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rummageo.md

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1# RummaGEO — GEO signature search and enrichment

3Public GraphQL endpoint: `https://rummageo.com/graphql`.

4The official [application queries](https://github.com/MaayanLab/rummageo/blob/rummageo/src/graphql/core.graphql)

5and [server](https://github.com/MaayanLab/rummageo/blob/rummageo/src/lib/postgraphile.ts)

6define its query surface. The formerly suggested `/api/enrich` and `/api/table`

7REST recipes are not supported by that source.

9A small read-only term search (live-tested):

10```bash

11curl --fail-with-body 'https://rummageo.com/graphql' \

12 -H 'Content-Type: application/json' \

13 --data '{"query":"{ geneSetTermSearch(terms:[\"neuron\"],first:1,offset:0){ totalCount nodes{term} } }"}'

14```

16Gene-set enrichment uses `background(id: $id) { enrich(genes: $genes, first: $n,

17offset: $offset) { nodes { pvalue adjPvalue oddsRatio nOverlap } totalCount } }`.

18Select the appropriate species/background UUID from the service's current

19background catalogue before querying. Consult the source for supported filters;

20the gene list alone is insufficient to specify the analysis.

22Inspect GraphQL `errors` even with HTTP 200. Paginate with `first` and `offset`.

23Preserve background, species, signature direction, sample-group contrast and GEO

24accession. An enriched signature is an association with a study contrast, not

25proof of a causal drug or disease mechanism.

RummaGEO — GEO signature search and enrichment

Public GraphQL endpoint: https://rummageo.com/graphql. The official application queries and server define its query surface. The formerly suggested /api/enrich and /api/table REST recipes are not supported by that source.

A small read-only term search (live-tested):

curl --fail-with-body 'https://rummageo.com/graphql' \
  -H 'Content-Type: application/json' \
  --data '{"query":"{ geneSetTermSearch(terms:[\"neuron\"],first:1,offset:0){ totalCount nodes{term} } }"}'

Gene-set enrichment uses background(id: $id) { enrich(genes: $genes, first: $n, offset: $offset) { nodes { pvalue adjPvalue oddsRatio nOverlap } totalCount } }. Select the appropriate species/background UUID from the service's current background catalogue before querying. Consult the source for supported filters; the gene list alone is insufficient to specify the analysis.

Inspect GraphQL errors even with HTTP 200. Paginate with first and offset. Preserve background, species, signature direction, sample-group contrast and GEO accession. An enriched signature is an association with a study contrast, not proof of a causal drug or disease mechanism.

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