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[bioontology-support] BAO New Term Requests
jgraybeal at stanford.edu
Thu Apr 22 12:28:17 PDT 2021
Thanks for asking! You are using our Ontolobridge connection, currently configured for just a few of the BioPortal ontologies. These requests are processed through backend services that connect to the individual managers of each ontology.
In this case, the backend services for this ontology are supported by members of the BioAssay team, John Turner and Samantha Jeschonek. They are copied in this message.
For everyone else, if you want term requests for your ontology to be managed through Ontolobridge, please contact Samantha about getting it added. Thanks!
On Apr 16, 2021, at 3:43 PM, Benjamin Chittick <Benjamin_Chittick at vrtx.com<mailto:Benjamin_Chittick at vrtx.com>> wrote:
I have some new endpoints (pasted below) for the BioAssay ontology that I would like to request. Before I request these new terms I was wondering
1. How long will it take for the term to be accepted/rejected? If accepted how long until it would be added to the ontology?
2. What is the mechanism for reviewing new terms?
* Are there any changes that I could make below to help their submission?
Preferred Name: Emax
Definitions: Maximum induction effect (dimensionless)
subClassOf: graphical calculation endpoint
Justification: Emax is a common assay endpoint for CYP induction. It is not currently in the ontology.
Preffered Name: molar attenuation coefficient
Definitions: This is a measurement of how strongly a chemical species attenuates light at a given wavelength. Common units are L/(mol*cm).
subClassOf: physical property endpoint
Justification: this is a molecular property that is evaluated experimentally. Having a property like LogD in the ontology argues for other molecular property endpoints to be added.
Preffered Name: max fold increase
Definitions: The maximum observed fold increase.
subClassOf: fold change
Justification: If the percent response endpoints include a maximal effect (presumably max % activity) then there should be a maximal endpoint for other readouts like fold change.
Preffered Name: categorical endpoint
Justification: This is a generalization of the binary endpoint. The binary endpoint could move to be a subClassOf categorical endpoint.
Preffered Name: fraction unbound
Definitions: The fraction of compound that does not bind to plasma proteins.
subClassOf: physical property endpoint
Justification: It is common in medicinal chemistry to monitor the amount of compound that binds to plasma proteins. Used in calculating clearance.
Preffered Name: cell count
Definitions: cell count
subClassOf: quantified endpoint
Justification: If calculation endpoints like percent ### cells are in the ontology, the higher level readout of cell count should also be included.
Preffered Name: ratio
Justification: This endpoint would be the parent node for endpoints like blood to plasma ratio and AC50 ratio.
Preffered Name: blood to plasma ratio
Definitions: The ratio of the concentration of molecule in whole blood (i.e. contains both red blood cells and plasma) to the concentration of molecule in plasma, namely CB/CP.
Justification: The ontology has a blood to plasma ratio assay, but no matching endpoint.
Preffered Name: AC50 ratio
Definitions: Ratio of AC50 values
Justification: This is the endpoint several assays, for example a time dependent CYP inhibition reads out the ratio of the IC50s with and without NADPH.
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Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
Stanford Center for Biomedical Informatics Research
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