In [1]:

    

import pygraphviz as pgv
from IPython.core.display import Image


    

In [2]:

    

import requests
 
ensembl_server = 'http://rest.ensembl.org'

def do_request(server, service, *args, **kwargs):
    params = ''
    for a in args:
        if a is not None:
            params += '/' + a
    req = requests.get('%s/%s%s' % (server, service, params),
                       params=kwargs,
                       headers={'Content-Type': 'application/json'})
 
    if not req.ok:
        req.raise_for_status()
    return req.json()


    

In [3]:

    

lct_id = 'ENSG00000115850'


    

In [4]:

    

refs = do_request(ensembl_server, 'xrefs/id', lct_id, external_db='GO', all_levels='1')
print(len(refs))
print(refs[0].keys())
for ref in refs:
    go_id = ref['primary_id']
    details = do_request(ensembl_server, 'ontology/id', go_id)
    print('%s %s %s' % (go_id,  details['namespace'], ref['description']))
    print('%s\n' % details['definition'])


    

    




13
[u'display_id', u'description', u'db_display_name', u'info_text', u'linkage_types', u'info_type', u'primary_id', u'synonyms', u'version', u'dbname']
GO:0000016 molecular_function lactase activity
"Catalysis of the reaction: lactose + H2O = D-glucose + D-galactose." [EC:3.2.1.108]

GO:0004553 molecular_function hydrolase activity, hydrolyzing O-glycosyl compounds
"Catalysis of the hydrolysis of any O-glycosyl bond." [GOC:mah]

GO:0005886 cellular_component plasma membrane
"The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins." [ISBN:0716731363]

GO:0005887 cellular_component integral component of plasma membrane
"The component of the plasma membrane consisting of gene products and protein complexes that have some part that penetrates at least one leaflet of the membrane bilayer. This component includes gene products that are buried in the bilayer with no exposure outside the bilayer." [GOC:dos, GOC:go_curators]

GO:0005975 biological_process carbohydrate metabolic process
"The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule." [GOC:mah, ISBN:0198506732]

GO:0009405 biological_process pathogenesis
"The set of specific processes that generate the ability of an organism to cause disease in another." [GOC:go_curators]

GO:0016020 cellular_component membrane
"Double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins." [GOC:mah, ISBN:0815316194]

GO:0016324 cellular_component apical plasma membrane
"The region of the plasma membrane located at the apical end of the cell." [GOC:curators]

GO:0017042 molecular_function glycosylceramidase activity
"Catalysis of the reaction: glycosyl-N-acylsphingosine + H2O = a sugar + N-acylsphingosine." [EC:3.2.1.62]

GO:0044245 biological_process polysaccharide digestion
"The whole of the physical, chemical, and biochemical processes carried out by living organisms to break down ingested polysaccharides into components that may be easily absorbed and directed into metabolism." [GOC:go_curators]

GO:0044281 biological_process small molecule metabolic process
"The chemical reactions and pathways involving small molecules, any low molecular weight, monomeric, non-encoded molecule." [GOC:curators, GOC:pde, GOC:vw]

GO:0004553 molecular_function hydrolase activity, hydrolyzing O-glycosyl compounds
"Catalysis of the hydrolysis of any O-glycosyl bond." [GOC:mah]

GO:0005975 biological_process carbohydrate metabolic process
"The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule." [GOC:mah, ISBN:0198506732]

In [5]:

    

go_id = 'GO:0000016'
my_data = do_request(ensembl_server, 'ontology/id', go_id)
for k, v in my_data.items():
    if k == 'parents':
        for parent in v:
            print(parent)
            parent_id = parent['accession']
    else:
        print('%s: %s' % (k, str(v)))

parent_data = do_request(ensembl_server, 'ontology/id', parent_id)
print(parent_id, len(parent_data['children']))


    

    




definition: "Catalysis of the reaction: lactose + H2O = D-glucose + D-galactose." [EC:3.2.1.108]
name: lactase activity
subsets: []
namespace: molecular_function
accession: GO:0000016
synonyms: [u'"lactase-phlorizin hydrolase activity" [EC:3.2.1.108]', u'"lactose galactohydrolase activity" [EC:3.2.1.108]']
{u'definition': u'"Catalysis of the hydrolysis of any O-glycosyl bond." [GOC:mah]', u'name': u'hydrolase activity, hydrolyzing O-glycosyl compounds', u'subsets': [u'gosubset_prok'], u'namespace': u'molecular_function', u'accession': u'GO:0004553', u'synonyms': [u'"O-glucosyl hydrolase activity" []'], u'ontology': u'GO'}
ontology: GO
children: []
(u'GO:0004553', 97)

In [6]:

    

refs = do_request(ensembl_server, 'ontology/ancestors/chart', go_id)
for go, entry in refs.items():
    print(go)
    term = entry['term']
    print('%s %s' % (term['name'], term['definition']))
    is_a = entry.get('is_a', [])
    print('\t is a: %s\n' % ', '.join([x['accession'] for x in is_a]))


    

    




GO:0016787
hydrolase activity "Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3." [ISBN:0198506732]
	 is a: GO:0003824

GO:0000016
lactase activity "Catalysis of the reaction: lactose + H2O = D-glucose + D-galactose." [EC:3.2.1.108]
	 is a: GO:0004553

GO:0016798
hydrolase activity, acting on glycosyl bonds "Catalysis of the hydrolysis of any glycosyl bond." [GOC:jl]
	 is a: GO:0016787

GO:0003824
catalytic activity "Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic." [ISBN:0198506732]
	 is a: GO:0003674

GO:0003674
molecular_function "Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions." [GOC:go_curators]
	 is a: 

GO:0004553
hydrolase activity, hydrolyzing O-glycosyl compounds "Catalysis of the hydrolysis of any O-glycosyl bond." [GOC:mah]
	 is a: GO:0016798

In [7]:

    

def get_upper(go_id):
    parents = {}
    node_data = {}
    refs = do_request(ensembl_server, 'ontology/ancestors/chart', go_id)
    for ref, entry in refs.items():
        my_data = do_request(ensembl_server, 'ontology/id', ref)
        node_data[ref] = {'name': entry['term']['name'], 'children': my_data['children']}
        try:
            parents[ref] = [x['accession'] for x in entry['is_a']]
        except KeyError:
            pass  # Top of hierarchy
    return parents, node_data


    

In [8]:

    

parents, node_data = get_upper(go_id)


    

In [9]:

    

g = pgv.AGraph(directed=True)
for ofs, ofs_parents in parents.items():
    ofs_text = '%s\n(%s)' % (node_data[ofs]['name'].replace(', ', '\n'), ofs)
    for parent in ofs_parents:
        parent_text = '%s\n(%s)' % (node_data[parent]['name'].replace(', ', '\n'), parent)
        children = node_data[parent]['children']
        if len(children) < 3:
            for child in children:
                if child['accession'] in node_data:
                    continue
                g.add_edge(parent_text, child['accession'])
        else:
            g.add_edge(parent_text, '...%d...' % (len(children) - 1))
        g.add_edge(parent_text, ofs_text)
print(g)
g.graph_attr['label']='Ontology tree for Lactase activity'
g.node_attr['shape']='rectangle'
g.layout(prog='dot')
g.draw('graph.png')
Image("graph.png")


    

    




strict digraph {
	"catalytic activity
(GO:0003824)" -> "...27...";
	"catalytic activity
(GO:0003824)" -> "hydrolase activity
(GO:0016787)";
	"hydrolase activity
(GO:0016787)" -> "hydrolase activity
acting on glycosyl bonds
(GO:0016798)";
	"hydrolase activity
(GO:0016787)" -> "...22...";
	"hydrolase activity
acting on glycosyl bonds
(GO:0016798)" -> "GO:0016799";
	"hydrolase activity
acting on glycosyl bonds
(GO:0016798)" -> "hydrolase activity
hydrolyzing O-glycosyl compounds
(GO:0004553)";
	"hydrolase activity
hydrolyzing O-glycosyl compounds
(GO:0004553)" -> "...96...";
	"hydrolase activity
hydrolyzing O-glycosyl compounds
(GO:0004553)" -> "lactase activity
(GO:0000016)";
	"molecular_function
(GO:0003674)" -> "catalytic activity
(GO:0003824)";
	"molecular_function
(GO:0003674)" -> "...21...";
}







    
Out[9]:

In [10]:

    

print(go_id)
refs = do_request(ensembl_server, 'ontology/descendants', go_id)
for go in refs:
    print(go['accession'], go['name'], go['definition'])


    

    




GO:0000016
(u'GO:0004553', u'hydrolase activity, hydrolyzing O-glycosyl compounds', u'"Catalysis of the hydrolysis of any O-glycosyl bond." [GOC:mah]')
(u'GO:0016798', u'hydrolase activity, acting on glycosyl bonds', u'"Catalysis of the hydrolysis of any glycosyl bond." [GOC:jl]')
(u'GO:0016787', u'hydrolase activity', u'"Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3." [ISBN:0198506732]')
(u'GO:0003824', u'catalytic activity', u'"Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic." [ISBN:0198506732]')
(u'GO:0003674', u'molecular_function', u'"Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions." [GOC:go_curators]')

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