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MetaBase--the wiki-database of biological databases

D. M. Bolser, P.-Y. Chibon, N. Palopoli, S. Gong, D. Jacob, V. D. D. Angel, D. Swan, S. Bassi, V. Gonzalez, P. Suravajhala, S. Hwang, P. Romano (+9 others)
2011 Nucleic Acids Research  
MetaBase (MB) (http:// MetaDatabase.Org) is a community-curated database containing more than 2000 commonly used biological databases.  ...  The initial release of MB was derived from the content of the 2007 Nucleic Acids Research (NAR) Database Issue.  ...  To address these problems, we have created MetaBase (MB), a wiki-based database of biological databases.  ... 
doi:10.1093/nar/gkr1099 pmid:22139927 pmcid:PMC3245051 fatcat:zrv3w2wuabgxtbmdcmxozlstde

D8.6_Mirri_Report On Human And Programmatic Access

B. Bunk, DP Colobraro, P. Dawyndt, P. De Vos, F.O. Glöckner, A. Kopf, V. Robert, P. Romano, D. Smith, C. Söhngen, F. Van Hauwenhuyse, A. Vasilenko
2015 Zenodo  
It intends to get the maximum compliance with databases, ontologies and the standards for applications like human health, veterinary science, pharma, agriculture, food production, winemaking, brewing and  ...  This report outlines the optimal approach following technology produced in the World Wide Web Consortium (W3C), as well as in the ELIXIR system and in the BioMedBriges project.  ...  Institute ENVO Community ontology for the concise, controlled description of environments WDCM World Data Center for Microorganisms SPARQL Abbreviations MB MetaBase mBRC microbial Biological Resource  ... 
doi:10.5281/zenodo.49970 fatcat:xjddke3a7zaivn5x3zqmu2htuy

Internet Databases of the Properties, Enzymatic Reactions, and Metabolism of Small Molecules—Search Options and Applications in Food Science

Piotr Minkiewicz, Małgorzata Darewicz, Anna Iwaniak, Justyna Bucholska, Piotr Starowicz, Emilia Czyrko
2016 International Journal of Molecular Sciences  
Data summarized in computer databases may be used for calculation of daily intake of bioactive compounds, prediction of metabolism of food components, and their biological activity as well as for prediction  ...  Application of databases follows recent worldwide trends in the use of information resources.  ...  ., databases of phytochemicals important from the point of view of food science [4] , Metabases, Biochemical reactions; Metabolites and metabolic pathways [33] LabWorm Metabases  ... 
doi:10.3390/ijms17122039 pmid:27929431 pmcid:PMC5187839 fatcat:rbggkt4xcbbu3pnkh33zpovxju

DaTo: an atlas of biological databases and tools

Qilin Li, Yincong Zhou, Yingmin Jiao, Zhao Zhang, Lin Bai, Li Tong, Xiong Yang, Björn Sommer, Ralf Hofestädt, Ming Chen
2016 Journal of Integrative Bioinformatics  
This work presents DaTo, a semi-automatically generated world atlas of biological databases and tools.  ...  Using DaTo, the geographical locations, the health statuses, as well as the journal associations were evaluated with respect to the historical development of bioinformatics tools and databases over the  ...  ., MetaBasethe wiki-database of biological databases.  ... 
doi:10.1515/jib-2016-297 fatcat:72j7or3fhfgllifn2dpptw5w2e

RDFIO: extending Semantic MediaWiki for interoperable biomedical data management

Samuel Lampa, Egon Willighagen, Pekka Kohonen, Ali King, Denny Vrandečić, Roland Grafström, Ola Spjuth
2017 Journal of Biomedical Semantics  
This stresses the need for efficient ways of integrating these data in a coherent description of biological systems. In many cases, biological data needs organization before integration.  ...  Biological sciences are characterised not only by an increasing amount but also the extreme complexity of its data.  ...  Acknowledgements The authors thank Joel Sachs for mentoring AK during the Gnome FOSS OPW 2014 project.  ... 
doi:10.1186/s13326-017-0136-y pmid:28870259 pmcid:PMC5584330 fatcat:6oevr7fjwvcsba73u2h6fbxq3y

Taking Open Innovation to the Molecular Level - Strengths and Limitations

Barbara Zdrazil, Niklas Blomberg, Gerhard F. Ecker
2012 Molecular Informatics  
Acknowledgements We want to thank Paul Groth (VU University of Amsterdam) for discussion.The research leading to these results has received support from the Innovative Medicines Initiative Joint Undertaking  ...  under Grant Agreement n8 115191 (Open PHACTS), resources of which are composed of financial con-  ...  for databases termed MetaBase (MB) (  ... 
doi:10.1002/minf.201200014 pmid:23226167 pmcid:PMC3507005 fatcat:agxqiy375fbc5dw46x26bdgyh4

In Silico Toxicology Data Resources to Support Read-Across and (Q)SAR

Gopal Pawar, Judith C. Madden, David Ebbrell, James W. Firman, Mark T. D. Cronin
2019 Frontiers in Pharmacology  
This review also specifically addresses the need for solutions for mapping and integration of databases into a common platform for better translatability of preclinical data to clinical data.  ...  ), exposure, omics, pathways, Absorption, Distribution, Metabolism and Elimination (ADME) properties, clinical trials, pharmacovigilance, patents-related databases, biological (genes, enzymes, proteins  ...  Biological Databases There are 268 biological databases.  ... 
doi:10.3389/fphar.2019.00561 pmid:31244651 pmcid:PMC6580867 fatcat:t3junhqvxfeslcu37pihztlxiq

NDEx: A Community Resource for Sharing and Publishing of Biological Networks [chapter]

Rudolf T. Pillich, Jing Chen, Vladimir Rynkov, David Welker, Dexter Pratt
2017 Msphere  
NDEx, the Network Data Exchange, is an online commons to enable new modes of collaboration and publication using biological networks.  ...  In doing this, the NDEx project does not compete with existing pathway and interaction databases, such as KEGG or Reactome; instead, NDEx provides a novel, common distribution channel for these efforts  ...  Primary financial support for The NDEx Project is from the National Cancer Institute (U24 CA-184427), F. Hoffmann-La Roche Ltd., Janssen Research and Development, LLC, and Pfizer, Inc.  ... 
doi:10.1007/978-1-4939-6783-4_13 pmid:28150243 fatcat:g7o7npnizjgingotcpqmsgkpc4

BIOPEP-UWM Database of Bioactive Peptides: Current Opportunities

Minkiewicz, Iwaniak, Darewicz
2019 International Journal of Molecular Sciences  
The addition of new peptides and the introduction of new information about the existing ones (e.g., chemical codes and references to other databases) is in progress.  ...  The database is continuously updated and modified.  ...  Chemical databases and metabases are attributed to this category.  ... 
doi:10.3390/ijms20235978 pmid:31783634 pmcid:PMC6928608 fatcat:kllch44xkvbp5fizp2qaklfg3m

Knowledge-Driven Manufacturing Process Innovation: A Case Study on Problem Solving in Micro-Turbine Machining

Dong Zhang, Gangfeng Wang, Yupeng Xin, Xiaolin Shi, Richard Evans, Biao Guo, Pu Huang
2021 Micromachines  
However, due to their high-precision machining requirements, and the knowledge-intensive characteristics of miniaturized parts, complex manufacturing process problems often hinder production.  ...  Subsequently, a knowledge-driven heuristic design system for machining process innovation was integrated in the Computer-Aided Process Innovation (CAPI) platform.  ...  Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/mi12111357 pmid:34832769 pmcid:PMC8625213 fatcat:ssqvqn7qdzddjh5rlwp4eh4mq4

Specification of Web-based Analytics Methods and Tools D3.1

Laia Albó, Miriam Calvera Isabal, Sven Manske, David Roldán Álvarez
2021 Zenodo  
One of the central characteristics of the CS Track approach to investigating citizen science projects and activities is to focus on underlying types of participation, collaboration and knowledge creation  ...  The final section explains the intended usage of the methodology regarding the interplay with other work packages and information provided to the outside.  ...  Accessed: 2020-08-06.4 Metabase, Metabase (2020). Accessed: 2020-08-06. On the other hand, MongoDB Atlas is a free of charge tool focused on MongoDB databases.  ... 
doi:10.5281/zenodo.5653454 fatcat:hq6g3lzdlbdm7pj5cmrccnilfa

A systems-level framework for drug discovery identifies Csf1R as an anti-epileptic drug target

Prashant K. Srivastava, Jonathan van Eyll, Patrice Godard, Manuela Mazzuferi, Andree Delahaye-Duriez, Juliette Van Steenwinckel, Pierre Gressens, Benedicte Danis, Catherine Vandenplas, Patrik Foerch, Karine Leclercq, Georges Mairet-Coello (+14 others)
2018 Nature Communications  
The identification of drug targets is highly challenging, particularly for diseases of the brain.  ...  The predicted effect of Csf1R blockade in attenuating epilepsy seizures was validated in three pre-clinical models of epilepsy.  ...  Acknowledgements We acknowledge funding from UCB Pharma, Imperial College NIHR Biomedical Research Center (BRC) Scheme, the Singapore Ministry of Health, and the European Union's Seventh Framework Programme  ... 
doi:10.1038/s41467-018-06008-4 pmid:30177815 pmcid:PMC6120885 fatcat:puzx6l4klrby3nl62wazz35mki

Genome-wide miRNA response to anacardic acid in breast cancer cells

David J. Schultz, Penn Muluhngwi, Negin Alizadeh-Rad, Madelyn A. Green, Eric C. Rouchka, Sabine J. Waigel, Carolyn M. Klinge, Bernard Mari
2017 PLoS ONE  
To identify potential mediators of AnAc action in breast cancer, we profiled the genome-wide microRNA transcriptome (microRNAome) in these two cell lines altered by the AnAc 24:1n5 congener.  ...  Whole genome expression profiling (RNAseq) and subsequent network analysis in MetaCore Gene Ontology (GO) algorithm was used to characterize the biological pathways altered by AnAc.  ...  Radde for performing the cell treatments and isolating the RNA for RNA seq.  ... 
doi:10.1371/journal.pone.0184471 pmid:28886127 pmcid:PMC5590942 fatcat:ro2uvqywlrfrtnv3jcb72orqty


Dissertation, Roberto Vera Alvarez, Sándor Pongor
Hence, in this thesis, we developed a biological data integration framework (JBioWH) that has a modular design for the integration of the most important biological databases.  ...  Therefore, the integration of biological data, as a product of those technological advances, is far from being a solved task although it is one of the most important and basic element inside the bioinformatics  ...  Acknowledgements This work is the result of an exceptionally fruitful collaboration between institutions from Cuba,  ... 

SNP based literature and data retrieval

Werner Veldsman
A second novel feature is the inclusion of the email address of a correspondence author in the results returned to the user, which promotes communication between scientists.  ...  The purpose is to allow scientists searching for relevant literature to query a database using refSNP identifiers and potential keywords assigned to scientific literature by the authors.  ...  Bolser et al. (2015) tabulated ten upper databases as being similar in scope to their upper database called MetaBase.  ... 
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