bcorrie
commented
1 month ago I should note that a few weeks ago I added the above to the Consolidated Mapping sheet. With the YAML files I have generated this should be pretty easy to add, no?
Open bcorrie opened 1 month ago
bcorrie
commented
1 month ago I should note that a few weeks ago I added the above to the Consolidated Mapping sheet. With the YAML files I have generated this should be pretty easy to add, no?
The AIRR Standard has a very rich set of metadata about how samples are processed for sequencing, including sample processing, cell processing, nucleic acid processing, and sequence data processing.
In the AKC we currently have the following objects that are related to this:
Dataset- maybe a representation of the final set of annotated sequencesAssay- I think this might fit in in the spectrum somewhere, but its current definition is very narrow. It essentially has a single value, clearly designed to measure an Assay for reactivity/specificity between a receptor and antigen/epitope. As it is I don't think it makes sense for BCR/TCR sequencing???PlannedProcess- an abstract class that seems to capture the AIRR concepts aboveSpecimenCollection- a subclass ofPlannedProcessthat describes how specimens are collected, but currently it doesn't have any process slots that describe how the specimen was collected, it only has a pointer to a specimen.In my conversion of ADC data to AKC, there is nothing in the AKC data model for me to map the 40 odd ADC fields from the above objects.
The simple and straightforward approach would be to create the following AKC LinkML classes:
CellProcessing- subclass ofPlannedProcesswith all of the fields in the AIRR CellProcessing object: https://github.com/airr-knowledge/ak-schema/blob/airr-export/src/ak_schema/schema/airr/ak_slot_CellProcessing.yamlNucleicAcidProcessing- subclass ofPlannedProcesswith all of the fields in the AIRR NucleicAcidProcessing object: https://github.com/airr-knowledge/ak-schema/blob/airr-export/src/ak_schema/schema/airr/ak_slot_NucleicAcidProcessing.yamlSequencingRun- subclass ofPlannedProcesswith all of the fields in the AIRR SequencingRun object: https://github.com/airr-knowledge/ak-schema/blob/airr-export/src/ak_schema/schema/airr/ak_slot_SequencingRun.yamlSequencingData- subclass ofPlannedProcesswith all of the fields in the AIRR SequencingData object: https://github.com/airr-knowledge/ak-schema/blob/airr-export/src/ak_schema/schema/airr/ak_slot_SequencingData.yamlDataProcessing- subclass ofPlannedProcesswith all of the fields in the AIRR DataProcessing object: https://github.com/airr-knowledge/ak-schema/blob/airr-export/src/ak_schema/schema/airr/ak_slot_DataProcessing.yamlA
DataSetin the AKC currently consists of a list ofassessmentsorassaysas a slots. If we added aprocessesslot, we could then use the AKC represent an ADCDataSetthat has had a set ofprocessesapplied (as above).This still leaves me not really understanding how
Assayfits into describing and ADC data set.@schristley thoughts? This would result in us having a mapping of a significant percentage of the ADC fields in the AKC. The relationships between the classes still needs to be resolved, but at least all of the data would be mapped.
I suppose the main question is, do we want/need all of the ADC
Repertoirefields mapped to the AKC?If we do create the above LinkML classes, then field -> field translation of the ADC to AKC is probably 80% - 90% complete. What would remain is the transformation of any fields that don't have a direct mapping.