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UniProt Protein Knowledgebase [chapter]

Sangya Pundir, Maria J. Martin, Claire O'Donovan
2017 Msphere  
The entry provides all annotated Fig. 3 Fig. 4 34 Advanced UniProtKB search results page Sangya Pundir et al.  ... 
doi:10.1007/978-1-4939-6783-4_2 pmid:28150232 pmcid:PMC5565770 fatcat:sem3wywevbcancpfdfx3lvpqse

ProtVista: visualization of protein sequence annotations

Xavier Watkins, Leyla J Garcia, Sangya Pundir, Maria J Martin, Alfonso Valencia
2017 Bioinformatics  
ProtVista is a comprehensive visualization tool for the graphical representation of protein sequence features in the UniProt Knowledgebase, experimental proteomics and variation public datasets. The complexity and relationships in this wealth of data pose a challenge in interpretation. Integrative visualization approaches such as provided by ProtVista are thus essential for researchers to understand the data and, for instance, discover patterns affecting function and disease associations.
more » ... bility and Implementation: ProtVista is a JavaScript component released as an open source project under the Apache 2 License. Documentation and source code are available at http://ebi-uni Contact: Supplementary information: Supplementary data are available at Bioinformatics online. Visualization ProtVista's display consists of three sections (see Fig. 1 ). The first, located at the top, is used for navigation and zooming. It represents the full length of the protein sequence. Elements on both sides of the component can be dragged to specify the zoom level, as well as navigating along the sequence. The second section, on the left, consists of categories of the feature types. The third and main section of the visualization is the area where the features are displayed in tracks. Each category track is collapsed by default, providing a feature-
doi:10.1093/bioinformatics/btx120 pmid:28334231 pmcid:PMC5963392 fatcat:fzl2glx3tvgqpjs5amex7y6rl4

Searching and Navigating UniProt Databases

Sangya Pundir, Michele Magrane, Maria J. Martin, Claire O'Donovan
2015 Current Protocols in Bioinformatics  
Author Manuscript Author Manuscript Pundir et al.  ... 
doi:10.1002/0471250953.bi0127s50 pmid:26088053 pmcid:PMC4522465 fatcat:o2ggn5ojxvaajfkymbfhifi7vi

Ten Simple Rules for Running Interactive Workshops

Katrina Pavelin, Sangya Pundir, Jennifer A. Cham, Philip E. Bourne
2014 PLoS Computational Biology  
doi:10.1371/journal.pcbi.1003485 pmid:24586135 pmcid:PMC3937100 fatcat:klepndwb7jccnnbm5rg44ri3rm

Designing an intuitive web application for drug discovery scientists [article]

Nikiforos Karamanis, Denise Carvalho-Silva, Jennifer A. Cham, Luca Fumis, Samiul Hasan, David Hulcoop, Gautier Koscielny, Michael Maguire, William Newell, ChuangKee Ong, Eliseo Papa, Andrea Pierleoni (+7 others)
2017 bioRxiv   pre-print
Although a scientific web application that is intuitive can help scientists utilize data more easily and advance their research, there is little guidance on how to design such an application in the academic literature. We discuss how we designed an intuitive application for bench scientists working in drug discovery following an approach that can be applied to the design and development of scientific resources in a broad range of disciplines.
doi:10.1101/169193 fatcat:iiqgbd2qpbhzldk7b35gdcqgtq

The EBI Search engine: providing search and retrieval functionality for biological data from EMBL-EBI

Silvano Squizzato, Young Mi Park, Nicola Buso, Tamer Gur, Andrew Cowley, Weizhong Li, Mahmut Uludag, Sangya Pundir, Jennifer A. Cham, Hamish McWilliam, Rodrigo Lopez
2015 Nucleic Acids Research  
The European Bioinformatics Institute (EMBL-EBI-- provides free and unrestricted access to data across all major areas of biology and biomedicine. Searching and extracting knowledge across these domains requires a fast and scalable solution that addresses the requirements of domain experts as well as casual users. We present the EBI Search engine, referred to here as 'EBI Search', an easy-to-use fast text search and indexing system with powerful data navigation and
more » ... l capabilities. API integration provides access to analytical tools, allowing users to further investigate the results of their search. The interconnectivity that exists between data resources at EMBL-EBI provides easy, quick and precise navigation and a better understanding of the relationship between different data types including sequences, genes, gene products, proteins, protein domains, protein families, enzymes and macromolecular structures, together with relevant life science literature.
doi:10.1093/nar/gkv316 pmid:25855807 pmcid:PMC4489232 fatcat:m6wp7w7c4zdbrpsunzxlzqy4mi

ELIXIR Belgium services for research data management

Flora D'Anna
2022 Zenodo  
" Sangya Pundir, CC BY-SA 4.0 Open means anyone can freely access, use, modify, and share for any purpose (subject, at most, to requirements that preserve provenance  ... 
doi:10.5281/zenodo.6602262 fatcat:2xw2jzj2gnf2hhhfbk6p7tisp4

An introduction to ELIXIR's tools for Research Data Management

Flora D'Anna, Rafael Andrade Buono
2022 Zenodo  
• Scalable from small local installations to "••• Sangya Pundir, CC BY-SA 4.0 Open means anyone can freely access, use, modify, and share for any purpose (subject  ... 
doi:10.5281/zenodo.7120491 fatcat:mmk4iuvdvfh4vaw3fizsqonqdi

Overview of the interactive task in BioCreative V

Qinghua Wang, Shabbir S. Abdul, Lara Almeida, Sophia Ananiadou, Yalbi I. Balderas-Martínez, Riza Batista-Navarro, David Campos, Lucy Chilton, Hui-Jou Chou, Gabriela Contreras, Laurel Cooper, Hong-Jie Dai (+44 others)
2016 Database: The Journal of Biological Databases and Curation  
Fully automated text mining (TM) systems promote efficient literature searching, retrieval, and review but are not sufficient to produce ready-to-consume curated documents. These systems are not meant to replace biocurators, but instead to assist them in one or more literature curation steps. To do so, the user interface is an important aspect that needs to be considered for tool adoption. The BioCreative Interactive task (IAT) is a track designed for exploring user-system interactions,
more » ... g development of useful TM tools, and providing a communication channel between the biocuration and the TM communities. In BioCreative V, the IAT track followed a format similar to previous interactive tracks, where the utility and usability of TM tools, as well as the generation of use cases, have been the focal points. The proposed curation tasks are user-centric and formally evaluated by biocurators. In BioCreative V IAT, seven TM systems and 43 biocurators participated. Two levels of user participation were offered to broaden curator involvement and obtain more feedback on usability aspects. The full level participation involved training on the system, curation of a set of documents with and without TM assistance, tracking of time-on-task, and completion of a user survey. The partial level participation was designed to focus on usability aspects of the interface and not the performance per se. In this case, biocurators navigated the system by performing predesigned tasks and then were asked whether they were able to achieve the task and the level of difficulty in completing the task. In this manuscript, we describe the development
doi:10.1093/database/baw119 pmid:27589961 pmcid:PMC5009325 fatcat:ldpn6gjxircjlibqtysi57cztq

Forschungsdaten & Open Access - so publizieren Sie Ihre Daten

Frauke Ziedorn
2021 Zenodo  
 Bilder: Sangya Pundir CC-BY-SA 4.Wer darf Daten einstellen?  In welchen Formaten werden Daten und Metadaten akzeptiert?  ... 
doi:10.5281/zenodo.4529739 fatcat:muciax32r5gbnopfz6bvvxbzie

Introductory workshop on research data management for data representatives (in environmental science)

Helen Kollai, Paul Remmler
2021 Zenodo  
, Sangya under CC-BY-SA-4.0 license] [1] Wilkinson, M.  ...  naming • Data transfer and conversion • Deployed software, infrastructures and tools • Actors and responsibilities • Rights and licenses 12 The FAIR principles [Graphic: Pundir  ... 
doi:10.5281/zenodo.4557620 fatcat:rl257crexjeshaccghe244ipwy

FAIR data stewardship. The need for capacity building & the role of communities

Mijke Jetten
2021 Zenodo  
Pundir, Wikimedia Commons FAIR data stewardship The responsible planning and executing of all actions on (digital) data before, during and after a research project, with the aim of optimising the  ...  stimulates an integrated health data infrastructure accessible for researchers, citizens and care providers • provides services, expertise and communities CC-BY-SA-4.0, Sangya  ... 
doi:10.5281/zenodo.5036442 fatcat:n7f63j4envg2bpxc4dz2nmdrmi

Towards a Community-Endorsed Data Steward Profession for Supporting Research

Mijke Jetten, Inge Slouwerhof, Salome Scholtens, Marije Van der Geest, Cecilia Van Gelder, Nelly Anbeek, Mirjam Brullemans
2019 Zenodo  
Pundir, Wikimedia Commons 4  ...  is and does; -education/certification • Collaborative approach: -creating a standardised job description/formalising the function; -creating visibility of the function; -develop training CC-BY-SA-4.0, Sangya  ... 
doi:10.5281/zenodo.3259654 fatcat:h3wyplraazfgvgrqeywanwiq4m

Comment sensibiliser les chercheur.e.s en SHS à la gestion des données ? [article]

Laetitia Bracco, Stéphanie Cheviron, Caroline-Sophie Donati, Delphine Du Pasquier, France Martin
2021 Zenodo  
(Sangya Pundir, CC BY-SA 4.0) Comment aider les chercheur·e·s à rapprocher leur pratique personnelle de gestion des données de la pratique développée ou en cours d'élaboration par leur communauté scientifique  ... 
doi:10.5281/zenodo.4639590 fatcat:te2swqrm6jarfn5bmkb5nij7k4

Comment sensibiliser les chercheur.e.s en SHS à la gestion des données ? [article]

Laetitia Bracco, Stéphanie Cheviron, Caroline-Sophie Donati, Delphine Du Pasquier, France Martin
2021 Zenodo  
(Sangya Pundir, CC BY-SA 4.0) Comment aider les chercheur•e•s à rapprocher leur pratique personnelle de gestion des données de la pratique développée ou en cours d'élaboration par leur communauté scientifique  ... 
doi:10.5281/zenodo.6854322 fatcat:hpherun7ljbvjin3lbxtt7khhe
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