Class: StudyTable

NMDC research studies with ecosystem classification and investigator information. Links to GOLD study identifiers and DOIs.

TOTAL STUDIES: 48

ECOSYSTEM DISTRIBUTION: - Environmental/Terrestrial/Soil: 3 studies - Environmental/Aquatic/Freshwater: 3 studies - Environmental/Terrestrial/Deep subsurface: 1 study - Host-associated/Plants: 1 study - Unclassified: 40 studies

STUDY TYPES: - research_study: Individual PI-led studies (most common) - consortium: Multi-institution projects like NEON

EXAMPLE STUDIES: - Deep shale microbiomes (Kelly Wrighton, Colorado State) - SPRUCE peatland experiment (Christopher Schadt, ORNL) - Columbia River hyporheic zone (James Stegen, PNNL) - NEON soil metagenomes (Kate Thibault, nationwide)

URI: https://w3id.org/kbase/nmdc_core/StudyTable

classDiagram class StudyTable click StudyTable href "../StudyTable/" StudyTable : associated_dois StudyTable : description StudyTable : ecosystem StudyTable --> "0..1" Ecosystem : ecosystem click Ecosystem href "../Ecosystem/" StudyTable : ecosystem_category StudyTable --> "0..1" EcosystemCategory : ecosystem_category click EcosystemCategory href "../EcosystemCategory/" StudyTable : ecosystem_subtype StudyTable : ecosystem_type StudyTable --> "0..1" EcosystemType : ecosystem_type click EcosystemType href "../EcosystemType/" StudyTable : funding_sources StudyTable : gold_study_identifiers StudyTable : name StudyTable : principal_investigator_name StudyTable : principal_investigator_orcid StudyTable : specific_ecosystem StudyTable : study_category StudyTable --> "0..1" StudyCategory : study_category click StudyCategory href "../StudyCategory/" StudyTable : study_id StudyTable : title StudyTable : websites

Slots

Name	Cardinality and Range	Description	Inheritance
study_id	1 String	NMDC study identifier	direct
name	0..1 String	Study short name	direct
description	0..1 String	Detailed study description including goals, methods, and context	direct
title	0..1 String	Formal study title (may differ from name)	direct
ecosystem	0..1 Ecosystem	Top-level ecosystem classification	direct
ecosystem_category	0..1 EcosystemCategory	Ecosystem category (second level)	direct
ecosystem_type	0..1 EcosystemType	Specific ecosystem type (third level)	direct
ecosystem_subtype	0..1 String	Ecosystem subtype for further classification	direct
specific_ecosystem	0..1 String	Most specific ecosystem classification	direct
principal_investigator_name	0..1 String	PI name	direct
principal_investigator_orcid	0..1 String	PI ORCID identifier for disambiguation	direct
study_category	0..1 StudyCategory	Category of study	direct
funding_sources	0..1 String	JSON array of funding sources	direct
gold_study_identifiers	0..1 String	JSON array of GOLD study IDs	direct
associated_dois	0..1 String	JSON array of DOI objects with doi_value, doi_category (dataset_doi, award_do...	direct
websites	0..1 String	JSON array of associated website URLs	direct

Identifier and Mapping Information

Annotations

property	value
source_table	study_table

Schema Source

from schema: https://w3id.org/kbase/nmdc_core

Mappings

Mapping Type	Mapped Value
self	https://w3id.org/kbase/nmdc_core/StudyTable
native	https://w3id.org/kbase/nmdc_core/StudyTable

LinkML Source

Direct

name: StudyTable
annotations:
  source_table:
    tag: source_table
    value: study_table
description: 'NMDC research studies with ecosystem classification and investigator
  information. Links to GOLD study identifiers and DOIs.

  TOTAL STUDIES: 48

  ECOSYSTEM DISTRIBUTION: - Environmental/Terrestrial/Soil: 3 studies - Environmental/Aquatic/Freshwater:
  3 studies - Environmental/Terrestrial/Deep subsurface: 1 study - Host-associated/Plants:
  1 study - Unclassified: 40 studies

  STUDY TYPES: - research_study: Individual PI-led studies (most common) - consortium:
  Multi-institution projects like NEON

  EXAMPLE STUDIES: - Deep shale microbiomes (Kelly Wrighton, Colorado State) - SPRUCE
  peatland experiment (Christopher Schadt, ORNL) - Columbia River hyporheic zone (James
  Stegen, PNNL) - NEON soil metagenomes (Kate Thibault, nationwide)'
from_schema: https://w3id.org/kbase/nmdc_core
attributes:
  study_id:
    name: study_id
    description: 'NMDC study identifier. Format: nmdc:sty-NN-XXXXXXXX where NN is
      a two-digit code and X is alphanumeric.'
    examples:
    - value: nmdc:sty-11-8fb6t785
      description: Deep subsurface shale study (Kelly Wrighton)
    - value: nmdc:sty-11-33fbta56
      description: SPRUCE peatland study (Christopher Schadt)
    - value: nmdc:sty-11-aygzgv51
      description: Columbia River study (James Stegen)
    - value: nmdc:sty-11-34xj1150
      description: NEON soil metagenomes (Kate Thibault)
    from_schema: https://w3id.org/kbase/nmdc_core
    rank: 1000
    identifier: true
    domain_of:
    - StudyTable
    range: string
    required: true
    pattern: nmdc:sty-\d{2}-[a-z0-9]+
  name:
    name: name
    description: Study short name
    examples:
    - value: Deep subsurface shale carbon reservoir microbial communities from Ohio
        and West Virginia, USA
    - value: Peatland microbial communities from Minnesota, USA, analyzing carbon
        cycling and trace gas fluxes
    - value: 'National Ecological Observatory Network: soil metagenomes (DP1.10107.001)'
    from_schema: https://w3id.org/kbase/nmdc_core
    domain_of:
    - AnnotationTermsUnified
    - GoTerms
    - EcTerms
    - KeggKoTerms
    - KeggPathwayTerms
    - StudyTable
    - MetabolomicsGold
    - MetacycPathways
    range: string
  description:
    name: description
    description: Detailed study description including goals, methods, and context.
      Often includes information about sampling locations and conditions.
    from_schema: https://w3id.org/kbase/nmdc_core
    domain_of:
    - AnnotationTermsUnified
    - EcTerms
    - CogCategories
    - StudyTable
    - MetacycPathways
    range: string
  title:
    name: title
    description: Formal study title (may differ from name)
    examples:
    - value: Fungal, bacterial, and archaeal communities mediating C cycling and trace
        gas flux in peatland ecosystems subject to climate change
    - value: Riverbed sediment microbial communities from the Columbia River, Washington,
        USA
    from_schema: https://w3id.org/kbase/nmdc_core
    rank: 1000
    domain_of:
    - StudyTable
    range: string
  ecosystem:
    name: ecosystem
    description: Top-level ecosystem classification
    examples:
    - value: Environmental
      description: Most NMDC studies are environmental
    - value: Host-associated
      description: Host-associated microbiomes
    from_schema: https://w3id.org/kbase/nmdc_core
    rank: 1000
    domain_of:
    - StudyTable
    range: Ecosystem
  ecosystem_category:
    name: ecosystem_category
    description: Ecosystem category (second level)
    examples:
    - value: Terrestrial
      description: Land-based environments
    - value: Aquatic
      description: Water environments
    - value: Plants
      description: Plant-associated
    from_schema: https://w3id.org/kbase/nmdc_core
    rank: 1000
    domain_of:
    - StudyTable
    range: EcosystemCategory
  ecosystem_type:
    name: ecosystem_type
    description: Specific ecosystem type (third level)
    examples:
    - value: Deep subsurface
      description: Shale formations, aquifers
    - value: Freshwater
      description: Rivers, wetlands, lakes
    - value: Soil
      description: Surface and subsurface soils
    from_schema: https://w3id.org/kbase/nmdc_core
    rank: 1000
    domain_of:
    - StudyTable
    range: EcosystemType
  ecosystem_subtype:
    name: ecosystem_subtype
    description: Ecosystem subtype for further classification
    examples:
    - value: Wetlands
      description: Peatlands, marshes
    - value: River
      description: River sediments
    - value: Unclassified
      description: Not further classified
    from_schema: https://w3id.org/kbase/nmdc_core
    rank: 1000
    domain_of:
    - StudyTable
    range: string
  specific_ecosystem:
    name: specific_ecosystem
    description: Most specific ecosystem classification
    examples:
    - value: Sediment
      description: River or lake sediments
    - value: Forest Soil
      description: Forest soil microbiomes
    - value: Unclassified
    from_schema: https://w3id.org/kbase/nmdc_core
    rank: 1000
    domain_of:
    - StudyTable
    range: string
  principal_investigator_name:
    name: principal_investigator_name
    description: PI name
    examples:
    - value: Kelly Wrighton
      description: Colorado State University
    - value: Christopher Schadt
      description: Oak Ridge National Lab
    - value: James Stegen
      description: Pacific Northwest National Lab
    - value: Kate Thibault
      description: NEON/Battelle Ecology
    from_schema: https://w3id.org/kbase/nmdc_core
    rank: 1000
    domain_of:
    - StudyTable
    range: string
  principal_investigator_orcid:
    name: principal_investigator_orcid
    description: PI ORCID identifier for disambiguation
    examples:
    - value: orcid:0000-0003-0434-4217
      description: Kelly Wrighton
    - value: orcid:0000-0001-8759-2448
      description: Christopher Schadt
    - value: orcid:0000-0001-9135-7424
      description: James Stegen
    from_schema: https://w3id.org/kbase/nmdc_core
    rank: 1000
    domain_of:
    - StudyTable
    range: string
    pattern: orcid:\d{4}-\d{4}-\d{4}-\d{3}[0-9X]
  study_category:
    name: study_category
    description: Category of study
    examples:
    - value: research_study
      description: Most studies are individual research
    - value: consortium
      description: NEON is a consortium
    from_schema: https://w3id.org/kbase/nmdc_core
    rank: 1000
    domain_of:
    - StudyTable
    range: StudyCategory
  funding_sources:
    name: funding_sources
    description: JSON array of funding sources
    examples:
    - value: '["National Sciences Foundation Dimensions of Biodiversity (award no.
        1342701)"]'
    - value: '["U.S. Department of Energy, Office of Science, Office of Biological
        and Environmental Research (BER)"]'
    from_schema: https://w3id.org/kbase/nmdc_core
    rank: 1000
    domain_of:
    - StudyTable
    range: string
  gold_study_identifiers:
    name: gold_study_identifiers
    description: JSON array of GOLD study IDs
    examples:
    - value: '["gold:Gs0114675"]'
      description: Single GOLD ID
    - value: '["gold:Gs0144570", "gold:Gs0161344"]'
      description: Multiple GOLD IDs (NEON)
    from_schema: https://w3id.org/kbase/nmdc_core
    rank: 1000
    domain_of:
    - StudyTable
    range: string
  associated_dois:
    name: associated_dois
    description: JSON array of DOI objects with doi_value, doi_category (dataset_doi,
      award_doi, publication_doi), and doi_provider (jgi, emsl, etc.)
    examples:
    - value: '[{"doi_value": "doi:10.25585/1487763", "doi_category": "dataset_doi",
        "doi_provider": "jgi"}]'
    - value: '[{"doi_value": "doi:10.1371/journal.pone.0228165", "doi_category": "publication_doi"}]'
      description: Publication DOI
    from_schema: https://w3id.org/kbase/nmdc_core
    rank: 1000
    domain_of:
    - StudyTable
    range: string
  websites:
    name: websites
    description: JSON array of associated website URLs
    examples:
    - value: '["https://mnspruce.ornl.gov/project/overview"]'
      description: SPRUCE project website
    - value: '["https://www.pnnl.gov/projects/river-corridor-hydrobiogeochemistry-science-focus-area"]'
      description: PNNL project page
    from_schema: https://w3id.org/kbase/nmdc_core
    rank: 1000
    domain_of:
    - StudyTable
    range: string

Induced

name: StudyTable
annotations:
  source_table:
    tag: source_table
    value: study_table
description: 'NMDC research studies with ecosystem classification and investigator
  information. Links to GOLD study identifiers and DOIs.

  TOTAL STUDIES: 48

  ECOSYSTEM DISTRIBUTION: - Environmental/Terrestrial/Soil: 3 studies - Environmental/Aquatic/Freshwater:
  3 studies - Environmental/Terrestrial/Deep subsurface: 1 study - Host-associated/Plants:
  1 study - Unclassified: 40 studies

  STUDY TYPES: - research_study: Individual PI-led studies (most common) - consortium:
  Multi-institution projects like NEON

  EXAMPLE STUDIES: - Deep shale microbiomes (Kelly Wrighton, Colorado State) - SPRUCE
  peatland experiment (Christopher Schadt, ORNL) - Columbia River hyporheic zone (James
  Stegen, PNNL) - NEON soil metagenomes (Kate Thibault, nationwide)'
from_schema: https://w3id.org/kbase/nmdc_core
attributes:
  study_id:
    name: study_id
    description: 'NMDC study identifier. Format: nmdc:sty-NN-XXXXXXXX where NN is
      a two-digit code and X is alphanumeric.'
    examples:
    - value: nmdc:sty-11-8fb6t785
      description: Deep subsurface shale study (Kelly Wrighton)
    - value: nmdc:sty-11-33fbta56
      description: SPRUCE peatland study (Christopher Schadt)
    - value: nmdc:sty-11-aygzgv51
      description: Columbia River study (James Stegen)
    - value: nmdc:sty-11-34xj1150
      description: NEON soil metagenomes (Kate Thibault)
    from_schema: https://w3id.org/kbase/nmdc_core
    rank: 1000
    identifier: true
    alias: study_id
    owner: StudyTable
    domain_of:
    - StudyTable
    range: string
    required: true
    pattern: nmdc:sty-\d{2}-[a-z0-9]+
  name:
    name: name
    description: Study short name
    examples:
    - value: Deep subsurface shale carbon reservoir microbial communities from Ohio
        and West Virginia, USA
    - value: Peatland microbial communities from Minnesota, USA, analyzing carbon
        cycling and trace gas fluxes
    - value: 'National Ecological Observatory Network: soil metagenomes (DP1.10107.001)'
    from_schema: https://w3id.org/kbase/nmdc_core
    alias: name
    owner: StudyTable
    domain_of:
    - AnnotationTermsUnified
    - GoTerms
    - EcTerms
    - KeggKoTerms
    - KeggPathwayTerms
    - StudyTable
    - MetabolomicsGold
    - MetacycPathways
    range: string
  description:
    name: description
    description: Detailed study description including goals, methods, and context.
      Often includes information about sampling locations and conditions.
    from_schema: https://w3id.org/kbase/nmdc_core
    alias: description
    owner: StudyTable
    domain_of:
    - AnnotationTermsUnified
    - EcTerms
    - CogCategories
    - StudyTable
    - MetacycPathways
    range: string
  title:
    name: title
    description: Formal study title (may differ from name)
    examples:
    - value: Fungal, bacterial, and archaeal communities mediating C cycling and trace
        gas flux in peatland ecosystems subject to climate change
    - value: Riverbed sediment microbial communities from the Columbia River, Washington,
        USA
    from_schema: https://w3id.org/kbase/nmdc_core
    rank: 1000
    alias: title
    owner: StudyTable
    domain_of:
    - StudyTable
    range: string
  ecosystem:
    name: ecosystem
    description: Top-level ecosystem classification
    examples:
    - value: Environmental
      description: Most NMDC studies are environmental
    - value: Host-associated
      description: Host-associated microbiomes
    from_schema: https://w3id.org/kbase/nmdc_core
    rank: 1000
    alias: ecosystem
    owner: StudyTable
    domain_of:
    - StudyTable
    range: Ecosystem
  ecosystem_category:
    name: ecosystem_category
    description: Ecosystem category (second level)
    examples:
    - value: Terrestrial
      description: Land-based environments
    - value: Aquatic
      description: Water environments
    - value: Plants
      description: Plant-associated
    from_schema: https://w3id.org/kbase/nmdc_core
    rank: 1000
    alias: ecosystem_category
    owner: StudyTable
    domain_of:
    - StudyTable
    range: EcosystemCategory
  ecosystem_type:
    name: ecosystem_type
    description: Specific ecosystem type (third level)
    examples:
    - value: Deep subsurface
      description: Shale formations, aquifers
    - value: Freshwater
      description: Rivers, wetlands, lakes
    - value: Soil
      description: Surface and subsurface soils
    from_schema: https://w3id.org/kbase/nmdc_core
    rank: 1000
    alias: ecosystem_type
    owner: StudyTable
    domain_of:
    - StudyTable
    range: EcosystemType
  ecosystem_subtype:
    name: ecosystem_subtype
    description: Ecosystem subtype for further classification
    examples:
    - value: Wetlands
      description: Peatlands, marshes
    - value: River
      description: River sediments
    - value: Unclassified
      description: Not further classified
    from_schema: https://w3id.org/kbase/nmdc_core
    rank: 1000
    alias: ecosystem_subtype
    owner: StudyTable
    domain_of:
    - StudyTable
    range: string
  specific_ecosystem:
    name: specific_ecosystem
    description: Most specific ecosystem classification
    examples:
    - value: Sediment
      description: River or lake sediments
    - value: Forest Soil
      description: Forest soil microbiomes
    - value: Unclassified
    from_schema: https://w3id.org/kbase/nmdc_core
    rank: 1000
    alias: specific_ecosystem
    owner: StudyTable
    domain_of:
    - StudyTable
    range: string
  principal_investigator_name:
    name: principal_investigator_name
    description: PI name
    examples:
    - value: Kelly Wrighton
      description: Colorado State University
    - value: Christopher Schadt
      description: Oak Ridge National Lab
    - value: James Stegen
      description: Pacific Northwest National Lab
    - value: Kate Thibault
      description: NEON/Battelle Ecology
    from_schema: https://w3id.org/kbase/nmdc_core
    rank: 1000
    alias: principal_investigator_name
    owner: StudyTable
    domain_of:
    - StudyTable
    range: string
  principal_investigator_orcid:
    name: principal_investigator_orcid
    description: PI ORCID identifier for disambiguation
    examples:
    - value: orcid:0000-0003-0434-4217
      description: Kelly Wrighton
    - value: orcid:0000-0001-8759-2448
      description: Christopher Schadt
    - value: orcid:0000-0001-9135-7424
      description: James Stegen
    from_schema: https://w3id.org/kbase/nmdc_core
    rank: 1000
    alias: principal_investigator_orcid
    owner: StudyTable
    domain_of:
    - StudyTable
    range: string
    pattern: orcid:\d{4}-\d{4}-\d{4}-\d{3}[0-9X]
  study_category:
    name: study_category
    description: Category of study
    examples:
    - value: research_study
      description: Most studies are individual research
    - value: consortium
      description: NEON is a consortium
    from_schema: https://w3id.org/kbase/nmdc_core
    rank: 1000
    alias: study_category
    owner: StudyTable
    domain_of:
    - StudyTable
    range: StudyCategory
  funding_sources:
    name: funding_sources
    description: JSON array of funding sources
    examples:
    - value: '["National Sciences Foundation Dimensions of Biodiversity (award no.
        1342701)"]'
    - value: '["U.S. Department of Energy, Office of Science, Office of Biological
        and Environmental Research (BER)"]'
    from_schema: https://w3id.org/kbase/nmdc_core
    rank: 1000
    alias: funding_sources
    owner: StudyTable
    domain_of:
    - StudyTable
    range: string
  gold_study_identifiers:
    name: gold_study_identifiers
    description: JSON array of GOLD study IDs
    examples:
    - value: '["gold:Gs0114675"]'
      description: Single GOLD ID
    - value: '["gold:Gs0144570", "gold:Gs0161344"]'
      description: Multiple GOLD IDs (NEON)
    from_schema: https://w3id.org/kbase/nmdc_core
    rank: 1000
    alias: gold_study_identifiers
    owner: StudyTable
    domain_of:
    - StudyTable
    range: string
  associated_dois:
    name: associated_dois
    description: JSON array of DOI objects with doi_value, doi_category (dataset_doi,
      award_doi, publication_doi), and doi_provider (jgi, emsl, etc.)
    examples:
    - value: '[{"doi_value": "doi:10.25585/1487763", "doi_category": "dataset_doi",
        "doi_provider": "jgi"}]'
    - value: '[{"doi_value": "doi:10.1371/journal.pone.0228165", "doi_category": "publication_doi"}]'
      description: Publication DOI
    from_schema: https://w3id.org/kbase/nmdc_core
    rank: 1000
    alias: associated_dois
    owner: StudyTable
    domain_of:
    - StudyTable
    range: string
  websites:
    name: websites
    description: JSON array of associated website URLs
    examples:
    - value: '["https://mnspruce.ornl.gov/project/overview"]'
      description: SPRUCE project website
    - value: '["https://www.pnnl.gov/projects/river-corridor-hydrobiogeochemistry-science-focus-area"]'
      description: PNNL project page
    from_schema: https://w3id.org/kbase/nmdc_core
    rank: 1000
    alias: websites
    owner: StudyTable
    domain_of:
    - StudyTable
    range: string