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
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' to 'gen/colomoto92w0em0_2329.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'}
In most models on CellCollective, authors attached to nodes several metadata, including identifiers of biological species:
sbml.species_metadata("Cas3")
{'GeneName': 'CASP3', 'NCBIGeneID': '836', 'UniProtID': 'P42574'}
The link to UnitProt knowledge or NCBI gene database can be obtained as follows:
sbml.species_uniprotkb("Cas3")
sbml.species_ncbi_gene("Cas3")
There exists several python interfaces to programmatically query information from these databases:
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)