Public-Health-Bioinformatics / LexMapr
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Classification (#93)

* A temporary owl file for terms available for curation.

This is a temporary owl file for terms (currently not available in ontologies) available for further considearion and curation in the ontologies which is used to enable classification in the interim.

* Revamping of classification component based on newer IFSAC+ classification schema.

Includes updated predefined resources.
Addition of some new predefined resources.
Functionality to deal with multi class label values in bucket labels.
Functionality to customize ordering of class labels in the final class assignment.
Updated and newer rules for post-classification refinement of  IFSAC labels.
Excluded "hasBroadSynonym" from the mapping considerations
Functionality to convert the matched component to standard Upper case Ontology Ids
Four new modules for assignment of confidence level in mapping (for future use)

* Update lexmapr/predefined_resources/ifsac-refinement.csv

Co-authored-by: ivansg44 <ivan.gill@bccdc.ca>

* Update lexmapr/pipeline.py

Co-authored-by: ivansg44 <ivan.gill@bccdc.ca>

* Update lexmapr/pipeline.py

Co-authored-by: ivansg44 <ivan.gill@bccdc.ca>

* Update lexmapr/pipeline.py

Co-authored-by: ivansg44 <ivan.gill@bccdc.ca>

* Update lexmapr/pipeline_classification.py

Co-authored-by: ivansg44 <ivan.gill@bccdc.ca>

* Update lexmapr/pipeline_classification.py

Co-authored-by: ivansg44 <ivan.gill@bccdc.ca>

* Update lexmapr/pipeline_classification.py

Co-authored-by: ivansg44 <ivan.gill@bccdc.ca>

* Update lexmapr/pipeline_classification.py

Co-authored-by: ivansg44 <ivan.gill@bccdc.ca>

* Update lexmapr/pipeline_classification.py

Co-authored-by: ivansg44 <ivan.gill@bccdc.ca>

* Update lexmapr/pipeline_helpers.py

Co-authored-by: ivansg44 <ivan.gill@bccdc.ca>

* Update lexmapr/pipeline_helpers.py

Co-authored-by: ivansg44 <ivan.gill@bccdc.ca>

* Update lexmapr/pipeline.py

Co-authored-by: ivansg44... (continued)

1032 of 1285 relevant lines covered (80.31%)

1.61 hits per line

Relevant lines Covered
1285 RELEVANT LINES 1032 COVERED LINES
1.61 HITS PER LINE
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687 v0.7.0 Classification (#93) * A temporary owl file for terms available for curation. This is a temporary owl file for terms (currently not available in ontologies) available for further considearion and curation in the ontologies which is used to ena... push web-flow travis-ci pending completion  
686 master Classification (#93) * A temporary owl file for terms available for curation. This is a temporary owl file for terms (currently not available in ontologies) available for further considearion and curation in the ontologies which is used to ena... push web-flow travis-ci pending completion  
685 classification Merge e284e2fbe into 909306316 Pull #93 web-flow travis-ci pending completion  
684 classification Update lexmapr/pipeline_helpers.py Co-authored-by: ivansg44 <ivan.gill@bccdc.ca> push web-flow travis-ci pending completion  
674 classification Update lexmapr/pipeline_helpers.py Co-authored-by: ivansg44 <ivan.gill@bccdc.ca> push web-flow travis-ci pending completion  
669 classification Merge 6b8c38e60 into 909306316 Pull #93 web-flow travis-ci pending completion  
668 classification Update lexmapr/pipeline_helpers.py Co-authored-by: ivansg44 <ivan.gill@bccdc.ca> push web-flow travis-ci pending completion  
661 classification Merge 85bf01f93 into 909306316 Pull #93 web-flow travis-ci pending completion  
660 classification Update lexmapr/pipeline_classification.py Co-authored-by: ivansg44 <ivan.gill@bccdc.ca> push web-flow travis-ci pending completion  
654 classification Update tests and classification table push ivansg44 travis-ci pending completion  
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