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Merge pull request #1002 from GenomicsStandardsConsortium/1001-add-misip-mims
add MISIP-MIMS checklist
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‎src/data/examples/invalid/MimsMisipSoil-isotopolog_atom_frac.yaml‎

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mimsmisip_soil_data:
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- collection_date: "2013-03-25T12:42:31+01:00"
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depth: 1.234 units
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elev: 1.234 units
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env_broad_scale: term [ONTOLOGY:123]
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env_local_scale: term [ONTOLOGY:123]
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env_medium: term [ONTOLOGY:123]
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geo_loc_name: "text: text, text"
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lat_lon: 45.1 45.9
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project_name: absolutely any text
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samp_name: msd1
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samp_taxon_id: Gut Metagenome [NCBITaxon:749906]
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seq_meth: absolutely any text
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isotope: 13C | 15N
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isotopolog: toluene [pubchem.compound:1140] | water [pubchem.compound:962]
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isotopolog_label: natural abundance
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isotopolog_approach: multiple
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gradient_position: 1
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gradient_pos_density: 1.725 g/mL
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gradient_pos_rel_am: 0.1
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sip_method: https://doi.org/10.1038/s41396-018-0279-6
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isotopolog_atom_frac: 95 # invalid, should be a fraction like 0.95
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isotopolog_atom_pos: 1S/C7H8/c1-7-5-3-2-4-6-7/h2-6H,1H3/i1+1,2+1,3+1,4+1,5+1,6+1,7+1 | 1S/C6H12O6/c7-1-3(9)5(11)6(12)4(10)2-8/h1,3-6,8-12H,2H2/t3-,4+,5+,6+/m0/s1
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isotopolog_dose: 10 ppm
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nucleobase_atom_frac: 0.25
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isotopolog_incu_time: 12 hour
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internal_standard: https://doi.org/10.1101/2022.12.20.521340

‎src/data/examples/invalid/MimsMisipSoil-isotopolog_incu_time.yaml‎

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mimsmisip_soil_data:
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- collection_date: "2013-03-25T12:42:31+01:00"
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depth: 1.234 units
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elev: 1.234 units
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env_broad_scale: term [ONTOLOGY:123]
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env_local_scale: term [ONTOLOGY:123]
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env_medium: term [ONTOLOGY:123]
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geo_loc_name: "text: text, text"
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lat_lon: 45.1 45.9
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project_name: absolutely any text
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samp_name: msd1
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samp_taxon_id: Gut Metagenome [NCBITaxon:749906]
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seq_meth: absolutely any text
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isotope: 13C | 15N
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isotopolog: toluene [pubchem.compound:1140] | water [pubchem.compound:962]
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isotopolog_label: natural abundance
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isotopolog_approach: multiple
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gradient_position: 1
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gradient_pos_density: 1.725 g/mL
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gradient_pos_rel_am: 0.1
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sip_method: https://doi.org/10.1038/s41396-018-0279-6
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isotopolog_atom_frac: 0.95
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isotopolog_atom_pos: 1S/C7H8/c1-7-5-3-2-4-6-7/h2-6H,1H3/i1+1,2+1,3+1,4+1,5+1,6+1,7+1 | 1S/C6H12O6/c7-1-3(9)5(11)6(12)4(10)2-8/h1,3-6,8-12H,2H2/t3-,4+,5+,6+/m0/s1
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isotopolog_dose: 10 ppm
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nucleobase_atom_frac: 0.25
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isotopolog_incu_time: 12 # invalid, should include units like "12 hour"
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internal_standard: https://doi.org/10.1101/2022.12.20.521340

‎src/data/examples/invalid/MimsMisipSoil-nucleobase_atom_frac.yaml‎

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mimsmisip_soil_data:
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- collection_date: "2013-03-25T12:42:31+01:00"
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depth: 1.234 units
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elev: 1.234 units
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env_broad_scale: term [ONTOLOGY:123]
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env_local_scale: term [ONTOLOGY:123]
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env_medium: term [ONTOLOGY:123]
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geo_loc_name: "text: text, text"
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lat_lon: 45.1 45.9
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project_name: absolutely any text
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samp_name: msd1
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samp_taxon_id: Gut Metagenome [NCBITaxon:749906]
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seq_meth: absolutely any text
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isotope: 13C | 15N
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isotopolog: toluene [pubchem.compound:1140] | water [pubchem.compound:962]
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isotopolog_label: natural abundance
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isotopolog_approach: multiple
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gradient_position: 1
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gradient_pos_density: 1.725 g/mL
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gradient_pos_rel_am: 0.1
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sip_method: https://doi.org/10.1038/s41396-018-0279-6
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isotopolog_atom_frac: 0.95
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isotopolog_atom_pos: 1S/C7H8/c1-7-5-3-2-4-6-7/h2-6H,1H3/i1+1,2+1,3+1,4+1,5+1,6+1,7+1 | 1S/C6H12O6/c7-1-3(9)5(11)6(12)4(10)2-8/h1,3-6,8-12H,2H2/t3-,4+,5+,6+/m0/s1
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isotopolog_dose: 10 ppm
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nucleobase_atom_frac: 25 # invalid, should be a fraction like 0.25
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isotopolog_incu_time: 12 hour
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internal_standard: https://doi.org/10.1101/2022.12.20.521340

‎src/data/examples/valid/MixsCompliantData-MimsMisipSoil-example.yaml‎

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mimsmisip_soil_data:
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- collection_date: "2013-03-25T12:42:31+01:00"
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depth: 1.234 units
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elev: 1.234 units
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env_broad_scale: term [ONTOLOGY:123]
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env_local_scale: term [ONTOLOGY:123]
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env_medium: term [ONTOLOGY:123]
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geo_loc_name: "text: text, text"
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lat_lon: 45.1 45.9
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project_name: absolutely any text
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samp_name: msd1
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samp_taxon_id: Gut Metagenome [NCBITaxon:749906]
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seq_meth: absolutely any text
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samp_dna_conc: 12.34 ng/µL
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isotope:
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- 13C
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- 15N
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isotopolog:
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- toluene [pubchem.compound:1140]
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- water [pubchem.compound:962]
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isotopolog_label: natural abundance
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isotopolog_approach: multiple
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gradient_position: 1
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gradient_pos_density: 1.725 g/mL
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gradient_pos_rel_am: 0.1
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sip_method: https://doi.org/10.1038/s41396-018-0279-6
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isotopolog_atom_frac: 0.95 | 0.98
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isotopolog_atom_pos: 1S/C7H8/c1-7-5-3-2-4-6-7/h2-6H,1H3/i1+1,2+1,3+1,4+1,5+1,6+1,7+1 | 1S/C6H12O6/c7-1-3(9)5(11)6(12)4(10)2-8/h1,3-6,8-12H,2H2/t3-,4+,5+,6+/m0/s1
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isotopolog_dose: 10 ppm
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nucleobase_atom_frac: 0.25
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isotopolog_incu_time: 12 hour
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internal_standard: https://doi.org/10.1101/2022.12.20.521340

‎src/data/examples/valid/MixsCompliantData-MimsSoil-example2.yaml‎

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mims_soil_data:
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- collection_date: "2013-03-25T12:42:31+01:00"
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depth: 1.234 units
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elev: 1.234 units
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env_broad_scale: term [ONTOLOGY:123]
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env_local_scale: term [ONTOLOGY:123]
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env_medium: term [ONTOLOGY:123]
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geo_loc_name: "text: text, text"
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lat_lon: 45.1 45.9
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project_name: absolutely any text
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samp_name: msd1
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samp_taxon_id: Gut Metagenome [NCBITaxon:749906]
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seq_meth: absolutely any text
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- collection_date: "2013-03-25T12:42:31+01:00"
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depth: 1.234 units
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elev: 1.234 units
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env_broad_scale: term [ONTOLOGY:123]
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env_local_scale: term [ONTOLOGY:123]
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env_medium: term [ONTOLOGY:123]
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geo_loc_name: "text: text, text"
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lat_lon: 45.1 45.9
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project_name: absolutely any text
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samp_name: msd2
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samp_taxon_id: Gut Metagenome [NCBITaxon:749906]
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seq_meth: absolutely any text

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