There are two main methods of loading data for Xenbase and Echinobase: one is bulk loads through scripts, that read the data from remote sites or local files (e.g. GFF3) and save them in the database following various quality checks; the other method is adding data through the curation interface. Echinobase, like Xenbase, has been using these scripts to consume data from sites such as NCBI (Entrez), UniProt, Disease Ontology, the GO consortium and others. The various data curation interfaces have also been activated for Echinobase, and manual data entry initiated for features such as publications and experimental reagents (e.g. antisense-morpholino-oligonucleotide sequences, antibodies and guide RNA sequences).
The new expanded JBrowse resource contains a large amount of novel content, including all echinoderm genomes currently annotated by the NCBI data processing systems. This includes genome sequence and gene/CDS and protein sequences from two sea urchin species; S. purpuratus and Lytechinus variegatus, three sea stars Acanthaster planci, Patiria miniata and Asterias rubens and a feather star, Anneissia japonica. Where previous genome builds were available in the legacy resource, we have generated liftover tracks so users can compare the old gene models to the new versions. Various additional datasets have also been mapped to the new genome builds such as various RNA-seq and ATAC-seq data and enhancer RNAs (eRNAs). We also map NCBI gene model names to genomes so users have useful gene identifiers within the browser. Some genomes also have in-house generated transcription factor binding sites, created using Xenbase protocols. Echinobase plans to support most new echinoderm genomes with both genome browser and BLAST support. Full support, where gene models are integrated into the database and linked to genes in other echinoderms on Gene Pages, will be provided for species that are widely used in developmental biology or systems biology- the core focus of the Echinobase resource. Currently these are three species; S. purpuratus (both genome version 3 and version 5), Acanthaster planci and Patiria miniata. We include additional genomes either into BLAST and JBrowse functions or as fully integrated datasets through consultation with the echinoderm researchers.
The new expanded JBrowse resource contains a large amount of novel content, including all echinoderm genomes currently annotated by the NCBI data processing systems. This includes genome sequence and gene/CDS and protein sequences from two sea urchin species; S. purpuratus and Lytechinus variegatus, three sea stars Acanthaster planci, Patiria miniata and Asterias rubens and a feather star, Anneissia japonica. Where previous genome builds were available in the legacy resource, we have generated liftover tracks so users can compare the old gene models to the new versions. Various additional datasets have also been mapped to the new genome builds such as various RNA-seq and ATAC-seq data and enhancer RNAs (eRNAs). We also map NCBI gene model names to genomes so users have useful gene identifiers within the browser. Some genomes also have in-house generated transcription factor binding sites, created using Xenbase protocols. Echinobase plans to support most new echinoderm genomes with both genome browser and BLAST support. Full support, where gene models are integrated into the database and linked to genes in other echinoderms on Gene Pages, will be provided for species that are widely used in developmental biology or systems biology- the core focus of the Echinobase resource. Currently these are three species; S. purpuratus (both genome version 3 and version 5), Acanthaster planci and Patiria miniata. We include additional genomes either into BLAST and JBrowse functions or as fully integrated datasets through consultation with the echinoderm researchers.
