Add application files

[help]Commands.txt

@@ -0,0 +1 @@
+git add -A && git commit -m "Add application files" && git push

abstract.txt

@@ -1,36 +1 @@
-Title: β-Catenin Is Required for the cGAS/STING Signaling Pathway but Antagonized by the Herpes Simplex Virus 1 US3 Protein
-Text:
-The cGAS/STING-mediated DNA-sensing signaling pathway is crucial
-for interferon (IFN) production and host antiviral
-responses. Herpes simplex virus I (HSV-1) is a DNA virus that has
-evolved multiple strategies to evade host immune responses. Here,
-we demonstrate that the highly conserved β-catenin protein in the
-Wnt signaling pathway is an important factor to enhance the
-transcription of type I interferon (IFN-I) in the cGAS/STING
-signaling pathway, and the production of IFN-I mediated by
-β-catenin was antagonized by HSV-1 US3 protein via its kinase
-activity. Infection by US3-deficienct HSV-1 and its kinase-dead
-variants failed to downregulate IFN-I and IFN-stimulated
-gene (ISG) production induced by β-catenin. Consistent with this,
-absence of β-catenin enhanced the replication of US3-deficienct
-HSV-1, but not wild-type HSV-1. The underlying mechanism was the
-interaction of US3 with β-catenin and its hyperphosphorylation of
-β-catenin at Thr556 to block its nuclear translocation. For the
-first time, HSV-1 US3 has been shown to inhibit IFN-I production
-through hyperphosphorylation of β-catenin and to subvert host
-antiviral innate immunity.IMPORTANCE Although increasing evidence
-has demonstrated that HSV-1 subverts host immune responses and
-establishes lifelong latent infection, the molecular mechanisms
-by which HSV-1 interrupts antiviral innate immunity, especially
-the cGAS/STING-mediated cellular DNA-sensing signaling pathway,
-have not been fully explored. Here, we show that β-catenin
-promotes cGAS/STING-mediated activation of the IFN pathway, which
-is important for cellular innate immune responses and intrinsic
-resistance to DNA virus infection. The protein kinase US3
-antagonizes the production of IFN by targeting β-catenin via its
-kinase activity. The findings in this study reveal a novel
-mechanism for HSV-1 to evade host antiviral immunity and add new
-knowledge to help in understanding the interaction between the
-host and HSV-1 infection.
-
-Keywords: HSV-1; US3; type I IFN; β-catenin.
+Patient John Smith (HSI-5421) underwent a tissue biopsy at the bladder collection site. The histopathology report confirmed the presence of cancer in the bladder. The tumor, identified as T-BC5421, measures 4 cm in its longest dimension. The cancer has been staged as T2, indicating its progression beyond the bladder wall. The cancer was asserted on January 10, 2022. The tumor marker test revealed elevated levels of urinary bladder tumor antigen (UBTA). John Smith, a Caucasian male born on April 15, 1975, is non-Hispanic and resides in zip code 90210. He is still alive, with no reported death date at this time. For any further information, please contact John Smith at jsmith@email.com or (555) 123-4567.

app.py

@@ -17,12 +17,12 @@ import subprocess
 # demo.launch()   
     
     
-def greet(name1, name2, name3, name4):
+def greet(name1, name2):
     # Storing each input in a variable, you can process or save them as you like
-    str1 = name1
-    str2 = name2
-    str3 = name3
-    str4 = name4
+    str1 = name1 ## openai
+    str2 = "213e22ba-4c3b-402b-bd36-6e9d4e86b1b5"   #bioportal
+    str3 = "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"   # huggingface
+    str4 = name2
 
     with open('abstractsave.txt', 'w') as f:
         f.write(name4)
@@ -41,7 +41,7 @@ def greet(name1, name2, name3, name4):
     run_command(f"poetry run runoak set-apikey -e bioportal {str2}")
     run_command(f"poetry run runoak set-apikey -e hfhub-key {str3}")
 #     output = run_command(f"ontogpt extract -t gocam.GoCamAnnotations -i ./abstract.txt")
-    output = run_command(f"ontogpt extract -t gocam.GoCamAnnotations -i ./abstractsave.txt")
+    output = run_command(f"cancerontogpt extract -t cancer -i ./abstractsave.txt")
 
 #     output_string1, error_string1=run_command("poetry")# ontogpt")
 
@@ -56,8 +56,6 @@ def greet(name1, name2, name3, name4):
 # Define 5 text input boxes with labels
 input_boxes = [
     gr.inputs.Textbox(label="openai api key"),
-    gr.inputs.Textbox(label="bioportal api key"),
-    gr.inputs.Textbox(label="HuggingFace Hub api key"),
     gr.inputs.Textbox(label="Input data"),
 ]