pybel/pybel-notebooks

Notebooks demonstrating the usage of PyBEL and PyBEL Tools

PyBEL Notebooks

This repository contains Jupyter notebooks demonstrating the PyBEL and PyBEL Tools packages.

Cookbook

This directory contains notebooks that address small problems.

Summary

This directory contains notebooks that analyze the contents of a BEL graph.

1. Graph Summary
2. Citation Summary
3. Error Analysis

Integration

This directory contains notebooks dealing with input/output and data integration.

1. Parsing JGIF
2. Resolving Protein Complexes

Algorithms

This directory contains notebooks demonstrating algorithms implemented with PyBEL and NetworkX.

1. Generation of Unbiased Candidate Mechanisms
2. Subgraph Expansion
3. Subgraph Comparison
4. Candidate Mechanism Pertubation Amplitude
5. Time Series Analysis with CMPA
6. Concordance Analysis

Root Directory

Template Notebook (source)

This notebook serves as a style guide for other notebooks in this repository.

BEL Compiler Comparison Notebook (source) (nbviewer)

The speed and usability of the PyBEL compiler is compared to the two legacy options: bel.rb and the OpenBEL Framework.

test.py (source)

This file can be run with python3 -m nose to check that notebooks run to completion.

pybel-notebooks's Issues

Change HGNC Gene Families to use "is_a" relationship

Show export of BEL to natural language with INDRA

The data sources used in the documentation no longer exist

Hello guys.

I found that there is no more data sources that you used in documentation, like:
https://github.com/pybel/pybel-notebooks/blob/master/summary/Citation%20Analysis.ipynb

No more BEL models in repo: https://tor-2.scai.fraunhofer.de/gf/project/bms/

Could you please update documentation regarding to the new data sources?

Converting single node to list in pybel.struct.mutation.get_subgraph_by_neighborhood

Currently pybel.struct.mutation.get_subgraph_by_neighborhood doesn't accept a single node for the node argument.

Simple fix: convert node to list with node as only element

Write tox file to test notebooks all run to completion

This might require also writing a new python file that introspects on the current directory and builds up test cases automatically

Can I download BMS and BANANA as suggested in the notebook?

I have registed on https://tor-2.scai.fraunhofer.de/gf/project/bms. And click request to join.

But I'm still not permitted to git clone the bms and banana repository.

Do these two repository only allowwed to be downloaded by internally ?

Sorry for the bothering.
Hope for your reply.

Graph expansion notebook

Error analysis notebook

Adapt the notebook on tor-2 for public usage

Show loading of Reactome with INDRA

CausalR Demo Notebook

Cool San Diego Demo

Collapsing of Orthologous genes

Juliane said this is a post-processing feature that would be really nice.

• Get data from OpenBEL Framework (in BEL) and HGNC (in JSON)
• Parse into new graph
• Collapse all rat and mouse genes to orthologous human genes
• Statistics
  • Change in degree distribution
  • Change in other graph statistics - betweeness, centrality, characteristic path length

Later:

• Data model for orthology in sqlalchemy
• External scripts for download and versioning

New pybel breaks indra dependencies in BEL to Natural Language

The latest version of pybel breaks indra dependencies in the BEL to Natural Language notebook

pybel.get_version()

'0.14.11-dev'

indra.util.get_version.get_version()

'1.17.0-c8f35a6f7a00e8a6116b707b6a034f57a72f22ae'

pbp = process_pybel_graph(sialic_acid_graph)
pbp.statements

---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
<ipython-input-17-2420ef54593c> in <module>
----> 1 pbp = process_pybel_graph(sialic_acid_graph)
      2 pbp.statements

~/Projects/Proposals/MARS/Pathogenesis/indra/indra/sources/bel/api.py in process_pybel_graph(graph)
    150     """
    151     bp = PybelProcessor(graph)
--> 152     bp.get_statements()
    153     if bp.annot_manager.failures:
    154         logger.warning('missing %d annotation pairs',

~/Projects/Proposals/MARS/Pathogenesis/indra/indra/sources/bel/processor.py in get_statements(self)
     90             for node_ix, node in enumerate((u_data, v_data)):
     91                 if isinstance(node, dsl.ComplexAbundance):
---> 92                     self._get_enum_complex(u_data, v_data, k, d, node_ix)
     93             subj_activity = _get_activity_condition(d.get(pc.SUBJECT))
     94             obj_activity = _get_activity_condition(d.get(pc.OBJECT))

~/Projects/Proposals/MARS/Pathogenesis/indra/indra/sources/bel/processor.py in _get_enum_complex(self, u_data, v_data, k, edge_data, node_ix)
    187         cplx_agent.bound_conditions = []
    188         agents.append(cplx_agent)
--> 189         ev = self._get_evidence(u_data, v_data, k, edge_data)
    190         stmt = Complex(agents, evidence=[ev])
    191         self.statements.append(stmt)

~/Projects/Proposals/MARS/Pathogenesis/indra/indra/sources/bel/processor.py in _get_evidence(self, u_data, v_data, k, edge_data)
    327         ev_pmid = None
    328         if ev_citation:
--> 329             cit_type = ev_citation[pc.CITATION_DB]
    330             cit_ref = ev_citation[pc.CITATION_IDENTIFIER]
    331             if cit_type == pc.CITATION_TYPES[pc.CITATION_TYPE_PUBMED]:

AttributeError: module 'pybel.constants' has no attribute 'CITATION_DB'

Impossible to use notebooks due to problems with pybel_tools package

Hello guys.

notebooks in that repo heavy related on 'pybel_tools' package, but you can't use it with the latest version of the 'pybel_tools' because of the
pybel/pybel-tools#144

Finding Complex and Composite Names

Change HGNC Gene Families to use "is_a" relationship

Candidate Mechanism Pertubation Amplitude notebook missing

Candidate mechanism generation and overlap with cute mechanisms

Load multiple bel files with same manager

This demonstrates how to improve caching time