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Task (Assay) code, categories #2

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bwalsh opened this issue Mar 19, 2023 · 4 comments
Open

Task (Assay) code, categories #2

bwalsh opened this issue Mar 19, 2023 · 4 comments

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@bwalsh
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bwalsh commented Mar 19, 2023

As an ACED user, in order to identify assay type, I need Task's category and code set to the correct ontology values.
@bwalsh
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bwalsh commented Mar 20, 2023

We have the same issue on MCF10, see slack conversation from. https://ohsucomputationalbio.slack.com/archives/C043HPV0VMY/p1675450583003219?thread_ts=1675379318.084749&cid=C043HPV0VMY

@bwalsh bwalsh mentioned this issue Mar 20, 2023
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@jordan2lee
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I would suggest that we place
“ATACSeq”
“Cyclic Immunoflourescence”
“Global Chromatin Profiling”
“Immunofluorescence”
“L1000”
“Reverse Phase Protein Array”
“immunofluorescence”
“live cell imaging”
“rnaSeq”
into Assay bioassay component > bioassay specification/experimental specification > assay description. The distinction between bioassay specification and experimental specification seems blurred and overlapping, so either should work, but i would say experimental specification is better fit longterm when we introduce different datasets into the system
https://www.ebi.ac.uk/ols/ontologies/bao

@bwalsh
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bwalsh commented Mar 28, 2023

@jordan2lee We can place the particular string the study uses in description as you suggest above

However, we still need to normalize these strings into a specific system, code combination that we will use across studies.

study-string system code text
ATACSeq http://www.bioassayontology.org/bao BAO_0010038 ATAC-seq epigenetic profiling assay
Cyclic Immunoflourescence ? ? ?
etc... ? ? ?

These codings will be used in https://hl7.org/fhir/r4b/task.html and https://hl7.org/fhir/r4b/observation.html code

@jordan2lee
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“Cyclic Immunoflourescence”

“Global Chromatin Profiling”

“Immunofluorescence”

“L1000”

“Reverse Phase Protein Array”

“immunofluorescence”

“live cell imaging”

“rnaSeq”

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@bwalsh @jordan2lee