Pathogen-drug network

Question

[sagi.polani]

Hi,

I'm looking for an online pathogen-drug network, in which you can input a list of pathogens and retrieve a list of relevant drug treatments.

For example: Input a list of pathogens and retrieve a list of relevant antibacterial therapy.

Would appreciate any help on this matter.

Thanks

Answer 1

[Pratik]

Search google for "antibacterial drug database" you could change antibacterial with antimicrobial or other relevant terms. If you can find a database/tsv/csv file you could extract the information you need from it.

I think this is the best one I found for antivirals:

https://www.viprbrc.org/brc/antiviralDrug_search.spg?method=ShowCleanSearch&decorator=picorna_entero

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This one might give you some information:

http://patho.phenomebrowser.net/#/search

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Not sure if this would be helpful:

http://target.sbg.qb.fcen.uba.ar/patho/

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This what I wrote originally which could help you out:

I know this may not be exactly what you are looking for, but in case no one else has a good answer, here is one to help you get started maybe?

I use ctdbase.org (Comparative Toxicogenomics Database) for gene-pathway associations. However, they also have chemical-phenotype and chemical-disease that could be helpful to you.

For example if you go to the CTDbase.org Downloads You will find Chemical-disease associations and Chemical–phenotype interactions in .tsv and .csv format gzipped. These as well as maybe Chemical–GO enriched associations.

These could serve helpful for your purpose because if you search these in terminal using grep you may be able to find some useful information.

For example:

If you download the Chemical–phenotype interactions.tsv.gz file and extract it so you have the a file named CTD_pheno_term_ixns.tsv, you could use grep to just profile the database to see if theres anything you are looking for.

You could do something like:

grep Tetrodotoxin  /the/path/to/the/following/file/CTD_pheno_term_ixns.csv | grep Esch

which would search for Tetrodotoxin (an antibiotic) and also search for Esch (as in Escherichia coli) give the output:

cariporide,C093373,,reactive oxygen species metabolic process,GO:0072593,"lipopolysaccharide, Escherichia coli O111 B4^C440499^MESH|Tetrodotoxin^D013779^MESH",Mus musculus,10090,"[Tetrodotoxin co-treated with cariporide] inhibits the reaction [lipopolysaccharide, Escherichia coli O111 B4 results in increased reactive oxygen species metabolic process]",affects^cotreatment|decreases^reaction|increases^phenotype,"1^Microglia^D017628|2^Cell Line, Transformed^D002461",CAT^847^GENE,24070585,
cariporide,C093373,,reactive oxygen species metabolic process,GO:0072593,"lipopolysaccharide, Escherichia coli O111 B4^C440499^MESH|Tetrodotoxin^D013779^MESH",Mus musculus,10090,"[Tetrodotoxin co-treated with cariporide] inhibits the reaction [lipopolysaccharide, Escherichia coli O111 B4 results in increased reactive oxygen species metabolic process]",affects^cotreatment|decreases^reaction|increases^phenotype,"1^Microglia^D017628|2^Cells, Cultured^D002478",CAT^847^GENE,24070585,
"lipopolysaccharide, Escherichia coli O111 B4",C440499,,reactive oxygen species metabolic process,GO:0072593,cariporide^C093373^MESH|Tetrodotoxin^D013779^MESH,Mus musculus,10090,"[Tetrodotoxin co-treated with cariporide] inhibits the reaction [lipopolysaccharide, Escherichia coli O111 B4 results in increased reactive oxygen species metabolic process]",affects^cotreatment|decreases^reaction|increases^phenotype,"1^Microglia^D017628|2^Cell Line, Transformed^D002461",BCL2^596^GENE|CAT^847^GENE|P2RX7^5027^GENE|SOD1^6647^GENE|SOD2^6648^GENE,24070585,
"lipopolysaccharide, Escherichia coli O111 B4",C440499,,reactive oxygen species metabolic process,GO:0072593,cariporide^C093373^MESH|Tetrodotoxin^D013779^MESH,Mus musculus,10090,"[Tetrodotoxin co-treated with cariporide] inhibits the reaction [lipopolysaccharide, Escherichia coli O111 B4 results in increased reactive oxygen species metabolic process]",affects^cotreatment|decreases^reaction|increases^phenotype,"1^Microglia^D017628|2^Cells, Cultured^D002478",BCL2^596^GENE|CAT^847^GENE|P2RX7^5027^GENE|SOD1^6647^GENE|SOD2^6648^GENE,24070585,
"lipopolysaccharide, Escherichia coli O111 B4",C440499,,reactive oxygen species metabolic process,GO:0072593,Tetrodotoxin^D013779^MESH,Mus musculus,10090,"Tetrodotoxin inhibits the reaction [lipopolysaccharide, Escherichia coli O111 B4 results in increased reactive oxygen species metabolic process]",decreases^reaction|increases^phenotype,"1^Microglia^D017628|2^Cell Line, Transformed^D002461",BCL2^596^GENE|CAT^847^GENE|P2RX7^5027^GENE|SOD1^6647^GENE|SOD2^6648^GENE,24070585,
"lipopolysaccharide, Escherichia coli O111 B4",C440499,,reactive oxygen species metabolic process,GO:0072593,Tetrodotoxin^D013779^MESH,Mus musculus,10090,"Tetrodotoxin inhibits the reaction [lipopolysaccharide, Escherichia coli O111 B4 results in increased reactive oxygen species metabolic process]",decreases^reaction|increases^phenotype,"1^Microglia^D017628|2^Cells, Cultured^D002478",BCL2^596^GENE|CAT^847^GENE|P2RX7^5027^GENE|SOD1^6647^GENE|SOD2^6648^GENE,24070585,
"lipopolysaccharide, Escherichia coli O111 B4",C440499,,sodium ion import across plasma membrane,GO:0098719,Tetrodotoxin^D013779^MESH,Mus musculus,10090,"Tetrodotoxin affects the reaction [lipopolysaccharide, Escherichia coli O111 B4 results in increased sodium ion import across plasma membrane]",affects^reaction|increases^phenotype,"1^Microglia^D017628|2^Cell Line, Transformed^D002461",HCN2^610^GENE|SLC9A1^6548^GENE,24070585,
"lipopolysaccharide, Escherichia coli O111 B4",C440499,,sodium ion import across plasma membrane,GO:0098719,Tetrodotoxin^D013779^MESH,Mus musculus,10090,"Tetrodotoxin affects the reaction [lipopolysaccharide, Escherichia coli O111 B4 results in increased sodium ion import across plasma membrane]",affects^reaction|increases^phenotype,"1^Microglia^D017628|2^Cells, Cultured^D002478",HCN2^610^GENE|SLC9A1^6548^GENE,24070585,
Tetrodotoxin,D013779,4368-28-9,reactive oxygen species metabolic process,GO:0072593,"cariporide^C093373^MESH|lipopolysaccharide, Escherichia coli O111 B4^C440499^MESH",Mus musculus,10090,"[Tetrodotoxin co-treated with cariporide] inhibits the reaction [lipopolysaccharide, Escherichia coli O111 B4 results in increased reactive oxygen species metabolic process]",affects^cotreatment|decreases^reaction|increases^phenotype,"1^Microglia^D017628|2^Cell Line, Transformed^D002461",,24070585,
Tetrodotoxin,D013779,4368-28-9,reactive oxygen species metabolic process,GO:0072593,"cariporide^C093373^MESH|lipopolysaccharide, Escherichia coli O111 B4^C440499^MESH",Mus musculus,10090,"[Tetrodotoxin co-treated with cariporide] inhibits the reaction [lipopolysaccharide, Escherichia coli O111 B4 results in increased reactive oxygen species metabolic process]",affects^cotreatment|decreases^reaction|increases^phenotype,"1^Microglia^D017628|2^Cells, Cultured^D002478",,24070585,
Tetrodotoxin,D013779,4368-28-9,reactive oxygen species metabolic process,GO:0072593,"lipopolysaccharide, Escherichia coli O111 B4^C440499^MESH",Mus musculus,10090,"Tetrodotoxin inhibits the reaction [lipopolysaccharide, Escherichia coli O111 B4 results in increased reactive oxygen species metabolic process]",decreases^reaction|increases^phenotype,"1^Microglia^D017628|2^Cell Line, Transformed^D002461",,24070585,
Tetrodotoxin,D013779,4368-28-9,reactive oxygen species metabolic process,GO:0072593,"lipopolysaccharide, Escherichia coli O111 B4^C440499^MESH",Mus musculus,10090,"Tetrodotoxin inhibits the reaction [lipopolysaccharide, Escherichia coli O111 B4 results in increased reactive oxygen species metabolic process]",decreases^reaction|increases^phenotype,"1^Microglia^D017628|2^Cells, Cultured^D002478",,24070585,
Tetrodotoxin,D013779,4368-28-9,sodium ion import across plasma membrane,GO:0098719,"lipopolysaccharide, Escherichia coli O111 B4^C440499^MESH",Mus musculus,10090,"Tetrodotoxin affects the reaction [lipopolysaccharide, Escherichia coli O111 B4 results in increased sodium ion import across plasma membrane]",affects^reaction|increases^phenotype,"1^Microglia^D017628|2^Cell Line, Transformed^D002461",SCN5A^6331^GENE|SLC9A1^6548^GENE,24070585,
Tetrodotoxin,D013779,4368-28-9,sodium ion import across plasma membrane,GO:0098719,"lipopolysaccharide, Escherichia coli O111 B4^C440499^MESH",Mus musculus,10090,"Tetrodotoxin affects the reaction [lipopolysaccharide, Escherichia coli O111 B4 results in increased sodium ion import across plasma membrane]",affects^reaction|increases^phenotype,"1^Microglia^D017628|2^Cells, Cultured^D002478",SCN5A^6331^GENE|SLC9A1^6548^GENE,24070585,
pratik@Pratiks-Air ~ % 

Good luck!

[sagi.polani]

Thanks Pratik!

I'll look into it and update you accordingly.