Ontology & Vocabularies

SynDB uses controlled vocabularies to standardize dataset metadata — brain regions, species, microscopy techniques, and neurotransmitter types.

Browsing Terms

List All Vocabularies

curl https://api.syndb.xyz/v1/ontology/vocabularies

List Terms in a Vocabulary

curl "https://api.syndb.xyz/v1/ontology/terms?vocabulary=brain_region"

Search Terms

curl "https://api.syndb.xyz/v1/ontology/terms?q=mushroom"

Term Hierarchy

# Get child terms
curl https://api.syndb.xyz/v1/ontology/terms/{term_id}/children

# Get ancestor terms
curl https://api.syndb.xyz/v1/ontology/terms/{term_id}/ancestors

Validating Terms

Before submitting dataset metadata, validate that your terms exist:

curl -X POST -H "Content-Type: application/json" \
  https://api.syndb.xyz/v1/ontology/terms/validate \
  -d '{"terms": ["mushroom_body", "lateral_horn"]}'

Returns which terms are valid and which are unrecognized.

Administration (SuperUser)

Create a Term

curl -X POST -H "Authorization: Bearer $TOKEN" \
  -H "Content-Type: application/json" \
  https://api.syndb.xyz/v1/ontology/terms \
  -d '{
    "vocabulary": "brain_region",
    "code": "MB_CALYX",
    "label": "calyx",
    "parent_id": "00000000-0000-0000-0000-000000000001",
    "uri": "https://example.org/terms/mb-calyx",
    "metadata": {
      "source": "manual"
    }
  }'

Update a Term

curl -X PUT -H "Authorization: Bearer $TOKEN" \
  -H "Content-Type: application/json" \
  https://api.syndb.xyz/v1/ontology/terms/{term_id} \
  -d '{
    "label": "calyx",
    "uri": "https://example.org/terms/mb-calyx",
    "metadata": {
      "status": "reviewed"
    }
  }'

Deprecate a Term

curl -X DELETE -H "Authorization: Bearer $TOKEN" \
  https://api.syndb.xyz/v1/ontology/terms/{term_id}

Deprecated terms remain in the system but are flagged in search results and validation.

Bulk Import

curl -X POST -H "Authorization: Bearer $TOKEN" \
  -H "Content-Type: application/json" \
  https://api.syndb.xyz/v1/ontology/import/csv \
  -d '{
    "vocabulary": "brain_region",
    "csv_data": "code,label,uri,parent_code\nMB,mushroom body,https://example.org/terms/mb,\nMB_CALYX,calyx,https://example.org/terms/mb-calyx,MB"
  }'

CSV format: code,label,uri,parent_code

Integration with Datasets

When creating or updating dataset metadata, brain region, species, and microscopy fields are validated against the ontology. Invalid terms are rejected with an error listing the closest matches.

External References

SynDB’s ontology system draws from established biomedical and neuroscience ontologies:

• OBO Foundry — community-maintained interoperable ontologies for biology and biomedicine
• UBERON — multi-species anatomy ontology used for brain region terms
• ChEBI — Chemical Entities of Biological Interest, covering neurotransmitter classifications
• Allen Brain Atlas — reference atlas for mouse and human brain region parcellations
• Virtual Fly Brain — Drosophila neuroanatomy ontology browser and data integration hub