File type profiles
Every BIO·STOR object has two type layers: an extension that drives format validation and statistics extraction, and a profile that declares the object's domain role. Pass any profile name from this page as profile=<name> on upload.
Image profiles
Photography of a physical specimen or sample. Carries full copyright, taxonomy, and catalogue linkage metadata.
photographer, copyright_holder, copyright_year,
copyright_license, copyright_institution,
measurement, measurement_type, instrument, camera
A scientific chart or graph — phylogenetic trees, alignments, electropherograms, distance matrices, and other analytical visuals.
chart_type: bar · line · scatter · pie · histogram
box · heatmap · network · phylogenetic_tree
alignment · electropherogram · other
Sequence profiles
Raw sequencing reads supporting a consensus or assembly. The standard profile for FASTQ output from a single sequencing run.
sequencing_direction, sequencing_run_date
Single-end metabarcoding FASTQ — environmental DNA from a bulk collection, water filter, soil core, or malaise trap. Collection coordinates, sampling methodology, habitat scope, and collection date supplied at upload.
primers_forward, primers_reverse,
sequencing_direction, sequencing_run_date,
platform, instrument_model
sampling_protocol:
malaise_trap · pitfall_trap · aquatic_net
water_filter · soil_core · light_trap
aerial_net · passive_bulk_collection · other
habitat_scope:
terrestrial · freshwater · marine
soil · estuarine · human_managed
collection_date_start, collection_date_end,
latitude, longitude
A multiple sequence alignment (MSA) in FASTA format. Used for aligned sets fed into tree-building or distance jobs.
Trace profiles
A Sanger sequencing trace from a single-reaction run. Quality scoring and a rendered chromatogram preview are produced automatically.
Microsatellite profiles
Fragment analysis file from a microsatellite or STR panel run. Records the locus name and allele calls for a single sample.
Document profiles
General supporting documentation attached to a specimen or sample record.
document_version, title,
annotation, processids, sampleids
Signed statement related to sample collection — sample collection, sample opening, or analyst declarations.
sample_collection
sample_opening
analyst
processids, sampleids
Chain-of-custody tracking form for specimens or extracts through the laboratory workflow.
coc_datasheet
accession
retrieval
processids, sampleids
Formal taxonomic identification record assigned to a specimen by a qualified identifier.
method, confidence,
processids, sampleids
Published or preprint scientific paper attached to a project or specimen record.
doi, volume, issue, pages
Collection or research permit issued by a regulatory authority, with a defined validity window.
issue_date, expiration_date,
collection_scope
Spreadsheet profiles
A completed lab data entry worksheet from a defined template — extraction plates, PCR runs, QC sheets, gel documentation.
performed_by, processids, sampleids
Free-form lab notebook in spreadsheet format, not bound to a specific template structure.
Audio profiles
A field recording of animal vocalisation or acoustic environment. Duration, sample rate, and a spectrogram preview are extracted automatically.
Archive profiles
Tar archives have no default profile — a profile is required on every .tar upload. These two profiles trigger L2 auto-parsing procedures that validate the archive's internal structure and populate domain fields without any additional API calls.
A batch acoustic survey deployment: a tar of recordings plus index.tsv and sensor.json manifests. Both manifests are validated, then parsed into profile fields automatically during postprocessing.
sensor.json — deployment metadata
individual .mp3 / .wav recording files
deployment_date, retrieval_date, habitat_description
A paired-end metabarcoding run: a tar containing exactly two FASTQ files (R1 + R2). Read counts, lengths, and quality scores are extracted from both files automatically.
platform, instrument_model,
sampling_protocol, habitat_scope,
collection_date_start, collection_date_end,
latitude, longitude
r1_read_count, r2_read_count,
r1_mean_length, r2_mean_length,
r1_mean_qv, r2_mean_qv
Tabular data profiles
All three tabular formats share the same four profiles. Row counts, column names, and a preview.json sidecar (schema + 3 sample rows) are extracted automatically for every tabular upload regardless of profile.
Biodiversity occurrence records — GBIF exports, BOLD data downloads, field survey data. Default profile for .parquet and .jsonl.
taxon_scope, geographic_scope,
collection_date_start, collection_date_end,
source_doi, source_institution, coordinate_system
compression codec (Parquet only)
Tabular output from a BioStor analysis pipeline job — identification results, distance summaries, barcode gap reports, phylogenetic outputs.
analysis_date, record_count_in, record_count_out
job_type: identification · distance-summary
barcode-gap · phylogenetic-tree
sequence-composition · diagnostic-characters · …
Bulk specimen submission sheet — BWP batch ingest templates or BOLD upload TSVs. Default profile for .tsv.
submitter_name, submitter_institution,
collection_date_start, collection_date_end, has_gps
Stable reference datasets — species lists, barcode reference libraries, CITES appendix tables, controlled vocabularies. Versioned with a validity window.
controlled_vocabulary · distance_matrix · other
authority, version, taxon_scope, valid_from, valid_until
compression codec (Parquet only)
Ready to integrate?
The Swagger UI has live request forms for every endpoint. Pass any profile identifier from this page as the profile= query parameter on upload.