--- a +++ b/docs/aitrika/usage.mdx @@ -0,0 +1,103 @@ +--- +title: 'Usage' +description: 'Use AItrika' +icon: 'code' +--- + +## 🔍 Usage + +You can easily get informations of a paper by passing a PubMed ID: + +```python +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: + +```python +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: + +```python +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: + +```python +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: + +```python +## 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: + +```python +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 +``` \ No newline at end of file