Whole-brain annotation and multi-connectome cell typing of Drosophila.

Autor: Schlegel P; Neurobiology Division, MRC Laboratory of Molecular Biology, Cambridge, UK.; Drosophila Connectomics Group, Department of Zoology, University of Cambridge, Cambridge, UK., Yin Y; Drosophila Connectomics Group, Department of Zoology, University of Cambridge, Cambridge, UK., Bates AS; Neurobiology Division, MRC Laboratory of Molecular Biology, Cambridge, UK.; Department of Neurobiology and Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA.; Centre for Neural Circuits and Behaviour, University of Oxford, Oxford, UK., Dorkenwald S; Computer Science Department, Princeton University, Princeton, NJ, USA.; Princeton Neuroscience Institute, Princeton University, Princeton, NJ, USA., Eichler K; Drosophila Connectomics Group, Department of Zoology, University of Cambridge, Cambridge, UK., Brooks P; Drosophila Connectomics Group, Department of Zoology, University of Cambridge, Cambridge, UK., Han DS; Neurobiology Division, MRC Laboratory of Molecular Biology, Cambridge, UK.; School of Mathematics and Statistics, University of New South Wales, Sydney, New South Wales, Australia., Gkantia M; Drosophila Connectomics Group, Department of Zoology, University of Cambridge, Cambridge, UK., Dos Santos M; Drosophila Connectomics Group, Department of Zoology, University of Cambridge, Cambridge, UK., Munnelly EJ; Drosophila Connectomics Group, Department of Zoology, University of Cambridge, Cambridge, UK., Badalamente G; Drosophila Connectomics Group, Department of Zoology, University of Cambridge, Cambridge, UK., Serratosa Capdevila L; Drosophila Connectomics Group, Department of Zoology, University of Cambridge, Cambridge, UK., Sane VA; Drosophila Connectomics Group, Department of Zoology, University of Cambridge, Cambridge, UK., Fragniere AMC; Drosophila Connectomics Group, Department of Zoology, University of Cambridge, Cambridge, UK., Kiassat L; Drosophila Connectomics Group, Department of Zoology, University of Cambridge, Cambridge, UK., Pleijzier MW; Neurobiology Division, MRC Laboratory of Molecular Biology, Cambridge, UK., Stürner T; Neurobiology Division, MRC Laboratory of Molecular Biology, Cambridge, UK.; Drosophila Connectomics Group, Department of Zoology, University of Cambridge, Cambridge, UK., Tamimi IFM; Drosophila Connectomics Group, Department of Zoology, University of Cambridge, Cambridge, UK., Dunne CR; Drosophila Connectomics Group, Department of Zoology, University of Cambridge, Cambridge, UK., Salgarella I; Drosophila Connectomics Group, Department of Zoology, University of Cambridge, Cambridge, UK., Javier A; Drosophila Connectomics Group, Department of Zoology, University of Cambridge, Cambridge, UK., Fang S; Drosophila Connectomics Group, Department of Zoology, University of Cambridge, Cambridge, UK., Perlman E; Yikes, Baltimore, MD, USA., Kazimiers T; kazmos, Dresden, Germany., Jagannathan SR; Drosophila Connectomics Group, Department of Zoology, University of Cambridge, Cambridge, UK., Matsliah A; Princeton Neuroscience Institute, Princeton University, Princeton, NJ, USA., Sterling AR; Princeton Neuroscience Institute, Princeton University, Princeton, NJ, USA.; Eyewire, Boston, MA, USA., Yu SC; Princeton Neuroscience Institute, Princeton University, Princeton, NJ, USA., McKellar CE; Princeton Neuroscience Institute, Princeton University, Princeton, NJ, USA., Costa M; Drosophila Connectomics Group, Department of Zoology, University of Cambridge, Cambridge, UK., Seung HS; Computer Science Department, Princeton University, Princeton, NJ, USA.; Princeton Neuroscience Institute, Princeton University, Princeton, NJ, USA., Murthy M; Princeton Neuroscience Institute, Princeton University, Princeton, NJ, USA., Hartenstein V; Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA, USA., Bock DD; Department of Neurological Sciences, Larner College of Medicine, University of Vermont, Burlington, VT, USA. dbock@uvm.edu., Jefferis GSXE; Neurobiology Division, MRC Laboratory of Molecular Biology, Cambridge, UK. jefferis@mrc-lmb.cam.ac.uk.; Drosophila Connectomics Group, Department of Zoology, University of Cambridge, Cambridge, UK. jefferis@mrc-lmb.cam.ac.uk.

Publikováno v: Nature [Nature] 2024 Oct; Vol. 634 (8032), pp. 139-152. Date of Electronic Publication: 2024 Oct 02.

Automated annotation of scientific texts for ML-based keyphrase extraction and validation.

Autor: Amusat OO; Scientific Data Division, Lawrence Berkeley National Laboratory, 1 Cyclotron road, Berkeley, CA 94720, United States., Hegde H; Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, 1 Cyclotron road, Berkeley, CA 94720, United States., Mungall CJ; Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, 1 Cyclotron road, Berkeley, CA 94720, United States., Giannakou A; Scientific Data Division, Lawrence Berkeley National Laboratory, 1 Cyclotron road, Berkeley, CA 94720, United States., Byers NP; DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron road, Berkeley, CA 94720, United States., Gunter D; Scientific Data Division, Lawrence Berkeley National Laboratory, 1 Cyclotron road, Berkeley, CA 94720, United States., Fagnan K; DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron road, Berkeley, CA 94720, United States., Ramakrishnan L; Scientific Data Division, Lawrence Berkeley National Laboratory, 1 Cyclotron road, Berkeley, CA 94720, United States.

Publikováno v: Database : the journal of biological databases and curation [Database (Oxford)] 2024 Sep 27; Vol. 2024.

Functional implications of glycans and their curation: insights from the workshop held at the 16th Annual International Biocuration Conference in Padua, Italy.

Autor: Martinez K; Department of Biochemistry & Molecular Medicine, The George Washington University School of Medicine and Health Sciences, 2300 I St. NW, Washington, DC 20052, United States., Agirre J; York Structural Biology Laboratory, Department of Chemistry, University of York, Wentworth Way, York YO10 5DD, United Kingdom., Akune Y; The Glycosciences Laboratory, Imperial College London, Hammersmith Campus, Du Cane Road, London W12 0NN, United Kingdom., Aoki-Kinoshita KF; Glycan and Life Systems Integration Center (GaLSIC), Soka University, 1-236 Tangi-machi, Hachioji, Tokyo 192-8577, Japan., Arighi C; Department of Computer and Information Sciences, University of Delaware, 18 Amstel Ave, Newark, DE 19716, United States., Axelsen KB; Swiss-Prot Group, Swiss Institute of Bioinformatics (SIB), CMU, 1 rue Michel Servet, Geneva 4 1211, Switzerland., Bolton E; National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, United States., Bordeleau E; Michael Smith Laboratories, The University of British Columbia, 2185 East Mall, Vancouver, British Columbia V6T 1Z4, Canada., Edwards NJ; Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, 2115 Wisconsin Ave NW, Washington, DC 20007, United States., Fadda E; Department of Chemistry and Hamilton Institute, Maynooth University, Kilcock Road, Maynooth, Co. Kildare W23 AH3Y, Ireland., Feizi T; The Glycosciences Laboratory, Imperial College London, Hammersmith Campus, Du Cane Road, London W12 0NN, United Kingdom., Hayes C; Proteome Informatics Group, Swiss Institute of Bioinformatics (SIB), route de Drize 7, Geneva CH-1227, Switzerland., Ives CM; Department of Chemistry and Hamilton Institute, Maynooth University, Kilcock Road, Maynooth, Co. Kildare W23 AH3Y, Ireland., Joshi HJ; Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen DK-2200, Denmark., Krishna Prasad K; ELI Beamlines Facility, The Extreme Light Infrastructure ERIC, Za Radnicí 835, Dolní Břežany 25241, Czech Republic., Kossida S; IMGT, The International ImMunoGeneTics Information System, National Center for Scientific Research (CNRS), Institute of Human Genetics (IGH), University of Montpellier (UM), 141 rue de la Cardonille, Montpellier 34 090, France., Lisacek F; Proteome Informatics Group, Swiss Institute of Bioinformatics (SIB), route de Drize 7, Geneva CH-1227, Switzerland., Liu Y; The Glycosciences Laboratory, Imperial College London, Hammersmith Campus, Du Cane Road, London W12 0NN, United Kingdom., Lütteke T; Institute of Veterinary Physiology and Biochemistry, Justus-Liebig-University Gießen, Frankfurter Str. 100, Gießen 35392, Germany., Ma J; Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, 3900 Reservior Road NW, Washington, DC 20007, United States., Malik A; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom., Martin M; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom., Mehta AY; Department of Surgery, Beth Israel Deaconess Medical Center, National Center for Functional Glycomics, Harvard Medical School, 330 Brookline Avenue, Boston, MA 02215, United States., Neelamegham S; Departments of Chemical & Biological Engineering, Biomedical Engineering and Medicine, University at Buffalo, State University of New York, 906 Furnas Hall, Buffalo, NY 14260, United States., Panneerselvam K; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom., Ranzinger R; Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd, Athens, GA 30602, United States., Ricard-Blum S; Institute of Molecular and Supramolecular Chemistry and Biochemistry (ICBMS), UMR 5246, University Lyon 1, CNRS, 43 Boulevard du 11 novembre 1918, Villeurbanne cedex F-69622, France., Sanou G; IMGT, The International ImMunoGeneTics Information System, National Center for Scientific Research (CNRS), Institute of Human Genetics (IGH), University of Montpellier (UM), 141 rue de la Cardonille, Montpellier 34 090, France., Shanker V; Department of Computer and Information Sciences, University of Delaware, 18 Amstel Ave, Newark, DE 19716, United States., Thomas PD; Department of Population and Public Health Sciences, University of Southern California, 2001 N Soto Street, Los Angeles, CA 90032, United States., Tiemeyer M; Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd, Athens, GA 30602, United States., Urban J; Department of Chemistry and Molecular Biology, University of Gothenburg, Medicinaregatan 7 B, Gothenburg 41390, Sweden., Vita R; Immune Epitope Database and Analysis Project, La Jolla Institute for Allergy & Immunology, 9420 Athena Circle, La Jolla, CA 92037, United States., Vora J; Department of Biochemistry & Molecular Medicine, The George Washington University School of Medicine and Health Sciences, 2300 I St. NW, Washington, DC 20052, United States., Yamamoto Y; Database Center for Life Science, Joint Support-Center for Data Science Research, Research Organization of Information and Systems, 178-4-4 Wakashiba, Kashiwa, Chiba 277-0871, Japan., Mazumder R; Department of Biochemistry & Molecular Medicine, The George Washington University School of Medicine and Health Sciences, 2300 I St. NW, Washington, DC 20052, United States.

Publikováno v: Database : the journal of biological databases and curation [Database (Oxford)] 2024 Aug 13; Vol. 2024.

OMD Curation Toolkit: a workflow for in-house curation of public omics datasets.

Autor: Piquer-Esteban S; Institute for Integrative Systems Biology (I2SysBio), University of Valencia and Spanish National Research Council, Valencia, Spain. samuel.piquer@uv.es.; Area of Genomics and Health, Foundation for the Promotion of Sanitary and Biomedical Research of Valencia Region (FISABIO-Public Health), Valencia, Spain. samuel.piquer@uv.es., Arnau V; Institute for Integrative Systems Biology (I2SysBio), University of Valencia and Spanish National Research Council, Valencia, Spain.; Area of Genomics and Health, Foundation for the Promotion of Sanitary and Biomedical Research of Valencia Region (FISABIO-Public Health), Valencia, Spain.; Biomedical Research Networking Centre for Epidemiology and Public Health (CIBEResp), Madrid, Spain., Diaz W; Institute for Integrative Systems Biology (I2SysBio), University of Valencia and Spanish National Research Council, Valencia, Spain.; Area of Genomics and Health, Foundation for the Promotion of Sanitary and Biomedical Research of Valencia Region (FISABIO-Public Health), Valencia, Spain.; Biomedical Research Networking Centre for Epidemiology and Public Health (CIBEResp), Madrid, Spain., Moya A; Institute for Integrative Systems Biology (I2SysBio), University of Valencia and Spanish National Research Council, Valencia, Spain. andres.moya@uv.es.; Area of Genomics and Health, Foundation for the Promotion of Sanitary and Biomedical Research of Valencia Region (FISABIO-Public Health), Valencia, Spain. andres.moya@uv.es.; Biomedical Research Networking Centre for Epidemiology and Public Health (CIBEResp), Madrid, Spain. andres.moya@uv.es.

Publikováno v: BMC bioinformatics [BMC Bioinformatics] 2024 May 09; Vol. 25 (1), pp. 184. Date of Electronic Publication: 2024 May 09.

A study on formalizing the knowledge of data curation activities across different fields.

Autor: Minamiyama Y; Research Center for Open Science and Data Platform, National Institute of Informatics, Chiyoda-City, Tokyo, Japan., Takeda H; Principles of Informatics Research Division, National Institute of Informatics, Chiyoda-City, Tokyo, Japan., Hayashi M; Research Center for Open Science and Data Platform, National Institute of Informatics, Chiyoda-City, Tokyo, Japan., Asaoka M; Research Center for Open Science and Data Platform, National Institute of Informatics, Chiyoda-City, Tokyo, Japan., Yamaji K; Research Center for Open Science and Data Platform, National Institute of Informatics, Chiyoda-City, Tokyo, Japan.

Publikováno v: PloS one [PLoS One] 2024 Apr 25; Vol. 19 (4), pp. e0301772. Date of Electronic Publication: 2024 Apr 25 (Print Publication: 2024).