<commit_before># Graph extractor v2.0

## Objective: 

Extract a graph composed by vertices and edges that represents the hierarchical structure of pathways, reactions, complexes, sets and proteins defined in Reactome.

## Graph definition

Vertices:
  * Proteins
  * Complexes/Sets
  * Reactions
  * Pathways

Edges:

* Vertical:
    - [ ] complex has a protein (Cp).
    - [ ] set has a protein (Sp).
    - [ ] complex has a complex (CC).
    - [ ] set has a complex (SC).
    - [ ] complex has a set (CS).
    - [ ] set has a set (SS).
    - [ ] reaction has a protein (Rp).
    - [ ] reaction has a complex (RC).
    - [ ] reaction has a set (RS).
    - [ ] pathway has a reaction (PR).
    - [ ] pathway has a pathway (PP).
* Horizontal:
    - [ ] Interaction between proteins: input-output, catalyst-input, catalyst-output, regulator-input, regulator-output
    - [ ] Interaction between Complexes or Sets:  input-output, catalyst-input, catalyst-output, regulator-input, regulator-output
    - [ ] Binary interactions between proteins obtained from Uniprot, which in turn gets them from IntAct.
    - [ ] Reactions chained: Two reactions _R1_ and _R2_ are chained if the output of _R1_ is the input of _R2_. Where the input and output can be a protein, complex or set, but not a small molecule such as water, ATP or others.

## Input

* **Case 1:** Generate a graph in respect to a set of proteins.<commit_msg>Updated list of edge types that are included in the graph extractor.<commit_after># Graph extractor v2.0

## Objective: 

Extract a graph composed by vertices and edges that represents the hierarchical structure of pathways, reactions, complexes, sets and proteins defined in Reactome.

## Graph definition

Vertices:
  * Proteins
  * Complexes/Sets
  * Reactions
  * Pathways

Edges:

* Vertical:
    - [X] complex has a protein (Cp).
    - [X] set has a protein (Sp).
    - [X] complex has a complex (CC).
    - [X] set has a complex (SC).
    - [X] complex has a set (CS).
    - [X] set has a set (SS).
    - [X] reaction has a protein (Rp).
    - [X] reaction has a complex (RC).
    - [X] reaction has a set (RS).
    - [X] pathway has a reaction (PR).
    - [X] pathway has a pathway (PP).
* Horizontal:
    - [X] Interaction between proteins: input-output, catalyst-input, catalyst-output, regulator-input, regulator-output
    - [ ] Interaction between Complexes or Sets:  input-output, catalyst-input, catalyst-output, regulator-input, regulator-output
    - [ ] Binary interactions between proteins obtained from Uniprot, which in turn gets them from IntAct.
    - [ ] Reactions chained: Two reactions _R1_ and _R2_ are chained if the output of _R1_ is the input of _R2_. Where the input and output can be a protein, complex or set, but not a small molecule such as water, ATP or others.

## Input

* **Case 1:** Generate a graph in respect to a set of proteins.
{'fraction_non_alphanumeric': 0.09726548978885427, 'fraction_numerical': 0.004845967462789893, 'mean_word_length': 3.0646976090014064, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 3, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '6885111', 'n_tokens_mistral': 890, 'n_tokens_neox': 831, 'n_words': 382}