canonical: https://jentic.com/apis/geodesystems.com/geodesystems

# Geode Systems RAMADDA API

Jentic publishes the only available OpenAPI specification for the Geode Systems RAMADDA repository, keeping it validated and agent-ready. RAMADDA is a content and data repository used by scientific and research organisations to manage documents, photos, geospatial layers, biological datasets, and dashboards. The 241 endpoints expose entry-show and typed search operations across a wide catalogue of repository entry types - from FASTA biological sequences to OME-TIFF imagery and election expenditure datasets - so external clients can query and retrieve repository entries directly. It targets earth-science labs, conservation projects, and research informatics teams.

## For AI agents

Search and retrieve typed entries from a Geode Systems RAMADDA repository - documents, photos, geospatial layers, biological datasets, and dashboards.

## Scope

Does not handle sequence alignment, variant calling, or interactive viewer rendering - use for RAMADDA repository entry search and retrieval only.

## Capabilities

- Show a specific RAMADDA repository entry by ID with its metadata
- Search the repository by entry type for biological data such as FASTA, FASTQ, or HMMER index files
- Query OME-TIFF and DICOM imagery entries for biological imaging projects
- Retrieve ontology-typed entries for assays, cohorts, samples, and persons
- Run a type=any search across the full repository catalogue

## Use cases

### Research Repository Browse

Research informatics teams expose a RAMADDA repository to internal users through a custom dashboard. The `/repository/entry/show` endpoint fetches a specific entry by ID and the `/repository/search/type`/* endpoints return matching entries by type, so the dashboard can render typed views of biological data, imagery, and supporting documents without scraping the RAMADDA UI.

Example prompt: Render a typed-search panel that calls `/repository/search/type/bio_fasta` to list FASTA entries the user has access to

### Biological Imagery Pipeline

Imaging labs ingest OME-TIFF, DICOM, and FASTQ files into RAMADDA and want downstream pipelines to pick them up automatically. Polling `/repository/search/type/bio_ome_tiff` and `/repository/search/type/bio_dicom` returns the latest imagery entries so a pipeline can fetch them via `/repository/entry/show` and route them into analysis tools.

Example prompt: Poll `/repository/search/type/bio_ome_tiff` hourly and queue any new entries for downstream ImageJ analysis

### Ontology-Driven Cohort Discovery

Translational research teams use ontology-typed entries to organise cohorts, samples, and assays. The `/repository/search/type/bio_ontology_cohort`, _sample, _assay, and _person endpoints expose these typed records, letting an agent assemble a cross-referenced cohort view from a single repository.

Example prompt: Search `/repository/search/type/bio_ontology_cohort`, then for each cohort call `/repository/search/type/bio_ontology_sample` to assemble the sample list

### AI Agent Data Discovery

An AI agent helping a researcher find the right dataset can issue typed searches across RAMADDA via Jentic. The agent searches for 'find FASTA entries' or 'list DICOM imagery', loads the matching schema, and executes the call. The basic-auth credentials remain in your Jentic One instance and the agent receives structured entry lists.

Example prompt: Search Jentic for 'find FASTA entries in RAMADDA', execute `/repository/search/type/bio_fasta` with the project filter, and return the matching entry list to the researcher

## Key endpoints

| Method | Path | Description |
| --- | --- | --- |
| GET | `/repository/entry/show` | Show a specific repository entry by ID |
| GET | `/repository/search/type/any` | Search across all entry types in the repository |
| GET | `/repository/search/type/bio_fasta` | Search for FASTA biological sequence entries |
| GET | `/repository/search/type/bio_dicom` | Search for DICOM medical imaging entries |
| GET | `/repository/search/type/bio_ome_tiff` | Search for OME-TIFF microscopy imagery entries |
| GET | `/repository/search/type/bio_ontology_cohort` | Search ontology cohort entries |
| GET | `/repository/search/type/bio_ontology_sample` | Search ontology sample entries |

## Key resources

- **Repository Entries** — Show or list typed entries in a RAMADDA repository
- **Biological Datasets** — Search for FASTA, FASTQ, HMMER, OME-TIFF, and DICOM entries
- **Ontology Records** — Query ontology-typed cohort, sample, assay, and person records
- **General Search** — Run typed searches including type=any across the catalogue

## Why Jentic

- **Setup:** Wiring the Geode Systems RAMADDA API by hand means setting up basic auth, building the Authorization header on every call, and navigating a large typed-search surface yourself. Through Jentic you install once, import RAMADDA from the API Directory, store the username and password once, and your agent calls it.
- **Permission scoping:** RAMADDA's search and show operations take their query in the query string rather than the URL path, so scope the agent to the operations it needs, such as searching for FASTA entries and showing a repository entry. You choose the operations it may call, so search types you do not need are not included unless you add them.
- **Credential handling:** Your RAMADDA username and password are stored once, encrypted, by your own Jentic One instance, and the Authorization header is built at execution time. They never enter the agent's prompt, logs, or context.
- **Discovery method:** Agents search Jentic by intent such as 'search RAMADDA for FASTA entries' or 'show a repository entry', and Jentic returns the matching typed-search operation with its parameter schema so the agent calls the right endpoint without memorizing RAMADDA's large surface.

## Related APIs

- **EMBL-EBI** — European bioinformatics APIs covering Ensembl, sequence, and proteomics data
- **NCBI Datasets** — NCBI Datasets API for genome assemblies, gene records, and taxonomy
- **UCSC Genome Browser** — Pair UCSC reference genome data with project-specific entries stored in RAMADDA

## FAQ

### Why is there no official OpenAPI spec for the Geode Systems RAMADDA API?

Geode Systems documents RAMADDA's API in HTML reference pages but does not publish an OpenAPI specification. Jentic generates and maintains this spec so that AI agents and developers can call Geode Systems RAMADDA API via structured tooling. It is validated against the live API and kept up to date. Get started with Jentic One, the self-hosted execution layer.

### What authentication does the Geode Systems RAMADDA API use?

RAMADDA uses HTTP Basic authentication - the username and password of a repository account are sent in the Authorization header. Through Jentic the credentials live in the vault and are injected per call, so an agent never sees the raw password.

### Can I search for FASTA or DICOM entries in the repository?

Yes. Use GET `/repository/search/type/bio_fasta` for FASTA sequences and GET `/repository/search/type/bio_dicom` for DICOM imagery. Both endpoints accept standard search filters and return matching entry summaries you can deep-fetch via `/repository/entry/show.`

### What are the rate limits for the Geode Systems RAMADDA API?

The OpenAPI spec does not declare explicit rate limits. RAMADDA is typically self-hosted by the research organisation, so practical limits depend on the host's server capacity - coordinate batch jobs with the repository administrator and avoid tight polling on high-cardinality search endpoints.

### How do I retrieve a specific repository entry through Jentic?

Run pip install jentic, search Jentic for 'show RAMADDA repository entry', and call `/repository/entry/show` with the entry ID. The response includes the entry's metadata and links to associated files in the repository.

### Does the API cover non-biological entry types?

Yes. The 241-endpoint surface includes generic types such as type/any, beforeafter, biblio, and election-expenditure datasets alongside the biological types - RAMADDA catalogues a wide range of research artefacts.

### Can I limit what my agent is allowed to do with the Geode Systems RAMADDA API?

Yes. Because Jentic One runs on your own infrastructure, your rules decide which RAMADDA operations the agent may call, so you can allow only what it needs, such as searching for FASTA entries with `/repository/search/type/bio_fasta` and fetching a single record with `/repository/entry/show.` Search types you do not grant, like DICOM or ontology cohort queries, stay unavailable unless you add them. The basic-auth username and password stay in your self-hosted instance and are injected into the Authorization header at call time, so the agent never receives the raw credentials.