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Cell Line Ontology: Redesigning the Cell Line Knowledgebase to Aid Integrative Translational Informatics

Sirarat Sarntivijai, Zuoshuang Xiang, Terrence F. Meehan, Alexander D. Diehl, Uma Vempati, Stephan C. Schürer, Chao Pang, James Malone, Helen E. Parkinson, Brian D. Athey, Yongqun He
2011 International Conference on Biomedical Ontology  
dblp:conf/icbo/SarntivijaiXMDVSPMPAH11 fatcat:axdjrwyai5gvhngyg3h6kwqjve

The Year of the Rat: The Rat Genome Database at 20: a multi-species knowledgebase and analysis platform

2019 Nucleic Acids Research  
for >150 years, RGD has always been disease-focused and committed to providing data and tools for researchers doing comparative genomics and translational studies.  ...  Formed in late 1999, the Rat Genome Database (RGD, https://rgd.mcw.edu) will be 20 in 2020, the Year of the Rat.  ...  Functional data in the form of disease, gene ontology, and pathway ontology annotations have been informatically 'inferred' to these genes from their orthologs in human, mouse and rat.  ... 
doi:10.1093/nar/gkz1041 pmid:31713623 pmcid:PMC7145519 fatcat:4a6ja3vobncmtbp7m2hivrebr4

Open Targets Platform: new developments and updates two years on

Denise Carvalho-Silva, Andrea Pierleoni, Miguel Pignatelli, ChuangKee Ong, Luca Fumis, Nikiforos Karamanis, Miguel Carmona, Adam Faulconbridge, Andrew Hercules, Elaine McAuley, Alfredo Miranda, Gareth Peat (+6 others)
2018 Nucleic Acids Research  
In addition to target-disease associations, we also aggregate and display data at the target and disease levels to aid target prioritisation.  ...  The Open Targets Platform integrates evidence from genetics, genomics, transcriptomics, drugs, animal models and scientific literature to score and rank target-disease associations for drug target identification  ...  The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.  ... 
doi:10.1093/nar/gky1133 pmid:30462303 fatcat:2elh777ogbhknky33z5xfvaxfa

Unlocking Big Data for better health

Steven Munevar
2017 Nature Biotechnology  
The UniProt GO annotation (GOA) program aims to add high-quality Gene Ontology (GO) annotations to proteins in the UniProt Knowledgebase (UniProtKB).  ...  We also added BioAssay Ontology (BAO) indexing of many assays, and classified cell-line assays with standard ontology terms; this enhanced search-and-retrieval functionality.  ... 
doi:10.1038/nbt.3918 pmid:28700551 fatcat:oqiurm5cgzec7lfenvjvlemxoy

The Alphaviral Capsid Protein Inhibits IRAK1-Dependent TLR Signaling

V. Douglas Landers, Daniel W. Wilkey, Michael L. Merchant, Thomas C. Mitchell, Kevin J. Sokoloski
2021 Viruses  
Here we detail the use of a BioID2 biotin ligase system to identify the protein–protein interactions of the Sindbis virus capsid protein.  ...  These efforts led to the discovery of a series of novel host–pathogen interactions, including the identification of an interaction between the alphaviral capsid protein and the host IRAK1 protein.  ...  The funding agencies had no role in the study design, data collection and analysis, decision to publish, or the preparation of the manuscript.  ... 
doi:10.3390/v13030377 pmid:33673546 pmcid:PMC7997285 fatcat:xb4texc3evehpltpnyvrlvcksa

Computational Toxicology as Implemented by the U.S. EPA: Providing High Throughput Decision Support Tools for Screening and Assessing Chemical Exposure, Hazard and Risk

Robert Kavlock, David Dix
2010 Journal of Toxicology and Environmental Health. Part B, Critical Reviews  
on in vitro assays, especially those using human cell lines.  ...  Large-scale knowledgebased approaches have become feasible because of semantic Web technology and available ontologies for different levels of biological organization.  ...  statistical language R, submitted to CRAN (8) Description of ontologically aware PBPK language working name "SemanticPK" drafted, and translator to R completed (using code developed for RDynamic) (9)  ... 
doi:10.1080/10937404.2010.483935 pmid:20574897 fatcat:4gh7hecabfduhc7uqvuautko3e

Crystal ball - 2011

2011 Microbial Biotechnology  
Acknowledgements I am indebted to my collaborator, Prof. Stratos Pistikopoulos, for the privilege of working together on this research and I am grateful to members of my group, Dr.  ...  Acknowledgements We gratefully acknowledge the financial support from the Foreign Office of UK and the Ministry of Science and Technology of P. R. China.  ...  Biology as a discipline will rely on the creation of an integrated data storage and analysis tool, also referred as Knowledgebase.  ... 
doi:10.1111/j.1751-7915.2010.00245.x fatcat:4t3p675ig5caba5mjsowpazh54

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

Thibault Robin, Amos Marc Bairoch, Frédérique Lisacek
2020
To separate sperm cells from seminal plasma and round cells, we loaded the pooled sperm sample onto 1 mL of a 50% suspension of silica particles (SupraSperm, Origio, Malov, Denmark) diluted in Sperm Washing  ...  The supernatant was removed, and the cell pellet was flash-frozen in liquid nitrogen.  ...  The Cellosaurus has planned to refine the tissue sources of cell lines using the Uberon ontology [117] .  ... 
doi:10.13097/archive-ouverte/unige:143042 fatcat:yspp2pj2bbho7py3m5jebbqqqm

Rational Vaccine Design by Reverse & Structural Vaccinology and Ontology

Edison Ong, University, My
2021
Furthermore, I created a community-based Ontology of Host-Pathogen Interactions (OHPI), which served as a platform to semantically represent the interactions between host and virulence factors that are  ...  These works can be further expanded and integrated with other technologies such as epitope prediction, molecular epidemiology, and high-throughput sequencing to build the foundation of precision vaccinology  ...  Vaccine-informatics and Ontology With the exponential growth of data accumulated in vaccine informatics, there is a challenge to translate the high volume, variety, and variability of vaccine-related data  ... 
doi:10.7302/1424 fatcat:khq2a4zisfexbf7cbmcrqr32fu

A Nonproprietary Language for the Command and Control of Cyber Defenses - OpenC2

Vasileios Mavroeidis, Joe Brule
2020 Computers & security  
the potential to process, correlate, and analyze that information to understand adversaries better.  ...  Defenders need to establish the capability necessary to represent and interpret those new polymorphic threats in a format that both human and machine agents can understand, and use that intelligence to  ...  Acknowledgements I would like to express my gratitude to Professor Audun Jøsang for the fruitful discussions and support in this long research journey.  ... 
doi:10.1016/j.cose.2020.101999 fatcat:5wyfkpkvarcktbnxuuepvxvsru

Cross-Covariance Models [chapter]

2017 Encyclopedia of GIS  
Efficient tools for extracting information from geo-spatial data are crucial to organizations which make decisions based on large spatial datasets, including the National Aeronautics and Space Administration  ...  Acknowledgements We would like to thank Keith Harries, Dan Helms, Chris Maxwell and Susan Wernicke-Smith for providing comments on this entry in a very short time.  ...  Thus a large task ahead is to elicit this knowledge and integrate it with relevant existing conceptual structures and ontologies.  ... 
doi:10.1007/978-3-319-17885-1_100240 fatcat:2ojzb7es7rhofinw4abol6dgc4

The Fourth Paradigm – Data-Intensive Scientific Discovery [chapter]

Tony Hey
2012 Communications in Computer and Information Science  
The F o u r T H Data-In t e n s I v e scIen t I f I c DIs c o v e r y P a r a d i g m MiCroSoF T reSe arCH REDMOND, WASHINGTON  ...  very helpful discussion on a draft of this material. to all the contributors to this book for sharing their visions within the Fourth Paradigm.  ...  Acknowledgments My thanks to the participants at the April 24, 2009, Buckland-Lynch-Larsen "Friday Seminar" on information access at the University of California, Berkeley, School of Information for a  ... 
doi:10.1007/978-3-642-33299-9_1 fatcat:etue636ubrandga5corvkx3d7u

Leveraging Knowledge-Based Approaches to Promote Antiretroviral Toxicity Monitoring in Underserved Settings

William Ogallo
2017
As access and use of antiretroviral therapy continue to increase, the need to improve antiretroviral toxicity monitoring becomes more critical.  ...  Next, a quantitative validation study was used to evaluate the structure and behavior of the prototype's knowledge base.  ...  Health Organization (WHO) clinical staging of HIV/AIDS or the CD4 cell count of the patient.  ... 
doi:10.7916/d8tm7pn4 fatcat:eon2mla52raohe42oue6w32bhu

From Research to Innovation: Exploring the Translation Journey with OpenInnoTrain [article]

Anne-Laure Mention, Massimo Menichinelli
2021 Zenodo  
As we cross the 2-year mark of the project, the intent of this book is to provide glimpses on OpenInnoTrain's current reflections and achievements with a variety of illustrations featuring activities across  ...  The European funded OpenInnoTrain project precisely aims to explore those mechanisms, across four specific contemporary settings, so to as equip researchers and practitioners with actionable knowledge  ...  Distinct approach to knowledge production and use At this juncture, it needs to be noted that most of the research translation and UIC literature has been based on patent data or studies involving natural  ... 
doi:10.5281/zenodo.5536932 fatcat:7pfwvjaznfagjgcapb2bm2zkuu

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

Julien Mariethoz, Frédérique Lisacek
2022
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.  ...  Vincenzo Daponte, Francisco Lorenzo for the good time we shared during those last years.  ...  . ¶ ¶ To whom correspondence should be addressed: SIB Swiss Institute of Bioinformatics, Proteome Informatics Group, Route de Drize 7, 1227 Geneva, Switzerland.  ... 
doi:10.13097/archive-ouverte/unige:159753 fatcat:uadamnb5yrhgfmcess2ukrh3n4
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