Biology subjects

Karis, K.

Publications and source records attributed to Karis, K..

2 recordsLinked to original sources

bioRxiv2022

NDEx IQuery: a multi-method network gene set analysis leveraging the Network Data Exchange

MotivationThe investigation of sets of genes using biological pathways is a common task for researchers and is supported by a wide variety of software tools. This type of analysis generates hypotheses about the biological processes active or modulated in a specific experimental context. ResultsThe NDEx Integrated Query (IQuery) is a new tool for network and pathway-based gene set interpretation that complements or extends existing resources. It combines novel sources of pathways, integration with Cytoscape, and the ability to store and share analysis results. The IQuery web application performs multiple gene set analyses based on diverse pathways and networks stored in NDEx. These include curated pathways from WikiPathways and SIGNOR, published pathway figures from the last 27 years, machine-assembled networks using the INDRA system, and the new NCI-PID v2.0, an updated version of the popular NCI Pathway Interaction Database. IQuerys integration with MSigDB and cBioPortal now provides pathway analysis in the context of these two resources. Availability and ImplementationIQuery is available at https://www.ndexbio.org/iquery and is implemented in Javascript and Java. ContactDexter Pratt (depratt@health.ucsd.edu)

bioinformatics↗

bioRxiv2022

The Bioregistry: Unifying the Identification of Biomedical Entities through an Integrative, Open, Community-driven Metaregistry

The standardized identification of biomedical entities is a cornerstone of interoperability, reuse, and data integration in the life sciences. Several registries have been developed to catalog resources maintaining identifiers for biomedical entities such as small molecules, proteins, cell lines, and clinical trials. However, existing registries have struggled to provide sufficient coverage and metadata standards that meet the evolving needs of modern life sciences researchers. Here, we introduce the Bioregistry, an integrative, open, community-driven metaregistry that synthesizes and substantially expands upon 23 existing registries. The Bioregistry addresses the need for a sustainable registry by leveraging public infrastructure and automation, and employing a progressive governance model centered around open code and open data to foster community contribution. The Bioregistry can be used to support the standardized annotation of data, models, ontologies, and scientific literature, thereby promoting their interoperability and reuse. The Bioregistry can be accessed through https://bioregistry.io and its source code and data are available under the MIT and CC0 Licenses at https://github.com/biopragmatics/bioregistry.

bioinformatics↗