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Merging and scoring molecular interactions utilising existing community standards: tools, use-cases and a case study
2015
Database: The Journal of Biological Databases and Curation
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Merging and scoring molecular interactions utilising existing community standards: tools, use-cases and a case study. ...
We have developed both a merging algorithm and a scoring system for molecular interactions based on the proteomics standard initiative-molecular interaction standards. ...
The community has, however, not agreed yet on a generally accepted common scoring system for molecular interactions (7) ]. A set of different confidence measures for molecular interactions exist. ...
doi:10.1093/database/bau131
pmid:25652942
pmcid:PMC4316181
fatcat:n2oauiczgjgqtlgpkv6tuopexm
PARTHENOS D4.2 Report on Standardization
2017
Zenodo
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to fulfil the research task, we present here a systematic review of the activities that have to be carried out to provide support to researchers in using, but also contributing to, these standards. ...
On the basis of the various user scenarios presented in Deliverable 4.1, where each stage of the research process has been annotated according to the actual standards that are actually needed in order ...
an overview of tools and projects that utilise MEI (more on tools and projects below). ...
doi:10.5281/zenodo.2668414
fatcat:gog5jmigdjag7hexhjbdrlldc4
Standard methods for characterising subspecies and ecotypes ofApis mellifera
2013
Journal of Apicultural Research
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In this paper, we give an overview of methods that are currently available and used for recognition of honey bee subspecies and ecotypes, or that can be utilised to verify the genetic origin of colonies ...
A multitude of reasons lead to a loss of both genetic diversity and specific adaptations to local conditions. ...
This is a serious limitation, and we strongly urge the community to develop commonly available standards, to increase reproducibility and comparability of data between labs and studies. ...
doi:10.3896/ibra.1.52.4.05
fatcat:2ew6js3y3zfsjbxixopflk7lpi
A Beta-Version Of Phenomenal Integration Vmi Capable Of Proof- Of-Concept Integration With Other Vmis. Initial Services Online Supporting Phenomenal Data Standards - D5.2
2016
Zenodo
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We describe the architecture of the e-infrastructure, the workflow systems chosen, and case studies demonstrating the capabilities of integrating services. ...
We present a number of case studies that demonstrate the capabilities of the VRE, which are: I. R-based metabolomics workflow II. Fluxomics Tools III. ...
Since data formats are all agreed-upon and following open standards like mzML, nmrML and ISA-Tab, the communication and data sent between tools is simplified. ...
doi:10.5281/zenodo.832271
fatcat:g4j4vgsgpbfz7fmxf5cxbupq6i
PathNER: a tool for systematic identification of biological pathway mentions in the literature
2013
BMC Systems Biology
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The rules utilise general pathway-specific keywords, syntactic information and gene/protein mentions. Detection results from both components are merged. ...
On a goldstandard corpus, PathNER achieved an F1-score of 84%. ...
Acknowledgements We would like to thank Geraint Duck (University of Manchester) for his help in using GATE. CW is co-funded by Biotechnology ...
doi:10.1186/1752-0509-7-s3-s2
pmid:24555844
pmcid:PMC3852116
fatcat:ax462pg6azfjpprwqpjsiihbk4
PINOT: an intuitive resource for integrating protein-protein interactions
2020
Cell Communication and Signaling
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Then each PPI is confidence scored based on the number of distinct methods used for interaction detection and the number of publications that report the specific interaction. ...
PINOT extracts a similar numbers of PPIs as other, analogous, tools and incorporates a set of innovative features. ...
Funding
Availability of data and materials This resource is available as a fully automated web-server at: http://www. reading.ac.uk/bioinf/PINOT/PINOT_form.html; R scripts, which underlie this bioinformatics ...
doi:10.1186/s12964-020-00554-5
pmid:32527260
pmcid:PMC7291677
fatcat:5e3xducnmfghbibewctqnxpcgm
PINOT: An Intuitive Resource for Integrating Protein-Protein Interactions
[article]
2019
biorxiv/medrxiv
pre-print
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PPI data is downloaded, merged, quality checked, and confidence scored based on the number of distinct methods and publications in which each interaction has been reported. ...
Examples of PINOT applications are provided to highlight the performance, the ease of use and the potential applications of this tool. ...
Funding
Availability of data and materials This resource is available as a fully automated web-server at: http://www. reading.ac.uk/bioinf/PINOT/PINOT_form.html; R scripts, which underlie this bioinformatics ...
doi:10.1101/788000
fatcat:cwyyefdt4fb3tihisq2e2hffdm
In Silico Designing of a Multi-Epitope Based Vaccine Candidate Against Human Adenovirus Type B3 Respiratory Infections by Utilising Various Immunoinformatics Approaches
2021
Pertanika journal of science & technology
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The allergenicity, antigenicity, structure, physicochemical properties along with molecular docking with TLR-3 and TLR-9 had also been predicted. The constructed vaccine had 23 different epitopes. ...
It showed non-allergic but antigenic nature with 30hours of half-life in vitro and exhibited thermostable nature. ...
The geometric shape complementarity score of the best-docked model in this case was estimated to be 13944, the calculated interface region of interaction was 2231. ...
doi:10.47836/pjst.29.1.32
fatcat:mf4gpfy5qraanejhrkodznpswy
Towards a unified open access dataset of molecular interactions
2020
Nature Communications
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Additionally, we provide examples of how IMEx data are being used by biomedical researchers and integrated in other bioinformatic tools and resources. ...
The International Molecular Exchange (IMEx) Consortium provides scientists with a single body of experimentally verified protein interactions curated in rich contextual detail to an internationally agreed ...
Acknowledgements The IntAct team at EMBL-EBI received funding from EMBL core funding, Open Targets (grant agreements OTAR-044 and OTAR02-048) and the Wellcome Trust ...
doi:10.1038/s41467-020-19942-z
pmid:33262342
pmcid:PMC7708836
fatcat:soyrqsypencbrkmqwxzjz6crp4
A Critical Comparative Study On The National Accreditation Standards For Hospitals Of India, Australia, Denmark And South Africa
2021
Zenodo
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A Critical Comparative Study On The National Accreditation Standards For Hospitals Of India, Australia, Denmark And South Africa: D.Litt thesis Part-1 ...
Standard scoring methodology is used to score each measurable element as per the national and international healthcare organizations. ...
Hence, all such duplicated chapters, standards and measurable elements were eliminated by mapping, filtration and merging of Chapters, Standards and Measurable Elements and a new list of chapters, standards ...
doi:10.5281/zenodo.5151605
fatcat:feje66575jarldm5ukkbeo36pe
QPHAR: quantitative pharmacophore activity relationship: method and validation
2021
Journal of Cheminformatics
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Furthermore, a well‐crafted quantitative pharmacophore model can generalise to underrepresented or even missing molecular features in the training set by using pharmacophoric interaction patterns only. ...
The abstract depiction of molecular interactions avoids a bias towards overrepresented functional groups in small datasets. ...
Metadata of all datasets used for CV studies are provided in Additional File 1 and Additional File 2 for CV-split 20-80 and CV-split 80-20, respectively. ...
doi:10.1186/s13321-021-00537-9
fatcat:rycewxpxl5bgnjynvkmhf5lgiq
Key Topics in Molecular Docking for Drug Design
2019
International Journal of Molecular Sciences
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their advantages and caveats, (ii) the advances in consensus methods, (iii) recent algorithms and applications using fragment-based approaches, and (iv) the use of machine learning algorithms in molecular ...
Molecular docking has been widely employed as a fast and inexpensive technique in the past decades, both in academic and industrial settings. ...
Nonetheless, existing prospective studies show positive results (Table 4 ). In 2011, Kinnings et al. ...
doi:10.3390/ijms20184574
pmid:31540192
pmcid:PMC6769580
fatcat:ye5rdnonofc3jjaizbncrdx2yu
Incorporating digital technologies into science classes: Two case studies from the field
2013
International Journal of Pedagogies and Learning
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In the case study described here, a 10week chemistry unit was adapted to incorporate a range of multimedia tools, including molecular modelling software, animations and simulations, as a means of promoting ...
Case Study 2 focuses on the use of molecular modelling and simulation software in secondary school chemistry classrooms. ...
Aim of this activity In this activity, you will learn to use a program called ChemSketch and use it to create different representations of molecular compounds and elements. Using ChemSketch 1. ...
doi:10.5172/ijpl.2013.8.3.153
fatcat:2j4kqhgjjveazo5zjovvkepg2m
Genetically informed precision drug repurposing for lung function and implications for respiratory infection
[article]
2020
medRxiv
pre-print
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by transcriptome-wide association studies to identify drug-gene interactions with potential lung function increasing modes of action. ...
Measures of pulmonary function are heritable, and thus, we sought to utilise genomics to propose novel drug repurposing candidates which could improve respiratory outcomes. ...
spirometry measures in theHunter Community Study cohortThe z value is the PES model coefficient divided by its standard error. ...
doi:10.1101/2020.06.25.20139816
fatcat:zhfoyy55wnd7ph5soqzza23b34
COVID-19 Disease Map, a computational knowledge repository of SARS-CoV-2 virus-host interaction mechanisms
[article]
2020
bioRxiv
pre-print
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We discuss the tools, platforms, and guidelines necessary for the distributed development of its contents by a multi-faceted community of biocurators, domain experts, bioinformaticians, and computational ...
We hereby describe a large-scale community effort to build an open-access, interoperable, and computable repository of COVID-19 molecular mechanisms - the COVID-19 Disease Map. ...
Preliminary results of such efforts are illustrated in case studies above. ...
doi:10.1101/2020.10.26.356014
fatcat:gbxecdcnhbb3jehkhdjxmkdlbq
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