diff --git a/datasets/anvilproject.yaml b/datasets/anvilproject.yaml new file mode 100644 index 000000000..481a10885 --- /dev/null +++ b/datasets/anvilproject.yaml @@ -0,0 +1,221 @@ +Name: NHGRI AnVIL Project + +Description: "The NHGRI Analysis, Visualization, and Informatics Lab-space + (AnVIL) Project (https://anvilproject.org/) is the National Human Genome + Research Institute's cloud-based platform for genomic data sharing and + analysis. AnVIL hosts widely used human genome reference datasets generated + through NHGRI-funded research. AnVIL on Open Data on AWS provides public + access to open-access datasets available through AnVIL. The project is a + collaborative effort involving NHGRI, the Broad Institute, Johns Hopkins + University, the University of California Santa Cruz, Vanderbilt University + Medical Center, Brigham and Women's Hospital, the Carnegie Institution for + Science, the City University of New York, the Fred Hutchinson Cancer Research + Center, Harvard University, Oregon Health & Science University, Massachusetts + General Hospital, Moffitt Cancer Center, Penn State University, and Washington + University." + +Documentation: "https://explore.anvilproject.org/datasets" + +Contact: "https://anvilproject.org/help" + +ManagedBy: "The AnVIL Project, and UC Santa Cruz Genomics Institute, University + of California, Santa Cruz (UCSC)" + +UpdateFrequency: Quarterly + +Tags: + - life sciences + - biology + - genome + - genomic + - gene expression + - Homo sapiens + +License: "https://anvilproject.org/faq/data-security" + +Citation: "Schatz MC, Philippakis AA, Afgan E, Banks E, Carey VJ, Carroll RJ, et + al. [Inverting the model of genomics data sharing with the NHGRI Genomic Data + Science Analysis, Visualization, and Informatics Lab-space + (AnVIL)](https://www.cell.com/cell-genomics/fulltext/S2666-979X(21)00106-3). + Cell Genomics. 2022;2. doi:10.1016/j.xgen.2021.100085" + +Resources: + - Description: "An S3 bucket containing all publicly accessible data files in + The AnVIL Project. The bucket layout and access procedures are documented + at + + https://github.com/DataBiosphere/azul/blob/develop/docs/mirror.rst + + and metadata can be viewed at + + https://explore.anvilproject.org/datasets + + or accessed programmatically at + + https://service.explore.anvilproject.org/" + ARN: arn:aws:s3:::humancellatlas + Region: us-east-1 + Type: S3 Bucket + Explore: + - "[Data Browser UI](https://explore.anvilproject.org/datasets)" + - "[Azul REST Web Service](https://service.explore.anvilproject.org/)" + +DataAtWork: + Publications: + - Title: "Inverting the model of genomics data sharing with the NHGRI + Genomic Data Science Analysis, Visualization, and Informatics Lab-space + (AnVIL)" + URL: "https://doi.org/10.1016/j.xgen.2021.100085" + AuthorName: "Michael C. Schatz, Anthony A. Philippakis, Enis Afgan, Eric + Banks, Vincent J. Carey, Robert J. Carroll, Alessandro Culotti, Kyle + Ellrott, Jeremy Goecks, Robert L. Grossman, Ira M. Hall, Kasper D. + Hansen, Jonathan Lawson, Jeffrey T. Leek, Anne O’Donnell Luria, Stephen + Mosher, Martin Morgan, Anton Nekrutenko, Brian D. O’Connor, Kevin + Osborn, Benedict Paten, Candace Patterson, Frederick J. Tan, Casey + Overby Taylor, Jennifer Vessio, Levi Waldron, Ting Wang, Kristin + Wuichet, AnVIL Team" + - Title: "Beyond the Human Genome Project: The Age of Complete Human Genome + Sequences and Pangenome References" + URL: "https://doi.org/10.1146/annurev-genom-021623-081639" + AuthorName: "Dylan J. Taylor, Jordan M. Eizenga, Qiuhui Li, Arun Das, + Katharine M. Jenike, Eimear E. Kenny, Karen H. Miga, Jean Monlong, Rajiv + C. McCoy, Benedict Paten, and Michael C. Schatz" + - Title: "CNPI: Rapid Analyses of Human Copy Number Data" + URL: "https://doi.org/10.1016/j.jmb.2025.169313" + AuthorName: "Jack Ustanik, Tychele N. Turner" + - Title: "The Galaxy platform for accessible, reproducible, and + collaborative data analyses: 2024 update" + URL: "https://doi.org/10.1093/nar/gkae410" + AuthorName: "The Galaxy Community" + - Title: "The complete sequence of a human Y chromosome" + URL: "https://doi.org/10.1038/s41586-023-06457-y" + AuthorName: "Arang Rhie, Sergey Nurk, Monika Cechova, Savannah J. Hoyt, + Dylan J. Taylor, Nicolas Altemose, Paul W. Hook, Sergey Koren, Mikko + Rautiainen, Ivan A. Alexandrov, Jamie Allen, Mobin Asri, Andrey V. + Bzikadze, Nae-Chyun Chen, Chen-Shan Chin, Mark Diekhans, Paul Flicek, + Giulio Formenti, Arkarachai Fungtammasan, Carlos Garcia Giron, Erik + Garrison, Ariel Gershman, Jennifer L. Gerton, Patrick G. S. Grady, + Andrea Guarracino, Leanne Haggerty, Reza Halabian, Nancy F. Hansen, + Robert Harris, Gabrielle A. Hartley, William T. Harvey, Marina Haukness, + Jakob Heinz, Thibaut Hourlier, Robert M. Hubley, Sarah E. Hunt, Stephen + Hwang, Miten Jain, Rupesh K. Kesharwani, Alexandra P. Lewis, Heng Li, + Glennis A. Logsdon, Julian K. Lucas, Wojciech Makalowski, Christopher + Markovic, Fergal J. Martin, Ann M. Mc Cartney, Rajiv C. McCoy, Jennifer + McDaniel, Brandy M. McNulty, Paul Medvedev, Alla Mikheenko, Katherine M. + Munson, Terence D. Murphy, Hugh E. Olsen, Nathan D. Olson, Luis F. + Paulin, David Porubsky, Tamara Potapova, Fedor Ryabov, Steven L. + Salzberg, Michael E. G. Sauria, Fritz J. Sedlazeck, Kishwar Shafin, + Valery A. Shepelev, Alaina Shumate, Jessica M. Storer, Likhitha + Surapaneni, Angela M. Taravella Oill, Françoise Thibaud-Nissen, Winston + Timp, Marta Tomaszkiewicz, Mitchell R. Vollger, Brian P. Walenz, Allison + C. Watwood, Matthias H. Weissensteiner, Aaron M. Wenger, Melissa A. + Wilson, Samantha Zarate, Yiming Zhu, Justin + M. Zook, Evan E. Eichler, Rachel J. O’Neill, Michael C. Schatz, Karen H. + Miga, Kateryna D. Makova, Adam M. Phillippy" + - Title: "Approaching complete genomes, transcriptomes and epi-omes with + accurate long-read sequencing" + URL: "https://doi.org/10.1038/s41592-022-01716-8" + AuthorName: "Sam Kovaka, Shujun Ou, Katharine M. Jenike, Michael C. + Schatz" + - Title: "The complete sequence and comparative analysis of ape sex + chromosomes" + URL: "https://doi.org/10.1038/s41586-024-07473-2" + AuthorName: "Kateryna D. Makova, Brandon D. Pickett, Robert S. Harris, + Gabrielle A. Hartley, Monika Cechova, Karol Pal, Sergey Nurk, DongAhn + Yoo, Qiuhui Li, Prajna Hebbar, Barbara C. McGrath, Francesca Antonacci, + Margaux Aubel, Arjun Biddanda, Matthew Borchers, Erich Bornberg-Bauer, + Gerard G. Bouffard, Shelise Y. Brooks, Lucia Carbone, Laura Carrel, + Andrew Carroll, Pi-Chuan Chang, Chen-Shan Chin, Daniel E. Cook, Sarah J. + C. Craig, Luciana de Gennaro, Mark Diekhans, Amalia Dutra, Gage H. + Garcia, Patrick G. S. Grady, Richard E. Green, Diana Haddad, Pille + Hallast, William T. Harvey, Glenn Hickey, David A. Hillis, Savannah J. + Hoyt, Hyeonsoo Jeong, Kaivan Kamali, Sergei L. Kosakovsky Pond, Troy + M. LaPolice, Charles Lee, Alexandra P. Lewis, Yong-Hwee E. Loh, + Patrick Masterson, Kelly M. McGarvey, Rajiv C. McCoy, Paul Medvedev, + Karen H. Miga, Katherine M. Munson, Evgenia Pak, Benedict Paten, + Brendan J. Pinto, Tamara Potapova, Arang Rhie, Joana L. Rocha, Fedor + Ryabov, Oliver A. Ryder, Samuel Sacco, Kishwar Shafin, Valery A. + Shepelev, Viviane Slon, Steven J. Solar, Jessica M. Storer, Peter H. + Sudmant, Sweetalana, Alex Sweeten, Michael G. Tassia, Françoise + Thibaud-Nissen, Mario Ventura, Melissa A. Wilson, Alice C. Young, + Huiqing Zeng, Xinru Zhang, Zachary A. Szpiech, Christian D. Huber, + Jennifer L. Gerton, Soojin V. Yi, Michael C. Schatz, Ivan A. + Alexandrov, Sergey Koren, Rachel J. O’Neill, Evan E. Eichler, Adam M. + Phillippy" + - Title: "Scalable Nanopore sequencing of human genomes provides a + comprehensive view of haplotype-resolved variation and methylation" + URL: "https://doi.org/10.1038/s41592-023-01993-x" + AuthorName: "Mikhail Kolmogorov, Kimberley J. Billingsley, Mira Mastoras, + Melissa Meredith, Jean Monlong, Ryan Lorig-Roach, Mobin Asri, Pilar + Alvarez Jerez, Laksh Malik, Ramita Dewan, Xylena Reed, Rylee M. Genner, + Kensuke Daida, Sairam Behera, Kishwar Shafin, Trevor Pesout, Jeshuwin + Prabakaran, Paolo Carnevali, Jianzhi Yang, Arang Rhie, Sonja W. Scholz, + Bryan J. Traynor, Karen H. Miga, Miten Jain, Winston Timp, Adam M. + Phillippy, Mark Chaisson, Fritz J. Sedlazeck, Cornelis Blauwendraat, + Benedict Paten" + - Title: "The Human Pangenome Project: a global resource to map genomic + diversity" + URL: "https://doi.org/10.1038/s41586-022-04601-8" + AuthorName: "Ting Wang, Lucinda Antonacci-Fulton, Kerstin Howe, Heather A. + Lawson, Julian K. Lucas, Adam M. Phillippy, Alice B. Popejoy, Mobin + Asri, Caryn Carson, Mark J. P. Chaisson, Xian Chang, Robert Cook-Deegan, + Adam L. Felsenfeld, Robert S. Fulton, Erik P. Garrison, Nanibaa’ A. + Garrison, Tina A. Graves-Lindsay, Hanlee Ji, Eimear E. Kenny, Barbara A. + Koenig, Daofeng Li, Tobias Marschall, Joshua F. McMichael, Adam M. + Novak, Deepak Purushotham, Valerie A. Schneider, Baergen I. Schultz, + Michael W. Smith, Heidi J. Sofia, Tsachy Weissman, Paul Flicek, Heng Li, + Karen H. Miga, Benedict Paten, Erich D. Jarvis, Ira M. Hall, Evan E. + Eichler, David Haussler, the Human Pangenome Reference Consortium" + - Title: "Deciphering the impact of genomic variation on function" + URL: "https://doi.org/10.1038/s41586-024-07510-0" + AuthorName: "IGVF Consortium" + - Title: "A complete reference genome improves analysis of human genetic variation" + URL: "https://doi.org/10.1126/science.abl3533" + AuthorName: "Sergey Aganezov, Stephanie M. Yan, Daniela C. Soto, Melanie + Kirsche, Samantha Zarate, Pavel Avdeyev, Dylan J. Taylor, Kishwar + Shafin, Alaina Shumate, Chunlin Xiao, Justin Wagner, Jennifer McDaniel, + Nathan D. Olson, Michael E. G. Sauria, Mitchell R. Vollger, Arang Rhie, + Melissa Meredith, Skylar Martin, Joyce Lee, Sergey Koren, Jeffrey A. + Rosenfeld, Benedict Paten, Ryan Layer, Chen-Shan Chin, Fritz J. + Sedlazeck, Nancy F. Hansen, Danny E. Miller, Adam M. Phillippy, Karen H. + Miga, Rajiv C. McCoy, Megan Y. Dennis, Justin M. Zook, Michael C. + Schatz" + - Title: "Jasmine and Iris: population-scale structural variant comparison + and analysis" + URL: "https://doi.org/10.1038/s41592-022-01753-3" + AuthorName: "Melanie Kirsche, Gautam Prabhu, Rachel Sherman, Bohan Ni, + Alexis Battle, Sergey Aganezov, Michael C. Schatz" + - Title: "A draft human pangenome reference" + URL: "https://www.nature.com/articles/s41586-023-05896-x" + AuthorName: "Wen-Wei Liao, Mobin Asri, Jana Ebler, Daniel Doerr, Marina + Haukness, Glenn Hickey, Shuangjia Lu, Julian K. Lucas, Jean Monlong, + Haley J. Abel, Silvia Buonaiuto, Xian H. Chang, Haoyu Cheng, Justin Chu, + Vincenza Colonna, Jordan M. Eizenga, Xiaowen Feng, Christian Fischer, + Robert S. Fulton, Shilpa Garg, Cristian Groza, Andrea Guarracino, + William T. Harvey, Simon Heumos, Kerstin Howe, Miten Jain, Tsung-Yu Lu, + Charles Markello, Fergal J. Martin, Matthew W. Mitchell, Katherine M. + Munson, Moses Njagi Mwaniki, Adam M. Novak, Hugh E. Olsen, Trevor + Pesout, David Porubsky, Pjotr Prins, Jonas A. Sibbesen, Jouni Sirén, + Chad Tomlinson, Flavia Villani, Mitchell R. Vollger, Lucinda L. + Antonacci-Fulton, Gunjan Baid, Carl A. Baker, Anastasiya Belyaeva, + Konstantinos Billis, Andrew Carroll, Pi-Chuan Chang, Sarah Cody, Daniel + E. Cook, Robert M. Cook-Deegan, Omar E. Cornejo, Mark Diekhans, Peter + Ebert, Susan Fairley, Olivier Fedrigo, Adam L. Felsenfeld, Giulio + Formenti, Adam Frankish, Yan Gao, Nanibaa’ A. Garrison, Carlos Garcia + Giron, Richard E. Green, Leanne Haggerty, Kendra Hoekzema, Thibaut + Hourlier, Hanlee P. Ji, Eimear E. Kenny, Barbara A. Koenig, Alexey + Kolesnikov, Jan O. Korbel, Jennifer Kordosky, Sergey Koren, HoJoon Lee, + Alexandra P. Lewis, Hugo Magalhães, Santiago Marco-Sola, Pierre Marijon, + Ann McCartney, Jennifer McDaniel, Jacquelyn Mountcastle, Maria + Nattestad, Sergey Nurk, Nathan D. Olson, Alice B. Popejoy, Daniela Puiu, + Mikko Rautiainen, Allison A. Regier, Arang Rhie, Samuel Sacco, Ashley D. + Sanders, Valerie A. Schneider, Baergen I. Schultz, Kishwar Shafin, + Michael W. Smith, Heidi J. Sofia, Ahmad N. Abou Tayoun, Françoise + Thibaud-Nissen, Francesca Floriana Tricomi, Justin Wagner, Brian Walenz, + Jonathan M. D. Wood, Aleksey V. Zimin, Guillaume Bourque, Mark J. P. + Chaisson, Paul Flicek, Adam M. Phillippy, Justin M. Zook, Evan E. + Eichler, David Haussler, Ting Wang, Erich D. Jarvis, Karen H. Miga, Erik + Garrison, Tobias Marschall, Ira M. Hall, Heng Li, Benedict Paten" + +ADXCategories: + - Healthcare & Life Sciences Data