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New linkers #246

Merged
merged 7 commits into from
Jul 8, 2020
Merged

New linkers #246

merged 7 commits into from
Jul 8, 2020

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DeNeutoy
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@DeNeutoy DeNeutoy commented Jul 7, 2020

  • use jsonl files for new linkers, as they are easier to work with
  • add paths to new linkers: rxnorm, go, hpo and updated umls linker.

@DeNeutoy DeNeutoy requested a review from dakinggg July 7, 2020 23:54
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dakinggg approved these changes Jul 8, 2020
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LGTM

README.md Outdated
The linker simply performs a string overlap search on named entities,
comparing them with a knowledge base of 2.7 million concepts using an approximate nearest neighbours search.
The `EntityLinker` is a SpaCy component which performs linking to a knowledge base. The linker simply performs
a string overlap based search on named entities, comparing them with a knowledge base of 2.7 million concepts
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its a little unclear what the 2.7 number is referring to here because there are 5 options below. probably mention the 2.7 refers to the default, umls option.

scispacy/umls_utils.py
@@ -37,7 +37,7 @@ def read_umls_file_headers(meta_path: str, filename: str) -> List[str]:
return None


def read_umls_concepts(meta_path: str, concept_details: Dict):
def read_umls_concepts(meta_path: str, concept_details: Dict, source: str = None):
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add source arg to the docstring?

@DeNeutoy DeNeutoy merged commit 8994934 into allenai:master Jul 8, 2020
@diegoolano diegoolano mentioned this pull request Jul 11, 2020
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@DeNeutoy @dakinggg