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QuickUMLS v.1.4 #55

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May 13, 2020
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more docs
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Soldaini, Luca committed May 10, 2020
commit edf88171acfbf9a4f48b028d99c9e3d28c1e0892
4 changes: 3 additions & 1 deletion README.md
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Expand Up @@ -16,7 +16,7 @@ This project should be compatible with Python 3 (Python 2 is [no longer supporte
- `-L` / `--lowercase`: if used, all concept terms are folded to lowercase before being processed. This option typically increases recall, but it might reduce precision;
- `-U` / `--normalize-unicode`: if used, expressions with non-ASCII characters are converted to the closest combination of ASCII characters.
- `-E` / `--language`: Specify the language to consider for UMLS concepts; by default, English is used. For a complete list of languages, please see [this table provided by NLM](https://www.nlm.nih.gov/research/umls/knowledge_sources/metathesaurus/release/abbreviations.html#LAT).
- `-d` / `--database-backend`: Specify which database backend to use for QuickUMLS. The two options are `leveldb` and `unqlite`. The former is set as default for compatibility reasons, while the latter support multi-process reading and has better unicode compatibility. More info about differences between the two databases and migration info are available [here](https://github.com/Georgetown-IR-Lab/QuickUMLS/wiki/Migration-QuickUMLS-1.3-to-1.4).
- `-d` / `--database-backend`: Specify which database backend to use for QuickUMLS. The two options are `leveldb` and `unqlite`. The latter supports multi-process reading and has better unicode compatibility, and it used as default for all new 1.4 installations; the former is still used as default when instantiating a QuickUMLS client. More info about differences between the two databases and migration info are available [here](https://github.com/Georgetown-IR-Lab/QuickUMLS/wiki/Migration-QuickUMLS-1.3-to-1.4).


**†**: If the installation fails on macOS when using Anaconda, install `leveldb` first by running `conda install -c conda-forge python-leveldb`.
Expand Down Expand Up @@ -50,6 +50,8 @@ matcher.match(text, best_match=True, ignore_syntax=False)

Set `best_match` to `False` if you want to return overlapping candidates, `ignore_syntax` to `True` to disable all heuristics introduced in (Soldaini and Goharian, 2016).

If the matcher throws a warning during initialization, read [this page](https://github.com/Georgetown-IR-Lab/QuickUMLS/wiki/Migration-QuickUMLS-1.3-to-1.4) to learn why and how to stop it from doing so.


## Server / Client Support

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2 changes: 1 addition & 1 deletion quickumls/install.py
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Expand Up @@ -154,7 +154,7 @@ def parse_args():
help='Normalize unicode strings to their closest ASCII representation'
)
ap.add_argument(
'-d', '--database-backend', choices=('leveldb', 'unqlite'), default='leveldb',
'-d', '--database-backend', choices=('leveldb', 'unqlite'), default='unqlite',
help='KV database to use to store CUIs and semantic types'
)
ap.add_argument(
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