Evidence profiles
The profiles that give a file its meaning, and which file types each accepts.
Reference
A profile states what a file is for. The file's extension decides how BioStor checks and renders it; the profile decides which domain fields it carries, which values those fields may take and, in two cases, which extra parsing runs on it. Choosing the right profile at upload is what makes a PDF a permit rather than a generic document, and what lets a reviewer see the collection date of a recording rather than only its duration. BioStor declares 24 profiles.
How profiles work
Each profile has a description, a list of accepted extensions, its own metadata table and, where a field is enumerated, a controlled vocabulary. You may name a profile at upload; otherwise the extension's default profile applies. The profile must accept the extension, so a .pdf cannot be filed as chromatogram. Tar archives have no default: every .tar upload must name acoustic_survey or paired_end_metabarcoding.
Profile fields are supplied as form fields at upload, or in the metadata manifest of a batch package. Account holders can later edit one profile field at a time on the object's page in the portal; computed (derived_*) and protected fields cannot be edited there, and each edit is audited. The live field schema of any profile is available through the API (BioStor API).
Profile metadata and file metadata
| Kind | Describes | Set by |
|---|---|---|
| File-type metadata | The file as a technical artefact: dimensions, read counts, trace statistics, audio properties, row counts | Computed by post-processing; read-only |
| Profile metadata | The file as evidence: which specimen, which statement type, which permit, which species or dataset | The uploader; editable in the portal |
The two are stored separately, so adding a profile never changes how a file type is processed.
The 24 profiles
| Profile | For | Accepts |
|---|---|---|
specimen_image |
Photograph of a biological specimen | jpg |
chart |
Chart, diagram or data visualisation; chart_type from bar, line, scatter, pie, histogram, box, heatmap, network, phylogenetic_tree, alignment, electropherogram, other |
png, gif |
specimen_documentation |
Legal or regulatory document about specimens (agreements, MTAs, affidavits); document_type names the kind |
pdf |
collection_statement |
Sworn affidavit describing how a specimen sample was collected; statement_type from sample_collection, sample_opening, analyst |
pdf |
evidence_seal_break_statement |
Sworn affidavit describing the breaking of an evidence seal and the sub-sampling of the specimen (point 2 of the chain of custody) | pdf |
analyst_statement |
Sworn affidavit by the analyst who performed the DNA barcode analysis (point 3 of the chain of custody) | pdf |
chain_of_custody |
Provenance and handling form; form_type from coc_datasheet, accession, retrieval |
pdf |
taxonomic_identification |
Expert identification or verification of a voucher specimen (taxon, identifier, method, confidence) | pdf |
lab_worksheet |
Laboratory procedure worksheet; worksheet_type from dna_isolation, dna_quantification, pcr, gel_electrophoresis, pcr_cleanup, cycle_sequencing, cycle_seq_purification, capillary_electrophoresis, sequence_assembly |
pdf, xlsx |
permit |
Regulatory permit for collection, possession, export or transport; permit_type from collection, hunt, convey, export, standing, section_20, possession |
pdf |
scientific_paper |
Publication with bibliographic metadata (title, authors, journal, DOI, year) | pdf |
supporting_reads |
Raw sequencing reads with quality scores | fastq |
sequence_alignment |
Consensus or aligned sequence data | fasta |
chromatogram |
Sanger trace chromatogram | ab1, scf |
genetic_fingerprint |
STR or SNP genotyping fingerprint data | fsa |
lab_notebook |
Experimental records and observations | xlsx |
acoustic_survey |
Bioacoustic sensor-day archive: a tar of WAV recordings with index.tsv and sensor.json manifests, stored as one object |
tar |
paired_end_metabarcoding |
Paired-end Illumina metabarcoding sample: a tar of the R1 and R2 FASTQ files, stored as one object | tar |
metabarcoding |
Single-end metabarcoding FASTQ from a bulk or environmental sample, with coordinates, sampling protocol, habitat scope and date range supplied at upload | fastq |
bioacoustic_recording |
Single audio recording, with species, coordinates and recording date supplied at upload | mp3, wav |
occurrence_dataset |
Biodiversity occurrence records (GBIF or BOLD exports, survey data); data_standard from DwC, ABCD, BOLD, custom |
parquet, jsonl, tsv |
analysis_result |
Tabular output of an analysis job, linked to its job and pipeline version; job_type names the job |
parquet, jsonl, tsv |
specimen_batch |
Bulk specimen submission sheet, with submitter, dataset code and template version | tsv, jsonl |
reference_table |
Stable reference dataset with a validity window; table_type from species_list, barcode_reference, controlled_vocabulary, distance_matrix, other |
parquet, tsv |
Default profiles by extension: jpg is specimen_image; png and gif are chart; pdf is specimen_documentation; fastq is supporting_reads; fasta is sequence_alignment; ab1 and scf are chromatogram; fsa is genetic_fingerprint; xlsx is lab_notebook; mp3 and wav are bioacoustic_recording; parquet and jsonl are occurrence_dataset; tsv is specimen_batch.
Only acoustic_survey and paired_end_metabarcoding run additional procedures of their own; the other 22 profiles are metadata-only. See File types, pipelines and size limits.
Profiles the workbench exposes
The workbench's batch forms choose the profile for you: images are filed as specimen_image, traces as chromatogram, and documents, FASTQ, microsatellite and spreadsheet packages under their extension defaults. Enrich record attaches one file to a record under any of 12 profiles: specimen_image, specimen_documentation, chain_of_custody, collection_statement, permit, taxonomic_identification, lab_worksheet, scientific_paper, chromatogram, supporting_reads, genetic_fingerprint and lab_notebook. The other profiles are reached through the BioStor portal and API. See Attach to one record.
Good to know
- Searches by file family (for example documents or FASTQ) filter on the domain fields of the extension's default profile only. A PDF filed as
permitis found by its identifier and in thepermitprofile listing, not through a domain-field search on documents. - Changing an object's profile after upload does not move the profile fields already recorded, so set the profile correctly at upload.