Protocol Workflow Extraction Tool
Langchain tools that execute zero-shot extraction over a local database of full text papers previously imported into our database.
BaseProtocolExtractionTool
BaseProtocolExtractionTool (db:alhazen.utils.ceifns_db.Ceifns_Literature Db, llm:Optional[langchain_core.language_mode ls.chat_models.BaseChatModel]=None, slm:Optio nal[langchain_core.language_models.chat_model s.BaseChatModel]=None, name:str='protocol_workflow_extraction', description:str='Runs a specified protocol extraction pipeline over a research paper that has been loaded in the local literature database.', args_schema:Optional[Type[pydanti c.v1.main.BaseModel]]=None, return_direct:bool=True, verbose:bool=False, callbacks:Union[List[langchain_core.callbacks .base.BaseCallbackHandler],langchain_core.cal lbacks.base.BaseCallbackManager,NoneType]=Non e, callback_manager:Optional[langchain_core.c allbacks.base.BaseCallbackManager]=None, tags:Optional[List[str]]=None, metadata:Optional[Dict[str,Any]]=None, handle _tool_error:Union[bool,str,Callable[[langchai n_core.tools.ToolException],str],NoneType]=Fa lse, handle_validation_error:Union[bool,str,C allable[[pydantic.v1.error_wrappers.Validatio nError],str],NoneType]=False)
Runs a specified protocol extraction pipeline over a research paper that has been loaded in the local literature database.
ProtocolExtractionToolSchema
ProtocolExtractionToolSchema (paper_id:str)
Create a new model by parsing and validating input data from keyword arguments.
Raises ValidationError if the input data cannot be parsed to form a valid model.
ProcotolDiagramExtractionTool
ProcotolDiagramExtractionTool (db:alhazen.utils.ceifns_db.Ceifns_Literat ureDb, llm:Optional[langchain_core.languag e_models.chat_models.BaseChatModel]=None, slm:Optional[langchain_core.language_model s.chat_models.BaseChatModel]=None, name:str='protocol_diagram_extraction', description:str='Extracts a mermaid diagram of the protocol from a paper.', ar gs_schema:Optional[Type[pydantic.v1.main.B aseModel]]=None, return_direct:bool=True, verbose:bool=False, callbacks:Union[List[l angchain_core.callbacks.base.BaseCallbackH andler],langchain_core.callbacks.base.Base CallbackManager,NoneType]=None, callback_m anager:Optional[langchain_core.callbacks.b ase.BaseCallbackManager]=None, tags:Optional[List[str]]=None, metadata:Optional[Dict[str,Any]]=None, han dle_tool_error:Union[bool,str,Callable[[la ngchain_core.tools.ToolException],str],Non eType]=False, handle_validation_error:Unio n[bool,str,Callable[[pydantic.v1.error_wra ppers.ValidationError],str],NoneType]=Fals e)
Extracts a mermaid diagram of the protocol from a paper.
ProcotolEntitiesExtractionTool
ProcotolEntitiesExtractionTool (db:alhazen.utils.ceifns_db.Ceifns_Litera tureDb, llm:Optional[langchain_core.langu age_models.chat_models.BaseChatModel]=Non e, slm:Optional[langchain_core.language_m odels.chat_models.BaseChatModel]=None, name:str='protocol_entities_extraction', description:str='Extracts all entities used in a protocol.', args_schema:Optiona l[Type[pydantic.v1.main.BaseModel]]=None, return_direct:bool=True, verbose:bool=False, callbacks:Union[List[ langchain_core.callbacks.base.BaseCallbac kHandler],langchain_core.callbacks.base.B aseCallbackManager,NoneType]=None, callba ck_manager:Optional[langchain_core.callba cks.base.BaseCallbackManager]=None, tags:Optional[List[str]]=None, metadata:Optional[Dict[str,Any]]=None, ha ndle_tool_error:Union[bool,str,Callable[[ langchain_core.tools.ToolException],str], NoneType]=False, handle_validation_error: Union[bool,str,Callable[[pydantic.v1.erro r_wrappers.ValidationError],str],NoneType ]=False)
Extracts all entities used in a protocol.
ProcotolProcessesExtractionTool
ProcotolProcessesExtractionTool (db:alhazen.utils.ceifns_db.Ceifns_Liter atureDb, llm:Optional[langchain_core.lan guage_models.chat_models.BaseChatModel]= None, slm:Optional[langchain_core.langua ge_models.chat_models.BaseChatModel]=Non e, name:str='protocol_processes_extracti on', description:str='Extracts all processes used in a protocol.', args_sch ema:Optional[Type[pydantic.v1.main.BaseM odel]]=None, return_direct:bool=True, verbose:bool=False, callbacks:Union[List [langchain_core.callbacks.base.BaseCallb ackHandler],langchain_core.callbacks.bas e.BaseCallbackManager,NoneType]=None, ca llback_manager:Optional[langchain_core.c allbacks.base.BaseCallbackManager]=None, tags:Optional[List[str]]=None, metadata:Optional[Dict[str,Any]]=None, h andle_tool_error:Union[bool,str,Callable [[langchain_core.tools.ToolException],st r],NoneType]=False, handle_validation_er ror:Union[bool,str,Callable[[pydantic.v1 .error_wrappers.ValidationError],str],No neType]=False)
Extracts all processes used in a protocol.