Xenbase - Curation

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Component: CURATION PROJECT SUMMARY/ABSTRACT Xenbase’s mandate is to curate the data from Xenopus research and generate the definitive reference dataset for this key model organism. In order to fulfill this mandate, the data in Xenbase must be accurately annotated, comprehensive, and up-to-date. Xenbase contains many different data types (genomes and genes, orthology, RNA, proteins, genomic data (RNA/ChIP-seq), gene expression, gene function, anatomy, reagents (MOs and antibodies), mutant and transgenic lines, phenotypes and disease associations) that data come from published literature, direct community submissions and from other. We curate, annotate and index data types using ontologies (i.e., standardized vocabularies), which make the data computer readable and FAIR compliant. This allows us to inter-relate different data types within Xenbase and to link Xenopus data to humans and other model organisms. Our literature module contains >52,000 Xenopus research papers. We have curated ~4,800 of these primarily for gene expression patterns, transgenic lines and reagents, yet we estimate that about 10,000 additional papers contain valuable data, including phenotypes and GO, two of our main curation priorities in this renewal. Another major goal is to curate the metadata associated with Xenopus RNA-seq and ChIP-seq datasets in the NCBI Gene Expression Omnibus (GEO) so that we can process the data and make it available on Xenbase. Our plan to support single cell transcriptomics will be a third major curation effort in this renewal. In order to manage this volume of new data, our curation workflow implements several innovative semi-automated pipelines, texting mining and machine learning. Our curation goals are to stay current with new publications, clear the backlog of to-be-curated papers (giving priority to those with phenotypes/models of human disease), and add additional data types, including diverse omic data sets. Aim 1. Continue curation of Xenopus research data. Aim 2. Curate Xenopus phenotypes and human disease models. Aim 3. Curate new omics and cell biological data.