OpenScience provides a common way to search its registered scientific databases. The database directory lists every included source and the formats it declares.
Discover the right source
Ask which databases are available for your domain and which one fits the question. The agent can inspect the current catalog before choosing a database identifier.
List available protein and structure databases. Explain which one should
supply a reference sequence and which one should supply an experimental
structure for the protein I am studying.
A general web search and a structured database query answer different questions. Use the direct database when exact identifiers, organisms, versions, or downloadable records matter.
Search with explicit identifiers and constraints
Search UniProt for human insulin. Return the accession, organism, record
title, source URL, and any ambiguity. Do not fetch a structure until we
have selected the intended protein record.
Queries use the source's native syntax. Organism filters apply where the source supports them. Search requests return a bounded set of hits, up to 50, so a single search is not a full database export.
Use accession identifiers from the returned records rather than inventing one from a protein or compound name. Similar names can refer to different isoforms, organisms, structures, or chemical forms.
Fetch a record or a file
Once you select a result, ask for its structured record or a declared file format:
Fetch the selected accession in FASTA format if the database supports it.
Keep the database name, accession, retrieval date, and source URL beside
the downloaded file. Show the output path and inspect the sequence.
Common declared formats include FASTA, PDB, CIF, and SDF, depending on the database. Some sources support only structured metadata. A catalog entry does not guarantee that every record has every advertised format.
Validate the retrieved material
Find a simulation tool with BioSimulators
Search biosimulators for SBML CVODE, KISAO:0000019, CellML, NeuroML, or BNGL. Combined model-format and algorithm queries match a single supported capability. Search results include versioned identifiers, so fetching a selected result preserves its version.
Fetch tellurium for its latest registry record or tellurium/2.2.10 for an exact version. The record describes supported formats, algorithms, and installation metadata; this connector does not execute simulations. No API key is required. Enable Genomics and biology in Network settings if the source needs approval.
| Material | Checks to request |
|---|---|
| Sequence | Organism, accession/version, alphabet, length, record count. |
| Structure | Record identity, chains, ligands, experimental versus predicted origin. |
| Compound | Identifier, chemical form, stereochemistry, units and property provenance. |
| Literature record | Title, authors, year, identifier, and available full-text link. |
| Dataset record | Version, access conditions, size, files, and whether data were actually downloaded. |
A metadata record is useful evidence that a resource exists; it is not the same as having its underlying dataset or complete paper.
Recover from source problems
Rate limits and source errors are reported separately from an empty search. Wait and retry a bounded request when a source is temporarily unavailable. If the format or operation is unsupported, use a supported alternative or the source's own authorized download process.
Keep failed retrievals in the task report when they affect coverage. Do not silently substitute a different accession or omit failed inputs from a comparison.
Build a reproducible collection
Ask OpenScience to save a manifest containing database, accession, format, URL, retrieval date, local path, and any error. Then use Scientific viewers to inspect the files and the relevant research workflow for analysis.