Search the literature and write a cited summary

Turn one narrow question into a short evidence summary: find studies through the built-in literature connectors, extract what each one reports, and get a report whose references you can open.

Time: about 15–25 minutes. Most of it is the run; retrieval speed depends on the sources and your network.
You need: a working task model, and network access from the machine that runs ScienceDiscovery to PubMed and Europe PMC.
Input: no file. The question is in the prompt.
Skills and connectors: the bundled literature-searcher, evidence-extractor and report-writer Skills; the PubMed and Europe PMC connectors.
You end with: biochar-yield-summary.md among the Artifacts, plus the source list and evidence table it was built from.

This lesson follows Analyze a dataset. For a full-length review that takes one to two hours, see the migratory bird navigation case.

1. Turn on the literature connectors

Create a Project, for example biochar-evidence, and open its Session. In the bar under the message box, open Data connectors. Under Data sources, turn on PubMed and Europe PMC.

A new Session enables only web access by default, so this step is what lets the Agent query the two literature databases. The choice applies to this Session; see Runtime behavior for Project and global defaults.

2. Attach the three Skills

All bundled Skills are available by default. To point the Agent at the three this lesson exercises, type / in the message box and choose literature-searcher; repeat for evidence-extractor and report-writer. Each appears as a chip in the message box. Naming them in the prompt, as below, also works.

3. Send the task

Write a short, cited evidence summary on this question:
Does adding biochar to soil increase crop yield, and does the effect depend on soil pH?

Work in three steps:
1. With literature-searcher, find 6 to 10 relevant studies in PubMed and Europe PMC, preferring meta-analyses and field trials. Record the queries you ran.
2. With evidence-extractor, record for each study its design, crops, soil pH range and reported yield effect, with the source of each row.
3. With report-writer, write biochar-yield-summary.md: a one-paragraph answer, the evidence table, where the studies disagree, and limitations. Every factual sentence needs an inline citation that points to a reference with a DOI or URL.

Keep it short: this is an evidence summary, not a full review. Declare biochar-yield-summary.md as an artifact and name it in your final reply.

4. Approve connector searches

Each new kind of action pauses on a Permission required card. Here the cards name the connector tool and the query, for example mcp__pubmed__search with the search terms, and later the first code execution. Several cards can arrive at once because searches run in parallel. Allow same type approves one tool for the rest of the Session; you approve each connector tool once.

5. What you should see

The exact studies, numbers and wording depend on the model and on what the databases return that day. Expect this shape:

A plan or to-do list, then the work split into Subagents cards: a search, an extraction and a writing step, each run by a built-in Specialist of the same name as the Skill. Open a card to see its own tool calls.
Search calls to PubMed and Europe PMC in the timeline. A query that returns nothing is normal; the Agent usually rephrases it.
Intermediate Artifacts such as a source list and an evidence table, then biochar-yield-summary.md.
A report with a short answer, a table with one row per study, a section on disagreement, limitations, and a numbered reference list whose entries carry a DOI or a PubMed or Europe PMC link.
Usually a remark that some evidence comes from abstracts only. Search results and abstracts are not full papers; the summary should not claim it read text it did not retrieve.
A Reviewer card a minute or so after the report is registered, often listing claims whose evidence is not yet linked. The last lesson shows how to act on such findings.

6. Check your result

The timeline shows searches against PubMed or Europe PMC that you approved.
biochar-yield-summary.md is listed among the Artifacts.
Every row of the evidence table names a source, and the references open to real records.
Open two or three references and confirm they say what the summary attributes to them.

The last check is the important one. A well-formed citation does not prove that the source supports the sentence; see ScienceMemory and Reviewer.

If the Agent reports that a connector is unavailable, check the Data connectors selection and the network of the machine running ScienceDiscovery. A source that could not be reached is a coverage gap, not evidence that no research exists.

Continue with Use and write Skills.