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2. Rapid and sensitive detection of genome contamination at scale with FCS-GX

Author

Astashyn, Alexander, Tvedte, Eric S., Sweeney, Deacon, Sapojnikov, Victor, Bouk, Nathan, Joukov, Victor, Mozes, Eyal, Strope, Pooja K., Sylla, Pape M., Wagner, Lukas, Bidwell, Shelby L., Brown, Larissa C., Clark, Karen, Davis, Emily W., Smith-White, Brian, Hlavina, Wratko, Pruitt, Kim D., Schneider, Valerie A., and Murphy, Terence D.

Published
2024
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3. The status of the human gene catalogue

Author

Amaral, Paulo, Carbonell-Sala, Silvia, De La Vega, Francisco M., Faial, Tiago, Frankish, Adam, Gingeras, Thomas, Guigo, Roderic, Harrow, Jennifer L, Hatzigeorgiou, Artemis G., Johnson, Rory, Murphy, Terence D., Pertea, Mihaela, Pruitt, Kim D., Pujar, Shashikant, Takahashi, Hazuki, Ulitsky, Igor, Varabyou, Ales, Wells, Christine A., Yandell, Mark, Carninci, Piero, and Salzberg, Steven L.

Subjects
Quantitative Biology - Genomics, Quantitative Biology - Quantitative Methods
Abstract

Scientists have been trying to identify all of the genes in the human genome since the initial draft of the genome was published in 2001. Over the intervening years, much progress has been made in identifying protein-coding genes, and the estimated number has shrunk to fewer than 20,000, although the number of distinct protein-coding isoforms has expanded dramatically. The invention of high-throughput RNA sequencing and other technological breakthroughs have led to an explosion in the number of reported non-coding RNA genes, although most of them do not yet have any known function. A combination of recent advances offers a path forward to identifying these functions and towards eventually completing the human gene catalogue. However, much work remains to be done before we have a universal annotation standard that includes all medically significant genes, maintains their relationships with different reference genomes, and describes clinically relevant genetic variants., Comment: 14 pages

Published
2023

4. Standards recommendations for the Earth BioGenome Project

Author

Lawniczak, Mara KN, Durbin, Richard, Flicek, Paul, Lindblad-Toh, Kerstin, Wei, Xiaofeng, Archibald, John M, Baker, William J, Belov, Katherine, Blaxter, Mark L, Bonet, Tomas Marques, Childers, Anna K, Coddington, Jonathan A, Crandall, Keith A, Crawford, Andrew J, Davey, Robert P, Di Palma, Federica, Fang, Qi, Haerty, Wilfried, Hall, Neil, Hoff, Katharina J, Howe, Kerstin, Jarvis, Erich D, Johnson, Warren E, Johnson, Rebecca N, Kersey, Paul J, Liu, Xin, Lopez, Jose Victor, Myers, Eugene W, Pettersson, Olga Vinnere, Phillippy, Adam M, Poelchau, Monica F, Pruitt, Kim D, Rhie, Arang, Castilla-Rubio, Juan Carlos, Sahu, Sunil Kumar, Salmon, Nicholas A, Soltis, Pamela S, Swarbreck, David, Thibaud-Nissen, Françoise, Wang, Sibo, Wegrzyn, Jill L, Zhang, Guojie, Zhang, He, Lewin, Harris A, and Richards, Stephen

Subjects
Human Genome, Genetics, Animals, Base Sequence, Biodiversity, Eukaryota, Genomics, Humans, Reference Standards, Reference Values, Sequence Analysis, DNA, Earth BioGenome Project, genomics, ethics, genome assembly
Abstract

A global international initiative, such as the Earth BioGenome Project (EBP), requires both agreement and coordination on standards to ensure that the collective effort generates rapid progress toward its goals. To this end, the EBP initiated five technical standards committees comprising volunteer members from the global genomics scientific community: Sample Collection and Processing, Sequencing and Assembly, Annotation, Analysis, and IT and Informatics. The current versions of the resulting standards documents are available on the EBP website, with the recognition that opportunities, technologies, and challenges may improve or change in the future, requiring flexibility for the EBP to meet its goals. Here, we describe some highlights from the proposed standards, and areas where additional challenges will need to be met.

Published
2022

5. A joint NCBI and EMBL-EBI transcript set for clinical genomics and research

Author

Morales, Joannella, Pujar, Shashikant, Loveland, Jane E., Astashyn, Alex, Bennett, Ruth, Berry, Andrew, Cox, Eric, Davidson, Claire, Ermolaeva, Olga, Farrell, Catherine M., Fatima, Reham, Gil, Laurent, Goldfarb, Tamara, Gonzalez, Jose M., Haddad, Diana, Hardy, Matthew, Hunt, Toby, Jackson, John, Joardar, Vinita S., Kay, Michael, Kodali, Vamsi K., McGarvey, Kelly M., McMahon, Aoife, Mudge, Jonathan M., Murphy, Daniel N., Murphy, Michael R., Rajput, Bhanu, Rangwala, Sanjida H., Riddick, Lillian D., Thibaud-Nissen, Françoise, Threadgold, Glen, Vatsan, Anjana R., Wallin, Craig, Webb, David, Flicek, Paul, Birney, Ewan, Pruitt, Kim D., Frankish, Adam, Cunningham, Fiona, and Murphy, Terence D.

Published
2022
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6. The NCBI Comparative Genome Viewer (CGV) is an interactive visualization tool for the analysis of whole-genome eukaryotic alignments

Author

Rangwala, Sanjida H., primary, Rudnev, Dmitry V., additional, Ananiev, Victor V., additional, Oh, Dong-Ha, additional, Asztalos, Andrea, additional, Benica, Barrett, additional, Borodin, Evgeny A., additional, Bouk, Nathan, additional, Evgeniev, Vladislav I., additional, Kodali, Vamsi K., additional, Lotov, Vadim, additional, Mozes, Eyal, additional, Omelchenko, Marina V., additional, Savkina, Sofya, additional, Sukharnikov, Ekaterina, additional, Virothaisakun, Joël, additional, Murphy, Terence D., additional, Pruitt, Kim D., additional, and Schneider, Valerie A., additional

Published
2024
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7. A New Chicken Genome Assembly Provides Insight into Avian Genome Structure

Author

Warren, Wesley C, Hillier, LaDeana W, Tomlinson, Chad, Minx, Patrick, Kremitzki, Milinn, Graves, Tina, Markovic, Chris, Bouk, Nathan, Pruitt, Kim D, Thibaud-Nissen, Francoise, Schneider, Valerie, Mansour, Tamer A, Brown, C Titus, Zimin, Aleksey, Hawken, Rachel, Abrahamsen, Mitch, Pyrkosz, Alexis B, Morisson, Mireille, Fillon, Valerie, Vignal, Alain, Chow, William, Howe, Kerstin, Fulton, Janet E, Miller, Marcia M, Lovell, Peter, Mello, Claudio V, Wirthlin, Morgan, Mason, Andrew S, Kuo, Richard, Burt, David W, Dodgson, Jerry B, and Cheng, Hans H

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Biotechnology, Human Genome, Generic health relevance, Animals, Chickens, Chromosomes, Artificial, Bacterial, Computational Biology, Contig Mapping, Genome, Molecular Sequence Annotation, Sequence Analysis, DNA, Gallus gallus, genome assembly, MHC, Biochemistry and cell biology, Statistics
Abstract

The importance of the Gallus gallus (chicken) as a model organism and agricultural animal merits a continuation of sequence assembly improvement efforts. We present a new version of the chicken genome assembly (Gallus_gallus-5.0; GCA_000002315.3), built from combined long single molecule sequencing technology, finished BACs, and improved physical maps. In overall assembled bases, we see a gain of 183 Mb, including 16.4 Mb in placed chromosomes with a corresponding gain in the percentage of intact repeat elements characterized. Of the 1.21 Gb genome, we include three previously missing autosomes, GGA30, 31, and 33, and improve sequence contig length 10-fold over the previous Gallus_gallus-4.0. Despite the significant base representation improvements made, 138 Mb of sequence is not yet located to chromosomes. When annotated for gene content, Gallus_gallus-5.0 shows an increase of 4679 annotated genes (2768 noncoding and 1911 protein-coding) over those in Gallus_gallus-4.0. We also revisited the question of what genes are missing in the avian lineage, as assessed by the highest quality avian genome assembly to date, and found that a large fraction of the original set of missing genes are still absent in sequenced bird species. Finally, our new data support a detailed map of MHC-B, encompassing two segments: one with a highly stable gene copy number and another in which the gene copy number is highly variable. The chicken model has been a critical resource for many other fields of study, and this new reference assembly will substantially further these efforts.

Published
2017

8. Creating a specialist protein resource network: a meeting report for the protein bioinformatics and community resources retreat

Author

Babbitt, Patricia C, Bagos, Pantelis G, Bairoch, Amos, Bateman, Alex, Chatonnet, Arnaud, Chen, Mark Jinan, Craik, David J, Finn, Robert D, Gloriam, David, Haft, Daniel H, Henrissat, Bernard, Holliday, Gemma L, Isberg, Vignir, Kaas, Quentin, Landsman, David, Lenfant, Nicolas, Manning, Gerard, Nagano, Nozomi, Srinivasan, Narayanaswamy, O’Donovan, Claire, Pruitt, Kim D, Sowdhamini, Ramanathan, Rawlings, Neil D, Saier, Milton H, Sharman, Joanna L, Spedding, Michael, Tsirigos, Konstantinos D, Vastermark, Ake, and Vriend, Gerrit

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Human Genome, 2.6 Resources and infrastructure (aetiology), 1.5 Resources and infrastructure (underpinning), Aetiology, Underpinning research, Generic health relevance, Computational Biology, Congresses as Topic, Databases, Nucleic Acid, Databases, Protein, Humans, Molecular Sequence Annotation, Proteins, Data Format, Library and Information Studies, Bioinformatics and computational biology, Data management and data science
Abstract

During 11-12 August 2014, a Protein Bioinformatics and Community Resources Retreat was held at the Wellcome Trust Genome Campus in Hinxton, UK. This meeting brought together the principal investigators of several specialized protein resources (such as CAZy, TCDB and MEROPS) as well as those from protein databases from the large Bioinformatics centres (including UniProt and RefSeq). The retreat was divided into five sessions: (1) key challenges, (2) the databases represented, (3) best practices for maintenance and curation, (4) information flow to and from large data centers and (5) communication and funding. An important outcome of this meeting was the creation of a Specialist Protein Resource Network that we believe will improve coordination of the activities of its member resources. We invite further protein database resources to join the network and continue the dialogue.

Published
2015

9. Current status and new features of the Consensus Coding Sequence database

Author

Farrell, Catherine M, O’Leary, Nuala A, Harte, Rachel A, Loveland, Jane E, Wilming, Laurens G, Wallin, Craig, Diekhans, Mark, Barrell, Daniel, Searle, Stephen MJ, Aken, Bronwen, Hiatt, Susan M, Frankish, Adam, Suner, Marie-Marthe, Rajput, Bhanu, Steward, Charles A, Brown, Garth R, Bennett, Ruth, Murphy, Michael, Wu, Wendy, Kay, Mike P, Hart, Jennifer, Rajan, Jeena, Weber, Janet, Snow, Catherine, Riddick, Lillian D, Hunt, Toby, Webb, David, Thomas, Mark, Tamez, Pamela, Rangwala, Sanjida H, McGarvey, Kelly M, Pujar, Shashikant, Shkeda, Andrei, Mudge, Jonathan M, Gonzalez, Jose M, Gilbert, James GR, Trevanion, Stephen J, Baertsch, Robert, Harrow, Jennifer L, Hubbard, Tim, Ostell, James M, Haussler, David, and Pruitt, Kim D

Subjects
Human Genome, Genetics, Animals, Databases, Genetic, Exons, Genomics, Humans, Internet, Mice, Molecular Sequence Annotation, Proteins, Sequence Analysis, Environmental Sciences, Biological Sciences, Information and Computing Sciences, Developmental Biology
Abstract

The Consensus Coding Sequence (CCDS) project (http://www.ncbi.nlm.nih.gov/CCDS/) is a collaborative effort to maintain a dataset of protein-coding regions that are identically annotated on the human and mouse reference genome assemblies by the National Center for Biotechnology Information (NCBI) and Ensembl genome annotation pipelines. Identical annotations that pass quality assurance tests are tracked with a stable identifier (CCDS ID). Members of the collaboration, who are from NCBI, the Wellcome Trust Sanger Institute and the University of California Santa Cruz, provide coordinated and continuous review of the dataset to ensure high-quality CCDS representations. We describe here the current status and recent growth in the CCDS dataset, as well as recent changes to the CCDS web and FTP sites. These changes include more explicit reporting about the NCBI and Ensembl annotation releases being compared, new search and display options, the addition of biologically descriptive information and our approach to representing genes for which support evidence is incomplete. We also present a summary of recent and future curation targets.

Published
2014

10. Database resources of the National Center for Biotechnology Information

Author

Sayers, Eric W, primary, Beck, Jeff, additional, Bolton, Evan E, additional, Brister, J Rodney, additional, Chan, Jessica, additional, Comeau, Donald C, additional, Connor, Ryan, additional, DiCuccio, Michael, additional, Farrell, Catherine M, additional, Feldgarden, Michael, additional, Fine, Anna M, additional, Funk, Kathryn, additional, Hatcher, Eneida, additional, Hoeppner, Marilu, additional, Kane, Megan, additional, Kannan, Sivakumar, additional, Katz, Kenneth S, additional, Kelly, Christopher, additional, Klimke, William, additional, Kim, Sunghwan, additional, Kimchi, Avi, additional, Landrum, Melissa, additional, Lathrop, Stacy, additional, Lu, Zhiyong, additional, Malheiro, Adriana, additional, Marchler-Bauer, Aron, additional, Murphy, Terence D, additional, Phan, Lon, additional, Prasad, Arjun B, additional, Pujar, Shashikant, additional, Sawyer, Amanda, additional, Schmieder, Erin, additional, Schneider, Valerie A, additional, Schoch, Conrad L, additional, Sharma, Shobha, additional, Thibaud-Nissen, Françoise, additional, Trawick, Barton W, additional, Venkatapathi, Thilakam, additional, Wang, Jiyao, additional, Pruitt, Kim D, additional, and Sherry, Stephen T, additional

Published
2023
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11. Interactive visualization of whole eukaryote genome alignments using NCBI’s Comparative Genome Viewer (CGV)

Author

Rangwala, Sanjida H, primary, Rudnev, Dmitry V, additional, Ananiev, Victor V, additional, Asztalos, Andrea, additional, Benica, Barrett, additional, Borodin, Evgeny A, additional, Bouk, Nathan, additional, Evgeniev, Vladislav I, additional, Kodali, Vamsi K, additional, Lotov, Vadim, additional, Mozes, Eyal, additional, Oh, Dong-Ha, additional, Omelchenko, Marina V, additional, Savkina, Sofya, additional, Sukharnikov, Ekaterina, additional, Virothaisakun, Joël, additional, Murphy, Terence D., additional, Pruitt, Kim D, additional, and Schneider, Valerie A., additional

Published
2023
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12. GenBank 2024 Update

Author

Sayers, Eric W, primary, Cavanaugh, Mark, additional, Clark, Karen, additional, Pruitt, Kim D, additional, Sherry, Stephen T, additional, Yankie, Linda, additional, and Karsch-Mizrachi, Ilene, additional

Published
2023
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13. The status of the human gene catalogue

Author

Amaral, Paulo, primary, Carbonell-Sala, Silvia, additional, De La Vega, Francisco M., additional, Faial, Tiago, additional, Frankish, Adam, additional, Gingeras, Thomas, additional, Guigo, Roderic, additional, Harrow, Jennifer L., additional, Hatzigeorgiou, Artemis G., additional, Johnson, Rory, additional, Murphy, Terence D., additional, Pertea, Mihaela, additional, Pruitt, Kim D., additional, Pujar, Shashikant, additional, Takahashi, Hazuki, additional, Ulitsky, Igor, additional, Varabyou, Ales, additional, Wells, Christine A., additional, Yandell, Mark, additional, Carninci, Piero, additional, and Salzberg, Steven L., additional

Published
2023
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14. GenBank 2024 Update.

Author

Sayers, Eric W, Cavanaugh, Mark, Clark, Karen, Pruitt, Kim D, Sherry, Stephen T, Yankie, Linda, and Karsch-Mizrachi, Ilene

Published
2024
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15. Clonal polymorphism and high heterozygosity in the celibate genome of the Amazon molly

Author

Warren, Wesley C., García-Pérez, Raquel, Xu, Sen, Lampert, Kathrin P., Chalopin, Domitille, Stöck, Matthias, Loewe, Laurence, Lu, Yuan, Kuderna, Lukas, Minx, Patrick, Montague, Michael J., Tomlinson, Chad, Hillier, LaDeana W., Murphy, Daniel N., Wang, John, Wang, Zhongwei, Garcia, Constantino Macias, Thomas, Gregg C. W., Volff, Jean-Nicolas, Farias, Fabiana, Aken, Bronwen, Walter, Ronald B., Pruitt, Kim D., Marques-Bonet, Tomas, Hahn, Matthew W., Kneitz, Susanne, Lynch, Michael, and Schartl, Manfred

Published
2018
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16. Rapid and sensitive detection of genome contamination at scale with FCS-GX

Author

Astashyn, Alexander, primary, Tvedte, Eric S., additional, Sweeney, Deacon, additional, Sapojnikov, Victor, additional, Bouk, Nathan, additional, Joukov, Victor, additional, Mozes, Eyal, additional, Strope, Pooja K., additional, Sylla, Pape M., additional, Wagner, Lukas, additional, Bidwell, Shelby L., additional, Clark, Karen, additional, Davis, Emily W., additional, Smith-White, Brian, additional, Hlavina, Wratko, additional, Pruitt, Kim D., additional, Schneider, Valerie A., additional, and Murphy, Terence D., additional

Published
2023
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17. Rapid and sensitive detection of genome contamination at scale with FCS-GX

Author

Astashyn, Alexander, Tvedte, Eric S, Sweeney, Deacon, Sapojnikov, Victor, Bouk, Nathan, Joukov, Victor, Mozes, Eyal, Strope, Pooja K, Sylla, Pape M, Wagner, Lukas, Bidwell, Shelby L, Clark, Karen, Davis, Emily W, Smith-White, Brian, Hlavina, Wratko, Pruitt, Kim D, Schneider, Valerie A, and Murphy, Terence D

Subjects
Article
Abstract

Assembled genome sequences are being generated at an exponential rate. Here we present FCS-GX, part of NCBI's Foreign Contamination Screen (FCS) tool suite, optimized to identify and remove contaminant sequences in new genomes. FCS-GX screens most genomes in 0.1-10 minutes. Testing FCS-GX on artificially fragmented genomes demonstrates sensitivity >95% for diverse contaminant species and specificity >99.93%. We used FCS-GX to screen 1.6 million GenBank assemblies and identified 36.8 Gbp of contamination (0.16% of total bases), with half from 161 assemblies. We updated assemblies in NCBI RefSeq to reduce detected contamination to 0.01% of bases. FCS-GX is available at https://github.com/ncbi/fcs/.

Published
2023

18. Database resources of the National Center for Biotechnology Information in 2023

Author

Sayers, Eric W, primary, Bolton, Evan E, additional, Brister, J Rodney, additional, Canese, Kathi, additional, Chan, Jessica, additional, Comeau, Donald C, additional, Farrell, Catherine M, additional, Feldgarden, Michael, additional, Fine, Anna M, additional, Funk, Kathryn, additional, Hatcher, Eneida, additional, Kannan, Sivakumar, additional, Kelly, Christopher, additional, Kim, Sunghwan, additional, Klimke, William, additional, Landrum, Melissa J, additional, Lathrop, Stacy, additional, Lu, Zhiyong, additional, Madden, Thomas L, additional, Malheiro, Adriana, additional, Marchler-Bauer, Aron, additional, Murphy, Terence D, additional, Phan, Lon, additional, Pujar, Shashikant, additional, Rangwala, Sanjida H, additional, Schneider, Valerie A, additional, Tse, Tony, additional, Wang, Jiyao, additional, Ye, Jian, additional, Trawick, Barton W, additional, Pruitt, Kim D, additional, and Sherry, Stephen T, additional

Published
2022
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19. GenBank 2023 update

Author

Sayers, Eric W, primary, Cavanaugh, Mark, additional, Clark, Karen, additional, Pruitt, Kim D, additional, Sherry, Stephen T, additional, Yankie, Linda, additional, and Karsch-Mizrachi, Ilene, additional

Published
2022
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20. Towards increased accuracy and reproducibility in SARS-CoV-2 next generation sequence analysis for public health surveillance

Author

Connor, Ryan, primary, Yarmosh, David A., additional, Maier, Wolfgang, additional, Shakya, Migun, additional, Martin, Ross, additional, Bradford, Rebecca, additional, Brister, J. Rodney, additional, Chain, Patrick SG, additional, Copeland, Courtney A., additional, di Iulio, Julia, additional, Hu, Bin, additional, Ebert, Philip, additional, Gunti, Jonathan, additional, Jin, Yumi, additional, Katz, Kenneth S., additional, Kochergin, Andrey, additional, LaRosa, Tré, additional, Li, Jiani, additional, Li, Po-E, additional, Lo, Chien-Chi, additional, Rashid, Sujatha, additional, Maiorova, Evguenia S., additional, Xiao, Chunlin, additional, Zalunin, Vadim, additional, and Pruitt, Kim D., additional

Published
2022
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21. Standards recommendations for the Earth BioGenome Project

Author

Lawniczak, Mara K.N., Durbin, Richard, Flicek, Paul, Lindblad-Toh, Kerstin, Wei, Xiaofeng, Archibald, John M., Baker, William J, Belov, Katherine, Blaxter, Mark, Marques-Bonet, Tomas, Childers, Anna K., Coddington, Jonathan A., Crandall, Keith A., Crawford, Andrew J., Davey, Robert P., Di Palma, Federica, Fang, Qi, Haerty, Wilfried, Hall, Neil, Hoff, Katharina, Howe, Kerstin, Jarvis, Erich D., Johnson, Warren E., Johnson, Rebecca, Kersey, Paul J., Liu, Xin, Lopez, Jose V., Myers, Eugene W., Vinnere Pettersson, Olga, Phillippy, Adam M., Poelchau, Monica, Pruitt, Kim D., Rhie, Arang, Castilla-Rubio, Juan Carlos, Sahu, Sunil Kumar, Salmon, Nicholas A., Soltis, Pamela, Swarbreck, David, Thibaud-Nissen, Francoise, Wang, Sibo, Wegrzyn, Jill, Zhang, Guojie, Zhang, He, Lewin, Harris A., Richards, Stephen, Lawniczak, Mara K.N., Durbin, Richard, Flicek, Paul, Lindblad-Toh, Kerstin, Wei, Xiaofeng, Archibald, John M., Baker, William J, Belov, Katherine, Blaxter, Mark, Marques-Bonet, Tomas, Childers, Anna K., Coddington, Jonathan A., Crandall, Keith A., Crawford, Andrew J., Davey, Robert P., Di Palma, Federica, Fang, Qi, Haerty, Wilfried, Hall, Neil, Hoff, Katharina, Howe, Kerstin, Jarvis, Erich D., Johnson, Warren E., Johnson, Rebecca, Kersey, Paul J., Liu, Xin, Lopez, Jose V., Myers, Eugene W., Vinnere Pettersson, Olga, Phillippy, Adam M., Poelchau, Monica, Pruitt, Kim D., Rhie, Arang, Castilla-Rubio, Juan Carlos, Sahu, Sunil Kumar, Salmon, Nicholas A., Soltis, Pamela, Swarbreck, David, Thibaud-Nissen, Francoise, Wang, Sibo, Wegrzyn, Jill, Zhang, Guojie, Zhang, He, Lewin, Harris A., and Richards, Stephen

Abstract

A global international initiative, such as the Earth BioGenome Project (EBP), requires both agreement and coordination on standards to ensure that the collective effort generates rapid progress toward its goals. To this end, the EBP initiated five technical standards committees comprising volunteer members from the global genomics scientific community: Sample Collection and Processing, Sequencing and Assembly, Annotation, Analysis, and IT and Informatics. The current versions of the resulting standards documents are available on the EBP website, with the recognition that opportunities, technologies, and challenges may improve or change in the future, requiring flexibility for the EBP to meet its goals. Here, we describe some highlights from the proposed standards, and areas where additional challenges will need to be met.

Published
2022

22. Standards recommendations for the Earth BioGenome Project

Author

Lawniczak, Mara K. N., Durbin, Richard, Flicek, Paul, Lindblad-Toh, Kerstin, Wei, Xiaofeng, Archibald, John M., Baker, William J., Belov, Katherine, Blaxter, Mark L., Bonet, Tomas Marques, Childers, Anna K., Coddington, Jonathan A., Crandall, Keith A., Crawford, Andrew J., Davey, Robert P., Di Palma, Federica, Fang, Qi, Haerty, Wilfried, Hall, Neil, Hoff, Katharina J., Howe, Kerstin, Jarvis, Erich D., Johnson, Warren E., Johnson, Rebecca N., Kersey, Paul J., Liu, Xin, Lopez, Jose Victor, Myers, Eugene W., Vinnere Pettersson, Olga, Phillippy, Adam M., Poelchau, Monica F., Pruitt, Kim D., Rhie, Arang, Castilla-Rubio, Juan Carlos, Sahu, Sunil Kumar, Salmon, Nicholas A., Soltis, Pamela S., Swarbreck, David, Thibaud-Nissen, Francoise, Wang, Sibo, Wegrzyn, Jill L., Zhang, Guojie, Zhang, He, Lewin, Harris A., Richards, Stephen, Lawniczak, Mara K. N., Durbin, Richard, Flicek, Paul, Lindblad-Toh, Kerstin, Wei, Xiaofeng, Archibald, John M., Baker, William J., Belov, Katherine, Blaxter, Mark L., Bonet, Tomas Marques, Childers, Anna K., Coddington, Jonathan A., Crandall, Keith A., Crawford, Andrew J., Davey, Robert P., Di Palma, Federica, Fang, Qi, Haerty, Wilfried, Hall, Neil, Hoff, Katharina J., Howe, Kerstin, Jarvis, Erich D., Johnson, Warren E., Johnson, Rebecca N., Kersey, Paul J., Liu, Xin, Lopez, Jose Victor, Myers, Eugene W., Vinnere Pettersson, Olga, Phillippy, Adam M., Poelchau, Monica F., Pruitt, Kim D., Rhie, Arang, Castilla-Rubio, Juan Carlos, Sahu, Sunil Kumar, Salmon, Nicholas A., Soltis, Pamela S., Swarbreck, David, Thibaud-Nissen, Francoise, Wang, Sibo, Wegrzyn, Jill L., Zhang, Guojie, Zhang, He, Lewin, Harris A., and Richards, Stephen

Abstract

A global international initiative, such as the Earth BioGenome Project (EBP), requires both agreement and coordination on standards to ensure that the collective effort generates rapid progress toward its goals. To this end, the EBP initiated five technical standards committees comprising volunteer members from the global genomics scientific community: Sample Collection and Processing, Sequencing and Assembly, Annotation, Analysis, and IT and Informatics. The current versions of the resulting standards documents are available on the EBP website, with the recognition that opportunities, technologies, and challenges may improve or change in the future, requiring flexibility for the EBP to meet its goals. Here, we describe some highlights from the proposed standards, and areas where additional challenges will need to be met.

Published
2022
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23. Standards recommendations for the Earth BioGenome Project

Author

National Library of Medicine (US), National Institutes of Health (US), Swedish Research Council, National Museum of Natural History Smithsonian Institution, Howard Hughes Medical Institute, Wellcome, European Molecular Biology Laboratory, National Science Foundation (US), Department of Agriculture (US), Agricultural Research Service (US), Lawniczak, Mara K. N., Durbin, Richard, Flicek, Paul, Lindblad-Toh, Kerstin, Wei, Xiaofeng, Archibald, John M., Baker, William J., Belov, Katherine, Blaxter, Mark, Marqués-Bonet, Tomàs, Childers, Anna K., Coddington, Jonathan A., Crandall, Keith A., Crawford, Andrew J., Davey, Robert P., Di Palma, Federica, Fang, Qi, Haerty, Wilfried, Hall, Neil, Hoff, Katharina J., Howe, Kerstin, Jarvis, Erich D., Johnson, Warren E., Johnson, Rebecca N., Kersey, Paul J., Liu, Xin, López, José Víctor, Myers, Eugene W., Vinnere Pettersson, Olga, Phillippy, Adam M., Poelchau, Monica F., Pruitt, kim D., Rhie, Arang, Castilla-Rubio, Juan Carlos, Kumar Sahu, Sunil, Salmon, Nicholas A., Soltis, Pamela S., Swarbreck, David, Thibaud-Nissen, Francoise, Wang, Sibo, Wegrzyn, Jill L., Zhang, Guojie, Zhang, He, Lewin, Harris A., Richards, Stephen, National Library of Medicine (US), National Institutes of Health (US), Swedish Research Council, National Museum of Natural History Smithsonian Institution, Howard Hughes Medical Institute, Wellcome, European Molecular Biology Laboratory, National Science Foundation (US), Department of Agriculture (US), Agricultural Research Service (US), Lawniczak, Mara K. N., Durbin, Richard, Flicek, Paul, Lindblad-Toh, Kerstin, Wei, Xiaofeng, Archibald, John M., Baker, William J., Belov, Katherine, Blaxter, Mark, Marqués-Bonet, Tomàs, Childers, Anna K., Coddington, Jonathan A., Crandall, Keith A., Crawford, Andrew J., Davey, Robert P., Di Palma, Federica, Fang, Qi, Haerty, Wilfried, Hall, Neil, Hoff, Katharina J., Howe, Kerstin, Jarvis, Erich D., Johnson, Warren E., Johnson, Rebecca N., Kersey, Paul J., Liu, Xin, López, José Víctor, Myers, Eugene W., Vinnere Pettersson, Olga, Phillippy, Adam M., Poelchau, Monica F., Pruitt, kim D., Rhie, Arang, Castilla-Rubio, Juan Carlos, Kumar Sahu, Sunil, Salmon, Nicholas A., Soltis, Pamela S., Swarbreck, David, Thibaud-Nissen, Francoise, Wang, Sibo, Wegrzyn, Jill L., Zhang, Guojie, Zhang, He, Lewin, Harris A., and Richards, Stephen

Abstract

A global international initiative, such as the Earth BioGenome Project (EBP), requires both agreement and coordination on standards to ensure that the collective effort generates rapid progress toward its goals. To this end, the EBP initiated five technical standards committees comprising volunteer members from the global genomics scientific community: Sample Collection and Processing, Sequencing and Assembly, Annotation, Analysis, and IT and Informatics. The current versions of the resulting standards documents are available on the EBP website, with the recognition that opportunities, technologies, and challenges may improve or change in the future, requiring flexibility for the EBP to meet its goals. Here, we describe some highlights from the proposed standards, and areas where additional challenges will need to be met.

Published
2022

24. Mouse genome annotation by the RefSeq project

Author

McGarvey, Kelly M., Goldfarb, Tamara, Cox, Eric, Farrell, Catherine M., Gupta, Tripti, Joardar, Vinita S., Kodali, Vamsi K., Murphy, Michael R., O’Leary, Nuala A., Pujar, Shashikant, Rajput, Bhanu, Rangwala, Sanjida H., Riddick, Lillian D., Webb, David, Wright, Mathew W., Murphy, Terence D., and Pruitt, Kim D.

Published
2015
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27. RefSeq Functional Elements as experimentally assayed nongenic reference standards and functional interactions in human and mouse

Author

Farrell, Catherine M., primary, Goldfarb, Tamara, additional, Rangwala, Sanjida H., additional, Astashyn, Alexander, additional, Ermolaeva, Olga D., additional, Hem, Vichet, additional, Katz, Kenneth S., additional, Kodali, Vamsi K., additional, Ludwig, Frank, additional, Wallin, Craig L., additional, Pruitt, Kim D., additional, and Murphy, Terence D., additional

Published
2021
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28. Database resources of the national center for biotechnology information

Author

Sayers, Eric W, primary, Bolton, Evan E, additional, Brister, J Rodney, additional, Canese, Kathi, additional, Chan, Jessica, additional, Comeau, Donald C, additional, Connor, Ryan, additional, Funk, Kathryn, additional, Kelly, Chris, additional, Kim, Sunghwan, additional, Madej, Tom, additional, Marchler-Bauer, Aron, additional, Lanczycki, Christopher, additional, Lathrop, Stacy, additional, Lu, Zhiyong, additional, Thibaud-Nissen, Francoise, additional, Murphy, Terence, additional, Phan, Lon, additional, Skripchenko, Yuri, additional, Tse, Tony, additional, Wang, Jiyao, additional, Williams, Rebecca, additional, Trawick, Barton W, additional, Pruitt, Kim D, additional, and Sherry, Stephen T, additional

Published
2021
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29. GenBank

Author

Sayers, Eric W, primary, Cavanaugh, Mark, additional, Clark, Karen, additional, Pruitt, Kim D, additional, Schoch, Conrad L, additional, Sherry, Stephen T, additional, and Karsch-Mizrachi, Ilene, additional

Published
2021
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32. Supplementary Tables and Legends Standards Recommendations for the Earth BioGenome Project

Author

Lawniczak, Mara K. N., Durbin, Richard, Flicek, Paul, Lindblad-Toh, Kerstin, Wei, Xiaofeng, Archibald, John M., Baker, William J., Belov, Katherine, Blaxter, Mark, Marqués-Bonet, Tomàs, Childers, Anna K., Coddington, Jonathan A., Crandall, Keith A., Crawford, Andrew J., Davey, Robert P., Di Palma, Federica, Fang, Qi, Haerty, Wilfried, Hall, Neil, Hoff, Katharina J., Howe, Kerstin, Jarvis, Erich D., Johnson, Warren E., Johnson, Rebecca N., Kersey, Paul J., Liu, Xin, López, José Víctor, Myers, Eugene W., Vinnere Pettersson, Olga, Phillippy, Adam M., Poelchau, Monica F., Pruitt, kim D., Rhie, Arang, Castilla-Rubio, Juan Carlos, Kumar Sahu, Sunil, Salmon, Nicholas A., Soltis, Pamela S., Swarbreck, David, Thibaud-Nissen, Francoise, Wang, Sibo, Wegrzyn, Jill L., Zhang, Guojie, Zhang, He, Lewin, Harris A., Richards, Stephen, Lawniczak, Mara K. N., Durbin, Richard, Flicek, Paul, Lindblad-Toh, Kerstin, Wei, Xiaofeng, Archibald, John M., Baker, William J., Belov, Katherine, Blaxter, Mark, Marqués-Bonet, Tomàs, Childers, Anna K., Coddington, Jonathan A., Crandall, Keith A., Crawford, Andrew J., Davey, Robert P., Di Palma, Federica, Fang, Qi, Haerty, Wilfried, Hall, Neil, Hoff, Katharina J., Howe, Kerstin, Jarvis, Erich D., Johnson, Warren E., Johnson, Rebecca N., Kersey, Paul J., Liu, Xin, López, José Víctor, Myers, Eugene W., Vinnere Pettersson, Olga, Phillippy, Adam M., Poelchau, Monica F., Pruitt, kim D., Rhie, Arang, Castilla-Rubio, Juan Carlos, Kumar Sahu, Sunil, Salmon, Nicholas A., Soltis, Pamela S., Swarbreck, David, Thibaud-Nissen, Francoise, Wang, Sibo, Wegrzyn, Jill L., Zhang, Guojie, Zhang, He, Lewin, Harris A., and Richards, Stephen

Published
2021

33. RefSeq: an update on mammalian reference sequences

Author

Pruitt, Kim D., Brown, Garth R., Hiatt, Susan M., Thibaud-Nissen, Françoise, Astashyn, Alexander, Ermolaeva, Olga, Farrell, Catherine M., Hart, Jennifer, Landrum, Melissa J., McGarvey, Kelly M., Murphy, Michael R., OʼLeary, Nuala A., Pujar, Shashikant, Rajput, Bhanu, Rangwala, Sanjida H., Riddick, Lillian D., Shkeda, Andrei, Sun, Hanzhen, Tamez, Pamela, Tully, Raymond E., Wallin, Craig, Webb, David, Weber, Janet, Wu, Wendy, DiCuccio, Michael, Kitts, Paul, Maglott, Donna R., Murphy, Terence D., and Ostell, James M.

Published
2014
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36. Database resources of the National Center for Biotechnology Information

Author

Sayers, Eric W., Barrett, Tanya, Benson, Dennis A., Bolton, Evan, Bryant, Stephen H., Canese, Kathi, Chetvernin, Vyacheslav, Church, Deanna M., DiCuccio, Michael, Federhen, Scott, Feolo, Michael, Fingerman, Ian M., Geer, Lewis Y., Helmberg, Wolfgang, Kapustin, Yuri, Krasnov, Sergey, Landsman, David, Lipman, David J., Lu, Zhiyong, Madden, Thomas L., Madej, Tom, Maglott, Donna R., Marchler-Bauer, Aron, Miller, Vadim, Karsch-Mizrachi, Ilene, Ostell, James, Panchenko, Anna, Phan, Lon, Pruitt, Kim D., Schuler, Gregory D., Sequeira, Edwin, Sherry, Stephen T., Shumway, Martin, Sirotkin, Karl, Slotta, Douglas, Souvorov, Alexandre, Starchenko, Grigory, Tatusova, Tatiana A., Wagner, Lukas, Wang, Yanli, Wilbur, W. John, Yaschenko, Eugene, and Ye, Jian

Published
2012
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37. Database resources of the National Center for Biotechnology Information

Author

Sayers, Eric W., Barrett, Tanya, Benson, Dennis A., Bolton, Evan, Bryant, Stephen H., Canese, Kathi, Chetvernin, Vyacheslav, Church, Deanna M., DiCuccio, Michael, Federhen, Scott, Feolo, Michael, Fingerman, Ian M., Geer, Lewis Y., Helmberg, Wolfgang, Kapustin, Yuri, Landsman, David, Lipman, David J., Lu, Zhiyong, Madden, Thomas L., Madej, Tom, Maglott, Donna R., Marchler-Bauer, Aron, Miller, Vadim, Mizrachi, Ilene, Ostell, James, Panchenko, Anna, Phan, Lon, Pruitt, Kim D., Schuler, Gregory D., Sequeira, Edwin, Sherry, Stephen T., Shumway, Martin, Sirotkin, Karl, Slotta, Douglas, Souvorov, Alexandre, Starchenko, Grigory, Tatusova, Tatiana A., Wagner, Lukas, Wang, Yanli, Wilbur, W. John, Yaschenko, Eugene, and Ye, Jian

Published
2011
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39. GenBank

Author

Sayers, Eric W, primary, Cavanaugh, Mark, additional, Clark, Karen, additional, Pruitt, Kim D, additional, Schoch, Conrad L, additional, Sherry, Stephen T, additional, and Karsch-Mizrachi, Ilene, additional

Published
2020
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40. Database resources of the National Center for Biotechnology Information

Author

Sayers, Eric W, primary, Beck, Jeffrey, additional, Bolton, Evan E, additional, Bourexis, Devon, additional, Brister, James R, additional, Canese, Kathi, additional, Comeau, Donald C, additional, Funk, Kathryn, additional, Kim, Sunghwan, additional, Klimke, William, additional, Marchler-Bauer, Aron, additional, Landrum, Melissa, additional, Lathrop, Stacy, additional, Lu, Zhiyong, additional, Madden, Thomas L, additional, O’Leary, Nuala, additional, Phan, Lon, additional, Rangwala, Sanjida H, additional, Schneider, Valerie A, additional, Skripchenko, Yuri, additional, Wang, Jiyao, additional, Ye, Jian, additional, Trawick, Barton W, additional, Pruitt, Kim D, additional, and Sherry, Stephen T, additional

Published
2020
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41. Database resources of the National Center for Biotechnology Information

Author

Sayers, Eric W., Barrett, Tanya, Benson, Dennis A., Bolton, Evan, Bryant, Stephen H., Canese, Kathi, Chetvernin, Vyacheslav, Church, Deanna M., DiCuccio, Michael, Federhen, Scott, Feolo, Michael, Geer, Lewis Y., Helmberg, Wolfgang, Kapustin, Yuri, Landsman, David, Lipman, David J., Lu, Zhiyong, Madden, Thomas L., Madej, Tom, Maglott, Donna R., Marchler-Bauer, Aron, Miller, Vadim, Mizrachi, Ilene, Ostell, James, Panchenko, Anna, Pruitt, Kim D., Schuler, Gregory D., Sequeira, Edwin, Sherry, Stephen T., Shumway, Martin, Sirotkin, Karl, Slotta, Douglas, Souvorov, Alexandre, Starchenko, Grigory, Tatusova, Tatiana A., Wagner, Lukas, Wang, Yanli, John Wilbur, W., Yaschenko, Eugene, and Ye, Jian

Published
2010
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42. Database resources of the National Center for Biotechnology Information

Author

Agarwala, Richa, Barrett, Tanya, Beck, Jeff, Benson, Dennis A, Bollin, Colleen, Bolton, Evan, Bourexis, Devon, Brister, J Rodney, Bryant, Stephen H, Canese, Kathi, Cavanaugh, Mark, Charowhas, Chad, Clark, Karen, Dondoshansky, Ilya, Feolo, Michael, Fitzpatrick, Lawrence, Funk, Kathryn, Geer, Lewis Y, Gorelenkov, Viatcheslav, Graeff, Alan, Hlavina, Wratko, Holmes, Brad, Johnson, Mark, Kattman, Brandi, Khotomlianski, Viatcheslav, Kimchi, Avi, Kimelman, Michael, Kimura, Masato, Kitts, Paul, Klimke, William, Kotliarov, Alex, Krasnov, Sergey, Kuznetsov, Anatoliy, Landrum, Melissa J, Landsman, David, Lathrop, Stacy, Lee, Jennifer M, Leubsdorf, Carl, Lu, Zhiyong, Madden, Thomas L, Marchler-Bauer, Aron, Malheiro, Adriana, Meric, Peter, Karsch-Mizrachi, Ilene, Mnev, Anatoly, Murphy, Terence, Orris, Rebecca, Ostell, James, O'Sullivan, Christopher, Palanigobu, Vasuki, Panchenko, Anna R, Phan, Lon, Pierov, Borys, Pruitt, Kim D, Rodarmer, Kurt, Sayers, Eric W, Schneider, Valerie, Schoch, Conrad L, Schuler, Gregory D, Sherry, Stephen T, Siyan, Karanjit, Soboleva, Alexandra, Soussov, Vladimir, Starchenko, Grigory, Tatusova, Tatiana A, Thibaud-Nissen, Francoise, Todorov, Kamen, Trawick, Bart W, Vakatov, Denis, Ward, Minghong, Yaschenko, Eugene, Zasypkin, Aleksandr, and Zbicz, Kerry

Subjects
0301 basic medicine, Internet, PubMed, National Library of Medicine (U.S.), 010402 general chemistry, Databases, Bibliographic, 01 natural sciences, United States, 0104 chemical sciences, 03 medical and health sciences, ComputingMethodologies_PATTERNRECOGNITION, 030104 developmental biology, Databases, Genetic, Genetics, Database Issue, Database Management Systems, Humans, Databases, Nucleic Acid, Databases, Chemical, Biotechnology
Abstract

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 database of citations and abstracts for published life science journals. The Entrez system provides search and retrieval operations for most of these data from 39 distinct databases. The E-utilities serve as the programming interface for the Entrez system. Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. New resources released in the past year include PubMed Data Management, RefSeq Functional Elements, genome data download, variation services API, Magic-BLAST, QuickBLASTp, and Identical Protein Groups. Resources that were updated in the past year include the genome data viewer, a human genome resources page, Gene, virus variation, OSIRIS, and PubChem. All of these resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov.

Published
2017
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45. Database resources of the National Center for Biotechnology Information

Author

Sayers, Eric W., Barrett, Tanya, Benson, Dennis A., Bryant, Stephen H., Canese, Kathi, Chetvernin, Vyacheslav, Church, Deanna M., DiCuccio, Michael, Edgar, Ron, Federhen, Scott, Feolo, Michael, Geer, Lewis Y., Helmberg, Wolfgang, Kapustin, Yuri, Landsman, David, Lipman, David J., Madden, Thomas L., Maglott, Donna R., Miller, Vadim, Mizrachi, Ilene, Ostell, James, Pruitt, Kim D., Schuler, Gregory D., Sequeira, Edwin, Sherry, Stephen T., Shumway, Martin, Sirotkin, Karl, Souvorov, Alexandre, Starchenko, Grigory, Tatusova, Tatiana A., Wagner, Lukas, Yaschenko, Eugene, and Ye, Jian

Published
2009

46. GenBank.

Author

Sayers, Eric W, Cavanaugh, Mark, Clark, Karen, Pruitt, Kim D, Schoch, Conrad L, Sherry, Stephen T, and Karsch-Mizrachi, Ilene

Published
2022
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47. Database resources of the National Center for Biotechnology Information

Author

Wheeler, David L., Barrett, Tanya, Benson, Dennis A., Bryant, Stephen H., Canese, Kathi, Chetvernin, Vyacheslav, Church, Deanna M., DiCuccio, Michael, Edgar, Ron, Federhen, Scott, Feolo, Michael, Geer, Lewis Y., Helmberg, Wolfgang, Kapustin, Yuri, Khovayko, Oleg, Landsman, David, Lipman, David J., Madden, Thomas L., Maglott, Donna R., Miller, Vadim, Ostell, James, Pruitt, Kim D., Schuler, Gregory D., Shumway, Martin, Sequeira, Edwin, Sherry, Steven T., Sirotkin, Karl, Souvorov, Alexandre, Starchenko, Grigory, Tatusov, Roman L., Tatusova, Tatiana A., Wagner, Lukas, and Yaschenko, Eugene

Published
2008

48. Database resources of the National Center for Biotechnology Information

Author

Wheeler, David L., Barrett, Tanya, Benson, Dennis A., Bryant, Stephen H., Canese, Kathi, Chetvernin, Vyacheslav, Church, Deanna M., DiCuccio, Michael, Edgar, Ron, Federhen, Scott, Geer, Lewis Y., Kapustin, Yuri, Khovayko, Oleg, Landsman, David, Lipman, David J., Madden, Thomas L., Maglott, Donna R., Ostell, James, Miller, Vadim, Pruitt, Kim D., Schuler, Gregory D., Sequeira, Edwin, Sherry, Steven T., Sirotkin, Karl, Souvorov, Alexandre, Starchenko, Grigory, Tatusov, Roman L., Tatusova, Tatiana A., Wagner, Lukas, and Yaschenko, Eugene

Published
2007

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