Glossary
SDF structure file
SDF structure file is structure-Data File distributing chemical structures together with associated data fields; the standard bulk format for molecule structure dumps. In Datadory's catalog of 1,744 datasets, DrugBank Open Data (commercial delivery terms) and PubChem PUG REST API are working examples.
What is SDF structure file?
A Structure-Data File distributing chemical structures together with associated data fields; the standard bulk format for molecule structure dumps.
In this catalog it appears concretely: - DrugBank Open Data (commercial delivery terms) — "Structures SDF 5.16 MB". - PubChem PUG REST API — "CURRENT-Full SDF chunks run ~280-320 MB per 500,000 compounds". - ChEMBL Web Services API — "SDF among its output formats".
PubChem PUG REST API is the second reference point worth knowing: "CURRENT-Full SDF chunks run ~280-320 MB per 500,000 compounds". Reading the two together shows how much variation sits underneath one shared label.
Why does SDF structure file matter when choosing a dataset?
A label on a listing is not a deliverable. Teams that license on the strength of a product-name match routinely find the shipped files cover a narrower slice than they assumed, and backfilling history afterwards costs more than the license ever did.
The failure mode is concrete: the label appears in a listing, the delivered files tell a different story, and the gap surfaces mid-project when fixing it is most expensive.
You rarely have to take a vendor's word for it. 82.4% of the 1,744 datasets Datadory catalogs are free to access, and DrugBank Open Data (commercial delivery terms) lets you inspect the real artifact before any budget is committed.
How do you evaluate SDF structure file in a data source?
Treat every claim of this attribute as testable:
- Open DrugBank Open Data (commercial delivery terms) and confirm its record — "Structures SDF 5.16 MB" — against the files you actually receive.
- Open PubChem PUG REST API and confirm its record — "CURRENT-Full SDF chunks run ~280-320 MB per 500,000 compounds" — against the files you actually receive.
- Open ChEMBL Web Services API and confirm its record — "SDF among its output formats" — against the files you actually receive.
See the term applied to real records: biotechnology data, pharmaceuticals data.
Related terms
Adjacent concepts worth reading next: - bulk download access - commercial delivery terms commercial delivery terms release - SMILES notation
Frequently asked questions
What is an example of SDF structure file?
DrugBank Open Data (commercial delivery terms) is the clearest example in this catalog. Its record states: "Structures SDF 5.16 MB". Across all 1,744 datasets Datadory averages a quality score of 7.81 out of 10, so a named example can be weighed rather than trusted blindly.
Is data described as "SDF structure file" free to use?
Treat access and permission separately. 82.4% of the 1,744 datasets in this catalog are free to access, but 235 are freemium and 61 are paid outright, so confirm both the price and the license on the exact distribution before building on it.
How do I verify a source really provides SDF structure file?
Open DrugBank Open Data (commercial delivery terms) next to PubChem PUG REST API and compare the promise with the download. Field definitions are verified for 1495 of 1,744 datasets (85.7%), which makes that check fast inside the catalog and manual outside it.
Datasets containing this field
Datasets containing SDF structure file
6 datasets carry sdf structure file in the catalog. Open one, count the fields, judge for yourself.
ChEMBL
ClinicalTrials.gov
DrugBank Online
Ensembl Genome Browser
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