Add Noodle Biomedical Literature Discovery to the Research Software Encyclopedia

[helena-good-outreach]

Please add the following public research software repository to the Research Software Encyclopedia:

• Repository: https://github.com/helena-bioinformatics/noodle-mcp
• Name: Noodle Biomedical Literature Discovery MCP
• Website: https://noodle.helena.bio
• Description: Public, read-only biomedical literature discovery software for natural-language and PMID/DOI/PMCID search, source-linked publication inspection, bounded citation and semantic graph traversal, and corpus coverage inspection.
• Software DOI: https://doi.org/10.5281/zenodo.22166486
• Concept DOI: https://doi.org/10.5281/zenodo.22166485
• Licence: Apache-2.0
• Provider: Helena Bioinformatics
• Primary research-software source: the GitHub repository above

The repository is also the official public adapter for the canonical hosted Model Context Protocol service at https://api.helena.bio/noodle/v1/mcp. The product website and MCP interface should be represented as facets of the same software, not as duplicate records.

I verified that neither the canonical repository nor the task-first software title currently appears in https://rseng.github.io/software/data.json, and no matching open or closed issue was found.

If you prefer a pull request generated with the rse CLI instead of a maintainer-side addition, please indicate the current supported workflow and I will follow it.

[vsoch]

Hi @helena-good-outreach - if you are interested in adding a scraper, that is part of the software at https://github.com/rseng/rse.

[helena-good-outreach]

Hi Vanessa, Thank you. I inspected rseng/rse and found that the existing BioToolsScraper already provides the appropriate general ingestion route; a Noodle-specific scraper would duplicate that mechanism. The current call: rse scrape biotools Noodle resolves the live bio.tools record with biotoolsID "noodle". That record exposes: - repository: https://github.com/helena-bioinformatics/noodle-mcp - homepage: https://noodle.helena.bio - software DOI: 10.5281/zenodo.22166486 - Apache-2.0 public adapter metadata The rseng/software weekly workflow already invokes the biotools scraper, but BioToolsScraper.latest() defaults to the first page only. A targeted search is therefore the deterministic way to ingest this record without creating a brand-specific scraper. Would you prefer that I contribute a small general workflow enhancement allowing an optional query value for the existing on-demand biotools scraper, or can you trigger the targeted biotools search for "Noodle" in the current ingestion workflow? Best, Vladimir

[vsoch]

If you just need to add that one repository (and not as a scraper) you can use rse add

https://rseng.github.io/rse/getting-started/index.html#quick-start

And then contribute the entry to the database.

[helena-good-outreach]

Thanks, that clarifies the intended path. I’ll use rse add to generate the single Noodle repository entry, validate the generated metadata against the current database schema, and contribute the entry to rseng/software; no scraper change is needed.

[helena-good-outreach]

Thank you, Vanessa. I followed the documented `rse add` route and contributed the generated metadata record in PR #491: #491 The PR contains only the generated `database/github/helena-bioinformatics/noodle-mcp/metadata.json` entry and links back to this issue. Best, Vladimir