<commit_before>[![Build Status](https://travis-ci.org/sorgerlab/indra.svg?branch=travis_ci)](https://travis-ci.org/sorgerlab/indra) [![Documentation Status](https://readthedocs.org/projects/indra/badge/?version=latest)](https://indra.readthedocs.io/en/latest/?badge=latest)

# INDRA

<img align="left" src="/doc/indra_logo.png?raw=True" width="300" height="224" />

INDRA (Integrated Network and Dynamical Reasoning Assembler) is an automated
model assembly system, originally developed for molecular systems biology and
currently being generalized to other domains. INDRA draws on natural language
processing systems and structured databases to collect mechanistic and causal
assertions, represents them in a standardized form (INDRA Statements), and
assembles them into various modeling formalisms including causal graphs and
dynamical models.

Importantly, INDRA isn't merely an import/export hub or a multi-reader
integrator. Its core added value in
assembling knowledge sources into coherent models comes from
providing knowledge-level assembly procedures that
operate on INDRA Statements and correct certain errors, find and resolve
redundancies, infer missing information, filter to a scope of interest and
assess belief.

The detailed INDRA documentation is available at
[http://indra.readthedocs.io](http://indra.readthedocs.io).

### Knowledge sources

INDRA is currently integrated with the following natural language processing
systems and structured databases. These input modules (available in
`indra.sources`) all produce INDRA Statements.

General purpose causal relation reading systems:

| Reader     | Module                | Reference                                 |
|------------|-----------------------|-------------------------------------------|
| Eidos      | `indra.sources.eidos` | https://github.com/clulab/eidos           |
| TRIPS/CWMS | `indra.sources.cwms`  | http://trips.ihmc.us/parser/cgi/cwmsreader|
| Hume       | `indra.sources.hume`  | https://github.com/BBN-E/Hume             |
| Sofia      | `indra.sources.sofia` | https://sofia.worldmodelers.com/ui/       |

Biology-oriented reading systems:

| Reader     | Module                  | Reference                                       |
|------------|-------------------------|-------------------------------------------------|
| TRIPS/DRUM | `indra.sources.trips`   | http://trips.ihmc.us/parser/cgi/drum            |
| REACH      | `indra.sources.reach`   | https://github.com/clulab/reach                 |
| Sparser    | `indra.sources.sparser` | https://github.com/ddmcdonald/sparser           |
| TEES       | `indra.sources.tees`    | https://github.com/jbjorne/TEES                 |
| MedScan    | `indra.sources.medscan` | https://doi.org/10.1093/bioinformatics/btg207   |<commit_msg>Improve description of knowledge assembly<commit_after>[![Build Status](https://travis-ci.org/sorgerlab/indra.svg?branch=travis_ci)](https://travis-ci.org/sorgerlab/indra) [![Documentation Status](https://readthedocs.org/projects/indra/badge/?version=latest)](https://indra.readthedocs.io/en/latest/?badge=latest)

# INDRA

<img align="left" src="/doc/indra_logo.png?raw=True" width="300" height="224" />

INDRA (Integrated Network and Dynamical Reasoning Assembler) is an automated
model assembly system, originally developed for molecular systems biology and
currently being generalized to other domains. INDRA draws on natural language
processing systems and structured databases to collect mechanistic and causal
assertions, represents them in a standardized form (INDRA Statements), and
assembles them into various modeling formalisms including causal graphs and
dynamical models.

At the core of INDRA are its knowledge-level assembly procedures, allowing
sources to be assembled into coherent models, a process that involves
correcting systematic input errors, finding and resolving redundancies,
inferring missing information, filtering to a relevant scope and assessing the
reliability of causal information.

The detailed INDRA documentation is available at
[http://indra.readthedocs.io](http://indra.readthedocs.io).

### Knowledge sources

INDRA is currently integrated with the following natural language processing
systems and structured databases. These input modules (available in
`indra.sources`) all produce INDRA Statements.

General purpose causal relation reading systems:

| Reader     | Module                | Reference                                 |
|------------|-----------------------|-------------------------------------------|
| Eidos      | `indra.sources.eidos` | https://github.com/clulab/eidos           |
| TRIPS/CWMS | `indra.sources.cwms`  | http://trips.ihmc.us/parser/cgi/cwmsreader|
| Hume       | `indra.sources.hume`  | https://github.com/BBN-E/Hume             |
| Sofia      | `indra.sources.sofia` | https://sofia.worldmodelers.com/ui/       |

Biology-oriented reading systems:

| Reader     | Module                  | Reference                                       |
|------------|-------------------------|-------------------------------------------------|
| TRIPS/DRUM | `indra.sources.trips`   | http://trips.ihmc.us/parser/cgi/drum            |
| REACH      | `indra.sources.reach`   | https://github.com/clulab/reach                 |
| Sparser    | `indra.sources.sparser` | https://github.com/ddmcdonald/sparser           |
| TEES       | `indra.sources.tees`    | https://github.com/jbjorne/TEES                 |
| MedScan    | `indra.sources.medscan` | https://doi.org/10.1093/bioinformatics/btg207   |
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