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HendrikBorgeltHendrikBorgelt
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updated git action pipeline, toml and config file for changing to LinkML 1.11
1 parent d5a4529 commit 9e8f726

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‎.github/workflows/main.yaml‎

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runs-on: ubuntu-latest
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strategy:
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matrix:
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python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
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python-version: ["3.10", "3.11", "3.12", "3.13"]
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fail-fast: false
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steps:

‎config.yaml‎

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mergeimports: true
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shacl:
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mergeimports: true
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use_class_uri_names: false
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shex:
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mergeimports: true
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sqlddl:

‎examples/output/AnalysisDataset-001.json‎

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{
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"id": "https://dx.doi.org/10.14272/UGRXAOUDHZOHPF-UHFFFAOYSA-N/CHMO0000595.1",
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"id": "doi:10.14272/UGRXAOUDHZOHPF-UHFFFAOYSA-N/CHMO0000595.1",
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"description": [
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"Dataset for 13C nuclear magnetic resonance spectroscopy (13C NMR)"
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],
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],
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"was_generated_by": [
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{
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"id": "https://dx.doi.org/10.14272/UGRXAOUDHZOHPF-UHFFFAOYSA-N/CHMO0000595.1#NMRSpectralAnalysis",
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"id": "doi:10.14272/UGRXAOUDHZOHPF-UHFFFAOYSA-N/CHMO0000595.1#NMRSpectralAnalysis",
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"description": [
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"Analysis of NMR spectra."
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],
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},
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"evaluated_entity": [
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{
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"id": "https://dx.doi.org/10.14272/UGRXAOUDHZOHPF-UHFFFAOYSA-N/CHMO0000595.1#CDCl3_13C_NMR_Spectrum",
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"id": "doi:10.14272/UGRXAOUDHZOHPF-UHFFFAOYSA-N/CHMO0000595.1#CDCl3_13C_NMR_Spectrum",
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"was_generated_by": [
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{
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"id": "https://dx.doi.org/10.14272/UGRXAOUDHZOHPF-UHFFFAOYSA-N/CHMO0000595.1#CDCl3_13C_NMR",
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"id": "doi:10.14272/UGRXAOUDHZOHPF-UHFFFAOYSA-N/CHMO0000595.1#CDCl3_13C_NMR",
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"title": [
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"CDCl3_13C_NMR"
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],
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"carried_out_by": [
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{
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"id": "https://dx.doi.org/10.14272/UGRXAOUDHZOHPF-UHFFFAOYSA-N/CHMO0000595.1#CDCl3_13C_NMR_Spectrometer",
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"id": "doi:10.14272/UGRXAOUDHZOHPF-UHFFFAOYSA-N/CHMO0000595.1#CDCl3_13C_NMR_Spectrometer",
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"title": "Bruker 400 MHz",
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"description": "The NMR spectrometer used.",
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"rdf_type": {
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}
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},
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{
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"id": "https://dx.doi.org/10.14272/UGRXAOUDHZOHPF-UHFFFAOYSA-N/CHMO0000595.1#CDCl3_13C_NMR_Solvent",
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"id": "doi:10.14272/UGRXAOUDHZOHPF-UHFFFAOYSA-N/CHMO0000595.1#CDCl3_13C_NMR_Solvent",
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"description": "used solvent",
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"has_part": [
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{
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},
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"evaluated_entity": [
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{
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"id": "https://dx.doi.org/10.14272/UGRXAOUDHZOHPF-UHFFFAOYSA-N.2",
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"id": "doi:10.14272/UGRXAOUDHZOHPF-UHFFFAOYSA-N.2",
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"title": "CRS-50440"
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}
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]
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}
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]
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},
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{
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"id": "https://dx.doi.org/10.14272/UGRXAOUDHZOHPF-UHFFFAOYSA-N/CHMO0000595.1#DMSO_13C_NMR_Spectrum",
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"id": "doi:10.14272/UGRXAOUDHZOHPF-UHFFFAOYSA-N/CHMO0000595.1#DMSO_13C_NMR_Spectrum",
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"was_generated_by": [
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{
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"id": "https://dx.doi.org/10.14272/UGRXAOUDHZOHPF-UHFFFAOYSA-N/CHMO0000595.1#DMSO_13C_NMR",
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"id": "doi:10.14272/UGRXAOUDHZOHPF-UHFFFAOYSA-N/CHMO0000595.1#DMSO_13C_NMR",
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"title": [
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"DMSO_13C_NMR"
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],
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"carried_out_by": [
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{
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"id": "https://dx.doi.org/10.14272/UGRXAOUDHZOHPF-UHFFFAOYSA-N/CHMO0000595.1#DMSO_13C_NMR_Spectrometer",
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"id": "doi:10.14272/UGRXAOUDHZOHPF-UHFFFAOYSA-N/CHMO0000595.1#DMSO_13C_NMR_Spectrometer",
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"title": "Bruker 400 MHz",
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"description": "used spectrometer",
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"rdf_type": {
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}
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},
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{
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"id": "https://dx.doi.org/10.14272/UGRXAOUDHZOHPF-UHFFFAOYSA-N/CHMO0000595.1#DMSO_13C_NMR_Solvent",
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"id": "doi:10.14272/UGRXAOUDHZOHPF-UHFFFAOYSA-N/CHMO0000595.1#DMSO_13C_NMR_Solvent",
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"description": "used solvent",
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"has_part": [
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{
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},
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"evaluated_entity": [
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{
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"id": "https://dx.doi.org/10.14272/UGRXAOUDHZOHPF-UHFFFAOYSA-N.2",
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"id": "doi:10.14272/UGRXAOUDHZOHPF-UHFFFAOYSA-N.2",
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"title": "CRS-50440"
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}
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]
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],
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"is_about_entity": [
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{
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"id": "https://dx.doi.org/10.14272/UGRXAOUDHZOHPF-UHFFFAOYSA-N.2",
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"id": "doi:10.14272/UGRXAOUDHZOHPF-UHFFFAOYSA-N.2",
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"title": "CRS-50440",
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"description": "The analysed chemical substance sample CRS-50440.",
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"has_part": [
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{
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"id": "https://dx.doi.org/10.14272/UGRXAOUDHZOHPF-UHFFFAOYSA-N.2#EvaluatedCompound",
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"description": "compound assigned to https://dx.doi.org/10.14272/UGRXAOUDHZOHPF-UHFFFAOYSA-N.2",
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"id": "doi:10.14272/UGRXAOUDHZOHPF-UHFFFAOYSA-N.2#EvaluatedCompound",
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"description": "compound assigned to doi:10.14272/UGRXAOUDHZOHPF-UHFFFAOYSA-N.2",
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"other_identifier": [
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{
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"notation": "https://pubchem.ncbi.nlm.nih.gov/compound/26248854"
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}
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],
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"@type": "AnalysisDataset"
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}
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}

‎examples/output/AnalysisDataset-001.yaml‎

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id: https://dx.doi.org/10.14272/UGRXAOUDHZOHPF-UHFFFAOYSA-N/CHMO0000595.1
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id: doi:10.14272/UGRXAOUDHZOHPF-UHFFFAOYSA-N/CHMO0000595.1
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description:
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- Dataset for 13C nuclear magnetic resonance spectroscopy (13C NMR)
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title:
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- 13C nuclear magnetic resonance spectroscopy (13C NMR)
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was_generated_by:
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- id: https://dx.doi.org/10.14272/UGRXAOUDHZOHPF-UHFFFAOYSA-N/CHMO0000595.1#NMRSpectralAnalysis
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- id: doi:10.14272/UGRXAOUDHZOHPF-UHFFFAOYSA-N/CHMO0000595.1#NMRSpectralAnalysis
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description:
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- Analysis of NMR spectra.
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rdf_type:
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id: NMR:1400042
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title: NMR data processing
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evaluated_entity:
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- id: https://dx.doi.org/10.14272/UGRXAOUDHZOHPF-UHFFFAOYSA-N/CHMO0000595.1#CDCl3_13C_NMR_Spectrum
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- id: doi:10.14272/UGRXAOUDHZOHPF-UHFFFAOYSA-N/CHMO0000595.1#CDCl3_13C_NMR_Spectrum
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was_generated_by:
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- id: https://dx.doi.org/10.14272/UGRXAOUDHZOHPF-UHFFFAOYSA-N/CHMO0000595.1#CDCl3_13C_NMR
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- id: doi:10.14272/UGRXAOUDHZOHPF-UHFFFAOYSA-N/CHMO0000595.1#CDCl3_13C_NMR
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title:
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- CDCl3_13C_NMR
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carried_out_by:
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- id: https://dx.doi.org/10.14272/UGRXAOUDHZOHPF-UHFFFAOYSA-N/CHMO0000595.1#CDCl3_13C_NMR_Spectrometer
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- id: doi:10.14272/UGRXAOUDHZOHPF-UHFFFAOYSA-N/CHMO0000595.1#CDCl3_13C_NMR_Spectrometer
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title: Bruker 400 MHz
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description: The NMR spectrometer used.
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rdf_type:
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id: OBI:0000566
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title: NMR instrument
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- id: https://dx.doi.org/10.14272/UGRXAOUDHZOHPF-UHFFFAOYSA-N/CHMO0000595.1#CDCl3_13C_NMR_Solvent
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- id: doi:10.14272/UGRXAOUDHZOHPF-UHFFFAOYSA-N/CHMO0000595.1#CDCl3_13C_NMR_Solvent
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description: used solvent
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has_part:
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- id: https://pubchem.ncbi.nlm.nih.gov/compound/71583
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id: CHMO:0000595
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title: 13C nuclear magnetic resonance spectroscopy
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evaluated_entity:
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- id: https://dx.doi.org/10.14272/UGRXAOUDHZOHPF-UHFFFAOYSA-N.2
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- id: doi:10.14272/UGRXAOUDHZOHPF-UHFFFAOYSA-N.2
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title: CRS-50440
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- id: https://dx.doi.org/10.14272/UGRXAOUDHZOHPF-UHFFFAOYSA-N/CHMO0000595.1#DMSO_13C_NMR_Spectrum
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- id: doi:10.14272/UGRXAOUDHZOHPF-UHFFFAOYSA-N/CHMO0000595.1#DMSO_13C_NMR_Spectrum
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was_generated_by:
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- id: https://dx.doi.org/10.14272/UGRXAOUDHZOHPF-UHFFFAOYSA-N/CHMO0000595.1#DMSO_13C_NMR
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- id: doi:10.14272/UGRXAOUDHZOHPF-UHFFFAOYSA-N/CHMO0000595.1#DMSO_13C_NMR
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title:
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- DMSO_13C_NMR
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carried_out_by:
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- id: https://dx.doi.org/10.14272/UGRXAOUDHZOHPF-UHFFFAOYSA-N/CHMO0000595.1#DMSO_13C_NMR_Spectrometer
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- id: doi:10.14272/UGRXAOUDHZOHPF-UHFFFAOYSA-N/CHMO0000595.1#DMSO_13C_NMR_Spectrometer
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title: Bruker 400 MHz
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id: OBI:0000566
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title: NMR instrument
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- id: https://dx.doi.org/10.14272/UGRXAOUDHZOHPF-UHFFFAOYSA-N/CHMO0000595.1#DMSO_13C_NMR_Solvent
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- id: doi:10.14272/UGRXAOUDHZOHPF-UHFFFAOYSA-N/CHMO0000595.1#DMSO_13C_NMR_Solvent
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description: used solvent
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has_part:
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- id: https://pubchem.ncbi.nlm.nih.gov/compound/679
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id: CHMO:0000595
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title: 13C nuclear magnetic resonance spectroscopy
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evaluated_entity:
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- id: https://dx.doi.org/10.14272/UGRXAOUDHZOHPF-UHFFFAOYSA-N.2
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- id: doi:10.14272/UGRXAOUDHZOHPF-UHFFFAOYSA-N.2
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title: CRS-50440
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other_identifier:
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- notation: https://www.chemotion-repository.net/pid/50434
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theme:
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- preferred_label:
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- TECH
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is_about_entity:
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- id: https://dx.doi.org/10.14272/UGRXAOUDHZOHPF-UHFFFAOYSA-N.2
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- id: doi:10.14272/UGRXAOUDHZOHPF-UHFFFAOYSA-N.2
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title: CRS-50440
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description: The analysed chemical substance sample CRS-50440.
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has_part:
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- id: https://dx.doi.org/10.14272/UGRXAOUDHZOHPF-UHFFFAOYSA-N.2#EvaluatedCompound
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description: compound assigned to https://dx.doi.org/10.14272/UGRXAOUDHZOHPF-UHFFFAOYSA-N.2
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- id: doi:10.14272/UGRXAOUDHZOHPF-UHFFFAOYSA-N.2#EvaluatedCompound
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description: compound assigned to doi:10.14272/UGRXAOUDHZOHPF-UHFFFAOYSA-N.2
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other_identifier:
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- notation: https://pubchem.ncbi.nlm.nih.gov/compound/26248854
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has_qualitative_attribute:

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