diff --git a/.gitignore b/.gitignore
index 7bc089e..e75ca98 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,12 +1,12 @@
 # Boilerplate
 /*.json
+/*.owl
 /env/*
 !/env/.env.example
 /.idea/
 /.run/
 /venv/
-*/cache/*
-!*/cache/.keep
+cache/*
 __pycache__/
 _archive/
 _dev/
diff --git a/owl_on_fhir/__main__.py b/owl_on_fhir/__main__.py
index dbb3a0d..932b147 100644
--- a/owl_on_fhir/__main__.py
+++ b/owl_on_fhir/__main__.py
@@ -1,6 +1,7 @@
 """Convert OWL to FHIR"""
 import json
 import os
+import shutil
 import subprocess
 from argparse import ArgumentParser
 from typing import Dict, List
@@ -61,7 +62,7 @@ def _preprocess_rxnorm(path: str) -> str:
     return outpath
 
 
-def download(url: str, path: str, download_if_cached=True):
+def download(url: str, path: str, save_to_cache=False, download_if_cached=True):
     """Download file at url to local path
 
     :param download_if_cached: If True and file at `path` already exists, download anyway."""
@@ -72,8 +73,12 @@ def download(url: str, path: str, download_if_cached=True):
         with open(path, 'wb') as f:
             response = requests.get(url, verify=False)
             f.write(response.content)
+    if save_to_cache:
+        cache_path = os.path.join(CACHE_DIR, os.path.basename(path))
+        shutil.copy(path, cache_path)
 
 
+# todo: owl_to_semsql: this may need similar updates to caching that were done for obographs on 2023/04/15
 def owl_to_semsql(inpath: str, use_cache=False) -> str:
     """Converts OWL (or RDF, I think) to a SemanticSQL sqlite DB.
     Docs: https://incatools.github.io/ontology-access-kit/intro/tutorial07.html?highlight=semsql
@@ -101,46 +106,28 @@ def owl_to_semsql(inpath: str, use_cache=False) -> str:
     return outpath
 
 
-def owl_to_obograph(inpath: str, native_uri_stems: List[str] = None, use_cache=False) -> str:
+def owl_to_obograph(inpath: str, out_dir: str, use_cache=False, cache_output=False) -> str:
     """Convert OWL to Obograph
-    # todo: TTL and RDF also supported? not just OWL?"""
+    todo: TTL and RDF also supported? not just OWL?"""
     # Vars
-    outpath = os.path.join(CACHE_DIR, inpath + '.obographs.json')
-    outdir = os.path.realpath(os.path.dirname(outpath))
+    infile = os.path.basename(inpath)
+    cache_path = os.path.join(CACHE_DIR, infile + '.obographs.json')
+    outpath = os.path.join(out_dir, infile + '.obographs.json')
     command = f'java -jar {ROBOT_PATH}.jar convert -i {inpath} -o {outpath} --format json'
 
     # Convert
-    if not os.path.exists(outdir):
-        os.makedirs(outdir)
-    if use_cache and os.path.exists(outpath):
-        return outpath
+    if not os.path.exists(out_dir):
+        os.makedirs(out_dir)
+    if use_cache and os.path.exists(cache_path):
+        return cache_path
     # todo: Switch back to `bioontologies` when complete: https://github.com/biopragmatics/bioontologies/issues/9
     # from bioontologies import robot
     # parse_results: robot.ParseResults = robot.convert_to_obograph_local(inpath)
     # graph = parse_results.graph_document.graphs[0]
     _run_shell_command(command)
 
-    # Patch missing roots / etc issue (until resolved: https://github.com/ontodev/robot/issues/1082)
-    if native_uri_stems:
-        with open(outpath, 'r') as f:
-            data = json.load(f)
-        nodes = data['graphs'][0]['nodes']
-        node_ids = set([node['id'] for node in nodes])
-        edges = data['graphs'][0]['edges']
-        # edges = [x for x in edges if x['pred'] in missing_nodes_from_important_edge_preds]
-        edge_subs = set([edge['sub'] for edge in edges])
-        edge_objs = set([edge['obj'] for edge in edges])
-        edge_ids = edge_subs.union(edge_objs)
-        missing = set([x for x in edge_ids if x not in node_ids])  # all missing
-        missing = [x for x in missing if any([x.startswith(y) for y in native_uri_stems])]  # filter
-
-        if missing:
-            print(f'INFO: The following nodes were found in Obographs edges, but not nodes. Adding missing '
-                  f'declarations: {missing}')
-            for node_id in missing:
-                nodes.append({'id': node_id})
-            with open(outpath, 'w') as f:
-                json.dump(data, f)
+    if cache_output:
+        shutil.copy(outpath, cache_path)
 
     return outpath
 
@@ -151,7 +138,7 @@ def owl_to_obograph(inpath: str, native_uri_stems: List[str] = None, use_cache=F
 #  - https://github.com/geneontology/obographs/issues/89
 def obograph_to_fhir(
     inpath: str, out_dir: str, out_filename: str = None, code_system_id: str = None, code_system_url: str = None,
-    include_all_predicates=False, native_uri_stems: List[str] = None, dev_oak_path: str = None,
+    include_all_predicates=True, native_uri_stems: List[str] = None, dev_oak_path: str = None,
     dev_oak_interpreter_path: str = None
 ) -> str:
     """Convert Obograph to FHIR"""
@@ -176,9 +163,15 @@ def obograph_to_fhir(
     else:
         converter = OboGraphToFHIRConverter()
         converter.curie_converter = curies.Converter.from_prefix_map(get_default_prefix_map())
-        gd: GraphDocument = json_loader.load(inpath, target_class=GraphDocument)
-        converter.dump(gd, out_path, include_all_predicates=include_all_predicates)
-        # todo: update w/ these params when released
+        gd: GraphDocument = json_loader.load(str(inpath), target_class=GraphDocument)
+        converter.dump(
+            gd,
+            out_path,
+            code_system_id=code_system_id,
+            code_system_url=code_system_url,
+            include_all_predicates=include_all_predicates,
+            native_uri_stems=native_uri_stems)
+        # TODO: add these params once supported: use_curies_native_concepts, use_curies_foreign_concepts
         # converter.dump(
         #     gd, out_path, code_system_id='', code_system_url='', include_all_predicates=include_all_predicates,
         #     native_uri_stems=native_uri_stems, use_curies_native_concepts=False, use_curies_foreign_concepts=True)
@@ -219,18 +212,21 @@ def owl_to_fhir(
     input_path = input_path_or_url
     url = None
     maybe_url = urlparse(input_path_or_url)
+    out_dir = out_dir if out_dir else os.getcwd()
+    if out_dir.startswith('~'):
+        out_dir = os.path.expanduser('~/Desktop')
     if maybe_url.scheme and maybe_url.netloc:
         url = input_path_or_url
     if url:
-        input_path = os.path.join(CACHE_DIR, out_filename.replace('.json', '.owl'))
-        download(url, input_path)
+        download_path = os.path.join(out_dir, out_filename.replace('.json', '.owl'))
+        input_path = download_path
+        download(url, download_path, use_cached_intermediaries)
     if not out_filename:
         if not code_system_id:
             code_system_id = '.'.join(os.path.basename(input_path).split('.')[0:-1])  # removes file extension
         out_filename = f'CodeSystem-{code_system_id}.json'
     if not code_system_id and out_filename and out_filename.startswith('CodeSystem-'):
         code_system_id = out_filename.split('-')[1].split('.')[0]
-    input_path = input_path if os.path.exists(input_path) else os.path.join(os.getcwd(), input_path)
     out_dir = os.path.realpath(out_dir if out_dir else os.path.dirname(input_path))
     intermediary_outdir = intermediary_outdir if intermediary_outdir else out_dir
 
@@ -240,13 +236,14 @@ def owl_to_fhir(
 
     # Convert
     if intermediary_type == 'obographs' or input_path.endswith('.ttl'):  # semsql only supports .owl
-        intermediary_path = owl_to_obograph(input_path, native_uri_stems, use_cached_intermediaries)
+        intermediary_path = owl_to_obograph(input_path, out_dir, use_cached_intermediaries, use_cached_intermediaries)
         obograph_to_fhir(
             inpath=intermediary_path, out_dir=intermediary_outdir, out_filename=out_filename,
             code_system_id=code_system_id, code_system_url=code_system_url, native_uri_stems=native_uri_stems,
             include_all_predicates=include_all_predicates, dev_oak_path=dev_oak_path,
             dev_oak_interpreter_path=dev_oak_interpreter_path)
     else:  # semsql
+        # todo: owl_to_semsql: this may need similar updates to caching that were done for obographs on 2023/04/15
         intermediary_path = owl_to_semsql(input_path, use_cached_intermediaries)
         semsql_to_fhir(
             inpath=intermediary_path, out_dir=intermediary_outdir, out_filename=out_filename,
@@ -304,7 +301,7 @@ def cli():
              'convert that to FHIR.')
     parser.add_argument(
         '-c', '--use-cached-intermediaries', action='store_true', required=False, default=False,
-        help='Use cached intermediaries if they exist?')
+        help='Use cached intermediaries if they exist? Also will save intermediaries to owl-on-fhir\'s cache/ dir.')
     parser.add_argument(
         '-r', '--retain-intermediaries', action='store_true', default=False, required=False,
         help='Retain intermediary files created during conversion process (e.g. Obograph JSON)?')
diff --git a/requirements.txt b/requirements.txt
index 3716289..75c2437 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,45 +1,57 @@
 aiohttp==3.8.3
 aiosignal==1.3.1
-alabaster==0.7.12
+airium==0.2.5
+alabaster==0.7.13
 antlr4-python3-runtime==4.9.3
 appdirs==1.4.4
 arrow==1.2.3
 async-timeout==4.0.2
-attrs==22.1.0
+attrs==22.2.0
 Babel==2.11.0
 bcp47==0.0.4
+beautifulsoup4==4.12.2
 bioontologies==0.2.1
-bioregistry==0.5.143
-certifi==2022.9.24
+bioregistry==0.6.99
+bleach==6.0.0
+certifi==2022.12.7
 CFGraph==0.2.1
-chardet==4.0.0
+chardet==5.1.0
 charset-normalizer==2.1.1
-class-resolver==0.3.10
+class-resolver==0.4.2
 click==8.1.3
-curies==0.4.0
+colorama==0.4.6
+contourpy==1.0.7
+curies==0.4.2
+cycler==0.11.0
 decorator==5.1.1
 Deprecated==1.2.13
 deprecation==2.1.0
 distlib==0.3.6
 docutils==0.17.1
+EditorConfig==0.12.3
 et-xmlfile==1.1.0
-exceptiongroup==1.0.4
+exceptiongroup==1.1.0
 fastobo==0.12.2
-filelock==3.8.2
+filelock==3.9.0
+fonttools==4.39.3
 fqdn==1.5.1
 frozenlist==1.3.3
-fsspec==2022.11.0
-funowl==0.1.12
+fsspec==2023.1.0
+funowl==0.1.13
+ghp-import==2.1.0
 graphviz==0.20.1
-greenlet==2.0.1
+greenlet==2.0.2
 hbreader==0.9.1
 idna==3.4
+ijson==3.2.0.post0
 imagesize==1.4.1
 importlib-metadata==4.13.0
-iniconfig==1.1.1
+iniconfig==2.0.0
 isodate==0.6.1
 isoduration==20.11.0
+jaraco.classes==3.2.3
 Jinja2==3.1.2
+jsbeautifier==1.14.7
 json-flattener==0.1.9
 jsonasobj==1.3.1
 jsonasobj2==1.0.4
@@ -47,94 +59,120 @@ jsonpatch==1.32
 jsonpath-ng==1.5.3
 jsonpointer==2.3
 jsonschema==4.17.3
+keyring==23.13.1
 kgcl-rdflib==0.3.0
-kgcl-schema==0.3.1
+kgcl-schema==0.3.6
+kiwisolver==1.4.4
 lark==1.1.5
-linkml==1.3.15
+linkml==1.4.3
 linkml-dataops==0.1.0
-linkml-runtime==1.3.7
-markdown-it-py==2.1.0
-MarkupSafe==2.1.1
+linkml-renderer==0.1.2
+linkml-runtime==1.4.3
+Markdown==3.3.7
+markdown-it-py==2.2.0
+MarkupSafe==2.1.2
+matplotlib==3.7.1
 mdit-py-plugins==0.3.3
 mdurl==0.1.2
+mergedeep==1.3.4
+mkdocs==1.4.2
+mkdocs-material==9.1.6
+mkdocs-material-extensions==1.1.1
+mkdocs-mermaid2-plugin==0.6.0
 more-click==0.1.2
-multidict==6.0.3
+more-itertools==9.1.0
+multidict==6.0.4
 myst-parser==0.18.1
+ndex2==3.5.1
 networkx==2.8.8
-numpy==1.23.5
+numpy==1.24.1
 nxontology==0.4.1
-oaklib==0.1.67
+oaklib==0.5.1
 ols-client==0.1.2
 ontoportal-client==0.0.3
 openpyxl==3.0.10
-packaging==21.3
-pandas==1.5.2
+packaging==23.0
+pandas==1.5.3
 pandasql==0.7.3
+pansql==0.0.1
 parse==1.19.0
-pbr==5.11.0
-platformdirs==2.5.4
+pbr==5.11.1
+Pillow==9.5.0
+pkginfo==1.9.6
+platformdirs==2.6.2
 pluggy==1.0.0
 ply==3.11
 prefixcommons==0.1.12
 prefixmaps==0.1.4
-pronto==2.5.1
+pronto==2.5.3
 py==1.11.0
-pydantic==1.10.2
-Pygments==2.13.0
+pydantic==1.10.4
+Pygments==2.14.0
 PyJSG==0.11.10
+pymdown-extensions==9.11
 pyparsing==3.0.9
-pyrsistent==0.19.2
+pyrsistent==0.19.3
 PyShEx==0.8.1
 PyShExC==0.9.1
-pystow==0.4.7
-pytest==7.2.0
+pystow==0.5.0
+pytest==7.2.1
 pytest-logging==2015.11.4
 python-dateutil==2.8.2
 PyTrie==0.4.0
-pytz==2022.6
+pytz==2022.7.1
 PyYAML==6.0
+pyyaml_env_tag==0.1
 ratelimit==2.2.1
 rdflib==6.2.0
 rdflib-jsonld==0.6.1
 rdflib-shim==1.0.3
-requests==2.28.1
+readme-renderer==37.3
+regex==2023.3.23
+requests==2.28.2
+requests-toolbelt==0.10.1
 rfc3339-validator==0.1.4
+rfc3986==2.0.0
 rfc3987==1.3.8
+rich==13.3.2
 ruamel.yaml==0.17.21
 ruamel.yaml.clib==0.2.7
-scipy==1.9.3
-semsql==0.2.5
+scipy==1.10.0
+semsql==0.3.2
 ShExJSG==0.8.2
 six==1.16.0
 snowballstemmer==2.2.0
 sortedcontainers==2.4.0
+soupsieve==2.4
 sparqlslurper==0.5.1
 SPARQLWrapper==2.0.0
 Sphinx==5.3.0
 sphinx-click==4.4.0
 sphinx-rtd-theme==1.1.1
-sphinxcontrib-applehelp==1.0.2
+sphinxcontrib-applehelp==1.0.4
 sphinxcontrib-devhelp==1.0.2
 sphinxcontrib-htmlhelp==2.0.0
 sphinxcontrib-jsmath==1.0.1
 sphinxcontrib-qthelp==1.0.3
 sphinxcontrib-serializinghtml==1.1.5
-SQLAlchemy==1.4.44
+SQLAlchemy==1.4.46
 SQLAlchemy-Utils==0.38.3
-sssom==0.3.17
-sssom-schema==0.9.4
+sssom==0.3.28
+sssom-schema==0.11.0
 stevedore==4.1.1
 tomli==2.0.1
-tox==3.27.1
+tox==3.28.0
 tqdm==4.64.1
+twine==4.0.2
 typing_extensions==4.4.0
+UpSetPlot==0.8.0
 uri-template==1.2.0
-urllib3==1.26.13
+urllib3==1.26.14
 validators==0.20.0
 virtualenv==20.17.1
 virtualenv-clone==0.5.7
-watchdog==2.2.0
+watchdog==2.2.1
 webcolors==1.12
+webencodings==0.5.1
 wrapt==1.14.1
 yarl==1.8.2
-zipp==3.11.0
+zipp==3.12.0
diff --git a/setup.py b/setup.py
index d888c03..dc6cd52 100644
--- a/setup.py
+++ b/setup.py
@@ -15,12 +15,12 @@
 EMAIL = 'jflack@jhu.edu'
 AUTHOR = 'Joe Flack'
 REQUIRES_PYTHON = '>=3.9.0'
-VERSION = '0.1.11'
+VERSION = '1.0.0'
 
 # Requirements
 REQUIRED = [
     'bioontologies',
-    'oaklib>=0.1.58',
+    'oaklib>=0.5.1',
     'requests',
 ]