bio2bel / mirtarbase

Serializes text-mined miRNA-target interactions to BEL

Bio2BEL

Bio2BEL is a project aimed at bringing biological databases and other structured knowledge sources in a wide variety of schemata into the unified framework of the Biological Expression Language [1].

Two important places to look:

• How to make a Bio2BEL Repository
• How to use the CLI

Installation

Download the latest stable code from PyPI with:

$ python -m pip install bio2bel

or get the latest from GitHub with:

$ git clone https://github.com/bio2bel/bio2bel.git
$ cd bio2bel
$ python -m pip install -e .

or check the installation instructions.

Citation

If you find Bio2BEL useful for your work, please consider citing:

[1]	Hoyt, C. T., et al. (2019). Integration of Structured Biological Data Sources using Biological Expression Language. bioRxiv, 631812.

mirtarbase's Issues

Make SQLAlchemy Models

Database query for all MTI for given miRNA

Calculate co-occurrence network

which miRNAs share a significant number of the same targets? This is one way to collapse the entire bipartite network into a homogoneous network that might be more informative

Serialize to BEL

Enable passing custom PyHGNC connection to populate function

Promiscuity calculations for both miRNA and target

The promiscuity of an miRNA is the number of targets it hits / number of targets in database and likewise for the target. Targets with lower promiscuity are somehow more informative

Pluralize backrefs

https://github.com/bio2bel/miRTarBase/blob/835330f25a9e981c8359fee3257f8c8c79beca55/src/bio2bel_mirtarbase/build_db.py#L52

Since this is a one-to-many relationship, the back-reference points to multiple "interactions" so we should name this variable with a plural

Enrich pybel.BELGraph with MTIs from database

Make data uploader

Add tox script

Add tox.ini to miRTarBase repository that just runs the unit tests. Should match the same format as all the other repositories we made.

Get data

Add setup.py

Unit test uploaded data

Setup Travis CI

Database query for all MTIs given target gene