#!/usr/bin/env python
# coding: utf-8

# # CellCollective Knowledge Base
# 
# Models from [CellCollective.org](https://cellcollective.org) can be directly imported by CoLoMoTo tools (such as `bioLQM` or `Pint`) by giving their URL as the argument of the ``.load`` function, for instance, ``lqm = biolqm.load("https://cellcollective.org/#2329/apoptosis-network")``.
# 
# In this notebook, we show how to use the API of the `cellcollective` python module to access metadata of network species, such as UnitProt and NCBI gene identifiers.

# In[1]:


import cellcollective


# ### Model loading from cellcollective.org
# 
# A CellCollective model can be imported using its URL on https://cellcollective.org.
# Alternatively, you can also use "cellcollective://MODEL_ID" syntax.

# In[2]:


sbml = cellcollective.load("https://cellcollective.org/#2329/apoptosis-network")


# The cellcollective python module supports basic access to the SBML-qual file, including the list of defined qualitative species:

# In[3]:


sbml.species


# ### Access metadata
# 
# In most models on CellCollective, authors attached to nodes several metadata, including identifiers of biological species:

# In[4]:


sbml.species_metadata("Cas3")


# The link to UnitProt knowledge or NCBI gene database can be obtained as follows:

# In[5]:


sbml.species_uniprotkb("Cas3")


# In[6]:


sbml.species_ncbi_gene("Cas3")


# There exists several python interfaces to programmatically query information from these databases:
# - using NBCI Gene ID: https://github.com/biocommons/eutils
# - using UniProt ID: https://github.com/jdrudolph/uniprot

# ### Convert to bioLQM for model analysis
# 
# Finally, a CellCollective model can be imported in the `bioLQM` tool, for further processing, such as dynamical analysis and simulations.

# In[7]:


lqm = cellcollective.to_biolqm(sbml)


# In[8]:


set([str(c) for c in lqm.getComponents()])


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