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The neXtProt knowledgebase in 2020: data, tools and usability improvements

2019 Nucleic Acids Research  
The neXtProt knowledgebase (https://www.nextprot.org) is an integrative resource providing both data on human protein and the tools to explore these.  ...  We have improved the peptide uniqueness checker and have implemented a new protein digestion tool.  ...  ACKNOWLEDGEMENTS We thank the UniProtKB groups at SIB, EBI and PIR for their dedication in providing up-to-date high-quality annotations for the human proteins in UniProtKB/Swiss-Prot thus providing neXtProt  ... 
doi:10.1093/nar/gkz995 pmid:31724716 pmcid:PMC7145669 fatcat:o22obm2ffbef3isbk2qjtp3m5y

14th Annual Biocuration Conference (virtual) - Abstracts from the invited speakers talks and poster session presentations [article]

Federica Quaglia
2021 Zenodo  
booklet of the 14th Annual Biocuration Conference (virtual), including invited speakers talks and poster session presentations  ...  RepeatsDB in 2021: improved data and extended classification for protein tandem repeat structures Category: Curation and Data Visualization Tools Almost twenty years ago the discovery of non-globular  ...  15th Category: Curation and Data Visualization Tools; Functional Annotation The UniProt Knowledgebase (UniProtKB, https://www.uniprot.org) is a comprehensive, high quality and freely accessible resource  ... 
doi:10.5281/zenodo.5570276 fatcat:nlbkkzkhfvhdddqu4ypzh247iy

Case Report: Combination of Olaparib With Chemotherapy in a Patient With ATM-Deficient Colorectal Cancer

Georgios I. Papageorgiou, Evangelos Fergadis, Nikos Skouteris, Evridiki Christakos, Sergios A. Tsakatikas, Evangelos Lianos, Christos Kosmas
2021 Frontiers in Oncology  
combination after exhaustion of all available treatment choices; furthermore, we discuss the existing data providing evidence for the use of PARP inhibitors in ATM-deficient CRC and encourage the implementation  ...  Preclinical data support the investigation of PARP inhibitors in other neoplasms exhibiting "BRCAness" or homologous recombination deficiency (HRD) as monotherapy as well as in combination with chemotherapy  ...  The Nextprot Knowledgebase in 2020: Data, Tools and Usability Improvements.  ... 
doi:10.3389/fonc.2021.788809 pmid:35004311 pmcid:PMC8728007 fatcat:7wkr7kaeufcofbl3efwp7k5pfi

Development of Bioinformatics Tools and Workflows for the Analysis of Cell Line Data

Thibault Robin, Amos Marc Bairoch, Frédérique Lisacek
2020
The authors would like to thank Alain Gateau for help with checking peptide uniqueness, the neXtProt team for help with neXtProt API, David Shteynberg for his assistance with the PTMProphet tool and Jean-Luc  ...  The supernatant was removed, and the cell pellet was flash-frozen in liquid nitrogen.  ...  The main advantage of developing such applications is the overall enhanced user experience resulting from improved web page usability and performance.  ... 
doi:10.13097/archive-ouverte/unige:143042 fatcat:yspp2pj2bbho7py3m5jebbqqqm

Corbel Review Of Identifier Schemes, Standards And Interoperability Maps And Proposed Harmonization Strategy

Carol Goble, Helen Parkinson, Simon Jupp, Renzo Kottmann, Jan-Willem Boiten, Frank Oliver Glöckner, Eleanor Williams, Jason Swedlow, Morris Swertz, David van Enckevort, Nick Juty, Anna Gaulton
2017 Zenodo  
This work addresses identifier recommendations and harmonisation in the context of the BMS Research Infrastructures (RIs) participating in CORBEL.  ...  We use six case studies to guide the work. We also define priorities and document existing services that can be adopted, or extended in support of CORBEL.  ...  Acknowledgements We wish to acknowledge the contributions of the following people: Julie  ... 
doi:10.5281/zenodo.376236 fatcat:jnrelmcl5vd7vnr4butpx2g6me

ELIXIR Scientific Programme 2019-2023 [article]

ELIXIR
2019
and thus usable in major tools.  ...  comprehensive guidelines for software curation, and through workshops for training best practices, and improving the usability of the Tools Platform products.  ...  and members of the various Working Groups. © 2018 ELIXIR.  ... 
doi:10.7490/f1000research.1117352.1 fatcat:aaocjeqix5dfbgwxvkfazdjcsi

Heterogeneous Data Processing for Information and Knowledge Management in Glycomics and Glycoproteomics

Julien Mariethoz, Frédérique Lisacek
2022
Still, it includes individuals from SIB's internal teams such as NextProt, ViralZone, Cellosaurus, and Uniprot and external organizations or projects including Cermav, MatrixDB, Göteborg University, Beilstein  ...  During the multiple projects related to this thesis, I was also privileged to collaborate and learn from many individuals and groups. There are too many people to name them all.  ...  ■ ACKNOWLEDGMENTS We thank our UniCarbKB collaborators Nicki Packer for fruitful discussions and Matthew Campbell for his help on using the data.  ... 
doi:10.13097/archive-ouverte/unige:159753 fatcat:uadamnb5yrhgfmcess2ukrh3n4