marcin p. joachimiak
marcin p. joachimiak
A curated resource of information about 80,000 microbes. This includes viruses which we can deprioritize for now. The source data tables from The Microbe Directory can be build using 'make'...
The data used for figure 3 is publicly available and the source is listed in the figure legend. It was taken from Table S3 and S5 from Oh et al....
General info here: http://www.webofmicrobes.org/about Download SQLite via 'download' button. This is the primary relevant data: "The Web", links the actions of microorganisms on metabolites from within a single environment." And...
These are the two main public resources with this data: https://www.frontiersin.org/articles/10.3389/fcimb.2018.00424/full https://academic.oup.com/nar/article/49/D1/D776/5943835
"Towards the biogeography of prokaryotic genes" https://www.nature.com/articles/s41586-021-04233-4 Downloads here: https://gmgc.embl.de/download.cgi More info soon ...
The gutMEGA resource provides a few useful files for KG-Microbe. http://gutmega.omicsbio.info/download.php The first set of ingests cover different microbial taxonomy resources, including NCBITaxonomy which is already present in KG-Microbe. Looking...
The data is from this paper: Exploring the functional composition of the human microbiome using a hand-curated microbial trait database https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-021-04216-2 The dataset itself is Additional File 1: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-021-04216-2#MOESM1 To...
https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0272473
Here are the edge file headers for current transforms: @bsantan ==> BacDive/edges.tsv BactoTraits/edges.tsv MediaDive/edges.tsv ontologies/chebi_edges.tsv ontologies/ec_edges.tsv ontologies/envo_edges.tsv ontologies/go_edges.tsv ontologies/ncbitaxon_edges.tsv ontologies/upa_edges.tsv RheaMappings/edges.tsv traits/edges.tsv uniprot_genome_features/edges.tsv uniprot_genome_features/uniprot_bacdive_edges.tsv