marcin p. joachimiak

Regarding BacDive-to-media edges, a total of 32513 edges for NCBITaxon -> medium are ingested from BacDive. However, there are 1609 unmatched BacDive taxa (vs NCBITaxon). In addition there are 257...

https://www.uniprot.org/help/downloads

http://protraits.irb.hr

https://bacdive.dsmz.de/api-test-finder

http://dbbact.org/main REST API http://api.dbbact.org/docs

ProGenomes3 has over 900k annotated prokaryotic genomes. The download provides: - contigs - genes - proteins - habitats - marker genes - https://progenomes.embl.de/download.cgi

BacDive stats: https://bacdive.dsmz.de/dashboard CSV download: https://bacdive.dsmz.de/isolation-sources/csv?filter-domain=&filter-phylum=&filter-class=&filter-ordo=&filter-family=&filter-genus=&iso_3_country=&polygon-strain-ids=&sort_by_order=ASC&sort_by=st.species&pfc=&csv=1

Download full csv across ~1200 taxa here (CSV button): https://services.bromberglab.org/fusiondb/explore

Most likely this will involve running this tool on select genomes/MAGs/metagenomes and then modeling the source data and inferences and knowledge. https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-021-01213-8 https://github.com/AnantharamanLab/METABOLIC

19 traits for 19,455 bacterial strains https://www.sciencedirect.com/science/article/pii/S1470160X21007123 Possible complete download here: https://www.sciencedirect.com/science/article/pii/S1470160X21007123 Website: https://bacdive.dsmz.de/ No direct download on website, there is an API: https://api.bacdive.dsmz.de