AItrika
Usage
Use AItrika
🔍 Usage
You can easily get informations of a paper by passing a PubMed ID:
from aitrika.engine.aitrika import OnlineAItrika
aitrika_engine = OnlineAItrika(pubmed_id=pubmed_id)
title = aitrika_engine.get_title()
print(title)
Or you can parse a local pdf:
from aitrika.engine.aitrika import LocalAItrika
aitrika_engine = LocalAItrika(pdf_path = pdf_path)
title = aitrika_engine.get_title()
print(title)
Breast cancer genes: beyond BRCA1 and BRCA2.
You can get other informations, like the associations between genes and diseases:
associations = aitrika_engine.get_associations()
[
{
"gene": "BRIP1",
"disease": "Breast Neoplasms"
},
{
"gene": "PTEN",
"disease": "Breast Neoplasms"
},
{
"gene": "CHEK2",
"disease": "Breast Neoplasms"
},
]
...
Or you can get a nice formatted DataFrame:
associations = aitrika_engine.associations(dataframe = True)
gene disease
0 BRIP1 Breast Neoplasms
1 PTEN Breast Neoplasms
2 CHEK2 Breast Neoplasms
...
With the power of RAG, you can query your document:
## Prepare the documents
documents = generate_documents(content=abstract)
## Set the LLM
llm = GroqLLM(documents=documents, api_key=os.getenv("GROQ_API_KEY"))
## Query your document
query = "Is BRCA1 associated with breast cancer?"
print(llm.query(query=query))
The provided text suggests that BRCA1 is associated with breast cancer, as it is listed among the high-penetrance genes identified in family linkage studies as responsible for inherited syndromes of breast cancer.
Or you can extract other informations:
results = engine.extract_results(llm=llm)
print(results)
** RESULTS **
- High-penetrance genes - BRCA1, BRCA2, PTEN, TP53 - responsible for inherited syndromes
- Moderate-penetrance genes - CHEK2, ATM, BRIP1, PALB2, RAD51C - associated with moderate BC risk
- Low-penetrance alleles - common alleles - associated with slightly increased or decreased risk of BC
- Current clinical practice - high-penetrance genes - widely used
- Future prospect - all familial breast cancer genes - to be included in genetic test
- Research need - clinical management - of moderate and low-risk variants