Scientific databases
Use this page to choose a data source, understand what it can return, and make its tools available in Open-Science. For step-by-step research examples with screenshots and output files, see Research workflows.
Supported databases
Open-Science v0.34.0 includes 28 data-source Connectors with 298 operations. The separate offline Molecule Connector adds two operations, bringing the full registry to 300. Connector names below match Settings → Connectors; each family can expose several databases. Listing a source does not mean every feature of its website is available.
| Connector | Sources | Operations | Use it for |
|---|---|---|---|
Chemistry · chemistry | PubChem, ChEBI, Rhea, BindingDB | 12 | Small-molecule chemistry via PubChem, ChEBI, Rhea and BindingDB. |
Literature Graph · literature | OpenAlex, arXiv, Crossref, DataCite | 13 | Papers, authors, citations, DOI updates and dataset/software records. |
PubMed · pubmed | PubMed, PMC, Europe PMC | 7 | Biomedical literature via NCBI E-utilities, the PMC ID Converter and Europe PMC — search, metadata, related articles, citation lookup, ID conversion, full text and copyright. |
Genes & Ontologies · genes | MyGene, UniProt, OLS, QuickGO, Reactome, g:Profiler, Enrichr | 15 | Gene/protein identifiers, UniProt sequence discovery, GO and Reactome annotations, and g:Profiler and Enrichr gene-set enrichment. |
Genomes · genomes | Ensembl, UCSC, NCBI, BLAST, Clustal Omega | 20 | Genome annotation, homology and sequence; NCBI taxon/assembly/sequence identity; BLAST search and Clustal Omega multiple sequence alignment. |
Variants · variants | gnomAD, ClinVar, dbSNP | 15 | Human genetic variants — gnomAD population frequencies/constraint, ClinVar records/search (direct NCBI), dbSNP, structural and mitochondrial variants. |
Clinical Trials · clinical-trials | ClinicalTrials.gov | 6 | Clinical trials from ClinicalTrials.gov — search, details, sponsors, investigators, endpoints, and eligibility. |
Clinical Genomics · clinical-genomics | ClinGen, CIViC, Open Targets, ClinPGx | 30 | Clinical genomics knowledge bases: ClinGen curations, CIViC clinical evidence, and the Open Targets Platform, plus ClinPGx pharmacogenomic records. |
Structures & Interactions · structures | PDB, AlphaFold, EMDB, Complex Portal, IntAct | 16 | Structures and molecular interactions — PDB structures, AlphaFold predictions, EMDB cryo-EM entries, Complex Portal complexes, IntAct interaction networks. |
ChEMBL · chembl | ChEMBL | 6 | Bioactive compounds, drugs, targets, bioactivity, and mechanisms via the ChEMBL REST API. |
bioRxiv · biorxiv | bioRxiv, medRxiv, ROR | 7 | bioRxiv/medRxiv preprints — search by date/category, metadata by DOI, journal-publication links, funder listings, and platform statistics. |
Drug Regulatory · drug-regulatory | openFDA | 10 | Drugs@FDA, labels, FAERS adverse-event reports and drug recalls. |
Human Genetics · human-genetics | GWAS Catalog, eQTL Catalogue, PheWeb | 14 | Human genetic association evidence — GWAS Catalog, eQTL Catalogue, and PheWeb PheWAS portals (FinnGen, BioBank Japan). |
Expression · expression | GTEx, Bgee | 16 | Human GTEx tissue expression and eQTLs; Bgee cross-species baseline expression. |
Protein Annotation · protein-annotation | InterPro, Pfam, Human Protein Atlas, STRING | 14 | Protein domain architecture, family/clan membership, expression atlas and interaction networks via InterPro/Pfam, the Human Protein Atlas and STRING, including network interaction enrichment. |
Cancer Models · cancer-models | cBioPortal | 10 | Studies, mutations, copy number, samples, patients, clinical attributes and molecular-profile expression. |
RNA · rna | Rfam | 9 | Non-coding RNA family data (metadata, alignments, models, structures) via Rfam. |
Omics Archives · omics-archives | ArrayExpress, GEO, MetaboLights, MGnify, PRIDE, ENA | 23 | Omics studies and runs; ENA FASTQ/submission inventories, PRIDE and MGnify result-file metadata. |
CellGuide · cellguide | CELLxGENE | 5 | Cell-type identity, marker genes, source datasets, and tissues via CELLxGENE CellGuide. |
Regulation · regulation | ENCODE, JASPAR, UniBind | 16 | Gene-regulation functional genomics — ENCODE experiments/biosamples/files, JASPAR TF binding profiles, and UniBind ChIP-seq TFBS. |
Research Resources · research-resources | Grants.gov, Antibody Registry | 5 | Funding-opportunity search (Grants.gov) and antibody catalog lookups (Antibody Registry). |
BioMart · biomart | Ensembl BioMart | 8 | Ensembl BioMart attribute queries and identifier translation. |
ZINC · zinc | ZINC | 5 | ZINC22 purchasable chemical space (CartBlanche22) — compound lookup by ZINC id, SMILES exact/similarity search, supplier-code resolution, random sampling, 3D structure locations for docking. |
GDC · gdc | NCI GDC | 5 | Cancer projects, cases, file metadata, open/controlled labels and transfer manifests; no download or access grant. |
Zenodo · zenodo | Zenodo | 2 | Public dataset, software and publication discovery, version-specific metadata and file inventories; no upload or download. |
HMMER · hmmer | EMBL-EBI HMMER3 | 3 | Program-specific protein/profile/alignment search, job status and results. |
InterProScan · interproscan | EMBL-EBI InterProScan | 2 | Status and TSV reports for existing annotation jobs; no submission. |
Pathway Commons · pathway-commons | Pathway Commons / Reactome | 4 | Pathway search, top pathways, graph queries and BioPAX submodel exports. |
The offline Molecule tools are covered in Scientific viewers. For the exact operations exposed by each data source, use the Connector operation reference.
What you can do
| Research task | Start with | Typical output |
|---|---|---|
| Find papers, trace citations and check DOI relationships | Literature Graph, PubMed, bioRxiv | Literature records, identifiers, citation links and full-text availability |
| Find genes or proteins and compare sequences | Genes & Ontologies, Genomes | Identifier mappings, protein records, FASTA and BLAST reports |
| Discover public omics data and inspect available files | Omics Archives | Study/run metadata and file inventories with source locations, sizes and available checksums |
| Interpret a gene list or inspect an interaction network | Genes & Ontologies, Protein Annotation | Enrichment tables, ontology annotations and network records |
| Check variants, expression and regulatory evidence | Variants, Clinical Genomics, Human Genetics, Expression, Regulation | Source records with organism, tissue, reference build and relevant evidence fields |
| Retrieve compound, structure or clinical-study records | Chemistry, ChEMBL, Structures & Interactions, Clinical Trials | Chemical identifiers/properties, structure records and trial metadata |
For batch identifier conversion, Genes & Ontologies adds submit_uniprot_id_mapping, get_uniprot_id_mapping_status and get_uniprot_id_mapping_results. Save the job ID, poll at least three seconds apart, then retrieve every result page. Preserve one-to-many mappings and explicit failed_ids; missing from one page does not mean unmatched. The service accepts up to 100,000 identifiers and expires results after up to seven days. See exact mapping fields.
Zenodo exposes public record metadata without authentication. Keep the version-specific record ID and access/license fields with the file inventory. GDC exposes public metadata; a manifest is not download authorization, and controlled files require GDC permission. GDC operations · Zenodo operations.
A database response can support a research step; it does not automatically download data, add every paper to the literature library or run a complete analysis. Specify which records and files you want to save.
Connect and start using a database
1. Enable the built-in Connector
- Open Settings → Connectors and search for the family listed above, such as Omics Archives.
- Open its detail and expand Tools. Read the chosen operation's inputs, result limits and third-party requirements.
- Enable availability for Main and check Used by. Use Manage access on the resource to adjust Main Agent and Specialist associations. Availability and per-tool approval policies are separate controls.
These Connectors are built in; you do not need to add a custom server for them. For an external service you operate yourself, see custom Connector setup. A listed or enabled Connector is not proof that authentication or a query succeeded.
2. Add credentials when the operation requires them
| Service or condition | Where to configure it |
|---|---|
| OpenAlex | Optional key. To configure one, open Settings → Connectors → Literature Graph → Manage credentials → OpenAlex, validate it, then save. |
| Direct NCBI variant queries requiring contact information | Settings → Connectors → Manage credentials → Literature access. Fill in Contact email and select Save. An NCBI API key is optional. |
| Another operation with a credential requirement | Follow that tool's requirements and the credentials guide. Bind the credential to the intended service. |
Enter keys in the credential form, not in a research prompt or a shared output file. Configure requirements for the selected operation; the contact-email requirement above does not mean that every NCBI tool has the same requirement.
Literature Graph also offers crossref_get_work, crossref_get_updates, datacite_search_records and datacite_get_record. These four public methods do not require the OpenAlex key. For OpenAlex citation directions, openalex_citations finds works citing a work, while openalex_references finds the works it cites. Literature Graph parameters.
3. Confirm access with a small query
Enable Genes & Ontologies, open a conversation with a connected model, and send:
Example Check a known human gene identifier
Use Genes & Ontologies query_genes to resolve TP53 with scopes="symbol",
species="human" and fields="symbol,name,entrezgene". Return the input query,
matched records and any unmatched identifiers. Keep the response in English.
Inspect the actual tool result. For human TP53, check query, symbol, Entrez Gene 7157 and the name tumor protein p53. Retain multiple matches until you have confirmed the organism and record. A successful query confirms this particular operation; it does not establish access to all sources. Exact fields.
Follow a research workflow
Each article below includes the inputs, steps, actual English-interface screenshots and downloadable example outputs.
Find public omics data
Find public omics data and build a file inventory: start with a known run or a topic, inspect ENA and PRIDE records, and save source locations and checksums. Downloading the data remains a separate step.
Compare a protein sequence
Find a protein sequence and complete a BLAST search: retrieve UniProt FASTA, retain the BLAST job ID, then inspect the completed alignments, identity and query coverage.
Analyze a candidate gene set
Run functional enrichment for a candidate gene set: choose the organism, identifiers and background, run g:Profiler, and interpret corrected probabilities with source versions.
Confirm a reference genome
Check species, reference genome and chromosome identifiers: resolve the taxon, versioned assembly and chromosome aliases before joining records.
Inspect a pathway network
Inspect a pathway and its interaction network: find a human Reactome pathway through Pathway Commons, preserve its returned URI, export the interactions and distinguish a selected network from evidence of pathway activity.
For other tasks, follow structured PubChem records, cross-checking scientific records or literature discovery for a group meeting.
Use the returned data correctly
- Retain the query, source, organism, tissue, units and accession versions. Database records, predictions and generated summaries are different kinds of evidence.
- Check returned counts, pagination and truncation flags before treating a response as complete. Zero matches, a partial response and a request error need different follow-up actions.
- A file inventory provides locations and metadata. Downloading bytes, checking checksums and analyzing the data are separate operations.
- If a request needs credentials, complete the relevant form before retrying. For rate limits, follow the service's delay; for timeouts, reduce the request size. See Troubleshooting.
Population frequencies and interaction networks
For get_variant, set include_populations: true only when population details are needed. Retain the dataset and reference build. Exome and genome observations remain separate. An unavailable value is null, not zero; overlapping population or sex strata must not be summed. These are observed frequencies, not filtering allele frequencies. gnomAD parameters
From v0.31.0, get_string_network.nodes includes returned neighbors and isolated mapped inputs. A single mapped input requests neighbors; multiple mapped inputs are not expanded. Filter is_query to recover input nodes, and use queries for all mapped aliases. n_nodes counts the graph; n_mapped counts input mappings. Update scripts that equated the two before reusing them. STRING parameters
Find operation parameters
The Connector operation reference lists required inputs, allowed values and exact calls. Use this page to choose a source and connect it; use the reference for a particular tool's fields.
Catalog source: catalog.ts, registry.ts.
Sequence searches and alignment
HMMER provides program-specific protein-sequence, profile-HMM and alignment searches. Choose the program and database together, retain the job ID, and retrieve results only after SUCCESS. HMMER operations.
InterProScan retrieves annotations for an existing job submitted through the EMBL-EBI service. Keep its job ID, check status at least ten seconds apart, and fetch the TSV after FINISHED. This Connector cannot submit a new job. InterProScan operations.
Genomes → Clustal Omega aligns at least three uniquely named protein, DNA or RNA FASTA records. Configure the contact email requested by the service, submit once, retain the job ID, then check status and save the returned alignment. Multiple sequence alignment workflow.
Enrichr, STRING and ClinPGx
- Genes & Ontologies → Enrichr: list current libraries, then query gene-set enrichment for functions, transcription factors, perturbations, drugs, diseases, tissues or cell types. Select a library appropriate to the organism and question, and retain its name, background and adjusted P values.
- Protein Annotation → STRING: test whether a protein network has more interactions than expected from its background. This asks a different question from pathway over-representation; its network P value is not a pathway test. Follow the gene-set enrichment workflow.
- Clinical Genomics → ClinPGx: retrieve drug, gene or variant annotations, guidelines, regulatory labels and population frequencies. Resolve identifiers first, supply the fields required by the operation, and retain original sources and evidence levels. This retrieves research records; it does not automatically produce an individual treatment plan.
Enable the relevant Connector for the active agent in Settings → Connectors. These built-in entries do not require a custom MCP server. See the operation reference for exact fields and conditional requirements.
Pathways, expression and clinical data
Enable the corresponding family in Settings → Connectors, then tell the agent the organism, source, identifiers and intended scope. These additions use built-in Connectors; no custom MCP server is required.
| Entry | What it can do | Connection and interpretation |
|---|---|---|
| Pathway Commons | Search pathways, list top pathways, query paths between genes or export a submodel | Public service; retain the returned URI, organism and source. Graph queries differ from enrichment tests. Follow the pathway interaction workflow. |
| Expression → Bgee | Cross-species present/absent calls, normalized scores, bounded SPARQL queries and download links | Discover species first and retain the NCBI taxonomy ID. SPARQL requires gene, species and tissue. Healthy wild-type baseline calls are not differential expression; download links are not downloaded files. |
| Cancer Models → cBioPortal | List samples/patients and query clinical attributes or mRNA/protein expression | Select a study, discover its profiles and choose measurement/normalization. Supply IDs matching the clinical sample/patient level; molecular data needs explicit genes and exactly one of sample_ids or sample_list_id. Missing rows are not zeros. |
| Drug Regulatory → openFDA | Search/count FAERS reports and search drug recalls | Bound dates and products and retain truncation information. Report counts are not incidence or causal evidence. Multi-valued buckets may overlap; their sum is not a unique report total. |
| Omics Archives → MGnify | List result files by MGYA analysis accession | Returns type, category, upstream URL and size when reported. No file bytes are downloaded; missing sizes or URLs stay null. |
See the Connector operation reference for exact required fields, conditions and examples.