This component provides a standardized and abstracted interface for interacting with various external bioinformatics APIs and services. It encapsulates the logic for querying and retrieving data from sources such as NCBI Entrez databases (e.g., PubMed, SRA), Google Cloud BigQuery for large-scale data, and the UBERON tissue ontology service for standardized biological annotations. It acts as a crucial wrapper, simplifying external interactions for other components like AI agents and workflows.

Components

External Service Integration

This component provides a standardized and abstracted interface for interacting with various external bioinformatics APIs and services. It encapsulates the logic for querying and retrieving data from sources such as NCBI Entrez databases (e.g., PubMed, SRA), Google Cloud BigQuery for large-scale data, and the UBERON tissue ontology service for standardized biological annotations. It acts as a crucial wrapper, simplifying external interactions for other components like AI agents and workflows.

SRAgent.tools.esearch

Handles search queries against NCBI Entrez databases (e.g., SRA, PubMed, GEO). It's crucial for initiating data retrieval by identifying relevant entries based on user queries.

SRAgent.tools.efetch

Retrieves full records from NCBI Entrez databases based on IDs obtained from `esearch` or other means. This is vital for getting detailed information about biological entities.

SRAgent.tools.elink

Facilitates linking between related entries across different NCBI Entrez databases. This is essential for navigating the interconnectedness of biological data (e.g., linking a SRA experiment to a PubMed article).

SRAgent.tools.esummary

Retrieves summaries of records from NCBI Entrez databases. This is useful for quickly getting an overview of an entry without fetching the entire detailed record.

SRAgent.tools.ncbi_fetch

A more general-purpose tool for fetching data from NCBI, potentially encapsulating or orchestrating calls to `esearch`, `efetch`, `elink`, and `esummary` for more complex NCBI interactions.

SRAgent.tools.entrez_db

Likely provides utilities or configurations related to managing and interacting with different Entrez databases, such as listing available databases or setting up database-specific parameters.

SRAgent.tools.sequences

Focuses on retrieving and potentially processing biological sequence data, likely from NCBI or other sequence repositories.

SRAgent.tools.bigquery

Provides an interface for querying and retrieving data from Google Cloud BigQuery, enabling access to large-scale public or private bioinformatics datasets.

SRAgent.tools.tissue_ontology

Interacts with the UBERON tissue ontology service, allowing for standardized annotation and retrieval of information based on anatomical structures and tissues.

SRAgent.tools.utils

Contains common utility functions used across various external service interactions, such as XML parsing, error handling, or request formatting.

AI Agents

AI agents (e.g., Entrez Agent, SRAgent Agent, Tissue-ontology Agent, Find-datasets Agent) that utilize external service integration.

Workflows

Workflows (e.g., Convert Workflow, Find Datasets Workflow, Metadata Workflow, SRX Info Workflow) that orchestrate calls to external service integration.