Reference
biomappings.gilda_utils Module
Utilities for generating predictions with pyobo/gilda.
Functions
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Add gilda predictions to the Biomappings predictions.tsv file. |
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Iterate over prediction tuples for a given prefix. |
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Filter out custom mappings. |
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Filter predictions that match xrefs already loaded through PyOBO. |
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Check if there's already a mapping available for this entity in a target namespace. |
biomappings.utils Module
Utilities.
Functions
Get the git hash. |
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Get the source path for this script. |
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Get the canonical tuple from a mapping entry. |
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Check the prefix/identifier pair is valid. |
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Get a normalized curie from a pre-parsed prefix/identifier pair. |
Classes
Raised for an invalid prefix. |
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Raised for an unstandardized prefix. |
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Raised for an invalid identifier. |
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Raised for an invalid normalized identifier. |
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Raised for an identifier that doesn't match the pattern. |
Class Inheritance Diagram
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Validation tests for biomappings
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Classes
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Data integrity tests. |
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A test case that can be configured with paths. |
Class Inheritance Diagram
digraph inheritance91366e06bd { bgcolor=transparent; rankdir=LR; size="8.0, 12.0"; "IntegrityTestCase" [URL="api/biomappings.testing.IntegrityTestCase.html#biomappings.testing.IntegrityTestCase",fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",target="_top",tooltip="Data integrity tests."]; "TestCase" -> "IntegrityTestCase" [arrowsize=0.5,style="setlinewidth(0.5)"]; "PathIntegrityTestCase" [URL="api/biomappings.testing.PathIntegrityTestCase.html#biomappings.testing.PathIntegrityTestCase",fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",target="_top",tooltip="A test case that can be configured with paths."]; "IntegrityTestCase" -> "PathIntegrityTestCase" [arrowsize=0.5,style="setlinewidth(0.5)"]; "TestCase" [fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",tooltip="A class whose instances are single test cases."]; }biomappings.resources Package
Biomappings resources.
Functions
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Load the mappings table. |
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Get a dictionary of 1-1 mappings from the source prefix to the target prefix. |
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Append new lines to the mappings table. |
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Append new lines to the mappings table. |
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Write mappigns to the true mappings file. |
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Load the false mappings table. |
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Append new lines to the false mappings table. |
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Write mappings to the false mappings file. |
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Load the unsure table. |
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Append new lines to the "unsure" mappings table. |
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Write mappings to the unsure mappings file. |
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Load the predictions table. |
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Append new lines to the predictions table. |
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Append new lines to the predictions table that come as canonical tuples. |
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Write new content to the predictions table. |
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Remove the first set of mappings from the second. |
Load the curators table. |
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Filter all the predictions by removing what's in the custom filter then re-write. |
Get a filter over all curated mappings. |
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Get prediction tuples from SeMRA mappings. |
Classes
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A named tuple class for mappings. |
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A named tuple class for predictions. |