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      Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking.

      1 , 2 , 1 , 2 , 3 , 3 , 3 , 4 , 4 , 3 , 4 , 3 , 3 , 3 , 3 , 3 , 5 , 6 , 6 , 7 , 8 , 9 , 3 , 10 , 11 , 6 , 4 , 4 , 12 , 6 , 13 , 14 , 15 , 16 , 17 , 18 , 18 , 8 , 2 , 1 , 19 , 20 , 21 , 20 , 22 , 23 , 6 , 24 , 25 , 26 , 18 , 27 , 28 , 29 , 29 , 30 , 12 , 18 , 6 , 31 , 12 , 12 , 3 , 31 , 32 , 33 , 32 , 32 , 7 , 6 , 6 , 34 , 22 , 35 , 6 , 22 , 7 , 2 , 6 , 4 , 22 , 36 , 37 , 38 , 18 , 7 , 23 , 39 , 40 , 3 , 38 , 28 , 32 , 6 , 15 , 13 , 7 , 41 , 42 , 43 , 43 , 43 , 43 , 32 , 44 , 45 , 3 , 3 , 3 , 46 , 47 , 48 , 47 , 48 , 46 , 49 , 49 , 50 , 50 , 50 , 50 , 50 , 41 , 49 , 20 , 51 , 51 , 52 , 6 , 37 , 44 , 36 , 12 , 32 , 3 , 6 , 3 , 6 , 42 , 3 , 6 , 31 , 2 , 3 , 31
      Nature biotechnology
          There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

          Abstract

          The potential of the diverse chemistries present in natural products (NP) for biotechnology and medicine remains untapped because NP databases are not searchable with raw data and the NP community has no way to share data other than in published papers. Although mass spectrometry (MS) techniques are well-suited to high-throughput characterization of NP, there is a pressing need for an infrastructure to enable sharing and curation of data. We present Global Natural Products Social Molecular Networking (GNPS; http://gnps.ucsd.edu), an open-access knowledge base for community-wide organization and sharing of raw, processed or identified tandem mass (MS/MS) spectrometry data. In GNPS, crowdsourced curation of freely available community-wide reference MS libraries will underpin improved annotations. Data-driven social-networking should facilitate identification of spectra and foster collaborations. We also introduce the concept of 'living data' through continuous reanalysis of deposited data.

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          Most cited references34

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          MassBank: a public repository for sharing mass spectral data for life sciences.

          MassBank is the first public repository of mass spectra of small chemical compounds for life sciences (<3000 Da). The database contains 605 electron-ionization mass spectrometry (EI-MS), 137 fast atom bombardment MS and 9276 electrospray ionization (ESI)-MS(n) data of 2337 authentic compounds of metabolites, 11 545 EI-MS and 834 other-MS data of 10,286 volatile natural and synthetic compounds, and 3045 ESI-MS(2) data of 679 synthetic drugs contributed by 16 research groups (January 2010). ESI-MS(2) data were analyzed under nonstandardized, independent experimental conditions. MassBank is a distributed database. Each research group provides data from its own MassBank data servers distributed on the Internet. MassBank users can access either all of the MassBank data or a subset of the data by specifying one or more experimental conditions. In a spectral search to retrieve mass spectra similar to a query mass spectrum, the similarity score is calculated by a weighted cosine correlation in which weighting exponents on peak intensity and the mass-to-charge ratio are optimized to the ESI-MS(2) data. MassBank also provides a merged spectrum for each compound prepared by merging the analyzed ESI-MS(2) data on an identical compound under different collision-induced dissociation conditions. Data merging has significantly improved the precision of the identification of a chemical compound by 21-23% at a similarity score of 0.6. Thus, MassBank is useful for the identification of chemical compounds and the publication of experimental data. 2010 John Wiley & Sons, Ltd.
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            Is Open Access

            NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy

            The National Center for Biotechnology Information (NCBI) Reference Sequence (RefSeq) database is a collection of genomic, transcript and protein sequence records. These records are selected and curated from public sequence archives and represent a significant reduction in redundancy compared to the volume of data archived by the International Nucleotide Sequence Database Collaboration. The database includes over 16 000 organisms, 2.4 × 106 genomic records, 13 × 106 proteins and 2 × 106 RNA records spanning prokaryotes, eukaryotes and viruses (RefSeq release 49, September 2011). The RefSeq database is maintained by a combined approach of automated analyses, collaboration and manual curation to generate an up-to-date representation of the sequence, its features, names and cross-links to related sources of information. We report here on recent growth, the status of curating the human RefSeq data set, more extensive feature annotation and current policy for eukaryotic genome annotation via the NCBI annotation pipeline. More information about the resource is available online (see http://www.ncbi.nlm.nih.gov/RefSeq/).
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              Is Open Access

              MetaboLights—an open-access general-purpose repository for metabolomics studies and associated meta-data

              MetaboLights (http://www.ebi.ac.uk/metabolights) is the first general-purpose, open-access repository for metabolomics studies, their raw experimental data and associated metadata, maintained by one of the major open-access data providers in molecular biology. Metabolomic profiling is an important tool for research into biological functioning and into the systemic perturbations caused by diseases, diet and the environment. The effectiveness of such methods depends on the availability of public open data across a broad range of experimental methods and conditions. The MetaboLights repository, powered by the open source ISA framework, is cross-species and cross-technique. It will cover metabolite structures and their reference spectra as well as their biological roles, locations, concentrations and raw data from metabolic experiments. Studies automatically receive a stable unique accession number that can be used as a publication reference (e.g. MTBLS1). At present, the repository includes 15 submitted studies, encompassing 93 protocols for 714 assays, and span over 8 different species including human, Caenorhabditis elegans, Mus musculus and Arabidopsis thaliana. Eight hundred twenty-seven of the metabolites identified in these studies have been mapped to ChEBI. These studies cover a variety of techniques, including NMR spectroscopy and mass spectrometry.
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                Author and article information

                Journal
                Nat. Biotechnol.
                Nature biotechnology
                1546-1696
                1087-0156
                Aug 9 2016
                : 34
                : 8
                Affiliations
                [1 ] Computer Science and Engineering, University of California (UC) San Diego, La Jolla, California, USA.
                [2 ] Center for Computational Mass Spectrometry, UC San Diego, La Jolla, California, USA.
                [3 ] Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, California, USA.
                [4 ] Department of Chemistry and Biochemistry, UC San Diego, La Jolla, California, USA.
                [5 ] Department of Microbiology and Immunology, Stanford University, Palo Alto, California, USA.
                [6 ] Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, California, USA.
                [7 ] Sirenas Marine Discovery, San Diego, California, USA.
                [8 ] Centro de Ciencias Genómicas, Universidad Nacional Autonoma de Mexico, Cuernavaca, Mexico.
                [9 ] Salk Institute, Salk Institute, La Jolla, California, USA.
                [10 ] Biology Department, San Diego State University, San Diego, California, USA.
                [11 ] Scottish Association for Marine Science, Scottish Marine Institute, Oban, UK.
                [12 ] Center for Drug Discovery and Biodiversity, INDICASAT, City of Knowledge, Panama.
                [13 ] Genome Dynamics, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
                [14 ] FAS Center for Systems Biology, Harvard, Cambridge, Massachusetts, USA.
                [15 ] Produits naturels - Synthèses - Chimie Médicinale, University of Rennes 1, Rennes Cedex, France.
                [16 ] Department of Chemistry, University of Minnesota, Minneapolis, Minnesota, USA.
                [17 ] Dynamique des Génomes et Adaptation Microbienne, University of Lorraine, Vandœuvre-lès-Nancy, France.
                [18 ] Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark.
                [19 ] Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, California, USA.
                [20 ] School of Dentistry, UC Los Angeles, Los Angeles, California, USA.
                [21 ] Department of Periodontics, University of Washington, Seattle, Washington, USA.
                [22 ] Institute of Microbiology, ETH Zurich, Zurich, Switzerland.
                [23 ] Department of Medicinal Chemistry and Pharmacognosy, University of Illinois Chicago, Chicago, Illinois, USA.
                [24 ] Department of Marine Biotechnology and Resources, National Sun Yat-sen University, Kaohsiung, Taiwan.
                [25 ] Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan.
                [26 ] Institute of Food Chemistry, University of Münster, Münster, Germany.
                [27 ] School of Chemical &Physical Sciences, and Centre for Biodiscovery, Victoria University of Wellington, Wellington, New Zealand.
                [28 ] Gillings School of Global Public Health, Department of Epidemiology, University of North Carolina Chapel Hill, Chapel Hill, North Carolina, USA.
                [29 ] Department of Chemistry, Indiana University, Bloomington, Indiana, USA.
                [30 ] Smithsonian Tropical Research Institute, Ancón, Panama.
                [31 ] Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, California, USA.
                [32 ] School of Pharmaceutical Sciences of Ribeirao Preto, University of São Paulo, São Paulo, Brazil.
                [33 ] Centro de Ciencias Biologicas e da Saude, Universidade Federal de Mato Grosso do Sul, Campo Grande, Brazil.
                [34 ] UMR CNRS 6553 ECOBIO, University of Rennes 1, Rennes Cedex, France.
                [35 ] Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA.
                [36 ] PBSci-Chemistry &Biochemistry Department, UC Santa Cruz, Santa Cruz, California, USA.
                [37 ] Department of Bioengineering, UC San Diego, La Jolla, California, USA.
                [38 ] Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon, USA.
                [39 ] Department of Plant and Microbial Biology, UC Berkeley, Berkeley, California, USA.
                [40 ] Department of Biological Sciences, Florida International University, Miami, Florida, USA.
                [41 ] Department of Pharmaceutical Biotechnology, Helmholtz Institute for Pharmaceutical Research Saarland, Saarbrücken, Germany.
                [42 ] Center for Oceans and Human Health, Scripps Institute of Oceanography, UC San Diego, La Jolla, California, USA.
                [43 ] Department of Chemistry, University of Hawaii at Manoa, Honolulu, Hawaii, USA.
                [44 ] Division of Biological Sciences, UC San Diego, La Jolla, California, USA.
                [45 ] Department of Nanoengineering, UC San Diego, La Jolla, California, USA.
                [46 ] School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland.
                [47 ] Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany.
                [48 ] Institut de Chimie des Substances Naturelles, CNRS-ICSN, UPR 2301, Labex CEBA, University of Paris-Saclay, Gif-sur-Yvette, France.
                [49 ] Biological Sciences, Pacific Northwest National Laboratory, Richland, Washington, USA.
                [50 ] National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA.
                [51 ] Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
                [52 ] Department of Pediatrics, UC San Diego, La Jolla, California, USA.
                Article
                nbt.3597
                10.1038/nbt.3597
                27504778
                e5d7cc61-d360-4b7c-b102-537f6fd20dc5
                History

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