nt.gml

graph [
  node [
    id 0
    label "0"
    pathway [u'Hemostasis']
    domain [u'pfam05109']
    compartment [u'GO:0001931', u' GO:0005604', u' GO:0005615', u' GO:0005886', u' GO:0005887']
    name "SPN"
    disease [u'MYL003', u'MNT214', u'WSK001', u'MRG003', u'MYL040', u'BCL009']
  ]
  node [
    id 1
    label "1"
    pathway [u'Cell Cycle', u'Disease', u'Hemostasis', u'Immune System', u'Metabolism', u'Transmembrane transport of small molecules', u'Signal Transduction']
    domain [u'smart00220', u'cd05580']
    compartment [u'GO:0005634', u' GO:0005737', u' GO:0005739', u' GO:0005813', u' GO:0005829']
    name "PRKACA"
    disease [u'PRM051', u'CSH005', u'HPT012']
  ]
  node [
    id 2
    label "2"
    pathway []
    domain [u'pfam08788', u'pfam07531', u'pfam01753']
    compartment [u'GO:0005634', u' GO:0016363']
    name "RUNX1T1"
    disease [u'ACT194', u'RFR010', u'LPP002', u'MYL006', u'ACT019', u'LKM002']
  ]
  node [
    id 3
    label "3"
    pathway []
    domain [u'cd00076']
    compartment [u'GO:0000786', u' GO:0005576', u' GO:0005634', u' GO:0005654', u' GO:0005730']
    name "HIST4H4"
    disease [u'CLR023']
  ]
  node [
    id 4
    label "4"
    pathway [u'Disease', u'Cellular responses to stress', u'Signal Transduction', u'Cell Cycle']
    domain [u'smart00428', u'PTZ00018']
    compartment [u'GO:0000786', u' GO:0005654', u' GO:0070062']
    name "HIST3H3"
    disease []
  ]
  node [
    id 5
    label "5"
    pathway [u'Signal Transduction', u'Disease', u'Chromatin organization']
    domain [u'cl17011']
    compartment [u'GO:0000118', u' GO:0000228', u' GO:0005634', u' GO:0005737', u' GO:0005829']
    name "HDAC8"
    disease [u'CLR023', u'CRN209', u'TRN020', u'WLS004', u'HDC004', u'WLS003', u'CRN015', u'ARC004', u'CRN139', u'OBS005']
  ]
  node [
    id 6
    label "6"
    pathway [u'Metabolism', u'Disease']
    domain [u'cd03793', u'pfam05693']
    compartment [u'GO:0005737', u' GO:0005829', u' GO:0016234']
    name "GYS1"
    disease [u'INS005', u'GLC003', u'CMR002']
  ]
  edge [
    source 0
    target 2
    color "green"
    features [0.0, 0.0, 0.0, 1.96]
    weight 1.96
  ]
  edge [
    source 1
    target 5
    color "green"
    features [0.25, 0.0, 0.0, 9.26]
    weight 9.26
  ]
  edge [
    source 1
    target 6
    color "green"
    features [0.2857142857142857, 0.0, 0.0, 6.44]
    weight 6.44
  ]
  edge [
    source 2
    target 5
    color "green"
    features [0.0, 0.0, 0.0, 6.4]
    weight 6.4
  ]
  edge [
    source 3
    target 4
    color "green"
    features [0.0, 0.0, 0.0, 6.53]
    weight 6.53
  ]
  edge [
    source 4
    target 5
    color "green"
    features [0.4, 0.0, 0.0, 8.58]
    weight 8.58
  ]
]

nt.gpickle

test.py

import networkx as nx

print "Networkx v{}\n".format(nx.__version__)

G = nx.read_gpickle('nt.gpickle')
nx.write_gml(G, 'nt.gml')
G = nx.read_gml('nt.gml')