Class: STORMSChecklist

A checklist of items that should be reported in a microbiome study. Try and provide a value for ALL items. If an item is not reported, say NOT REPORTED.

URI: storms:STORMSChecklist

erDiagram STORMSChecklist { string abstract_structured_or_unstructured string abstract_study_design string abstract_sequencing_methods string abstract_specimens string introduction_background_and_rationale string introduction_hypotheses string methods_study_design string methods_participants string methods_geographic_location string methods_relevant_dates string methods_eligibility_criteria string methods_antibiotics_usage string methods_analytic_sample_size string methods_longitudinal_studies string methods_matching string methods_ethics string methods_laboratory_methods string methods_specimen_collection string methods_shipping string methods_storage string methods_dna_extraction string methods_human_dna_sequence_depletion_or_microbial_dna_enrichment string methods_primer_selection string methods_positive_controls string methods_negative_controls string methods_contaminant_mitigation_and_identification string methods_replication string methods_sequencing_strategy string methods_sequencing_methods string methods_batch_effects string methods_metatranscriptomics string methods_metaproteomics string methods_metabolomics string results_descriptive_data string results_microbiome_data string results_taxonomy string results_differential_abundance string results_other_data_types string results_other_statistical_analysis string discussion_key_results string discussion_interpretation string discussion_limitations string discussion_bias string discussion_generalizability string discussion_ongoing_future_work string other_information_funding string other_information_acknowledgements string other_information_conflicts_of_interest string other_information_supplements string other_information_supplementary_data }

Slots

Name	Cardinality and Range	Description	Inheritance
abstract_structured_or_unstructured	0..1 String	Abstract should include information on background, methods, results, and conc...	direct
abstract_study_design	0..1 String	State study design in abstract	direct
abstract_sequencing_methods	0..1 String	State the strategy used for metagenomic classification	direct
abstract_specimens	0..1 String	Describe body site(s) studied	direct
introduction_background_and_rationale	0..1 String	Summarize the underlying background, scientific evidence, or theory driving t...	direct
introduction_hypotheses	0..1 String	State the pre-specified hypothesis	direct
methods_study_design	0..1 String	Describe the study design	direct
methods_participants	0..1 String	State what the population of interest is, and the method by which participant...	direct
methods_geographic_location	0..1 String	State the geographic region(s) where participants were sampled from	direct
methods_relevant_dates	0..1 String	State the start and end dates for recruitment, follow-up, and data collection	direct
methods_eligibility_criteria	0..1 String	List any criteria for inclusion and exclusion of recruited participants	direct
methods_antibiotics_usage	0..1 String	List what is known about antibiotics usage before or during sample collection	direct
methods_analytic_sample_size	0..1 String	Explain how the final analytic sample size was calculated, including the numb...	direct
methods_longitudinal_studies	0..1 String	For longitudinal studies, state how many follow-ups were conducted, describe ...	direct
methods_matching	0..1 String	For matched studies, give matching criteria	direct
methods_ethics	0..1 String	State the name of the institutional review board that approved the study and ...	direct
methods_laboratory_methods	0..1 String	State the laboratory/center where laboratory work was done	direct
methods_specimen_collection	0..1 String	State the body site(s) sampled from and how specimens were collected	direct
methods_shipping	0..1 String	Describe how samples were stored and shipped to the laboratory	direct
methods_storage	0..1 String	Describe how the laboratory stored samples, including time between collection...	direct
methods_dna_extraction	0..1 String	Provide DNA extraction method, including kit and version if relevant	direct
methods_human_dna_sequence_depletion_or_microbial_dna_enrichment	0..1 String	Describe whether human DNA sequence depletion or enrichment of microbial or v...	direct
methods_primer_selection	0..1 String	Provide primer selection and DNA amplification methods as well as variable re...	direct
methods_positive_controls	0..1 String	Describe any positive controls (mock communities) if used	direct
methods_negative_controls	0..1 String	Describe any negative controls if used	direct
methods_contaminant_mitigation_and_identification	0..1 String	Provide any laboratory or computational methods used to control for or identi...	direct
methods_replication	0..1 String	Describe any biological or technical replicates included in the sequencing, i...	direct
methods_sequencing_strategy	0..1 String	Major divisions of strategy, such as shotgun or amplicon sequencing	direct
methods_sequencing_methods	0..1 String	State whether experimental quantification was used (QMP/cell count based, spi...	direct
methods_batch_effects	0..1 String	Detail any blocking or randomization used in study design to avoid confoundin...	direct
methods_metatranscriptomics	0..1 String	Detail whether any mRNA enrichment was performed and whether/how retrotranscr...	direct
methods_metaproteomics	0..1 String	Detail which protease was used for digestion	direct
methods_metabolomics	0..1 String	Specify the analytic method used (such as nuclear magnetic resonance spectros...	direct
results_descriptive_data	0..1 String	Give characteristics of study participants (e	direct
results_microbiome_data	0..1 String	Report descriptive findings for microbiome analyses with all applicable outco...	direct
results_taxonomy	0..1 String	Identify taxonomy using standardized taxon classifications that are sufficien...	direct
results_differential_abundance	0..1 String	Report results of differential abundance analysis by the variable of interest...	direct
results_other_data_types	0..1 String	Report other data analyzed--e	direct
results_other_statistical_analysis	0..1 String	Report any statistical data analysis not covered above	direct
discussion_key_results	0..1 String	Summarize key results with reference to study objectives	direct
discussion_interpretation	0..1 String	Give a cautious overall interpretation of results considering objectives, lim...	direct
discussion_limitations	0..1 String	Discuss limitations of the study, taking into account sources of potential bi...	direct
discussion_bias	0..1 String	Discuss any potential for bias to influence study findings	direct
discussion_generalizability	0..1 String	Discuss the generalizability (external validity) of the study results	direct
discussion_ongoing_future_work	0..1 String	Describe potential future research or ongoing research based on the study's f...	direct
other_information_funding	0..1 String	Give the source of funding and the role of the funders for the present study ...	direct
other_information_acknowledgements	0..1 String	Include acknowledgements of those who contributed to the research but did not...	direct
other_information_conflicts_of_interest	0..1 String	Include a conflicts of interest statement	direct
other_information_supplements	0..1 String	Indicate where supplements may be accessed and what materials they contain	direct
other_information_supplementary_data	0..1 String	Provide supplementary data files of results with all taxa and all outcome var...	direct

Identifier and Mapping Information

Annotations

property	value
prompt	Try and provide a value for ALL items. If an item is not reported, say NOT REPORTED

Schema Source

from schema: https://w3id.org/ontogpt/storms

Mappings

Mapping Type	Mapped Value
self	storms:STORMSChecklist
native	storms:STORMSChecklist

LinkML Source

Direct

name: STORMSChecklist
annotations:
  prompt:
    tag: prompt
    value: Try and provide a value for ALL items. If an item is not reported, say
      NOT REPORTED
description: A checklist of items that should be reported in a microbiome study. Try
  and provide a value for ALL items. If an item is not reported, say NOT REPORTED.
from_schema: https://w3id.org/ontogpt/storms
attributes:
  abstract_structured_or_unstructured:
    name: abstract_structured_or_unstructured
    description: Abstract should include information on background, methods, results,
      and conclusions in structured or unstructured format.
    from_schema: https://w3id.org/ontogpt/storms
    rank: 1000
    domain_of:
    - STORMSChecklist
    slot_group: abstract
    range: string
  abstract_study_design:
    name: abstract_study_design
    description: State study design in abstract.
    from_schema: https://w3id.org/ontogpt/storms
    rank: 1000
    domain_of:
    - STORMSChecklist
    slot_group: abstract
    range: string
  abstract_sequencing_methods:
    name: abstract_sequencing_methods
    description: State the strategy used for metagenomic classification.
    from_schema: https://w3id.org/ontogpt/storms
    rank: 1000
    domain_of:
    - STORMSChecklist
    slot_group: abstract
    range: string
  abstract_specimens:
    name: abstract_specimens
    description: Describe body site(s) studied.
    from_schema: https://w3id.org/ontogpt/storms
    rank: 1000
    domain_of:
    - STORMSChecklist
    slot_group: abstract
    range: string
  introduction_background_and_rationale:
    name: introduction_background_and_rationale
    description: Summarize the underlying background, scientific evidence, or theory
      driving the current hypothesis as well as the study objectives.
    from_schema: https://w3id.org/ontogpt/storms
    rank: 1000
    domain_of:
    - STORMSChecklist
    slot_group: introduction
    range: string
  introduction_hypotheses:
    name: introduction_hypotheses
    description: State the pre-specified hypothesis. If the study is exploratory,
      state any pre-specified study objectives.
    from_schema: https://w3id.org/ontogpt/storms
    rank: 1000
    domain_of:
    - STORMSChecklist
    slot_group: introduction
    range: string
  methods_study_design:
    name: methods_study_design
    description: Describe the study design.
    from_schema: https://w3id.org/ontogpt/storms
    rank: 1000
    domain_of:
    - STORMSChecklist
    slot_group: methods
    range: string
  methods_participants:
    name: methods_participants
    description: State what the population of interest is, and the method by which
      participants are sampled from that population.
    from_schema: https://w3id.org/ontogpt/storms
    rank: 1000
    domain_of:
    - STORMSChecklist
    slot_group: methods
    range: string
  methods_geographic_location:
    name: methods_geographic_location
    description: State the geographic region(s) where participants were sampled from.
    from_schema: https://w3id.org/ontogpt/storms
    rank: 1000
    domain_of:
    - STORMSChecklist
    slot_group: methods
    range: string
  methods_relevant_dates:
    name: methods_relevant_dates
    description: State the start and end dates for recruitment, follow-up, and data
      collection.
    from_schema: https://w3id.org/ontogpt/storms
    rank: 1000
    domain_of:
    - STORMSChecklist
    slot_group: methods
    range: string
  methods_eligibility_criteria:
    name: methods_eligibility_criteria
    description: List any criteria for inclusion and exclusion of recruited participants.
    from_schema: https://w3id.org/ontogpt/storms
    rank: 1000
    domain_of:
    - STORMSChecklist
    slot_group: methods
    range: string
  methods_antibiotics_usage:
    name: methods_antibiotics_usage
    description: List what is known about antibiotics usage before or during sample
      collection.
    from_schema: https://w3id.org/ontogpt/storms
    rank: 1000
    domain_of:
    - STORMSChecklist
    slot_group: methods
    range: string
  methods_analytic_sample_size:
    name: methods_analytic_sample_size
    description: Explain how the final analytic sample size was calculated, including
      the number of cases and controls if relevant, and reasons for dropout at each
      stage of the study.
    from_schema: https://w3id.org/ontogpt/storms
    rank: 1000
    domain_of:
    - STORMSChecklist
    slot_group: methods
    range: string
  methods_longitudinal_studies:
    name: methods_longitudinal_studies
    description: For longitudinal studies, state how many follow-ups were conducted,
      describe sample size at follow-up by group or condition, and discuss any loss
      to follow-up.
    from_schema: https://w3id.org/ontogpt/storms
    rank: 1000
    domain_of:
    - STORMSChecklist
    slot_group: methods
    range: string
  methods_matching:
    name: methods_matching
    description: For matched studies, give matching criteria.
    from_schema: https://w3id.org/ontogpt/storms
    rank: 1000
    domain_of:
    - STORMSChecklist
    slot_group: methods
    range: string
  methods_ethics:
    name: methods_ethics
    description: State the name of the institutional review board that approved the
      study and protocols, protocol number and date of approval, and procedures for
      obtaining informed consent from participants.
    from_schema: https://w3id.org/ontogpt/storms
    rank: 1000
    domain_of:
    - STORMSChecklist
    slot_group: methods
    range: string
  methods_laboratory_methods:
    name: methods_laboratory_methods
    description: State the laboratory/center where laboratory work was done.
    from_schema: https://w3id.org/ontogpt/storms
    rank: 1000
    domain_of:
    - STORMSChecklist
    slot_group: methods
    range: string
  methods_specimen_collection:
    name: methods_specimen_collection
    description: State the body site(s) sampled from and how specimens were collected.
    from_schema: https://w3id.org/ontogpt/storms
    rank: 1000
    domain_of:
    - STORMSChecklist
    slot_group: methods
    range: string
  methods_shipping:
    name: methods_shipping
    description: Describe how samples were stored and shipped to the laboratory.
    from_schema: https://w3id.org/ontogpt/storms
    rank: 1000
    domain_of:
    - STORMSChecklist
    slot_group: methods
    range: string
  methods_storage:
    name: methods_storage
    description: Describe how the laboratory stored samples, including time between
      collection and storage and any preservation buffers or refrigeration used.
    from_schema: https://w3id.org/ontogpt/storms
    rank: 1000
    domain_of:
    - STORMSChecklist
    slot_group: methods
    range: string
  methods_dna_extraction:
    name: methods_dna_extraction
    description: Provide DNA extraction method, including kit and version if relevant.
    from_schema: https://w3id.org/ontogpt/storms
    rank: 1000
    domain_of:
    - STORMSChecklist
    slot_group: methods
    range: string
  methods_human_dna_sequence_depletion_or_microbial_dna_enrichment:
    name: methods_human_dna_sequence_depletion_or_microbial_dna_enrichment
    description: Describe whether human DNA sequence depletion or enrichment of microbial
      or viral DNA was performed.
    from_schema: https://w3id.org/ontogpt/storms
    rank: 1000
    domain_of:
    - STORMSChecklist
    slot_group: methods
    range: string
  methods_primer_selection:
    name: methods_primer_selection
    description: Provide primer selection and DNA amplification methods as well as
      variable region sequenced (if applicable).
    from_schema: https://w3id.org/ontogpt/storms
    rank: 1000
    domain_of:
    - STORMSChecklist
    slot_group: methods
    range: string
  methods_positive_controls:
    name: methods_positive_controls
    description: Describe any positive controls (mock communities) if used.
    from_schema: https://w3id.org/ontogpt/storms
    rank: 1000
    domain_of:
    - STORMSChecklist
    slot_group: methods
    range: string
  methods_negative_controls:
    name: methods_negative_controls
    description: Describe any negative controls if used.
    from_schema: https://w3id.org/ontogpt/storms
    rank: 1000
    domain_of:
    - STORMSChecklist
    slot_group: methods
    range: string
  methods_contaminant_mitigation_and_identification:
    name: methods_contaminant_mitigation_and_identification
    description: Provide any laboratory or computational methods used to control for
      or identify microbiome contamination from the environment, reagents, or laboratory.
    from_schema: https://w3id.org/ontogpt/storms
    rank: 1000
    domain_of:
    - STORMSChecklist
    slot_group: methods
    range: string
  methods_replication:
    name: methods_replication
    description: Describe any biological or technical replicates included in the sequencing,
      including which steps were replicated between them.
    from_schema: https://w3id.org/ontogpt/storms
    rank: 1000
    domain_of:
    - STORMSChecklist
    slot_group: methods
    range: string
  methods_sequencing_strategy:
    name: methods_sequencing_strategy
    description: Major divisions of strategy, such as shotgun or amplicon sequencing.
    from_schema: https://w3id.org/ontogpt/storms
    rank: 1000
    domain_of:
    - STORMSChecklist
    slot_group: methods
    range: string
  methods_sequencing_methods:
    name: methods_sequencing_methods
    description: State whether experimental quantification was used (QMP/cell count
      based, spike-in based) or whether relative abundance methods were applied.
    from_schema: https://w3id.org/ontogpt/storms
    rank: 1000
    domain_of:
    - STORMSChecklist
    slot_group: methods
    range: string
  methods_batch_effects:
    name: methods_batch_effects
    description: Detail any blocking or randomization used in study design to avoid
      confounding of batches with exposures or outcomes. Discuss any likely sources
      of batch effects, if known.
    from_schema: https://w3id.org/ontogpt/storms
    rank: 1000
    domain_of:
    - STORMSChecklist
    slot_group: methods
    range: string
  methods_metatranscriptomics:
    name: methods_metatranscriptomics
    description: Detail whether any mRNA enrichment was performed and whether/how
      retrotranscription was performed prior to sequencing. Provide size range of
      isolated transcripts. Describe whether the sequencing library was stranded or
      not. Provide details on sequencing methods and platforms.
    from_schema: https://w3id.org/ontogpt/storms
    rank: 1000
    domain_of:
    - STORMSChecklist
    slot_group: methods
    range: string
  methods_metaproteomics:
    name: methods_metaproteomics
    description: Detail which protease was used for digestion. Provide details on
      proteomic methods and platforms (e.g. LC-MS/MS, instrument type, column type,
      mass range, resolution, scan speed, maximum injection time, isolation window,
      normalised collision energy, and resolution).
    from_schema: https://w3id.org/ontogpt/storms
    rank: 1000
    domain_of:
    - STORMSChecklist
    slot_group: methods
    range: string
  methods_metabolomics:
    name: methods_metabolomics
    description: Specify the analytic method used (such as nuclear magnetic resonance
      spectroscopy or mass spectrometry). For mass spectrometry, detail which fractions
      were obtained (polar and/or non polar) and how these were analyzed. Provide
      details on metabolomics methods and platforms (e.g. derivatization, instrument
      type, injection type, column type and instrument settings).
    from_schema: https://w3id.org/ontogpt/storms
    rank: 1000
    domain_of:
    - STORMSChecklist
    slot_group: methods
    range: string
  results_descriptive_data:
    name: results_descriptive_data
    description: Give characteristics of study participants (e.g. dietary, demographic,
      clinical, social) and information on exposures and potential confounders.
    from_schema: https://w3id.org/ontogpt/storms
    rank: 1000
    domain_of:
    - STORMSChecklist
    slot_group: results
    range: string
  results_microbiome_data:
    name: results_microbiome_data
    description: Report descriptive findings for microbiome analyses with all applicable
      outcomes and covariates.
    from_schema: https://w3id.org/ontogpt/storms
    rank: 1000
    domain_of:
    - STORMSChecklist
    slot_group: results
    range: string
  results_taxonomy:
    name: results_taxonomy
    description: Identify taxonomy using standardized taxon classifications that are
      sufficient to uniquely identify taxa.
    from_schema: https://w3id.org/ontogpt/storms
    rank: 1000
    domain_of:
    - STORMSChecklist
    slot_group: results
    range: string
  results_differential_abundance:
    name: results_differential_abundance
    description: Report results of differential abundance analysis by the variable
      of interest and (if applicable) by time, clearly indicating the direction of
      change and total number of taxa tested.
    from_schema: https://w3id.org/ontogpt/storms
    rank: 1000
    domain_of:
    - STORMSChecklist
    slot_group: results
    range: string
  results_other_data_types:
    name: results_other_data_types
    description: Report other data analyzed--e.g. metabolic function, functional potential,
      MAG assembly, and RNAseq.
    from_schema: https://w3id.org/ontogpt/storms
    rank: 1000
    domain_of:
    - STORMSChecklist
    slot_group: results
    range: string
  results_other_statistical_analysis:
    name: results_other_statistical_analysis
    description: Report any statistical data analysis not covered above.
    from_schema: https://w3id.org/ontogpt/storms
    rank: 1000
    domain_of:
    - STORMSChecklist
    slot_group: results
    range: string
  discussion_key_results:
    name: discussion_key_results
    description: Summarize key results with reference to study objectives.
    from_schema: https://w3id.org/ontogpt/storms
    rank: 1000
    domain_of:
    - STORMSChecklist
    slot_group: discussion
    range: string
  discussion_interpretation:
    name: discussion_interpretation
    description: Give a cautious overall interpretation of results considering objectives,
      limitations, multiplicity of analyses, results from similar studies, and other
      relevant evidence.
    from_schema: https://w3id.org/ontogpt/storms
    rank: 1000
    domain_of:
    - STORMSChecklist
    slot_group: discussion
    range: string
  discussion_limitations:
    name: discussion_limitations
    description: Discuss limitations of the study, taking into account sources of
      potential bias or imprecision.
    from_schema: https://w3id.org/ontogpt/storms
    rank: 1000
    domain_of:
    - STORMSChecklist
    slot_group: discussion
    range: string
  discussion_bias:
    name: discussion_bias
    description: Discuss any potential for bias to influence study findings.
    from_schema: https://w3id.org/ontogpt/storms
    rank: 1000
    domain_of:
    - STORMSChecklist
    slot_group: discussion
    range: string
  discussion_generalizability:
    name: discussion_generalizability
    description: Discuss the generalizability (external validity) of the study results.
    from_schema: https://w3id.org/ontogpt/storms
    rank: 1000
    domain_of:
    - STORMSChecklist
    slot_group: discussion
    range: string
  discussion_ongoing_future_work:
    name: discussion_ongoing_future_work
    description: Describe potential future research or ongoing research based on the
      study's findings.
    from_schema: https://w3id.org/ontogpt/storms
    rank: 1000
    domain_of:
    - STORMSChecklist
    slot_group: discussion
    range: string
  other_information_funding:
    name: other_information_funding
    description: Give the source of funding and the role of the funders for the present
      study and, if applicable, for the original study on which the present article
      is based.
    from_schema: https://w3id.org/ontogpt/storms
    rank: 1000
    domain_of:
    - STORMSChecklist
    slot_group: other_information
    range: string
  other_information_acknowledgements:
    name: other_information_acknowledgements
    description: Include acknowledgements of those who contributed to the research
      but did not meet criteria for authorship.
    from_schema: https://w3id.org/ontogpt/storms
    rank: 1000
    domain_of:
    - STORMSChecklist
    slot_group: other_information
    range: string
  other_information_conflicts_of_interest:
    name: other_information_conflicts_of_interest
    description: Include a conflicts of interest statement.
    from_schema: https://w3id.org/ontogpt/storms
    rank: 1000
    domain_of:
    - STORMSChecklist
    slot_group: other_information
    range: string
  other_information_supplements:
    name: other_information_supplements
    description: Indicate where supplements may be accessed and what materials they
      contain.
    from_schema: https://w3id.org/ontogpt/storms
    rank: 1000
    domain_of:
    - STORMSChecklist
    slot_group: other_information
    range: string
  other_information_supplementary_data:
    name: other_information_supplementary_data
    description: Provide supplementary data files of results with all taxa and all
      outcome variables analyzed. Indicate the taxonomic level of all taxa.
    from_schema: https://w3id.org/ontogpt/storms
    rank: 1000
    domain_of:
    - STORMSChecklist
    slot_group: other_information
    range: string
tree_root: true

Induced

name: STORMSChecklist
annotations:
  prompt:
    tag: prompt
    value: Try and provide a value for ALL items. If an item is not reported, say
      NOT REPORTED
description: A checklist of items that should be reported in a microbiome study. Try
  and provide a value for ALL items. If an item is not reported, say NOT REPORTED.
from_schema: https://w3id.org/ontogpt/storms
attributes:
  abstract_structured_or_unstructured:
    name: abstract_structured_or_unstructured
    description: Abstract should include information on background, methods, results,
      and conclusions in structured or unstructured format.
    from_schema: https://w3id.org/ontogpt/storms
    rank: 1000
    alias: abstract_structured_or_unstructured
    owner: STORMSChecklist
    domain_of:
    - STORMSChecklist
    slot_group: abstract
    range: string
  abstract_study_design:
    name: abstract_study_design
    description: State study design in abstract.
    from_schema: https://w3id.org/ontogpt/storms
    rank: 1000
    alias: abstract_study_design
    owner: STORMSChecklist
    domain_of:
    - STORMSChecklist
    slot_group: abstract
    range: string
  abstract_sequencing_methods:
    name: abstract_sequencing_methods
    description: State the strategy used for metagenomic classification.
    from_schema: https://w3id.org/ontogpt/storms
    rank: 1000
    alias: abstract_sequencing_methods
    owner: STORMSChecklist
    domain_of:
    - STORMSChecklist
    slot_group: abstract
    range: string
  abstract_specimens:
    name: abstract_specimens
    description: Describe body site(s) studied.
    from_schema: https://w3id.org/ontogpt/storms
    rank: 1000
    alias: abstract_specimens
    owner: STORMSChecklist
    domain_of:
    - STORMSChecklist
    slot_group: abstract
    range: string
  introduction_background_and_rationale:
    name: introduction_background_and_rationale
    description: Summarize the underlying background, scientific evidence, or theory
      driving the current hypothesis as well as the study objectives.
    from_schema: https://w3id.org/ontogpt/storms
    rank: 1000
    alias: introduction_background_and_rationale
    owner: STORMSChecklist
    domain_of:
    - STORMSChecklist
    slot_group: introduction
    range: string
  introduction_hypotheses:
    name: introduction_hypotheses
    description: State the pre-specified hypothesis. If the study is exploratory,
      state any pre-specified study objectives.
    from_schema: https://w3id.org/ontogpt/storms
    rank: 1000
    alias: introduction_hypotheses
    owner: STORMSChecklist
    domain_of:
    - STORMSChecklist
    slot_group: introduction
    range: string
  methods_study_design:
    name: methods_study_design
    description: Describe the study design.
    from_schema: https://w3id.org/ontogpt/storms
    rank: 1000
    alias: methods_study_design
    owner: STORMSChecklist
    domain_of:
    - STORMSChecklist
    slot_group: methods
    range: string
  methods_participants:
    name: methods_participants
    description: State what the population of interest is, and the method by which
      participants are sampled from that population.
    from_schema: https://w3id.org/ontogpt/storms
    rank: 1000
    alias: methods_participants
    owner: STORMSChecklist
    domain_of:
    - STORMSChecklist
    slot_group: methods
    range: string
  methods_geographic_location:
    name: methods_geographic_location
    description: State the geographic region(s) where participants were sampled from.
    from_schema: https://w3id.org/ontogpt/storms
    rank: 1000
    alias: methods_geographic_location
    owner: STORMSChecklist
    domain_of:
    - STORMSChecklist
    slot_group: methods
    range: string
  methods_relevant_dates:
    name: methods_relevant_dates
    description: State the start and end dates for recruitment, follow-up, and data
      collection.
    from_schema: https://w3id.org/ontogpt/storms
    rank: 1000
    alias: methods_relevant_dates
    owner: STORMSChecklist
    domain_of:
    - STORMSChecklist
    slot_group: methods
    range: string
  methods_eligibility_criteria:
    name: methods_eligibility_criteria
    description: List any criteria for inclusion and exclusion of recruited participants.
    from_schema: https://w3id.org/ontogpt/storms
    rank: 1000
    alias: methods_eligibility_criteria
    owner: STORMSChecklist
    domain_of:
    - STORMSChecklist
    slot_group: methods
    range: string
  methods_antibiotics_usage:
    name: methods_antibiotics_usage
    description: List what is known about antibiotics usage before or during sample
      collection.
    from_schema: https://w3id.org/ontogpt/storms
    rank: 1000
    alias: methods_antibiotics_usage
    owner: STORMSChecklist
    domain_of:
    - STORMSChecklist
    slot_group: methods
    range: string
  methods_analytic_sample_size:
    name: methods_analytic_sample_size
    description: Explain how the final analytic sample size was calculated, including
      the number of cases and controls if relevant, and reasons for dropout at each
      stage of the study.
    from_schema: https://w3id.org/ontogpt/storms
    rank: 1000
    alias: methods_analytic_sample_size
    owner: STORMSChecklist
    domain_of:
    - STORMSChecklist
    slot_group: methods
    range: string
  methods_longitudinal_studies:
    name: methods_longitudinal_studies
    description: For longitudinal studies, state how many follow-ups were conducted,
      describe sample size at follow-up by group or condition, and discuss any loss
      to follow-up.
    from_schema: https://w3id.org/ontogpt/storms
    rank: 1000
    alias: methods_longitudinal_studies
    owner: STORMSChecklist
    domain_of:
    - STORMSChecklist
    slot_group: methods
    range: string
  methods_matching:
    name: methods_matching
    description: For matched studies, give matching criteria.
    from_schema: https://w3id.org/ontogpt/storms
    rank: 1000
    alias: methods_matching
    owner: STORMSChecklist
    domain_of:
    - STORMSChecklist
    slot_group: methods
    range: string
  methods_ethics:
    name: methods_ethics
    description: State the name of the institutional review board that approved the
      study and protocols, protocol number and date of approval, and procedures for
      obtaining informed consent from participants.
    from_schema: https://w3id.org/ontogpt/storms
    rank: 1000
    alias: methods_ethics
    owner: STORMSChecklist
    domain_of:
    - STORMSChecklist
    slot_group: methods
    range: string
  methods_laboratory_methods:
    name: methods_laboratory_methods
    description: State the laboratory/center where laboratory work was done.
    from_schema: https://w3id.org/ontogpt/storms
    rank: 1000
    alias: methods_laboratory_methods
    owner: STORMSChecklist
    domain_of:
    - STORMSChecklist
    slot_group: methods
    range: string
  methods_specimen_collection:
    name: methods_specimen_collection
    description: State the body site(s) sampled from and how specimens were collected.
    from_schema: https://w3id.org/ontogpt/storms
    rank: 1000
    alias: methods_specimen_collection
    owner: STORMSChecklist
    domain_of:
    - STORMSChecklist
    slot_group: methods
    range: string
  methods_shipping:
    name: methods_shipping
    description: Describe how samples were stored and shipped to the laboratory.
    from_schema: https://w3id.org/ontogpt/storms
    rank: 1000
    alias: methods_shipping
    owner: STORMSChecklist
    domain_of:
    - STORMSChecklist
    slot_group: methods
    range: string
  methods_storage:
    name: methods_storage
    description: Describe how the laboratory stored samples, including time between
      collection and storage and any preservation buffers or refrigeration used.
    from_schema: https://w3id.org/ontogpt/storms
    rank: 1000
    alias: methods_storage
    owner: STORMSChecklist
    domain_of:
    - STORMSChecklist
    slot_group: methods
    range: string
  methods_dna_extraction:
    name: methods_dna_extraction
    description: Provide DNA extraction method, including kit and version if relevant.
    from_schema: https://w3id.org/ontogpt/storms
    rank: 1000
    alias: methods_dna_extraction
    owner: STORMSChecklist
    domain_of:
    - STORMSChecklist
    slot_group: methods
    range: string
  methods_human_dna_sequence_depletion_or_microbial_dna_enrichment:
    name: methods_human_dna_sequence_depletion_or_microbial_dna_enrichment
    description: Describe whether human DNA sequence depletion or enrichment of microbial
      or viral DNA was performed.
    from_schema: https://w3id.org/ontogpt/storms
    rank: 1000
    alias: methods_human_dna_sequence_depletion_or_microbial_dna_enrichment
    owner: STORMSChecklist
    domain_of:
    - STORMSChecklist
    slot_group: methods
    range: string
  methods_primer_selection:
    name: methods_primer_selection
    description: Provide primer selection and DNA amplification methods as well as
      variable region sequenced (if applicable).
    from_schema: https://w3id.org/ontogpt/storms
    rank: 1000
    alias: methods_primer_selection
    owner: STORMSChecklist
    domain_of:
    - STORMSChecklist
    slot_group: methods
    range: string
  methods_positive_controls:
    name: methods_positive_controls
    description: Describe any positive controls (mock communities) if used.
    from_schema: https://w3id.org/ontogpt/storms
    rank: 1000
    alias: methods_positive_controls
    owner: STORMSChecklist
    domain_of:
    - STORMSChecklist
    slot_group: methods
    range: string
  methods_negative_controls:
    name: methods_negative_controls
    description: Describe any negative controls if used.
    from_schema: https://w3id.org/ontogpt/storms
    rank: 1000
    alias: methods_negative_controls
    owner: STORMSChecklist
    domain_of:
    - STORMSChecklist
    slot_group: methods
    range: string
  methods_contaminant_mitigation_and_identification:
    name: methods_contaminant_mitigation_and_identification
    description: Provide any laboratory or computational methods used to control for
      or identify microbiome contamination from the environment, reagents, or laboratory.
    from_schema: https://w3id.org/ontogpt/storms
    rank: 1000
    alias: methods_contaminant_mitigation_and_identification
    owner: STORMSChecklist
    domain_of:
    - STORMSChecklist
    slot_group: methods
    range: string
  methods_replication:
    name: methods_replication
    description: Describe any biological or technical replicates included in the sequencing,
      including which steps were replicated between them.
    from_schema: https://w3id.org/ontogpt/storms
    rank: 1000
    alias: methods_replication
    owner: STORMSChecklist
    domain_of:
    - STORMSChecklist
    slot_group: methods
    range: string
  methods_sequencing_strategy:
    name: methods_sequencing_strategy
    description: Major divisions of strategy, such as shotgun or amplicon sequencing.
    from_schema: https://w3id.org/ontogpt/storms
    rank: 1000
    alias: methods_sequencing_strategy
    owner: STORMSChecklist
    domain_of:
    - STORMSChecklist
    slot_group: methods
    range: string
  methods_sequencing_methods:
    name: methods_sequencing_methods
    description: State whether experimental quantification was used (QMP/cell count
      based, spike-in based) or whether relative abundance methods were applied.
    from_schema: https://w3id.org/ontogpt/storms
    rank: 1000
    alias: methods_sequencing_methods
    owner: STORMSChecklist
    domain_of:
    - STORMSChecklist
    slot_group: methods
    range: string
  methods_batch_effects:
    name: methods_batch_effects
    description: Detail any blocking or randomization used in study design to avoid
      confounding of batches with exposures or outcomes. Discuss any likely sources
      of batch effects, if known.
    from_schema: https://w3id.org/ontogpt/storms
    rank: 1000
    alias: methods_batch_effects
    owner: STORMSChecklist
    domain_of:
    - STORMSChecklist
    slot_group: methods
    range: string
  methods_metatranscriptomics:
    name: methods_metatranscriptomics
    description: Detail whether any mRNA enrichment was performed and whether/how
      retrotranscription was performed prior to sequencing. Provide size range of
      isolated transcripts. Describe whether the sequencing library was stranded or
      not. Provide details on sequencing methods and platforms.
    from_schema: https://w3id.org/ontogpt/storms
    rank: 1000
    alias: methods_metatranscriptomics
    owner: STORMSChecklist
    domain_of:
    - STORMSChecklist
    slot_group: methods
    range: string
  methods_metaproteomics:
    name: methods_metaproteomics
    description: Detail which protease was used for digestion. Provide details on
      proteomic methods and platforms (e.g. LC-MS/MS, instrument type, column type,
      mass range, resolution, scan speed, maximum injection time, isolation window,
      normalised collision energy, and resolution).
    from_schema: https://w3id.org/ontogpt/storms
    rank: 1000
    alias: methods_metaproteomics
    owner: STORMSChecklist
    domain_of:
    - STORMSChecklist
    slot_group: methods
    range: string
  methods_metabolomics:
    name: methods_metabolomics
    description: Specify the analytic method used (such as nuclear magnetic resonance
      spectroscopy or mass spectrometry). For mass spectrometry, detail which fractions
      were obtained (polar and/or non polar) and how these were analyzed. Provide
      details on metabolomics methods and platforms (e.g. derivatization, instrument
      type, injection type, column type and instrument settings).
    from_schema: https://w3id.org/ontogpt/storms
    rank: 1000
    alias: methods_metabolomics
    owner: STORMSChecklist
    domain_of:
    - STORMSChecklist
    slot_group: methods
    range: string
  results_descriptive_data:
    name: results_descriptive_data
    description: Give characteristics of study participants (e.g. dietary, demographic,
      clinical, social) and information on exposures and potential confounders.
    from_schema: https://w3id.org/ontogpt/storms
    rank: 1000
    alias: results_descriptive_data
    owner: STORMSChecklist
    domain_of:
    - STORMSChecklist
    slot_group: results
    range: string
  results_microbiome_data:
    name: results_microbiome_data
    description: Report descriptive findings for microbiome analyses with all applicable
      outcomes and covariates.
    from_schema: https://w3id.org/ontogpt/storms
    rank: 1000
    alias: results_microbiome_data
    owner: STORMSChecklist
    domain_of:
    - STORMSChecklist
    slot_group: results
    range: string
  results_taxonomy:
    name: results_taxonomy
    description: Identify taxonomy using standardized taxon classifications that are
      sufficient to uniquely identify taxa.
    from_schema: https://w3id.org/ontogpt/storms
    rank: 1000
    alias: results_taxonomy
    owner: STORMSChecklist
    domain_of:
    - STORMSChecklist
    slot_group: results
    range: string
  results_differential_abundance:
    name: results_differential_abundance
    description: Report results of differential abundance analysis by the variable
      of interest and (if applicable) by time, clearly indicating the direction of
      change and total number of taxa tested.
    from_schema: https://w3id.org/ontogpt/storms
    rank: 1000
    alias: results_differential_abundance
    owner: STORMSChecklist
    domain_of:
    - STORMSChecklist
    slot_group: results
    range: string
  results_other_data_types:
    name: results_other_data_types
    description: Report other data analyzed--e.g. metabolic function, functional potential,
      MAG assembly, and RNAseq.
    from_schema: https://w3id.org/ontogpt/storms
    rank: 1000
    alias: results_other_data_types
    owner: STORMSChecklist
    domain_of:
    - STORMSChecklist
    slot_group: results
    range: string
  results_other_statistical_analysis:
    name: results_other_statistical_analysis
    description: Report any statistical data analysis not covered above.
    from_schema: https://w3id.org/ontogpt/storms
    rank: 1000
    alias: results_other_statistical_analysis
    owner: STORMSChecklist
    domain_of:
    - STORMSChecklist
    slot_group: results
    range: string
  discussion_key_results:
    name: discussion_key_results
    description: Summarize key results with reference to study objectives.
    from_schema: https://w3id.org/ontogpt/storms
    rank: 1000
    alias: discussion_key_results
    owner: STORMSChecklist
    domain_of:
    - STORMSChecklist
    slot_group: discussion
    range: string
  discussion_interpretation:
    name: discussion_interpretation
    description: Give a cautious overall interpretation of results considering objectives,
      limitations, multiplicity of analyses, results from similar studies, and other
      relevant evidence.
    from_schema: https://w3id.org/ontogpt/storms
    rank: 1000
    alias: discussion_interpretation
    owner: STORMSChecklist
    domain_of:
    - STORMSChecklist
    slot_group: discussion
    range: string
  discussion_limitations:
    name: discussion_limitations
    description: Discuss limitations of the study, taking into account sources of
      potential bias or imprecision.
    from_schema: https://w3id.org/ontogpt/storms
    rank: 1000
    alias: discussion_limitations
    owner: STORMSChecklist
    domain_of:
    - STORMSChecklist
    slot_group: discussion
    range: string
  discussion_bias:
    name: discussion_bias
    description: Discuss any potential for bias to influence study findings.
    from_schema: https://w3id.org/ontogpt/storms
    rank: 1000
    alias: discussion_bias
    owner: STORMSChecklist
    domain_of:
    - STORMSChecklist
    slot_group: discussion
    range: string
  discussion_generalizability:
    name: discussion_generalizability
    description: Discuss the generalizability (external validity) of the study results.
    from_schema: https://w3id.org/ontogpt/storms
    rank: 1000
    alias: discussion_generalizability
    owner: STORMSChecklist
    domain_of:
    - STORMSChecklist
    slot_group: discussion
    range: string
  discussion_ongoing_future_work:
    name: discussion_ongoing_future_work
    description: Describe potential future research or ongoing research based on the
      study's findings.
    from_schema: https://w3id.org/ontogpt/storms
    rank: 1000
    alias: discussion_ongoing_future_work
    owner: STORMSChecklist
    domain_of:
    - STORMSChecklist
    slot_group: discussion
    range: string
  other_information_funding:
    name: other_information_funding
    description: Give the source of funding and the role of the funders for the present
      study and, if applicable, for the original study on which the present article
      is based.
    from_schema: https://w3id.org/ontogpt/storms
    rank: 1000
    alias: other_information_funding
    owner: STORMSChecklist
    domain_of:
    - STORMSChecklist
    slot_group: other_information
    range: string
  other_information_acknowledgements:
    name: other_information_acknowledgements
    description: Include acknowledgements of those who contributed to the research
      but did not meet criteria for authorship.
    from_schema: https://w3id.org/ontogpt/storms
    rank: 1000
    alias: other_information_acknowledgements
    owner: STORMSChecklist
    domain_of:
    - STORMSChecklist
    slot_group: other_information
    range: string
  other_information_conflicts_of_interest:
    name: other_information_conflicts_of_interest
    description: Include a conflicts of interest statement.
    from_schema: https://w3id.org/ontogpt/storms
    rank: 1000
    alias: other_information_conflicts_of_interest
    owner: STORMSChecklist
    domain_of:
    - STORMSChecklist
    slot_group: other_information
    range: string
  other_information_supplements:
    name: other_information_supplements
    description: Indicate where supplements may be accessed and what materials they
      contain.
    from_schema: https://w3id.org/ontogpt/storms
    rank: 1000
    alias: other_information_supplements
    owner: STORMSChecklist
    domain_of:
    - STORMSChecklist
    slot_group: other_information
    range: string
  other_information_supplementary_data:
    name: other_information_supplementary_data
    description: Provide supplementary data files of results with all taxa and all
      outcome variables analyzed. Indicate the taxonomic level of all taxa.
    from_schema: https://w3id.org/ontogpt/storms
    rank: 1000
    alias: other_information_supplementary_data
    owner: STORMSChecklist
    domain_of:
    - STORMSChecklist
    slot_group: other_information
    range: string
tree_root: true