How to use the bioservices.ChEBI function in bioservices

To help you get started, we’ve selected a few bioservices examples, based on popular ways it is used in public projects.

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github cokelaer / bioservices / test / test_chebi.py View on Github external
def test_chebi():
    ch = ChEBI()
    ch.getCompleteEntity("CHEBI:10102")
    res = ch.conv("CHEBI:10102", "KEGG COMPOUND accession")
    assert res == ['C07484']

    try:
        res = ch.conv("CHEBI:10102", "wrong db")
        assert False
    except:
        assert True

    ch.getOntologyChildren("CHEBI:27732")
    ch.getOntologyParents("CHEBI:27732")
    ch.getUpdatedPolymer("CHEBI:27732")
github cokelaer / bioservices / test / test_chebi.py View on Github external
def test_chebi_mass():
    ch = ChEBI()
    mass1 = ch.getCompleteEntity("CHEBI:27732").mass
    assert float(mass1) == 194.19076
github RuleWorld / bionetgen / parsers / dragon-001 / stats.py View on Github external
def resolveAnnotation(annotation):
    if not hasattr(resolveAnnotation, 'db'):
        resolveAnnotation.db = {}
        resolveAnnotation.ch = bioservices.ChEBI(verbose=False)
        resolveAnnotation.bio = bioservices.BioModels(verbose=False)
        resolveAnnotation.uni = bioservices.UniProt(verbose=False)
        resolveAnnotation.k = bioservices.kegg.KeggParser(verbose=False)
        resolveAnnotation.s = bioservices.Service('name')
        resolveAnnotation.qg = bioservices.QuickGO(verbose=False)
        resolveAnnotation.db['http://identifiers.org/uniprot/P62988'] = 'http://identifiers.org/uniprot/P62988'
        resolveAnnotation.db['http://identifiers.org/uniprot/P06842'] = 'http://identifiers.org/uniprot/P06842'
        resolveAnnotation.db['http://identifiers.org/uniprot/P07006'] = 'http://identifiers.org/uniprot/P06842'
        
    if annotation in resolveAnnotation.db:
        return resolveAnnotation.db[annotation]
    
        
    tAnnotation = annotation.replace('%3A',':')
    tAnnotation = annotation.split('/')[-1]
    #tAnnotation = re.search(':([^:]+:[^:]+$)',tAnnotation).group(1)
github RuleWorld / bionetgen / parsers / SBMLparser / SBMLparser / utils / annotationResolver.py View on Github external
def resolveAnnotationHelper(annotation):
    if not hasattr(resolveAnnotation, 'db'):
        resolveAnnotation.db = {}
        resolveAnnotation.ch = bioservices.ChEBI(verbose=False)
        resolveAnnotation.uni = bioservices.UniProt(verbose=False)
        resolveAnnotation.k = bioservices.kegg.KEGG(verbose=False)
        resolveAnnotation.qg = bioservices.QuickGO(verbose=False)
        resolveAnnotation.t = bioservices.Taxon()
        resolveAnnotation.db['http://identifiers.org/uniprot/P62988'] = 'http://identifiers.org/uniprot/P62988'
        resolveAnnotation.db['http://identifiers.org/uniprot/P06842'] = 'http://identifiers.org/uniprot/P06842'
        resolveAnnotation.db['http://identifiers.org/uniprot/P07006'] = 'http://identifiers.org/uniprot/P06842'
        
    if annotation in resolveAnnotation.db:
        return annotation,resolveAnnotation.db[annotation]
    
        
    tAnnotation = annotation.replace('%3A',':')
    tAnnotation = annotation.split('/')[-1]
    #tAnnotation = re.search(':([^:]+:[^:]+$)',tAnnotation).group(1)
    try:
github sys-bio / tellurium / tellurium / notebooks / speciessearch.py View on Github external
def __init__(self, debug=False):
        """ Creates and displays the search form. """
        self.debug = debug

        self.s = bioservices.BioModels()
        self.ch = bioservices.ChEBI()

        # Define widgets
        # 
        self.wSearchTerm = w.Text(description='Search biomodels by species:', value="CHEBI:17925")
        self.wSearchTerm.on_submit(self.searchChebi)
        self.wSearchButton = w.Button(description='Search')
        self.wSearchButton.on_click(self.searchChebi)
        self.wSearchChebi = w.HBox(children=[
            self.wSearchTerm, self.wSearchButton
        ])

        self.wSelectChebis = w.Select(description='Matching ChEBI:', width='600px', height='250px')
        # FIXME: update the deprecated functions
        self.wSelectChebis.on_trait_change(self.selectChebi)
        self.wSelectModels = w.Select(description='Matching BioModels:', width='200px')
        self.wSelectModels.on_trait_change(self.selectedModel)
github RuleWorld / bionetgen / bng2 / SBMLparser / stats.py View on Github external
def resolveAnnotation(annotation):
    if not hasattr(resolveAnnotation, 'db'):
        resolveAnnotation.db = {}
        resolveAnnotation.ch = bioservices.ChEBI(verbose=False)
        resolveAnnotation.uni = bioservices.UniProt(verbose=False)
        resolveAnnotation.k = bioservices.kegg.KeggParser(verbose=False)
        resolveAnnotation.qg = bioservices.QuickGO(verbose=False)
        resolveAnnotation.db['http://identifiers.org/uniprot/P62988'] = 'http://identifiers.org/uniprot/P62988'
        resolveAnnotation.db['http://identifiers.org/uniprot/P06842'] = 'http://identifiers.org/uniprot/P06842'
        resolveAnnotation.db['http://identifiers.org/uniprot/P07006'] = 'http://identifiers.org/uniprot/P06842'
        
    if annotation in resolveAnnotation.db:
        return resolveAnnotation.db[annotation]
    
        
    tAnnotation = annotation.replace('%3A',':')
    tAnnotation = annotation.split('/')[-1]
    #tAnnotation = re.search(':([^:]+:[^:]+$)',tAnnotation).group(1)
    try:
        if 'obo.go' in annotation:
github sys-bio / tellurium / tellurium / notebooks / ontologysearch.py View on Github external
def __init__(self):
        self.ch = bioservices.ChEBI()
        self.kegg = bioservices.KEGG()

        self.wOntologySelect = w.Dropdown(description='Ontology:', options=['ChEBI', 'KEGG.Reaction'])
        self.wSearchTerm = w.Text(description='Search Term:', value="glucose")
        self.wSearchTerm.on_submit(self.search)
        self.wSearchButton = w.Button(description='Search')
        self.wSearchButton.on_click(self.search)

        self.wResultsSelect = w.Select(description='Results:', width='100%')
        self.wResultsSelect.on_trait_change(self.selectedTerm)
        self.wResultsURL = w.Textarea(description='URL:', width='100%')
        self.wResults = w.VBox(children=[
                self.wResultsSelect,
                self.wResultsURL
        ], width='100%')
        for ch in self.wResults.children:
github RuleWorld / bionetgen / parsers / dragon-001 / twistedStats.py View on Github external
def resolveAnnotation(annotation):
    if not hasattr(resolveAnnotation, 'db'):
        resolveAnnotation.db = {}
        resolveAnnotation.ch = bioservices.ChEBI(verbose=False)
        resolveAnnotation.bio = bioservices.BioModels(verbose=False)
        resolveAnnotation.uni = bioservices.UniProt(verbose=False)
        resolveAnnotation.k = bioservices.kegg.KeggParser(verbose=False)
        resolveAnnotation.s = bioservices.Service('name')
        resolveAnnotation.qg = bioservices.QuickGO(verbose=False)
        resolveAnnotation.db['http://identifiers.org/uniprot/P62988'] = 'http://identifiers.org/uniprot/P62988'
        resolveAnnotation.db['http://identifiers.org/uniprot/P06842'] = 'http://identifiers.org/uniprot/P06842'
        resolveAnnotation.db['http://identifiers.org/uniprot/P07006'] = 'http://identifiers.org/uniprot/P06842'
        
    if annotation in resolveAnnotation.db:
        return resolveAnnotation.db[annotation]
    
        
    tAnnotation = annotation.replace('%3A',':')
    tAnnotation = annotation.split('/')[-1]
    #tAnnotation = re.search(':([^:]+:[^:]+$)',tAnnotation).group(1)