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High-throughput Multimodal Automated Phenotyping (MAP) with Application to PheWAS
[article]
2019
bioRxiv
pre-print
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The objective of this study was to develop an automated high-throughput phenotyping method integrating International Classification of Diseases (ICD) codes and narrative data extracted using natural language ...
The PheWAS results suggest that the MAP approach detected previously validated associations with higher power when compared to the standard PheWAS method based on ICD codes.ConclusionThe MAP approach increased ...
In this paper, we propose an unsupervised multimodal automated phenotyping (MAP) method with application in PheWAS. ...
doi:10.1101/587436
fatcat:gn773e7dkbdmhm43gseq2ez6v4
Pharmacogenomics in the Age of GWAS, Omics Atlases, and PheWAS
[article]
2018
arXiv
pre-print
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in an automated parallel process. ...
We conclude with a vision for a pharmacophenomic atlas, in which omics atlas data, PheWAS associations, and biobank data would be used with AI to design thousands of genetic tests for clinical deployment ...
The construction of tissue files on an automated basis requires a degree of natural language processing. ...
arXiv:1808.09481v1
fatcat:7tys2l3qlfgifjxtgjq4jejoma
The anatomy of phenotype ontologies: principles, properties and applications
2017
Briefings in Bioinformatics
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Along with this comes the challenge of dealing with the related phenotype data, which is not only large but also highly multidimensional. ...
The Phenotype And Trait Ontology framework provides a method for formal definitions of phenotypes and associated data sets and has proved to be key to our ability to develop methods for the integration ...
Funding The National Science Foundation (IOS:1340112 to G.V.G.), the European Commission H2020 (grant agreement number 731075) to G.V.G. and the King Abdullah University of Science and Technology (to R.H ...
doi:10.1093/bib/bbx035
pmid:28387809
fatcat:eouajqukvncvfjlazgmsnmyxbe
PS4DR: a multimodal workflow for identification and prioritization of drugs based on pathway signatures
2020
BMC Bioinformatics
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Here, we present a customizable workflow (PS4DR) which not only integrates high-throughput data such as genome-wide association study (GWAS) data and gene expression signatures from disease and drug perturbations ...
We showcase PS4DR with applications demonstrating how this tool can be used for repositioning and identifying new drugs as well as proposing drugs that can simulate disease dysregulations. ...
Programming language: R. Other Requirements: R 3.5.1. License: Apache License 2.0. Any restrictions to use by non-academics: None. ...
doi:10.1186/s12859-020-03568-5
pmid:32503412
fatcat:72oupapphzcntipdawrhkgyqgm
Linking brain structure, activity and cognitive function through computation
2022
eNeuro
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In 2013 the European Union launched the Human Brain Project (HBP) with the mission to integrate spatial and temporal scales of brain sciences within a common framework, ultimately leading to the digital ...
community of researchers united by the quest to understand the brain, with fascinating insights and perspectives for societal benefits.Significance statementTheoretical and methodological integration ...
Likewise, much work remains to be done to elucidate how the brain interacts with the natural and cultural environment, e.g., how epigenetic mechanisms act on the brain, how genotype-phenotype relationships ...
doi:10.1523/eneuro.0316-21.2022
pmid:35217544
pmcid:PMC8925650
fatcat:k7obyuqb5vcenossdwrlcbg4eu
Romano_columbia_0054D_15271.pdf
[article]
2019
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VenomSeq is a biotechnology workflow that is designed to generate new high-throughput sequencing data for incorporation into VenomKB. ...
To provide a platform for structuring, representing, retrieving, and integrating venom data relevant to drug discovery, VenomKB provides a database-backed web application and knowledge base for computational ...
VenomSeq is a biotechnology workflow that is designed to generate new high-throughput sequencing data for incorporation into VenomKB. ...
doi:10.7916/d8-spcd-yh22
fatcat:qj4yn44c6nd7jj3fegklasfrua