Init

Parameters.py

@@ -0,0 +1,28 @@
+from audioop import reverse
+
+GNBRfile = '../GNBRdata/'
+PubTatorfile = '../pubtator/'
+UMLSfile = '../umls/META/'
+Pubmedfile = '../pubmed/'
+
+edge_type_dict = {
+    'chemical-gene':(['A+', 'A-', 'B', 'E+', 'E-', 'E', 'N', 'O', 'K', 'Z'],
+    ['agonism, activation', 'antagonism, blocking', 'binding, ligand', 'increases expression/production', 'decreases expression/production', 'affects expression/production', 'inhibits', 'transport, channels', 'metabolism, pharmacokinetics', 'enzyme activity']),
+    'chemical-disease':(['T', 'C', 'Sa', 'Pr', 'Pa', 'J', 'Mp'],
+    ['treatment/therapy', 'inhibits cell growth', 'side effect/adverse event', 'prevents, suppresses', 'alleviates, reduces', 'role in disease pathogenesis', 'biomarkers']),
+    'gene-disease':(['U', 'Ud', 'D', 'J', 'Te', 'Y', 'G', 'Md', 'X', 'L'],
+    ['causal mutations', 'mutations affecting disease course', 'drug targets', 'role in pathogenesis', 'possible therapeutic effect', 'polymorphisms alter risk', 'promotes progression', 'biomarkers', 'overexpression in disease', 'improper regulation linked to disease']),
+    'gene-gene':(['B', 'W', 'V+', 'E+', 'E', 'I', 'H', 'Rg', 'Q'],
+    ['binding, ligand', 'enhances response', 'activates, stimulates', 'increases expression/production', 'affects expression/production', 'signaling pathway', 'same protein or complex', 'regulation', 'production by cell population'])
+}
+
+reverse_mask = {
+    'chemical-gene':[0, 0, 0, 0, 0, 0, 0, 1, 1, 1],
+    'chemical-disease':[0, 0, 0, 0, 0, 0, 1],
+    'gene-disease': [0, 0, 0, 0, 0, 0, 0, 1, 1, 1],
+    'gene-gene': [0, 0, 0, 0, 0, 0, 0, 0, 0]
+}
+
+edge_id_to_type = ['chemical-gene:agonism, activation', 'chemical-gene:antagonism, blocking', 'chemical-gene:binding, ligand', 'chemical-gene:increases expression/production', 'chemical-gene:decreases expression/production', 'chemical-gene:affects expression/production', 'chemical-gene:inhibits', 'chemical-gene:transport, channels', 'chemical-gene:metabolism, pharmacokinetics', 'chemical-gene:enzyme activity', 'chemical-disease:treatment/therapy', 'chemical-disease:inhibits cell growth', 'chemical-disease:side effect/adverse event', 'chemical-disease:prevents, suppresses', 'chemical-disease:alleviates, reduces', 'chemical-disease:role in disease pathogenesis', 'chemical-disease:biomarkers', 'gene-disease:causal mutations', 'gene-disease:mutations affecting disease course', 'gene-disease:drug targets', 'gene-disease:role in pathogenesis', 'gene-disease:possible therapeutic effect', 'gene-disease:polymorphisms alter risk', 'gene-disease:promotes progression', 'gene-disease:biomarkers', 'gene-disease:overexpression in disease', 'gene-disease:improper regulation linked to disease', 'gene-gene:binding, ligand', 'gene-gene:enhances response', 'gene-gene:activates, stimulates', 'gene-gene:increases expression/production', 'gene-gene:affects expression/production', 'gene-gene:signaling pathway', 'gene-gene:same protein or complex', 'gene-gene:regulation', 'gene-gene:production by cell population']
+
+edge_type_to_id = {'chemical-gene': [0, 1, 2, 3, 4, 5, 6, 7, 8, 9], 'chemical-disease': [10, 11, 12, 13, 14, 15, 16], 'gene-disease': [17, 18, 19, 20, 21, 22, 23, 24, 25, 26], 'gene-gene': [27, 28, 29, 30, 31, 32, 33, 34, 35]}

README.md

@@ -4,8 +4,9 @@ emoji: 👀
 colorFrom: red
 colorTo: gray
 sdk: gradio
+python_version: 3.8.12
 sdk_version: 3.41.2
-app_file: app.py
+app_file: server/server.py
 pinned: false
 license: mit
 ---

requirements.txt

@@ -0,0 +1,158 @@
+aiofiles==23.2.1
+aiohttp==3.8.5
+aiosignal==1.3.1
+altair==5.0.1
+annotated-types==0.5.0
+anyio==3.7.1
+argon2-cffi==20.1.0
+async-generator==1.10
+async-timeout==4.0.3
+attrs==21.2.0
+backcall==0.2.0
+backports.functools-lru-cache==1.6.4
+bleach==4.0.0
+blis==0.7.10
+Bottleneck==1.3.2
+brotlipy==0.7.0
+catalogue==2.0.9
+certifi==2022.12.7
+cffi==1.14.6
+charset-normalizer==2.0.4
+click==8.1.7
+confection==0.1.1
+cryptography==37.0.1
+cycler==0.11.0
+cymem==2.0.7
+debugpy==1.5.1
+decorator==5.1.0
+defusedxml==0.7.1
+dill==0.3.7
+en-core-web-md==3.6.0
+en-core-web-sm==3.6.0
+entrypoints==0.3
+exceptiongroup==1.1.3
+fastapi==0.102.0
+ffmpy==0.3.1
+filelock==3.12.2
+flit_core==3.6.0
+fonttools==4.25.0
+frozenlist==1.4.0
+fsspec==2023.6.0
+gradio==3.41.2
+gradio_client==0.5.0
+h11==0.14.0
+httpcore==0.17.3
+httpx==0.24.1
+huggingface-hub==0.16.4
+idna==3.3
+importlib-metadata==4.8.2
+importlib-resources==6.0.1
+ipykernel==6.6.0
+ipython==7.30.1
+ipython-genutils==0.2.0
+ipywidgets==7.6.5
+jedi==0.18.1
+Jinja2==3.0.2
+joblib==1.3.2
+jsonschema==3.2.0
+jupyter==1.0.0
+jupyter-client==7.1.0
+jupyter-console==6.4.0
+jupyter-core==4.9.1
+jupyterlab-pygments==0.1.2
+jupyterlab-widgets==1.0.0
+kiwisolver==1.3.1
+langcodes==3.3.0
+MarkupSafe==2.0.1
+matplotlib==3.5.0
+matplotlib-inline==0.1.3
+mistune==0.8.4
+mkl-fft==1.3.1
+mkl-random==1.2.2
+mkl-service==2.4.0
+multidict==6.0.4
+munkres==1.1.4
+murmurhash==1.0.9
+nbclient==0.5.3
+nbconvert==6.3.0
+nbformat==5.1.3
+nest-asyncio==1.5.4
+networkx==2.6.3
+notebook==6.4.6
+numexpr==2.8.1
+numpy==1.21.5
+olefile==0.46
+openai==0.27.6
+orjson==3.9.5
+packaging==21.3
+pandas==1.3.4
+pandocfilters==1.4.3
+parso==0.8.3
+pathy==0.10.2
+pexpect==4.8.0
+pickleshare==0.7.5
+Pillow==8.4.0
+pip==21.2.4
+preshed==3.0.8
+prometheus-client==0.12.0
+prompt-toolkit==3.0.20
+ptyprocess==0.7.0
+pycparser==2.21
+pydantic==2.3.0
+pydantic_core==2.6.3
+pydub==0.25.1
+Pygments==2.11.1
+pyOpenSSL==22.0.0
+pyparsing==3.0.4
+pyrsistent==0.18.0
+PySocks==1.7.1
+python-dateutil==2.8.2
+python-multipart==0.0.6
+pytz==2021.3
+PyYAML==6.0.1
+pyzmq==19.0.2
+qtconsole==5.1.1
+QtPy==1.10.0
+regex==2023.8.8
+requests==2.28.1
+sacremoses==0.0.46
+scipy==1.7.3
+seaborn==0.11.2
+semantic-version==2.10.0
+Send2Trash==1.8.0
+setuptools==58.0.4
+shadowsocks==3.0.0
+sip==4.19.13
+six==1.16.0
+smart-open==6.3.0
+sniffio==1.3.0
+spacy==3.6.1
+spacy-legacy==3.0.12
+spacy-loggers==1.0.4
+srsly==2.4.7
+starlette==0.27.0
+terminado==0.9.4
+testpath==0.5.0
+thinc==8.1.12
+tokenizers==0.13.3
+toolz==0.12.0
+torch==1.12.1
+torchaudio==0.12.1
+torchvision==0.13.1
+tornado==6.1
+tqdm==4.62.3
+traitlets==5.7.1
+transformers==4.26.0
+typer==0.4.2
+typing_extensions==4.7.1
+urllib3==1.26.11
+uvicorn==0.23.2
+wasabi==0.10.1
+wcwidth==0.2.5
+webencodings==0.5.1
+websockets==11.0.3
+wheel==0.37.0
+widgetsnbextension==3.5.1
+xlwt==1.3.0
+yarl==1.9.2
+zipp==3.6.0