Merge branch 'BioDataFuse:main' into main

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,24 @@
+---
+name: Bug report
+about: Create a report to help us improve
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+
+**To Reproduce**
+Steps to reproduce the behavior:
+1. Provide the Gene List used in the workflow
+2. Provide the script/notebook where the error occur
+3. State at which point the code is failing or resulting unexpected behavior.
+4. Add any relevant information to reproduce the problem
+
+**Expected behavior**
+A clear and concise description of what you expected to happen. For example, the report may not be about a programmatic error but about unexpected behavior (like empty annotation result set, or different graph structure than expected or even missing nodes or edges)
+
+**Screenshots**
+If applicable, add screenshots to help explain your problem.

.github/ISSUE_TEMPLATE/custom.md

@@ -0,0 +1,10 @@
+---
+name: Custom issue template
+about: Describe this issue template's purpose here.
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+

.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,20 @@
+---
+name: Feature request
+about: Suggest an idea for this project
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**Is your feature request related to a problem? Please describe.**
+A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+
+**Describe the solution you'd like**
+A clear and concise description of what you want to happen.
+
+**Describe alternatives you've considered**
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Additional context**
+Add any other context or screenshots about the feature request here.

MANIFEST.in

@@ -2,6 +2,7 @@ graft src
 graft tests
 graft resources
 graft viz
+graft graph
 prune scripts
 prune notebooks
 prune examples
@@ -14,6 +15,7 @@ recursive-include docs/source *.py
 recursive-include docs/source *.rst
 recursive-include docs/source *.png
 recursive-include resources *.csv
+recursive-include src *.py
 
 global-exclude *.py[cod] __pycache__ *.so *.dylib .DS_Store *.gpickle
 

README.md

@@ -38,12 +38,10 @@
     </a>
 </p>
 
-A python package for integrating data from multiple resources
 
 ## 💪 Getting Started
 
-> TODO show in a very small amount of space the **MOST** useful thing your package can do.
-> Make it as short as possible! You have an entire set of docs for later.
+> A python package for integrating data from multiple existsing biomedical resources and assist in generating a knowledge graph on the data. 
 
 ### Command Line Interface
 

docs/source/conf.py

@@ -47,7 +47,7 @@
 
 # If true, the current module name will be prepended to all description
 # unit titles (such as .. function::).
-add_module_names = False
+add_module_names = True
 
 # A list of prefixes that are ignored when creating the module index. (new in Sphinx 0.6)
 modindex_common_prefix = ["pyBiodatafuse."]

docs/source/datasources.rst

@@ -0,0 +1,77 @@
+Data sources
+============
+
+Here you can find the different data resources that you can successfully query with the pyBiodatafuse package.
+
+.. module:: pyBiodatafuse.annotators
+
+Bgee
+~~~~~~~~~~~~~~~
+
+`Bgee <https://www.bgee.org/>` is a database for retrieval and comparison of gene expression patterns across multiple animal species.
+
+.. autofunction:: pyBiodatafuse.annotators.bgee.get_gene_expression
+
+DisGeNET
+~~~~~~~~~~~~~~~
+
+`DisGeNET <https://www.disgenet.org/home/>` is a discovery platform containing one of the largest publicly available collections of genes and variants associated to human diseases.
+
+.. autofunction:: pyBiodatafuse.annotators.disgenet.get_gene_disease
+
+MolMeDB
+~~~~~~~~~~~~~~~
+
+`MolMeDB <https://molmedb.upol.cz/detail/intro>` is an open chemistry database about interactions of molecules with membranes.
+
+.. autofunction:: pyBiodatafuse.annotators.molmedb.get_gene_mol_inhibitor
+
+.. autofunction:: pyBiodatafuse.annotators.molmedb.get_mol_gene_inhibitor
+
+OpenTargets
+~~~~~~~~~~~~~~~
+
+`OpenTargets database <https://www.opentargets.org/>` uses human genetics and genomics data for systematic drug target identification and prioritisation.
+
+.. autofunction:: pyBiodatafuse.annotators.opentargets.get_gene_location
+
+.. autofunction:: pyBiodatafuse.annotators.opentargets.get_gene_go_process
+
+.. autofunction:: pyBiodatafuse.annotators.opentargets.get_gene_reactome_pathways
+
+.. autofunction:: pyBiodatafuse.annotators.opentargets.get_gene_tractability
+
+.. autofunction:: pyBiodatafuse.annotators.opentargets.get_gene_drug_interactions
+
+.. autofunction:: pyBiodatafuse.annotators.opentargets.get_targetgene_disease_associations
+
+StringDB
+~~~~~~~~~~~~~~~
+
+`StringDB <https://string-db.org/>` aims to collect, score and integrate all publicly available sources of protein-protein interaction information, and to complement these with computational predictions.
+
+.. autofunction:: pyBiodatafuse.annotators.stringdb.get_ppi
+
+Wikidata
+~~~~~~~~~~~~~~~
+
+`Wikidata <https://www.wikidata.org/>` acts as central storage for the structured data of its Wikimedia sister projects including Wikipedia, Wikivoyage, Wiktionary, Wikisource, and others.
+
+.. autofunction:: pyBiodatafuse.annotators.wikidata.get_gene_literature
+
+.. autofunction:: pyBiodatafuse.annotators.wikidata.get_gene_cellular_component
+
+WikiPathways
+~~~~~~~~~~~~~~~
+
+`Wikipathways <https://www.wikipathways.org/>` is an open science platform for biological pathways contributed, updated, and used by the research community.
+
+.. autofunction:: pyBiodatafuse.annotators.wikipathways.get_gene_wikipathway
+
+MINERVA
+~~~~~~~~~~~~~~~
+
+`MINERVA <https://minerva.pages.uni.lu/doc/>` is a standalone webserver for visual exploration, analysis and management of molecular networks encoded in following systems biology formats.
+
+.. autofunction:: pyBiodatafuse.annotators.minerva.get_minerva_components
+.. autofunction:: pyBiodatafuse.annotators.minerva.get_gene_minerva_pathways

docs/source/graph_plotters.rst

@@ -0,0 +1,25 @@
+Graph Plotters
+==============
+
+Here you can find the different graph loading, storing, and plotting functions in the package.
+
+.. module:: pyBiodatafuse.graph
+
+NetworkX
+~~~~~~~~~~~~~~~
+
+.. autofunction:: pyBiodatafuse.graph.generate_networkx_graph
+
+Cytoscape
+~~~~~~~~~~~~~~~
+
+.. autofunction:: pyBiodatafuse.graph.generator.convert_graph_to_cytoscape_json
+
+.. autofunction:: pyBiodatafuse.graph.cytoscape.save_cytoscape_json_to_file
+
+Neo4J
+~~~~~~~~~~~~~~~
+
+.. autofunction:: pyBiodatafuse.graph.neo4j_exporter.save_graph_to_neo4j_graphml
+
+.. autofunction:: pyBiodatafuse.graph.neo4j_exporter.export

docs/source/index.rst

@@ -1,34 +1,13 @@
 pyBioDataFuse |release| Documentation
 =====================================
 
-Cookiecutter
-------------
-This package was created with the `cookiecutter <https://github.com/cookiecutter/cookiecutter>`_
-package using `cookiecutter-snekpack <https://github.com/cthoyt/cookiecutter-snekpack>`_ template.
-It comes with the following:
-
-- Standard `src/` layout
-- Declarative setup with `setup.cfg` and `pyproject.toml`
-- Reproducible tests with `pytest` and `tox`
-- A command line interface with `click`
-- A vanity CLI via python entrypoints
-- Version management with `bumpversion`
-- Documentation build with `sphinx`
-- Testing of code quality with `flake8` in `tox`
-- Testing of documentation coverage with `docstr-coverage` in `tox`
-- Testing of documentation format and build in `tox`
-- Testing of package metadata completeness with `pyroma` in `tox`
-- Testing of MANIFEST correctness with `check-manifest` in `tox`
-- Testing of optional static typing with `mypy` in `tox`
-- A `py.typed` file so other packages can use your type hints
-- Automated running of tests on each push with GitHub Actions
-- Configuration for `ReadTheDocs <https://readthedocs.org/>`_
-- A good base `.gitignore` generated from `gitignore.io <https://gitignore.io>`_.
-- A pre-formatted README with badges
-- A pre-formatted LICENSE file with the MIT License (you can change this to whatever you want, though)
-- A pre-formatted CONTRIBUTING guide
-- Automatic tool for releasing to PyPI with ``tox -e finish``
-- A copy of the `Contributor Covenant <https://www.contributor-covenant.org>`_ as a basic code of conduct
+.. automodule:: pyBioDataFuse
+
+## 💪 Getting Started
+
+- pyBioDataFuse is a python package for integrating data from multiple existing biomedical resources and
+- assist in generating a knowledge graph on the data.
+
 
 Table of Contents
 -----------------
@@ -38,11 +17,17 @@ Table of Contents
    :name: start
 
    installation
-   usage
-   cli
+   datasources
+   graph_plotters
 
 Indices and Tables
 ------------------
 * :ref:`genindex`
 * :ref:`modindex`
 * :ref:`search`
+
+
+Disclaimer
+------------
+This package was created with the `cookiecutter <https://github.com/cookiecutter/cookiecutter>`_
+package using `cookiecutter-snekpack <https://github.com/cthoyt/cookiecutter-snekpack>`_ template.

docs/source/installation.rst

@@ -1,5 +1,6 @@
 Installation
 ============
+
 The most recent release can be installed from
 `PyPI <https://pypi.org/project/pyBiodatafuse>`_ with: