Quartz sync: Jul 30, 2024, 8:50 PM

content/Entries/prolog_to_folder.py

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+import os
+import re
+
+def parse_prolog_file(file_path):
+    with open(file_path, 'r') as file:
+        content = file.read()
+
+    arity_1_predicates = {}
+    arity_2_predicates = []
+
+    # Parse arity 1 predicates
+    for match in re.finditer(r'(\w+)\((\w+)\)\.', content):
+        predicate, parameter = match.groups()
+        if predicate not in arity_1_predicates:
+            arity_1_predicates[predicate] = set()
+        arity_1_predicates[predicate].add(parameter)
+
+    # Parse arity 2 predicates
+    for match in re.finditer(r'(\w+)\((\w+),\s*(\w+)\)\.', content):
+        predicate, param1, param2 = match.groups()
+        arity_2_predicates.append((predicate, param1, param2))
+
+    return arity_1_predicates, arity_2_predicates
+def create_folders_and_files(arity_1_predicates, arity_2_predicates, output_dir):
+    os.makedirs(output_dir, exist_ok=True)
+
+    # Create folders and files for arity 1 predicates
+    for predicate, parameters in arity_1_predicates.items():
+        predicate_dir = os.path.join(output_dir, predicate)
+        os.makedirs(predicate_dir, exist_ok=True)
+        pred_file_path = os.path.join(predicate_dir, f"{predicate}.md")
+        with open(pred_file_path, 'a') as file:
+            file.write("%% Waypoint ")
+            file.write("%% \n")
+
+        for parameter in parameters:
+            file_path = os.path.join(predicate_dir, f"{parameter}.md")
+            with open(file_path, 'w') as file:
+                file.write(f"# {parameter}\n\n")
+
+    # Add arity 2 predicates as links
+    for predicate, param1, param2 in arity_2_predicates:
+        # Find which arity 1 predicate contains param1
+        for arity_1_pred, params in arity_1_predicates.items():
+            if param1 in params:
+                param_file_path = os.path.join(output_dir, arity_1_pred, f"{param1}.md")
+                with open(param_file_path, 'a') as file:
+                    file.write(f"{predicate}::[[{param2}]]\n")
+                break
+        else:
+            uncategorized_dir = os.path.join(output_dir, "uncategorized")
+            print(f"Warning: No matching arity 1 predicate found for {param1} in {predicate}({param1}, {param2}). Saving in {uncategorized_dir}")
+            os.makedirs(uncategorized_dir, exist_ok=True)
+            param_file_path = os.path.join(uncategorized_dir, f"{param1}.md")
+            with open(param_file_path, 'a') as file:
+                file.write(f"{predicate}::[[{param2}]]\n")
+
+    print("Folders and files created successfully!")
+
+def main():
+    input_file = "./test.pl"  # Change this to your Prolog file name
+    output_dir = "output"    # Change this to your desired output directory
+
+    arity_1_predicates, arity_2_predicates = parse_prolog_file(input_file)
+    create_folders_and_files(arity_1_predicates, arity_2_predicates, output_dir)
+
+    print("Folders and files created successfully!")
+
+if __name__ == "__main__":
+    main()

content/Entries/text_to_prolog.py

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+import openai
+import os
+from textwrap import wrap
+
+# Set up your OpenAI API key
+openai.api_key = 'keyhere'
+
+def split_text(text, chunk_size):
+    """Split the text into chunks of specified size."""
+    return wrap(text, chunk_size, break_long_words=False)
+
+def call_gpt_api(chunk, prompt):
+    """Call the GPT API with the given chunk and prompt."""
+    try:
+        response = openai.ChatCompletion.create(
+            model="gpt-4o-mini",
+            messages=[
+                {"role": "system", "content": prompt},
+                {"role": "user", "content": chunk}
+            ]
+        )
+        return response.choices[0].message['content']
+    except Exception as e:
+        return f"Error: {str(e)}"
+
+def process_text(input_file, output_file, chunk_size, prompt):
+    """Process the input text file and save results to the output file."""
+    with open(input_file, 'r') as f:
+        text = f.read()
+
+    chunks = split_text(text, chunk_size)
+
+    with open(output_file, 'w') as f:
+        for i, chunk in enumerate(chunks):
+            print(f"Processing chunk {i+1}/{len(chunks)}")
+            result = call_gpt_api(chunk, prompt)
+            f.write(f"% Chunk {i+1}\n{result}\n\n")
+
+# Example usage
+input_file = 'input.txt'
+output_file = 'output.txt'
+chunk_size = 2000  # Adjust this based on your needs and API limitations
+prompt = '''can you parse concepts and relationships from this text into prolog code? Please use the predicates below.  When a predicate is missing, create a new one of arity 1 or 2. You will likely need to create more relations of arity 2. Please respond with prolog code only.
+
+abstract_concept/1
+physical_entity/1
+country/1
+person/1
+theoretical_framework/1
+model/1
+
+parent/2
+category/2
+property/2
+has/2
+contributes/2
+
+Text:'''
+
+process_text(input_file, output_file, chunk_size, prompt)

content/References/blogPost/Encouraging results for Knowledge Graph Extraction by LLM Ontology-prompting.md

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+[🇿](zotero://select/library/items/I9GKP7GD)
+
+[[Entries/Individuals/Peter Lawrence, answering users' data questions]] 
+# Encouraging results for Knowledge Graph Extraction by LLM Ontology-prompting (2023)
+

content/References/computerProgram/OntoGPT.md

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+[🇿](zotero://select/library/items/GNA7T4FQ)
+
+[[Entries/Individuals/J. Harry Caufield]] [[Entries/Individuals/Harshad Hegde]] [[Entries/Individuals/Vincent Emonet]] [[Entries/Individuals/Nomi L. Harris]] [[Entries/Individuals/Marcin P. Joachimiak]] [[Entries/Individuals/Nicolas Matentzoglu]] [[Entries/Individuals/HyeongSik Kim]] [[Entries/Individuals/Sierra A.T. Moxon]] [[Entries/Individuals/Justin T. Reese]] [[Entries/Individuals/Melissa A. Haendel]] [[Entries/Individuals/Peter N. Robinson]] [[Entries/Individuals/Christopher J. Mungall]] 
+# OntoGPT (2024)
+

content/References/conferencePaper/OLaLa Ontology Matching with Large Language Models.md

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+[🇿](zotero://select/library/items/EQ38M8HE)
+
+[[Entries/Individuals/Sven Hertling]] [[Entries/Individuals/Heiko Paulheim]] 
+# OLaLa: Ontology Matching with Large Language Models (2023)
+

content/References/journalArticle/Structured information extraction from scientific text with large language models.md

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+[🇿](zotero://select/library/items/INL5CWJC)
+
+[[Entries/Individuals/John Dagdelen]] [[Entries/Individuals/Alexander Dunn]] [[Entries/Individuals/Sanghoon Lee]] [[Entries/Individuals/Nicholas Walker]] [[Entries/Individuals/Andrew S. Rosen]] [[Entries/Individuals/Gerbrand Ceder]] [[Entries/Individuals/Kristin A. Persson]] [[Entries/Individuals/Anubhav Jain]] 
+# Structured information extraction from scientific text with large language models (2024)
+

content/References/preprint/Enhancing Knowledge Graph Construction Using Large Language Models.md

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+[🇿](zotero://select/library/items/46X2B48B)
+
+[[Entries/Individuals/Milena Trajanoska]] [[Entries/Individuals/Riste Stojanov]] [[Entries/Individuals/Dimitar Trajanov]] 
+# Enhancing Knowledge Graph Construction Using Large Language Models (2023)
+

content/References/preprint/Structured prompt interrogation and recursive extraction of semantics (SPIRES) A method for populating knowledge bases using zero-shot learning.md

@@ -0,0 +1,7 @@
+[🇿](zotero://select/library/items/43JB77SY)
+
+[[Entries/Individuals/J. Harry Caufield]] [[Entries/Individuals/Harshad Hegde]] [[Entries/Individuals/Vincent Emonet]] [[Entries/Individuals/Nomi L. Harris]] [[Entries/Individuals/Marcin P. Joachimiak]] [[Entries/Individuals/Nicolas Matentzoglu]] [[Entries/Individuals/HyeongSik Kim]] [[Entries/Individuals/Sierra A. T. Moxon]] [[Entries/Individuals/Justin T. Reese]] [[Entries/Individuals/Melissa A. Haendel]] [[Entries/Individuals/Peter N. Robinson]] [[Entries/Individuals/Christopher J. Mungall]] 
+# Structured prompt interrogation and recursive extraction of semantics (SPIRES): A method for populating knowledge bases using zero-shot learning (2023)
+
+Comment: Updated 2023-12-22
+

content/References/webpage/Leveraging Large Language Models for Ontology Extraction through Question-Answering.md

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+[🇿](zotero://select/library/items/RARZ7ZYI)
+
+
+# Leveraging Large Language Models for Ontology Extraction through Question-Answering
+