NDEx Signor Content Loader

https://coveralls.io/repos/github/ndexcontent/ndexsignorloader/badge.svg?branch=master

Python application that loads Signor data into NDEx

This tool downloads data files from Signor and performs the following operations:

1) The text files are loaded into a network using this loadplan

2) The edge attribute direct is set to True if value is 't' otherwise its set to False

3) Using values in the databasea and databaseb data files, the represents field found on each node is prefixed with uniprot: if the database value is UNIPROT and signor: if the database value is SIGNOR

4) The location node attribute is set to cytoplasm if its not set (which is case for all nodes in Signor Complete - Human, Signor Complete - Rat, and Signor Complete - Mouse networks)

5) The location node attribute with value phenotypeList is set to empty string

6) Any negative or non-numeric citations are removed from the citation edge attribute (There were multiple cases of -1 and Other). In addition, a specific PMC:## is updated to its pubmed id.

7) IF --edgecollapse flag is set on commandline, then edges between same nodes are collapsed if they have same interaction with attributes stored in lists with exception of direct which is a bool. The pubmed id is prepended (as html link) to each sentence attribute entry.: In addition, a network attribute named notes is added with following text: Edges have been collapsed with attributes converted to lists with exception of direct attribute

8) The layout of the network is created using the spring layout, but with additional logic that positions nodes in a vertical based on value of the location node attribute. The ordering is as follows:

extracellular are placed at the top
receptor are below extracellular
cytoplasm are placed in the middle
factor are below cytoplasm
If attribute is empty, nodes are placed at the bottom

9) The following network attributes are set

name is set to data from Signor service getPathwayData.php?pathway= (except for the full/complete networks which have a more generic description)
author is set to data from Signor service getPathwayData.php?pathway= (unless its empty in which case its not added to network)
organism is set to Human, 9606, Homo sapiens (except for Signor Complete - Rat, and Signor Complete - Mouse networks)
prov:wasGeneratedBy is set to ndexsignorloader <VERSION> (example: ndexsignorloader 1.1.0)
prov:wasDerivedFrom set to URL to download data file (or in case of full networks its set to Signor site)
version is set to Abbreviated day-month-year (example: 05-Jun-2019)
description is taken from Signor service getPathwayData.php?pathway=
rightsHolder is set to Prof. Gianni Cesareni
rights is set to Attribution-ShareAlike 4.0 International (CC BY-SA 4.0)
reference is set to citation for SIGNOR: a database of causal relationships between biological entities
labels is set to data from Signor service getPathwayData.php?pathway= (not set for full networks)
type is set to a list with pathway and if known type of pathway
__normalizationversion is set to 0.1

Dependencies

Compatibility

Python 3.4+

Installation

git clone https://github.com/ndexcontent/ndexsignorloader
cd ndexsignorloader
make dist
pip install dist/ndexloadsignor*whl

Run make command with no arguments to see other build/deploy options including creation of Docker image

make

Output:

clean                remove all build, test, coverage and Python artifacts
clean-build          remove build artifacts
clean-pyc            remove Python file artifacts
clean-test           remove test and coverage artifacts
lint                 check style with flake8
test                 run tests quickly with the default Python
test-all             run tests on every Python version with tox
coverage             check code coverage quickly with the default Python
docs                 generate Sphinx HTML documentation, including API docs
servedocs            compile the docs watching for changes
testrelease          package and upload a TEST release
release              package and upload a release
dist                 builds source and wheel package
install              install the package to the active Python's site-packages
dockerbuild          build docker image and store in local repository
dockerpush           push image to dockerhub

Configuration

The ndexloadsignor.py requires a configuration file in the following format be created. The default path for this configuration is ~/.ndexutils.conf but can be overridden with --conf flag.

Format of configuration file

[<value in --profile (default ndexsignorloader)>]

user = <NDEx username>
password = <NDEx password>
server = <NDEx server(omit http) ie public.ndexbio.org>

Example configuration file

[ndexsignorloader_dev]

user = joe123
password = somepassword123
server = dev.ndexbio.org

Usage

For information invoke ndexloadsignor.py -h

Example usage

TODO: Add information about example usage

mkdir signor
ndexloadsignor.py signor/

Via Docker