Geode Systems RAMADDA API
Agent-ready OpenAPI document · curated by JenticStorageDocument Managementbasic241 EndpointsREST
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For Agents
Search and retrieve typed entries from a Geode Systems RAMADDA repository - documents, photos, geospatial layers, biological datasets, and dashboards.
Use for: I need to fetch repository entry 0a1b-... by ID, Search the repository for FASTA biological sequence entries, List all OME-TIFF imagery entries in the repository, Find DICOM imaging records uploaded in the last week
Not supported: Does not handle sequence alignment, variant calling, or interactive viewer rendering - use for RAMADDA repository entry search and retrieval only.
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.
Install Jentic One Beta
Connect the Geode Systems RAMADDA API to your agent
Jentic One is a self-hosted execution layer for AI agents. It lets your agent call the Geode Systems RAMADDA API, or any other public or private API you need. You set the rules, the agent never sees your credentials, and every call is logged.
Two steps, two machines. Install the instance in a safe environment, then register your agent from wherever it runs.
1
Step 1: Jentic One Host machine
# On the machine that will host your Jentic One instance:
curl -fsSL "https://jentic.com/install.sh?src=apis&api=%2Fapis%2Fgeodesystems.com%2Fgeodesystems" | sh2
Step 2: Agent machine
# On the machine where your agent runs (keep this separate from the instance):
curl -fsSL "https://jentic.com/install.sh?src=apis&api=%2Fapis%2Fgeodesystems.com%2Fgeodesystems" | sh
jentic register # connects your agent to your Jentic One instanceJentic One is in public beta. The setup above keeps your agent separate from the instance, which is what you want before using real credentials: an agent running as the same OS user as Jentic One can read its stored keys directly. Just evaluating? A single local install is fine to start. See the secure deployment guide for the tiers.
Capabilities
What an agent can do with Geode Systems RAMADDA API.
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
Patterns agents use Geode Systems RAMADDA API for, with concrete tasks.
★ 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.
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.
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.
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.
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
241 endpoints — jentic publishes the only available openapi specification for the geode systems ramadda repository, keeping it validated and agent-ready.
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
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
Why Jentic?
What agents get from Jentic-routed access to this vendor.
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 isolation
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.
Intent-based discovery
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
Alternatives and complements available in the Jentic catalogue.
FAQs
Specific to using Geode Systems RAMADDA API through Jentic.
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.
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