*********************************
e(BE:L) |docs| |python_versions|
*********************************
e(BE:L) is a Python package built for both validating and modeling information extracted from publications using `Biological Expression Language (BEL) <https://language.bel.bio/>`_.
This software package serves a comprehensive tool for all of your BEL needs and serves to create enriched knowledge graphs
for developing and testing new theories and hypotheses.
**e(BE:L)** have implemented several other knowledge bases to extend the BEL knowledge graph or map identifiers.
* `BioGrid <https://thebiogrid.org/>`_
* `ChEBI <https://www.ebi.ac.uk/chebi/>`_
* `ClinicalTrials.gov <https://clinicaltrials.gov/>`_
* `ClinVar <https://www.ncbi.nlm.nih.gov/clinvar/>`_
* `DisGeNET <https://www.disgenet.org/>`_
* `DrugBank <https://go.drugbank.com/>`_
* `Ensembl`_
* `Expression Atlas <https://www.ebi.ac.uk/gxa/home>`_
* `GWAS Catalog <https://www.ebi.ac.uk/gxa/home>`_
* `HGNC <https://www.genenames.org/>`_
* `IntAct`_
* `Guide to PHARMACOLOGY <https://www.guidetopharmacology.org/>`_
* `KEGG <https://www.genome.jp/kegg/>`_
* `MirTarBase <https://mirtarbase.cuhk.edu.cn/~miRTarBase/miRTarBase_2022/php/index.php>`_
* `Different resources from NCBI <https://www.ncbi.nlm.nih.gov/>`_
* `OffSides <http://tatonettilab.org/offsides/>`_
* `Pathway Commons <https://www.pathwaycommons.org/>`_
* `The Human Protein Atlas <https://www.proteinatlas.org/>`_
* `Reactome <https://reactome.org/>`_
* `STRING <https://string-db.org/>`_
* `UniProt`_
Installation |pypi_version| |pypi_license|
==========================================
The easiest way to install ebel is to use `docker-compose`. See below instructions to use the docker installation.
``ebel`` can be directly installed from PyPi with pip::
$ pip install ebel
But we want to encourage you to use the latest development version which can be installed with::
$ pip install git+https://github.com/e-bel/ebel
Package Requirements
====================
Installing OrientDB
-------------------
This software package is designed to work in conjunction with `OrientDB`_, a NoSQL, multi-model database
that acts as both a graph and relational database. e(BE:L) uses OrientDB for generating the knowledge graph derived from BEL files. To get
started with e(BE:L), first `download OrientDB`_ and get a server up and running.
The first time the server is ran, you will need to create a root password. Once it is up and running, you can get
start importing BEL files into it!
On Linux you can use following commands::
wget https://repo1.maven.org/maven2/com/orientechnologies/orientdb-community/3.2.2/orientdb-community-3.2.2.tar.gz
tar -xvzf orientdb-community-3.2.2.tar.gz
cd orientdb-community-3.2.2/bin
./server.sh
SQL Databases
--------------
This package is capable of enriching the compiled knowledge graphs with a lot of external information, however, this requires
a SQL databases for storage. While, a SQLite database can be used, this is not recommended as the amount of data and
complexity of queries will be quite slow. Additionally, SQLite will not be directly supported, the methods will be built
such that they should work with both SQLite and MySQL, but we will not address performance issues due to using SQLite.
Instead, we recommend setting up a `MySQL server <https://www.mysql.com/downloads/>`_ or
`MariaDB`_ to use with e(BE:L). By default, `PyMySQL <https://pypi.org/project/PyMySQL/>`_
is installed as a driver by e(BE:L), but others can also be used.
On Lunux Ubuntu you can use following command::
sudo apt install mysql-server -y
or::
sudo apt install mariadb-server -y
Configuration
=============
Before you start working with e(BE:L), a simple to use wizard helps you to setup all configurations. Make sure OrientDB
and MySQL (or MariaDB) are running. Then start the configuration wizard with::
ebel settings
The wizard will create the needed databases and users in OrientDB and MySQL/MariaDB.
Package Components
==================
To test the different components you find `here <https://github.com/e-bel/covid19_knowledge_graph/>`_ several BEL and
already compiled JSON files.
BEL Validation
==============
BEL is a domain-specific language designed to capture biological relationships in a computer- and human-readable format.
The rules governing BEL statement generation can be quite complex and often mistakes are made during curation.
e(BE:L) includes a grammar and syntax checker that reads through given BEL files and validates whether each statement
satisfies the guidelines provided by `BEL.bio <https://language.bel.bio/>`_. Should any BEL statement within the file
not adhere to the rules, a report file is created by e(BE:L) explaining the error and offering suggested fixes.
You can use the following command to validate your BEL file::
$ ebel validate /path/to/bel_file.bel
In a single command, you can validate your BEL file as well as generate error reports if there are errors and if there
are none, produce an importable JSON file::
$ ebel validate /path/to/bel_file.bel -r error_report.xlsx -j
BEL documents should be properly formatted prior to validation. e(BE:L) contains a repair tool that will check the format
and it is highly recommended that this is used prior to validation. The repaired will overwrite the original if a new file
path is not specified. Here is an example::
$ ebel repair /path/to/bel_file.bel -n /path/to/repaired_file.bel
Import Process
==============
BEL Modeling - OrientDB
-----------------------
BEL files that have passed the validation process can be imported into the
database individually or *en masse*. During the import process, e(BE:L) automatically creates all of the relevant nodes and edges
as described in the BEL files. Additionally, e(BE:L) also automatically adds in missing nodes and edges that are known to exist
e.g. protein nodes with a respective RNA or gene node with have these automatically added to the graph with the appropriate ``translatedTo`` and
``transcribedTo`` edges.
Model Enrichment - MySQL
------------------------
e(BE:L) goes one step farther when compiling your BEL statements into a knowledge graph by supplementing your new graph model with information derived from several
publicly available repositories. Data is automatically downloaded from several useful sites including `UniProt`_ ,
`Ensembl`_, and `IntAct`_ and added as generic tables in your newly built database.
Information from these popular repositories are then linked to the nodes and edges residing in your graph model, allowing for more complex and
useful queries to be made against your data. This data is automatically downloaded, parsed, and imported into a specified SQL database.
Importing - Getting Started
---------------------------
e(BE:L) supports OrientDB as graph database and `MySQL <https://www.mysql.com>`_ and `MariaDB`_ as `RDBMS <https://en.wikipedia.org/wiki/Relational_database>`_
Make sure you have downloaded/installed and running
1. `OrientDB`_
2. MySQL or MariaDB
a. MySQL
- `Windows <https://dev.mysql.com/doc/refman/8.0/en/windows-installation.html>`__
- `MacOS <https://dev.mysql.com/doc/refman/8.0/en/macos-installation.html>`_
- Linux
- `Ubuntu, Debian, Linux Mint, ... <https://dev.mysql.com/doc/mysql-apt-repo-quick-guide/en/>`__
- `RedHat, Fedora, CentOS, OpenSUSE, Scientific Linux, ... <https://dev.mysql.com/doc/refman/8.0/en/linux-installation-yum-repo.html>`__
b. MariaDB
- `Windows <https://mariadb.com/kb/en/installing-mariadb-msi-packages-on-windows/>`__
- MacOS (`PKG <https://mariadb.com/kb/en/installing-mariadb-server-pkg-packages-on-macos/>`_, `Homebrew <https://mariadb.com/kb/en/installing-mariadb-on-macos-using-homebrew/>`_)
- Linux
- `Ubuntu, Debian, Linux Mint, ... <https://mariadb.com/kb/en/yum/>`__
- `RedHat, Fedora, CentOS, OpenSUSE, Scientific Linux, ... <https://mariadb.com/kb/en/installing-mariadb-deb-files/>`__
This can be configured as a service in both Windows and Unix systems.
Set your MySQL connection parameters in e(BE:L)::
$ ebel set-mysql --host localhost --user root --password myPassWord --database ebel
Once you have made sure both OrientDB and MySQL are running, you can now import an e(BE:L) compiled JSON file::
$ ebel import-json /path/to/checked_bel.json -u root -p orientdbPassword -d ebel -h localhost -p 2424
After you have successfully connected to the OrientDB database at least once, the login credentials will be written to the config file and no longer need to be passed (same with ``enrich`` command)::
$ ebel import-json /path/to/checked_bel.json
You can also import all e(BE:L) compiled JSON files in a passed directory::
$ ebel import-json /path/to/bel_json/dir/
If you do no wish to enrich the graph, or wish to disable the protein/RNA/gene extension step, you can toggle these with the following options::
$ ebel import-json /path/to/checked_bel.json -e -g
You can run an enrichment step later using the ``enrich`` command::
$ ebel enrich
This command can also be given a list of resources to either skip or include during enrichment::
$ ebel enrich -i uniprot,hgnc
or::
$ ebel enrich -s intact,kegg
Querying the Graph
==================
Once the knowledge graph has been created (and optionally enriched), one can use e(BE:L) to query it directly.
.. code-block:: python
from ebel import Bel
bel = Bel()
relation_query = "SELECT out.bel as subject, @class as relation, in.bel as object FROM bel_relation"
df = bel.query(relation_query) # Returns results as pandas DataFrame
result_list = bel.query_get_dict(relation_query) # Returns results as a list of dicts
To specify a different graph database to connect to than the one in your config file, you can pass connection parameters when initializing the `Bel` class:
.. code-block:: python
from ebel import Bel
config_params = {
"db": "my_db",
"user": "superdude",
"password": "password123",
"server": "localhost", # defaults to localhost if none given
"port": "2424", # defaults to 2424 if none given
}
bel = Bel(graph_config=config_params)
# To overwrite your default values in the config file
bel = Bel(graph_config=config_params, overwrite_config=True)
Docker installation
===================
Make sure `docker <https://docs.docker.com/get-docker/>`_ and `docker-compose <https://docs.docker.com/compose/install/>`_ are installed.
.. code-block::
docker-compose up --build -d
docker exec -it ebel_ebel ebel settings
Several question will follow. You can accept the default values (just press RETURN) except the following questions:
.. code-block::
OrientDB server [localhost] ?
ebel_orientdb
OrientDB root password (to create database and users)
ebel
MySQL/MariaDB sever name [localhost]
ebel_mysql
MySQL root password (will be not stored) to create database and user
ebel
It's strongly recommended, if you are using ebel in the production environment, to change the
standard root MySQL and OrientDB passwords in the docker-compose.yml file.
To load example files in container and import.
.. code-block::
docker exec -it ebel_ebel git clone https://github.com/e-bel/example_json_bel_files.git
docker exec -it ebel_ebel ebel import-json example_json_bel_files/phago.bel.json -e
To enrich the network:
.. code-block::
docker exec -it ebel_ebel ebel enrich
Following services are now available:
1. `OrientDB Studio <http://localhost:2480/studio/index.html#/>`_
2. `e(BE:L) REST server <http://localhost:5000/ui/>`_
3. `phpMyAdmin <http://localhost:8089>`_
API
===
Finally, this package comes equipped with a built-in RESTful API using Flask. Users that have a running and populated set of databases
can also create a running API server which contains several queries for retrieving information from both the network itself, as well
as the downloaded enrichment information stored in the SQL database.
This server can be activated using::
$ ebel serve
You can also specify certain parameters as options::
$ ebel serve -p 5000 --debug-mode
Disclaimer
==========
e(BE:L) is a scientific software that has been developed in an academic capacity, and thus comes with no warranty or
guarantee of maintenance, support, or back-up of data.
.. |docs| image:: http://readthedocs.org/projects/ebel/badge/?version=latest
:target: https://ebel.readthedocs.io/en/latest/
:alt: Documentation Status
.. |python_versions| image:: https://img.shields.io/pypi/pyversions/ebel.svg
:alt: Stable Supported Python Versions
.. |pypi_version| image:: https://img.shields.io/pypi/v/ebel.svg
:alt: Current version on PyPI
.. |pypi_license| image:: https://img.shields.io/pypi/l/ebel.svg
:alt: MIT
.. _UniProt: https://https://uniprot.org/
.. _OrientDB: https://orientdb.org/
.. _download OrientDB: https://www.orientdb.org/download/
.. _MariaDB: https://mariadb.org/
.. _Ensembl: https://www.ensembl.org/index.html
.. _IntAct: https://www.ebi.ac.uk/intact/
Raw data
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"name": "ebel",
"maintainer": "Christian Ebeling",
"docs_url": null,
"requires_python": ">=3.9,<4.0",
"maintainer_email": "christian.ebeling@scai.fraunhofer.de",
"keywords": "Biomedical Database,Biological Expression Lnaguage,Graph Database",
"author": "Bruce Schultz",
"author_email": "bruce.schultz@scai.fraunhofer.de",
"download_url": "https://files.pythonhosted.org/packages/c4/da/5b67d0f1b0e1669138ca78f4ba7f1eea8a1ecb5b78f886b988b793adb0a1/ebel-1.0.37.tar.gz",
"platform": null,
"description": "*********************************\ne(BE:L) |docs| |python_versions|\n*********************************\ne(BE:L) is a Python package built for both validating and modeling information extracted from publications using `Biological Expression Language (BEL) <https://language.bel.bio/>`_.\nThis software package serves a comprehensive tool for all of your BEL needs and serves to create enriched knowledge graphs\nfor developing and testing new theories and hypotheses.\n\n**e(BE:L)** have implemented several other knowledge bases to extend the BEL knowledge graph or map identifiers.\n\n* `BioGrid <https://thebiogrid.org/>`_\n* `ChEBI <https://www.ebi.ac.uk/chebi/>`_\n* `ClinicalTrials.gov <https://clinicaltrials.gov/>`_\n* `ClinVar <https://www.ncbi.nlm.nih.gov/clinvar/>`_\n* `DisGeNET <https://www.disgenet.org/>`_\n* `DrugBank <https://go.drugbank.com/>`_\n* `Ensembl`_\n* `Expression Atlas <https://www.ebi.ac.uk/gxa/home>`_\n* `GWAS Catalog <https://www.ebi.ac.uk/gxa/home>`_\n* `HGNC <https://www.genenames.org/>`_\n* `IntAct`_\n* `Guide to PHARMACOLOGY <https://www.guidetopharmacology.org/>`_\n* `KEGG <https://www.genome.jp/kegg/>`_\n* `MirTarBase <https://mirtarbase.cuhk.edu.cn/~miRTarBase/miRTarBase_2022/php/index.php>`_\n* `Different resources from NCBI <https://www.ncbi.nlm.nih.gov/>`_\n* `OffSides <http://tatonettilab.org/offsides/>`_\n* `Pathway Commons <https://www.pathwaycommons.org/>`_\n* `The Human Protein Atlas <https://www.proteinatlas.org/>`_\n* `Reactome <https://reactome.org/>`_\n* `STRING <https://string-db.org/>`_\n* `UniProt`_\n\n\nInstallation |pypi_version| |pypi_license|\n==========================================\n\nThe easiest way to install ebel is to use `docker-compose`. See below instructions to use the docker installation.\n\n\n``ebel`` can be directly installed from PyPi with pip::\n\n $ pip install ebel\n\nBut we want to encourage you to use the latest development version which can be installed with::\n\n $ pip install git+https://github.com/e-bel/ebel\n\nPackage Requirements\n====================\n\nInstalling OrientDB\n-------------------\n\nThis software package is designed to work in conjunction with `OrientDB`_, a NoSQL, multi-model database\nthat acts as both a graph and relational database. e(BE:L) uses OrientDB for generating the knowledge graph derived from BEL files. To get\nstarted with e(BE:L), first `download OrientDB`_ and get a server up and running.\nThe first time the server is ran, you will need to create a root password. Once it is up and running, you can get\nstart importing BEL files into it!\n\nOn Linux you can use following commands::\n\n wget https://repo1.maven.org/maven2/com/orientechnologies/orientdb-community/3.2.2/orientdb-community-3.2.2.tar.gz\n tar -xvzf orientdb-community-3.2.2.tar.gz\n cd orientdb-community-3.2.2/bin\n ./server.sh\n\n\nSQL Databases\n--------------\n\nThis package is capable of enriching the compiled knowledge graphs with a lot of external information, however, this requires\na SQL databases for storage. While, a SQLite database can be used, this is not recommended as the amount of data and\ncomplexity of queries will be quite slow. Additionally, SQLite will not be directly supported, the methods will be built\nsuch that they should work with both SQLite and MySQL, but we will not address performance issues due to using SQLite.\n\nInstead, we recommend setting up a `MySQL server <https://www.mysql.com/downloads/>`_ or \n`MariaDB`_ to use with e(BE:L). By default, `PyMySQL <https://pypi.org/project/PyMySQL/>`_\nis installed as a driver by e(BE:L), but others can also be used.\n\nOn Lunux Ubuntu you can use following command::\n\n sudo apt install mysql-server -y\n\nor::\n\n sudo apt install mariadb-server -y\n\n\nConfiguration\n=============\n\nBefore you start working with e(BE:L), a simple to use wizard helps you to setup all configurations. Make sure OrientDB \nand MySQL (or MariaDB) are running. Then start the configuration wizard with::\n\n ebel settings\n\nThe wizard will create the needed databases and users in OrientDB and MySQL/MariaDB.\n\nPackage Components\n==================\n\nTo test the different components you find `here <https://github.com/e-bel/covid19_knowledge_graph/>`_ several BEL and \nalready compiled JSON files.\n\nBEL Validation\n==============\n\nBEL is a domain-specific language designed to capture biological relationships in a computer- and human-readable format.\nThe rules governing BEL statement generation can be quite complex and often mistakes are made during curation.\ne(BE:L) includes a grammar and syntax checker that reads through given BEL files and validates whether each statement\nsatisfies the guidelines provided by `BEL.bio <https://language.bel.bio/>`_. Should any BEL statement within the file\nnot adhere to the rules, a report file is created by e(BE:L) explaining the error and offering suggested fixes.\n\nYou can use the following command to validate your BEL file::\n\n $ ebel validate /path/to/bel_file.bel\n\nIn a single command, you can validate your BEL file as well as generate error reports if there are errors and if there\nare none, produce an importable JSON file::\n\n $ ebel validate /path/to/bel_file.bel -r error_report.xlsx -j\n\nBEL documents should be properly formatted prior to validation. e(BE:L) contains a repair tool that will check the format\nand it is highly recommended that this is used prior to validation. The repaired will overwrite the original if a new file\npath is not specified. Here is an example::\n\n $ ebel repair /path/to/bel_file.bel -n /path/to/repaired_file.bel\n\nImport Process\n==============\n\nBEL Modeling - OrientDB\n-----------------------\n\nBEL files that have passed the validation process can be imported into the\ndatabase individually or *en masse*. During the import process, e(BE:L) automatically creates all of the relevant nodes and edges\nas described in the BEL files. Additionally, e(BE:L) also automatically adds in missing nodes and edges that are known to exist\ne.g. protein nodes with a respective RNA or gene node with have these automatically added to the graph with the appropriate ``translatedTo`` and\n``transcribedTo`` edges.\n\n\nModel Enrichment - MySQL\n------------------------\n\ne(BE:L) goes one step farther when compiling your BEL statements into a knowledge graph by supplementing your new graph model with information derived from several\npublicly available repositories. Data is automatically downloaded from several useful sites including `UniProt`_ ,\n`Ensembl`_, and `IntAct`_ and added as generic tables in your newly built database.\nInformation from these popular repositories are then linked to the nodes and edges residing in your graph model, allowing for more complex and\nuseful queries to be made against your data. This data is automatically downloaded, parsed, and imported into a specified SQL database.\n\nImporting - Getting Started\n---------------------------\n\ne(BE:L) supports OrientDB as graph database and `MySQL <https://www.mysql.com>`_ and `MariaDB`_ as `RDBMS <https://en.wikipedia.org/wiki/Relational_database>`_\n\nMake sure you have downloaded/installed and running\n\n1. `OrientDB`_\n2. MySQL or MariaDB\n a. MySQL\n - `Windows <https://dev.mysql.com/doc/refman/8.0/en/windows-installation.html>`__\n - `MacOS <https://dev.mysql.com/doc/refman/8.0/en/macos-installation.html>`_\n - Linux\n - `Ubuntu, Debian, Linux Mint, ... <https://dev.mysql.com/doc/mysql-apt-repo-quick-guide/en/>`__\n - `RedHat, Fedora, CentOS, OpenSUSE, Scientific Linux, ... <https://dev.mysql.com/doc/refman/8.0/en/linux-installation-yum-repo.html>`__\n b. MariaDB\n - `Windows <https://mariadb.com/kb/en/installing-mariadb-msi-packages-on-windows/>`__\n - MacOS (`PKG <https://mariadb.com/kb/en/installing-mariadb-server-pkg-packages-on-macos/>`_, `Homebrew <https://mariadb.com/kb/en/installing-mariadb-on-macos-using-homebrew/>`_)\n - Linux\n - `Ubuntu, Debian, Linux Mint, ... <https://mariadb.com/kb/en/yum/>`__\n - `RedHat, Fedora, CentOS, OpenSUSE, Scientific Linux, ... <https://mariadb.com/kb/en/installing-mariadb-deb-files/>`__\n\nThis can be configured as a service in both Windows and Unix systems.\n\nSet your MySQL connection parameters in e(BE:L)::\n\n $ ebel set-mysql --host localhost --user root --password myPassWord --database ebel\n\nOnce you have made sure both OrientDB and MySQL are running, you can now import an e(BE:L) compiled JSON file::\n\n $ ebel import-json /path/to/checked_bel.json -u root -p orientdbPassword -d ebel -h localhost -p 2424\n\nAfter you have successfully connected to the OrientDB database at least once, the login credentials will be written to the config file and no longer need to be passed (same with ``enrich`` command)::\n\n $ ebel import-json /path/to/checked_bel.json\n\nYou can also import all e(BE:L) compiled JSON files in a passed directory::\n\n $ ebel import-json /path/to/bel_json/dir/\n\nIf you do no wish to enrich the graph, or wish to disable the protein/RNA/gene extension step, you can toggle these with the following options::\n\n $ ebel import-json /path/to/checked_bel.json -e -g\n\nYou can run an enrichment step later using the ``enrich`` command::\n\n $ ebel enrich\n\nThis command can also be given a list of resources to either skip or include during enrichment::\n\n $ ebel enrich -i uniprot,hgnc\n\nor::\n\n $ ebel enrich -s intact,kegg\n\n\nQuerying the Graph\n==================\nOnce the knowledge graph has been created (and optionally enriched), one can use e(BE:L) to query it directly.\n\n.. code-block:: python\n\n from ebel import Bel\n bel = Bel()\n\n relation_query = \"SELECT out.bel as subject, @class as relation, in.bel as object FROM bel_relation\"\n df = bel.query(relation_query) # Returns results as pandas DataFrame\n result_list = bel.query_get_dict(relation_query) # Returns results as a list of dicts\n\nTo specify a different graph database to connect to than the one in your config file, you can pass connection parameters when initializing the `Bel` class:\n\n.. code-block:: python\n\n from ebel import Bel\n config_params = {\n \"db\": \"my_db\",\n \"user\": \"superdude\",\n \"password\": \"password123\",\n \"server\": \"localhost\", # defaults to localhost if none given\n \"port\": \"2424\", # defaults to 2424 if none given\n }\n\n bel = Bel(graph_config=config_params)\n\n # To overwrite your default values in the config file\n bel = Bel(graph_config=config_params, overwrite_config=True)\n\nDocker installation\n===================\n\nMake sure `docker <https://docs.docker.com/get-docker/>`_ and `docker-compose <https://docs.docker.com/compose/install/>`_ are installed.\n\n.. code-block::\n\n docker-compose up --build -d\n docker exec -it ebel_ebel ebel settings\n\nSeveral question will follow. You can accept the default values (just press RETURN) except the following questions:\n\n.. code-block::\n\n OrientDB server [localhost] ?\n ebel_orientdb\n OrientDB root password (to create database and users)\n ebel\n MySQL/MariaDB sever name [localhost]\n ebel_mysql\n MySQL root password (will be not stored) to create database and user\n ebel\n\nIt's strongly recommended, if you are using ebel in the production environment, to change the\nstandard root MySQL and OrientDB passwords in the docker-compose.yml file.\n\nTo load example files in container and import.\n\n.. code-block::\n\n docker exec -it ebel_ebel git clone https://github.com/e-bel/example_json_bel_files.git\n docker exec -it ebel_ebel ebel import-json example_json_bel_files/phago.bel.json -e\n\n\nTo enrich the network:\n\n.. code-block::\n\n docker exec -it ebel_ebel ebel enrich\n\nFollowing services are now available:\n\n1. `OrientDB Studio <http://localhost:2480/studio/index.html#/>`_\n2. `e(BE:L) REST server <http://localhost:5000/ui/>`_\n3. `phpMyAdmin <http://localhost:8089>`_\n\nAPI\n===\nFinally, this package comes equipped with a built-in RESTful API using Flask. Users that have a running and populated set of databases\ncan also create a running API server which contains several queries for retrieving information from both the network itself, as well\nas the downloaded enrichment information stored in the SQL database.\n\nThis server can be activated using::\n\n $ ebel serve\n\nYou can also specify certain parameters as options::\n\n $ ebel serve -p 5000 --debug-mode\n\nDisclaimer\n==========\ne(BE:L) is a scientific software that has been developed in an academic capacity, and thus comes with no warranty or\nguarantee of maintenance, support, or back-up of data.\n\n\n.. |docs| image:: http://readthedocs.org/projects/ebel/badge/?version=latest\n :target: https://ebel.readthedocs.io/en/latest/\n :alt: Documentation Status\n\n.. |python_versions| image:: https://img.shields.io/pypi/pyversions/ebel.svg\n :alt: Stable Supported Python Versions\n\n.. |pypi_version| image:: https://img.shields.io/pypi/v/ebel.svg\n :alt: Current version on PyPI\n\n.. |pypi_license| image:: https://img.shields.io/pypi/l/ebel.svg\n :alt: MIT\n\n.. _UniProt: https://https://uniprot.org/\n\n.. _OrientDB: https://orientdb.org/\n\n.. _download OrientDB: https://www.orientdb.org/download/\n\n.. _MariaDB: https://mariadb.org/\n\n.. _Ensembl: https://www.ensembl.org/index.html\n\n.. _IntAct: https://www.ebi.ac.uk/intact/",
"bugtrack_url": null,
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