API

Every record on this site is readable over HTTP as JSON. The API needs no key and no account. Two families are served: the v1 resources, which keep the field names and the response shape the LungMAP API has always used, and the documented endpoints, which describe themselves through OpenAPI and carry paging.

Start here

curl "https://www.lungmap.net/api/datasets?limit=3"
curl "https://www.lungmap.net/api/samples?limit=3"
curl "https://www.lungmap.net/api/v2/analyses?limit=3&offset=0"

A v1 resource answers with a bare JSON array. A documented endpoint answers with {total, offset, limit, count, items}. limit defaults to and is capped at 1,000,000.

Interactive reference (OpenAPI)  |  openapi.json  |  coverage report

v1 resources

18 of 29 paths declared by the original API answer with records from this data release. The rest answer an empty array, which is what the live site answers for them.

analyses

GET/api/analyses

Fields: analysis_id, dataset_id, parent_analysis_id, species, species_common_name, submission_stage_id, submission_stage_label, taxon_id, type_id

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biological_database_entities

GET/api/biological_database_entities

Fields: entity_id, id_type_id, name, symbol

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biological_replicates

GET/api/biological_replicates

Fields: analysis_id, biological_replicate_id, dataset_id, sample_id

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datasets

GET/api/datasets

Fields: dataset_id, dataset_type_category_id, dataset_type_category_label, dataset_type_id, dataset_type_label, default, description, label, molecule_type_id, molecule_type_label, molecule_type_plural_label, sample_count, sample_type_id, sample_type_label, species, species_common_name, submission_stage_id, submission_stage_label, taxon_id

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entity_lungmap_data

GET/api/entity_lungmap_data

Fields: associated_id, associated_id_type, id

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entity_sets

GET/api/entity_sets

Fields: description, entity_set_id, label, source_analysis_id

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entrez_genes

GET/api/entrez_genes

Fields: entrez_id, name, species, species_common_name, symbol, taxon_id

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files

GET/api/files

Fields: description, file_id, file_size, file_type_id, label, path

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images

GET/api/images

Fields: dataset_id, description, image_id, label

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probes

GET/api/probes

Fields: label, manufacturer, probe_id, probe_type_id, probe_type_label, product_number

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publications

GET/api/publications

Fields: doi, label, pmid, publication_id

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researchers

GET/api/researchers

Fields: label, researcher_id, site_id, site_label, site_short_label

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samples

GET/api/samples

Fields: age_range_id, age_range_label, age_unit_display_order, age_unit_id, age_unit_label, age_value, alternate_id, sample_id, sex_id, sex_label, species, species_common_name, taxon_id, weight

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sites

GET/api/sites

Fields: label, short_label, site_id, type_id, type_label

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synonyms

GET/api/synonyms

Fields: id, synonym

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technical_replicates

GET/api/technical_replicates

Fields: age_id, age_label, age_range_id, age_range_label, analysis_id, biological_replicate_id, dataset_id, sample_alternate_id, sample_id, technical_replicate_id

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technologies

GET/api/technologies

Fields: description, label, manufacturer_id, manufacturer_label, technology_id

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tools

GET/api/tools

Fields: display_order, icon, label, tool_id, tutorial

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charts

GET/api/charts

No records in this data release.

controlled_vocabulary

GET/api/controlled_vocabulary

No records in this data release.

entity_properties

GET/api/entity_properties

No records in this data release.

entity_set_entities

GET/api/entity_set_entities

No records in this data release.

heatmaps

GET/api/heatmaps

No records in this data release.

image_feature_annotations

GET/api/image_feature_annotations

No records in this data release.

image_feature_sets

GET/api/image_feature_sets

No records in this data release.

image_features

GET/api/image_features

No records in this data release.

ontologies

GET/api/ontologies

No records in this data release.

search_helper

GET/api/search_helper

No records in this data release.

species

GET/api/species

No records in this data release.

Documented endpoints

Built from the running application's OpenAPI document, so this list is always what the server serves.

Home page

GET/

Search the CellRef2 atlas: features, cell states and comparisons

GET/api/agent/cellref2/search

Parameters: q, limit

Return a prompt-ready context block for one dataset

GET/api/agent/context/{experiment_id}

Parameters: experiment_id, max_tokens

Every comparison this atlas ran, by its readable name

GET/api/agent/contrasts

Parameters: q, contrast_class, dataset, limit

Find datasets an agent can then analyse

GET/api/agent/datasets

Parameters: q, anatomy, organism, limit, offset

What one acronym or label means, and what the atlas holds of it

GET/api/agent/define

Parameters: term

Differential statistics for a feature or a cell type

GET/api/agent/differential

Parameters: feature, cell_type, disease, modality, contrast, comparison, dataset, order, contrast_class, max_fdr, limit

The disease and cell setting of a figure, with its definitions

GET/api/agent/figure-context

Parameters: contrast, cell_state

Write a comparison label out in full

GET/api/agent/label

Parameters: text, budget

Describe every capability an agent may call

GET/api/agent/manifest

Every modality's evidence about one gene

GET/api/agent/modalities

Parameters: feature, cell_type, contrast_class, comparison, max_fdr, limit

Protocol documents for a technique, and the datasets that used it

GET/api/agent/protocols

Parameters: q, limit

Turn free text into LungMAP identifiers

GET/api/agent/resolve

Parameters: q, limit

Every disease, cell state and study this atlas names

GET/api/agent/vocabulary

Parameters: kind

Find a disease, cell state, study or measured field by any words

GET/api/agent/vocabulary/search

Parameters: q, limit

Read a viewer question

POST/api/assistant/viewer-intent

List the database classes and their sizes

GET/api/classes

Return one entity and its properties

GET/api/entities/{entity_id}

Parameters: entity_id

List experiments

GET/api/experiments

Parameters: experiment_type, organism, format, limit, offset

Return one experiment

GET/api/experiments/{experiment_id}

Parameters: experiment_id

Report whether the database answers

GET/api/health

Single-cell releases and their status

GET/api/sc/datasets

Top correlated genes in one state

POST/api/sc/{key}/correlated

Parameters: key

How many cells match a selection

POST/api/sc/{key}/count

Parameters: key

Prepare selected cells x ALL genes

POST/api/sc/{key}/export

Parameters: key

Download a prepared export

GET/api/sc/{key}/export/direct/{token}

Parameters: key, token

Export job status

GET/api/sc/{key}/export/{export_id}

Parameters: key, export_id

Finished export

GET/api/sc/{key}/export/{export_id}/download

Parameters: key, export_id

Selected cells x selected genes

POST/api/sc/{key}/matrix

Parameters: key

Turn a request into a gene list for this release

POST/api/sc/{key}/resolve-genes

Parameters: key

Filterable fields for a release

GET/api/sc/{key}/schema

Parameters: key

Categories and cell counts

GET/api/sc/{key}/values/{field}

Parameters: key, field

Start an embedding job

POST/api/sc/{key}/viewer

Parameters: key

Embedding job status

GET/api/sc/{key}/viewer/{job_id}

Parameters: key, job_id

Finished embedding payload

GET/api/sc/{key}/viewer/{job_id}/data

Parameters: key, job_id

Search labels and descriptions

GET/api/search

Parameters: query, category, format, limit, offset

Return the record counts of the database

GET/api/statistics

List analyses (envelope form)

GET/api/v2/analyses

Parameters: experiment, format, limit, offset

List samples (envelope form)

GET/api/v2/samples

Parameters: organism, format, limit, offset

Assistant

GET/ask/

Parameters: query, q, no_redirect, expand

Heatmap, charts and entity list for one analysis

GET/breath-omics-analysis-page/

Parameters: dataset_id, experiment_id, analysis_id, tab, entity_set_id

One dataset

GET/dataset/

Parameters: dataset_id, experiment_id

Explore Data

GET/explore-data/

What the corpus contains, by covariate

GET/explore-data/analytics/

Parameters: species, disease

Ontology browser

GET/explore-data/ontology-browser/

Parameters: term

Browse every dataset by assay

GET/explore-data/visualize-data/

Parameters: tab_id, main_tab_id, spatial_tab_id, entity_id

Previous home page

GET/home-classic/

One image, with its details

GET/image-visualization/

Parameters: datasetid, imageId

Full-size heatmap

GET/morpheus/

Parameters: dataset_id, analysis_id, entity_set_id, tab, entity_source

News index

GET/news

One news item

GET/news/{slug}

Parameters: slug

Lung CellCards

GET/research/cell-cards/

Parameters: cell_cards_id

LungMAP publications

GET/research/publication-page/

Parameters: q, year, offset, limit

API reference

GET/resources/api/

Single-Cell Matrix Service

GET/resources/single-cell-service/

Single-cell embedding viewer

GET/resources/single-cell-service/viewer/

Parameters: dataset, job, state

Search results

GET/search/

Parameters: q, query, has_data, search_category_id, taxon_ids, experiment_type_ids, offset, limit

Bring your own data

GET/submit-data/

One content page

GET/{slug}

Parameters: slug

Terms

The data are open. Cite LungMAP as described on the Citing LungMAP page, and cite the dataset you used by its LungMAP identifier. Please keep automated requests to a few per second so the service stays available to everyone.