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Storms Evaluation Template

A template for extracting information using STORMS checklist

URI: https://w3id.org/ontogpt/storms

Name: storms-template

Schema Diagram

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 }

Classes

Class Description
AnnotatorResult None
Any None
CompoundExpression None
        Triple Abstract parent for Relation Extraction tasks
ExtractionResult A result of extracting knowledge on text
NamedEntity None
        RelationshipType None
Publication None
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.
TextWithEntity A text containing one or more instances of a single type of entity.
TextWithTriples A text containing one or more relations of the Triple type.

Slots

Slot Description
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
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
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

Enumerations

Enumeration Description
NullDataOptions

Types

Type Description
Boolean A binary (true or false) value
Curie a compact URI
Date a date (year, month and day) in an idealized calendar
DateOrDatetime Either a date or a datetime
Datetime The combination of a date and time
Decimal A real number with arbitrary precision that conforms to the xsd:decimal speci...
Double A real number that conforms to the xsd:double specification
Float A real number that conforms to the xsd:float specification
Integer An integer
Jsonpath A string encoding a JSON Path
Jsonpointer A string encoding a JSON Pointer
Ncname Prefix part of CURIE
Nodeidentifier A URI, CURIE or BNODE that represents a node in a model
Objectidentifier A URI or CURIE that represents an object in the model
Sparqlpath A string encoding a SPARQL Property Path
String A character string
Time A time object represents a (local) time of day, independent of any particular...
Uri a complete URI
Uriorcurie a URI or a CURIE

Subsets

Subset Description