This data dictionary describes the major VaxSEA tables, identifiers, and relationships
used to integrate vaccine-related study, experiment, subject, sample, intervention,
assay, documentation, and result metadata.
VaxSEA integrates data from heterogeneous sources such as ImmPort, VIGET, GEO, PubMed,
and biomedical ontologies. Because these sources use different identifier systems,
VaxSEA stores both original source identifiers and normalized internal keys used for
search and display.
VaxSEA uses several kinds of identifiers. Some are local VaxSEA import identifiers, while
others are original source accessions from ImmPort, GEO, PubMed, or biomedical ontologies.
Identifier Pattern
Meaning
Notes
IMMP...
Local ImmPort-style import identifier
Often used as a VaxSEA-local identifier for imported ImmPort records.
Example: IMMP100.
IMP_...
Prefixed ImmPort source identifier
Prefix commonly appears before source identifiers such as
SUB, PV, or
ARM. Example:
IMP_SUB00240.
SDY...
ImmPort study accession
Original ImmPort study identifier. Commonly stored in
study.reference_source_id.
PV...
Planned visit / experiment accession
Used in ImmPort-style data to connect experiments, subjects, samples, and visits.
SUB...
Subject accession
Used to identify subjects and connect subject-level data to samples,
interventions, occurrences, and some result records.
ARM...
Arm or group accession
Used for study arm, group, or cohort references.
BS...
Biosample accession
Identifies collected biological samples.
ES...
Experiment sample accession
Frequently used to connect sample records to result records.
GSE...
GEO Series accession
Represents a GEO dataset or expression series.
GSM...
GEO Sample accession
Represents an individual GEO sample.
GPL...
GEO Platform accession
Represents an expression platform or microarray/sequencing platform.
PMID
PubMed identifier
Used in documentation and citation metadata.
Core Tables
The main data model is study-centered. A study may contain experiments, documentation,
groups, subjects, samples, interventions, assays, and results. In VaxSEA, exact join
paths differ between VIGET-style and ImmPort-style data, so normalized clean keys are used
to make relationships more consistent.
Table
Purpose
Primary Use
study
Top-level study metadata
Study name, description, type, focus, keywords, and source accession.
experiment
Experiment or visit-level metadata
Connects studies to planned visits, experiment types, and experiment subjects.
subject
Subject or organism metadata
Species, sex, age, race, lineage/strain, group assignment, and source subject accession.
sample
Biosample and experiment sample metadata
Sample type, collection time, subject linkage, biosample accession, and experiment sample accession.
intervention
Intervention or exposure metadata
Vaccination, disease occurrence labels, materials, routes, dosages, and timing.
assay
Assay reference metadata
Assay name, assay type, platform/device, reagents, and ontology identifiers.
results
Result dataset/file references
Assay result references, file paths, file type, datatype, and links to subjects/samples/groups.
documentation
Documentation, source files, publications
Study files, source documents, citations, PubMed IDs, and supplemental files.
Table: study
The study table is the root-level table for study metadata.
In many ImmPort-style imports, study.study_id is a local
VaxSEA identifier, while study.reference_source_id stores
the original ImmPort accession such as SDY984.
Column
Description
study_id
Local VaxSEA study identifier.
study_name
Study title or name.
study_description
Free-text study description, when available.
study_type
Study type classification, when available.
study_focus
Study focus area, such as vaccine response, immune response, epidemiology, or allergy/atopy.
study_keywords
Keyword list or source-provided tags.
reference_source_id
Original source study accession, commonly an ImmPort SDY identifier.
reference_source
Source repository or provider, such as ImmPort.
Table: experiment
The experiment table stores experiment-level or visit-level
records. In VIGET-style data, numeric local identifiers are often used consistently.
In ImmPort-style data, downstream tables often connect through
experiment.reference_source_id, such as a
PV accession.
Column
Description
experiment_id
Local experiment identifier.
study_id
Study identifier or source-prefixed study accession.
experiment_type
Type of experiment, visit, or response being represented.
experiment_subject
Subject focus for the experiment, such as human or organism.
reference_source_id
Original experiment or visit accession, commonly PV... in ImmPort-style data.
clean_study_accession
Normalized study key used to connect experiment records to studies.
clean_experiment_local_id
Normalized local experiment identifier.
clean_experiment_accession
Normalized source experiment accession, such as a PV value.
Table: subject
Column
Description
subject_id
Local or source-prefixed subject identifier.
experiment_id
Experiment or visit identifier associated with the subject.
group_id
Group or arm identifier associated with the subject.
species
Species name, such as Homo sapiens, Mus musculus, or Macaca mulatta.
subject_lineage
Subject lineage, strain, or related classification, when available.
subject_race
Race or ancestry category, when available.
subject_age
Subject age value, when available.
subject_age_unit
Age unit, such as years.
subject_sex
Subject sex, when available.
reference_source_id
Original source subject accession, commonly SUB....
clean_experiment_key
Normalized experiment key used to connect subject records to experiments.
clean_subject_local_id
Normalized local subject identifier.
clean_subject_accession
Normalized source subject accession, usually SUB....
clean_group_key
Normalized group or arm key.
Table: sample
Column
Description
sample_id
Local sample identifier.
experiment_id
Experiment or visit identifier associated with the sample.
Sample collection timing information. Field availability depends on source/import format.
t0_definition
Definition of baseline or time zero.
biosample_type
Biosample type, such as PBMC, serum, plasma, saliva, spleen, or lymph node.
biosample_reference_id
Original biosample accession, commonly BS....
expsample_reference_id
Original experiment sample accession, commonly ES... or GSM....
clean_experiment_key
Normalized experiment key used to connect samples to experiments.
clean_subject_key
Normalized subject key used to connect samples to subjects.
clean_sample_accession
Normalized experiment sample accession used to connect samples to result records.
Table: intervention
Column
Description
intervention_id
Local intervention record identifier.
experiment_id
Experiment associated with the intervention, when available.
subject_id
Subject associated with the intervention.
material_name
Name of vaccine, material, disease state, or exposure.
material_name_id
Ontology or controlled vocabulary identifier for the material, when available.
intervention_type
Type of intervention, such as vaccination or disease occurrence.
dosage / dosage_unit
Dosage value and unit, when available.
intervention_route
Administration route, when available.
intervention_time
Intervention timing relative to baseline, when available.
clean_subject_key
Normalized subject key used to connect interventions to subjects.
Table: assay
Column
Description
assay_id
Assay identifier or local assay row identifier.
assay_name
Name of the assay, such as ELISA, CITE-Seq, Bulk RNA-seq assay, or microarray.
assay_type
Assay type or evidence/category classification.
assay_type_id
Ontology identifier for assay type, when available.
reagents
Reagent information, when available.
device
Platform or device identifier. In VIGET/GEO-style data, this may be a GPL... accession.
clean_assay_key
Normalized assay identifier.
clean_device_key
Normalized platform/device key used for GEO platform matching.
Table: results
The results table stores references to result datasets and
assay output files. Some records contain direct public URLs, while others contain source
file references or internal path references.
Column
Description
results_id
Local result row identifier.
experiment_id
Experiment identifier, when directly populated.
subject_id
Subject identifier associated with the result.
group_id
Group identifier associated with the result.
sample_id
Sample identifier associated with the result. Often matches sample.expsample_reference_id.
documentation_id
Documentation or source-file reference identifier.
assay_id
Assay identifier or platform identifier associated with the result.
analysis_id
Analysis record identifier, when available.
original_assay_type
Original assay type label from the source data.
datatype
Data type, such as numeric or spreadsheet.
file_access
URL, source file reference, or internal file path reference.
file_type
File format, such as txt, csv, or spreadsheet.
clean_sample_key
Normalized sample key used to connect result records to sample records.
clean_subject_key
Normalized subject key used to connect result records to subject records.
clean_experiment_key
Normalized experiment key used for direct experiment-result linking.
Table: documentation
Column
Description
documentation_id
Local documentation identifier.
study_id
Study identifier or source-prefixed study accession associated with the document.
document_name
Name of document, study file, publication, or supplemental data record.
documentation_type
Type of documentation, such as research, lab test results, or assessment results.
documentation_file_access
URL or source file reference for the documentation record.
documentation_reference_source
Reference source, such as PubMed or ImmPort.
documentation_reference_id
Reference ID, such as PMID or source file accession.
citation
Publication citation text, when available.
clean_study_accession
Normalized study key used to connect documentation to studies.
clean_documentation_key
Normalized documentation/source-file key used to connect documentation to results.
Table: group
The group table represents study arms, groups, or sample
groupings. In SQL, group may be a reserved word and often
needs to be quoted as `group`.
Column
Description
group_id
Local group ID or source group identifier.
experiment_id
Experiment or study/expression dataset label associated with the group.
subject_group_type
Subject group type, such as organism or humans.
sample_group_type
Sample group type, when available.
group_size
Group size, when available.
min_age / max_age
Age range for the group, when available.
reference_source_id
Original group or arm accession, such as ARM... or GSE....
clean_experiment_key
Normalized experiment key used to connect groups to experiments.
clean_group_key
Normalized group key used to connect groups to subjects, samples, or results.
Table: material
Column
Description
material_id
Local material identifier.
material_name
Material or vaccine name, such as Zostavax or Fluzone.
material_name_id
Ontology identifier for the material, often from Vaccine Ontology.
reference_id
Reference identifier associated with the material.
clean_material_key
Normalized material key used to connect material records to interventions.
Table: occurrence
The occurrence table stores disease, health status, or event
occurrence records. Some source exports use the spelling
occurence in column names.
Column
Description
occurence_id
Occurrence/event identifier. Source spelling may be occurence.
subject_id
Subject associated with the occurrence.
occurence_name
Occurrence name, such as healthy, disease name, or condition.
occurence_name_id
Ontology identifier for the occurrence name, when available.
occurence_severity
Severity value, when available.
clean_subject_key
Normalized subject key used to connect occurrence records to subjects.
Table: analysis
Column
Description
analysis_id
Analysis identifier.
group_id
Group associated with the analysis, when available.
documentation_id
Documentation or source reference associated with the analysis.
input_data
Input dataset or data source label.
analysis_name
Name or type of analysis.
file_access
Analysis file reference or source URL.
Table: ontology
Column
Description
ontology_id
Ontology row identifier.
ontology_name
Name of the ontology, such as Vaccine Ontology.
ontology_string
Ontology prefix or abbreviation, such as VO.
Common Relationships
VaxSEA supports both VIGET-style and ImmPort-style relationship paths. VIGET records often
use local numeric identifiers consistently, while ImmPort-style records often connect using
original source accessions.
VIGET-style common paths
study.study_id = experiment.study_id
experiment.experiment_id = subject.experiment_id
subject.subject_id = sample.subject_id
experiment.experiment_id = results.experiment_id
sample.expsample_reference_id = results.sample_id
assay.device = results.assay_id for GEO platform values such as GPL...
Note:
In ImmPort-style data, study.study_id may be a local VaxSEA
identifier such as IMMP100, while the real ImmPort accession
is stored in study.reference_source_id, such as
SDY100.
Normalized Clean Keys
To improve performance and avoid slow prefix-stripping operations during searches,
VaxSEA maintains normalized clean_* columns. These columns
remove source-specific prefixes such as IMP_ and
IMMP when appropriate and preserve the source accession needed
for joins.
Clean Key
Typical Source Column
Purpose
experiment.clean_study_accession
experiment.study_id
Connects experiment records to studies.
experiment.clean_experiment_accession
experiment.reference_source_id
Stores source experiment/visit accession, such as PV....
subject.clean_experiment_key
subject.experiment_id
Connects subjects to experiments.
subject.clean_subject_accession
subject.reference_source_id or subject.subject_id
Connects subjects to samples, interventions, occurrences, and some results.
sample.clean_subject_key
sample.subject_id
Connects samples to subjects.
sample.clean_sample_accession
sample.expsample_reference_id
Connects samples to result records.
results.clean_sample_key
results.sample_id
Connects results to samples.
results.clean_subject_key
results.subject_id
Connects results to subjects when sample linkage is not available.
documentation.clean_documentation_key
documentation.documentation_reference_id
Connects documentation records to result/document references.
Important:
VaxSEA data is integrated from multiple source systems. Not every field is populated for
every source. Some fields are source-specific, and some relationships may only be available
through normalized keys or source accessions.
