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ChIPSeq Template Created #543
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is_a: EpigenomicsAssayTemplate | ||
description: Template for describing raw data from ChIP-Seq assays, typically used to identify DNA-protein interactions. | ||
slots: | ||
- antibodyID |
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You can add a more specific ChIPseqAntibodyName
property with the NCIT meaning as suggested and use it here. We can either keep it free text or import a list of ChIPseq antibody names, but I'd prefer people use the antibodyID
as the preferred field anyway -- you can make antibodyID
required. For additional context, it looks like HTAN just uses single free text antibodyName
primarily https://github.com/ncihtan/data-models/blob/4b9bb3cfcbb979694479a4a60b7dac71becfbf96/HTAN.model.csv#L226
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Is the antibodyID already in free text form?
https://github.com/nf-osi/nf-metadata-dictionary/blob/main/modules/props.yaml#L73-L75
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Yes
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If we make this antibodyID
slot required, would this also effect other templates that might been using the slot?
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Yes, because the feature to set contextual required is not implemented in schematic yet. In this case, I think it's OK to make it required across all templates that use it -- you would only add antibodyID to the template if you really needed it anyway.
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Update props.yaml
Test Suite Report 24.7.2Template Generation
Manifest Validation
Manifest Submission
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added peakCallingAlgorithms for ChIP-Seq
removed the comment for peakcallingalgorithm
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LGTM
is_a: EpigenomicsAssayTemplate | ||
description: Template for describing raw data from ChIP-Seq assays, typically used to identify DNA-protein interactions. | ||
slots: | ||
- antibodyID |
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Choose a reason for hiding this comment
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If we make this antibodyID
slot required, would this also effect other templates that might been using the slot?
@changtotheintothemoon Once this template is considered "production-ready", to surface this in the app, you should add the template id and display name to the list here: https://github.com/nf-osi/nf-metadata-dictionary/blob/main/dca-template-config.json |
added ChIP-SeqTemplate to the DCA App
@changtotheintothemoon Thanks! I think you're all done except one small issue. So in this review I discovered we have a typo for "EpigenomiscAssayTemplate" 😅 in the existing classes (#550), which is why inheritance is not working in the rendered preview link the tests above -- your version is correct. If you fix it, everything should be good for a 2-for-1 deal! (Please update dca-template-config again as well to reference the corrected class ids) |
replaced "EpigenomiscAssayTemplate" to "EpigenomicsAssayTemplate"
Hi @allaway @anngvu
I created a new initial branch for adding a new template for the ChIP-Seq assay:
Related Issue: #532
Please review the template and let me know if there are additional sections that need to be added.
@allaway mentioned creating a new section for the antibody in
modules/Sample/SpecimenProcessing.yaml
. I have not modified this yet.He suggested using the OLS/NCIT definition for the ChIP-Seq Antibody Name: NCIT_C177613
@anngvu, what are your suggestions regarding adding the antibody to the template?
Thanks,
James