The Cellosaurus, a Cell-Line Knowledge Resource.
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TLDR
The Cellosaurus is a key resource to help researchers identify potentially contaminated/misidentified cell lines, thus contributing to improving the quality of research in the life sciences.Abstract:
The Cellosaurus is a knowledge resource on cell lines. It aims to describe all cell lines used in biomedical research. Its scope encompasses both vertebrates and invertebrates. Currently, information for >100,000 cell lines is provided. For each cell line, it provides a wealth of information, cross-references, and literature citations. The Cellosaurus is available on the ExPASy server (https://web.expasy.org/cellosaurus/) and can be downloaded in a variety of formats. Among its many uses, the Cellosaurus is a key resource to help researchers identify potentially contaminated/misidentified cell lines, thus contributing to improving the quality of research in the life sciences.read more
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Search and sequence analysis tools services from EMBL-EBI in 2022
Fábio Madeira,Matt Pearce,Adrian Tivey,Prasad Basutkar,Joon Seung Lee,Ossama Edbali,Nandana Madhusoodanan,A. Kolesnikov,Rodrigo Lopez +8 more
TL;DR: Recent improvements to EBI Search and Job Dispatcher tools frameworks are described and updates made to accommodate the increasing data requirements during the COVID-19 pandemic are described.
Journal ArticleDOI
OUP accepted manuscript
TL;DR: The EMBL-EBI search and sequence analysis tools frameworks as discussed by the authors provide integrated access to EMBL EBI's data resources and core bioinformatics analytical tools, allowing users to interact through user-friendly web applications, as well as via RESTful and SOAP-based APIs.
Journal ArticleDOI
PubTator central: automated concept annotation for biomedical full text articles
TL;DR: The full text results in PTC significantly increase biomedical concept coverage and it is anticipated this expansion will both enhance existing downstream applications and enable new use cases.
Journal ArticleDOI
Expasy, the Swiss Bioinformatics Resource Portal, as designed by its users.
Séverine Duvaud,Chiara Gabella,Frédérique Lisacek,Frédérique Lisacek,Heinz Stockinger,Vassilios Ioannidis,Christine Durinx +6 more
TL;DR: The Swiss Bioinformatics Resource Portal (expasy) as mentioned in this paper provides a portfolio of reliable and state-of-the-art resources for the storage, analysis and interpretation of biological data.
Journal ArticleDOI
DrugComb: an integrative cancer drug combination data portal.
Bulat Zagidullin,Jehad Aldahdooh,Shuyu Zheng,Wenyu Wang,Yinyin Wang,Joseph Saad,Alina Malyutina,Mohieddin Jafari,Ziaurrehman Tanoli,Alberto Pessia,Jing Tang +10 more
TL;DR: It was shown that linear regression approaches, when considering chemical fingerprints as predictors, have the potential to achieve high accuracy of predicting the sensitivity of drug combinations and are freely available in DrugComb.
References
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TL;DR: The Swiss-Prot, TrEMBL and PIR protein database activities have united to form the Universal Protein Knowledgebase (UniProt), which is to provide a comprehensive, fully classified, richly and accurately annotated protein sequence knowledgebase, with extensive cross-references and query interfaces.
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TL;DR: The Gene Expression Omnibus is an international public repository for high-throughput microarray and next-generation sequence functional genomic data sets submitted by the research community and supports archiving of raw data, processed data and metadata which are indexed, cross-linked and searchable.
Journal ArticleDOI
The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity
Jordi Barretina,Giordano Caponigro,Nicolas Stransky,Kavitha Venkatesan,Adam A. Margolin,Adam A. Margolin,Sungjoon Kim,Christine D. Wilson,Joseph Lehar,Gregory V. Kryukov,Dmitriy Sonkin,Anupama Reddy,Manway Liu,Lauren Murray,Michael F. Berger,Michael F. Berger,John Monahan,Paula Morais,Jodi Meltzer,Adam Korejwa,Judit Jané-Valbuena,Judit Jané-Valbuena,Felipa A. Mapa,Joseph Thibault,Eva Bric-Furlong,Pichai Raman,Aaron Shipway,Ingo H. Engels,Jill Cheng,Guoying K. Yu,Jianjun Yu,Peter Aspesi,Melanie de Silva,Kalpana Jagtap,Michael D. Jones,Li Wang,Charlie Hatton,Emanuele Palescandolo,Supriya Gupta,Scott Mahan,Carrie Sougnez,Robert C. Onofrio,Ted Liefeld,Laura E. MacConaill,Wendy Winckler,Michael R. Reich,Nanxin Li,Jill P. Mesirov,Stacey Gabriel,Gad Getz,Kristin G. Ardlie,Vivien W. Chan,Vic E. Myer,Barbara L. Weber,Jeffrey A. Porter,Markus Warmuth,Peter Finan,Jennifer L. Harris,Matthew Meyerson,Matthew Meyerson,Todd R. Golub,Michael Morrissey,William R. Sellers,Robert Schlegel,Levi A. Garraway,Levi A. Garraway +65 more
TL;DR: The results indicate that large, annotated cell-line collections may help to enable preclinical stratification schemata for anticancer agents and the generation of genetic predictions of drug response in the preclinical setting and their incorporation into cancer clinical trial design could speed the emergence of ‘personalized’ therapeutic regimens.
Journal ArticleDOI
2016 update of the PRIDE database and its related tools
Juan Antonio Vizcaíno,Attila Csordas,Noemi del-Toro,José A. Dianes,Johannes Griss,Ilias Lavidas,Gerhard Mayer,Yasset Perez-Riverol,Florian Reisinger,Tobias Ternent,Qing Wei Xu,Rui Wang,Henning Hermjakob +12 more
TL;DR: The developments in PRIDE resources and related tools are summarized and a brief update on the resources under development 'PRIDE Cluster' and 'PRide Proteomes', which provide a complementary view and quality-scored information of the peptide and protein identification data available inPRIDE Archive are given.
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