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Schema Field Reference

Complete reference for all metadata fields in pulse sequence annotations.

Required Fields

Field Type Description Example
schema_version string Schema version "0.0.1"
sequence_version string Sequence version (semantic) "1.2.0"
title string Descriptive sequence name "SOFAST-HMQC"
authors array List of contributors ["Name <email>"]
created string Creation date (YYYY-MM-DD) "2024-01-15"
last_modified string Last modification date "2024-08-17"
repository string Repository identifier "github.com/user/repo"
status string Development status "stable"

Optional Fields

Field Type Description Example
experiment_type array Experiment keywords ["hsqc", "2d"]
description string Detailed description "1H,15N SOFAST-HMQC..."
features array Technical features ["trosy", "sofast"]
nuclei_hint array Suggested mapping of nuclei to channels ["1H", "15N"]
citation array Literature references ["Author et al., Journal (Year)"]
doi array DOI identifiers ["10.1021/ja051306e"]

Controlled Vocabularies

Status Values

  • experimental: Under development, use with caution
  • beta: Testing phase, mostly stable
  • stable: Production ready, well tested
  • deprecated: No longer recommended

Nuclei Format

Use standard isotope notation: 1H, 13C, 15N, 31P, 19F, etc.

Common Experiment Types

  • 1d, 2d, 3d
  • cosy, tocsy, noesy
  • hsqc, hmqc, trosy
  • relaxation
  • diffusion
  • r1rho, cest

Common Experiment Features

  • watergate
  • hahn echo, perfect echo (relaxation)
  • ste, xste (diffusion)
  • relaxation dispersion
  • temperature compensation
  • on-resonance (r1rho)

Details by Experiment Type / Feature

Relaxation

Experiments with type relaxation should include an object relaxation with fields describing the following additional parameters:

  • type: R1, R2
  • model: exponential-decay, inversion-recovery, saturation-recovery
  • channel: corresponding to observed nucleus
  • duration: relaxation time

For example:

;@ experiment_type: [relaxation, 1d]
;@ relaxation: {type: R1, model: inversion-recovery, channel: f1, duration: <$VDLIST>}

cest, r1rho

Experiments with type cest or r1rho should include an object spinlock with fields describing the spinlock parameters:

  • channel: corresponding to observed nucleus
  • power
  • duration
  • offset
  • alignment (optional): hard pulse

For example:

;@ experiment_type: [r1rho, 1d]
;@ spinlock: {channel: f1, power: <$VALIST>, duration: <$VPLIST>, offset: 0, alignment: hard pulse}

diffusion

Experiments with type diffusion should include an object diffusion with fields describing the following parameters:

  • type: bipolar
  • coherence: specifying the order of the encoding coherence [channel, coherence_order]
  • big-delta: diffusion delay
  • little-delta: total encoding pulse length
  • tau: delay between bipolar gradients
  • Gmax: maximum gradient strength
  • g: reference to diff ramp file, or specify a calculated ramp ([linear, cnst1, cnst2])
  • shape: encoding gradient pulse name

For example:

;@ experiment_type: [diffusion, 1d]
;@ diffusion:
;@ - type: bipolar
;@ - coherence: [f1, 1]
;@ - big-delta: d20
;@ - little-delta: p31
;@ - tau: d17
;@ - Gmax: gpz6
;@ - g: [linear, cnst1, cnst2]
;@ - shape: gpnam6