biomappings
latest
Getting Started
Reference
Command Line Interface
Adding Predictions
Deploying a Custom Biomappings Instance
biomappings
Index
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Index
Symbols
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A
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B
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C
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F
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G
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H
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I
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L
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M
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P
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R
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S
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T
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U
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W
Symbols
--negatives-path
biomappings-web command line option
--password
biomappings-ndex command line option
--path
biomappings-curate command line option
--positives-path
biomappings-web command line option
--predictions-path
biomappings-web command line option
--standardize
biomappings-lint command line option
--unsure-path
biomappings-web command line option
--username
biomappings-ndex command line option
--version
biomappings command line option
A
append_false_mappings() (in module biomappings.resources)
append_gilda_predictions() (in module biomappings.gilda_utils)
append_prediction_tuples() (in module biomappings.resources)
append_predictions() (in module biomappings.resources)
append_true_mapping_tuples() (in module biomappings.resources)
append_true_mappings() (in module biomappings.resources)
append_unsure_mappings() (in module biomappings.resources)
as_dict() (MappingTuple method)
(PredictionTuple method)
assert_canonical_identifier() (IntegrityTestCase method)
assert_no_internal_redundancies() (IntegrityTestCase method)
B
biomappings
module
biomappings command line option
--version
biomappings-curate command line option
--path
biomappings-lint command line option
--standardize
biomappings-ndex command line option
--password
--username
biomappings-prune command line option
PREFIXES
biomappings-web command line option
--negatives-path
--positives-path
--predictions-path
--unsure-path
biomappings.gilda_utils
module
biomappings.resources
module
biomappings.testing
module
biomappings.utils
module
C
check_valid_prefix_id() (in module biomappings.utils)
confidence (PredictionTuple attribute)
F
filter_custom() (in module biomappings.gilda_utils)
filter_existing_xrefs() (in module biomappings.gilda_utils)
filter_predictions() (in module biomappings.resources)
from_dict() (MappingTuple class method)
(PredictionTuple class method)
from_semra() (PredictionTuple class method)
G
get_canonical_tuple() (in module biomappings.utils)
get_curated_filter() (in module biomappings.resources)
get_curie() (in module biomappings.utils)
get_git_hash() (in module biomappings.utils)
get_script_url() (in module biomappings.utils)
H
has_mapping() (in module biomappings.gilda_utils)
I
IntegrityTestCase (class in biomappings.testing)
InvalidIdentifier
InvalidIdentifierPattern
InvalidNormIdentifier
iter_prediction_tuples() (in module biomappings.gilda_utils)
L
load_curators() (in module biomappings.resources)
load_false_mappings() (in module biomappings.resources)
load_mappings() (in module biomappings.resources)
load_mappings_subset() (in module biomappings.resources)
load_predictions() (in module biomappings.resources)
load_unsure() (in module biomappings.resources)
M
MappingTuple (class in biomappings.resources)
module
biomappings
biomappings.gilda_utils
biomappings.resources
biomappings.testing
biomappings.utils
P
PathIntegrityTestCase (class in biomappings.testing)
prediction_confidence (MappingTuple attribute)
prediction_source (MappingTuple attribute)
prediction_tuples_from_semra() (in module biomappings.resources)
prediction_type (MappingTuple attribute)
PredictionTuple (class in biomappings.resources)
PREFIXES
biomappings-prune command line option
R
relation (MappingTuple attribute)
(PredictionTuple attribute)
remove_mappings() (in module biomappings.resources)
S
setUpClass() (PathIntegrityTestCase class method)
source (MappingTuple attribute)
(PredictionTuple attribute)
source_curie (MappingTuple attribute)
(PredictionTuple attribute)
source_id (MappingTuple attribute)
(PredictionTuple attribute)
source_name (MappingTuple attribute)
(PredictionTuple attribute)
source_prefix (MappingTuple attribute)
(PredictionTuple attribute)
T
target_curie (MappingTuple attribute)
(PredictionTuple attribute)
target_identifier (MappingTuple attribute)
(PredictionTuple attribute)
target_name (MappingTuple attribute)
(PredictionTuple attribute)
target_prefix (MappingTuple attribute)
(PredictionTuple attribute)
test_canonical_prefixes() (IntegrityTestCase method)
test_contributors() (IntegrityTestCase method)
test_cross_redundancy() (IntegrityTestCase method)
test_curations_sorted() (IntegrityTestCase method)
test_false_mappings_sorted() (IntegrityTestCase method)
test_normalized_identifiers() (IntegrityTestCase method)
test_prediction_types() (IntegrityTestCase method)
test_predictions_sorted() (IntegrityTestCase method)
test_relations() (IntegrityTestCase method)
test_unsure_sorted() (IntegrityTestCase method)
type (MappingTuple attribute)
(PredictionTuple attribute)
U
UnregisteredPrefix
UnstandardizedPrefix
W
write_false_mappings() (in module biomappings.resources)
write_predictions() (in module biomappings.resources)
write_true_mappings() (in module biomappings.resources)
write_unsure_mappings() (in module biomappings.resources)
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