research

name	research
description	Use the /research skill when performing background research from the literature or the web to create a RESEARCH.md file; also covers use of `deep-research-client`

Context

You can use normal web search tools to find relevant literature. You can also use trusted encyclopedic sources such as wikipedia but it's good to follow up with the publications themselves. All research must be summarized in a file RESEARCH.md. This file is NOT to be committed, however, it MUST be communicated back appropriately to the user.

Remember, most of the time you are likely to be running in a GitHub actions context, when triggered from an issue (via a @ai4c-agent invocation). If this is the case, the RESEARCH.md contents should be copied onto the issue comments. Otherwise, the user has no way of seeing the RESEARCH.md file, as it disappears alongside the temporary github actions workspace.

This is especially true if the user asks you explicitly to research a topic - they want to see the full report! Even if you make the RESEARCH.md as part of a broader task, it is good to post the contents.

You can editorialize if need be

When to invoke

Use this appropriately. If the request is to fix a typo in a synonym or definition, there is no need to do research (write as N/A in any checklists). Similarly if the request pertains to a trivial compositional term then research is not required. But if there is any nuanced biology involved, it is good to do the appropriate level of research.

Always bear in mind:

• GO is pan-species; while human relevance is good, don't assume the term will only be used for human biology
• GO is primarily interested in evolved molecular and cellular biology, and not pleiotropic phenotypes
• For ontology terms, recent reviews are often better than older references, or references that focus on specific experimental results
• Encyclopedic and book references are perfectly fine for high level biology (e.g. "nucleus"); but even for well understood processes (e.g. apoptosis), recent reviews are favored

Deep Research

For detailed searches, you can do deep research queries:

deep-research-client research --provider perplexity "<DETAILED RESEARCH QUESTION HERE>" --output results.md --separate-citations citations.md

This will take around 5 minutes or so.

If the user wants to do more extensive research, or if perplexity credits are exhaustive, then use the cyberian provider:

deep-research-client research --provider cyberian ....

Caching PMIDs and DOIs

You can use linkml-reference-validator to cache references. This is in your path. Note that this will not always work for full texts.

Example: linkml-reference-validator cache reference PMID:28318978 ==> writes to references_cache/PMID_28318978.md

Always use this to check that there are no typos or hallucinations with reference IDs. If the title or abstract doesn't match with what the reference is purportedly supporting, there is likely a typo or hallucination.

Note that references_cache should NOT be checked back in to git.

Incorporating research results back into your work

PMIDs are preferred for most purposes. These are usually written as CURIEs, e.g. PMID:123456. Next best are DOIs, also curies DOI:<doi>

For GO, usually the best place to include citations is in definition provenance; e.g

def: "<genus and differentia>. <additional info>" [PMID:nnnn]

But you should ALWAYS include more detailed summaries of publications in RESEARCH.md

Entries in RESEARCH.md should have blocks in the following format:

## <PMID:nnnnnnn> "<TITLE>"

<brief summary>

* SUPPORT: <PMID:nnnnnn> "<EXACT excerpt from publication>"
    - finding 1
    - finding 2
    - ...

i.e. `^ SUPPORT: (\S+:\S+) "(.*)$"` all on one line, with no newlines between the `""`s

You MUST validate the supporting text like this:

`linkml-reference-validator validate text-file -r 'SUPPORT: (\S+:\S+) "(.*)"' -t 2 -R 1 RESEARCH.md`

In some cases, if a full text is not available and support cannot be found in the abstract, but support came from deep research, you can say:

* NO_FULL_TEXT: <PMID:nnnn> <say how you obtained the information>
    - finding 1
    - finding 2
    - ...

## What to at the end of the research phase

Remember that if the user is communicating with you via github action they will not see the RESEARCH.md file

On completion, this skill should produce a complete RESEARCH.md, with no fabricated results.