marcin p. joachimiak

A number of useful downloads https://www.tcdb.org/download.php

link Bacdive isolation source categories to each other to represent hierarchy

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"Cat1": "#Environmental", "Cat2": "#Aquatic", "Cat3": "#Mangrove NCBITaxon|Strain -> location_of -> Cat3/Cat2/Cat1 -> subclass_of -> Cat2 -> Cat1

This is somewhat complex in that there is a wide variety of terms with different specificities. Some look like titles of a study and will fail NER. Our first pass...

Publication: https://www.mdpi.com/2076-2607/10/2/293 Looks like entity extraction/annotations: tagger dictionary is the basis of knowledge of taxa, environments, processes and molecular functions that the tagger extracts. Available at: https://download.jensenlab.org/prego_dictionary.tar.gz, CC-BY license Dictionaries...

https://microbeatlas.org/index.html?action=taxon&taxon_id=90_107;96_2813;97_3454;98_5165;99_7030&stattab=map https://microbeatlas.org/index.html?action=download

https://genomes.atcc.org/genomes/130252a15510442f?tab=overview-tab https://genomes.atcc.org/genomes Name Isolation Tag Biosafety

https://europepmc.org/article/PPR/PPR28618

https://www.nature.com/articles/s41587-023-01872-y https://bugsigdb.org/Main_Page

ingest the EC hierarchy

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A bare minimum would be to ingest this file: https://ftp.expasy.org/databases/enzyme/enzclass.txt This has more useful info including a synonymous enzyme names, description, and reaction strings (but without chemical or reaction ids):...