VaxSEA Data Sources
VaxSEA integrates vaccine-related experimental, assay, subject, sample, intervention,
and result metadata from multiple public biomedical resources. The goal is to provide
a searchable view across heterogeneous datasets while preserving links back to the
original data sources whenever possible.
Because each source uses its own accession system and file-access policies, VaxSEA
stores both local VaxSEA identifiers and original source identifiers such as
SDY, SUB,
GSE, GSM,
and GPL.
Primary Data Sources
| Source |
Role in VaxSEA |
Common Identifiers |
External Resource |
| ImmPort |
Source of immunology study metadata, clinical study descriptions,
subject/sample/intervention metadata, assay metadata, and result-file references.
|
SDY study accessions
SUB subject accessions
ARM study arms/groups
PV planned visits/experiments
BS biosamples
ES experiment samples
SFL study files/documentation
|
ImmPort
Some ImmPort files may require user access or may be represented in VaxSEA
as file references rather than direct public downloads.
|
| VIGET |
Source of vaccine-induced host gene-expression study metadata and integrated
expression-analysis references.
|
VIGET study mappings
ImmPort SDY accessions
GEO expression identifiers
|
VIGET publication
VIGET Zenodo record
Publication: Brunson et al., Frontiers in Immunology, 2023. PMID: 37180100.
|
| GEO |
Source repository for gene-expression datasets, sample records, and platform records
referenced by VIGET and related studies.
|
GSE GEO Series
GSM GEO Sample
GPL GEO Platform
|
NCBI Gene Expression Omnibus |
| PubMed |
Source of publication metadata and citations linked to VaxSEA documentation records.
|
PMID identifiers
|
PubMed |
| Biomedical Ontologies |
Provide controlled terminology for assays, vaccines, organisms, units, diseases,
phenotypes, study types, and related biomedical concepts.
|
OBI,
VO,
NCIT,
EFO,
DOID,
UO,
PATO,
SWO
|
OBO Foundry
NCBO BioPortal |
Identifier Guide
| Identifier Pattern |
Meaning |
Example Use in VaxSEA |
| IMMP... |
Local VaxSEA/ImmPort-style imported identifier |
Used internally in VaxSEA for imported ImmPort rows.
Example: IMMP100.
|
| SDY... |
ImmPort study accession |
Stored as a source study accession, often in
study.reference_source_id.
|
| PV... |
ImmPort planned visit / experiment accession |
Used to connect experiments, subjects, samples, and visit-level metadata.
|
| SUB... |
ImmPort subject accession |
Used to connect subject metadata, samples, interventions, and some result records.
|
| ARM... |
ImmPort study arm or group accession |
Used for group or arm-level subject/sample/result organization.
|
| BS... |
ImmPort biosample accession |
Identifies biological samples collected from subjects.
|
| ES... |
ImmPort experiment sample accession |
Frequently used to connect sample records to result records.
|
| GSE... |
GEO Series accession |
Represents a GEO expression dataset or study-level expression series.
|
| GSM... |
GEO Sample accession |
Represents a specific GEO sample, often linked to expression results.
|
| GPL... |
GEO Platform accession |
Represents a microarray or sequencing platform.
|
How VaxSEA Integrates Source Data
VaxSEA imports data from heterogeneous sources that do not always use the same primary
keys. For example, VIGET data may use local numeric identifiers consistently, while
ImmPort-style imports often require matching source accessions such as
SDY, PV,
SUB, and ES.
To support faster search and linking, VaxSEA maintains normalized internal join keys
derived from source identifiers. These normalized keys help connect:
- studies to experiments,
- experiments to subjects and samples,
- subjects to interventions and occurrences,
- samples to result records, and
- results to documentation and assay metadata.
Note:
VaxSEA preserves original source identifiers whenever possible. A local VaxSEA ID such as
IMMP100 is not necessarily the same as the original source
accession. The original source accession is usually displayed separately, such as
SDY100.
Result Files and Download Availability
VaxSEA result records may contain a file reference, a repository URL, or an internal
source-path reference. Not every result entry is a direct public download link.
| Value Type |
Example |
How VaxSEA Displays It |
| Public web URL |
https://zenodo.org/records/7407195 |
Displayed as a clickable source link. |
| Repository accession |
GSE79396, GPL13158 |
Displayed as a link to the relevant source repository when possible. |
| Internal or source file reference |
ALLSTUDIES-DR56_Metadata/elisa_result.txt |
Displayed as a file reference only. It may not be directly downloadable from VaxSEA.
|
| Empty or unavailable link |
N/A |
Displayed as no direct source link available.
|
Important:
VaxSEA is primarily a metadata integration and search interface. Some raw or processed
datasets may need to be accessed through the original source repository, such as ImmPort,
GEO, or Zenodo. Some repositories may require authentication, data-use agreements, or
other access steps.
Citing Data Sources
When using data discovered through VaxSEA, please cite VaxSEA/VIOLIN as appropriate and
also cite the original source datasets, repositories, and publications. Source-specific
citations may include ImmPort study accessions, GEO series accessions, PubMed publications,
and VIGET-related publications.
If you notice a missing or incorrect source link, please contact the VaxSEA/VIOLIN team
so the metadata can be reviewed.
