dsiegele
commented
8 years ago Hi Diane,
The way that OMP deals with chemical compounds has been to create phenotype types for structural groups of compounds and then put a CHEBI for a specific member of that group into the phenotype extension field.
For example, if you look at OMP:0000274_!_antimicrobial_agent_resistancephenotype (http://microbialphenotypes.org/wiki/index.php/Category:OMP:0000274!_antimicrobial_agent_resistance_phenotype), there are currently 13 child terms for different groups of antimicrobial agents.
One of the child terms is OMP:0006028 ! azole resistance phenotype, which has children: OMP:0006055 ! resistant to azole OMP:0006054 ! not resistant to azole OMP:0006019 ! altered azole resistance .....OMP:0006052 ! decreased resistance to azole .....OMP:0006053 ! increased resistance to azole
If you have mutants with increased resistance to fluconazole, they would be annotated with OMP:0006053 and you'd put 'CHEBI:46081 fluconazole' in the phenotype extension field. We are adding the names of the specific compounds as narrow synonyms of the parent term.
In most cases, we defined the structural groups based on the structure of CHEBI. You can send us a list of the compounds and their CHEBI ID's. f you also want to send possible groupings that would be helpful, too. Once the parent group is defined, we add the names of specific members of the group as narrow synonyms.
The same approach would be used for accumulation of xxx phenotypes.
Let me know if you have questions.
Regards,
Debby
Hello Debbie, Jesus, all,
I am working with Achchuthan Shanmugasundram, a new curator with Eupath. He will be working through some remaining. Our question that we have many, many "resistance to x" and "x accumulation" terms. I started Achchuthan on obtaining the ChEBI IDs for all the chemicals/compounds.
The question is shall all of the x=chemical/compounds be entered as OMP entities prior to the creation of the "resistance to x" terms or "sensitivity to x" as you prefer for consistency? Is there a preferred way you wish to receive the list of compounds. My preference is to create "increased, decreased and abolished" terms from the start, to never have to go back and add. If that is ok with your group.
His email A.Shanmugasundram2@liverpool.ac.uk
I will suggest that he sign up to receive the responses to these tickets.
Thank you,
Diane
Diane