Merge pull request #51 from ncbo/restructure_1

Restructuring - Rewrite downloader

.github/workflows/main.yml

@@ -10,22 +10,11 @@ jobs:
       - uses: actions/setup-python@v2
         name: setup python
         with:
-          python-version: 3.8
+          python-version: "3.10"
       - name: Install Dependencies
         run: |
           python -m pip install --upgrade pip
           pip install .
           pip install .[test]
           pip install types-PyYAML
           pip install types-requests
-      - name: run pytest
-        run: |
-          coverage erase
-          pytest --cov=kg_bioportal --cov-report xml:coverage.xml
-          coverage combine --append || true
-          coverage report
-          coverage xml
-      - name: run mypy
-        run: mypy --strict-optional kg_bioportal
-      - name: run yamllint
-        run: yamllint -d relaxed merge.yaml download.yaml

README.md

@@ -1,25 +1,15 @@
 # KG-Bioportal
 
-[Bioportal](https://bioportal.bioontology.org/), as a Knowledge Graph.
+[Bioportal](https://bioportal.bioontology.org/), as a set of knowledge graphs.
 
 ## Data Sources
 
-In this graph pipeline, source data is primarily derived from [Bioportal-to-KGX](https://github.com/ncbo/BioPortal-to-KGX), starting from a 4store dump of the BioPortal ontologies.
+Source data is derived from the Bioportal API (<https://data.bioontology.org/documentation>).
 
 ## Components
 
-### Download
-
-The [download.yaml](download.yaml) contains all the URLs for source data. In this KG project, sources are pre-processed and this component is used for data transfer only.
-
-### Transform
-
-The [transform_utils](kg_bioportal/transform_utils) serve as a passthrough, allowing paths for sources to be stored.
-
-### Merge
-
-Implementation of the 'cat-merge' function from [cat-merge](https://github.com/monarch-initiative/cat-merge).
+TBA
 
 ## Example
 
-`python run.py catmerge --merge_all`
+TBA