In [1]:

    

from ontobio import OntologyFactory


    

In [2]:

    

ont = OntologyFactory().create('go')


    

In [3]:

    

relations=['subClassOf', 'BFO:0000050']
m = ont.create_slim_mapping(subset='goslim_generic', relations=relations)


    

In [4]:

    

m['GO:0016577']


    

    
Out[4]:





['GO:0051276', 'GO:0006464']

In [7]:

    

# show the first 20 GO terms plus their mappings
for n in ont.nodes()[0:20]:
    if n.startswith('GO:'):
        print('{} {}'.format(n, ont.label(n)))
        for x in m[n]:
              print('  --> {} {}'.format(x, ont.label(x)))


    

    




GO:0052060 evasion or tolerance by symbiont of host-produced nitric oxide
  --> GO:0044403 symbiosis, encompassing mutualism through parasitism
GO:0061698 protein deglutarylation
  --> GO:0006464 cellular protein modification process
GO:0061092 positive regulation of phospholipid translocation
  --> GO:0061024 membrane organization
GO:0048027 mRNA 5'-UTR binding
  --> GO:0003729 mRNA binding
GO:0048325 negative regulation of axial mesodermal cell fate determination
  --> GO:0008150 biological_process
GO:0061444 endocardial cushion cell development
  --> GO:0048856 anatomical structure development
  --> GO:0030154 cell differentiation
GO:0000332 template for synthesis of G-rich strand of telomere DNA activity
  --> GO:0009058 biosynthetic process
  --> GO:0006259 DNA metabolic process
  --> GO:0003677 DNA binding
  --> GO:0016779 nucleotidyltransferase activity
GO:0034367 macromolecular complex remodeling
  --> GO:0008150 biological_process
GO:2001238 positive regulation of extrinsic apoptotic signaling pathway
  --> GO:0008150 biological_process
GO:0003154 BMP signaling pathway involved in determination of left/right symmetry
  --> GO:0048856 anatomical structure development
  --> GO:0007165 signal transduction
GO:0098839 postsynaptic density membrane
  --> GO:0043226 organelle
  --> GO:0005886 plasma membrane
GO:2001116 methanopterin-containing compound biosynthetic process
  --> GO:0009058 biosynthetic process
  --> GO:0034641 cellular nitrogen compound metabolic process

In [8]:

    

from ontobio.assoc_factory import AssociationSetFactory

MOUSE = 'NCBITaxon:10090'

# Create association set
# Transparently uses remote Monarch service.
# (May take a few seconds to run first time, Jupyter will show '*'. BE PATIENT, do
# not re-execute cell)
afactory = AssociationSetFactory()
aset = afactory.create(ontology=ont,
                       subject_category='gene',
                       object_category='function',   # this is ALL GO, not just MF
                       taxon=MOUSE)


    

In [9]:

    

sample = aset.subjects[0:20]
sample


    

    
Out[9]:





['MGI:1349388',
 'MGI:3645524',
 'MGI:1916411',
 'MGI:2444552',
 'MGI:2444277',
 'MGI:106321',
 'MGI:2444891',
 'MGI:1933174',
 'MGI:2676815',
 'MGI:2152450',
 'MGI:1349400',
 'MGI:88460',
 'MGI:2142075',
 'MGI:2654437',
 'MGI:1342248',
 'MGI:2179723',
 'MGI:2686534',
 'MGI:1918361',
 'MGI:2449771',
 'MGI:1202388']

In [10]:

    

for g in sample:
    print('{} {}'.format(g,aset.label(g)))
    for a in aset.annotations(g):
        print('  {} {}'.format(a,ont.label(a)))
        for mn in m[a]:
            print('  --> {} {}'.format(mn,ont.label(mn)))


    

    




MGI:1349388 Cops7b
  GO:0000338 protein deneddylation
  --> GO:0006464 cellular protein modification process
  GO:0008180 COP9 signalosome
  --> GO:0043234 protein complex
  --> GO:0005634 nucleus
  GO:0005737 cytoplasm
  --> GO:0005737 cytoplasm
  GO:0005634 nucleus
  --> GO:0005634 nucleus
  GO:0003674 molecular_function
  --> GO:0003674 molecular_function
  GO:0005654 nucleoplasm
  --> GO:0005654 nucleoplasm
MGI:3645524 Vmn1r224
  GO:0003674 molecular_function
  --> GO:0003674 molecular_function
  GO:0007606 sensory perception of chemical stimulus
  --> GO:0050877 neurological system process
  GO:0005575 cellular_component
  --> GO:0005575 cellular_component
MGI:1916411 Manbal
  GO:0003674 molecular_function
  --> GO:0003674 molecular_function
  GO:0016020 membrane
  --> GO:0005575 cellular_component
  GO:0016021 integral component of membrane
  --> GO:0005575 cellular_component
  GO:0005575 cellular_component
  --> GO:0005575 cellular_component
  GO:0008150 biological_process
  --> GO:0008150 biological_process
MGI:2444552 Actbl2
  GO:0070062 extracellular exosome
  --> GO:0043226 organelle
  --> GO:0005615 extracellular space
  GO:0005737 cytoplasm
  --> GO:0005737 cytoplasm
  GO:0003674 molecular_function
  --> GO:0003674 molecular_function
  GO:0005856 cytoskeleton
  --> GO:0005856 cytoskeleton
  GO:0005615 extracellular space
  --> GO:0005615 extracellular space
  GO:0000166 nucleotide binding
  --> GO:0003674 molecular_function
  GO:0005524 ATP binding
  --> GO:0043167 ion binding
  GO:0008150 biological_process
  --> GO:0008150 biological_process
MGI:2444277 Islr2
  GO:0005515 protein binding
  --> GO:0003674 molecular_function
  GO:0016021 integral component of membrane
  --> GO:0005575 cellular_component
  GO:0005886 plasma membrane
  --> GO:0005886 plasma membrane
  GO:0045773 positive regulation of axon extension
  --> GO:0048856 anatomical structure development
  --> GO:0030154 cell differentiation
  GO:0007275 multicellular organism development
  --> GO:0048856 anatomical structure development
  GO:0016020 membrane
  --> GO:0005575 cellular_component
  GO:0007399 nervous system development
  --> GO:0048856 anatomical structure development
  GO:0009986 cell surface
  --> GO:0005623 cell
MGI:106321 Dock9
  GO:0045296 cadherin binding
  --> GO:0003674 molecular_function
  GO:0005085 guanyl-nucleotide exchange factor activity
  --> GO:0003674 molecular_function
  --> GO:0008150 biological_process
  GO:0017048 Rho GTPase binding
  --> GO:0019899 enzyme binding
  GO:0005089 Rho guanyl-nucleotide exchange factor activity
  --> GO:0003674 molecular_function
  --> GO:0008150 biological_process
  GO:0007264 small GTPase mediated signal transduction
  --> GO:0007165 signal transduction
  GO:0043547 positive regulation of GTPase activity
  --> GO:0008150 biological_process
  GO:0016020 membrane
  --> GO:0005575 cellular_component
MGI:2444891 Abra
  GO:0015031 protein transport
  --> GO:0006810 transport
  GO:0030016 myofibril
  --> GO:0043226 organelle
  --> GO:0005737 cytoplasm
  GO:0015629 actin cytoskeleton
  --> GO:0005856 cytoskeleton
  GO:0035025 positive regulation of Rho protein signal transduction
  --> GO:0008150 biological_process
  GO:0006810 transport
  --> GO:0006810 transport
  GO:0005737 cytoplasm
  --> GO:0005737 cytoplasm
  GO:0003779 actin binding
  --> GO:0008092 cytoskeletal protein binding
  GO:0000060 protein import into nucleus, translocation
  --> GO:0006913 nucleocytoplasmic transport
  GO:0030017 sarcomere
  --> GO:0043226 organelle
  --> GO:0005737 cytoplasm
  GO:0005856 cytoskeleton
  --> GO:0005856 cytoskeleton
  GO:0051091 positive regulation of sequence-specific DNA binding transcription factor activity
  --> GO:0008150 biological_process
  GO:0006355 regulation of transcription, DNA-templated
  --> GO:0008150 biological_process
  GO:0005886 plasma membrane
  --> GO:0005886 plasma membrane
  GO:0006351 transcription, DNA-templated
  --> GO:0009058 biosynthetic process
  --> GO:0034641 cellular nitrogen compound metabolic process
  GO:0045944 positive regulation of transcription from RNA polymerase II promoter
  --> GO:0008150 biological_process
  GO:0045893 positive regulation of transcription, DNA-templated
  --> GO:0008150 biological_process
MGI:1933174 Bri3
  GO:0016020 membrane
  --> GO:0005575 cellular_component
  GO:0016021 integral component of membrane
  --> GO:0005575 cellular_component
  GO:0042802 identical protein binding
  --> GO:0003674 molecular_function
MGI:2676815 Mir129-1
  GO:0045202 synapse
  --> GO:0005575 cellular_component
  GO:0060291 long-term synaptic potentiation
  --> GO:0008150 biological_process
  GO:0035195 gene silencing by miRNA
  --> GO:0008150 biological_process
MGI:2152450 Usp3
  GO:0006508 proteolysis
  --> GO:0008150 biological_process
  GO:0016578 histone deubiquitination
  --> GO:0051276 chromosome organization
  --> GO:0006464 cellular protein modification process
  GO:0006511 ubiquitin-dependent protein catabolic process
  --> GO:0009056 catabolic process
  GO:0000278 mitotic cell cycle
  --> GO:0000278 mitotic cell cycle
  GO:0007049 cell cycle
  --> GO:0007049 cell cycle
  GO:0031647 regulation of protein stability
  --> GO:0008150 biological_process
  GO:0008234 cysteine-type peptidase activity
  --> GO:0008233 peptidase activity
  GO:0008270 zinc ion binding
  --> GO:0043167 ion binding
  GO:0042393 histone binding
  --> GO:0042393 histone binding
  GO:0005634 nucleus
  --> GO:0005634 nucleus
  GO:0006281 DNA repair
  --> GO:0006259 DNA metabolic process
  --> GO:0006950 response to stress
  GO:0070938 contractile ring
  --> GO:0005623 cell
  GO:0016787 hydrolase activity
  --> GO:0003674 molecular_function
  GO:0016569 covalent chromatin modification
  --> GO:0051276 chromosome organization
  GO:0008233 peptidase activity
  --> GO:0008233 peptidase activity
  GO:0004843 thiol-dependent ubiquitin-specific protease activity
  --> GO:0008233 peptidase activity
  GO:0000790 nuclear chromatin
  --> GO:0000228 nuclear chromosome
  GO:0016579 protein deubiquitination
  --> GO:0006464 cellular protein modification process
  GO:0006974 cellular response to DNA damage stimulus
  --> GO:0006950 response to stress
  GO:0000122 negative regulation of transcription from RNA polymerase II promoter
  --> GO:0008150 biological_process
  GO:0001046 core promoter sequence-specific DNA binding
  --> GO:0003677 DNA binding
  GO:0006355 regulation of transcription, DNA-templated
  --> GO:0008150 biological_process
  GO:0005654 nucleoplasm
  --> GO:0005654 nucleoplasm
  GO:0046872 metal ion binding
  --> GO:0043167 ion binding
  GO:0003682 chromatin binding
  --> GO:0003674 molecular_function
  GO:0036459 thiol-dependent ubiquitinyl hydrolase activity
  --> GO:0008233 peptidase activity
MGI:1349400 Cops7a
  GO:0000338 protein deneddylation
  --> GO:0006464 cellular protein modification process
  GO:0008180 COP9 signalosome
  --> GO:0043234 protein complex
  --> GO:0005634 nucleus
  GO:0005829 cytosol
  --> GO:0005829 cytosol
  GO:0005737 cytoplasm
  --> GO:0005737 cytoplasm
  GO:0005634 nucleus
  --> GO:0005634 nucleus
  GO:0003674 molecular_function
  --> GO:0003674 molecular_function
  GO:0005654 nucleoplasm
  --> GO:0005654 nucleoplasm
MGI:88460 Col6a2
  GO:0031012 extracellular matrix
  --> GO:0005576 extracellular region
MGI:2142075 Nars2
  GO:0004812 aminoacyl-tRNA ligase activity
  --> GO:0016874 ligase activity
  GO:0016874 ligase activity
  --> GO:0016874 ligase activity
  GO:0006418 tRNA aminoacylation for protein translation
  --> GO:0006412 translation
  --> GO:0006520 cellular amino acid metabolic process
  --> GO:0006399 tRNA metabolic process
  GO:0005737 cytoplasm
  --> GO:0005737 cytoplasm
  GO:0005829 cytosol
  --> GO:0005829 cytosol
  GO:0006421 asparaginyl-tRNA aminoacylation
  --> GO:0006412 translation
  --> GO:0006520 cellular amino acid metabolic process
  --> GO:0006399 tRNA metabolic process
  GO:0006412 translation
  --> GO:0006412 translation
  GO:0000166 nucleotide binding
  --> GO:0003674 molecular_function
  GO:0005654 nucleoplasm
  --> GO:0005654 nucleoplasm
  GO:0004816 asparagine-tRNA ligase activity
  --> GO:0016874 ligase activity
  GO:0005524 ATP binding
  --> GO:0043167 ion binding
  GO:0003676 nucleic acid binding
  --> GO:0003674 molecular_function
  GO:0005739 mitochondrion
  --> GO:0005739 mitochondrion
MGI:2654437 Asb16
  GO:0000151 ubiquitin ligase complex
  --> GO:0005622 intracellular
  GO:0005737 cytoplasm
  --> GO:0005737 cytoplasm
  GO:0005634 nucleus
  --> GO:0005634 nucleus
  GO:0004842 ubiquitin-protein transferase activity
  --> GO:0003674 molecular_function
  --> GO:0006464 cellular protein modification process
  GO:0031625 ubiquitin protein ligase binding
  --> GO:0019899 enzyme binding
  GO:0035556 intracellular signal transduction
  --> GO:0007165 signal transduction
  GO:0008150 biological_process
  --> GO:0008150 biological_process
MGI:1342248 Slc25a17
  GO:0015908 fatty acid transport
  --> GO:0006810 transport
  GO:0055085 transmembrane transport
  --> GO:0055085 transmembrane transport
  GO:0015230 FAD transmembrane transporter activity
  --> GO:0022857 transmembrane transporter activity
  GO:0005779 integral component of peroxisomal membrane
  --> GO:0005777 peroxisome
  GO:0016020 membrane
  --> GO:0005575 cellular_component
  GO:0006810 transport
  --> GO:0006810 transport
  GO:0006635 fatty acid beta-oxidation
  --> GO:0044281 small molecule metabolic process
  --> GO:0006629 lipid metabolic process
  --> GO:0009056 catabolic process
  GO:0098655 cation transmembrane transport
  --> GO:0055085 transmembrane transport
  GO:0005737 cytoplasm
  --> GO:0005737 cytoplasm
  GO:0016021 integral component of membrane
  --> GO:0005575 cellular_component
  GO:0080121 AMP transport
  --> GO:0006810 transport
  GO:0005743 mitochondrial inner membrane
  --> GO:0005739 mitochondrion
  GO:0005739 mitochondrion
  --> GO:0005739 mitochondrion
  GO:0080122 AMP transmembrane transporter activity
  --> GO:0022857 transmembrane transporter activity
  GO:0015867 ATP transport
  --> GO:0006810 transport
  GO:0098656 anion transmembrane transport
  --> GO:0055085 transmembrane transport
  GO:0051087 chaperone binding
  --> GO:0003674 molecular_function
  GO:0015858 nucleoside transport
  --> GO:0006810 transport
  GO:0015228 coenzyme A transmembrane transporter activity
  --> GO:0022857 transmembrane transporter activity
  GO:0005778 peroxisomal membrane
  --> GO:0005777 peroxisome
  GO:0051724 NAD transporter activity
  --> GO:0003674 molecular_function
  --> GO:0006810 transport
  GO:0006839 mitochondrial transport
  --> GO:0006810 transport
  GO:0005347 ATP transmembrane transporter activity
  --> GO:0022857 transmembrane transporter activity
  GO:0015217 ADP transmembrane transporter activity
  --> GO:0022857 transmembrane transporter activity
  GO:0044610 FMN transmembrane transporter activity
  --> GO:0022857 transmembrane transporter activity
  GO:0005777 peroxisome
  --> GO:0005777 peroxisome
  GO:1901679 nucleotide transmembrane transport
  --> GO:0055085 transmembrane transport
MGI:2179723 Casc3
  GO:0051028 mRNA transport
  --> GO:0006810 transport
  GO:0031965 nuclear membrane
  --> GO:0005635 nuclear envelope
  GO:0030529 intracellular ribonucleoprotein complex
  --> GO:0005622 intracellular
  GO:0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay
  --> GO:0034655 nucleobase-containing compound catabolic process
  GO:0031625 ubiquitin protein ligase binding
  --> GO:0019899 enzyme binding
  GO:0006810 transport
  --> GO:0006810 transport
  GO:0019899 enzyme binding
  --> GO:0019899 enzyme binding
  GO:0005737 cytoplasm
  --> GO:0005737 cytoplasm
  GO:0008298 intracellular mRNA localization
  --> GO:0008150 biological_process
  GO:0005634 nucleus
  --> GO:0005634 nucleus
  GO:0006417 regulation of translation
  --> GO:0008150 biological_process
  GO:0006397 mRNA processing
  --> GO:0006397 mRNA processing
  GO:0042802 identical protein binding
  --> GO:0003674 molecular_function
  GO:0035145 exon-exon junction complex
  --> GO:0043234 protein complex
  --> GO:0005634 nucleus
  GO:0003723 RNA binding
  --> GO:0003723 RNA binding
  GO:0008380 RNA splicing
  --> GO:0034641 cellular nitrogen compound metabolic process
  GO:0005515 protein binding
  --> GO:0003674 molecular_function
MGI:2686534 A630073D07Rik
  GO:0003674 molecular_function
  --> GO:0003674 molecular_function
  GO:0005575 cellular_component
  --> GO:0005575 cellular_component
  GO:0008150 biological_process
  --> GO:0008150 biological_process
MGI:1918361 Gpr39
  GO:0030641 regulation of cellular pH
  --> GO:0042592 homeostatic process
  GO:0008343 adult feeding behavior
  --> GO:0008150 biological_process
  GO:0042632 cholesterol homeostasis
  --> GO:0042592 homeostatic process
  GO:0016020 membrane
  --> GO:0005575 cellular_component
  GO:0000187 activation of MAPK activity
  --> GO:0008150 biological_process
  GO:0051281 positive regulation of release of sequestered calcium ion into cytosol
  --> GO:0042592 homeostatic process
  GO:0005575 cellular_component
  --> GO:0005575 cellular_component
  GO:0007186 G-protein coupled receptor signaling pathway
  --> GO:0007165 signal transduction
  GO:0042391 regulation of membrane potential
  --> GO:0008150 biological_process
  GO:0016021 integral component of membrane
  --> GO:0005575 cellular_component
  GO:0019216 regulation of lipid metabolic process
  --> GO:0008150 biological_process
  GO:0004871 signal transducer activity
  --> GO:0004871 signal transducer activity
  GO:0007165 signal transduction
  --> GO:0007165 signal transduction
  GO:0004930 G-protein coupled receptor activity
  --> GO:0004871 signal transducer activity
  GO:0060455 negative regulation of gastric acid secretion
  --> GO:0008150 biological_process
  GO:0071294 cellular response to zinc ion
  --> GO:0008150 biological_process
  GO:0035774 positive regulation of insulin secretion involved in cellular response to glucose stimulus
  --> GO:0008150 biological_process
  GO:0035483 gastric emptying
  --> GO:0008150 biological_process
  GO:0042593 glucose homeostasis
  --> GO:0042592 homeostatic process
  GO:0005886 plasma membrane
  --> GO:0005886 plasma membrane
  GO:0032024 positive regulation of insulin secretion
  --> GO:0008150 biological_process
  GO:0002024 diet induced thermogenesis
  --> GO:0008150 biological_process
  GO:0046872 metal ion binding
  --> GO:0043167 ion binding
MGI:2449771 Cyp2r1
  GO:0004497 monooxygenase activity
  --> GO:0016491 oxidoreductase activity
  GO:0016705 oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen
  --> GO:0016491 oxidoreductase activity
  GO:0016491 oxidoreductase activity
  --> GO:0016491 oxidoreductase activity
  GO:0020037 heme binding
  --> GO:0003674 molecular_function
  GO:0043231 intracellular membrane-bounded organelle
  --> GO:0043226 organelle
  --> GO:0005622 intracellular
  GO:0005506 iron ion binding
  --> GO:0043167 ion binding
  GO:0030343 vitamin D3 25-hydroxylase activity
  --> GO:0044281 small molecule metabolic process
  --> GO:0009058 biosynthetic process
  --> GO:0016491 oxidoreductase activity
  --> GO:0006629 lipid metabolic process
  GO:0042359 vitamin D metabolic process
  --> GO:0044281 small molecule metabolic process
  --> GO:0006629 lipid metabolic process
  GO:0008395 steroid hydroxylase activity
  --> GO:0016491 oxidoreductase activity
  GO:0005783 endoplasmic reticulum
  --> GO:0005783 endoplasmic reticulum
  GO:0055114 oxidation-reduction process
  --> GO:0008150 biological_process
  GO:0016020 membrane
  --> GO:0005575 cellular_component
  GO:0046872 metal ion binding
  --> GO:0043167 ion binding
MGI:1202388 Gas7
  GO:0030182 neuron differentiation
  --> GO:0048856 anatomical structure development
  --> GO:0030154 cell differentiation
  GO:0008360 regulation of cell shape
  --> GO:0008150 biological_process
  GO:0030154 cell differentiation
  --> GO:0030154 cell differentiation
  GO:0005737 cytoplasm
  --> GO:0005737 cytoplasm
  GO:0051017 actin filament bundle assembly
  --> GO:0022607 cellular component assembly
  --> GO:0007010 cytoskeleton organization
  GO:0048812 neuron projection morphogenesis
  --> GO:0030154 cell differentiation
  --> GO:0000902 cell morphogenesis
  GO:0001726 ruffle
  --> GO:0005623 cell
  GO:0007275 multicellular organism development
  --> GO:0048856 anatomical structure development
  GO:0030041 actin filament polymerization
  --> GO:0006461 protein complex assembly
  --> GO:0007010 cytoskeleton organization
  GO:0005884 actin filament
  --> GO:0005856 cytoskeleton
  GO:0007399 nervous system development
  --> GO:0048856 anatomical structure development
  GO:0051015 actin filament binding
  --> GO:0008092 cytoskeletal protein binding

In [11]:

    

t='GO:0006681'
m[t]


    

    
Out[11]:





['GO:0006629', 'GO:0034641']

In [12]:

    

subont=ont.subontology(relations=relations)


    

In [13]:

    

subont.ancestors('GO:0034641')


    

    
Out[13]:





{'GO:0006807', 'GO:0008150', 'GO:0008152', 'GO:0009987', 'GO:0044237'}

In [14]:

    

subont.filter_redundant(m[t])


    

    
Out[14]:





{'GO:0006629', 'GO:0034641'}

In [ ]: