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