Class: Group¶
An aggregate participant group and its reported demographics.
URI: neurostudy_ex:Group
classDiagram
class Group
click Group href "../Group/"
Group : acquired_count
Group --> "0..1" ExtractedInteger : acquired_count
click ExtractedInteger href "../ExtractedInteger/"
Group : age_maximum
Group --> "0..1" ExtractedNumber : age_maximum
click ExtractedNumber href "../ExtractedNumber/"
Group : age_mean
Group --> "0..1" ExtractedNumber : age_mean
click ExtractedNumber href "../ExtractedNumber/"
Group : age_median
Group --> "0..1" ExtractedNumber : age_median
click ExtractedNumber href "../ExtractedNumber/"
Group : age_minimum
Group --> "0..1" ExtractedNumber : age_minimum
click ExtractedNumber href "../ExtractedNumber/"
Group : age_standard_deviation
Group --> "0..1" ExtractedNumber : age_standard_deviation
click ExtractedNumber href "../ExtractedNumber/"
Group : age_unit
Group --> "0..1" ExtractedString : age_unit
click ExtractedString href "../ExtractedString/"
Group : age_unit_normalized
Group --> "0..1" ExtractedString : age_unit_normalized
click ExtractedString href "../ExtractedString/"
Group : approached_count
Group --> "0..1" ExtractedInteger : approached_count
click ExtractedInteger href "../ExtractedInteger/"
Group : arm
Group --> "0..1" Arm : arm
click Arm href "../Arm/"
Group : clinical_characteristics
Group --> "0..1" ExtractedString : clinical_characteristics
click ExtractedString href "../ExtractedString/"
Group : consented_count
Group --> "0..1" ExtractedInteger : consented_count
click ExtractedInteger href "../ExtractedInteger/"
Group : description
Group --> "0..1" ExtractedString : description
click ExtractedString href "../ExtractedString/"
Group : diagnostic_instrument
Group --> "*" Assessment : diagnostic_instrument
click Assessment href "../Assessment/"
Group : diagnostic_system
Group --> "0..1" ExtractedString : diagnostic_system
click ExtractedString href "../ExtractedString/"
Group : education_summary
Group --> "0..1" ExtractedString : education_summary
click ExtractedString href "../ExtractedString/"
Group : enrolled_count
Group --> "0..1" ExtractedInteger : enrolled_count
click ExtractedInteger href "../ExtractedInteger/"
Group : ethnicity_distribution
Group --> "*" CategoryDistribution : ethnicity_distribution
click CategoryDistribution href "../CategoryDistribution/"
Group : excluded_count
Group --> "0..1" ExtractedInteger : excluded_count
click ExtractedInteger href "../ExtractedInteger/"
Group : exclusion_criteria
Group --> "0..1" ExtractedStringList : exclusion_criteria
click ExtractedStringList href "../ExtractedStringList/"
Group : gender_distribution
Group --> "*" CategoryDistribution : gender_distribution
click CategoryDistribution href "../CategoryDistribution/"
Group : handedness_distribution
Group --> "*" CategoryDistribution : handedness_distribution
click CategoryDistribution href "../CategoryDistribution/"
Group : inclusion_criteria
Group --> "0..1" ExtractedStringList : inclusion_criteria
click ExtractedStringList href "../ExtractedStringList/"
Group : is_healthy
Group --> "0..1" ExtractedBoolean : is_healthy
click ExtractedBoolean href "../ExtractedBoolean/"
Group : local_id
Group : medical_condition
Group --> "0..1" ExtractedStringList : medical_condition
click ExtractedStringList href "../ExtractedStringList/"
Group : medication_status
Group --> "0..1" ExtractedString : medication_status
click ExtractedString href "../ExtractedString/"
Group : medications
Group --> "0..1" ExtractedStringList : medications
click ExtractedStringList href "../ExtractedStringList/"
Group : name
Group --> "1" ExtractedString : name
click ExtractedString href "../ExtractedString/"
Group : other_characteristics
Group --> "0..1" ExtractedStringList : other_characteristics
click ExtractedStringList href "../ExtractedStringList/"
Group : population_characteristics
Group --> "0..1" ExtractedStringList : population_characteristics
click ExtractedStringList href "../ExtractedStringList/"
Group : race_distribution
Group --> "*" CategoryDistribution : race_distribution
click CategoryDistribution href "../CategoryDistribution/"
Group : recruitment_dates
Group --> "0..1" ExtractedString : recruitment_dates
click ExtractedString href "../ExtractedString/"
Group : recruitment_method
Group --> "0..1" ExtractedString : recruitment_method
click ExtractedString href "../ExtractedString/"
Group : sample_overlap_count
Group --> "0..1" ExtractedInteger : sample_overlap_count
click ExtractedInteger href "../ExtractedInteger/"
Group : sample_source
Group --> "0..1" ExtractedSampleSource : sample_source
click ExtractedSampleSource href "../ExtractedSampleSource/"
Group : sample_source_reference
Group --> "0..1" ExtractedString : sample_source_reference
click ExtractedString href "../ExtractedString/"
Group : sex_distribution
Group --> "*" CategoryDistribution : sex_distribution
click CategoryDistribution href "../CategoryDistribution/"
Group : socioeconomic_status_summary
Group --> "0..1" ExtractedString : socioeconomic_status_summary
click ExtractedString href "../ExtractedString/"
Group : species
Group --> "1" ExtractedSpecies : species
click ExtractedSpecies href "../ExtractedSpecies/"
Group : stable_id
Slots¶
| Name | Cardinality and Range | Description | Inheritance |
|---|---|---|---|
| stable_id | 0..1 String |
UUID minted by the store the first time this entity appears, never by an extr... | direct |
| local_id | 1 String |
direct | |
| name | 1 ExtractedString |
Study-local group label, for example healthy controls or patients with Parkin... | direct |
| description | 0..1 ExtractedString |
Narrative definition of the group and its role in the study | direct |
| species | 1 ExtractedSpecies |
The species of this cohort | direct |
| arm | 0..1 Arm |
The arm this cohort was allocated to | direct |
| approached_count | 0..1 ExtractedInteger |
Number of prospective participants approached for this group | direct |
| consented_count | 0..1 ExtractedInteger |
Number who consented or assented to participate | direct |
| enrolled_count | 0..1 ExtractedInteger |
Number enrolled after screening and before acquisition | direct |
| acquired_count | 0..1 ExtractedInteger |
Number for whom data were acquired or who were scanned | direct |
| excluded_count | 0..1 ExtractedInteger |
Number excluded after consent, enrollment, acquisition, and quality control | direct |
| inclusion_criteria | 0..1 ExtractedStringList |
Eligibility requirements that a participant had to satisfy for membership in ... | direct |
| exclusion_criteria | 0..1 ExtractedStringList |
Screening, imaging-safety, clinical, behavioral, or quality-control criteria ... | direct |
| recruitment_method | 0..1 ExtractedString |
How, where, and from what setting participants were recruited | direct |
| recruitment_dates | 0..1 ExtractedString |
Free-text recruitment period when the source does not support a precise norma... | direct |
| age_mean | 0..1 ExtractedNumber |
Mean participant age in the unit given by age_unit | direct |
| age_standard_deviation | 0..1 ExtractedNumber |
Standard deviation of participant age in the unit given by age_unit | direct |
| age_minimum | 0..1 ExtractedNumber |
Youngest age reported for the group | direct |
| age_maximum | 0..1 ExtractedNumber |
Oldest age reported for the group | direct |
| age_median | 0..1 ExtractedNumber |
Median participant age for the group | direct |
| age_unit | 0..1 ExtractedString |
Unit used for age summaries, normally years but potentially months, weeks, or... | direct |
| sex_distribution | * CategoryDistribution |
Aggregate phenotypic sex distribution | direct |
| gender_distribution | * CategoryDistribution |
Aggregate self-described gender distribution, kept separate from phenotypic s... | direct |
| handedness_distribution | * CategoryDistribution |
Aggregate handedness distribution | direct |
| race_distribution | * CategoryDistribution |
Aggregate racial distribution using the study-reported category labels | direct |
| ethnicity_distribution | * CategoryDistribution |
Aggregate ethnic distribution using the study-reported category labels | direct |
| population_characteristics | 0..1 ExtractedStringList |
How this cohort deviates from the typical, where no other field covers it... | direct |
| medical_condition | 0..1 ExtractedStringList |
Medical, neurological, psychiatric, developmental, or physiological condition... | direct |
| diagnostic_system | 0..1 ExtractedString |
Classification system and edition under which this group's `medical_condition... | direct |
| diagnostic_instrument | * Assessment |
The study assessment that established this group's defining condition -- the ... | direct |
| clinical_characteristics | 0..1 ExtractedString |
Disease duration, severity, treatment status, or other clinically relevant su... | direct |
| medications | 0..1 ExtractedStringList |
The drugs or other agents this cohort was taking, as the source names them, o... | direct |
| medication_status | 0..1 ExtractedString |
Whether the cohort was medicated, unmedicated, drug-naive, or withdrawn, and ... | direct |
| education_summary | 0..1 ExtractedString |
Aggregate education level and the measurement or coding system used | direct |
| socioeconomic_status_summary | 0..1 ExtractedString |
Aggregate socioeconomic status and the instrument or proxy used to measure it | direct |
| sample_source | 0..1 ExtractedSampleSource |
Where this group's participants came from | direct |
| sample_source_reference | 0..1 ExtractedString |
The dataset name, or the prior publication as the source cites it: an author-... | direct |
| sample_overlap_count | 0..1 ExtractedInteger |
How many of this group were in that prior report, when the source says so | direct |
| is_healthy | 0..1 ExtractedBoolean |
Whether this cohort is free of medical, neurological and psychiatric conditio... | direct |
| age_unit_normalized | 0..1 ExtractedString |
age_unit folded onto years / months / weeks / gestational_weeks / UNKNOWN b... |
direct |
| other_characteristics | 0..1 ExtractedStringList |
Cohort traits moved out of population_characteristics because every plausib... |
direct |
Usages¶
| used by | used in | type | used |
|---|---|---|---|
| AnalysisGroup | group | range | Group |
| FactorLevel | groups | range | Group |
| Study | groups | range | Group |
Identifier and Mapping Information¶
Schema Source¶
- from schema: https://neurostuff.org/schemas/neuroimaging-study-extraction
Mappings¶
| Mapping Type | Mapped Value |
|---|---|
| self | neurostudy_ex:Group |
| native | neurostudy_ex:Group |
LinkML Source¶
Direct¶
name: Group
description: An aggregate participant group and its reported demographics.
from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction
rank: 1000
attributes:
stable_id:
name: stable_id
description: UUID minted by the store the first time this entity appears, never
by an extractor, and kept across re-runs so a later extraction matches the same
entity.
from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/group
domain_of:
- Arm
- Timepoint
- Group
- Task
- Condition
- Assessment
- Region
- Acquisition
- Device
- Analysis
- Measure
- Preprocessing
- ModelEstimation
- ModelTerm
- InferenceSettings
- Table
- CoordinateSet
- Study
range: string
pattern: ^[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}$
local_id:
name: local_id
from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/group
identifier: true
domain_of:
- Arm
- Timepoint
- Group
- Task
- Condition
- Assessment
- Region
- Acquisition
- Device
- Analysis
- Measure
- Preprocessing
- ModelEstimation
- ModelTerm
- InferenceSettings
- Table
- CoordinateSet
- Study
range: string
required: true
name:
name: name
description: Study-local group label, for example healthy controls or patients
with Parkinson disease.
from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/group
domain_of:
- Arm
- Timepoint
- Group
- Task
- Condition
- Assessment
- Region
- Analysis
- ModelTerm
- ExternalDataset
- PerformanceMetric
range: ExtractedString
required: true
description:
name: description
description: Narrative definition of the group and its role in the study.
from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/group
domain_of:
- StudyDesign
- Arm
- Group
- Task
- Condition
- Assessment
- Region
- Preprocessing
- Table
- CoordinateSet
- Study
range: ExtractedString
species:
name: species
description: The species of this cohort.
from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/group
rank: 1000
domain_of:
- Group
range: ExtractedSpecies
required: true
arm:
name: arm
description: 'The arm this cohort was allocated to. Set it whenever a cohort was
allocated to one, which is the parallel-group case: every participant of this
cohort received this arm and no other. A crossover study allocates nobody to
one arm, so its cohorts leave this empty and an arm reaches an analysis only
as a level of a model term, through `FactorLevel.arms`. Distinct from `medication_status`,
which is the on/off state during acquisition rather than the allocation.'
from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/group
rank: 1000
domain_of:
- Group
range: Arm
inlined: false
approached_count:
name: approached_count
description: Number of prospective participants approached for this group.
from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/group
rank: 1000
domain_of:
- Group
range: ExtractedInteger
consented_count:
name: consented_count
description: Number who consented or assented to participate.
from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/group
rank: 1000
domain_of:
- Group
range: ExtractedInteger
enrolled_count:
name: enrolled_count
description: Number enrolled after screening and before acquisition.
from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/group
rank: 1000
domain_of:
- Group
range: ExtractedInteger
acquired_count:
name: acquired_count
description: Number for whom data were acquired or who were scanned.
from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/group
rank: 1000
domain_of:
- Group
range: ExtractedInteger
excluded_count:
name: excluded_count
description: Number excluded after consent, enrollment, acquisition, and quality
control.
from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/group
rank: 1000
domain_of:
- Group
range: ExtractedInteger
inclusion_criteria:
name: inclusion_criteria
description: Eligibility requirements that a participant had to satisfy for membership
in this group.
from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/group
rank: 1000
domain_of:
- Group
range: ExtractedStringList
exclusion_criteria:
name: exclusion_criteria
description: Screening, imaging-safety, clinical, behavioral, or quality-control
criteria causing exclusion.
from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/group
rank: 1000
domain_of:
- Group
range: ExtractedStringList
recruitment_method:
name: recruitment_method
description: How, where, and from what setting participants were recruited.
from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/group
rank: 1000
domain_of:
- Group
range: ExtractedString
recruitment_dates:
name: recruitment_dates
description: Free-text recruitment period when the source does not support a precise
normalized date range; examples include January 2021 to June 2022, 2018-2020,
or autumn 2023.
from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/group
rank: 1000
domain_of:
- Group
range: ExtractedString
age_mean:
name: age_mean
description: Mean participant age in the unit given by age_unit.
from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/group
rank: 1000
domain_of:
- Group
range: ExtractedNumber
age_standard_deviation:
name: age_standard_deviation
description: Standard deviation of participant age in the unit given by age_unit.
from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/group
rank: 1000
domain_of:
- Group
range: ExtractedNumber
age_minimum:
name: age_minimum
description: Youngest age reported for the group.
from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/group
rank: 1000
domain_of:
- Group
range: ExtractedNumber
age_maximum:
name: age_maximum
description: Oldest age reported for the group.
from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/group
rank: 1000
domain_of:
- Group
range: ExtractedNumber
age_median:
name: age_median
description: Median participant age for the group.
from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/group
rank: 1000
domain_of:
- Group
range: ExtractedNumber
age_unit:
name: age_unit
description: Unit used for age summaries, normally years but potentially months,
weeks, or gestational weeks.
from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/group
rank: 1000
domain_of:
- Group
range: ExtractedString
sex_distribution:
name: sex_distribution
description: 'Aggregate phenotypic sex distribution. Use one entry per reported
category, with the study''s category label and a count and/or percentage. A
cohort described wholly as one sex reports its distribution without ever printing
a breakdown: "22 male smokers", "young women (n = 8)" and "ten male patients"
are each one entry whose count is the whole group, plus a second entry for the
absent sex with a count of zero. Read a demographics table row ("N female |
5") exactly as you would read the same fact in a sentence.'
from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/group
rank: 1000
domain_of:
- Group
range: CategoryDistribution
multivalued: true
inlined_as_list: true
gender_distribution:
name: gender_distribution
description: Aggregate self-described gender distribution, kept separate from
phenotypic sex. Use one entry per reported category.
from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/group
rank: 1000
domain_of:
- Group
range: CategoryDistribution
multivalued: true
inlined_as_list: true
handedness_distribution:
name: handedness_distribution
description: Aggregate handedness distribution. Use one entry per reported category,
such as right-handed, left-handed, or ambidextrous.
from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/group
rank: 1000
domain_of:
- Group
range: CategoryDistribution
multivalued: true
inlined_as_list: true
race_distribution:
name: race_distribution
description: Aggregate racial distribution using the study-reported category labels.
from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/group
rank: 1000
domain_of:
- Group
range: CategoryDistribution
multivalued: true
inlined_as_list: true
ethnicity_distribution:
name: ethnicity_distribution
description: Aggregate ethnic distribution using the study-reported category labels.
from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/group
rank: 1000
domain_of:
- Group
range: CategoryDistribution
multivalued: true
inlined_as_list: true
population_characteristics:
name: population_characteristics
description: 'How this cohort **deviates from the typical**, where no other field
covers it: habitual exposure (heavy caffeine use, social drinkers, smoking status),
training or expertise (athletes, musicians, bilinguals, gamers), occupation
or social role (veterans, undergraduates, shift workers), lifestyle (sedentary,
vegetarian, meditation practitioners), and body habitus where it is atypical
(obese, overweight, underweight).
Deviation is the test, and it is what makes this field worth querying. A study
selects its cohort for something; that something is what belongs here. The unremarkable
does not: "normal weight", "healthy weight", "typically developing", "right-handed",
"no hearing loss" and an ordinary age range describe a cohort that was not selected
for anything, and recording them fills the field with the absence of information.
If every plausible cohort could carry the value, leave it out.
**Every other Group slot takes priority.** Nothing here that belongs in `age_mean`,
`age_minimum`, `age_maximum`, `age_median`, `sex_distribution`, `gender_distribution`,
`handedness_distribution`, `race_distribution`, `ethnicity_distribution`, `education_summary`,
`socioeconomic_status_summary`, `medications`, `medication_status`, `recruitment_method`,
`species`, `inclusion_criteria`, `exclusion_criteria` or `medical_condition`.
"All Caucasian" is `race_distribution`; "children aged 8-11" is `age_minimum`
and `age_maximum`; "five participants were female" is `sex_distribution`.
Not a diagnosis either. Where a trait is also the cohort''s condition -- alcohol
dependence, obesity as a diagnosed disease -- `medical_condition` takes it alone,
which is where a clinician would look.
What was screened out is not a characteristic. "Excluding caffeine" in an exclusion
list says nothing about caffeine use in the cohort.'
from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/group
rank: 1000
domain_of:
- Group
range: ExtractedStringList
medical_condition:
name: medical_condition
description: Medical, neurological, psychiatric, developmental, or physiological
condition(s) defining or characterizing the group. List the primary diagnosis
and all comorbidities.
from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/group
rank: 1000
domain_of:
- Group
range: ExtractedStringList
diagnostic_system:
name: diagnostic_system
description: 'Classification system and edition under which this group''s `medical_condition`
was diagnosed, such as DSM-5 or ICD-10. An edition that appears only inside
an instrument''s title does not establish it: "SCID for DSM-IV Axis II Disorders",
administered to screen comorbidities, says nothing about the system used to
diagnose the condition that defines the group.'
from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/group
rank: 1000
domain_of:
- Group
range: ExtractedString
diagnostic_instrument:
name: diagnostic_instrument
description: 'The study assessment that established this group''s defining condition
-- the `medical_condition` entries, or for a healthy group its confirmed absence.
Naming one here claims it classified this cohort, which is narrower than having
been administered to it: an interview screening a comorbidity the group is not
defined by, or grading the severity of a diagnosis made elsewhere, is recorded
in `assessments` and pointed at from nowhere. Groups defined by enrollment or
history rather than by an assessment -- a treatment programme''s patients, self-reported
users -- name nothing, as do sources reporting a diagnostic system but never
the instrument applying it. Every entry must also appear in the study''s `assessments`.'
from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/group
rank: 1000
domain_of:
- Group
range: Assessment
multivalued: true
inlined: false
clinical_characteristics:
name: clinical_characteristics
description: Disease duration, severity, treatment status, or other clinically
relevant summaries.
from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/group
rank: 1000
domain_of:
- Group
range: ExtractedString
medications:
name: medications
description: The drugs or other agents this cohort was taking, as the source names
them, one agent per entry. Names only.
from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/group
rank: 1000
domain_of:
- Group
range: ExtractedStringList
medication_status:
name: medication_status
description: 'Whether the cohort was medicated, unmedicated, drug-naive, or withdrawn,
and the on/off medication state during acquisition or testing. The state, not
the agents: which drugs they were taking is `medications`.'
from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/group
rank: 1000
domain_of:
- Group
range: ExtractedString
education_summary:
name: education_summary
description: Aggregate education level and the measurement or coding system used.
from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/group
rank: 1000
domain_of:
- Group
range: ExtractedString
socioeconomic_status_summary:
name: socioeconomic_status_summary
description: Aggregate socioeconomic status and the instrument or proxy used to
measure it.
from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/group
rank: 1000
domain_of:
- Group
range: ExtractedString
sample_source:
name: sample_source
description: 'Where this group''s participants came from. `recruited` when they
were enrolled for this study and no other source is stated; `public_dataset`
when they were drawn from a named public or consortium dataset; `previously_reported`
when the same or an overlapping sample was already reported in another publication.
On the group and not the study, because overlap is routinely partial: a study
may scan a fresh patient group against controls taken from an existing dataset,
and a study-level flag cannot say which. `Study.external_datasets` remains the
place for a named dataset the study as a whole used.
A protocol, preprocessing pipeline or analysis "described previously" is a shared
METHOD and leaves this `recruited`; so does comparing findings to earlier literature
in the discussion. Only a statement that these same people were scanned, studied
or reported before counts, and a source that means it normally says so in one
sentence.
`recruited` is an assertion and not the absence of one. A meta-analysis excluding
overlapping samples has to distinguish a study that recruited freshly from one
nobody checked, and an unfilled field cannot.'
from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/group
rank: 1000
domain_of:
- Group
range: ExtractedSampleSource
sample_source_reference:
name: sample_source_reference
description: 'The dataset name, or the prior publication as the source cites it:
an author-year citation, a bracketed reference number, or a trial registration
number, copied as written. Without it the overlap is known but not actionable
-- deciding whether two papers are one independent sample needs the identity
of the other one.'
from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/group
rank: 1000
domain_of:
- Group
range: ExtractedString
sample_overlap_count:
name: sample_overlap_count
description: How many of this group were in that prior report, when the source
says so. It is the difference between two papers being one sample and their
sharing part of one, which is the difference between dropping a study and down-weighting
it.
from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/group
rank: 1000
domain_of:
- Group
range: ExtractedInteger
is_healthy:
name: is_healthy
description: 'Whether this cohort is free of medical, neurological and psychiatric
conditions. Derived from `medical_condition` by `pondie.normalization.is_healthy`,
never extracted, so it cannot disagree with the field it summarises. Unset where
`medical_condition` was never read: that is an unread cohort, not a healthy
one.'
from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/group
rank: 1000
domain_of:
- Group
range: ExtractedBoolean
age_unit_normalized:
name: age_unit_normalized
description: '`age_unit` folded onto years / months / weeks / gestational_weeks
/ UNKNOWN by `pondie.normalization.age_unit`, never extracted. The source''s
own wording stays in `age_unit`.'
from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/group
rank: 1000
domain_of:
- Group
range: ExtractedString
other_characteristics:
name: other_characteristics
description: Cohort traits moved out of `population_characteristics` because every
plausible cohort could carry them. Written by `pondie.normalization.population_characteristics`,
never extracted.
from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/group
rank: 1000
domain_of:
- Group
range: ExtractedStringList
Induced¶
name: Group
description: An aggregate participant group and its reported demographics.
from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction
rank: 1000
attributes:
stable_id:
name: stable_id
description: UUID minted by the store the first time this entity appears, never
by an extractor, and kept across re-runs so a later extraction matches the same
entity.
from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/group
owner: Group
domain_of:
- Arm
- Timepoint
- Group
- Task
- Condition
- Assessment
- Region
- Acquisition
- Device
- Analysis
- Measure
- Preprocessing
- ModelEstimation
- ModelTerm
- InferenceSettings
- Table
- CoordinateSet
- Study
range: string
pattern: ^[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}$
local_id:
name: local_id
from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/group
identifier: true
owner: Group
domain_of:
- Arm
- Timepoint
- Group
- Task
- Condition
- Assessment
- Region
- Acquisition
- Device
- Analysis
- Measure
- Preprocessing
- ModelEstimation
- ModelTerm
- InferenceSettings
- Table
- CoordinateSet
- Study
range: string
required: true
name:
name: name
description: Study-local group label, for example healthy controls or patients
with Parkinson disease.
from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/group
owner: Group
domain_of:
- Arm
- Timepoint
- Group
- Task
- Condition
- Assessment
- Region
- Analysis
- ModelTerm
- ExternalDataset
- PerformanceMetric
range: ExtractedString
required: true
description:
name: description
description: Narrative definition of the group and its role in the study.
from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/group
owner: Group
domain_of:
- StudyDesign
- Arm
- Group
- Task
- Condition
- Assessment
- Region
- Preprocessing
- Table
- CoordinateSet
- Study
range: ExtractedString
species:
name: species
description: The species of this cohort.
from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/group
rank: 1000
owner: Group
domain_of:
- Group
range: ExtractedSpecies
required: true
arm:
name: arm
description: 'The arm this cohort was allocated to. Set it whenever a cohort was
allocated to one, which is the parallel-group case: every participant of this
cohort received this arm and no other. A crossover study allocates nobody to
one arm, so its cohorts leave this empty and an arm reaches an analysis only
as a level of a model term, through `FactorLevel.arms`. Distinct from `medication_status`,
which is the on/off state during acquisition rather than the allocation.'
from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/group
rank: 1000
owner: Group
domain_of:
- Group
range: Arm
inlined: false
approached_count:
name: approached_count
description: Number of prospective participants approached for this group.
from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/group
rank: 1000
owner: Group
domain_of:
- Group
range: ExtractedInteger
consented_count:
name: consented_count
description: Number who consented or assented to participate.
from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/group
rank: 1000
owner: Group
domain_of:
- Group
range: ExtractedInteger
enrolled_count:
name: enrolled_count
description: Number enrolled after screening and before acquisition.
from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/group
rank: 1000
owner: Group
domain_of:
- Group
range: ExtractedInteger
acquired_count:
name: acquired_count
description: Number for whom data were acquired or who were scanned.
from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/group
rank: 1000
owner: Group
domain_of:
- Group
range: ExtractedInteger
excluded_count:
name: excluded_count
description: Number excluded after consent, enrollment, acquisition, and quality
control.
from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/group
rank: 1000
owner: Group
domain_of:
- Group
range: ExtractedInteger
inclusion_criteria:
name: inclusion_criteria
description: Eligibility requirements that a participant had to satisfy for membership
in this group.
from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/group
rank: 1000
owner: Group
domain_of:
- Group
range: ExtractedStringList
exclusion_criteria:
name: exclusion_criteria
description: Screening, imaging-safety, clinical, behavioral, or quality-control
criteria causing exclusion.
from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/group
rank: 1000
owner: Group
domain_of:
- Group
range: ExtractedStringList
recruitment_method:
name: recruitment_method
description: How, where, and from what setting participants were recruited.
from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/group
rank: 1000
owner: Group
domain_of:
- Group
range: ExtractedString
recruitment_dates:
name: recruitment_dates
description: Free-text recruitment period when the source does not support a precise
normalized date range; examples include January 2021 to June 2022, 2018-2020,
or autumn 2023.
from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/group
rank: 1000
owner: Group
domain_of:
- Group
range: ExtractedString
age_mean:
name: age_mean
description: Mean participant age in the unit given by age_unit.
from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/group
rank: 1000
owner: Group
domain_of:
- Group
range: ExtractedNumber
age_standard_deviation:
name: age_standard_deviation
description: Standard deviation of participant age in the unit given by age_unit.
from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/group
rank: 1000
owner: Group
domain_of:
- Group
range: ExtractedNumber
age_minimum:
name: age_minimum
description: Youngest age reported for the group.
from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/group
rank: 1000
owner: Group
domain_of:
- Group
range: ExtractedNumber
age_maximum:
name: age_maximum
description: Oldest age reported for the group.
from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/group
rank: 1000
owner: Group
domain_of:
- Group
range: ExtractedNumber
age_median:
name: age_median
description: Median participant age for the group.
from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/group
rank: 1000
owner: Group
domain_of:
- Group
range: ExtractedNumber
age_unit:
name: age_unit
description: Unit used for age summaries, normally years but potentially months,
weeks, or gestational weeks.
from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/group
rank: 1000
owner: Group
domain_of:
- Group
range: ExtractedString
sex_distribution:
name: sex_distribution
description: 'Aggregate phenotypic sex distribution. Use one entry per reported
category, with the study''s category label and a count and/or percentage. A
cohort described wholly as one sex reports its distribution without ever printing
a breakdown: "22 male smokers", "young women (n = 8)" and "ten male patients"
are each one entry whose count is the whole group, plus a second entry for the
absent sex with a count of zero. Read a demographics table row ("N female |
5") exactly as you would read the same fact in a sentence.'
from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/group
rank: 1000
owner: Group
domain_of:
- Group
range: CategoryDistribution
multivalued: true
inlined: true
inlined_as_list: true
gender_distribution:
name: gender_distribution
description: Aggregate self-described gender distribution, kept separate from
phenotypic sex. Use one entry per reported category.
from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/group
rank: 1000
owner: Group
domain_of:
- Group
range: CategoryDistribution
multivalued: true
inlined: true
inlined_as_list: true
handedness_distribution:
name: handedness_distribution
description: Aggregate handedness distribution. Use one entry per reported category,
such as right-handed, left-handed, or ambidextrous.
from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/group
rank: 1000
owner: Group
domain_of:
- Group
range: CategoryDistribution
multivalued: true
inlined: true
inlined_as_list: true
race_distribution:
name: race_distribution
description: Aggregate racial distribution using the study-reported category labels.
from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/group
rank: 1000
owner: Group
domain_of:
- Group
range: CategoryDistribution
multivalued: true
inlined: true
inlined_as_list: true
ethnicity_distribution:
name: ethnicity_distribution
description: Aggregate ethnic distribution using the study-reported category labels.
from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/group
rank: 1000
owner: Group
domain_of:
- Group
range: CategoryDistribution
multivalued: true
inlined: true
inlined_as_list: true
population_characteristics:
name: population_characteristics
description: 'How this cohort **deviates from the typical**, where no other field
covers it: habitual exposure (heavy caffeine use, social drinkers, smoking status),
training or expertise (athletes, musicians, bilinguals, gamers), occupation
or social role (veterans, undergraduates, shift workers), lifestyle (sedentary,
vegetarian, meditation practitioners), and body habitus where it is atypical
(obese, overweight, underweight).
Deviation is the test, and it is what makes this field worth querying. A study
selects its cohort for something; that something is what belongs here. The unremarkable
does not: "normal weight", "healthy weight", "typically developing", "right-handed",
"no hearing loss" and an ordinary age range describe a cohort that was not selected
for anything, and recording them fills the field with the absence of information.
If every plausible cohort could carry the value, leave it out.
**Every other Group slot takes priority.** Nothing here that belongs in `age_mean`,
`age_minimum`, `age_maximum`, `age_median`, `sex_distribution`, `gender_distribution`,
`handedness_distribution`, `race_distribution`, `ethnicity_distribution`, `education_summary`,
`socioeconomic_status_summary`, `medications`, `medication_status`, `recruitment_method`,
`species`, `inclusion_criteria`, `exclusion_criteria` or `medical_condition`.
"All Caucasian" is `race_distribution`; "children aged 8-11" is `age_minimum`
and `age_maximum`; "five participants were female" is `sex_distribution`.
Not a diagnosis either. Where a trait is also the cohort''s condition -- alcohol
dependence, obesity as a diagnosed disease -- `medical_condition` takes it alone,
which is where a clinician would look.
What was screened out is not a characteristic. "Excluding caffeine" in an exclusion
list says nothing about caffeine use in the cohort.'
from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/group
rank: 1000
owner: Group
domain_of:
- Group
range: ExtractedStringList
medical_condition:
name: medical_condition
description: Medical, neurological, psychiatric, developmental, or physiological
condition(s) defining or characterizing the group. List the primary diagnosis
and all comorbidities.
from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/group
rank: 1000
owner: Group
domain_of:
- Group
range: ExtractedStringList
diagnostic_system:
name: diagnostic_system
description: 'Classification system and edition under which this group''s `medical_condition`
was diagnosed, such as DSM-5 or ICD-10. An edition that appears only inside
an instrument''s title does not establish it: "SCID for DSM-IV Axis II Disorders",
administered to screen comorbidities, says nothing about the system used to
diagnose the condition that defines the group.'
from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/group
rank: 1000
owner: Group
domain_of:
- Group
range: ExtractedString
diagnostic_instrument:
name: diagnostic_instrument
description: 'The study assessment that established this group''s defining condition
-- the `medical_condition` entries, or for a healthy group its confirmed absence.
Naming one here claims it classified this cohort, which is narrower than having
been administered to it: an interview screening a comorbidity the group is not
defined by, or grading the severity of a diagnosis made elsewhere, is recorded
in `assessments` and pointed at from nowhere. Groups defined by enrollment or
history rather than by an assessment -- a treatment programme''s patients, self-reported
users -- name nothing, as do sources reporting a diagnostic system but never
the instrument applying it. Every entry must also appear in the study''s `assessments`.'
from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/group
rank: 1000
owner: Group
domain_of:
- Group
range: Assessment
multivalued: true
inlined: false
clinical_characteristics:
name: clinical_characteristics
description: Disease duration, severity, treatment status, or other clinically
relevant summaries.
from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/group
rank: 1000
owner: Group
domain_of:
- Group
range: ExtractedString
medications:
name: medications
description: The drugs or other agents this cohort was taking, as the source names
them, one agent per entry. Names only.
from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/group
rank: 1000
owner: Group
domain_of:
- Group
range: ExtractedStringList
medication_status:
name: medication_status
description: 'Whether the cohort was medicated, unmedicated, drug-naive, or withdrawn,
and the on/off medication state during acquisition or testing. The state, not
the agents: which drugs they were taking is `medications`.'
from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/group
rank: 1000
owner: Group
domain_of:
- Group
range: ExtractedString
education_summary:
name: education_summary
description: Aggregate education level and the measurement or coding system used.
from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/group
rank: 1000
owner: Group
domain_of:
- Group
range: ExtractedString
socioeconomic_status_summary:
name: socioeconomic_status_summary
description: Aggregate socioeconomic status and the instrument or proxy used to
measure it.
from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/group
rank: 1000
owner: Group
domain_of:
- Group
range: ExtractedString
sample_source:
name: sample_source
description: 'Where this group''s participants came from. `recruited` when they
were enrolled for this study and no other source is stated; `public_dataset`
when they were drawn from a named public or consortium dataset; `previously_reported`
when the same or an overlapping sample was already reported in another publication.
On the group and not the study, because overlap is routinely partial: a study
may scan a fresh patient group against controls taken from an existing dataset,
and a study-level flag cannot say which. `Study.external_datasets` remains the
place for a named dataset the study as a whole used.
A protocol, preprocessing pipeline or analysis "described previously" is a shared
METHOD and leaves this `recruited`; so does comparing findings to earlier literature
in the discussion. Only a statement that these same people were scanned, studied
or reported before counts, and a source that means it normally says so in one
sentence.
`recruited` is an assertion and not the absence of one. A meta-analysis excluding
overlapping samples has to distinguish a study that recruited freshly from one
nobody checked, and an unfilled field cannot.'
from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/group
rank: 1000
owner: Group
domain_of:
- Group
range: ExtractedSampleSource
sample_source_reference:
name: sample_source_reference
description: 'The dataset name, or the prior publication as the source cites it:
an author-year citation, a bracketed reference number, or a trial registration
number, copied as written. Without it the overlap is known but not actionable
-- deciding whether two papers are one independent sample needs the identity
of the other one.'
from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/group
rank: 1000
owner: Group
domain_of:
- Group
range: ExtractedString
sample_overlap_count:
name: sample_overlap_count
description: How many of this group were in that prior report, when the source
says so. It is the difference between two papers being one sample and their
sharing part of one, which is the difference between dropping a study and down-weighting
it.
from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/group
rank: 1000
owner: Group
domain_of:
- Group
range: ExtractedInteger
is_healthy:
name: is_healthy
description: 'Whether this cohort is free of medical, neurological and psychiatric
conditions. Derived from `medical_condition` by `pondie.normalization.is_healthy`,
never extracted, so it cannot disagree with the field it summarises. Unset where
`medical_condition` was never read: that is an unread cohort, not a healthy
one.'
from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/group
rank: 1000
owner: Group
domain_of:
- Group
range: ExtractedBoolean
age_unit_normalized:
name: age_unit_normalized
description: '`age_unit` folded onto years / months / weeks / gestational_weeks
/ UNKNOWN by `pondie.normalization.age_unit`, never extracted. The source''s
own wording stays in `age_unit`.'
from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/group
rank: 1000
owner: Group
domain_of:
- Group
range: ExtractedString
other_characteristics:
name: other_characteristics
description: Cohort traits moved out of `population_characteristics` because every
plausible cohort could carry them. Written by `pondie.normalization.population_characteristics`,
never extracted.
from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/group
rank: 1000
owner: Group
domain_of:
- Group
range: ExtractedStringList