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Database-interleaved.yaml
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workflow_execution_set:
- id: nmdc:wfmtas-99-v9w6y.1
type: nmdc:MetatranscriptomeAssembly
asm_score: 0.85
ctg_n50: 10000.0
ended_at_time: '2023-08-04T14:00:00Z'
execution_resource: NERSC-Perlmutter
git_url: https://github.com/microbiomedata/metatranscriptome_assembly/releases/tag/v1.2.3
name: human gut metatranscriptome assembly
scaf_bp: 567890123.0
scaffolds: 1234.0
started_at_time: '2023-08-04T08:00:00Z'
was_informed_by: nmdc:dgns-12-dk484s
has_input:
- nmdc:dobj-99-7l49z
has_output:
- nmdc:dobj-99-9t74d
- id: nmdc:wfmp-99-74d83.1
type: nmdc:MetaproteomicsAnalysis
name: soil metaproteomics analysis
has_input:
- nmdc:dobj-99-74d83z
has_output:
- nmdc:dobj-99-74d83
ended_at_time: '2023-08-11T17:00:00Z'
execution_resource: EMSL
git_url: https://github.com/microbiomedata/metaproteomics_analysis/releases/tag/v0.6.3
was_informed_by: nmdc:dgms-12-384j8d
started_at_time: '2023-08-11T11:00:00Z'
metaproteomics_analysis_category: matched_metagenome
chemical_entity_set:
- id: nmdc:chem-99-000016
type: nmdc:ChemicalEntity
name: formic acid
alternative_identifiers:
- CHEBI:30751
chemical_formula: CH2O2
inchi_key: BDAGIHXWWSANSR-UHFFFAOYSA-N
- id: nmdc:chem-99-000001
type: nmdc:ChemicalEntity
name: glucose
description: generally considered the most abundant monosaccharide in nature
alternative_identifiers:
- wd:Q37525
chemical_formula: C6H12O6
inchi: 1S/C6H12O6/c7-1-2-3(8)4(9)5(10)6(11)12-2/h2-11H,1H2/t2-,3-,4+,5-,6?/m1/s1
inchi_key: WQZGKKKJIJFFOK-GASJEMHNSA-N
smiles:
- OC[C@H]1OC(O)[C@H](O)[C@@H](O)[C@@H]1O
- C([C@@H]1[C@H]([C@@H]([C@H]([C@H](O1)O)O)O)O)O
- id: nmdc:chem-99-000002
type: nmdc:ChemicalEntity
name: ammonium bicarbonate
alternative_identifiers:
- CHEBI:184335
- id: nmdc:chem-99-000014
type: nmdc:ChemicalEntity
name: trypsin
description: A serine protease that hydrolyzes peptide bonds at the C-terminus of
arginine and lysine.
alternative_identifiers:
- MS:1001251
- id: nmdc:chem-99-000003
type: nmdc:ChemicalEntity
name: methanol
alternative_identifiers:
- CHEBI:17790
chemical_formula: CH3OH
inchi_key: OKKJLVBELUTLKV-UHFFFAOYSA-N
- id: nmdc:chem-99-000004
type: nmdc:ChemicalEntity
name: water
alternative_identifiers:
- CHEBI:15377
chemical_formula: H2O
- id: nmdc:chem-99-000005
type: nmdc:ChemicalEntity
name: deionized water
- id: nmdc:chem-99-000015
type: nmdc:ChemicalEntity
name: hydrochloric acid
alternative_identifiers:
- CHEBI:7696
chemical_formula: HCl
- id: nmdc:chem-99-000006
type: nmdc:ChemicalEntity
name: triton-x 100
- id: nmdc:chem-99-000007
type: nmdc:ChemicalEntity
name: chymotrypsin
description: A serine protease that hydrolyzes peptide bonds at the C-terminus of
tryptophan, leucine, tyrosine, and phenylalanine.
alternative_identifiers:
- MS:1001306
- id: nmdc:chem-99-000008
type: nmdc:ChemicalEntity
name: Lys-C
description: A serine protease that hydrolyzes peptide, ester, and amide bonds at
the C-terminus of lysine.
alternative_identifiers:
- MS:1001309
- id: nmdc:chem-99-000009
type: nmdc:ChemicalEntity
name: Lys-N
description: A metalloendopeptidase that hydrolyzes peptide bonds at the C-terminus
of lysine.
alternative_identifiers:
- MS:1003093
- id: nmdc:chem-99-000010
type: nmdc:ChemicalEntity
name: Glu-C
description: A serine protease that hydrolyzes peptide and ester bonds at the C-terminus
of aspartic acid or glutamic acid
alternative_identifiers:
- MS:1001917
- id: nmdc:chem-99-000011
type: nmdc:ChemicalEntity
name: Arg-C
description: A cysteine protease that hydrolyzes peptide, ester, and amide bonds
at the C-terminus of arginine and with lower efficiency, lysine.
alternative_identifiers:
- MS:1001303
- id: nmdc:chem-99-000012
type: nmdc:ChemicalEntity
name: Asp-N
description: A zinc metalloendopeptidase that hydrolyzes peptide bonds at the N-terminus
of aspartic acid.
alternative_identifiers:
- MS:1001304
- id: nmdc:chem-99-000013
type: nmdc:ChemicalEntity
name: alphaLP
description: A serine protease that hydrolyzes peptide bonds at the C-terminus of
threonine, alanine, serine, and valine.
material_processing_set:
- id: nmdc:cspro-99-oW43DzG0
type: nmdc:ChromatographicSeparationProcess
has_input:
- nmdc:procsm-99-9gjxns61
has_output:
- nmdc:procsm-99-05g48p90
- nmdc:procsm-99-05g48p91
stationary_phase: "CN"
chromatographic_category: solid_phase_extraction
ordered_mobile_phases:
- type: nmdc:MobilePhaseSegment
substances_used:
- known_as: nmdc:chem-99-000003 # see src/data/valid/Database-chemical_entity_set-1.yaml
type: nmdc:PortionOfSubstance
final_concentration:
type: nmdc:QuantityValue
has_unit: '%'
has_numeric_value: 10
volume:
type: nmdc:QuantityValue
has_numeric_value: 700
has_unit: mL
- type: nmdc:MobilePhaseSegment
substances_used:
- known_as: nmdc:chem-99-000015 # see src/data/valid/Database-chemical_entity_set-1.yaml
type: nmdc:PortionOfSubstance
final_concentration:
type: nmdc:QuantityValue
has_unit: mM
has_numeric_value: 15
volume:
type: nmdc:QuantityValue
has_numeric_value: 700
has_unit: mL
- id: nmdc:subspr-99-oW43DzG0
type: nmdc:SubSamplingProcess
has_input:
- nmdc:bsm-99-oW43DzG1
container_size:
type: nmdc:QuantityValue
has_numeric_value: 50
has_unit: mL
contained_in: v-bottom_conical_tube
volume:
type: nmdc:QuantityValue
has_numeric_value: 20
has_unit: mL
temperature:
type: nmdc:QuantityValue
has_numeric_value: 25
has_unit: C
mass:
type: nmdc:QuantityValue
has_numeric_value: 30
has_unit: g
has_output:
- nmdc:procsm-99-05g48p90
sampled_portion:
- supernatant
storage_process_set:
- id: nmdc:storpr-99-zUCd5N
substances_used:
- known_as: nmdc:chem-99-000003 # see src/data/valid/Database-chemical_entity_set-1.yaml
type: nmdc:PortionOfSubstance
final_concentration:
type: nmdc:QuantityValue
has_unit: '%'
has_numeric_value: 1
contained_in: falcon_tube
start_date: "2021-01-14"
temperature:
type: nmdc:QuantityValue
has_unit: degrees Celsius
has_numeric_value: 80
has_input:
- nmdc:procsm-99-dtTMNb
has_output:
- nmdc:procsm-78-BZAPKH
type: nmdc:StorageProcess
protocol_execution_set:
- id: nmdc:pex-99-18sD2
type: nmdc:ProtocolExecution
has_input:
- nmdc:bsm-65-0002
has_process_parts:
- nmdc:extrp-71-r2pk
- nmdc:filtpr-22-32G2BS
protocol_execution_category: organic_matter_extraction
protocol_link:
type: nmdc:Protocol
url: https://www.protocols.io/view/water-extractable-organic-matter-weom-ewov1o4oylr2/v1
name: Water Extractable Organic Matter (WEOM)
material_processing_set:
- id: nmdc:cspro-99-xyzxyz
type: nmdc:ChromatographicSeparationProcess
has_input:
- nmdc:procsm-99-9gjxns61
has_output:
- nmdc:procsm-99-05g48p90
- nmdc:procsm-99-05g48p91
stationary_phase: BEH-HILIC
chromatographic_category: liquid_chromatography
temperature:
type: nmdc:QuantityValue
has_numeric_value: 25
has_unit: Cel
ordered_mobile_phases:
- type: nmdc:MobilePhaseSegment
duration:
type: nmdc:QuantityValue
has_unit: min
has_numeric_value: 60
substances_used:
- known_as: nmdc:chem-99-000003 # see src/data/valid/Database-chemical_entity_set-1.yaml
type: nmdc:PortionOfSubstance
final_concentration:
type: nmdc:QuantityValue
has_unit: '%'
has_numeric_value: 10
- type: nmdc:MobilePhaseSegment
substances_used:
- known_as: nmdc:chem-99-000015 # see src/data/valid/Database-chemical_entity_set-1.yaml
type: nmdc:PortionOfSubstance
final_concentration:
type: nmdc:QuantityValue
has_unit: mM
has_numeric_value: 15
material_processing_set:
- id: nmdc:mixpro-99-A74
type: nmdc:MixingProcess
has_input:
- nmdc:bsm-99-A67
- nmdc:bsm-99-A68
has_output:
- nmdc:procsm-11-abd123
duration:
type: nmdc:QuantityValue
has_numeric_value: 2
has_unit: hours
instrument_used:
- nmdc:inst-12-124
- id: nmdc:filtpr-22-32G2BS
type: nmdc:FiltrationProcess
has_input:
- nmdc:procsm-99-05g48p90
has_output:
- nmdc:procsm-99-05g48p91
conditionings:
- Methanol
- Sterile water #Milli-Q
filtration_category: pressure
instrument_used:
- nmdc:inst-12-125
is_pressurized: true
- id: nmdc:dispro-99-A74
type: nmdc:DissolvingProcess
has_input:
- nmdc:bsm-12-A67
has_output:
- nmdc:procsm-13-S67F
substances_used:
- known_as: nmdc:chem-99-000015 # see src/data/valid/Database-chemical_entity_set-1.yaml
type: nmdc:PortionOfSubstance
final_concentration:
type: nmdc:QuantityValue
has_unit: mM
has_numeric_value: 15
volume:
type: nmdc:QuantityValue
has_numeric_value: 500
has_unit: mL
- known_as: nmdc:chem-99-000006
type: nmdc:PortionOfSubstance
substance_role: solubilizing_agent
duration:
type: nmdc:QuantityValue
has_numeric_value: 2
has_unit: hours
instrument_used:
- nmdc:inst-12-124
- id: nmdc:chcpr-19-789
type: nmdc:ChemicalConversionProcess
# has_input:
# - nmdc-procsm-99-000001
# has_output:
# - nmdc-procsm-99-000002
chemical_conversion_category: acid_base
substances_used:
- known_as: nmdc:chem-99-000003 # see src/data/valid/Database-chemical_entity_set-1.yaml
type: nmdc:PortionOfSubstance
sample_state_information: liquid
volume:
type: nmdc:QuantityValue
has_numeric_value: 120
has_unit: mL
final_concentration:
type: nmdc:QuantityValue
has_unit: mM
has_numeric_value: 10
temperature:
type: nmdc:QuantityValue
has_numeric_value: 25
has_unit: Cel
duration:
type: nmdc:QuantityValue
has_numeric_value: 1
has_unit: h
- id: nmdc:chcpr-19-7890
type: nmdc:ChemicalConversionProcess
# has_input:
# - nmdc:procsm-37
# has_output:
# - nmdc:procsm-39
substances_used:
- known_as: nmdc:chem-99-000005 # see src/data/valid/Database-chemical_entity_set-1.yaml
type: nmdc:PortionOfSubstance
sample_state_information: liquid
substance_role: solvent
- known_as: nmdc:chem-99-000002
type: nmdc:PortionOfSubstance
substance_role: buffer
source_concentration:
type: nmdc:QuantityValue
has_unit: mM
has_numeric_value: 50
- known_as: nmdc:chem-99-000014
type: nmdc:PortionOfSubstance
substance_role: ms_proteolytic_enzyme
final_concentration:
type: nmdc:QuantityValue
has_unit: μg/μL
has_numeric_value: 0.05
substances_volume:
type: nmdc:QuantityValue
has_numeric_value: 75
has_unit: μL
temperature:
type: nmdc:QuantityValue
has_numeric_value: 37
has_unit: Cel
duration:
type: nmdc:QuantityValue
has_numeric_value: 3
has_unit: h
- id: nmdc:poolp-9x9-1x
type: nmdc:Pooling
name: first pooling process
description: xxx
alternative_identifiers:
- generic:xxx
has_input:
- nmdc:procsm-99-xyz1
- nmdc:procsm-99-xyz2
has_output:
- nmdc:procsm-99-xyz3
- id: nmdc:extrp-99-999999
type: nmdc:Extraction
has_input:
- nmdc:bsm-99-435737
has_output:
- nmdc:procsm-99-0938548
- id: nmdc:libprp-99-999999
type: nmdc:LibraryPreparation
has_input:
- nmdc:procsm-99-0938548
has_output:
- nmdc:procsm-99-sdsdll
functional_annotation_agg:
- gene_function_id: KEGG.ORTHOLOGY:K00627
count: 120
type: nmdc:FunctionalAnnotationAggMember
was_generated_by: nmdc:wfmgan-99-123456.1
biosample_set:
- id: nmdc:bsm-99-isqhuW
type: nmdc:Biosample
name: Permafrost microbial communities from Stordalen Mire, Sweden - 611E1M metaG
description: Permafrost microbial communities from Stordalen Mire, Sweden
associated_studies:
- nmdc:sty-99-8675309
env_broad_scale:
type: nmdc:ControlledIdentifiedTermValue
has_raw_value: ENVO:00002030
term:
id: ENVO:00002030
type: nmdc:OntologyClass
env_local_scale:
type: nmdc:ControlledIdentifiedTermValue
has_raw_value: ENVO:00002169
term:
id: ENVO:00002169
type: nmdc:OntologyClass
env_medium:
type: nmdc:ControlledIdentifiedTermValue
has_raw_value: ENVO:00005792
term:
id: ENVO:00005792
type: nmdc:OntologyClass
samp_name: 11E1M metaG
gold_biosample_identifiers:
- gold:Gb0150408
ecosystem: Environmental
ecosystem_category: Terrestrial
ecosystem_subtype: Wetlands
ecosystem_type: Soil
geo_loc_name:
type: nmdc:TextValue
has_raw_value: 'Sweden: Stordalen'
lat_lon:
type: nmdc:GeolocationValue
has_raw_value: 68.35 19.05
latitude: 68.35
longitude: 19.05
specific_ecosystem: Permafrost
add_date: 17-MAR-17 04.55.54.717000000 PM
community: microbial communities
habitat: Fen
location: Stordalen Mire, Sweden
mod_date: 08-JAN-20 02.49.23.000000000 PM
ncbi_taxonomy_name: permafrost metagenome
sample_collection_site: Mire fen
- id: nmdc:bsm-99-dge3H9
type: nmdc:Biosample
name: Forest soil microbial communities from Barre Woods Harvard Forest LTER site,
Petersham, Massachusetts, United States - Inc-BW-C-14-O
description: Forest soil from Barre Woods Harvard Forest LTER site was incubated
at 10C with heavy water. Sample is from a control plot at ambient soil temperature,
organic horizon - top 4cm of soil
associated_studies:
- nmdc:sty-99-8675309
env_broad_scale:
type: nmdc:ControlledIdentifiedTermValue
has_raw_value: ENVO:00002030
term:
id: ENVO:00002030
type: nmdc:OntologyClass
env_local_scale:
type: nmdc:ControlledIdentifiedTermValue
has_raw_value: ENVO:00002169
term:
id: ENVO:00002169
type: nmdc:OntologyClass
env_medium:
type: nmdc:ControlledIdentifiedTermValue
has_raw_value: ENVO:00005792
term:
id: ENVO:00005792
type: nmdc:OntologyClass
samp_name: Inc-BW-C-14-O
gold_biosample_identifiers:
- gold:Gb0157174
ecosystem: Environmental
ecosystem_category: Terrestrial
ecosystem_subtype: Unclassified
ecosystem_type: Soil
geo_loc_name:
type: nmdc:TextValue
has_raw_value: 'USA: Massachusetts'
lat_lon:
type: nmdc:GeolocationValue
has_raw_value: 42.481016 -72.178343
latitude: 42.481016
longitude: -72.178343
specific_ecosystem: Forest Soil
add_date: 17-AUG-17 05.38.34.719000000 PM
community: microbial communities
habitat: soil
location: Barre Woods Harvard Forest LTER site, Petersham, Massachusetts, United
States
mod_date: 08-JAN-20 02.49.23.000000000 PM
ncbi_taxonomy_name: soil metagenome
sample_collection_site: forest soil
- id: nmdc:bsm-99-dc6tg6
type: nmdc:Biosample
name: Rhizosphere microbial communities from Carex aquatilis grown in University
of Washington, Seatle, WA, United States - 4-1-23 metaG
description: Rhizosphere microbial communities from Carex aquatilis grown in submerged
peat from a thermokarst bog, University of Washington, Seatle, WA, United States
associated_studies:
- nmdc:sty-99-8675309
env_broad_scale:
type: nmdc:ControlledIdentifiedTermValue
has_raw_value: ENVO:00002030
term:
id: ENVO:00002030
type: nmdc:OntologyClass
env_local_scale:
type: nmdc:ControlledIdentifiedTermValue
has_raw_value: ENVO:00002169
term:
id: ENVO:00002169
type: nmdc:OntologyClass
env_medium:
type: nmdc:ControlledIdentifiedTermValue
has_raw_value: ENVO:00005792
term:
id: ENVO:00005792
type: nmdc:OntologyClass
samp_name: 4-1-23 metaG
gold_biosample_identifiers:
- gold:Gb0188037
ecosystem: Host-associated
ecosystem_category: Plants
ecosystem_subtype: Soil
ecosystem_type: Rhizosphere
geo_loc_name:
type: nmdc:TextValue
has_raw_value: 'USA: Seattle, Washington'
lat_lon:
type: nmdc:GeolocationValue
has_raw_value: 47.6516 -122.3045
latitude: 47.6516
longitude: -122.3045
specific_ecosystem: Unclassified
add_date: 29-MAR-18 01.27.40.709000000 PM
community: microbial communities
habitat: rhizosphere
host_name: Carex aquatilis
location: University of Washington, Seatle, WA, United States
mod_date: 08-JAN-20 02.49.25.000000000 PM
ncbi_taxonomy_name: rhizosphere metagenome
sample_collection_site: Peat Soil
- id: nmdc:bsm-99-dtTMNb
type: nmdc:Biosample
associated_studies:
- nmdc:sty-99-abc123
env_broad_scale:
type: nmdc:ControlledIdentifiedTermValue
has_raw_value: ENVO:00002030
term:
id: ENVO:00002030
type: nmdc:OntologyClass
env_local_scale:
type: nmdc:ControlledIdentifiedTermValue
has_raw_value: ENVO:00002169
term:
id: ENVO:00002169
type: nmdc:OntologyClass
env_medium:
type: nmdc:ControlledIdentifiedTermValue
has_raw_value: ENVO:00005792
term:
id: ENVO:00005792
type: nmdc:OntologyClass
dna_cont_type: tube
- id: nmdc:bsm-99-J9FcnC
type: nmdc:Biosample
name: Root microbial communities from poplar common garden site in Clatskanie, Oregon,
USA - BESC-13-CL1_35_33 endosphere
description: Root microbial communities from poplar common garden site in Clatskanie,
Oregon, USA
associated_studies:
- nmdc:sty-99-U21mUX
env_broad_scale:
type: nmdc:ControlledIdentifiedTermValue
has_raw_value: ENVO:00002030
term:
id: ENVO:00002030
type: nmdc:OntologyClass
env_local_scale:
type: nmdc:ControlledIdentifiedTermValue
has_raw_value: ENVO:00002169
term:
id: ENVO:00002169
type: nmdc:OntologyClass
env_medium:
type: nmdc:ControlledIdentifiedTermValue
has_raw_value: ENVO:00005792
term:
id: ENVO:00005792
type: nmdc:OntologyClass
collected_from: nmdc:frsite-99-SPreao
gold_biosample_identifiers:
- gold:Gb0305833
- id: nmdc:bsm-99-BdlWdQ
type: nmdc:Biosample
name: Rhizosphere soil microbial communities from poplar common garden site in Clatskanie,
Oregon, USA - BESC-13-CL1_35_33
description: Rhizosphere soil microbial communities from poplar common garden site
in Clatskanie, Oregon, USA
associated_studies:
- nmdc:sty-99-U21mUX
env_broad_scale:
type: nmdc:ControlledIdentifiedTermValue
has_raw_value: ENVO:00002030
term:
id: ENVO:00002030
type: nmdc:OntologyClass
env_local_scale:
type: nmdc:ControlledIdentifiedTermValue
has_raw_value: ENVO:00002169
term:
id: ENVO:00002169
type: nmdc:OntologyClass
env_medium:
type: nmdc:ControlledIdentifiedTermValue
has_raw_value: ENVO:00005792
term:
id: ENVO:00005792
type: nmdc:OntologyClass
collected_from: nmdc:frsite-99-SPreao
gold_biosample_identifiers:
- gold:Gb0291692
- id: nmdc:bsm-99-vn74Wq
type: nmdc:Biosample
name: Bulk soil microbial communities from poplar common garden site in Clatskanie,
Oregon, USA - BESC-13-CL1_35_33
description: Bulk soil microbial communities from poplar common garden site in Clatskanie,
Oregon, USA
associated_studies:
- nmdc:sty-99-U21mUX
env_broad_scale:
type: nmdc:ControlledIdentifiedTermValue
has_raw_value: ENVO:00002030
term:
id: ENVO:00002030
type: nmdc:OntologyClass
env_local_scale:
type: nmdc:ControlledIdentifiedTermValue
has_raw_value: ENVO:00002169
term:
id: ENVO:00002169
type: nmdc:OntologyClass
env_medium:
type: nmdc:ControlledIdentifiedTermValue
has_raw_value: ENVO:00005792
term:
id: ENVO:00005792
type: nmdc:OntologyClass
collected_from: nmdc:frsite-99-SPreao
gold_biosample_identifiers:
- gold:Gb0291582
- id: nmdc:bsm-99-P8FdpS
type: nmdc:Biosample
name: Root microbial communities from poplar common garden site in Clatskanie, Oregon,
USA - BESC-13-CL2_39_29 endosphere
description: Root microbial communities from poplar common garden site in Clatskanie,
Oregon, USA
associated_studies:
- nmdc:sty-99-U21mUX
env_broad_scale:
type: nmdc:ControlledIdentifiedTermValue
has_raw_value: ENVO:00002030
term:
id: ENVO:00002030
type: nmdc:OntologyClass
env_local_scale:
type: nmdc:ControlledIdentifiedTermValue
has_raw_value: ENVO:00002169
term:
id: ENVO:00002169
type: nmdc:OntologyClass
env_medium:
type: nmdc:ControlledIdentifiedTermValue
has_raw_value: ENVO:00005792
term:
id: ENVO:00005792
type: nmdc:OntologyClass
collected_from: nmdc:frsite-99-h2mYFG
gold_biosample_identifiers:
- gold:Gb0305834
- id: nmdc:bsm-99-ugBwz3
type: nmdc:Biosample
name: Rhizosphere soil microbial communities from poplar common garden site in Clatskanie,
Oregon, USA - BESC-13-CL2_39_29
description: Rhizosphere soil microbial communities from poplar common garden site
in Clatskanie, Oregon, USA
associated_studies:
- nmdc:sty-99-U21mUX
env_broad_scale:
type: nmdc:ControlledIdentifiedTermValue
has_raw_value: ENVO:00002030
term:
id: ENVO:00002030
type: nmdc:OntologyClass
env_local_scale:
type: nmdc:ControlledIdentifiedTermValue
has_raw_value: ENVO:00002169
term:
id: ENVO:00002169
type: nmdc:OntologyClass
env_medium:
type: nmdc:ControlledIdentifiedTermValue
has_raw_value: ENVO:00005792
term:
id: ENVO:00005792
type: nmdc:OntologyClass
collected_from: nmdc:frsite-99-h2mYFG
gold_biosample_identifiers:
- gold:Gb0291693
- id: nmdc:bsm-99-tN5lxM
type: nmdc:Biosample
name: Bulk soil microbial communities from poplar common garden site in Clatskanie,
Oregon, USA - BESC-13-CL2_39_29
description: Bulk soil microbial communities from poplar common garden site in Clatskanie,
Oregon, USA
associated_studies:
- nmdc:sty-99-U21mUX
env_broad_scale:
type: nmdc:ControlledIdentifiedTermValue
has_raw_value: ENVO:00002030
term:
id: ENVO:00002030
type: nmdc:OntologyClass
env_local_scale:
type: nmdc:ControlledIdentifiedTermValue
has_raw_value: ENVO:00002169
term:
id: ENVO:00002169
type: nmdc:OntologyClass
env_medium:
type: nmdc:ControlledIdentifiedTermValue
has_raw_value: ENVO:00005792
term:
id: ENVO:00005792
type: nmdc:OntologyClass
collected_from: nmdc:frsite-99-h2mYFG
gold_biosample_identifiers:
- gold:Gb0291583
- id: nmdc:bsm-99-n3ybxz
type: nmdc:Biosample
name: soil sample 1
description: soil sample collected from a grassland ecosystem
associated_studies:
- nmdc:sty-99-b27v55
env_broad_scale:
type: nmdc:ControlledIdentifiedTermValue
has_raw_value: ENVO:00000001
term:
id: ENVO:00000001
type: nmdc:OntologyClass
env_local_scale:
type: nmdc:ControlledIdentifiedTermValue
has_raw_value: ENVO:00000446
term:
id: ENVO:00000446
type: nmdc:OntologyClass
env_medium:
type: nmdc:ControlledIdentifiedTermValue
has_raw_value: ENVO:00001998
term:
id: ENVO:00001998
type: nmdc:OntologyClass
collected_from: nmdc:frsite-99-78f4bc
- id: nmdc:bsm-99-b316vq
type: nmdc:Biosample
name: soil sample 2
description: soil sample collected from a grassland ecosystem
associated_studies:
- nmdc:sty-99-b27v55
env_broad_scale:
type: nmdc:ControlledIdentifiedTermValue
has_raw_value: ENVO:00000001
term:
id: ENVO:00000001
type: nmdc:OntologyClass
env_local_scale:
type: nmdc:ControlledIdentifiedTermValue
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term:
id: ENVO:00000446
type: nmdc:OntologyClass
env_medium:
type: nmdc:ControlledIdentifiedTermValue
has_raw_value: ENVO:00001998
term:
id: ENVO:00001998
type: nmdc:OntologyClass
collected_from: nmdc:frsite-99-78f4bc
- id: nmdc:bsm-99-q9t93w
type: nmdc:Biosample
name: soil sample 3
description: soil sample collected from a grassland ecosystem
associated_studies:
- nmdc:sty-99-b27v55
env_broad_scale:
type: nmdc:ControlledIdentifiedTermValue
has_raw_value: ENVO:00000001
term:
id: ENVO:00000001
type: nmdc:OntologyClass
env_local_scale:
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term:
id: ENVO:00000446
type: nmdc:OntologyClass
env_medium:
type: nmdc:ControlledIdentifiedTermValue
has_raw_value: ENVO:00001998
term:
id: ENVO:00001998
type: nmdc:OntologyClass
collected_from: nmdc:frsite-99-78f4bc
- id: nmdc:bsm-99-t2r77l
type: nmdc:Biosample
name: water sample 1
description: water sample from a freshwater lake
associated_studies:
- nmdc:sty-99-t9w6g8
env_broad_scale:
type: nmdc:ControlledIdentifiedTermValue
has_raw_value: ENVO:00000001
term:
id: ENVO:00000001
type: nmdc:OntologyClass
env_local_scale:
type: nmdc:ControlledIdentifiedTermValue
has_raw_value: ENVO:00000234
term:
id: ENVO:00000234
type: nmdc:OntologyClass
env_medium:
type: nmdc:ControlledIdentifiedTermValue
has_raw_value: ENVO:00002004
term:
id: ENVO:00002004
type: nmdc:OntologyClass
collected_from: nmdc:frsite-99-k4m6j9
- id: nmdc:bsm-99-x971d3
type: nmdc:Biosample
name: water sample 2
description: water sample from a freshwater lake
associated_studies:
- nmdc:sty-99-t9w6g8
env_broad_scale:
type: nmdc:ControlledIdentifiedTermValue
has_raw_value: ENVO:00000001
term:
id: ENVO:00000001
type: nmdc:OntologyClass
env_local_scale:
type: nmdc:ControlledIdentifiedTermValue
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term:
id: ENVO:00000234
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env_medium:
type: nmdc:ControlledIdentifiedTermValue
has_raw_value: ENVO:00002004
term:
id: ENVO:00002004
type: nmdc:OntologyClass
collected_from: nmdc:frsite-99-k4m6j9
- id: nmdc:bsm-99-c6dlm7
type: nmdc:Biosample
name: water sample 3
description: water sample from a freshwater lake
associated_studies:
- nmdc:sty-99-t9w6g8
env_broad_scale:
type: nmdc:ControlledIdentifiedTermValue
has_raw_value: ENVO:00000001
term:
id: ENVO:00000001
type: nmdc:OntologyClass
env_local_scale:
type: nmdc:ControlledIdentifiedTermValue
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term:
id: ENVO:00000234
type: nmdc:OntologyClass
env_medium:
type: nmdc:ControlledIdentifiedTermValue
has_raw_value: ENVO:00002004
term:
id: ENVO:00002004
type: nmdc:OntologyClass
collected_from: nmdc:frsite-99-k4m6j9
- id: nmdc:bsm-99-p7k6v9
type: nmdc:Biosample
name: human gut sample 1
description: fecal sample from a human subject
associated_studies:
- nmdc:sty-99-q4g1z3
env_broad_scale:
type: nmdc:ControlledIdentifiedTermValue
has_raw_value: ENVO:00000001
term:
id: ENVO:00000001
type: nmdc:OntologyClass
env_local_scale:
type: nmdc:ControlledIdentifiedTermValue
has_raw_value: UBERON:0000059
term:
id: UBERON:0000059
type: nmdc:OntologyClass
env_medium:
type: nmdc:ControlledIdentifiedTermValue
has_raw_value: ENVO:00002005
term:
id: ENVO:00002005
type: nmdc:OntologyClass
host_taxid:
type: nmdc:ControlledIdentifiedTermValue
has_raw_value: NCBITaxon:9606
term:
id: NCBITaxon:9606
type: nmdc:OntologyClass
- id: nmdc:bsm-99-bbbbbb
type: nmdc:Biosample
name: human gut sample 2
description: fecal sample from a human subject
associated_studies:
- nmdc:sty-99-q4g1z3
env_broad_scale:
type: nmdc:ControlledIdentifiedTermValue
has_raw_value: ENVO:00000001
term:
id: ENVO:00000001
type: nmdc:OntologyClass
env_local_scale:
type: nmdc:ControlledIdentifiedTermValue
has_raw_value: UBERON:0000059
term:
id: UBERON:0000059
type: nmdc:OntologyClass
env_medium:
type: nmdc:ControlledIdentifiedTermValue
has_raw_value: ENVO:00002005
term:
id: ENVO:00002005
type: nmdc:OntologyClass
host_taxid:
type: nmdc:ControlledIdentifiedTermValue
has_raw_value: NCBITaxon:9606
term:
id: NCBITaxon:9606
type: nmdc:OntologyClass
- id: nmdc:bsm-99-d9j6n9
type: nmdc:Biosample
name: human gut sample 3
description: fecal sample from a human subject
associated_studies:
- nmdc:sty-99-q4g1z3
env_broad_scale:
type: nmdc:ControlledIdentifiedTermValue
has_raw_value: ENVO:00000001
term:
id: ENVO:00000001
type: nmdc:OntologyClass
env_local_scale:
type: nmdc:ControlledIdentifiedTermValue
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term:
id: UBERON:0000059
type: nmdc:OntologyClass
env_medium:
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has_raw_value: ENVO:00002005
term:
id: ENVO:00002005
type: nmdc:OntologyClass
host_taxid:
type: nmdc:ControlledIdentifiedTermValue
has_raw_value: NCBITaxon:9606
term:
id: NCBITaxon:9606
type: nmdc:OntologyClass
- id: nmdc:bsm-99-999999
type: nmdc:Biosample