CellCollective Knowledge Base

CellCollective Knowledge Base#

Models from 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.

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.

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

Downloading http://api.cellcollective.org/model/export/2329?type=SBML

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

sbml.species

{'A20',
 'AKT',
 'APC',
 'Apaf1',
 'Apoptosis',
 'BAD',
 'BID',
 'BclX',
 'Cas12',
 'Cas3',
 'Cas6',
 'Cas7',
 'Cas8',
 'Cas9',
 'DNADamageEvent',
 'FADD',
 'GF',
 'GFR',
 'IAP',
 'IKK',
 'IkB',
 'JNK',
 'JNKK',
 'MEKK1',
 'Mdm2',
 'Mito',
 'NFkB',
 'NIK',
 'PI3K',
 'PIP2',
 'PIP3',
 'PTEN',
 'RIP',
 'TNF',
 'TNFR1',
 'TNFR2',
 'TRADD',
 'TRAF',
 'TRAF2',
 'cFLIP',
 'p53'}

Access metadata#

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

sbml.species_metadata("Cas3")

{'UniProtID': 'P42574', 'GeneName': 'CASP3', 'NCBIGeneID': '836'}

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

sbml.species_uniprotkb("Cas3")

https://www.uniprot.org/uniprot/P42574

sbml.species_ncbi_gene("Cas3")

https://www.ncbi.nlm.nih.gov/gene/836

There exists several python interfaces to programmatically query information from these databases:

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.

lqm = cellcollective.to_biolqm(sbml)

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

{'A20',
 'AKT',
 'APC',
 'Apaf1',
 'Apoptosis',
 'BAD',
 'BID',
 'BclX',
 'Cas12',
 'Cas3',
 'Cas6',
 'Cas7',
 'Cas8',
 'Cas9',
 'DNADamageEvent',
 'FADD',
 'GF',
 'GFR',
 'IAP',
 'IKK',
 'IkB',
 'JNK',
 'JNKK',
 'MEKK1',
 'Mdm2',
 'Mito',
 'NFkB',
 'NIK',
 'PI3K',
 'PIP2',
 'PIP3',
 'PTEN',
 'RIP',
 'TNF',
 'TNFR1',
 'TNFR2',
 'TRADD',
 'TRAF',
 'TRAF2',
 'cFLIP',
 'p53'}