marcin p. joachimiak

Zenodo archive for rule mining paper https://zenodo.org/records/15106978 ZenodoZenodo [KG-Microbe-Core early release build 20241029](https://zenodo.org/records/15106978)] (https://berkeleybop.slack.com/archives/C032CTQSD8F/p1757721334969259) github releases https://github.com/Knowledge-Graph-Hub/kg-microbe/releases KG-Hub https://kg-hub.berkeleybop.io/kg-microbe/index.html KG-Registry https://kghub.org/kg-registry/resource/kg-microbe/kg-microbe.html

From OMP as a source https://www.ebi.ac.uk/ols4/ontologies/omp/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FOMP_0000001

currently 'human pathogen' is ingested from the keywords but there are cases of multi-pathogenicity (animal and human) that are not represented in keywords and just in 'risk assessment'. @sujaypatil96

https://pdfs.semanticscholar.org/21bd/0e4f28b745581dba67cc382ef570f56589e4.pdf?_gl=1*w9h60d*_gcl_au*MTkyMTk5NzUyLjE3NTcwMzkwNzg.*_ga*MTk5MjY5NjE0OS4xNzU3MDM5MDc4*_ga_H7P4ZT52H5*czE3NTcwMzkwNzgkbzEkZzAkdDE3NTcwMzk1NTEkajU5JGwwJGgw https://www.jmb.or.kr/journal/view.html?doi=10.4014/jmb.2311.11024

https://mediadb.systemsbiology.net/defined_media/

This means that there is something missing in the download step, likely specific API calls. Processing mediadive: medium:137: 4%|█████▊ | 142/3325 [07:01

new: https://raw.githubusercontent.com/bacteria-archaea-traits/bacteria-archaea-traits/refs/heads/master/output/condensed_traits_NCBI.csv

some of the transforms generate problematic URIs that then cause problems for KGX .nt conversion.

"unaccounted_compounds": [ "FeCl3 x 6 H2O", "NaHCO3", "NaH2PO4 x H2O", "NTA", "ZnCl2", "CoCl2 x 6 H2O", "Na2MoO4", "Na2WO4 x 2 H2O", "NiCl2 x 6 H2O", "H3BO3", "Thiamine", "Riboflavin", "Biotin", "Vitamin...