aurelian
Project description
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:
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:
https://github.com/geneontology/go-annotation/issues/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.
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