowledging the collaborative efforts of our colleagues at NCBI, INSDC and beyond, we remember the contributions of Scott Federhen, who initiated and guided many improvements to the NCBI  ... 
doi:10.1093/database/baaa062 pmid:32761142 fatcat:bnhdt2p6szf4rb2b2cerhg2bbq

Database resources of the National Center for Biotechnology Information

Eric W Sayers, Richa Agarwala, Evan E Bolton, J Rodney Brister, Kathi Canese, Karen Clark, Ryan Connor, Nicolas Fiorini, Kathryn Funk, Timothy Hefferon, J Bradley Holmes, Sunghwan Kim (+11 others)
2018 Nucleic Acids Research  
The National Center for Biotechnology Information (NCBI) provides a large suite of online resources for biological information and data, including the GenBank ® nucleic acid sequence database and the PubMed  ...  All of these resources can be accessed through the NCBI home page at www.ncbi. nlm.nih.gov.  ...  ACKNOWLEDGEMENTS The authors would like to thank all of the NCBI staff who through their dedicated efforts continue to allow NCBI to provide our full collection of services to the community.  ... 
doi:10.1093/nar/gky1069 pmid:30395293 fatcat:6myevv752rbsjkfofodo4lo3gu

Database resources of the National Center for Biotechnology Information

Richa Agarwala, Tanya Barrett, Jeff Beck, Dennis A Benson, Colleen Bollin, Evan Bolton, Devon Bourexis, J Rodney Brister, Stephen H Bryant, Kathi Canese, Mark Cavanaugh, Chad Charowhas (+61 others)
2017 Nucleic Acids Research  
The National Center for Biotechnology Information (NCBI) provides a large suite of online resources for biological information and data, including the GenBank ® nucleic acid sequence database and the PubMed  ...  All of these resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov.  ...  ACKNOWLEDGEMENTS Funding to pay the Open Access publication charges for this article was provided by the Intramural Research Program of the National Institutes of Health, National Library of Medicine.  ... 
doi:10.1093/nar/gkx1095 pmid:29140470 pmcid:PMC5753372 fatcat:v2wabu3mezcpnbvn7pnssppfdy

Database resources of the National Center for Biotechnology Information

Eric W Sayers, Jeffrey Beck, Evan E Bolton, Devon Bourexis, James R Brister, Kathi Canese, Donald C Comeau, Kathryn Funk, Sunghwan Kim, William Klimke, Aron Marchler-Bauer, Melissa Landrum (+13 others)
2020 Nucleic Acids Research  
The National Center for Biotechnology Information (NCBI) provides a large suite of online resources for biological information and data, including the GenBank® nucleic acid sequence database and the PubMed  ...  All of these resources can be accessed through the NCBI home page at https://www.ncbi.nlm.nih.gov.  ...  ACKNOWLEDGEMENTS The authors would like to thank all of the NCBI staff who through their dedicated efforts continue to allow NCBI to provide our full collection of services to the community. FUNDING  ... 
doi:10.1093/nar/gkaa892 pmid:33095870 fatcat:pptmq2emtjft7e62jnnm62t6ny

Cornejo.et.al.2019.detailed.methods [article]

Diego Cortez
2019 Figshare  
Full methods for the scientific paper "Viviparous reptile regarded to have temperature-dependent sex determination has 116 million year old XY chromosomes" by Cornejo et al.  ...  To establish Y gene identity, we searched NCBI GenBank (http://www.ncbi.nlm.nih.gov/genbank) for the closest homologs.  ...  Therefore, we worked with all synonyms obtained from the RedList database (http://www.iucnredlist.org/; version 3), the Reptile Database Generation of distributional ranges for additional species We  ... 
doi:10.6084/m9.figshare.9894500 fatcat:madhpevvmne3rjp4cnldiaohva

How to publish a new fungal species, or name, version 3.0

M Catherine Aime, Andrew N Miller, Takayuki Aoki, Konstanze Bensch, Lei Cai, Pedro W Crous, David L Hawksworth, Kevin D Hyde, Paul M Kirk, Robert Lücking, Tom W May, Elaine Malosso (+7 others)
2021 IMA Fungus  
In the meantime the International Code of Nomenclature for algae, fungi, and plants (ICNafp) has changed from its former name (the International Code of Botanical Nomenclature) and introduced new formal  ...  Additionally, we provide: (1) model papers for different fungal groups and circumstances; (2) a checklist to simplify meeting (i) the requirements of the ICNafp to ensure the effective, valid and legitimate  ...  Science Foundation (Th1672/ 19-1) and the LOEWE initiative of the Government of Hessen, in the framework of the centre for Translational Biodiversity Genomics (MT); the U.S.  ... 
doi:10.1186/s43008-021-00063-1 pmid:33934723 fatcat:4vwrdpg4j5gwlk2ejcdifpykja
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