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Expanding natural product chemistry resources at the EBI

Janna Hastings, Pablo Conesa, Adriano Dekker, Marcus Ennis, Kenneth Haug, Kalai Jayaseelan, Namrata Kale, Tejasvi Mahendraker, Pablo Moreno, Venkatesh Muthukrishnan, Gareth Owen, Reza Salek (+2 others)
2013 Journal of Cheminformatics  
product chemistry.  ...  The ChEBI database (http://www.ebi.ac.uk/chebi) and the MetaboLights database (http://www.ebi.ac.uk/metabolights/) aim to offer a comprehensive public resource suite for capturing and describing natural  ...  Open access provides opportunities to our colleagues in other parts of the globe, by allowing anyone to view the content free of charge.  ... 
doi:10.1186/1758-2946-5-s1-p43 fatcat:gui6pgmxznbhrjoimlkw2g37qa

The European Bioinformatics Institute's data resources 2014

Catherine Brooksbank, Mary Todd Bergman, Rolf Apweiler, Ewan Birney, Janet Thornton
2013 Nucleic Acids Research  
Molecular Biology has been at the heart of the 'big data' revolution from its very beginning, and the need for access to biological data is a common thread running from the 1965 publication of  ...  ACKNOWLEDGEMENTS The EMBL-EBI is indebted to the support of its funders: EMBL's member states, the European Commission, the Wellcome Trust, the UK Research Councils, the US National Institutes of Health  ...  The authors would like to thank the many colleagues who provided input to this manuscript.  ... 
doi:10.1093/nar/gkt1206 pmid:24271396 pmcid:PMC3964968 fatcat:7dgar73rqjhwzci6shbolfpvfq

Developing library bioinformatics services in context: the Purdue University Libraries bioinformationist program

Diane C Rein
2006 Journal of the Medical Library Association  
Based on the information gathered during the integration phase, several survey instruments were developed to facilitate more critical user assessment and the recovery of quantifiable data prior to planning  ...  The Purdue University Libraries (PUL) hired a molecular biosciences specialist to discover, engage, and support bioinformatics needs across the campus.  ...  Your primary departmental affiliation is: ❍ Agronomy ❍ Biochemistry ❍ Biological sciences ❍ Botany and plant pathology ❍ Chemistry ❍ Entomology ❍ Foods and nutrition ❍ Forestry and natural resources  ... 
pmid:16888666 pmcid:PMC1525331 fatcat:n7bpa3hxo5cj5o7xzybuwfa2by

Unlocking Big Data for better health

Steven Munevar
2017 Nature Biotechnology  
Major achievements In its third year, the Variation team moved the EVA project into full production, expanding the range of data and services to become a primary archive of genetic variation at EMBL-EBI  ...  The EBI Search engine in 2014 indexed over 1 billion data entries from all data resources at EMBL-EBI.  ... 
doi:10.1038/nbt.3918 pmid:28700551 fatcat:oqiurm5cgzec7lfenvjvlemxoy

Addressing standardization challenges through integrated approaches in biomedical and genomic data [article]

Lynn Schriml
2022 figshare.com  
Research on natural product biosynthesis is undergoing an extensive transformation, driven by technological developments in genomics, bioinformatics, analytical chemistry and synthetic biology.  ...  Many of these secondary metabolites nd use as natural products in medicine, agriculture and manufacturing.  ... 
doi:10.6084/m9.figshare.20633541.v1 fatcat:df2g6ur4xran7l3ckrdumgnz7a

Seed Set in Prairie Cordgrass

Arvid Boe, Vance Owens, Jose Gonzalez-Hernandez, D. K. Lee
2013 Crop science  
When the institute was soliciting project proposals in its first year, the three researchers noted that the fungus' appetite for burned-out grasses and trees in nature might yield clues into how organisms  ...  Louise Glass, who was among the first in the EBI to take on the ubiquitous fungus as a possible source of enzymatic deconstruction of biofuel feedstocks.  ...  Like our team at BP, EBI scientists are seeking to unlock the potential of nature to provide fuel for future generations.  ... 
doi:10.2135/cropsci2012.04.0250 fatcat:szrbjysivve4dggzwulsmwydwe

Plant Reactome: a knowledgebase and resource for comparative pathway analysis

2019 Nucleic Acids Research  
The Plant Reactome supports, implements and collaborates with the wider community to make data and tools related to genes, genomes, and pathways Findable, Accessible, Interoperable and Re-usable (FAIR)  ...  Plant Reactome (https://plantreactome.gramene.org) is an open-source, comparative plant pathway knowledgebase of the Gramene project.  ...  We extend our gratitude to the Ensembl Plants team at EBI for their support and interest in strong cross-platform data integration.  ... 
doi:10.1093/nar/gkz996 pmid:31680153 pmcid:PMC7145600 fatcat:ykzfjhf4hvgs7keopndswr5req

Boost that metabolomic confidence

Vivien Marx
2019 Nature Methods  
To let labs try it or use it regularly, they've added it to Global Natural Products Social Molecular Networking (GNPS), a cloudbased ecosystem based at the Dorrestein lab at the University of California  ...  metabolomics is as powerful as it can be. " At the EBI, experience with genomics and proteomics data and resources deliver useful lessons for metabolomics.  ... 
doi:10.1038/s41592-019-0694-2 pmid:31863087 fatcat:7ilxk3n6ujbzndgavgtveungmq

PDBe: Protein Data Bank in Europe

S. Velankar, Y. Alhroub, C. Best, S. Caboche, M. J. Conroy, J. M. Dana, M. A. Fernandez Montecelo, G. van Ginkel, A. Golovin, S. P. Gore, A. Gutmanas, P. Haslam (+20 others)
2011 Nucleic Acids Research  
In addition, PDBe develops tools, services and resources to make structure-related data more accessible to the biomedical community.  ...  in the PDB (UniPDB), chemistry-and taxonomy-based PDB-archive browsers (PDBeXplore), and a tool for interactive visualization of NMR structures, corresponding experimental data as well as validation and  ...  ACKNOWLEDGEMENTS The authors wish to thank all collaborators and partners in the EBI, EMBL, wwPDB, EMDB, BMRB, CCPN, CCP4, CCDC and other collaborative efforts, as well as the structural biology community  ... 
doi:10.1093/nar/gkr998 pmid:22110033 pmcid:PMC3245096 fatcat:q5b4mmkggbepdebpme7koi7hye

Description and evaluation of a detailed gas-phase chemistry scheme in the TM5-MP global chemistry transport model (r112)

Stelios Myriokefalitakis, Nikos Daskalakis, Angelos Gkouvousis, Andreas Hilboll, Twan van Noije, Jason E. Williams, Philippe Le Sager, Vincent Huijnen, Sander Houweling, Tommi Bergman, Johann Rasmus Nüß, Mihalis Vrekoussis (+2 others)
2020 Geoscientific Model Development  
Overall, the MOGUNTIA scheme simulates a large suite of oxygenated VOCs that are observed in the atmosphere at significant levels. This significantly expands the possible applications of TM5-MP.  ...  This work documents and evaluates the tropospheric gas-phase chemical mechanism MOGUNTIA in the three-dimensional chemistry transport model TM5-MP.  ...  Model simulations were performed at the GRNET HPC ARIS and the AETHER HPC cluster at the University of Bremen, funded by the DFG within the scope of the Excellence Initiative.  ... 
doi:10.5194/gmd-13-5507-2020 fatcat:sywp7c4o3fgdtcj2pnhdxtg34u

Bioinformatics training: a review of challenges, actions and support requirements

M. V. Schneider, J. Watson, T. Attwood, K. Rother, A. Budd, J. McDowall, A. Via, P. Fernandes, T. Nyronen, T. Blicher, P. Jones, M.-C. Blatter (+4 others)
2010 Briefings in Bioinformatics  
James Watson is the Senior Scientific Training Officer in the Outreach and Training Team at EMBL-EBI, prior to this he was a postdoctoral researcher in the Thornton group looking at protein structure-function  ...  The ideas presented in this article MariaVictoria Schneider is the Training Programme Project Leader in the Outreach and Training Team at EMBL-EBI where she is responsible for developing and coordinating  ...  The authors would also like to thank the many trainers, trainees and course hosts with whom we have worked, whose feedback has had a profound influence on the way that we train.  ... 
doi:10.1093/bib/bbq021 pmid:20562256 fatcat:bkc5qjb4hff5xaiotaiue5uoze

Petabyte-scale innovations at the European Nucleotide Archive

G. Cochrane, R. Akhtar, J. Bonfield, L. Bower, F. Demiralp, N. Faruque, R. Gibson, G. Hoad, T. Hubbard, C. Hunter, M. Jang, S. Juhos (+15 others)
2009 Nucleic Acids Research  
The European Nucleotide Archive (ENA; http://www.ebi.ac.uk/embl), comprising the EMBL Nucleotide Sequence Database and the Ensembl Trace Archive, has identified challenges in the storage, movement, analysis  ...  Sequence repositories, which provide the feed for these data sets into the worldwide computational infrastructure, are challenged by the impact of these data volumes.  ...  other tools and data resources available at EBI and beyond.  ... 
doi:10.1093/nar/gkn765 pmid:18978013 pmcid:PMC2686451 fatcat:xzwl3cvkjnarxbbbowzbnhazpi

Concepts, Historical Milestones and the Central Place of Bioinformatics in Modern Biology: A European Perspective [chapter]

T.K. Attwood, A. Gisel, N-E. Eriksson, E. Bongcam-Rudloff
2011 Bioinformatics - Trends and Methodologies  
In the decade that followed, time-consuming manual processes were gradually superseded with the advent of automated peptide sequencers, which increased the rate of sequence determination considerably.  ...  Meanwhile, another revolution was taking place, heralded by the elucidation of the 3D structures of the first proteins, those of myoglobin and haemoglobin, respectively (Kendrew et al., 1958; Muirhead  ...  of research infrastructure at the European level" (Nature Editorial, 1999) .  ... 
doi:10.5772/23535 fatcat:dwe4umftd5anrfobkciktbmg3m

Diverse Taxonomies for Diverse Chemistries: Enhanced Representation of Natural Product Metabolism in UniProtKB

Marc Feuermann, Emmanuel Boutet, Anne Morgat, Kristian Axelsen, Parit Bansal, Jerven Bolleman, Edouard de Castro, Elisabeth Coudert, Elisabeth Gasteiger, Sébastien Géhant, Damien Lieberherr, Thierry Lombardot (+7 others)
2021 Metabolites  
Here we describe work that enhances the utility of UniProtKB as a support for both the study of natural products and for their discovery.  ...  The foundation of this work is an improved representation of natural product metabolism in UniProtKB using Rhea, an expert-curated knowledgebase of biochemical reactions, that is built on the ChEBI (Chemical  ...  Acknowledgments: The authors would like to thank the Chemical Biology Team of EMBL-EBI for their work in maintaining and developing ChEBI, in particular Adnan Malik, Venkatesh Muthukrishnan (now at SIB  ... 
doi:10.3390/metabo11010048 pmid:33445429 pmcid:PMC7827101 fatcat:tatj2jy75refxbz3gqowk46nym

Climate Change and Cities: Challenges Ahead

Prashant Kumar
2021 Frontiers in Sustainable Cities  
Figure 3 shows that 83, 32, and 7% of cities, respectively, were at high risk of natural hazard-related mortality from at least one, two and three out of the six types of natural hazards.  ...  Of the studied metropolitan areas, almost 58% were highly exposed to at least one of the six natural hazards (Figure 3 ).  ...  NE/P016510/1) as a part of the UK-India NERC-MOES Programme on Atmospheric Pollution and Human Health in an Indian Megacity (Delhi), OPERANDUM (OPEn-air laboRAtories for Nature baseD solUtions to Manage  ... 
doi:10.3389/frsc.2021.645613 fatcat:qbcvfh44qvabjowhpjrhxmwjkm
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