المؤلفون: Davis, Paul, Zarowiecki, Magdalena, Arnaboldi, Valerio, Becerra, Andrés, Cain, Scott, Chan, Juancarlos, Chen, Wen J, Cho, Jaehyoung, da Veiga Beltrame, Eduardo, Diamantakis, Stavros, Gao, Sibyl, Grigoriadis, Dionysis, Grove, Christian A, Harris, Todd W, Kishore, Ranjana, Le, Tuan, Lee, Raymond YN, Luypaert, Manuel, Müller, Hans-Michael, Nakamura, Cecilia, Nuin, Paulo, Paulini, Michael, Quinton-Tulloch, Mark, Raciti, Daniela, Rodgers, Faye H, Russell, Matthew, Schindelman, Gary, Singh, Archana, Stickland, Tim, Van Auken, Kimberly, Wang, Qinghua, Williams, Gary, Wright, Adam J, Yook, Karen, Berriman, Matt, Howe, Kevin L, Schedl, Tim, Stein, Lincoln, Sternberg, Paul W

المصدر: Genetics. 220(4)

مصطلحات موضوعية: Biological Sciences, Genetics, Human Genome, Generic health relevance, Animals, Caenorhabditis, Caenorhabditis elegans, Databases, Genetic, Genome, Genomics, Humans, Nematoda, Caenorhabditis elegans, annotation, caenorhabditis, community, curation, data, database, gene, health, human, literature, mining, model, nematode, platform, research, resource, software, tools, Developmental Biology, Biochemistry and cell biology

الوصف: WormBase (www.wormbase.org) is the central repository for the genetics and genomics of the nematode Caenorhabditis elegans. We provide the research community with data and tools to facilitate the use of C. elegans and related nematodes as model organisms for studying human health, development, and many aspects of fundamental biology. Throughout our 22-year history, we have continued to evolve to reflect progress and innovation in the science and technologies involved in the study of C. elegans. We strive to incorporate new data types and richer data sets, and to provide integrated displays and services that avail the knowledge generated by the published nematode genetics literature. Here, we provide a broad overview of the current state of WormBase in terms of data type, curation workflows, analysis, and tools, including exciting new advances for analysis of single-cell data, text mining and visualization, and the new community collaboration forum. Concurrently, we continue the integration and harmonization of infrastructure, processes, and tools with the Alliance of Genome Resources, of which WormBase is a founding member.

وصف الملف: application/pdf

الوصول الحر: https://escholarship.org/uc/item/2ch788zmTest

المؤلفون: Agapite, Julie, Albou, Laurent-Philippe, Aleksander, Suzanne A, Alexander, Micheal, Anagnostopoulos, Anna V, Antonazzo, Giulia, Argasinska, Joanna, Arnaboldi, Valerio, Attrill, Helen, Becerra, Andrés, Bello, Susan M, Blake, Judith A, Blodgett, Olin, Bradford, Yvonne M, Bult, Carol J, Cain, Scott, Calvi, Brian R, Carbon, Seth, Chan, Juancarlos, Chen, Wen J, Cherry, J Michael, Cho, Jaehyoung, Christie, Karen R, Crosby, Madeline A, Davis, Paul, da Veiga Beltrame, Eduardo, De Pons, Jeffrey L, D’Eustachio, Peter, Diamantakis, Stavros, Dolan, Mary E, dos Santos, Gilberto, Douglass, Eric, Dunn, Barbara, Eagle, Anne, Ebert, Dustin, Engel, Stacia R, Fashena, David, Foley, Saoirse, Frazer, Ken, Gao, Sibyl, Gibson, Adam C, Gondwe, Felix, Goodman, Josh, Gramates, L Sian, Grove, Christian A, Hale, Paul, Harris, Todd, Hayman, G Thomas, Hill, David P, Howe, Douglas G, Howe, Kevin L, Hu, Yanhui, Jha, Sagar, Kadin, James A, Kaufman, Thomas C, Kalita, Patrick, Karra, Kalpana, Kishore, Ranjana, Kwitek, Anne E, Laulederkind, Stanley JF, Lee, Raymond, Longden, Ian, Luypaert, Manuel, MacPherson, Kevin A, Martin, Ryan, Marygold, Steven J, Matthews, Beverley, McAndrews, Monica S, Millburn, Gillian, Miyasato, Stuart, Motenko, Howie, Moxon, Sierra, Muller, Hans-Michael, Mungall, Christopher J, Muruganujan, Anushya, Mushayahama, Tremayne, Nalabolu, Harika S, Nash, Robert S, Ng, Patrick, Nuin, Paulo, Paddock, Holly, Paulini, Michael, Perrimon, Norbert, Pich, Christian, Quinton-Tulloch, Mark, Raciti, Daniela, Ramachandran, Sridhar, Richardson, Joel E, Gelbart, Susan Russo, Ruzicka, Leyla, Schaper, Kevin, Schindelman, Gary, Shimoyama, Mary, Simison, Matt, Shaw, David R, Shrivatsav, Ajay, Singer, Amy, Skrzypek, Marek, Smith, Constance M, Smith, Cynthia L

المصدر: Genetics. 220(4)

مصطلحات موضوعية: Biological Sciences, Bioinformatics and Computational Biology, Genetics, Biotechnology, Human Genome, Underpinning research, 1.5 Resources and infrastructure (underpinning), Alleles, Animals, Caenorhabditis elegans, Databases, Genetic, Drosophila, Gene Ontology, Humans, Internet, Mice, Molecular Sequence Annotation, Rats, Saccharomycetales, Zebrafish, Alliance of Genome Resources Consortium, biocuration, data mining, gene expression, gene function, gene interaction, genome, knowledgebase, phenotype, variants, Developmental Biology, Biochemistry and cell biology

الوصف: The Alliance of Genome Resources (the Alliance) is a combined effort of 7 knowledgebase projects: Saccharomyces Genome Database, WormBase, FlyBase, Mouse Genome Database, the Zebrafish Information Network, Rat Genome Database, and the Gene Ontology Resource. The Alliance seeks to provide several benefits: better service to the various communities served by these projects; a harmonized view of data for all biomedical researchers, bioinformaticians, clinicians, and students; and a more sustainable infrastructure. The Alliance has harmonized cross-organism data to provide useful comparative views of gene function, gene expression, and human disease relevance. The basis of the comparative views is shared calls of orthology relationships and the use of common ontologies. The key types of data are alleles and variants, gene function based on gene ontology annotations, phenotypes, association to human disease, gene expression, protein-protein and genetic interactions, and participation in pathways. The information is presented on uniform gene pages that allow facile summarization of information about each gene in each of the 7 organisms covered (budding yeast, roundworm Caenorhabditis elegans, fruit fly, house mouse, zebrafish, brown rat, and human). The harmonized knowledge is freely available on the alliancegenome.org portal, as downloadable files, and by APIs. We expect other existing and emerging knowledge bases to join in the effort to provide the union of useful data and features that each knowledge base currently provides.

وصف الملف: application/pdf

الوصول الحر: https://escholarship.org/uc/item/8xx9b11gTest

المؤلفون: Aleksander, Suzanne A., Anagnostopoulos, Anna V., Antonazzo, Giulia, Arnaboldi, Valerio, Attrill, Helen, Becerra, Andrés, Bello, Susan M., Blodgett, Olin, Bradford, Yvonne M., Bult, Carol J., Cain, Scott, Calvi, Brian R., Carbon, Seth, Chan, Juancarlos, Chen, Wen J., Cherry, J. Michael, Cho, Jaehyoung, Crosby, Madeline A., De Pons, Jeffrey L., D'Eustachio, Peter, Diamantakis, Stavros, Dolan, Mary E., dos Santos, Gilberto, Dyer, Sarah, Ebert, Dustin, Engel, Stacia R., Fashena, David, Fisher, Malcolm, Foley, Saoirse, Gibson, Adam C., Gollapally, Varun R., Gramates, L. Sian, Grove, Christian A., Hale, Paul, Harris, Todd, Hayman, G. Thomas, Hu, Yanhui, James-Zorn, Christina, Karimi, Kamran, Karra, Kalpana, Kishore, Ranjana, Kwitek, Anne E., Laulederkind, Stanley J. F., Lee, Raymond, Longden, Ian, Luypaert, Manuel, Markarian, Nicholas, Marygold, Steven J., Matthews, Beverley, McAndrews, Monica S., Millburn, Gillian, Miyasato, Stuart, Motenko, Howie, Moxon, Sierra, Muller, Hans-Michael, Mungall, Christopher J., Muruganujan, Anushya, Mushayahama, Tremayne, Nash, Robert S., Nuin, Paulo, Paddock, Holly, Pells, Troy, Perrimon, Norbert, Pich, Christian, Quinton-Tulloch, Mark, Raciti, Daniela, Ramachandran, Sridhar, Richardson, Joel E., Russo Gelbart, Susan, Ruzicka, Leyla, Schindelman, Gary, Shaw, David R., Sherlock, Gavin, Shrivatsav, Ajay, Singer, Amy, Smith, Constance M., Smith, Cynthia L., Smith, Jennifer R., Stein, Lincoln, Sternberg, Paul W, Tabone, Christopher J., Thomas, Paul D., Thorat, Ketaki, Thota, Jyothi, Tomczuk, Monika, Trovisco, Vitor, Tutaj, Marek A., Urbano, Jose-Maria, Van Auken, Kimberly, Van Slyke, Ceri E., Vize, Peter D., Wang, Qinghua, Weng, Shuai, Westerfield, Monte, Wilming, Laurens G., Wong, Edith D., Wright, Adam, Yook, Karen, Zhou, Pinglei, Zorn, Aaron, Zytkovicz, Mark, Alliance of Genome Resources Consortium

المصدر: Genetics, 227(1), iyae049, (2024-05)

الوصف: The Alliance of Genome Resources (Alliance) is an extensible coalition of knowledgebases focused on the genetics and genomics of intensively studied model organisms. The Alliance is organized as individual knowledge centers with strong connections to their research communities and a centralized software infrastructure, discussed here. Model organisms currently represented in the Alliance are budding yeast,Caenorhabditis elegans,Drosophila, zebrafish, frog, laboratory mouse, laboratory rat, and the Gene Ontology Consortium. The project is in a rapid development phase to harmonize knowledge, store it, analyze it, and present it to the community through a web portal, direct downloads, and application programming interfaces (APIs). Here, we focus on developments over the last 2 years. Specifically, we added and enhanced tools for browsing the genome (JBrowse), downloading sequences, mining complex data (AllianceMine), visualizing pathways, full-text searching of the literature (Textpresso), and sequence similarity searching (SequenceServer). We enhanced existing interactive data tables and added an interactive table of paralogs to complement our representation of orthology. To support individual model organism communities, we implemented species-specific “landing pages” and will add disease-specific portals soon; in addition, we support a common community forum implemented in Discourse software. We describe our progress toward a central persistent database to support curation, the data modeling that underpins harmonization, and progress toward a state-of-the-art literature curation system with integrated artificial intelligence and machine learning (AI/ML). ; © The Author(s) 2024. Published by Oxford University Press on behalf of The Genetics Society of America. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0Test/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work ...

العلاقة: https://doi.org/10.1101/2023.11.20.567935Test; https://www.ncbi.nlm.nih.gov/pmc/PMC10690154Test; https://doi.org/10.1093/genetics/iyae049Test; oai:authors.library.caltech.edu:agb38-ew637; https://www.ncbi.nlm.nih.gov/pmc/PMC11075569Test

الإتاحة: https://doi.org/10.1093/genetics/iyae04910.1101/2023.11.20.567935Test
https://www.ncbi.nlm.nih.gov/pmc/PMC11075569Test

المؤلفون: Sternberg, Paul W., Van Auken, Kimberly, Wang, Qinghua, Wright, Adam, Yook, Karen, Zarowiecki, Magdalena, Arnaboldi, Valerio, Becerra, Andrés, Brown, Stephanie, Cain, Scott, Chan, Juancarlos, Chen, Wen J., Cho, Jaehyoung, Davis, Paul, Diamantakis, Stavros, Dyer, Sarah, Grigoriadis, Dionysis, Grove, Christian A., Harris, Todd, Howe, Kevin, Kishore, Ranjana, Lee, Raymond, Longden, Ian, Luypaert, Manuel, Müller, Hans-Michael, Nuin, Paulo, Quinton-Tulloch, Mark, Raciti, Daniela, Schedl, Tim, Schindelman, Gary, Stein, Lincoln

المصدر: Genetics, 227(1), iyae050, (2024-05)

الوصف: WormBase has been the major repository and knowledgebase of information about the genome and genetics ofCaenorhabditis elegansand other nematodes of experimental interest for over 2 decades. We have 3 goals: to keep current with the fast-pacedC. elegansresearch, to provide better integration with other resources, and to be sustainable. Here, we discuss the current state of WormBase as well as progress and plans for moving core WormBase infrastructure to the Alliance of Genome Resources (the Alliance). As an Alliance member, WormBase will continue to interact with theC. elegans community, develop new features as needed, and curate key information from the literature and large-scale projects. ; © The Author(s) 2024. Published by Oxford University Press on behalf of The Genetics Society of America. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0Test/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. ; We thank our numerousC. elegans and other nematode colleagues for their continual feedback. We thank the National Human Genome Research Institute (NHGRI) Program Staff (Sandhya Xirasagar, Valentina di Francesco, Sarah Hutchison, and Helen Thompson) for guidance. ; The core funding for WormBase is from the National Human Genome Research Institute (NHGRI) U24HG002223 and Medical Research Council-UK grant MR/L001020/1; funding for the Alliance is from NHGRI and the National Heart, Lung and Blood Institute (U24HG010859). Curation tools are supported in part by the National Library of Medicine (NLM) R01LM013871. ; All WormBase and Alliance code and information are freely available. Specifically, WormBase code is freely available athttps://github.com/WormBase. WormBase data are available fordownloadand programmatically by API as described athttps://wormbase.org/about/userguide/for_developers/api-rest#10–10. Alliance data are ...

العلاقة: https://doi.org/10.1093/genetics/iyae050Test; oai:authors.library.caltech.edu:5sbp7-bgs69; https://www.ncbi.nlm.nih.gov/pmc/PMC11075546Test

الإتاحة: https://doi.org/10.1093/genetics/iyae050Test
https://www.ncbi.nlm.nih.gov/pmc/PMC11075546Test

المؤلفون: Yu, Corinna J., Chen, Wen J., Boyer, Tanna J.

المصدر: ASA Monitor ; volume 88, issue 3, page 28-28 ; ISSN 2380-4017 2380-4025

الإتاحة: https://doi.org/10.1097/01.asm.0001008292.72490.69Test
https://pubs.asahq.org/monitor/article-pdf/88/3/28/701013/20240300.0-00019.pdfTest

المؤلفون: Davis, Paul, Zarowiecki, Magdalena, Arnaboldi, Valerio, Becerra, Andrés, Cain, Scott, Chan, Juancarlos, Chen, Wen J., Cho, Jaehyoung, da Veiga Beltrame, Eduardo, Diamantakis, Stavros, Gao, Sibyl, Grigoriadis, Dionysis, Grove, Christian A., Harris, Todd W., Kishore, Ranjana, Le, Tuan, Lee, Raymond Y. N., Luypaert, Manuel, Müller, Hans-Michael, Nakamura, Cecilia, Nuin, Paulo, Paulini, Michael, Quinton-Tulloch, Mark, Raciti, Daniela, Rodgers, Faye H., Russell, Matthew, Schindelman, Gary, Singh, Archana, Stickland, Tim, Van Auken, Kimberly, Wang, Qinghua, Williams, Gary, Wright, Adam J., Yook, Karen, Berriman, Matt, Howe, Kevin L., Schedl, Tim, Stein, Lincoln, Sternberg, Paul W.

المصدر: Genetics, 220(4), Art. No. iyac003, (2022-04)

مصطلحات موضوعية: Caenorhabditis elegans, caenorhabditis, nematode, resource, model, database, data, community, software, gene, curation, annotation, research, literature, mining, tools, health, human, platform, Genetics

الوصف: WormBase (www.wormbase.org) is the central repository for the genetics and genomics of the nematode Caenorhabditis elegans. We provide the research community with data and tools to facilitate the use of C. elegans and related nematodes as model organisms for studying human health, development, and many aspects of fundamental biology. Throughout our 22-year history, we have continued to evolve to reflect progress and innovation in the science and technologies involved in the study of C. elegans. We strive to incorporate new data types and richer data sets, and to provide integrated displays and services that avail the knowledge generated by the published nematode genetics literature. Here, we provide a broad overview of the current state of WormBase in terms of data type, curation workflows, analysis, and tools, including exciting new advances for analysis of single-cell data, text mining and visualization, and the new community collaboration forum. Concurrently, we continue the integration and harmonization of infrastructure, processes, and tools with the Alliance of Genome Resources, of which WormBase is a founding member. ; © The Author(s) 2022. Published by Oxford University Press on behalf of Genetics Society of America. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0Test/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. The authors wish to thank the US National Human Genome Research Institute; UK Medical Research Council funding agencies for their ongoing support of WormBase and members of the C. elegans research community whose insights and explorations form the purpose of WormBase, all those contributing data through AFP or data submission forms, and all the WormBase users, for all your feedback, input and requests which inspire and guide us. Funding for WormBase is from US National Human Genome Research Institute [U24 HG002223]; UK ...

العلاقة: https://doi.org/10.1093/genetics/iyac003Test; oai:authors.library.caltech.edu:ax9qa-w5481; https://www.ncbi.nlm.nih.gov/pmc/PMC8982018Test; eprintid:113875; resolverid:CaltechAUTHORS:20220310-752284000

الإتاحة: https://doi.org/10.1093/genetics/iyac003Test
https://www.ncbi.nlm.nih.gov/pmc/PMC8982018Test

المؤلفون: Chen, Wen J.

الوصف: In the nematode C. elegans, heterotrimeric G proteins have been shown to regulate the behavior of locomotion, feeding and egg-laying. Go belongs to Gi family and only exists in organisms with a nervous system. The signaling downstream of Go has been a mystery since its discovery, and it is what we are determined to find out. Loss of Goα causes animals to be hyperactive and lay eggs constitutively. Overexpressing Goα causes opposite phenotypes. Another α protein a subunit, Gq, causes phenotypes opposite to Go. To identify G protein effectors in C. elegans, we performed a forward genetic screen for suppressors of activated Goα under the control of the heat-shock promoter hsp16-2. Because of the nature of the screen design, we identified two categories of genes. One category acts on heat shock response and the other category acts on G protein pathways. We characterized and positional cloned genes from both categories. The second chapter of the thesis described sag-4, a cyclin L homologue that specifically affects heat shock promoters and decreases heat-shock induced protein expression. We propose that cyclin Lis likely to be involved in heat shock induced transcription. Other genes in this category, sag-3, sag-5 and sag-8, may also function in similar mechanisms. The third chapter of the thesis focused on G protein signaling. eat-16 was identified in the screen for suppressors of activated Goα. We positional cloned it and found it encodes a RGS7 homologue. RGS proteins have been studied as GTPase Activating Protein for the α subunits of heterotrimeric G proteins. Although eat-16 was identified in a suppressor screen for activated Go (goa-1), both genetic and biochemical evidence showed that eat-16 is a GAP for Gq (egl-30). We propose that Go and Gq antagonize each other, thereby regulating behaviors. Go might negatively regulate Gq signaling, possibly through eat-16 or other unrevealed genes. Chapter four describes our reconstituted system in mammalian cell culture. EAT-16 decreases Gq/G11 mediated PLC activity. GOA-1 and GPB-2 (C. elegans Gβ5 homologue) also decrease PLC activity induced by Gq/G11. These results are consistent with the hypothesis that Go negatively regulate Gq signaling, and the interaction between Gβ5 and RGS7 can be one of the steps between Go and Gq.

وصف الملف: application/pdf

العلاقة: https://thesis.library.caltech.edu/13852Test/; https://resolver.caltech.edu/CaltechTHESIS:08112020-100312577Test; CaltechTHESIS:08112020-100312577

الإتاحة: https://thesis.library.caltech.edu/13852/1/Chen_WJ_2000.pdfTest

المؤلفون: Harris, Todd W., Arnaboldi, Valerio, Chan, Juancarlos, Chen, Wen J., Cho, Jaehyoung, Grove, Christian A., Kishore, Ranjana, Lee, Y. N., Müller, Hans-Michael, Nakamura, Cecilia, Raciti, Daniela, Schindelman, Gary, V. Auken, Kimberly, Wang, Qinghua, Yook, Karen, Sternberg, Paul W.

المصدر: Nucleic Acids Research, 48(D1), D762-D767, (2020-01-08)

الوصف: WormBase (https://wormbase.orgTest/) is a mature Model Organism Information Resource supporting researchers using the nematode Caenorhabditis elegans as a model system for studies across a broad range of basic biological processes. Toward this mission, WormBase efforts are arranged in three primary facets: curation, user interface and architecture. In this update, we describe progress in each of these three areas. In particular, we discuss the status of literature curation and recently added data, detail new features of the web interface and options for users wishing to conduct data mining workflows, and discuss our efforts to build a robust and scalable architecture by leveraging commercial cloud offerings. We conclude with a description of WormBase's role as a founding member of the nascent Alliance of Genome Resources. ; © The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0Test/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. Received: 15 September 2019; Revision received: 02 October 2019; Accepted: 07 October 2019; Published: 23 October 2019. The authors wish to thank funding agencies for their ongoing support of WormBase and members of the C. elegans research community whose results form the foundation and purpose of WormBase. Funding: US National Human Genome Research Institute [U24 HG002223]; UK Medical Research Council [MR/S000453/1]; UK Biotechnology and Biological Sciences Research Council [BB/P024602/1]. Funding for open access charge: US National Human Genome Research Institute [U24 HG002223]. Conflict of interest statement. None declared. ; Published - gkz920.pdf

العلاقة: https://doi.org/10.1093/nar/gkz920Test; oai:authors.library.caltech.edu:scabh-anq11; https://www.ncbi.nlm.nih.gov/pmc/PMC7145598Test; eprintid:99530; resolverid:CaltechAUTHORS:20191029-103634272

الإتاحة: https://doi.org/10.1093/nar/gkz920Test
https://www.ncbi.nlm.nih.gov/pmc/PMC7145598Test

المؤلفون: Agapite, Julie, Albou, Laurent-Philippe, Aleksander, Suzi, Argasinska, Joanna, Arnaboldi, Valerio, Attrill, Helen, Bello, Susan M., Blake, Judith A., Blodgett, Olin, Bradford, Yvonne M., Bult, Carol J., Cain, Scott, Calvi, Brian R., Carbon, Seth, Chan, Juancarlos, Chen, Wen J., Cherry, J. Michael, Cho, Jaehyoung, Christie, Karen R., Crosby, Madeline A., De Pons, Jeff, Dolan, Mary E, dos Santos, Gilberto, Dunn, Barbara, Dunn, Nathan, Eagle, Anne, Ebert, Dustin, Engel, Stacia R., Fashena, David, Frazer, Ken, Gao, Sibyl, Gondwe, Felix, Goodman, Josh, Gramates, L. Sian, Grove, Christian A., Harris, Todd, Harrison, Marie-Claire, Howe, Douglas G., Howe, Kevin L., Jha, Sagar, Kadin, James A., Kaufman, Thomas C., Kalita, Patrick, Karra, Kalpana, Kishore, Ranjana, Laulederkind, Stan, Lee, Raymond, MacPherson, Kevin A., Marygold, Steven J., Matthews, Beverley, Millburn, Gillian, Miyasato, Stuart, Moxon, Sierra, Mueller, Hans-Michael, Mungall, Christopher, Muruganujan, Anushya, Mushayahama, Tremayne, Nash, Robert S., Ng, Patrick, Paulini, Michael, Perrimon, Norbert, Pich, Christian, Raciti, Daniela, Richardson, Joel E., Russell, Matthew, Russo Gelbart, Susan, Ruzicka, Leyla, Schaper, Kevin, Shimoyama, Mary, Simison, Matt, Smith, Cynthia, Shaw, David R., Shrivatsav, Ajay, Skrzypek, Marek, Smith, Jennifer R., Sternberg, Paul W., Tabone, Christopher J., Thomas, Paul D., Thota, Jyothi, Toro, Sabrina, Tomczuk, Monika, Tutaj, Marek, Tutaj, Monika, Urbano, Jose-Maria, Van Auken, Kimberly, Van Slyke, Ceri E., Wang, Shur-Jen, Weng, Shuai, Westerfield, Monte, Williams, Gary, Wong, Edith D., Wright, Adam, Yook, Karen, Alliance of Genome Resources Consortium

المصدر: Nucleic Acids Research, 48(D1), D650-D658, (2020-01-08)

الوصف: The Alliance of Genome Resources (Alliance) is a consortium of the major model organism databases and the Gene Ontology that is guided by the vision of facilitating exploration of related genes in human and well-studied model organisms by providing a highly integrated and comprehensive platform that enables researchers to leverage the extensive body of genetic and genomic studies in these organisms. Initiated in 2016, the Alliance is building a central portal (www.alliancegenome.org) for access to data for the primary model organisms along with gene ontology data and human data. All data types represented in the Alliance portal (e.g. genomic data and phenotype descriptions) have common data models and workflows for curation. All data are open and freely available via a variety of mechanisms. Long-term plans for the Alliance project include a focus on coverage of additional model organisms including those without dedicated curation communities, and the inclusion of new data types with a particular focus on providing data and tools for the non-model-organism researcher that support enhanced discovery about human health and disease. Here we review current progress and present immediate plans for this new bioinformatics resource. ; © The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0Test/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. Received: 31 July 2019; Revision received: 03 September 2019; Accepted: 19 September 2019; Published: 25 September 2019. The Alliance platform is designed and implemented by a core group of developers and curators at SGD, WormBase, ZFIN, RGD, MGD, FlyBase and the GOC. We would particularly like to acknowledge other staff at those projects who continue to provide gold-standard curation of model organism data without which ...

العلاقة: https://doi.org/10.1093/nar/gkz813Test; oai:authors.library.caltech.edu:jskmd-kqf35; https://www.ncbi.nlm.nih.gov/pmc/PMC6943066Test; eprintid:102491; resolverid:CaltechAUTHORS:20200413-081503928

الإتاحة: https://doi.org/10.1093/nar/gkz813Test
https://www.ncbi.nlm.nih.gov/pmc/PMC6943066Test

المؤلفون: Grove, Christian, Cain, Scott, Chen, Wen J., Davis, Paul, Harris, Todd W., Howe, Kevin L., Kishore, Ranjana, Lee, Raymond, Paulini, Michael, Raciti, Daniela, Tuli, Mary Ann, Van Auken, Kimberly, Williams, Gary, WormBase Consortium

المساهمون: Kollmar, Martin

مصطلحات موضوعية: Data mining, Nematodes, Genomics, Genetics, Caenorhabditis elegans, Model organism database, Ontologies, User guide

الوصف: WormBase (www.wormbase.org) provides the nematode research community with a centralized database for information pertaining to nematode genes and genomes. As more nematode genome sequences are becoming available and as richer data sets are published, WormBase strives to maintain updated information, displays, and services to facilitate efficient access to and understanding of the knowledge generated by the published nematode genetics literature. This chapter aims to provide an explanation of how to use basic features of WormBase, new features, and some commonly used tools and data queries. Explanations of the curated data and step-by-step instructions of how to access the data via the WormBase website and available data mining tools are provided. ; © 2018 Springer Science+Business Media, LLC, part of Springer Nature. WormBase is supported by grant #U41 HG002223 from the National Human Genome Research Institute at the US National Institutes of Health, the UK Medical Research Council and the UK Biotechnology and Biological Sciences Research Council. At the time of writing, the WormBase Consortium included Paul W. Sternberg, Paul Kersey, Matthew Berriman, Lincoln Stein, Tim Schedl, Todd Harris, Scott Cain, Sibyl Gao, Paulo Nuin, Adam Wright, Kevin Howe, Bruce Bolt, Paul Davis, Michael Paulini, Faye Rodgers, Matthew Russell, Myriam Shafie, Gary Williams, Juancarlos Chan, Wen J. Chen, Christian Grove, Ranjana Kishore, Raymond Lee, Hans-Michael Müller, Cecilia Nakamura, Daniela Raciti, Gary Schindelman, Mary Ann Tuli, Kimberly Van Auken, Daniel Wang, and Karen Yook. ; Accepted Version - nihms-1011867.pdf

العلاقة: https://doi.org/10.1007/978-1-4939-7737-6_14Test; oai:authors.library.caltech.edu:sbxg2-b4p21; https://www.ncbi.nlm.nih.gov/pmc/PMC6424801Test; eprintid:94016; resolverid:CaltechAUTHORS:20190321-082336924

الإتاحة: https://doi.org/10.1007/978-1-4939-7737-6_14Test
https://www.ncbi.nlm.nih.gov/pmc/PMC6424801Test