BRC Genome Prioritization

[nekrut]

Taxa prioritization

For all genomes listed in VEuPathDb, NCBI Viruses and https://www.niaid.nih.gov/research/niaid-biodefense-pathogens generate a table (row per taxon) that summarized genome assembly quality, number of SRA entries, number of publications, and publication dynamics over time.

Tool prioritization

Given a corpus of publications from above use a ChapGPT-like approach to get a summary which software tools are used for data analysis, how current these tools are, how many papers do they have.

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[maximilianh]

For all NCBI genomes: this directory has a file gene2pubmed which gives PMIDs for every NCBI gene. gene_info.gz has gene -> taxonId. By joining them, one can create taxonId -> count of PMIDs. This should give a very simple way to prioritize taxons. And genes, if gene prioritization is needed. https://ftp.ncbi.nlm.nih.gov/gene/DATA/

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[nekrut]

For now we will be using https://docs.google.com/spreadsheets/d/1Gg9sw2Qw765tOx2To53XkTAn-RAMiBtqYrfItlLXXrc/edit?usp=sharing

[nekrut]

Some links from Michelle: https://docs.google.com/spreadsheets/d/1BSpv4EMUxb7JZyB51xMkGrFQ5SEnQKvTrml2y1F9T6s/edit?usp=sharing