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Publication of nuclear magnetic resonance experimental data with semantic web technology and the application thereof to biomedical research of proteins

Masashi Yokochi, Naohiro Kobayashi, Eldon L. Ulrich, Akira R. Kinjo, Takeshi Iwata, Yannis E. Ioannidis, Miron Livny, John L. Markley, Haruki Nakamura, Chojiro Kojima, Toshimichi Fujiwara
2016 Journal of Biomedical Semantics  
The nuclear magnetic resonance (NMR) spectroscopic data for biological macromolecules archived at the BioMagResBank (BMRB) provide a rich resource of biophysical information at atomic resolution.  ...  Conclusions: We have developed BMRB/XML and BMRB/RDF and demonstrate their use in performing a federated SPARQL query linking the BMRB to other databases through standard semantic web technologies.  ...  Findings Background The BioMagResBank (BMRB; http://www.bmrb.wisc.edu/) is a worldwide data repository for experimental and derived data gathered from nuclear magnetic resonance (NMR) spectroscopic studies  ... 
doi:10.1186/s13326-016-0057-1 pmid:27927232 pmcid:PMC5143449 fatcat:kidpbvthwbgzjko7jvgesbepqm

Biomedical Semantic Resources for Drug Discovery Platforms [chapter]

Ali Hasnain, Dietrich Rebholz-Schuhmann
2017 Lecture Notes in Computer Science  
Increasingly semantic Web technologies are being developed and used including ontologies, triple stores and combinations thereof.  ...  The biomedical research community is providing large-scale data sources to enable knowledge discovery from the data alone, or from novel scientific experiments in combination with the existing knowledge  ...  Similarly we categorise libraries and databases in five categories that comprise (i) Gene, Gene Expression and Protein Databases, (ii) Pathway databases, (iii) Chemical and Structure Databases including  ... 
doi:10.1007/978-3-319-70407-4_34 fatcat:2bzddzat5zdcrinfwd6m4xqlai

XGAP: a uniform and extensible data model and software platform for genotype and phenotype experiments

Morris A Swertz, K Joeri Velde, Bruno M Tesson, Richard A Scheltema, Danny Arends, Gonzalo Vera, Rudi Alberts, Martijn Dijkstra, Paul Schofield, Klaus Schughart, John M Hancock, Damian Smedley (+6 others)
2010 Genome Biology  
XGAP has simple load formats for any type of genotype, epigenotype, transcript, protein, metabolite or other phenotype data.  ...  Readers can download a standard XGAP (http://www.xgap.org) or auto-generate a custom version using MOLGENIS with programming interfaces to R-software and web-services or user interfaces for biologists.  ...  Acknowledgements The authors thank CASIMIR (funded by the European Commission under contract number LSHG-CT-2006-037811, [70] ; Table 7) , and GEN2PHEN, a FP7 project funded by the European Commission  ... 
doi:10.1186/gb-2010-11-3-r27 pmid:20214801 pmcid:PMC2864567 fatcat:kz73rzypunb5ll7f3oxxj2utve

Systems medicine: evolution of systems biology from bench to bedside

Rui-Sheng Wang, Bradley A. Maron, Joseph Loscalzo
2015 Wiley Interdisciplinary Reviews: Systems Biology and Medicine  
Systems biology integrates the mass of heterogeneous high-throughput data and predictive computational modeling to understand biological functions as system-level properties.  ...  At the same time, systems biology seeks to assist in drug discovery, drug optimization, drug combinations, and drug repositioning by investigating the molecular mechanisms of action of drugs at a system's  ...  This work was supported in part by NIH grants 1K08HL111207-01A1 (to BAM), and HL061795, HL108630 (MAPGen Consortium), HG007690 (to JL), and the Pulmonary Hypertension Association (to BAM).  ... 
doi:10.1002/wsbm.1297 pmid:25891169 pmcid:PMC4457580 fatcat:l4446pjeazanxakj2jwlt26l5m

Natural product drug discovery in the artificial intelligence era

Fernanda I Saldivar-Gonzalez, Victor Daniel Aldas-Bulos, José Luis Medina-Franco, Fabien Plisson
2022 Chemical Science  
Natural products (NPs) are primarily recognized as privileged structures to interact with protein drug targets.  ...  Their unique characteristics and structural diversity continue to marvel scientists for developing NP-inspired medicines, even...  ...  magnetic resonance (NMR) spectroscopy, mass spectrometry (MS), and combinations thereof.  ... 
doi:10.1039/d1sc04471k pmid:35282622 pmcid:PMC8827052 fatcat:jyfupubc2bgb7p4v6b62apgtfq

Biological and Medical Sciences

Detlev W. Bronk, Carl-Goran Heden, C. H. Waddington
1971 Annals of the New York Academy of Sciences  
Not surprisingly the percentage of basic research is high, in accordance with the horizontal nature of several of the BMS RIs.  ...  Figure 31 illustrates an estimate of the contribution of each individual BMS RI to research activities across this spectrum, from basic medical/ biological research and innovation activities to activities  ...  Conventional MRI is only the first of an array of methods that will eventually comprise the nuclear magnetic resonance (NMR) diagnostic armamentarium.  ... 
doi:10.1111/j.1749-6632.1971.tb41309.x fatcat:6zdkjtuojrdwhib3lpdzoq7i3u

Biological and Medical Sciences

G. J. Kennedy
1989 The gerontologist  
Not surprisingly the percentage of basic research is high, in accordance with the horizontal nature of several of the BMS RIs.  ...  Figure 31 illustrates an estimate of the contribution of each individual BMS RI to research activities across this spectrum, from basic medical/ biological research and innovation activities to activities  ...  Conventional MRI is only the first of an array of methods that will eventually comprise the nuclear magnetic resonance (NMR) diagnostic armamentarium.  ... 
doi:10.1093/geront/29.1.137a fatcat:32k4evfphzhdddo3ikpfvbwcgi

Identifying disease mutations in genomic medicine settings: current challenges and how to accelerate progress

Gholson J Lyon, Kai Wang
2012 Genome Medicine  
We thank Peter Krawitz, Degui Zhi, Shane McCarthy, Jason O'Rawe, Edwin Nyambi, Reid Robison and three anonymous reviewers for helpful comments and suggestions for the manuscript.  ...  Acknowledgements We apologize to those whose work we could not cite due to reference limitations.  ...  A compromise might be along the lines of what has occurred with the disruptive technology magnetic resonance imaging (MRI), which has been deployed in many hospitals but also at stand-alone MRI diagnostic  ... 
doi:10.1186/gm359 pmid:22830651 pmcid:PMC3580414 fatcat:c6ui7sn4gfetjbmvuqe4becloi

Machine Learning Methods for Histopathological Image Analysis: A Review [article]

Jonathan de Matos and Steve Tsham Mpinda Ataky and Alceu de Souza Britto Jr. and Luiz Eduardo Soares de Oliveira and Alessandro Lameiras Koerich
2021 arXiv   pre-print
One of the ways of accelerating such an analysis is to use computer-aided diagnosis (CAD) systems.  ...  In addition, we present a list of publicly available and private datasets that have been used in HI research.  ...  The number of publications related to the field of this research is presented in Figure 3 .  ... 
arXiv:2102.03889v1 fatcat:ylrsildl4nenho22erndvpjcjy

The value of universally available raw NMR data for transparency, reproducibility, and integrity in natural product research

James B. McAlpine, Shao-Nong Chen, Andrei Kutateladze, John B. MacMillan, Giovanni Appendino, Andersson Barison, Mehdi A. Beniddir, Maique W. Biavatti, Stefan Bluml, Asmaa Boufridi, Mark S. Butler, Robert J. Capon (+61 others)
2018 Natural product reports (Print)  
disseminating raw nuclear magnetic resonance (NMR) data, independently of, and in parallel with, classical publishing outlets.  ...  With contributions from the global natural product (NP) research community, and continuing the Raw Data Initiative, this review collects a comprehensive demonstration of the immense scientific value of  ...  Acknowledgements Acknowledgements The lead authors (JBM and GFP) and the CENAPT co-authors wish to acknowledge support through grant U41 AT008706 from NCCIH and ODS/NIH. We are also grateful to Ms.  ... 
doi:10.1039/c7np00064b pmid:30003207 pmcid:PMC6350634 fatcat:334k3rvc6ffyja6hflp7jeokji

Self-Organized Evolutionary Process in Sets of Interdependent Variables near the Midpoint of Phase Transition in K-Satisfiability [chapter]

Michael Korkin
2001 Lecture Notes in Computer Science  
Ackerman, John T Strategic Studies Quarterly: An Air Force-Sponsored Strategic Forum for Military, Government, and Academic Professionals. Volume 2, Number 1 -7 Acuff, Hugh F  ...  NRL's principal task is the development and orderly flow of research results for Navy applications and technology transfer.  ...  activities with potential application for nuclear weapons.  ... 
doi:10.1007/3-540-45443-8_20 fatcat:ght26tu6avh57kkp54kifofaee

Alternatives to animal use in research, testing, and education

G. Fillion
1988 Annales de l'Institut Pasteur: Immunologie  
Concerns focus on balancing societal needs for continued progress in biomedical and behavioral research, for toxicity testing to safeguard the public, and for education in the life sciences with desires  ...  In this assessment, OTA analyzes the scientific, regulatory, economic, legal, and ethical considerations involved in alternative technologies in biomedical and behavioral research, toxicity testing, and  ...  The Navy in fiscal year 1985 allocated $58 million for the life sciences or biomedical research.  ... 
doi:10.1016/0769-2625(88)90076-1 fatcat:6qph3stknzah7pu2zi6t5sh6ca

Alternatives to animal use in research, testing and education

David Lovell
1990 Food and Chemical Toxicology  
Concerns focus on balancing societal needs for continued progress in biomedical and behavioral research, for toxicity testing to safeguard the public, and for education in the life sciences with desires  ...  In this assessment, OTA analyzes the scientific, regulatory, economic, legal, and ethical considerations involved in alternative technologies in biomedical and behavioral research, toxicity testing, and  ...  The Navy in fiscal year 1985 allocated $58 million for the life sciences or biomedical research.  ... 
doi:10.1016/0278-6915(90)90029-m fatcat:twxfjmkepjelfjejuunmi2k2yi

Alternatives to animal use in research, testing, and education

1988 European Journal of Medicinal Chemistry  
Concerns focus on balancing societal needs for continued progress in biomedical and behavioral research, for toxicity testing to safeguard the public, and for education in the life sciences with desires  ...  In this assessment, OTA analyzes the scientific, regulatory, economic, legal, and ethical considerations involved in alternative technologies in biomedical and behavioral research, toxicity testing, and  ...  The Navy in fiscal year 1985 allocated $58 million for the life sciences or biomedical research.  ... 
doi:10.1016/0223-5234(88)90017-7 fatcat:upcuogj32rcuhiposqatpfjeu4

Alternatives to animal use in research, testing, and education

G. Fillon
1988 Annales de l Institut Pasteur Microbiologie  
Concerns focus on balancing societal needs for continued progress in biomedical and behavioral research, for toxicity testing to safeguard the public, and for education in the life sciences with desires  ...  In this assessment, OTA analyzes the scientific, regulatory, economic, legal, and ethical considerations involved in alternative technologies in biomedical and behavioral research, toxicity testing, and  ...  The Navy in fiscal year 1985 allocated $58 million for the life sciences or biomedical research.  ... 
doi:10.1016/0769-2609(88)90117-2 fatcat:57ydhlrq2ng7vgbvlqxtqpxgau
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