marcin p. joachimiak

Unfortunately the RIKEN media data seems to have some bad license: https://www.jcm.riken.jp/cgi-bin/jcm/jcm_grmd?GRMD=422 Copyright © 2023 Microbe Division (JCM) - All Rights Reserved https://jcm.brc.riken.jp/en/

Provides three additional properties for 3637 DSMZ media: Is Complex | Is Aerobic | Is SubMedium For a subset of DSMZ, here: https://komodo.modelseed.org/servlet/KomodoTomcatServerSideUtilitiesModelSeed?MediaList https://docs.google.com/spreadsheets/d/19q0re9z7ngOs1cKF9q-GWJRDXZmsoOMwktctBrNW0PY/edit#gid=0 Paper: https://www.nature.com/articles/ncomms9493 https://komodo.modelseed.org

https://conductscience.com/culture-media/ https://microbenotes.com/types-of-culture-media/#application-of-culture-media

1. ATCC (American Type Culture Collection) [ATCC Culture Guides](https://www.atcc.org/en/Support/Culture_Guides.aspx) ATCC offers a wide array of resources, including guidelines and recommendations for microbial culture media and their preparations. 2. DSMZ (German...

https://genomes.atcc.org/genomes https://genomes.atcc.org/genomes/bacteriology

https://github.com/cruizperez/MicrobeAnnotator

PREGO is a text-mined resource for information about microbes linked with additional information. Paper: https://www.mdpi.com/2076-2607/10/2/293/htm#app5-microorganisms-10-00293 Data sources for the PREGO association network are here: https://www.mdpi.com/2076-2607/10/2/293/htm#table_body_display_microorganisms-10-00293-t0A2

ingest gene knockout data from LBL microbial fitness experiments

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All of the data is here (84G total): http://genomics.lbl.gov/supplemental/bigfit/ The numerical relative growth data would have to be converted - growth vs no growth, via eg thresholding. Just taking the...

Ingest Disbiome microbiome data

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Disbiome database is a collection of microbiome compositional effects related to human disease https://disbiome.ugent.be/home Here is an example record for a disbiome entry: https://disbiome.ugent.be/experimentdetail/11342 The pertitent pieces of info for...

The core repo nodes header is: id category name description xref provided_by synonym deprecated iri object predicate relati on same_as subject subsets The merge repo header is similar but most...