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Merging and scoring molecular interactions utilising existing community standards: tools, use-cases and a case study

J. M. Villaveces, R. C. Jimenez, P. Porras, N. del-Toro, M. Duesbury, M. Dumousseau, S. Orchard, H. Choi, P. Ping, N. C. Zong, M. Askenazi, B. H. Habermann (+1 others)
2015 Database: The Journal of Biological Databases and Curation  
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

Laurent Romary, Piotr Banski, Jack Bowers, Emiliano Degl'Innocenti, Matej Ďurčo, Roberta Giacomi, Klaus Illmayer, Adeline Joffres, Fahad Khan, Mohamed Khemakhem, Nicolas Larrousse, Antonis Litke (+12 others)
2017 Zenodo  
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

Marina D Meixner, Maria Alice Pinto, Maria Bouga, Per Kryger, Evgeniya Ivanova, Stefan Fuchs
2013 Journal of Apicultural Research  
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. 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

PhenoMeNal Consortium
2016 Zenodo  
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

Chengkun Wu, Jean-Marc Schwartz, Goran Nenadic
2013 BMC Systems Biology  
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

James E. Tomkins, Raffaele Ferrari, Nikoleta Vavouraki, John Hardy, Ruth C. Lovering, Patrick A. Lewis, Liam J. McGuffin, Claudia Manzoni
2020 Cell Communication and Signaling  
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.; 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]

James E Tomkins, Raffaele Ferrari, Nikoleta Vavouraki, John Hardy, Ruth C Lovering, Patrick A Lewis, Liam J McGuffin, Claudia Manzoni
2019 biorxiv/medrxiv   pre-print
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.; 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

Somnath Panda, Urmila Banik, Arun Kumar Adhikary
2021 Pertanika journal of science & technology  
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

Pablo Porras, Elisabet Barrera, Alan Bridge, Noemi Del-Toro, Gianni Cesareni, Margaret Duesbury, Henning Hermjakob, Marta Iannuccelli, Igor Jurisica, Max Kotlyar, Luana Licata, Ruth C Lovering (+15 others)
2020 Nature Communications  
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

Dr. Zuber Mujeeb Shaikh
2021 Zenodo  
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

Stefan M. Kohlbacher, Thierry Langer, Thomas Seidel
2021 Journal of Cheminformatics  
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

Pedro H. M. Torres, Ana C. R. Sodero, Paula Jofily, Floriano P. Silva-Jr
2019 International Journal of Molecular Sciences  
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

Annette Hilton, Geoff Hilton
2013 International Journal of Pedagogies and Learning  
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]

William R Reay, Sahar El Shair, Michael P Geaghan, Carlos Riveros, Elizabeth G Holiday, Mark A McEvoy, Stephen Hancock, Roseanne Peel, Rodney J Scott, John R Attia, Murray J Cairns
2020 medRxiv   pre-print
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]

Marek Ostaszewski, Anna Niarakis, Alexander Mazein, Inna Kuperstein, Robert Phair, Aurelio Orta-Resendiz, Vidisha Singh, Sara Sadat Aghamiri, Marcio Luis Acencio, Enrico Glaab, Andreas Ruepp, Gisela Fobo (+125 others)
2020 bioRxiv   pre-print
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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