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Add JGI metagenomics long read class to submission schema #185

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merged 16 commits into from
Mar 5, 2024
Merged

Add JGI metagenomics long read class to submission schema #185

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e6c628a
Separate JGI MG into short and long read classes
bmeluch Jan 2, 2024
65a9a47
fix spacing
bmeluch Jan 2, 2024
4413089
fix spacing
bmeluch Jan 2, 2024
30cc26e
fix class names
bmeluch Jan 2, 2024
fa4d50d
break jgi_mg_data into long and short read classes
bmeluch Jan 2, 2024
c1bfa96
Change JgiMgInterface to JgiMgSr/LrInterface
bmeluch Jan 2, 2024
bd30e5e
add long/short read options to enums.tsv
bmeluch Jan 8, 2024
9052091
make dna_absorb slots required for JgiMgLrInterface
bmeluch Jan 11, 2024
11bba30
Merge branch 'main' into 168-add-jgi-metagenomics-long-read-class-to-…
pkalita-lbl Feb 13, 2024
238cf3e
Replace jgi_mg_data slot on SampleData class with jgi_mg_lr_data and …
pkalita-lbl Feb 13, 2024
07b2875
Rename example files to reflect updated slot name
pkalita-lbl Feb 13, 2024
ff001b2
Drop short read from class and slot names
pkalita-lbl Mar 2, 2024
f3762be
Remove enum which can be imported from nmdc-schema
pkalita-lbl Mar 2, 2024
8bde6d6
Upgrade to nmdc-schema v10.1.0
pkalita-lbl Mar 2, 2024
51f3fa0
Add metagenome long read example data files
pkalita-lbl Mar 4, 2024
9348b38
Add more informative descriptions for JGI metagenome classes
pkalita-lbl Mar 4, 2024
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5 changes: 3 additions & 2 deletions schemasheets/tsv_in/classes.tsv
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Expand Up @@ -8,7 +8,8 @@ EmslInterface Emsl emsl dh_interface DhInterface DhMultiviewCommonColumnsMixin
HcrCoresInterface Hcr Cores hcr_cores dh_interface DhInterface DhMultiviewCommonColumnsMixin
HcrFluidsSwabsInterface Hcr Fluids Swabs hcr_fluids_swabs dh_interface DhInterface DhMultiviewCommonColumnsMixin
HostAssociatedInterface Host Associated host_associated dh_interface DhInterface DhMultiviewCommonColumnsMixin|SampIdNewTermsMixin
JgiMgInterface JGI MG jgi_mg dh_interface DhInterface DhMultiviewCommonColumnsMixin dna_absorb1|dna_absorb2|dna_concentration|dna_cont_type|dna_cont_well|dna_container_id|dna_dnase|dna_isolate_meth|dna_project_contact|dna_samp_id|dna_sample_format|dna_sample_name|dna_seq_project|dna_seq_project_name|dna_seq_project_pi|dna_volume|proposal_dna
JgiMgInterface JGI MG jgi_mg DhInterface DhMultiviewCommonColumnsMixin dna_absorb1|dna_absorb2|dna_concentration|dna_cont_type|dna_cont_well|dna_container_id|dna_dnase|dna_isolate_meth|dna_project_contact|dna_samp_id|dna_sample_format|dna_sample_name|dna_seq_project|dna_seq_project_name|dna_seq_project_pi|dna_volume|proposal_dna
JgiMgLrInterface JGI MG (Long Read) jgi_mg_lr DhInterface DhMultiviewCommonColumnsMixin dna_absorb1|dna_absorb2|dna_concentration|dna_cont_type|dna_cont_well|dna_container_id|dna_dnase|dna_isolate_meth|dna_project_contact|dna_samp_id|dna_sample_format|dna_sample_name|dna_seq_project|dna_seq_project_name|dna_seq_project_pi|dna_volume|proposal_dna
JgiMtInterface JGI MT jgi_mt dh_interface DhInterface DhMultiviewCommonColumnsMixin dnase_rna|proposal_rna|rna_absorb1|rna_absorb2|rna_concentration|rna_cont_type|rna_cont_well|rna_container_id|rna_isolate_meth|rna_project_contact|rna_samp_id|rna_sample_format|rna_sample_name|rna_seq_project|rna_seq_project_name|rna_seq_project_pi|rna_volume
MiscEnvsInterface Misc Envs misc_envs dh_interface DhInterface DhMultiviewCommonColumnsMixin
PlantAssociatedInterface Plant Associated plant_associated dh_interface DhInterface DhMultiviewCommonColumnsMixin|SampIdNewTermsMixin
Expand All @@ -20,4 +21,4 @@ DhMultiviewCommonColumnsMixin Dh Mutliview Common Columns Mixin with DhMutliview
SampIdNewTermsMixin SampId New Terms Mixin with SampIdNew Terms TRUE sample_link
SoilMixsInspiredMixin Soil MIxS Inspired Mixin Mixin with SoilMixsInspired Terms TRUE collection_date_inc|collection_time|collection_time_inc|experimental_factor_other|filter_method|isotope_exposure|micro_biomass_c_meth|micro_biomass_n_meth|microbial_biomass_c|microbial_biomass_n|non_microb_biomass|non_microb_biomass_method|org_nitro_method|other_treatment|start_date_inc|start_time_inc
DhInterface Dh Root Interface One DataHarmonizer interface, for the specified combination of a checklist, enviornmental_package, and various standards, user facilities or analysis types
SampleData SampleData represents data produced by the DataHarmonizer tabs of the submission portal TRUE air_data|biofilm_data|built_env_data|host_associated_data|plant_associated_data|sediment_data|soil_data|wastewater_sludge_data|water_data|emsl_data|jgi_mg_data|jgi_mt_data
SampleData SampleData represents data produced by the DataHarmonizer tabs of the submission portal TRUE air_data|biofilm_data|built_env_data|host_associated_data|plant_associated_data|sediment_data|soil_data|wastewater_sludge_data|water_data|emsl_data|jgi_mg_lr_data|jgi_mg_data|jgi_mt_data
6 changes: 0 additions & 6 deletions schemasheets/tsv_in/enums.tsv
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Original file line number Diff line number Diff line change
@@ -1,12 +1,6 @@
DH pulldown column DH pulldown option description term_id old SNTC name MIxS see also notes
> enum permissible_value description ignore annotations see_also notes
> inner_key: sntc_name "internal_separator: ""|""" "internal_separator: ""|"""
AnalysisTypeEnum metabolomics placeholder PV descr
AnalysisTypeEnum metagenomics placeholder PV descr
AnalysisTypeEnum metaproteomics placeholder PV descr
AnalysisTypeEnum metatranscriptomics placeholder PV descr
AnalysisTypeEnum natural organic matter placeholder PV descr
AnalysisTypeEnum placeholder enum descr
BioticRelationshipEnum commensalism placeholder PV descr samp_biotic_relationship https://genomicsstandardsconsortium.github.io/mixs/biotic_relationship_enum/ biotic_relationship_enum: free living|parasitism|commensalism|symbiotic|mutualism
BioticRelationshipEnum free living placeholder PV descr
BioticRelationshipEnum mutualism placeholder PV descr
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3 changes: 2 additions & 1 deletion schemasheets/tsv_in/slots.tsv
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Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,8 @@ emsl_data aggregation slot relating emsl data collections to a SampleData contai
hcr_cores_data aggregation slot relating hcr_cores data collections to a SampleData container HcrCoresInterface TRUE TRUE TRUE
hcr_fluids_swabs_data aggregation slot relating hcr_fluids_swabs data collections to a SampleData container HcrFluidsSwabsInterface TRUE TRUE TRUE
host_associated_data aggregation slot relating host_associated data collections to a SampleData container HostAssociatedInterface TRUE TRUE TRUE
jgi_mg_data aggregation slot relating jgi_mg data collections to a SampleData container JgiMgInterface TRUE TRUE TRUE
jgi_mg_data aggregation slot relating jgi_mg data collections to a SampleData container JgiMgInterface TRUE TRUE TRUE
jgi_mg_lr_data aggregation slot relating jgi_mg_lr data collections to a SampleData container JgiMgLrInterface TRUE TRUE TRUE
jgi_mt_data aggregation slot relating jgi_mt data collections to a SampleData container JgiMtInterface TRUE TRUE TRUE
misc_envs_data aggregation slot relating misc_envs data collections to a SampleData container MiscEnvsInterface TRUE TRUE TRUE
plant_associated_data aggregation slot relating plant_associated data collections to a SampleData container PlantAssociatedInterface TRUE TRUE TRUE
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