Actogram LabScout

Find the labs, people and studies behind a research topic, and see on a map who works on it and where.

LabScout searches public sources, groups the papers by their senior author and organisation, and says in one sentence why each lab came up: how many papers on the topic it led, in which years, with what kind of data and which species. It also finds grants, registered trials and patents on a topic. You can use it in three ways:

• on the web page at actogram-labscout.hf.space: type a topic, get a map, a table and an Excel file;

• from an AI assistant, as an MCP server at https://actogram-labscout.hf.space/mcp;

• from the command line or your own Python code.

It grew out of pubmed2worldmap by Tim Pyrkov, and is part of Actogram Open Science.

What it uses

Only the official APIs are used. Requests are paced to each source's limits, sent with a clear User-Agent, and kept in a local cache for seven days, so a repeated search costs the sources nothing.

Related MCP server: PubMed MCP Server

Install

Python 3.10 or newer.

pip install "labscout @ git+https://github.com/actogram/scholar-mcp"

For development:

git clone https://github.com/actogram/scholar-mcp
cd scholar-mcp
python -m venv .venv && . .venv/bin/activate
pip install -e ".[dev]"

The web page

The hosted page is at https://actogram-labscout.hf.space. To run it on your own computer:

labscout serve                     # http://127.0.0.1:8000, with the MCP server at /mcp

Type a topic and press Find labs. A new topic takes 30 to 90 seconds; the page shows how long it has been searching and refreshes by itself. The report has a map of the labs with a known place, a table you can sort and filter with the papers behind each lab, and downloads as Excel, CSV and JSON.

From an AI assistant (MCP)

labscout mcp                       # stdio, for assistants on this computer
labscout mcp --http --port 8000    # Streamable HTTP at http://127.0.0.1:8000/mcp

Most MCP clients take a configuration like this:

{
  "mcpServers": {
    "labscout": { "command": "labscout", "args": ["mcp"] }
  }
}

The hosted LabScout works the same way: add https://actogram-labscout.hf.space/mcp as a custom connector.

The tools, all read-only:

From the command line

labscout labs "actigraphy sleep regularity older adults" --from 2020 --xlsx labs.xlsx --html labs.html
labscout labs "circadian rhythm shift work" --from 2022 --grants 5      # NIH grants for the five top labs
labscout papers "wearable step counts circadian" --max 20
labscout profile "Susan Redline" --topic "sleep regularity"
labscout grants --pi "Susan Redline"                                     # NIH RePORTER
labscout grants --text "circadian actigraphy"                            # NIH RePORTER and UKRI
labscout trials "actigraphy sleep"
labscout patents "actigraphy AND sleep"

Searches use PubMed syntax, so actigraphy AND "sleep regularity" and field tags such as [tiab] work. Each source gives at most --max papers, newest first.

Settings

Host it

The folder deploy/huggingface holds a Docker setup for a Hugging Face Docker Space, which also runs anywhere Docker does:

deploy/huggingface/build_space.sh build/space       # the Space files: Dockerfile, card, package
docker build -t labscout build/space
docker run -p 7860:7860 -e LABSCOUT_EMAIL=you@example.org labscout

To publish a Space, upload build/space to a new Docker Space and set LABSCOUT_EMAIL as a Space variable. The web page and the MCP endpoint (https://<space>.hf.space/mcp) then run together.

How a lab is found

1. Papers on the topic come from PubMed and Europe PMC and are merged by PMID, DOI or title and year.

2. The senior (last) author of each paper leads its lab. Older PubMed records list only the first author's affiliation; then the lab is placed with that one.

3. The affiliation is matched to an organisation in ROR. A match is accepted only when ROR is confident, or when a name search finds an organisation whose name words all appear in the affiliation and whose country agrees. Otherwise only the country is taken from the text. The column match (ror, ror-name or text) shows which.

4. One person at two organisations in the same city, such as a university and its hospital, is one lab. The same name in different cities stays apart, because it may be two people.

5. Labs are ranked by papers led, papers co-authored, recent work, the kinds of data mentioned and the search words found.

Privacy and fair use

LabScout shows information that researchers have made public in their work: names, affiliations, publications, grants, patents and registered studies. It removes e-mail addresses from affiliations and never returns them. Use the results to find research and collaborators, not to judge people. Organisation matching is automatic and can be wrong, so check before you act on a result.

Development

ruff check src tests && ruff format --check src tests
pytest                 # offline tests on recorded answers of the real APIs
pytest -m network      # a few live requests to the public APIs

See CONTRIBUTING.md. Planned next: newer patents through a patent office service, EU grants from CORDIS.

Cite

See CITATION.cff. Please cite the version you used.

Licence

MIT, see LICENSE. The data belongs to its sources and keeps their terms.