AmpliconSuite / AmpliconRepository

Website to host AmpliconSuite outputs, including AA outputs and resulting focal amplification classifications, such as ecDNA.
https://AmpliconRepository.org
BSD 3-Clause "New" or "Revised" License
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Improve linking the sample metadata to individual projects and samples #288

Open jluebeck opened 1 month ago

jluebeck commented 1 month ago

CCLE, PCAWG, and TCGA we can use the consortium-provided metadata and link it to samples.

For each sample it stores a reference to a metadata file - we already sort of have this, but the problem is that for most samples this is empty.

Users provide a self-created table with first column as sample name, other columns are all the metadata fields they want. Create functionality to inject this into the project database.

Is there a standard format we can leverage? Do we have required columns such as tissue of origin, cancer type, etc. ? Jens will check out how DepMap does this, and also how ICGC ARGO does it.

jluebeck commented 1 month ago

Future goal helped by adding this metadate - can we add an LLM that users can query about the results on the site?

Corpus of text it uses could be the database of the site + ecDNA literature.