Aurelian: Agentic Universal Research Engine for Literature, Integration, Annotation, and Navigation

| Documentation |

aurelian --help

Most commands will start up a different AI agent.

Examples of use

TALISMAN

gene set enrichment

Aria

checking papers against checklists

GO-CAM agent

This agent is for exploring, chatting with, and reviewing GO-CAMs

Docs: gocam_agent

It can be used to generate reviews according to guidelines for GO-CAMs:

• GO-CAM Reviews

It can also generate SVGs, demonstrating innate knowledge of both the visual grammar of pathway diagrams and the semantics of the underlying biology.

GO-Ann agent

This agent is for exploring, chatting with, and reviewing standard annotations

Docs: go_ann_agent

Example review using TF guidelines:

geneontology/go-annotation#5743

Troubleshooting

Installing linkml-store

Some agents require linkml-store pre-indexed. E.g. a mongodb with gocams for cam agent. Consult the linkml-store documentation for more information.

Semantic search over ontologies

If an agent requires ontology search it will use the semsql/OAK sqlite database. The first time querying it will use linkml-store to create an LLM index. Requires OAI key. This may be slow first iteration. Will be cached until your pystow cache regenerates.