neurommsig-epilepsy's Introduction

NeuroMMSig Epilepsy

Mechanistic pathway knowledge on Epilepsy encoded in Biological Expression Language.

Installation

To install the neurommsig_epilepsy python package for programmatic access to the BEL files in this repository, use the following code in your shell:

$ pip install neurommsig_epilepsy

To install the neurommsig_epilepsy python package for programmatic access to the BEL files in this repository, use the following code in your shell:

$ git clone https://github.com/neurommsig-epilepsy/neurommsig-epilepsy.git
$ cd neurommsig_epilepsy
$ pip install -e .

To optionally re-compile all of the BEL files, use

$ neurommsig-epilepsy compile

Usage

To get the knowledge and summarize it, use:

import neurommsig_epilepsy

graph = neurommsig_epilepsy.get_graph()
graph.summarize()

Contributors

Watchers

neurommsig-epilepsy's Issues

Fix missing famplex definition and other errors

Loading BEL:   0%|                                                                                                          | 0/7 [00:00<?, ?it/s/Users/cthoyt/dev/neurommsig-epilepsy/neurommsig_epilepsy_knowledge/epilepsy.bel:157:4 UndefinedAnnotationWarning "Evidence" is not defined, ?it/s]
                                                                                                                                                 /Users/cthoyt/dev/neurommsig-epilepsy/neurommsig_epilepsy_knowledge/epilepsy.bel:708:12 UndefinedNamespaceWarning "FPLX" is not a defined namespace
                                                                                                                                                 /Users/cthoyt/dev/neurommsig-epilepsy/neurommsig_epilepsy_knowledge/epilepsy.bel:776:24 UndefinedNamespaceWarning "FPLX" is not a defined namespace
/Users/cthoyt/dev/neurommsig-epilepsy/neurommsig_epilepsy_knowledge/epilepsy.bel:777:24 UndefinedNamespaceWarning "FPLX" is not a defined namespace
/Users/cthoyt/dev/neurommsig-epilepsy/neurommsig_epilepsy_knowledge/epilepsy.bel:781:42 UndefinedNamespaceWarning "FPLX" is not a defined namespace
/Users/cthoyt/dev/neurommsig-epilepsy/neurommsig_epilepsy_knowledge/epilepsy.bel:782:42 UndefinedNamespaceWarning "FPLX" is not a defined namespace
/Users/cthoyt/dev/neurommsig-epilepsy/neurommsig_epilepsy_knowledge/epilepsy.bel:783:50 UndefinedNamespaceWarning "FPLX" is not a defined namespace
/Users/cthoyt/dev/neurommsig-epilepsy/neurommsig_epilepsy_knowledge/epilepsy.bel:787:8 UndefinedNamespaceWarning "FPLX" is not a defined namespace
/Users/cthoyt/dev/neurommsig-epilepsy/neurommsig_epilepsy_knowledge/epilepsy.bel:788:8 UndefinedNamespaceWarning "FPLX" is not a defined namespace
/Users/cthoyt/dev/neurommsig-epilepsy/neurommsig_epilepsy_knowledge/epilepsy.bel:789:8 UndefinedNamespaceWarning "FPLX" is not a defined namespace
/Users/cthoyt/dev/neurommsig-epilepsy/neurommsig_epilepsy_knowledge/epilepsy.bel:793:12 UndefinedNamespaceWarning "FPLX" is not a defined namespace
/Users/cthoyt/dev/neurommsig-epilepsy/neurommsig_epilepsy_knowledge/epilepsy.bel:805:12 UndefinedNamespaceWarning "FPLX" is not a defined namespace
/Users/cthoyt/dev/neurommsig-epilepsy/neurommsig_epilepsy_knowledge/epilepsy.bel:806:12 UndefinedNamespaceWarning "FPLX" is not a defined namespace
/Users/cthoyt/dev/neurommsig-epilepsy/neurommsig_epilepsy_knowledge/epilepsy.bel:812:8 UndefinedNamespaceWarning "FPLX" is not a defined namespace
/Users/cthoyt/dev/neurommsig-epilepsy/neurommsig_epilepsy_knowledge/epilepsy.bel:813:8 UndefinedNamespaceWarning "FPLX" is not a defined namespace
/Users/cthoyt/dev/neurommsig-epilepsy/neurommsig_epilepsy_knowledge/epilepsy.bel:814:8 UndefinedNamespaceWarning "FPLX" is not a defined namespace
/Users/cthoyt/dev/neurommsig-epilepsy/neurommsig_epilepsy_knowledge/epilepsy.bel:839:25 UndefinedNamespaceWarning "FPLX" is not a defined namespace
/Users/cthoyt/dev/neurommsig-epilepsy/neurommsig_epilepsy_knowledge/epilepsy.bel:844:26 UndefinedNamespaceWarning "FPLX" is not a defined namespace
                                                                                                                                                 /Users/cthoyt/dev/neurommsig-epilepsy/neurommsig_epilepsy_knowledge/epilepsy.bel:2202:3 MissingNamespaceNameWarning "ion channel regulator activity" is not in the GOBP namespace
/Users/cthoyt/dev/neurommsig-epilepsy/neurommsig_epilepsy_knowledge/epilepsy.bel:2203:22 MissingNamespaceNameWarning "ion channel regulator activity" is not in the GOBP namespace
/Users/cthoyt/dev/neurommsig-epilepsy/neurommsig_epilepsy_knowledge/epilepsy.bel:2331:8 UndefinedNamespaceWarning "FPLX" is not a defined namespace
/Users/cthoyt/dev/neurommsig-epilepsy/neurommsig_epilepsy_knowledge/epilepsy.bel:2332:8 UndefinedNamespaceWarning "FPLX" is not a defined namespace
/Users/cthoyt/dev/neurommsig-epilepsy/neurommsig_epilepsy_knowledge/epilepsy.bel:2336:8 UndefinedNamespaceWarning "FPLX" is not a defined namespace
                                                                                                                                                 /Users/cthoyt/dev/neurommsig-epilepsy/neurommsig_epilepsy_knowledge/epilepsy.bel:2476:44 NakedNameWarning "maintenance of neuronal function" should be qualified with a valid namespace
                                                                                                                                                 /Users/cthoyt/dev/neurommsig-epilepsy/neurommsig_epilepsy_knowledge/epilepsy.bel:4128:4 IllegalAnnotationValueWarning "9940" is not defined in the Species annotation
                                                                                                                                                 /Users/cthoyt/dev/neurommsig-epilepsy/neurommsig_epilepsy_knowledge/epilepsy.bel:5965:5 MissingNamespaceNameWarning "Glucose transporter type 1 deficiency" is not in the EPT namespace
/Users/cthoyt/dev/neurommsig-epilepsy/neurommsig_epilepsy_knowledge/epilepsy.bel:5968:5 MissingNamespaceNameWarning "Glucose transporter type 1 deficiency" is not in the EPT namespace
/Users/cthoyt/dev/neurommsig-epilepsy/neurommsig_epilepsy_knowledge/epilepsy.bel:5969:5 MissingNamespaceNameWarning "Glucose transporter type 1 deficiency" is not in the EPT namespace
                                                                                                                                                 /Users/cthoyt/dev/neurommsig-epilepsy/neurommsig_epilepsy_knowledge/epilepsy.bel:6847:67 MissingNamespaceNameWarning "translation initiation" is not in the GOBP namespace
/Users/cthoyt/dev/neurommsig-epilepsy/neurommsig_epilepsy_knowledge/epilepsy.bel:6849:3 MissingNamespaceNameWarning "translation initiation" is not in the GOBP namespace
Epilepsy Curation v0.0.1-dev                                                                                                                      
Number of Nodes: 2216                                                                                                                             
Number of Edges: 6948
Number of Citations: 688
Number of Authors: 4417
Network Density: 1.42E-03
Number of Components: 23
Number of Warnings: 0