Search

Your search keyword '"Lynn Schriml"' showing total 20 results
Start Over Author "Lynn Schriml"
20 results on '"Lynn Schriml"'

1. Aligning Standards Communities for Omics Biodiversity Data: Sustainable Darwin Core-MIxS Interoperability

Author

Raïssa Meyer, Ward Appeltans, William Duncan, Mariya Dimitrova, Yi-Ming Gan, Thomas Stjernegaard Jeppesen, Christopher Mungall, Deborah Paul, Pieter Provoost, Tim Robertson, Lynn Schriml, Saara Suominen, Ramona Walls, Maxime Sweetlove, Visotheary Ung, Anton Van de Putte, Elycia Wallis, John Wieczorek, and Pier Buttigieg

Subjects
microbiome, eDNA, biodiversity, information standa, Biology (General), QH301-705.5
Abstract

The standardization of data, encompassing both primary and contextual information (metadata), plays a pivotal role in facilitating data (re-)use, integration, and knowledge generation. However, the biodiversity and omics communities, converging on omics biodiversity data, have historically developed and adopted their own distinct standards, hindering effective (meta)data integration and collaboration.In response to this challenge, the Task Group (TG) for Sustainable DwC-MIxS Interoperability was established. Convening experts from the Biodiversity Information Standards (TDWG) and the Genomic Standards Consortium (GSC) alongside external stakeholders, the TG aimed to promote sustainable interoperability between the Minimum Information about any (x) Sequence (MIxS) and Darwin Core (DwC) specifications.To achieve this goal, the TG utilized the Simple Standard for Sharing Ontology Mappings (SSSOM) to create a comprehensive mapping of DwC keys to MIxS keys. This mapping, combined with the development of the MIxS-DwC extension, enables the incorporation of MIxS core terms into DwC-compliant metadata records, facilitating seamless data exchange between MIxS and DwC user communities.Through the implementation of this translation layer, data produced in either MIxS- or DwC-compliant formats can now be efficiently brokered, breaking down silos and fostering closer collaboration between the biodiversity and omics communities. To ensure its sustainability and lasting impact, TDWG and GSC have both signed a Memorandum of Understanding (MoU) on creating a continuous model to synchronize their standards. These achievements mark a significant step forward in enhancing data sharing and utilization across domains, thereby unlocking new opportunities for scientific discovery and advancement.

Published
2023
Full Text
View/download PDF

2. A history of the MetaSUB consortium: Tracking urban microbes around the globe

Author

Krista A. Ryon, Braden T. Tierney, Alina Frolova, Andre Kahles, Christelle Desnues, Christos Ouzounis, Cynthis Gibas, Daniela Bezdan, Youping Deng, Ding He, Emmanuel Dias-Neto, Eran Elhaik, Evan Afshin, George Grills, Gregorio Iraola, Haruo Suzuki, Johannes Werner, Klas Udekwu, Lynn Schriml, Malay Bhattacharyya, Manuela Oliveira, Maria Mercedes Zambrano, Nur Hazlin Hazrin-Chong, Olayinka Osuolale, Paweł P. Łabaj, Prisca Tiasse, Sampath Rapuri, Silvia Borras, Sofya Pozdniakova, Tieliu Shi, Ugur Sezerman, Xavier Rodo, Zehra Hazal Sezer, and Christopher E. Mason

Subjects
Science
Abstract

Summary: The MetaSUB Consortium, founded in 2015, is a global consortium with an interdisciplinary team of clinicians, scientists, bioinformaticians, engineers, and designers, with members from more than 100 countries across the globe. This network has continually collected samples from urban and rural sites including subways and transit systems, sewage systems, hospitals, and other environmental sampling. These collections have been ongoing since 2015 and have continued when possible, even throughout the COVID-19 pandemic. The consortium has optimized their workflow for the collection, isolation, and sequencing of DNA and RNA collected from these various sites and processing them for metagenomics analysis, including the identification of SARS-CoV-2 and its variants. Here, the Consortium describes its foundations, and its ongoing work to expand on this network and to focus its scope on the mapping, annotation, and prediction of emerging pathogens, mapping microbial evolution and antibiotic resistance, and the discovery of novel organisms and biosynthetic gene clusters.

Published
2022
Full Text
View/download PDF

3. Diseasomics: Actionable machine interpretable disease knowledge at the point-of-care.

Author

Asoke K Talukder, Lynn Schriml, Arnab Ghosh, Rakesh Biswas, Prantar Chakrabarti, and Roland E Haas

Subjects
Computer applications to medicine. Medical informatics, R858-859.7
Abstract

Physicians establish diagnosis by assessing a patient's signs, symptoms, age, sex, laboratory test findings and the disease history. All this must be done in limited time and against the backdrop of an increasing overall workload. In the era of evidence-based medicine it is utmost important for a clinician to be abreast of the latest guidelines and treatment protocols which are changing rapidly. In resource limited settings, the updated knowledge often does not reach the point-of-care. This paper presents an artificial intelligence (AI)-based approach for integrating comprehensive disease knowledge, to support physicians and healthcare workers in arriving at accurate diagnoses at the point-of-care. We integrated different disease-related knowledge bodies to construct a comprehensive, machine interpretable diseasomics knowledge-graph that includes the Disease Ontology, disease symptoms, SNOMED CT, DisGeNET, and PharmGKB data. The resulting disease-symptom network comprises knowledge from the Symptom Ontology, electronic health records (EHR), human symptom disease network, Disease Ontology, Wikipedia, PubMed, textbooks, and symptomology knowledge sources with 84.56% accuracy. We also integrated spatial and temporal comorbidity knowledge obtained from EHR for two population data sets from Spain and Sweden respectively. The knowledge graph is stored in a graph database as a digital twin of the disease knowledge. We use node2vec (node embedding) as digital triplet for link prediction in disease-symptom networks to identify missing associations. This diseasomics knowledge graph is expected to democratize the medical knowledge and empower non-specialist health workers to make evidence based informed decisions and help achieve the goal of universal health coverage (UHC). The machine interpretable knowledge graphs presented in this paper are associations between various entities and do not imply causation. Our differential diagnostic tool focusses on signs and symptoms and does not include a complete assessment of patient's lifestyle and health history which would typically be necessary to rule out conditions and to arrive at a final diagnosis. The predicted diseases are ordered according to the specific disease burden in South Asia. The knowledge graphs and the tools presented here can be used as a guide.

Published
2022
Full Text
View/download PDF

4. Parasite microbiome project: Grand challenges.

Author

Nolwenn M Dheilly, Joaquín Martínez Martínez, Karyna Rosario, Paul J Brindley, Raina N Fichorova, Jonathan Z Kaye, Kevin D Kohl, Laura J Knoll, Julius Lukeš, Susan L Perkins, Robert Poulin, Lynn Schriml, and Luke R Thompson

Subjects
Immunologic diseases. Allergy, RC581-607, Biology (General), QH301-705.5
Published
2019
Full Text
View/download PDF

5. Annotating public fungal ITS sequences from the built environment according to the MIxS-Built Environment standard – a report from a May 23-24, 2016 workshop (Gothenburg, Sweden)

Author

Kessy Abarenkov, Rachel I. Adams, Irinyi Laszlo, Ahto Agan, Elia Ambrosio, Alexandre Antonelli, Mohammad Bahram, Johan Bengtsson-Palme, Gunilla Bok, Patrik Cangren, Victor Coimbra, Claudia Coleine, Claes Gustafsson, Jinhong He, Tobias Hofmann, Erik Kristiansson, Ellen Larsson, Tomas Larsson, Yingkui Liu, Svante Martinsson, Wieland Meyer, Marina Panova, Nuttapon Pombubpa, Camila Ritter, Martin Ryberg, Sten Svantesson, Ruud Scharn, Ola Svensson, Mats Töpel, Martin Unterseher, Cobus Visagie, Christian Wurzbacher, Andy F.S. Taylor, Urmas Kõljalg, Lynn Schriml, and R. Henrik Nilsson

Subjects
Botany, QK1-989
Abstract

Recent molecular studies have identified substantial fungal diversity in indoor environments. Fungi and fungal particles have been linked to a range of potentially unwanted effects in the built environment, including asthma, decay of building materials, and food spoilage. The study of the built mycobiome is hampered by a number of constraints, one of which is the poor state of the metadata annotation of fungal DNA sequences from the built environment in public databases. In order to enable precise interrogation of such data – for example, “retrieve all fungal sequences recovered from bathrooms” – a workshop was organized at the University of Gothenburg (May 23-24, 2016) to annotate public fungal barcode (ITS) sequences according to the MIxS-Built Environment annotation standard (http://gensc.org/mixs/). The 36 participants assembled a total of 45,488 data points from the published literature, including the addition of 8,430 instances of countries of collection from a total of 83 countries, 5,801 instances of building types, and 3,876 instances of surface-air contaminants. The results were implemented in the UNITE database for molecular identification of fungi (http://unite.ut.ee) and were shared with other online resources. Data obtained from human/animal pathogenic fungi will furthermore be verified on culture based metadata for subsequent inclusion in the ISHAM-ITS database (http://its.mycologylab.org).

Published
2016
Full Text
View/download PDF

6. Integrated Genomic Analysis of Diverse Induced Pluripotent Stem Cells from the Progenitor Cell Biology Consortium

Author

Nathan Salomonis, Phillip J. Dexheimer, Larsson Omberg, Robin Schroll, Stacy Bush, Jeffrey Huo, Lynn Schriml, Shannan Ho Sui, Mehdi Keddache, Christopher Mayhew, Shiva Kumar Shanmukhappa, James Wells, Kenneth Daily, Shane Hubler, Yuliang Wang, Elias Zambidis, Adam Margolin, Winston Hide, Antonis K. Hatzopoulos, Punam Malik, Jose A. Cancelas, Bruce J. Aronow, and Carolyn Lutzko

Subjects
Medicine (General), R5-920, Biology (General), QH301-705.5
Abstract

The rigorous characterization of distinct induced pluripotent stem cells (iPSC) derived from multiple reprogramming technologies, somatic sources, and donors is required to understand potential sources of variability and downstream potential. To achieve this goal, the Progenitor Cell Biology Consortium performed comprehensive experimental and genomic analyses of 58 iPSC from ten laboratories generated using a variety of reprogramming genes, vectors, and cells. Associated global molecular characterization studies identified functionally informative correlations in gene expression, DNA methylation, and/or copy-number variation among key developmental and oncogenic regulators as a result of donor, sex, line stability, reprogramming technology, and cell of origin. Furthermore, X-chromosome inactivation in PSC produced highly correlated differences in teratoma-lineage staining and regulator expression upon differentiation. All experimental results, and raw, processed, and metadata from these analyses, including powerful tools, are interactively accessible from a new online portal at https://www.synapse.org to serve as a reusable resource for the stem cell community.

Published
2016
Full Text
View/download PDF

7. A decade of GigaScience: 10 years of the evolving genomic and biomedical standards landscape

Author

Lynn Schriml

Subjects
Biomedical Research, Health Informatics, Genomics, Metagenomics, Reference Standards, Computer Science Applications
Abstract

Standardization of omics data drives FAIR data practices through community-built genomic data standards and biomedical ontologies. Use of standards has progressed from a foreign concept to a sought-after solution, moving from efforts to coordinate data within individual research projects to research communities coming together to identify solutions to common challenges. Today we are seeing the benefits of this multidecade groundswell to coordinate, exchange, and reuse data; to compare data across studies; and to integrate data across previously siloed resources.

Published
2022

8. eP063: Genetic variants associated with childhood cancers: Curation initiatives of the ClinGen Somatic Cancer Pediatric Taskforce

Author

Heather Williams, Kilannin Krysiak, Wan-Hsin Lin, Angshumoy Roy, Alanna Church, Jason Saliba, Shruti Rao, Deborah Ritter, Arpad Danos, Laura Corson, Kevin Fisher, Matthew Hiemenz, Katherine A. Janeway, Jianling Ji, Chimene Kesserwan, Ted Laetsch, Donald Parsons, Ryan Schmidt, Kristen Sund, Panieh Terraf, Xinjie Xu, Rashmi Kanagal-Shamana, Lisa Dyer, Marian Harris, Kristy Lee, Alex Wagner, Yassmine Akkari, Laveniya Satgunaseelan, Malachi Griffith, Obi Griffith, Shashikant Kulkarni, Lynn Schriml, Jeffrey Jean, Subha Madhavan, and Gordana Raca

Subjects
Genetics (clinical)
Published
2022

9. Reporting guidelines for human microbiome research: the STORMS checklist

Author

Dermot P.B. McGovern, Suzanne Devkota, Eran Segal, Rimsha Azhar, Thomas Sharpton, Douglas S Kwon, Massive Analysis, Elizabeth Grice, Eran Elinav, Jonathan Braun, Louise B. Thingholm, Paul Wilmes, Benjamin Haibe-Kains, Wendell D. Jones, Sofia Forslund, David Casero, Russell D. Wolfinger, Kirk Bergstrom, Ramona L Walls, Rebecca Kusko, Pamela Herd, Viswanath Devanarayan, Fatima Zohra, Brianna Lindsay, Aedin Culhane, Francesco Beghini, Heidi E. Jones, Maria Carmen Collado, Mingyu Zhang, Wenjun Bao, Robert D. Finn, Liping Zhao, Jonathan P Jacobs, Andreas Scherer, Xiaohui Fan, Omry Koren, Jennifer Fettweis, Morgan G. I. Langille, Weida Tong, Jordan E Bisanz, Malte Rühlemann, Curtis Huttenhower, Scott Handley, Rob Knight, Susanna-Assunta Sansone, Shannon McWeeney, Gregory A Buck, Sujatha Srinivasan, Jennifer B Dowd, Ekaterina Smirnova, Amy Loughman, Janneke van de Wijgert, Audrey Renson, Frederic D. Bushman, John F. Cryan, Christopher E. Mason, Levi Waldron, Harry Sokol, Susan Holmes, Andre Franke, Leming Shi, Anthony A. Fodor, Nicola Segata, Matthew R. Redinbo, Matthew Olm, Jeroen Raes, David A MacIntyre, Luigi Nezi, Joaquin Dopazo, Shaimaa Elsafoury, Kelly Eckenrode, Francine Z Marques, Peter J. Turnbaugh, Ni Zhao, Christopher Hunter, Lynn Schriml, Georg Zeller, Jack Gilbert, Ami Bhatt, Noah Palm, Ludwig Geistlinger, Juan S Escobar, Michelle Shardell, Dan Knights, Tim R Mercer, Vaibhav Upadhyay, Shraddha Thakkar, Noel T. Mueller, Manimozhiyan Arumugam, Paul D. Cotter, Gerard Clarke, Alice C. McHardy, Lisa Karstens, Cesare Furlanello, Edoardo Pasolli, Chloe Mirzayi, Justin L Sonnenburg, Ryan T Demmer, Patrick D. Schloss, Lora J. Kasselman, Takuji Yamada, Matthias Fischer, Hector Corrada Bravo, R Balfour Sartor, Consortium, Genomic Standards, Society, Massive Analysis and Quality Control, Mirzayi, Chloe, Renson, Audrey, Furlanello, Cesare, Sansone, Susanna-Assunta, Zohra, Fatima, Elsafoury, Shaimaa, Geistlinger, Ludwig, Kasselman, Lora J., Eckenrode, Kelly, van de Wijgert, Janneke, Loughman, Amy, Marques, Francine Z., Macintyre, David A., Arumugam, Manimozhiyan, Azhar, Rimsha, Beghini, Francesco, Bergstrom, Kirk, Bhatt, Ami, Bisanz, Jordan E., Braun, Jonathan, Bravo, Hector Corrada, Buck, Gregory A., Bushman, Frederic, Casero, David, Clarke, Gerard, Collado, Maria Carmen, Cotter, Paul D., Cryan, John F., Demmer, Ryan T., Devkota, Suzanne, Elinav, Eran, Escobar, Juan S., Fettweis, Jennifer, Finn, Robert D., Fodor, Anthony A., Forslund, Sofia, Franke, Andre, Gilbert, Jack, Grice, Elizabeth, Haibe-Kains, Benjamin, Handley, Scott, Herd, Pamela, Holmes, Susan, Jacobs, Jonathan P., Karstens, Lisa, Knight, Rob, Knights, Dan, Koren, Omry, Kwon, Douglas S., Langille, Morgan, Lindsay, Brianna, Mcgovern, Dermot, Mchardy, Alice C., Mcweeney, Shannon, Mueller, Noel T., Nezi, Luigi, Olm, Matthew, Palm, Noah, Pasolli, Edoardo, Raes, Jeroen, Redinbo, Matthew R., Rühlemann, Malte, Balfour Sartor, R., Schloss, Patrick D., Schriml, Lynn, Segal, Eran, Shardell, Michelle, Sharpton, Thoma, Smirnova, Ekaterina, Sokol, Harry, Sonnenburg, Justin L., Srinivasan, Sujatha, Thingholm, Louise B., Turnbaugh, Peter J., Upadhyay, Vaibhav, Walls, Ramona L., Wilmes, Paul, Yamada, Takuji, Zeller, Georg, Zhang, Mingyu, Zhao, Ni, Zhao, Liping, Bao, Wenjun, Culhane, Aedin, Devanarayan, Viswanath, Dopazo, Joaquin, Fan, Xiaohui, Fischer, Matthia, Jones, Wendell, Kusko, Rebecca, Mason, Christopher E., Mercer, Tim R., Scherer, Andrea, Shi, Leming, Thakkar, Shraddha, Tong, Weida, Wolfinger, Ru, Hunter, Christopher, Segata, Nicola, Huttenhower, Curti, Dowd, Jennifer B., Jones, Heidi E., and Waldron, Levi

Subjects
Biomedical, Microbiota, Human microbiome, MEDLINE, Translational medicine, Computational Biology, Dysbiosis, Humans, Observational Studies as Topic, Translational Science, Biomedical, Research Design, General Medicine, Data science, General Biochemistry, Genetics and Molecular Biology, Checklist, Comprehension, Genetic epidemiology, Observational study, Translational Science, Microbiome
Abstract

The particularly interdisciplinary nature of human microbiome research makes the organization and reporting of results spanning epidemiology, biology, bioinformatics, translational medicine and statistics a challenge. Commonly used reporting guidelines for observational or genetic epidemiology studies lack key features specific to microbiome studies. Therefore, a multidisciplinary group of microbiome epidemiology researchers adapted guidelines for observational and genetic studies to culture-independent human microbiome studies, and also developed new reporting elements for laboratory, bioinformatics and statistical analyses tailored to microbiome studies. The resulting tool, called ‘Strengthening The Organization and Reporting of Microbiome Studies’ (STORMS), is composed of a 17-item checklist organized into six sections that correspond to the typical sections of a scientific publication, presented as an editable table for inclusion in supplementary materials. The STORMS checklist provides guidance for concise and complete reporting of microbiome studies that will facilitate manuscript preparation, peer review, and reader comprehension of publications and comparative analysis of published results.

Published
2021

10. 16. Enhancement of pediatric cancer curation and representation through expert-guided data mining and ontology refinement

Author

Jason Saliba, Jake Lever, Kilannin Krysiak, Lana Sheta, Arpad Danos, Alex Wagner, Heather Williams, Chimene Kesserwan, Laura Corson, Jianling Ji, Catherine Cottrell, Alanna Church, Laveniya Satgunaseelan, David Meredith, Mark Evans, Wan-Hsin Lin, Kai Lee Yap, Shruti Rao, Lynn Schriml, Angshumoy Roy, Gordana Raca, Malachi Griffith, and Obi Griffith

Subjects
Cancer Research, Genetics, Molecular Biology
Published
2022

11. Annotating public fungal ITS sequences from the built environment according to the MIxS-Built Environment standard – a report from a May 23-24, 2016 workshop (Gothenburg, Sweden)

Author

Svante Martinsson, Mats Töpel, Wieland Meyer, Nuttapon Pombubpa, Martin Unterseher, Christian Wurzbacher, R. Henrik Nilsson, Victor R. M. Coimbra, Ahto Agan, Mohammad Bahram, Jinhong He, Tobias Hofmann, Ola Svensson, Sten Svantesson, Claudia Coleine, Martin Ryberg, Lynn Schriml, Cobus M. Visagie, Tomas Larsson, Marina Panova, Irinyi Laszlo, Patrik Cangren, Alexandre Antonelli, Gunilla Bok, Ellen Larsson, Erik Kristiansson, Rachel I. Adams, Andy F. S. Taylor, Yingkui Liu, Ruud Scharn, Johan Bengtsson-Palme, Claes G. R. Gustafsson, Kessy Abarenkov, Elia Ambrosio, Camila Duarte Ritter, and Urmas Kõljalg

Subjects
0301 basic medicine, Built environment, Annotation, 010501 environmental sciences, complex mixtures, 01 natural sciences, Civil engineering, Indoor fungi, 03 medical and health sciences, Fungal Diversity, lcsh:Botany, Biologiska vetenskaper, Biological sciences, Ecology, Evolution, Behavior and Systematics, 0105 earth and related environmental sciences, business.industry, fungi, Environmental resource management, Biological Sciences, lcsh:QK1-989, 030104 developmental biology, Geography, ITS, business, Biologie, human activities, Mycobiome
Abstract

Recent molecular studies have identified substantial fungal diversity in indoor environments. Fungi and fungal particles have been linked to a range of potentially unwanted effects in the built environment, including asthma, decay of building materials, and food spoilage. The study of the built mycobiome is hampered by a number of constraints, one of which is the poor state of the metadata annotation of fungal DNA sequences from the built environment in public databases. In order to enable precise interrogation of such data – for example, “retrieve all fungal sequences recovered from bathrooms” – a workshop was organized at the University of Gothenburg (May 23-24, 2016) to annotate public fungal barcode (ITS) sequences according to the MIxS-Built Environment annotation standard (http://gensc.org/mixs/). The 36 participants assembled a total of 45,488 data points from the published literature, including the addition of 8,430 instances of countries of collection from a total of 83 countries, 5,801 instances of building types, and 3,876 instances of surface-air contaminants. The results were implemented in the UNITE database for molecular identification of fungi (http://unite.ut.ee) and were shared with other online resources. Data obtained from human/animal pathogenic fungi will furthermore be verified on culture based metadata for subsequent inclusion in the ISHAM-ITS database (http://its.mycologylab.org).

Published
2016

12. Meeting Report from the Genomic Standards Consortium (GSC) Workshop 10

Author

Elizabeth Glass, Folker Meyer, Jack A Gilbert, Dawn Field, Sarah Hunter, Renzo Kottmann, Nikos Kyrpides, Susanna Sansone, Lynn Schriml, Peter Sterk, Owen White, and John Wooley

Subjects
0303 health sciences, 03 medical and health sciences, Community Dialog, 0302 clinical medicine, Genetics, 030217 neurology & neurosurgery, 030304 developmental biology
Abstract

This report summarizes the proceedings of the 10th workshop of the Genomic Standards Consortium (GSC), held at Argonne National Laboratory, IL, USA. It was the second GSC workshop to have open registration and attracted over 60 participants who worked together to progress the full range of projects ongoing within the GSC. Overall, the primary focus of the workshop was on advancing the M5 platform for next-generation collaborative computational infrastructures. Other key outcomes included the formation of a GSC working group focused on MIGS/MIMS/MIENS compliance using the ISA software suite and the formal launch of the GSC Developer Working Group. Further information about the GSC and its range of activities can be found at http://gensc.org/.

Published
2010

14. wikidata: a central hub of linked open life science data

Author

Andra Waagmeester, Elvira Mitraka, Benjamin M. Good, Sebastian Burgstaller-Muehlbacher, Paul Pavlidis, Gang Fu, Lynn Schriml, Andrew I. Su, Andra Waagmeester, Elvira Mitraka, Benjamin M. Good, Sebastian Burgstaller-Muehlbacher, Paul Pavlidis, Gang Fu, Lynn Schriml, and Andrew I. Su

Published
2015
Full Text
View/download PDF

15. The 'Minimum Information about an ENvironmental Sequence' (MIENS) specification

Author

Pelin Yilmaz, Renzo Kottmann, Dawn Field, Rob Knight, James R. Cole, Linda Amaral-Zettler, Jack A. Gilbert, Ilene Karsch-Mizrachi, Anjanette Johnston, Guy Cochrane, Robert Vaughan, Christopher Hunter, Joonhong Park, Norman Morrison, Phillipe Rocca-Serra, Peter Sterk, Mani Arumugam, Laura Baumgartner, Bruce W. Birren, Martin J. Blaser, Vivien Bonazzi, Peer Bork, Pier Luigi Buttigieg, Patrick Chain, Elizabeth K. Costello, Heather Huot-Creasy, Peter Dawyndt, Todd DeSantis, Noah Fierer, Jed Fuhrman, Rachel E. Gallery, Richard A. Gibbs, Michelle Gwinn Giglio, Inigo San Gil, Elizabeth M. Glass, Antonio Gonzalez, Jeffrey I. Gordon, Robert Guralnick, Wolfgang Hankeln, Sarah Highlander, Philip Hugenholtz, Janet Jansson, Jerry Kennedy, Dan Knights, Omry Koren, Justin Kuczynski, Nikos Kyrpides, Robert Larsen, Christian L. Lauber, Teresa Legg, Ruth E. Ley, Catherine A. Lozupone, Wolfgang Ludwig, Donna Lyons, Eamonn Maguire, Barbara A. Methé, Folker Meyer, Sara Nakielny, Karen E. Nelson, Diana Nemergut, Josh D. Neufeld, Norman R. Pace, Giriprakash Palanisamy, Jörg Peplies, Jane Peterson, Joseph Petrosino, Lita Proctor, Jeroen Raes, Sujeevan Ratnasingham, Jacques Ravel, David A. Relman, Susanna Assunta-Sansone, Lynn Schriml, Erica Sodergren, Aymé Spor, Jesse Stombaugh, James M. Tiedje, Doyle V. Ward, George M. Weinstock, Doug Wendel, Owen White, Andreas Wilke, Jennifer Wortmann, and Frank Oliver Glöckner

Subjects
Ecology, Bioinformatics, Earth & Environment, Data Standards, Genetics & Genomics, Microbiology, Biotechnology
Abstract

We present the Genomic Standards Consortium’s (GSC) “Minimum Information about an ENvironmental Sequence” (MIENS) standard for describing marker genes. Adoption of MIENS will enhance our ability to analyze natural genetic diversity across the Tree of Life as it is currently being documented by massive DNA sequencing efforts from myriad ecosystems in our ever-changing biosphere.

Published
2010
Full Text
View/download PDF

16. The 'Minimum Information about an ENvironmental Sequence' (MIENS) specification

Author

Frank Oliver Glöckner, Pelin Yilmaz, Renzo Kottmann, Dawn Field, Rob Knight, James Cole, Linda Amaral-Zettler, Jack Gilbert, Ilene Karsch-Mizrachi, Anjanette Johnston, Guy Cochrane, Robert Vaughan, Christopher Hunter, Joonhong Park, Norman Morrison, Phillipe Rocca-Serra, Peter Sterk, Mani Arumugam, Laura Baumgartner, Bruce Birren, Martin Blaser, Vivien Bonazzi, Peer Bork, Pier Luigi Buttigieg, Patrick Chain, Elizabeth Costello, Heather Huot-Creasy, Peter Dawyndt, Todd DeSantis, Noah Fierer, Jed Fuhrman, Rachel Gallery, Richard Gibbs, Michelle Gwinn Giglio, Inigo San Gil, Elizabeth Glass, Antonio Gonzalez, Jeffrey Gordon, Robert Guralnick, Wolfgang Hankeln, Sarah Highlander, Philip Hugenholtz, Janet Jansson, Jerry Kennedy, Dan Knights, Omry Koren, Justin Kuczynski, Nikos Kyrpides, Robert Larsen, Christian Lauber, Teresa Legg, Ruth Ley, Catherine Lozupone, Wolfgang Ludwig, Donna Lyons, Eamonn Maguire, Barbara Methé, Folker Meyer, Sara Nakielny, Karen Nelson, Diana Nemergut, Josh Neufeld, Norman Pace, Giriprakash Palanisamy, Jörg Peplies, Jane Peterson, Joseph Petrosino, Lita Proctor, Jeroen Raes, Sujeevan Ratnasingham, Jacques Ravel, David Relman, Susanna Assunta-Sansone, Lynn Schriml, Erica Sodergren, Aymé Spor, Jesse Stombaugh, James Tiedje, Doyle Ward, George Weinstock, Doug Wendel, Owen White, Andreas Wilke, and Jennifer Wortmann

Subjects
General Materials Science
Published
2010

17. Creating a Translational Medicine Ontology

Author

Christine Denney, Colin Batchelor, Olivier Bodenreider, Sam Cheng, John Hart, John Hill, John Madden, Mark Musen, Elgar Pichler, Matthias Samwald, Sándor Szalma, Lynn Schriml, David Sedlock, Larisa Soldatova, Koji Sonoda, David Statham, Holger Stenzhorn, Patricia Whetzel, Elizabeth Wu, and Susie Stephens

Subjects
General Materials Science
Published
2009

18. Database resources of the National Center for Biotechnology Information

Author

Wheeler, D. L., Barrett, T., Benson, D. A., Bryant, S. H., Canese, K., Chetvernin, V., Church, D. M., Dicuccio, M., Edgar, R., Federhen, S., Geer, L. Y., Helmberg, W., Kapustin, Y., Kenton, D. L., Khovayko, O., Lipman, D. J., Madden, T. L., Maglott, D. R., Ostell, J., Pruitt, K. D., Schuler, G. D., Lynn Schriml, Sequeira, E., Sherry, S. T., Sirotkin, K., Souvorov, A., Starchenko, G., Suzek, T. O., Tatusov, R., Tatusova, T. A., Wagner, L., and Yaschenko, E.

Subjects
Internet, PubMed, 0303 health sciences, National Library of Medicine (U.S.), Genomics, Sequence Analysis, DNA, United States, Article, 3. Good health, 03 medical and health sciences, 0302 clinical medicine, Gene Expression Regulation, Genes, Databases, Genetic, Genetics, Humans, natural sciences, Databases, Nucleic Acid, Databases, Protein, Sequence Alignment, Software, 030217 neurology & neurosurgery, 030304 developmental biology
Abstract

In addition to maintaining the GenBank nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data made available through NCBI's Web site. NCBI resources include Entrez, the Entrez Programming Utilities, MyNCBI, PubMed, PubMed Central, Entrez Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link (BLink), Electronic PCR, OrfFinder, Spidey, Splign, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, Cancer Chromosomes, Entrez Genomes and related tools, the Map Viewer, Model Maker, Evidence Viewer, Clusters of Orthologous Groups, Retroviral Genotyping Tools, HIV-1, Human Protein Interaction Database, SAGEmap, Gene Expression Omnibus, Entrez Probe, GENSAT, Online Mendelian Inheritance in Man, Online Mendelian Inheritance in Animals, the Molecular Modeling Database, the Conserved Domain Database, the Conserved Domain Architecture Retrieval Tool and the PubChem suite of small molecule databases. Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized datasets. All of the resources can be accessed through the NCBI home page at: http://www.ncbi.nlm.nih.gov.

Catalog

Books, media, physical & digital resources
See catalog results