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microbialphenotypes / OMP-ontology

This repository contains the editors's working copy of OMP and public release files.
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Need a term for Benzene #166

Open kylliechang opened 8 years ago

kylliechang commented 8 years ago

I want to annotate a strain that is resistant to Benzalkonium, which is a child of Benzene

pbuttigieg commented 8 years ago

Quick question: are these classes imports from CHEBI?

dsiegele commented 8 years ago

We are trying to use CHEBI as a guide to organize phenotypes for sensitivity/resistance to antibiotics and chemicals. Instead of creating terms for every individual compound, we want to create terms for groups of compounds and then indicate the specific compound by putting the CHEBI ID in the annotation extension field.

For example see the annotation for E. coli strain BW25113 on OMPWiki: http://microbialphenotypes.org/wiki/index.php/OMP_ST:800_!_Escherichia_coli_K-12_BW25113

Jguzman210 commented 8 years ago

Is it Benzalkonium chloride?

kylliechang commented 8 years ago

No, it is just Benzalkonium.

On Jul 26, 2016 3:28 PM, "Jguzman210" notifications@github.com wrote:

Is it Benzalkonium chloride?

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dsiegele commented 8 years ago

I checked with Nassos Typas (one of the authors of the Nichols paper) and he said that they used benzalkonium chloride. He sent me a list of chemicals and vendors that were used for the conditions. I will add the document to the google docs.

dsiegele commented 8 years ago

Benzalkonium chloride (CHEBI:3020) will be a narrow synonym of organic aromatic compound resistance phenotype. See issue #165.

dsiegele commented 7 years ago

Made a group of terms based on CHEBI:35273 - quaternary ammonium salt. "Derivatives of ammonium compounds, (NH4+)Y−, in which all four of the hydrogens bonded to nitrogen have been replaced with univalent (usually organyl) groups."

OMP:0007481 quaternary ammonium salts resistance phenotype .....OMP:0007484 altered resistance to quaternary ammonium salts ..........OMP:0007486 decreased resistance to quaternary ammonium salts ...............OMP:0007487 abolished resistance to quaternary ammonium salts ..........OMP:0007485 increased resistance to quaternary ammonium salts .....OMP:0007483 not resistant to quaternary ammonium salts .....OMP:0007482 resistant to quaternary ammonium salts

Added benzalkonium resistance phenotype as a narrow synonym of OMP:00007481.

Note: some of the terms need definitions.