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Project: pybel
(GitHub Link)
pybel-master
.codeclimate.yml
src
pybel
resources
resources.py
constants.py
__init__.py
update_resources.py
exceptions.py
config.py
examples
ampk_example.py
egf_example.py
various_example.py
braf_example.py
homology_example.py
tloc_example.py
sialic_acid_example.py
__init__.py
statin_example.py
vegf_example.py
cli.py
tokens.py
version.py
canonicalize.py
dsl
edges.py
constants.py
node_classes.py
exc.py
__init__.py
namespaces.py
constants.py
struct
graph.py
query
selection.py
seeding.py
query.py
constants.py
exc.py
__init__.py
grouping
provenance.py
__init__.py
annotations.py
getters.py
filters
edge_filters.py
node_predicate_builders.py
edge_predicate_builders.py
edge_predicates.py
__init__.py
utils.py
node_filters.py
node_predicates
relations.py
misc.py
modifications.py
__init__.py
utils.py
types.py
activities.py
typing.py
mutation
induction
upstream.py
random_subgraph.py
citation.py
neighborhood.py
__init__.py
utils.py
paths.py
annotations.py
expansion
upstream.py
neighborhood.py
__init__.py
metadata.py
__init__.py
utils.py
inference
transfer.py
protein_rna_origins.py
__init__.py
induction_expansion.py
collapse
protein_rna_origins.py
collapse.py
__init__.py
deletion
protein_rna_origins.py
deletion.py
__init__.py
__init__.py
utils.py
pipeline
decorators.py
pipeline.py
exc.py
__init__.py
node_utils.py
summary
provenance.py
supersummary.py
node_summary.py
__init__.py
errors.py
edge_summary.py
operations.py
__main__.py
io
lines.py
jinja_utils.py
jgif.py
jupyter
templates
graph_template.html
pybel_vis.js
pybel_jupyter.js
inline.py
constants.py
__init__.py
visualization.py
hipathia.py
pynpa.py
graphdati.py
biodati_client.py
neo4j.py
fraunhofer_orientdb.py
bel_commons_client.py
extras.py
pykeen.py
sbel.py
triples
api.py
converters.py
__init__.py
aws.py
api.py
spia.py
exc.py
hetionet
cli.py
hetionet.py
constants.py
__main__.py
__init__.py
__init__.py
gpickle.py
utils.py
cx.py
nodelink.py
umbrella_nodelink.py
line_utils.py
graphml.py
indra.py
emmaa.py
__init__.py
utils.py
manager
citation_utils.py
make_json_serializable.py
database_io.py
lookup_manager.py
models.py
exc.py
__init__.py
utils.py
base_manager.py
cache_manager.py
query_manager.py
language.py
grounding.py
parser
parse_control.py
baseparser.py
parse_bel.py
constants.py
parse_concept.py
exc.py
__init__.py
utils.py
parse_metadata.py
modifiers
variant.py
fragment.py
fusion.py
location.py
protein_modification.py
constants.py
truncation.py
__init__.py
gene_substitution.py
protein_substitution.py
gene_modification.py
testing
resources
belns
chebi-names.belns
go-names.belns
test_ns_empty.belns
disease-ontology.belns
test_ns_1_updated.belns
test_ns_1.belns
test_ns_2.belns
hgnc-names.belns
mesh-names.belns
belanno
mesh-diseases.belanno
cell-line.belanno
test_an_1.belanno
species-taxonomy-id.belanno
confidence-1.0.0.belanno
bel
misordered.bel
obo.bel
test_bel.bel
isolated.bel
slushy.bel
thorough.bel
cases.py
generate.py
mock_manager.py
constants.py
mocks.py
__init__.py
utils.py
typing.py
.pre-commit-config.yaml
LICENSE
.readthedocs.yml
.flake8
.appveyor.yml
README.rst
.bumpversion.cfg
notebooks
README.rst
Using Gilda to Help Curate.ipynb
loading.ipynb
hipathia_demo
alzheimers
output
Interleukin signaling subgraph.sif
Gamma secretase subgraph.sif
NMDA receptor.att
Response DNA damage.att
Wnt signaling subgraph.sif
ADAM Metallopeptidase subgraph.sif
Gamma secretase subgraph.att
Free radical formation subgraph.att
MAPK-ERK subgraph.att
Immunoglobulin subgraph.att
mTOR signaling subgraph.sif
Epigenetic modification subgraph.sif
Regulation of actin cytoskeleton subgraph.att
Innate immune system subgraph.att
Amylin subgraph.att
Metabolism of steroid hormones subgraph.att
Amyloidogenic subgraph.att
Albumin subgraph.sif
Glutamatergic subgraph.att
CREB subgraph.sif
Phosphatidylinositol 3 subgraph.sif
G-protein-mediated signaling.sif
Immunoglobulin subgraph.sif
Binding and Uptake of Ligands by Scavenger Receptors.att
Binding and Uptake of Ligands by Scavenger Receptors.sif
ATP binding cassette transport subgraph.att
MAPK-ERK subgraph.sif
Mitochondrial translocation subgraph.att
Cell cycle subgraph.sif
RhoA subgraph.sif
Phosphatidylinositol 3 subgraph.att
Calcium-dependent signal transduction.att
Electron transport chain.sif
GABA subgraph.att
Hypoxia response subgraph.att
Bcl-2 subgraph.att
GABA subgraph.sif
Eicosanoids signaling subgraph.att
mTOR signaling subgraph.att
Calpastatin-calpain subgraph.sif
Estrogen subgraph.sif
Inflammatory response subgraph.sif
MAPK-JNK subgraph.sif
Matrix metalloproteinase subgraph.sif
Calcium-dependent signal transduction.sif
miRNA subgraph.att
Cholesterol metabolism subgraph.att
Glutathione reductase subgraph.sif
Glutathione reductase subgraph.att
Acetylcholine signaling subgraph.sif
Free radical formation subgraph.sif
Axonal guidance subgraph.sif
Axonal transport subgraph.sif
Cholesterol metabolism subgraph.sif
Interferon signaling subgraph.sif
Nuclear factor Kappa beta subgraph.att
GSK3 subgraph.sif
CREB subgraph.att
Prostaglandin subgraph.att
Nerve growth factor subgraph.sif
Insulin signal transduction.att
Innate immune system subgraph.sif
Complement system subgraph.sif
Peroxisome proliferator activated receptor subgraph.sif
Bcl-2 subgraph.sif
Calpastatin-calpain subgraph.att
Peroxisome proliferator activated receptor subgraph.att
NMDA receptor.sif
Endoplasmic reticulum-Golgi protein export.att
Gap junctions subgraph.sif
Synapse assembly subgraph.att
Dopaminergic subgraph.sif
Eicosanoids signaling subgraph.sif
Smad subgraph.sif
Beta-Catenin subgraph.att
Apoptosis signaling subgraph.sif
Albumin subgraph.att
Glucagon subgraph.sif
DYRK1A subgraph.sif
Chaperone subgraph.att
Hypoxia response subgraph.sif
Plasminogen activator subgraph.sif
Prostaglandin subgraph.sif
G-protein-mediated signaling.att
p53 stabilization subgraph.att
Gap junctions subgraph.att
Tau protein subgraph.sif
Leptin subgraph.sif
Cell adhesion subgraph.att
Disaccharide metabolism subgraph.att
Metabolism of steroid hormones subgraph.sif
Akt subgraph.att
Renin-angiotensin subgraph.att
Calsyntenin subgraph.sif
Retinoblastoma subgraph.att
Leptin subgraph.att
Notch signaling subgraph.att
Toll like receptor subgraph.att
Disaccharide metabolism subgraph.sif
Mitochondrial translocation subgraph.sif
Beta secretase subgraph.sif
Neuroprotection subgraph.sif
Vitamin subgraph.att
Retinoblastoma subgraph.sif
Chemokine signaling subgraph.sif
Cell cycle subgraph.att
Alpha 2 macroglobulin subgraph.att
Non-amyloidogenic subgraph.sif
Tumor necrosis factor subgraph.att
Smad subgraph.att
Calsyntenin subgraph.att
DYRK1A subgraph.att
Lipid peroxidation subgraph.att
Synaptic vesicle endocytosis subgraph.att
Vitamin subgraph.sif
Endothelin subgraph.sif
Beta-Catenin subgraph.sif
Reactive oxygen species subgraph.att
Interferon signaling subgraph.att
DNA synthesis.att
Alpha 2 macroglobulin subgraph.sif
Toll like receptor subgraph.sif
Vascular endothelial growth factor subgraph.att
Endosomal lysosomal subgraph.att
APOE subgraph.sif
Estrogen subgraph.att
Insulin signal transduction.sif
DKK1 subgraph.att
Epigenetic modification subgraph.att
T cells signaling.sif
Apoptosis signaling subgraph.att
T cells signaling.att
Nitric oxide subgraph.att
Syndecan subgraph.sif
XIAP subgraph.sif
CRH subgraph.sif
Response to oxidative stress.sif
Cyclin-CDK subgraph.sif
Serotonergic subgraph.att
CRH subgraph.att
Endosomal lysosomal subgraph.sif
Low density lipoprotein subgraph.sif
Cell adhesion subgraph.sif
Amyloidogenic subgraph.sif
Synapse assembly subgraph.sif
APOE subgraph.att
DKK1 subgraph.sif
Response to oxidative stress.att
p53 stabilization subgraph.sif
Ubiquitin degradation subgraph.att
Inflammatory response subgraph.att
miRNA subgraph.sif
Axonal guidance subgraph.att
Wnt signaling subgraph.att
Endoplasmic reticulum-Golgi protein export.sif
Chemokine signaling subgraph.att
Caspase subgraph.att
Amylin subgraph.sif
Endothelin subgraph.att
Nitric oxide subgraph.sif
Matrix metalloproteinase subgraph.att
Acetylcholine signaling subgraph.att
Axonal transport subgraph.att
Tau protein subgraph.att
Sphingolipid metabolic subgraph.att
XIAP subgraph.att
Neuroprotection subgraph.att
Reactive oxygen species subgraph.sif
Plasminogen activator subgraph.att
Glucagon subgraph.att
Caspase subgraph.sif
Dopaminergic subgraph.att
Complement system subgraph.att
Unfolded protein response subgraph.sif
Interleukin signaling subgraph.att
Synaptic vesicle endocytosis subgraph.sif
Non-amyloidogenic subgraph.att
TGF-Beta subgraph.att
GSK3 subgraph.att
Unfolded protein response subgraph.att
Renin-angiotensin subgraph.sif
Regulation of actin cytoskeleton subgraph.sif
Nuclear factor Kappa beta subgraph.sif
Low density lipoprotein subgraph.att
Vascular endothelial growth factor subgraph.sif
Cytokine signaling subgraph.att
Sphingolipid metabolic subgraph.sif
Synuclein subgraph.sif
Chaperone subgraph.sif
JAK-STAT signaling subgraph.sif
Syndecan subgraph.att
Glutamatergic subgraph.sif
Autophagy signaling subgraph.att
ADAM Metallopeptidase subgraph.att
Reelin signaling subgraph.att
Ubiquitin degradation subgraph.sif
Response DNA damage.sif
DNA synthesis.sif
TGF-Beta subgraph.sif
Cytokine signaling subgraph.sif
Nerve growth factor subgraph.att
Synuclein subgraph.att
JAK-STAT signaling subgraph.att
Autophagy signaling subgraph.sif
MAPK-JNK subgraph.att
Notch signaling subgraph.sif
Beta secretase subgraph.att
Tumor necrosis factor subgraph.sif
Lipid peroxidation subgraph.sif
Cyclin-CDK subgraph.att
Akt subgraph.sif
ATP binding cassette transport subgraph.sif
Electron transport chain.att
Serotonergic subgraph.sif
Reelin signaling subgraph.sif
RhoA subgraph.att
_convert_alzheimers.py
covid19
COVID-19 Knowledge Graph.att
_convert_covid19kg.py
COVID-19 Knowledge Graph.sif
cbn
output
mTor-2.0-Hs.att
NFE2L2 Signaling-2.0-Hs.att
Angiogenesis-2.0-Hs.att
Hox-2.0-Hs.att
Mast cell activation-2.0-Hs.sif
Wnt-2.0-Hs.sif
Senescence-2.0-Hs.sif
NK Signaling-2.0-Hs.sif
Mapk-2.0-Hs.sif
Hox-2.0-Hs.sif
Growth Factor-2.0-Hs.att
Wound Healing-2.0-Hs.sif
Xenobiotic Metabolism Response-2.0-Hs.sif
Apoptosis-2.0-Hs.sif
Mast cell activation-2.0-Hs.att
Cell Cycle-2.0-Hs.att
Endoplasmic Reticulum Stress-2.0-Hs.sif
Neutrophil Signaling-2.0-Hs.sif
Necroptosis-2.0-Hs.att
Th17 Signaling-2.0-Hs.att
Hypoxic Stress-2.0-Hs.att
Oxidative Stress-2.0-Hs.sif
Necroptosis-2.0-Hs.sif
Cytotoxic T-cell Signaling-2.0-Hs.sif
Oxidative Stress-2.0-Hs.att
Jak Stat-2.0-Hs.sif
Calcium-2.0-Hs.att
Autophagy-2.0-Hs.att
Hedgehog-2.0-Hs.att
Fibrosis-2.0-Hs.att
PGE2-2.0-Hs.att
Wound Healing-2.0-Hs.att
Xenobiotic Metabolism Response-2.0-Hs.att
ECM Degradation-2.0-Hs.att
Growth Factor-2.0-Hs.sif
Cytotoxic T-cell Signaling-2.0-Hs.att
Hypoxic Stress-2.0-Hs.sif
Epigenetics-2.0-Hs.sif
Calcium-2.0-Hs.sif
Notch-2.0-Hs.sif
Treg Signaling-2.0-Hs.att
NK Signaling-2.0-Hs.att
Treg Signaling-2.0-Hs.sif
Tissue Damage-2.0-Hs.att
Nuclear Receptors-2.0-Hs.sif
Th1-Th2 Signaling-2.0-Hs.sif
Response to DNA Damage-2.0-Hs.sif
Epigenetics-2.0-Hs.att
Response to DNA Damage-2.0-Hs.att
Th1-Th2 Signaling-2.0-Hs.att
Fibrosis-2.0-Hs.sif
Hedgehog-2.0-Hs.sif
Clock-2.0-Hs.att
Dendritic Cell Signaling-2.0-Hs.att
Immune Regulation of Tissue Repair-2.0-Hs.sif
B-cell Signaling-2.0-Hs.sif
Endoplasmic Reticulum Stress-2.0-Hs.att
Nuclear Receptors-2.0-Hs.att
Senescence-2.0-Hs.att
Th17 Signaling-2.0-Hs.sif
Megakaryocyte Differentiation-2.0-Hs.att
Epithelial Mucus Hypersecretion-2.0-Hs.sif
NFE2L2 Signaling-2.0-Hs.sif
Osmotic Stress-2.0-Hs.sif
Epithelial Mucus Hypersecretion-2.0-Hs.att
Macrophage Signaling-2.0-Hs.att
Macrophage Signaling-2.0-Hs.sif
Notch-2.0-Hs.att
Mapk-2.0-Hs.att
Neutrophil Signaling-2.0-Hs.att
Endothelial Innate Immune Activation-2.0-Hs.sif
Cell Interaction-2.0-Hs.sif
Autophagy-2.0-Hs.sif
B-cell Signaling-2.0-Hs.att
Immune Regulation of Tissue Repair-2.0-Hs.att
PGE2-2.0-Hs.sif
mTor-2.0-Hs.sif
Megakaryocyte Differentiation-2.0-Hs.sif
Apoptosis-2.0-Hs.att
Cell Cycle-2.0-Hs.sif
Angiogenesis-2.0-Hs.sif
Clock-2.0-Hs.sif
Dendritic Cell Signaling-2.0-Hs.sif
Tissue Damage-2.0-Hs.sif
Epithelial Innate Immune Activation-2.0-Hs.sif
Endothelial Innate Immune Activation-2.0-Hs.att
Osmotic Stress-2.0-Hs.att
ECM Degradation-2.0-Hs.sif
Wnt-2.0-Hs.att
Epithelial Innate Immune Activation-2.0-Hs.att
Jak Stat-2.0-Hs.att
Cell Interaction-2.0-Hs.att
_convert_cbn.py
hemekg
HemeKG.att
_convert_hemekg.py
HemeKG.sif
selventa
_convert_selventa.py
BEL Framework Small Corpus Document.att
BEL Framework Small Corpus Document.sif
setup.py
CHANGELOG.rst
AUTHORS.rst
setup.cfg
.travis.yml
CONTRIBUTING.rst
tests
test_utils.py
test_dsl.py
constant_helper.py
constants.py
test_struct
test_struct_graph.py
test_filters
test_node_predicate_builders.py
test_struct_filters.py
test_node_selection.py
test_edge_predicate_builders.py
test_edge_predicates.py
__init__.py
test_node_predicates.py
test_query
test_query.py
__init__.py
test_mocks.py
test_struct_pipeline.py
test_seeding.py
test_getters.py
__init__.py
test_struct_operations.py
test_transformations
test_random.py
test_metadata.py
test_expansion.py
test_collapse.py
test_deletions.py
__init__.py
test_induction.py
test_transfer.py
test_summary
test_errors.py
test_summary_nodes.py
test_struct_summary_edges.py
test_provenance.py
__init__.py
test_node_utils.py
test_grouping.py
test_io
test_import.py
test_umbrella_nodelink.py
test_spia.py
test_pynpa.py
test_triples.py
test_jgif.py
test_cx
test_import.py
cases.py
__init__.py
examples.py
__init__.py
test_hipathia
test_hipathia.py
test_1.att
__init__.py
hsa04370.att
hsa04370.sif
test_1.sif
test_export.py
test_hetionet.py
test_jupyter.py
test_cli.py
__init__.py
test_parse
test_parse_utils.py
test_parse_identifier.py
test_parse_bel_relations.py
test_parse_control.py
test_parse_metadata.py
test_parse_bel.py
__init__.py
test_parse_bel_variants.py
test_canonicalization.py
test_tokens.py
test_manager
test_manager_definitions.py
test_connection.py
test_manager_model.py
test_manager_graph.py
__init__.py
test_citation_utils.py
test_manager_drop.py
test_seeding.py
.codecov.yml
.gitignore
docs
Makefile
source
reference
database
models.rst
manager.rst
logging.rst
io.rst
constants.rst
mutations
induction.rst
deletion.rst
inference.rst
mutations.rst
expansion.rst
induction_expansion.rst
metadata.rst
collapse.rst
struct
operators.rst
examples.rst
grouping.rst
summary.rst
filters.rst
query.rst
datamodel.rst
pipeline.rst
parser.rst
dsl.rst
introduction
overview.rst
installation.rst
topics
cli.rst
cookbook.rst
index.rst
conf.py
meta
technology.rst
postmortem.rst
references.rst
MANIFEST.in
tox.ini