Pipeline Managers

This module contains the pipelines used to update content and knowledge in the database, and move or transform that knowledge on a regular basis.

Content Manager (indra_db.managers.content_manager)

The Content Managers, as the name suggests, manage the text content that is stored in the database. A parent class is defined, and managers for different sources (e.g. PubMed) can be defined by inheriting from this parent. This file is also used as the shell command to run updates of the content.

Reading Manager (indra_db.managers.reading_manager)

The Reading Managers handle the reading of the text contend and the processing of those readings into statements. As with Content Managers, different reading pipelines can be handled by defining children of a parent class.

PreAssembly Manager (indra_db.managers.preassembly_manager)

The Preassembly Manager performs the complex process of preassembly, where after cleaning the raw extractions and fixing groundings and sites, the numerous duplicate Statements extracted from databases and literature are distilled into a corpus of unique statements, with links back to the raw Statements, and their history and provenance.

Knowledge Base Manager (indra_db.managers.knowledgebase_manager)

The INDRA Databases also derives much of its knowledge from external databases and other resources not extracted from plain text, referred to in this repo as “knowledge bases”, so as to avoid the ambiguity of “database”. This manager handles the updates of those knowledge bases, each of which requires different handling.

Readonly Manager (indra_db.managers.readonly_manager)

This handles the generation of the content for the readonly database from the principal database.