Develop

README.md

@@ -89,6 +89,17 @@ For the random walks method we have a similar factory method that can be found i
 
 ## List of contributors
 
+* [Fernando Zhapa](https://github.com/ferzcam)
+* [Maxat Kulmanov](https://github.com/coolmaksat)
+* [Sarah Alghamdi](https://github.com/smalghamdi)
+* [Robert Hoehndorf](https://github.com/leechuck)
+* [Carsten Jahn](https://github.com/carsten-jahn)
+* [Sonja Katz](https://github.com/sonjakatz)
+* [Marco Anteghini](https://github.com/MarcoAnteghini)
+* Francesco Gualdi
+* [luis-sribeiro](https://github.com/luis-sribeiro)
+* [Leduin Cuenca](https://github.com/leduin) (logo)
+
 ## License
 
 ## Documentation

build_jars.sh

@@ -3,4 +3,5 @@ gradle distZip
 cd build/distributions
 yes | unzip gateway.zip
 cd ../../../
+rm -f mowl/lib/*.jar
 cp -r gateway/build/distributions/gateway/lib mowl

docs/source/api/datasets/index.rst

@@ -14,3 +14,11 @@ PPI Yeast dataset
 .. automodule:: mowl.datasets.ppi_yeast
    :members:
    :show-inheritance:
+
+
+Extending ontologies
+========================
+
+.. automodule:: mowl.datasets.build_ontology
+   :members:
+   :show-inheritance:

docs/source/api/embedding/graph_based/index.rst

@@ -11,16 +11,13 @@ DL2Vec
    :undoc-members:
    :show-inheritance:
 
-Example of use
-^^^^^^^^^^^^^^^
-An example of use can be found at :doc:`../../../tutorials/DL2Vec`
 
 
 
 OWL2Vec*
 --------
 
-.. automodule:: mowl.embeddings.graph_based.owl2vec_star.model
+.. automodule:: mowl.embeddings.graph_based.owl2vec.model
    :members:
    :undoc-members:
    :show-inheritance:
@@ -35,6 +32,3 @@ Translational Embeddings
    :show-inheritance:
 
 
-Example of use
-^^^^^^^^^^^^^^^
-An example can be found at :doc:`../../../tutorials/Translational`

docs/source/api/embedding/semantic/index.rst

@@ -11,7 +11,3 @@ ELEmbeddings
    :show-inheritance:
 
 
-Example of use
-^^^^^^^^^^^^^^^
-An example can be found at :doc:`../../../tutorials/ELEmbeddings`
-

docs/source/api/walking/index.rst

@@ -26,6 +26,6 @@ Node2Vec
 Walk RDF and OWL
 ------------------
 
-.. automodule:: mowl.walking.walkRdfAndOwl.model
+.. automodule:: mowl.walking.rdf2vec.model
    :members:
    :show-inheritance:

docs/source/index.rst

@@ -1,29 +1,49 @@
 Welcome to mOWL's documentation!
 ===================================
 
-**mOWL** is a Python library for Machine Learning with Ontologies
+**mOWL** is a Python library for Machine Learning with Ontologies. Here you can find several methods to generate embeddings of ontology entities as described in the paper `Semantic similarity and machine learning with ontologies <https://academic.oup.com/bib/article/22/4/bbaa199/5922325>`_.
+
 
 Getting started
 ----------------
 
-Check out the how to :doc:`install/index` section of the project.
+.. note::
+
+   This project is under development.
+
+
 
+**mOWL** can be installed from the `source code <https://github.com/bio-ontology-research-group/mowl>`_ or from `Test PyPi <https://test.pypi.org/project/mowl-borg/>`_.
+
+Source code installation can be done with the following commands:
+
+.. code:: bash
+	  
+   git clone https://github.com/bio-ontology-research-group/mowl.git
+   
+   cd mowl
+
+   conda env create -f environment.yml
+   conda activate mowl
+
+   cd mowl
+   ./build_jars.sh
+
+
+
+For more details on installation check out the how to :doc:`install/index` section of the project.
 
 
 Authors
 ----------
 
-`BORG <https://cemse.kaust.edu.sa/borg>`_
+**mOWL** is a project initiated and developed by the `Bio-Ontology Research Group <https://cemse.kaust.edu.sa/borg>`_ from KAUST.
+Furthermore, mOWL had other collaboration by being part of the `Biohackathon Europe 2021 <https://2021.biohackathon-europe.org/>`_.
 
 License
 ---------------
 
-The package is released under the `DEFINE LICENSE`.
-
-
-.. note::
-
-   This project is under active development.
+The package is released under the BSD 3-Clause License.
 
 
 .. toctree::

docs/source/install/index.rst

@@ -7,12 +7,13 @@ System requirements
 - Ubuntu >16.04
 - Python version >3.8
 
-Install
--------------------
+Install from source code
+--------------------------
 
 Installation can be done with the following commands:
 
 .. code:: bash
+	  
    git clone https://github.com/bio-ontology-research-group/mowl.git
    
    cd mowl
@@ -21,7 +22,17 @@ Installation can be done with the following commands:
    conda activate mowl
 
    cd mowl
-   ./rebuild.sh
+   ./build_jars.sh
+
+Since mOWL needs to bind the Java Virtual Machine, the last line will generate the necessary `jar` files.
+
 
-The last line will generate the necessary `jar` files to bind Python with the code that runs in the JVM
 
+Install from PyPi
+------------------------------
+
+PyPi installation is on testing phase and can be done as follows:
+
+.. code:: bash
+	  
+   pip install -i https://test.pypi.org/simple/ mowl-borg