Add README metadata for PiLPC and PAPC datasets by AvNeEsH71-iam · Pull Request #374 · NMRLipids/BilayerData

AvNeEsH71-iam · 2026-03-24T12:16:33Z

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Copilot

Pull request overview

This PR updates/introduces README.yaml metadata for two OrderParameters experiment datasets (PAPC and PiLPC) under their respective DOI directories.

Changes:

Replaced the existing README metadata for 10.1039/c2cp42738a/1 with a new, expanded metadata schema.
Added a new README metadata file for 10.1021/bi3009399/1 using the same schema.

Reviewed changes

Copilot reviewed 2 out of 2 changed files in this pull request and generated 6 comments.

File	Description
experiments/OrderParameters/10.1039/c2cp42738a/1/README.yaml	Rewrites README metadata (composition/conditions/NMR details) for run `1`.
experiments/OrderParameters/10.1021/bi3009399/1/README.yaml	Adds new README metadata for the PiLPC dataset/run `1`.

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Copilot · 2026-03-24T12:21:24Z

+TEMPERATURE: 313
+MEMBRANE_COMPOSITION:
+  PAPC: 1.0


The metadata here indicates a PAPC membrane at 313 K, but the accompanying dataset files in this directory are clearly labeled as POPC at 300 K (e.g., POPC_Order_Parameters.dat starts with #POPC T300K). Please align MEMBRANE_COMPOSITION and TEMPERATURE with the actual data files, or (if this directory is intended to contain PAPC data) rename/move the data files and/or directory so the DOI/run folder consistently represents the PAPC dataset.

Suggested change

TEMPERATURE: 313

MEMBRANE_COMPOSITION:

PAPC: 1.0

TEMPERATURE: 300

MEMBRANE_COMPOSITION:

POPC: 1.0

Copilot · 2026-03-24T12:21:25Z

+REAGENT_SOURCES: |
+  Phosphatidylcholine lipids with arachidonoyl chains were synthesized and selectively deuterated.


REAGENT_SOURCES is provided as a free-form block string here, but other README.yaml files in this dataset use REAGENT_SOURCES as a mapping (e.g., lipid -> vendor, water -> source). Using a mapping will keep the structure machine-readable for downstream tooling; consider converting this to a map with at least the lipid, water, and buffer components as keys.

Suggested change

REAGENT_SOURCES: |

Phosphatidylcholine lipids with arachidonoyl chains were synthesized and selectively deuterated.

REAGENT_SOURCES:

lipid: "Phosphatidylcholine lipids with arachidonoyl chains were synthesized and selectively deuterated."

buffer: "20 mM Tris buffer, pH 7.5"

water: "Water used to achieve approximately 50 wt% hydration (source not specified)."

Again suggestion of AI is bad, but the error should be fixed.

Copilot · 2026-03-24T12:21:25Z

+DATA_REF: UNKNOWN
+TEMPERATURE: 313
+MEMBRANE_COMPOSITION:
+  PiLPC: 1.0


MEMBRANE_COMPOSITION uses 1.0 here, but other OrderParameters README.yaml files use 1 for single-component membranes (and reserve decimals for mixtures). Consider changing to PiLPC: 1 for consistency.

Suggested change

PiLPC: 1.0

PiLPC: 1

please capitalize PILPC

Copilot · 2026-03-24T12:21:26Z

+REAGENT_SOURCES: |
+  Deuterated isolinoleoyl fatty acids synthesized as described in the original publication.
+  Lipids purified by TLC and column chromatography.


REAGENT_SOURCES is formatted as a block string, but other OrderParameters README.yaml files use a mapping of reagent -> source (which is easier to consume programmatically). Consider converting this to a mapping (e.g., PiLPC: ..., water: ...) and moving any narrative text to SAMPLE_PROTOCOL/NMR.DETAILS if needed.

Suggested change

REAGENT_SOURCES: |

Deuterated isolinoleoyl fatty acids synthesized as described in the original publication.

Lipids purified by TLC and column chromatography.

REAGENT_SOURCES:

deuterated_isolinoleoyl_fatty_acids: "Synthesized as described in the original publication."

lipids: "Purified by TLC and column chromatography."

Suggestion of Copilot is bad but the error exists. format is

REAGENT_SOURCES: PILPC: bla-blabla

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

comcon1

Thanx for start! I applied a couple of suggestions and wrote some comments

comcon1 · 2026-03-24T13:34:34Z

+DATA_REF: UNKNOWN
+TEMPERATURE: 313
+MEMBRANE_COMPOSITION:
+  PiLPC: 1.0


please capitalize PILPC

comcon1 · 2026-03-24T13:35:41Z

+REAGENT_SOURCES: |
+  Deuterated isolinoleoyl fatty acids synthesized as described in the original publication.
+  Lipids purified by TLC and column chromatography.


Suggestion of Copilot is bad but the error exists. format is

REAGENT_SOURCES: PILPC: bla-blabla

comcon1 · 2026-03-24T13:38:16Z

+REAGENT_SOURCES: |
+  Phosphatidylcholine lipids with arachidonoyl chains were synthesized and selectively deuterated.


Again suggestion of AI is bad, but the error should be fixed.

comcon1 · 2026-03-24T13:38:49Z

+  Lipids were hydrated in buffer containing 20 mM Tris (pH 7.5)
+  to approximately 50 wt% hydration, forming bilayer dispersions.
+NMR:
+  INSTRUMENT: "2H NMR spectrometer"


Didn't they really write instrument name??

…ents

…rmatted)

comcon1

Thanks for progressing. Please see included comments

comcon1 · 2026-03-27T15:55:46Z

Universal atomnames have quite specific names. We must stick with them. Please consult https://nmrlipids.github.io/FAIRMD_lipids/latest/schemas/moleculesAndMapping.html

You also must investigate the sign of OP and define signes using your guess.

comcon1 · 2026-03-27T15:56:16Z

plz regenerate after you changed atomnames in DAT

comcon1 · 2026-03-27T15:57:59Z

+SAMPLE_PROTOCOL:
+  Lipids were hydrated in buffer containing 20 mM Tris (pH 7.5)
+  to approximately 50 wt% hydration, forming bilayer dispersions.


please check how multiline yamls are written. you must use > or | symbol

comcon1 · 2026-03-27T15:58:08Z

+REAGENT_SOURCES:
+  POPC: Avanti Polar Lipids, Birmingham, AL, USA
+  H2O: UNKNOWN
+SAMPLE_PROTOCOL:


comcon1 · 2026-03-27T15:58:29Z

+PH: UNKNOWN
+PH_METHOD: UNKNOWN


duplicated fields

comcon1 · 2026-03-27T16:00:02Z

Both JSON and DAT must be in folder 1/

Add README metadata for PiLPC and PAPC datasets

5f9b2e7

Copilot AI review requested due to automatic review settings March 24, 2026 12:16

Copilot started reviewing on behalf of AvNeEsH71-iam March 24, 2026 12:17 View session

Copilot AI reviewed Mar 24, 2026

View reviewed changes

Apply suggestions from code review

73e2de8

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

comcon1 requested changes Mar 24, 2026

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AvNeEsH71-iam added 6 commits March 24, 2026 22:34

Add README metadata for POPC dataset (10.1039/c2cp42738a)

e4e187d

Refine README metadata for PILPC and POPC datasets as per review comm…

d0ef30f

…ents

Fix README metadata properly

755264c

Added PILPC order parameter data from Fig. 5 (digitized and FAIRMD fo…

088cf5c

…rmatted)

Removed raw pilpc_scdo_fig5.dat file

77bdfcd

Moved PILPC data to correct DOI folder (10.1021/bi3009399)

71fb9a6

comcon1 requested changes Mar 27, 2026

View reviewed changes

comcon1 closed this Apr 3, 2026

		REAGENT_SOURCES: \|
		Phosphatidylcholine lipids with arachidonoyl chains were synthesized and selectively deuterated.

		PH: UNKNOWN
		PH_METHOD: UNKNOWN

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