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MetaBase--the wiki-database of biological databases
2011
Nucleic Acids Research
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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
2015
Zenodo
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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
2016
International Journal of Molecular Sciences
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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 https://labworm.com/ Metabases ...
doi:10.3390/ijms17122039
pmid:27929431
pmcid:PMC5187839
fatcat:rbggkt4xcbbu3pnkh33zpovxju
DaTo: an atlas of biological databases and tools
2016
Journal of Integrative Bioinformatics
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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 ...
., MetaBase—the wiki-database of
biological databases. ...
doi:10.1515/jib-2016-297
fatcat:72j7or3fhfgllifn2dpptw5w2e
RDFIO: extending Semantic MediaWiki for interoperable biomedical data management
2017
Journal of Biomedical Semantics
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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
2012
Molecular Informatics
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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) (http://metadatabase.org/wiki/Main_Page). ...
doi:10.1002/minf.201200014
pmid:23226167
pmcid:PMC3507005
fatcat:agxqiy375fbc5dw46x26bdgyh4
In Silico Toxicology Data Resources to Support Read-Across and (Q)SAR
2019
Frontiers in Pharmacology
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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]
2017
Msphere
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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
2019
International Journal of Molecular Sciences
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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
2021
Micromachines
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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
2021
Zenodo
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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). https://www.metabase.com/. 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
2018
Nature Communications
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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
2017
PLoS ONE
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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
LARGE SCALE ANNOTATION OF BIOMOLECULAR DATA USING INTEGRATED DATABASE MANAGEMENT TOOLS List of Publications
unpublished
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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, ...
fatcat:mxt7m3cjdzbezpcjwotpkjz4zm
SNP based literature and data retrieval
unpublished
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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. ...
fatcat:dffstcsv3nbwvoaxbvck2qzgcq
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