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Sage-Bionetworks / synapseAnnotations

Sage Bionetworks derived standards for annotating content in Synapse.
MIT License
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SOP for annotating cell lines by individualId and sampleId #233

Closed sgosline closed 4 years ago

sgosline commented 6 years ago

It will be helpful if we have a standard convention for annotating cell line data. For example - are cell lines individuals? or samples? We have some cell lines that are derived from the same patient but that's not necessarily the status quo.

I'd like to establish a convention so we can stick to it.

kdaily commented 6 years ago

In PCBC and OHSU-LINCS we had standalone annotations for cell line. Important to note OHSU-LINCS annotates in their own asset tracking database down to the aliquot (including growth conditions), but that is not propagated to Synapse.

I feel it's important to put into context of data use - if patient info is important, then cell line may have to go to sampleId.

sgosline commented 6 years ago

There is also a cellLine annotation for the PSON cell line repository. It's worth discussing adding it to the set, but what do we do for sampleId and patientId for cell line data?

sgosline commented 6 years ago

Decision is to create new terms "cellLine" and "cellLineSource" to experimentalData.json.