diff --git a/README.md b/README.md index f68f095..c1eb906 100644 --- a/README.md +++ b/README.md @@ -32,16 +32,17 @@ `biolexica` helps generate and apply coherent biomedical lexica. It takes care of the following: 1. Getting names and synonyms from a diverse set of inputs (ontologies, databases, custom) - using `pyobo`, `bioontologies`, `biosynonyms`, and more. + using [`pyobo`](https://github.com/pyobo/pyobo), [`bioontologies`](https://github.com/biopragmatics/bioontologies), + [`biosynonyms`](https://github.com/biopragmatics/biosynonyms), and more. 2. Merging equivalent terms to best take advantage of different synonyms for the same term from different sources - using `semra`. -3. Generating lexical index and doing NER using `gilda` + using [`semra`](https://github.com/biopragmatics/semra). +3. Generating lexical index and doing NER using [Gilda](https://github.com/gyorilab/gilda) Importantly, we pre-define lexica for several entity types that can be readily used with Gilda in the [`lexica/`](lexica/) folder including: -1. Cells and cell lines -2. Diseased, conditions, and other phenotypes +1. [Cells and cell lines](lexica/cell) +2. [Diseased, conditions, and other phenotypes](lexica/phenotype) ## 🚀 Installation @@ -78,15 +79,6 @@ The code in this package is licensed under the MIT License. Citation goes here! --> - -