Repository: linkml/dm-bip
Pull request #84: Add data annotation tool
Author: login: twhetzel
Created: 2025-05-16T07:21:08Z | Merged: 2025-05-19T16:15:01Z

This PR adds the data annotation tool Harmonica. The tool uses a config file and adds a new dependency for openai. A few new entries were added to conditions_simple.tsv also.


Diff:
diff --git a/.gitignore b/.gitignore
index 1352490..85181fd 100644
--- a/.gitignore
+++ b/.gitignore
@@ -131,3 +131,5 @@ dmypy.json
 # Pyre type checker
 .pyre/
 
+harmonica/tmp/
+config/config.yml
diff --git a/config/config.example.yml b/config/config.example.yml
new file mode 100644
index 0000000..b47f115
--- /dev/null
+++ b/config/config.example.yml
@@ -0,0 +1,8 @@
+ontologies:
+  - MONDO
+
+columns_to_annotate:
+  - condition_source_text
+
+# Optional output directory
+output_dir: data/output/
diff --git a/harmonica/README.md b/harmonica/README.md
new file mode 100644
index 0000000..992597b
--- /dev/null
+++ b/harmonica/README.md
@@ -0,0 +1,67 @@
+# Harmonica
+Annotate data with ontology terms.
+
+## Prerequisites
+The prerequisites to run the script are maintained within the `pyproject.toml` file. To update your virtual environment run `poetry install`.
+
+## Usage
+### Python
+```
+python harmonize.py annotate \
+    --config ../config/config.yml \
+    --input_file ../toy_data/raw_data_conditions/conditions_simple.tsv \
+    --output_dir tmp/output/ \
+    --refresh \
+    --no_openai
+```
+
+### Make Command
+`make annotate input_file=toy_data/raw_data_conditions/conditions_simple.tsv output_dir=harmonica/tmp/output refresh=true`
+(the `make` command is run from the root of the project)
+
+NOTES: 
+1. `--output_dir` is optional; it can be defined in the YAML config instead
+1. `--refresh` flag to update the cached OAK ontology database. To rely on the existing local copy, leave out `--refresh` or `refresh=true`
+1. `--no_openai` flag to skip LLM-based annotation
+
+
+## Ontology SQLite Database
+Using `get_adapter(f"sqlite:obo:{ontology_id}")` the ontology database is saved at `~/.data/oaklib/`.
+
+NOTE: This method downloads a version of an ontolgy from an AWS S3 bucket (https://s3.amazonaws.com/bbop-sqlite) managed by the OAK developers (https://github.com/INCATools/ontology-access-kit). Only one version of an ontology is present in the S3 bucket.
+
+Since OAK does not have a mechanism to automatically update the local cached ontology database (saved to `~/.data/oaklib/`), a custom method was added to harmonica. The `--refresh` flag will update your local database files with the content from the S3 bucket.
+
+There is a cache control option for OAK, however this manages the default cache expiry lifetime of 7 days. This does not ensure that when the data annotation is run that it's using the latest ontology content available from the S3 bucket. As of this code update (31-Mar-2025), the `refresh` option is only available in the OAK commandline and not in the Python code.
+
+OAK references:
+- Cached ontology database is out of date - https://incatools.github.io/ontology-access-kit/faq/troubleshooting.html#my-cached-sqlite-ontology-is-out-of-date
+
+- Cache control - https://incatools.github.io/ontology-access-kit/cli.html#cache-control
+
+
+## Configuration
+
+Copy the example config and customize it for your project:
+`cp config/config.example.yml config/config.yml`
+
+## OpenAI API
+Create an OpenAI API Key [here](https://platform.openai.com/api-keys) and then add this your environment as: 
+`export OPENAI_API_KEY=your-key-here>`
+
+## Data File
+The script reads and writes TSV files. The prefixes of the ontologies to be used for the annotation can be added into the config.yml file.
+
+### Input file
+See the file `conditions_simple.tsv` in `toy_data/raw_data_conditions`.
+
+### Output file
+_TBD_ Describe the format and content of the output data file.
+
+Example output file: 
+```
+condition_source_text	UUID	mondo_result_curie	mondo_result_label	mondo_result_match_type	annotation_source	annotation_method	ontology	alt_names	hpo_result_curie	hpo_result_label	hpo_result_match_type	maxo_result_curie	maxo_result_label	maxo_result_match_type
+ASD	7317c559-ff88-4c31-8608-77615b20b267	MONDO:0006664	atrial septal defect	MONDO_EXACT_ALIAS	oak	exact_synonym	mondo							
+ASD	7317c559-ff88-4c31-8608-77615b20b267				oak	exact_synonym	hp		HP:0000729, HP:0001631	Autistic behavior, Atrial septal defect	HPO_EXACT_ALIAS			
+ASD	7317c559-ff88-4c31-8608-77615b20b267				openai	no_match	maxo	autism spectrum disorder, atrial septal defect, advanced sleep phase disorder, asynchronous serial data, active server directory						
+```
diff --git a/harmonica/harmonize.py b/harmonica/harmonize.py
new file mode 100644
index 0000000..42e98ba
--- /dev/null
+++ b/harmonica/harmonize.py
@@ -0,0 +1,512 @@
+#!/usr/bin/env python3
+
+import click
+from datetime import datetime
+import uuid
+import logging
+from oaklib import get_adapter
+from oaklib.datamodels.search import SearchProperty, SearchConfiguration
+from oaklib.implementations.sqldb.sql_implementation import SqlImplementation
+import pandas as pd
+import numpy as np
+from pathlib import Path
+from tqdm import tqdm
+import sys
+import yaml
+from pathlib import Path
+import os
+import openai
+import json
+import re
+
+
+openai.api_key = os.getenv("OPENAI_API_KEY")
+
+
+__all__ = [
+    "main",
+]
+
+
+# Explicitly remove handlers that may have been added automatically
+for handler in logging.root.handlers[:]:
+    logging.root.removeHandler(handler)
+
+# Configure logger
+logger = logging.getLogger("harmonica")
+
+# logging.basicConfig(
+#     level=logging.DEBUG,
+#     format="%(asctime)s.%(msecs)03d [%(levelname)s] (%(module)s) (%(name)s): %(message)s",
+#     datefmt='%Y-%m-%d,%H:%M:%S',
+#     handlers=[
+#         logging.FileHandler("error.log"),
+#         logging.StreamHandler()
+#     ],
+#     force=True
+# )
+
+# Silence root logger
+logging.getLogger().setLevel(logging.WARNING)
+
+# Silence oak logger
+logging.getLogger("sql_implementation").setLevel(logging.WARNING)
+
+
+# Silence SQLAlchemy and related sub-loggers
+for name in [
+    "sqlalchemy",
+    "sqlalchemy.engine",
+    "sqlalchemy.engine.Engine",
+    "sqlalchemy.pool"
+]:
+    logging.getLogger(name).setLevel(logging.WARNING)
+    logging.getLogger(name).propagate = False
+
+
+@click.group()
+@click.option("-v", "--verbose", count=True)
+@click.option("-q", "--quiet")
+# @click.version_option(__version__)
+def main(verbose: int, quiet: bool):
+    """
+    The main click group containing with parameters for logging levels.
+    :param verbose: Levels of log messages to display.
+    :param quiet: Boolean to be quiet or verbose.
+    """
+    if verbose >= 2:
+        logger.setLevel(level=logging.DEBUG)
+    elif verbose == 1:
+        logger.setLevel(level=logging.INFO)
+    else:
+        logger.setLevel(level=logging.WARNING)
+    if quiet:
+        logger.setLevel(level=logging.ERROR)
+
+
+def clear_cached_db(ontology_id: str):
+    """Clear ontology database files (.db and .db.gz) cached by OAK."""
+    base_path = Path.home() / ".data" / "oaklib"
+    db_files = [
+        base_path / f"{ontology_id}.db",
+        base_path / f"{ontology_id}.db.gz"
+    ]
+
+    for file in db_files:
+        logger.debug("DB refresh set to True.")
+        if file.exists():
+            logger.debug(f"Removing cached DB: {file}")
+            file.unlink()
+        else:
+            logger.debug(f"No cached DB found at: {file}")
+
+
+
+
+def fetch_ontology(ontology_id: str, refresh: bool = False) -> SqlImplementation:
+    """
+    Download ontology of interest and convert to SQLite database.
+    :param ontology_id: The OBO identifier of the ontology.
+    :param refresh: Whether to force refresh the cached ontology.
+    :returns adapter: The connector to the ontology database.
+    """
+
+    if refresh:
+        clear_cached_db(ontology_id)
+
+    # Download and cache the ontology if not already present
+    adapter = get_adapter(f"sqlite:obo:{ontology_id}")
+
+    # Display ontology metadata
+    try:
+        for ont in adapter.ontologies():
+            metadata = adapter.ontology_metadata_map(ont)
+            version_iri = metadata.get("owl:versionIRI", "unknown")
+            logger.debug(f"{ontology_id.upper()} version: {version_iri}")
+    except Exception as e:
+        logger.debug(f"Could not fetch version metadata for {ontology_id}: {e}")
+
+    return adapter
+
+
+
+
+def load_config(config_path):
+    try:
+        with open(config_path, 'r') as f:
+            config = yaml.safe_load(f)
+    except Exception as e:
+        click.echo(f"Error reading config file: {e}", err=True)
+        sys.exit(1)
+
+    # Basic validation
+    required_keys = ["ontologies", "columns_to_annotate"]
+    for key in required_keys:
+        if key not in config:
+            click.echo(f"Missing required config key: {key}", err=True)
+            sys.exit(1)
+
+    if not isinstance(config["ontologies"], list) or not all(isinstance(o, str) for o in config["ontologies"]):
+        click.echo("Config error: 'ontologies' should be a list of strings", err=True)
+        sys.exit(1)
+
+    if not isinstance(config["columns_to_annotate"], list) or not all(isinstance(c, str) for c in config["columns_to_annotate"]):
+        click.echo("Config error: 'columns_to_annotate' should be a list of strings", err=True)
+        sys.exit(1)
+
+    return config
+
+
+def search_ontology(ontology_id: str, adapter: SqlImplementation, df: pd.DataFrame, columns: list, config: dict) -> pd.DataFrame:
+    """
+    Search for exact matches to the ontology term label.
+    :param adapter: The connector to the ontology database.
+    :param df: Dataframe containing terms to search and find matches to the ontology.
+    """
+
+    ontology_prefix = 'hpo' if ontology_id.lower() == 'hp' else ontology_id
+    exact_search_results = []
+
+    column_to_use = columns[0]  # assuming just one for now
+
+    # Create a tqdm instance to display search progress
+    #progress_bar = tqdm(total=len(df), desc="Processing Rows", unit="row")
+
+    for index, row in df.iterrows():
+        for result in adapter.basic_search(row[column_to_use], config=config):
+            exact_search_results.append([row["UUID"], result, adapter.label(result)])
+            # Update the progress bar
+            #progress_bar.update(1)
+
+    # Close the progress bar
+    #progress_bar.close()
+
+    # Convert search results to dataframe
+    results_df = pd.DataFrame(exact_search_results)
+    logger.debug(results_df.head())
+
+    # Add column headers
+    if results_df.empty:
+        results_df = pd.DataFrame(columns=['UUID', f'{ontology_prefix}_result_curie', f'{ontology_prefix}_result_label'])
+    else:
+        results_df.columns = ['UUID', f'{ontology_prefix}_result_curie', f'{ontology_prefix}_result_label']
+
+    # Filter rows to keep those where '{ontology}_result_curie' starts with the "ontology_id", keep in mind hp vs. hpo
+    # TODO: Decide whether these results should still be filtered out
+    results_df = results_df[results_df[f'{ontology_prefix}_result_curie'].str.startswith(f'{ontology_id}'.upper())]
+
+    # Group by 'UUID' and aggregate curie and label into lists
+    search_results_df = results_df.groupby('UUID').agg({
+        f'{ontology_prefix}_result_curie': list,
+        f'{ontology_prefix}_result_label': list
+    }).reset_index()
+
+    # Convert lists to strings
+    search_results_df[f'{ontology_prefix}_result_curie'] = search_results_df[f'{ontology_prefix}_result_curie'].astype(str).str.strip('[]').str.replace("'", "")
+    search_results_df[f'{ontology_prefix}_result_label'] = search_results_df[f'{ontology_prefix}_result_label'].astype(str).str.strip('[]').str.replace("'", "")
+
+    # TODO: Maintain individual columns of result_match_type for each ontology searched!
+    # Add column to indicate type of search match
+    if str(config.properties[0]) == 'LABEL':
+        search_results_df[f'{ontology_prefix}_result_match_type'] = np.where(
+            search_results_df[f'{ontology_prefix}_result_curie'].notnull(), f'{ontology_prefix.upper()}_EXACT_LABEL', '')
+    
+    if str(config.properties[0]) == 'ALIAS':
+        search_results_df[f'{ontology_prefix}_result_match_type'] = np.where(
+            search_results_df[f'{ontology_prefix}_result_curie'].notnull(), f'{ontology_prefix.upper()}_EXACT_ALIAS', '')
+
+    return search_results_df
+
+
+
+def clean_json_response(content: str) -> str:
+    """
+    Clean common formatting issues in GPT output before JSON parsing.
+    """
+    # Replace smart quotes with standard quotes
+    content = content.replace("“", "\"").replace("”", "\"").replace("‘", "'").replace("’", "'")
+
+    # Strip any leading junk like ```json ... ```
+    content = re.sub(r"^```(json)?\s*", "", content.strip())
+    content = re.sub(r"\s*```$", "", content.strip())
+
+    return content
+
+
+def get_alternative_names(term: str) -> dict:
+    prompt = (
+        f"For the term '{term}', return a JSON object with three keys:\n"
+        "- 'input': the original term\n"
+        "- 'alt_names': a list of up to five alternative names\n"
+        "- 'source': the string 'openai'\n\n"
+        "Example format:\n"
+        "{\n"
+        '  "input": "hole in heart",\n'
+        '  "alt_names": [\n'
+        '    "atrial septal defect",\n'
+        '    "ventricular septal defect",\n'
+        '    "congenital heart defect",\n'
+        '    "septal defect",\n'
+        '    "cardiac shunt"\n'
+        "  ],\n"
+        '  "source": "openai"\n'
+        "}"
+    )
+
+
+    try:
+        response = openai.ChatCompletion.create(
+            model="gpt-4o",
+            messages=[{"role": "user", "content": prompt}],
+            temperature=0.5,
+            max_tokens=150,
+        )
+        content = response['choices'][0]['message']['content']
+        cleaned = clean_json_response(content)
+        result = json.loads(cleaned)
+        return result
+    except json.JSONDecodeError:
+        logger.debug(f"Could not parse JSON: {content}")
+        return []
+    except Exception as e:
+        logger.debug(f"Error retrieving alt names for '{term}': {e}")
+        return []
+
+
+def generate_uuid() -> str:
+    """Function to generate UUID"""
+    return str(uuid.uuid4())
+
+
+def _clean_up_columns(df: pd.DataFrame, ontology_id: str) -> pd.DataFrame:
+    """
+    Copy over the search results to the columns from the input dataframe
+    amd remove the extra columns added with the search results.
+    :param df: The dataframe from the merge of the search results with the original dataframe.
+    :param ontology_id: The ontology identifier, ie. the ontology being searched  
+    """
+    ontology_prefix = 'hpo' if ontology_id.lower() == 'hp' else ontology_id
+
+    # Handle clean-up after a second round of synonym search
+    if f'{ontology_prefix}_result_match_type_x' in df.columns and f'{ontology_prefix}_result_match_type_y' in df.columns:
+        # Copy result label values to original df column and then drop result column
+        df[f'{ontology_prefix}Label'] = np.where(df[f'{ontology_prefix}_result_label'].notnull(), df[f'{ontology_prefix}_result_label'], df[f'{ontology_prefix}Label'])
+        df.drop([f'{ontology_prefix}_result_label'], axis=1, inplace=True)
+
+        # Copy result curie values to original df column and then drop result column
+        df[f'{ontology_prefix}Code'] = np.where(df[f'{ontology_prefix}_result_curie'].notnull(), df[f'{ontology_prefix}_result_curie'], df[f'{ontology_prefix}Code'])
+        df.drop([f'{ontology_prefix}_result_curie'], axis=1, inplace=True)
+
+        # Copy type of result match to original df column and then drop result column and rename original df column
+        df[f'{ontology_prefix}_result_match_type_x'] = np.where(df[f'{ontology_prefix}_result_match_type_y'].notnull(), df[f'{ontology_prefix}_result_match_type_y'], df[f'{ontology_prefix}_result_match_type_x'])
+        df.drop([f'{ontology_prefix}_result_match_type_y'], axis=1, inplace=True)
+        df = df.rename(columns={f'{ontology_prefix}_result_match_type_x': f'{ontology_prefix}_result_match_type'})
+    else:
+        # Update values in the existing columns
+        df[f'{ontology_prefix}Label'] = df[f'{ontology_prefix}_result_label']
+        df[f'{ontology_prefix}Code'] = df[f'{ontology_prefix}_result_curie']
+    
+        # Drop the search_results columns
+        df.drop([f'{ontology_prefix}_result_label'], axis=1, inplace=True)
+        df.drop([f'{ontology_prefix}_result_curie'], axis=1, inplace=True)
+
+
+    return df
+
+
+def _check_ontology_versions(ontology_ids: tuple):
+    """
+    Check and print the cached ontology versions for each ID.
+    :param ontology_ids: Tuple of ontology IDs to check.
+    """
+    logger.debug("\nChecking local ontology versions...")
+    for oid in ontology_ids:
+        try:
+            adapter = get_adapter(f"sqlite:obo:{oid}")
+            for ont in adapter.ontologies():
+                meta = adapter.ontology_metadata_map(ont)
+                version = meta.get("owl:versionIRI", "Unknown")
+                logger.debug(f"  - {oid.upper()}: {version}")
+        except Exception as e:
+            logger.debug(f"  - {oid.upper()}: Error loading version ({e})")
+
+
+
+def custom_join(series):
+    non_empty = series.dropna().astype(str).str.strip()
+    non_empty = [v for v in non_empty if v]
+    unique_vals = list(dict.fromkeys(non_empty))
+    return ', '.join(unique_vals) if unique_vals else ''
+
+
+
+@main.command("annotate")
+@click.option('--config', type=click.Path(exists=True), help='Path to YAML config file')
+@click.option('--input_file', type=click.Path(exists=True), required=True, help="Path to data file to annotate")
+@click.option('--output_dir', type=click.Path(), required=False, help='Optional override for output directory')
+@click.option('--refresh', is_flag=True, help='Force refresh of ontology cache')
+@click.option('--no_openai', is_flag=True, help='Disable OpenAI-based fallback searches')
+def annotate(config: str, input_file: str, output_dir: str, refresh: bool, no_openai: bool):
+    """
+    Annotate a data file with ontology terms.
+    :param config: Path to the config file.
+    :param data_filename: The name of the file with terms to search for ontology matches.
+    """
+
+    config_data = load_config(config)
+
+    ontologies = config_data["ontologies"]
+    columns = config_data["columns_to_annotate"]
+
+    if not ontologies or not columns:
+        raise click.ClickException("Config file must contain 'ontologies' and 'columns_to_annotate'.")
+    
+    # Determine output directory from CLI or config or fallback
+    output_dir = Path(output_dir or config_data.get("output_dir", "data/output/")).resolve()
+    output_dir.mkdir(parents=True, exist_ok=True)
+
+    click.echo(f"Using ontologies: {ontologies}")
+    click.echo(f"Annotating columns: {columns}")
+    click.echo(f"Output directory: {output_dir}")
+    if refresh:
+        click.echo("Refresh mode enabled")
+
+    oid = tuple(o.lower() for o in config_data["ontologies"])
+ 
+    filename_prefix = '_'.join(oid)
+
+    # Get the current formatted timestamp
+    timestamp = datetime.now()
+    formatted_timestamp = timestamp.strftime("%Y%m%d-%H%M%S")
+
+    # Read in the data file
+    file_path = Path(input_file).resolve()
+
+    data_df = pd.read_csv(file_path, sep='\t')
+    logger.debug(data_df[columns])
+    
+    # Add a new column 'UUID' with unique identifier values
+    data_df['UUID'] = data_df.apply(lambda row: generate_uuid(), axis=1)
+    logger.debug(data_df.nunique())
+    logger.info("Number of total rows in dataframe: %s", len(data_df))
+
+    # Check ontology versions 
+    _check_ontology_versions(oid)
+
+
+    # Collect all annotation results
+    all_final_results = []
+
+    for ontology_id in oid:
+        ontology_prefix = 'hpo' if ontology_id.lower() == 'hp' else ontology_id
+        adapter = fetch_ontology(ontology_id, refresh=refresh)
+
+        # === Exact LABEL match ===
+        label_config = SearchConfiguration(properties=[SearchProperty.LABEL], force_case_insensitive=True)
+        label_hits_df = search_ontology(ontology_id, adapter, data_df, columns, label_config)
+        label_hits_df["annotation_source"] = "oak"
+        label_hits_df["annotation_method"] = "exact_label"
+        label_hits_df["ontology"] = ontology_id.lower()
+
+        # Filter unmatched
+        matched_uuids_label = set(label_hits_df["UUID"])
+        filtered_df = data_df[~data_df["UUID"].isin(matched_uuids_label)]
+
+        # === Synonym match ===
+        synonym_config = SearchConfiguration(properties=[SearchProperty.ALIAS], force_case_insensitive=True)
+        synonym_hits_df = search_ontology(ontology_id, adapter, filtered_df, columns, synonym_config)
+        synonym_hits_df["annotation_source"] = "oak"
+        synonym_hits_df["annotation_method"] = "exact_synonym"
+        synonym_hits_df["ontology"] = ontology_id.lower()
+
+        matched_uuids_syn = set(synonym_hits_df["UUID"])
+        filtered_df = filtered_df[~filtered_df["UUID"].isin(matched_uuids_syn)]
+
+        # === OpenAI alternative names ===
+        openai_hits = []
+        if not no_openai:
+            for term in tqdm(filtered_df[columns[0]].dropna().unique()):
+                # Normalize the term
+                match = re.match(r"^(.*?)\s*\((\w{3,5})\)$", term.strip())
+                normalized_term = match.group(1).strip() if match else term.strip()
+
+                alt_response = get_alternative_names(normalized_term)
+                if not alt_response:
+                    continue
+
+                uuid_series = filtered_df[filtered_df[columns[0]] == term]["UUID"]
+                if uuid_series.empty:
+                    continue
+                uuid = uuid_series.iloc[0]
+
+                found_match = False
+
+                for alt in alt_response.get("alt_names", []):
+                    # First: exact label match
+                    df_search = pd.DataFrame({"UUID": [uuid], columns[0]: [alt]})
+                    label_match_df = search_ontology(ontology_id, adapter, df_search, columns, label_config)
+                    if not label_match_df.empty:
+                        label_match_df["annotation_source"] = "openai"
+                        label_match_df["annotation_method"] = "alt_term_label"
+                        label_match_df["original_term"] = normalized_term
+                        label_match_df["ontology"] = ontology_id.lower()
+                        openai_hits.append(label_match_df)
+                        found_match = True
+                        break
+
+                    # Then: synonym match if label fails
+                    synonym_match_df = search_ontology(ontology_id, adapter, df_search, columns, synonym_config)
+                    if not synonym_match_df.empty:
+                        synonym_match_df["annotation_source"] = "openai"
+                        synonym_match_df["annotation_method"] = "alt_term_synonym"
+                        synonym_match_df["original_term"] = normalized_term
+                        synonym_match_df["ontology"] = ontology_id.lower()
+                        openai_hits.append(synonym_match_df)
+                        found_match = True
+                        break
+
+                if not found_match:
+                    openai_hits.append(pd.DataFrame([{
+                        "UUID": uuid,
+                        "annotation_source": "openai",
+                        "annotation_method": "no_match",
+                        "original_term": normalized_term,
+                        "alt_names": ', '.join(alt_response.get("alt_names", [])),
+                        "ontology": ontology_id.lower()
+                    }]))
+
+
+        openai_hits_df = pd.concat(openai_hits, ignore_index=True) if openai_hits else pd.DataFrame()
+        results_sources = [label_hits_df, synonym_hits_df]
+        if not openai_hits_df.empty:
+            results_sources.append(openai_hits_df)
+
+        results_df = pd.concat(results_sources, ignore_index=True)
+        if not results_df.empty:
+            all_final_results.append(results_df)
+
+    # === Exit if no results  ===
+    if not all_final_results:
+        logger.warning("No annotation results found for any ontology.")
+        return
+
+    # === Combine all results ===
+    full_results = pd.concat(all_final_results, ignore_index=True)
+
+    # === Merge with input metadata ===
+    data_df["UUID"] = data_df["UUID"].astype(str).str.strip()
+    full_results["UUID"] = full_results["UUID"].astype(str).str.strip()
+    final_df = pd.merge(data_df, full_results, on="UUID", how="left")
+
+    # Drop duplicated or unnecessary columns
+    final_df.drop(columns=["source_column_value_y", "original_term"], inplace=True, errors="ignore")
+
+    # === Save final output ===
+    final_df = final_df.fillna("")
+    output_path = Path(output_dir) / f"{filename_prefix}-combined_ontology_annotations-{formatted_timestamp}.tsv"
+    final_df.to_csv(output_path, sep='\t', index=False)
+    print(f"\nAnnotation results written to: {output_path}")
+
+
+if __name__ == "__main__":
+    main()
\ No newline at end of file
diff --git a/pipeline.Makefile b/pipeline.Makefile
index a2779fb..7f14e6a 100644
--- a/pipeline.Makefile
+++ b/pipeline.Makefile
@@ -99,6 +99,17 @@ schema-create: $(SCHEMA_FILE)
 schema-lint: $(SCHEMA_FILE)
 	$(RUN) linkml-lint $<
 
+.PHONY: annotate
+annotate:
+	@echo "** Annotate data file with ontology terms using config and input_file: $(input_file)"
+	@cmd="python harmonica/harmonize.py annotate \
+		--config config/config.yml \
+		--input_file $(input_file)"; \
+	if [ -n "$(output_dir)" ]; then cmd="$$cmd --output_dir $(output_dir)"; fi; \
+	if [ -n "$(refresh)" ]; then cmd="$$cmd --refresh"; fi; \
+	echo $$cmd; \
+	eval $$cmd
+
 .PHONY: help
 .PHONY: schema-help
 help::
diff --git a/poetry.lock b/poetry.lock
index 6bca847..2e3747d 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,4 +1,134 @@
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+
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+]
+
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+]
+
+[package.dependencies]
+aiohappyeyeballs = ">=2.3.0"
+aiosignal = ">=1.1.2"
+attrs = ">=17.3.0"
+frozenlist = ">=1.1.1"
+multidict = ">=4.5,<7.0"
+propcache = ">=0.2.0"
+yarl = ">=1.17.0,<2.0"
+
+[package.extras]
+speedups = ["Brotli ; platform_python_implementation == \"CPython\"", "aiodns (>=3.2.0) ; sys_platform == \"linux\" or sys_platform == \"darwin\"", "brotlicffi ; platform_python_implementation != \"CPython\""]
+
+[[package]]
+name = "aiosignal"
+version = "1.3.2"
+description = "aiosignal: a list of registered asynchronous callbacks"
+optional = false
+python-versions = ">=3.9"
+groups = ["main"]
+files = [
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+]
+
+[package.dependencies]
+frozenlist = ">=1.1.0"
 
 [[package]]
 name = "airium"
@@ -96,12 +226,12 @@ files = [
 ]
 
 [package.extras]
-benchmark = ["cloudpickle", "hypothesis", "mypy (>=1.11.1)", "pympler", "pytest (>=4.3.0)", "pytest-codspeed", "pytest-mypy-plugins", "pytest-xdist[psutil]"]
-cov = ["cloudpickle", "coverage[toml] (>=5.3)", "hypothesis", "mypy (>=1.11.1)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"]
-dev = ["cloudpickle", "hypothesis", "mypy (>=1.11.1)", "pre-commit-uv", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"]
+benchmark = ["cloudpickle ; platform_python_implementation == \"CPython\"", "hypothesis", "mypy (>=1.11.1) ; platform_python_implementation == \"CPython\" and python_version >= \"3.10\"", "pympler", "pytest (>=4.3.0)", "pytest-codspeed", "pytest-mypy-plugins ; platform_python_implementation == \"CPython\" and python_version >= \"3.10\"", "pytest-xdist[psutil]"]
+cov = ["cloudpickle ; platform_python_implementation == \"CPython\"", "coverage[toml] (>=5.3)", "hypothesis", "mypy (>=1.11.1) ; platform_python_implementation == \"CPython\" and python_version >= \"3.10\"", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins ; platform_python_implementation == \"CPython\" and python_version >= \"3.10\"", "pytest-xdist[psutil]"]
+dev = ["cloudpickle ; platform_python_implementation == \"CPython\"", "hypothesis", "mypy (>=1.11.1) ; platform_python_implementation == \"CPython\" and python_version >= \"3.10\"", "pre-commit-uv", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins ; platform_python_implementation == \"CPython\" and python_version >= \"3.10\"", "pytest-xdist[psutil]"]
 docs = ["cogapp", "furo", "myst-parser", "sphinx", "sphinx-notfound-page", "sphinxcontrib-towncrier", "towncrier (<24.7)"]
-tests = ["cloudpickle", "hypothesis", "mypy (>=1.11.1)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"]
-tests-mypy = ["mypy (>=1.11.1)", "pytest-mypy-plugins"]
+tests = ["cloudpickle ; platform_python_implementation == \"CPython\"", "hypothesis", "mypy (>=1.11.1) ; platform_python_implementation == \"CPython\" and python_version >= \"3.10\"", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins ; platform_python_implementation == \"CPython\" and python_version >= \"3.10\"", "pytest-xdist[psutil]"]
+tests-mypy = ["mypy (>=1.11.1) ; platform_python_implementation == \"CPython\" and python_version >= \"3.10\"", "pytest-mypy-plugins ; platform_python_implementation == \"CPython\" and python_version >= \"3.10\""]
 
 [[package]]
 name = "babel"
@@ -264,7 +394,7 @@ pyproject_hooks = "*"
 
 [package.extras]
 docs = ["furo (>=2023.08.17)", "sphinx (>=7.0,<8.0)", "sphinx-argparse-cli (>=1.5)", "sphinx-autodoc-typehints (>=1.10)", "sphinx-issues (>=3.0.0)"]
-test = ["build[uv,virtualenv]", "filelock (>=3)", "pytest (>=6.2.4)", "pytest-cov (>=2.12)", "pytest-mock (>=2)", "pytest-rerunfailures (>=9.1)", "pytest-xdist (>=1.34)", "setuptools (>=42.0.0)", "setuptools (>=56.0.0)", "setuptools (>=56.0.0)", "setuptools (>=67.8.0)", "wheel (>=0.36.0)"]
+test = ["build[uv,virtualenv]", "filelock (>=3)", "pytest (>=6.2.4)", "pytest-cov (>=2.12)", "pytest-mock (>=2)", "pytest-rerunfailures (>=9.1)", "pytest-xdist (>=1.34)", "setuptools (>=42.0.0) ; python_version < \"3.10\"", "setuptools (>=56.0.0) ; python_version == \"3.10\"", "setuptools (>=56.0.0) ; python_version == \"3.11\"", "setuptools (>=67.8.0) ; python_version >= \"3.12\"", "wheel (>=0.36.0)"]
 typing = ["build[uv]", "importlib-metadata (>=5.1)", "mypy (>=1.9.0,<1.10.0)", "tomli", "typing-extensions (>=3.7.4.3)"]
 uv = ["uv (>=0.1.18)"]
 virtualenv = ["virtualenv (>=20.0.35)"]
@@ -322,8 +452,8 @@ attrs = ">=23.1.0"
 bson = ["pymongo (>=4.4.0)"]
 cbor2 = ["cbor2 (>=5.4.6)"]
 msgpack = ["msgpack (>=1.0.5)"]
-msgspec = ["msgspec (>=0.18.5)"]
-orjson = ["orjson (>=3.9.2)"]
+msgspec = ["msgspec (>=0.18.5) ; implementation_name == \"cpython\""]
+orjson = ["orjson (>=3.9.2) ; implementation_name == \"cpython\""]
 pyyaml = ["pyyaml (>=6.0)"]
 tomlkit = ["tomlkit (>=0.11.8)"]
 ujson = ["ujson (>=5.7.0)"]
@@ -578,7 +708,7 @@ click = ["click"]
 docs = ["sphinx (<8)", "sphinx-automodapi", "sphinx-rtd-theme"]
 numpy = ["numpy"]
 optuna = ["optuna"]
-ray = ["ray[tune] (<2.0.0)"]
+ray = ["ray[tune] (<2.0.0) ; python_version < \"3.9\""]
 sklearn = ["scikit-learn"]
 tabulate = ["tabulate"]
 tests = ["coverage", "docdata", "pytest"]
@@ -759,10 +889,10 @@ files = [
 cffi = {version = ">=1.12", markers = "platform_python_implementation != \"PyPy\""}
 
 [package.extras]
-docs = ["sphinx (>=5.3.0)", "sphinx-rtd-theme (>=3.0.0)"]
+docs = ["sphinx (>=5.3.0)", "sphinx-rtd-theme (>=3.0.0) ; python_version >= \"3.8\""]
 docstest = ["pyenchant (>=3)", "readme-renderer (>=30.0)", "sphinxcontrib-spelling (>=7.3.1)"]
-nox = ["nox (>=2024.4.15)", "nox[uv] (>=2024.3.2)"]
-pep8test = ["check-sdist", "click (>=8.0.1)", "mypy (>=1.4)", "ruff (>=0.3.6)"]
+nox = ["nox (>=2024.4.15)", "nox[uv] (>=2024.3.2) ; python_version >= \"3.8\""]
+pep8test = ["check-sdist ; python_version >= \"3.8\"", "click (>=8.0.1)", "mypy (>=1.4)", "ruff (>=0.3.6)"]
 sdist = ["build (>=1.0.0)"]
 ssh = ["bcrypt (>=3.1.5)"]
 test = ["certifi (>=2024)", "cryptography-vectors (==44.0.0)", "pretend (>=0.7)", "pytest (>=7.4.0)", "pytest-benchmark (>=4.0)", "pytest-cov (>=2.10.1)", "pytest-xdist (>=3.5.0)"]
@@ -832,7 +962,7 @@ files = [
 wrapt = ">=1.10,<2"
 
 [package.extras]
-dev = ["PyTest", "PyTest-Cov", "bump2version (<1)", "setuptools", "tox"]
+dev = ["PyTest", "PyTest-Cov", "bump2version (<1)", "setuptools ; python_version >= \"3.12\"", "tox"]
 
 [[package]]
 name = "deprecation"
@@ -1147,7 +1277,7 @@ files = [
 [package.extras]
 docs = ["furo (>=2024.8.6)", "sphinx (>=8.0.2)", "sphinx-autodoc-typehints (>=2.4.1)"]
 testing = ["covdefaults (>=2.3)", "coverage (>=7.6.1)", "diff-cover (>=9.2)", "pytest (>=8.3.3)", "pytest-asyncio (>=0.24)", "pytest-cov (>=5)", "pytest-mock (>=3.14)", "pytest-timeout (>=2.3.1)", "virtualenv (>=20.26.4)"]
-typing = ["typing-extensions (>=4.12.2)"]
+typing = ["typing-extensions (>=4.12.2) ; python_version < \"3.11\""]
 
 [[package]]
 name = "fqdn"
@@ -1161,6 +1291,120 @@ files = [
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 ]
 
+[[package]]
+name = "frozenlist"
+version = "1.6.0"
+description = "A list-like structure which implements collections.abc.MutableSequence"
+optional = false
+python-versions = ">=3.9"
+groups = ["main"]
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+
 [[package]]
 name = "funowl"
 version = "0.2.3"
@@ -1231,7 +1475,7 @@ gitdb = ">=4.0.1,<5"
 
 [package.extras]
 doc = ["sphinx (>=7.1.2,<7.2)", "sphinx-autodoc-typehints", "sphinx_rtd_theme"]
-test = ["coverage[toml]", "ddt (>=1.1.1,!=1.4.3)", "mock", "mypy", "pre-commit", "pytest (>=7.3.1)", "pytest-cov", "pytest-instafail", "pytest-mock", "pytest-sugar", "typing-extensions"]
+test = ["coverage[toml]", "ddt (>=1.1.1,!=1.4.3)", "mock ; python_version < \"3.8\"", "mypy", "pre-commit", "pytest (>=7.3.1)", "pytest-cov", "pytest-instafail", "pytest-mock", "pytest-sugar", "typing-extensions ; python_version < \"3.11\""]
 
 [[package]]
 name = "google"
@@ -1272,7 +1516,7 @@ requests = ">=2.18.0,<3.0.0.dev0"
 
 [package.extras]
 async-rest = ["google-auth[aiohttp] (>=2.35.0,<3.0.dev0)"]
-grpc = ["grpcio (>=1.33.2,<2.0dev)", "grpcio (>=1.49.1,<2.0dev)", "grpcio-status (>=1.33.2,<2.0.dev0)", "grpcio-status (>=1.49.1,<2.0.dev0)"]
+grpc = ["grpcio (>=1.33.2,<2.0dev)", "grpcio (>=1.49.1,<2.0dev) ; python_version >= \"3.11\"", "grpcio-status (>=1.33.2,<2.0.dev0)", "grpcio-status (>=1.49.1,<2.0.dev0) ; python_version >= \"3.11\""]
 grpcgcp = ["grpcio-gcp (>=0.2.2,<1.0.dev0)"]
 grpcio-gcp = ["grpcio-gcp (>=0.2.2,<1.0.dev0)"]
 
@@ -1698,12 +1942,12 @@ files = [
 zipp = ">=3.20"
 
 [package.extras]
-check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1)"]
+check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1) ; sys_platform != \"cygwin\""]
 cover = ["pytest-cov"]
 doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
 enabler = ["pytest-enabler (>=2.2)"]
 perf = ["ipython"]
-test = ["flufl.flake8", "importlib_resources (>=1.3)", "jaraco.test (>=5.4)", "packaging", "pyfakefs", "pytest (>=6,!=8.1.*)", "pytest-perf (>=0.9.2)"]
+test = ["flufl.flake8", "importlib_resources (>=1.3) ; python_version < \"3.9\"", "jaraco.test (>=5.4)", "packaging", "pyfakefs", "pytest (>=6,!=8.1.*)", "pytest-perf (>=0.9.2)"]
 type = ["pytest-mypy"]
 
 [[package]]
@@ -1719,7 +1963,7 @@ files = [
 ]
 
 [package.extras]
-check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1)"]
+check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1) ; sys_platform != \"cygwin\""]
 cover = ["pytest-cov"]
 doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
 enabler = ["pytest-enabler (>=2.2)"]
@@ -1743,7 +1987,7 @@ more_itertools = ">=8.5.0"
 typeguard = ">=4.0.1"
 
 [package.extras]
-check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1)"]
+check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1) ; sys_platform != \"cygwin\""]
 cover = ["pytest-cov"]
 doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
 enabler = ["pytest-enabler (>=2.2)"]
@@ -1834,7 +2078,7 @@ files = [
 
 [package.extras]
 doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
-test = ["portend", "pytest (>=6,!=8.1.*)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-mypy", "pytest-ruff (>=0.2.1)"]
+test = ["portend", "pytest (>=6,!=8.1.*)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-mypy", "pytest-ruff (>=0.2.1) ; sys_platform != \"cygwin\""]
 
 [[package]]
 name = "jaraco-functools"
@@ -1852,7 +2096,7 @@ files = [
 more-itertools = "*"
 
 [package.extras]
-check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1)"]
+check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1) ; sys_platform != \"cygwin\""]
 cover = ["pytest-cov"]
 doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
 enabler = ["pytest-enabler (>=2.2)"]
@@ -1874,7 +2118,7 @@ files = [
 
 [package.extras]
 test = ["async-timeout", "pytest", "pytest-asyncio (>=0.17)", "pytest-trio", "testpath", "trio"]
-trio = ["async_generator", "trio"]
+trio = ["async_generator ; python_version == \"3.6\"", "trio"]
 
 [[package]]
 name = "jinja2"
@@ -2061,7 +2305,7 @@ pywin32-ctypes = {version = ">=0.2.0", markers = "sys_platform == \"win32\""}
 SecretStorage = {version = ">=3.2", markers = "sys_platform == \"linux\""}
 
 [package.extras]
-check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1)"]
+check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1) ; sys_platform != \"cygwin\""]
 completion = ["shtab (>=1.1.0)"]
 cover = ["pytest-cov"]
 doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
@@ -2161,9 +2405,9 @@ watchdog = ">=0.9.0"
 
 [package.extras]
 black = ["black (>=24.0.0)"]
-numpydantic = ["numpydantic (>=1.6.1)"]
+numpydantic = ["numpydantic (>=1.6.1) ; python_version >= \"3.9\""]
 shacl = ["pyshacl (>=0.25.0,<0.26.0)"]
-tests = ["black (>=24.0.0)", "numpydantic (>=1.6.1)", "pyshacl (>=0.25.0,<0.26.0)"]
+tests = ["black (>=24.0.0)", "numpydantic (>=1.6.1) ; python_version >= \"3.9\"", "pyshacl (>=0.25.0,<0.26.0)"]
 
 [[package]]
 name = "linkml-dataops"
@@ -2569,7 +2813,7 @@ watchdog = ">=2.0"
 
 [package.extras]
 i18n = ["babel (>=2.9.0)"]
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 name = "mkdocs-get-deps"
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 tests = ["coverage", "pytest", "unittest-templates"]
 
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 python-dateutil = ">=2.8,<3.0"
 
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 [[package]]
 name = "proto-plus"
 version = "1.26.0"
@@ -3516,7 +4005,7 @@ typing-extensions = ">=4.12.2"
 
 [package.extras]
 email = ["email-validator (>=2.0.0)"]
-timezone = ["tzdata"]
+timezone = ["tzdata ; python_version >= \"3.9\" and platform_system == \"Windows\""]
 
 [[package]]
 name = "pydantic-core"
@@ -4484,7 +4973,7 @@ description = "C version of reader, parser and emitter for ruamel.yaml derived f
 optional = false
 python-versions = ">=3.9"
 groups = ["main"]
-markers = "platform_python_implementation == \"CPython\" and python_version < \"3.13\""
+markers = "platform_python_implementation == \"CPython\" and python_version == \"3.12\""
 files = [
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@@ -4679,7 +5168,7 @@ numpy = ">=1.23.5,<2.5"
 [package.extras]
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+test = ["Cython", "array-api-strict (>=2.0,<2.1.1)", "asv", "gmpy2", "hypothesis (>=6.30)", "meson", "mpmath", "ninja ; sys_platform != \"emscripten\"", "pooch", "pytest", "pytest-cov", "pytest-timeout", "pytest-xdist", "scikit-umfpack", "threadpoolctl"]
 
 [[package]]
 name = "secretstorage"
@@ -4728,13 +5217,13 @@ files = [
 ]
 
 [package.extras]
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-type = ["importlib_metadata (>=7.0.2)", "jaraco.develop (>=7.21)", "mypy (==1.14.*)", "pytest-mypy"]
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 [[package]]
 name = "shellingham"
@@ -5187,8 +5676,8 @@ intervals = ["intervals (>=0.7.1)"]
 password = ["passlib (>=1.6,<2.0)"]
 pendulum = ["pendulum (>=2.0.5)"]
 phone = ["phonenumbers (>=5.9.2)"]
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+test = ["Jinja2 (>=2.3)", "Pygments (>=1.2)", "backports.zoneinfo ; python_version < \"3.9\"", "docutils (>=0.10)", "flake8 (>=2.4.0)", "flexmock (>=0.9.7)", "isort (>=4.2.2)", "pg8000 (>=1.12.4)", "psycopg2 (>=2.5.1)", "psycopg2cffi (>=2.8.1)", "pymysql", "pyodbc", "pytest (>=2.7.1)", "python-dateutil (>=2.6)", "pytz (>=2014.2)"]
+test-all = ["Babel (>=1.3)", "Jinja2 (>=2.3)", "Pygments (>=1.2)", "arrow (>=0.3.4)", "backports.zoneinfo ; python_version < \"3.9\"", "colour (>=0.0.4)", "cryptography (>=0.6)", "docutils (>=0.10)", "flake8 (>=2.4.0)", "flexmock (>=0.9.7)", "furl (>=0.4.1)", "intervals (>=0.7.1)", "isort (>=4.2.2)", "passlib (>=1.6,<2.0)", "pendulum (>=2.0.5)", "pg8000 (>=1.12.4)", "phonenumbers (>=5.9.2)", "psycopg2 (>=2.5.1)", "psycopg2cffi (>=2.8.1)", "pymysql", "pyodbc", "pytest (>=2.7.1)", "python-dateutil", "python-dateutil (>=2.6)", "pytz (>=2014.2)"]
 timezone = ["python-dateutil"]
 url = ["furl (>=0.4.1)"]
 
@@ -5395,7 +5884,7 @@ typing_extensions = ">=4.10.0"
 
 [package.extras]
 doc = ["Sphinx (>=7)", "packaging", "sphinx-autodoc-typehints (>=1.2.0)", "sphinx-rtd-theme (>=1.3.0)"]
-test = ["coverage[toml] (>=7)", "mypy (>=1.2.0)", "pytest (>=7)"]
+test = ["coverage[toml] (>=7)", "mypy (>=1.2.0) ; platform_python_implementation != \"PyPy\"", "pytest (>=7)"]
 
 [[package]]
 name = "typer"
@@ -5522,7 +6011,7 @@ files = [
 ]
 
 [package.extras]
-brotli = ["brotli (>=1.0.9)", "brotlicffi (>=0.8.0)"]
+brotli = ["brotli (>=1.0.9) ; platform_python_implementation == \"CPython\"", "brotlicffi (>=0.8.0) ; platform_python_implementation != \"CPython\""]
 h2 = ["h2 (>=4,<5)"]
 socks = ["pysocks (>=1.5.6,!=1.5.7,<2.0)"]
 zstd = ["zstandard (>=0.18.0)"]
@@ -5561,7 +6050,7 @@ platformdirs = ">=3.9.1,<5"
 
 [package.extras]
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+test = ["covdefaults (>=2.3)", "coverage (>=7.2.7)", "coverage-enable-subprocess (>=1)", "flaky (>=3.7)", "packaging (>=23.1)", "pytest (>=7.4)", "pytest-env (>=0.8.2)", "pytest-freezer (>=0.4.8) ; platform_python_implementation == \"PyPy\" or platform_python_implementation == \"CPython\" and sys_platform == \"win32\" and python_version >= \"3.13\"", "pytest-mock (>=3.11.1)", "pytest-randomly (>=3.12)", "pytest-timeout (>=2.1)", "setuptools (>=68)", "time-machine (>=2.10) ; platform_python_implementation == \"CPython\""]
 
 [[package]]
 name = "watchdog"
@@ -5806,6 +6295,125 @@ files = [
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 ]
 
+[[package]]
+name = "yarl"
+version = "1.20.0"
+description = "Yet another URL library"
+optional = false
+python-versions = ">=3.9"
+groups = ["main"]
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+    {file = "yarl-1.20.0-cp39-cp39-win_amd64.whl", hash = "sha256:d4fad6e5189c847820288286732075f213eabf81be4d08d6cc309912e62be5b7"},
+    {file = "yarl-1.20.0-py3-none-any.whl", hash = "sha256:5d0fe6af927a47a230f31e6004621fd0959eaa915fc62acfafa67ff7229a3124"},
+    {file = "yarl-1.20.0.tar.gz", hash = "sha256:686d51e51ee5dfe62dec86e4866ee0e9ed66df700d55c828a615640adc885307"},
+]
+
+[package.dependencies]
+idna = ">=2.0"
+multidict = ">=4.0"
+propcache = ">=0.2.1"
+
 [[package]]
 name = "zipp"
 version = "3.21.0"
@@ -5819,14 +6427,14 @@ files = [
 ]
 
 [package.extras]
-check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1)"]
+check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1) ; sys_platform != \"cygwin\""]
 cover = ["pytest-cov"]
 doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
 enabler = ["pytest-enabler (>=2.2)"]
-test = ["big-O", "importlib-resources", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more-itertools", "pytest (>=6,!=8.1.*)", "pytest-ignore-flaky"]
+test = ["big-O", "importlib-resources ; python_version < \"3.9\"", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more-itertools", "pytest (>=6,!=8.1.*)", "pytest-ignore-flaky"]
 type = ["pytest-mypy"]
 
 [metadata]
 lock-version = "2.1"
 python-versions = "^3.12"
-content-hash = "5af5fddc1d4e6d4e05de67e335152c918b19b28a5c341b673f2d2758d77110aa"
+content-hash = "7a8783b86d6e85ae409950f34186a38a5c249d949ef53db307911da9b12f1dbf"
diff --git a/pyproject.toml b/pyproject.toml
index 0565328..1aafce8 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -12,6 +12,7 @@ click = "*"
 importlib-metadata = ">=8.2.0"
 pandas = "^2.2.3"
 schema-automator = "^0.5.3"
+openai = "0.28.0"
 
 [tool.poetry.group.dev.dependencies]
 pytest = {version = ">=8.3.2"}
diff --git a/toy_data/raw_data_conditions/conditions_simple.tsv b/toy_data/raw_data_conditions/conditions_simple.tsv
index 044caa7..39786f2 100644
--- a/toy_data/raw_data_conditions/conditions_simple.tsv
+++ b/toy_data/raw_data_conditions/conditions_simple.tsv
@@ -20,3 +20,5 @@ PDA
 Patent Ductus Arteriosu
 Brain MRI scan
 Hypothyroidism
+magnetic resonance imaging procedure
+therapeutic MRI


Reviews:
user: login: amc-corey-cox
body: This looks great to me Trish. I added some nit-pick comments about where things are output but feel free to ignore them.
state: APPROVED
author_association: COLLABORATOR
submitted_at: 2025-05-16T18:29:23Z
user: login: twhetzel
state: COMMENTED
author_association: COLLABORATOR
submitted_at: 2025-05-16T18:34:33Z

Review comments:
diff_hunk: @@ -131,3 +131,5 @@ dmypy.json
 # Pyre type checker
 .pyre/
 
+harmonica/tmp/
path: .gitignore
user: login: amc-corey-cox
body: I'd prefer to just have this in output/tmp. `output/` is already set to ignore anything in there with the local .gitignore in that folder. But this is fine if you prefer it this way.
created_at: 2025-05-16T18:24:50Z
author_association: COLLABORATOR
diff_hunk: @@ -0,0 +1,8 @@
+ontologies:
+  - MONDO
+
+columns_to_annotate:
+  - condition_source_text
+
+# Optional output directory
+output_dir: data/output/
path: config/config.example.yml
user: login: amc-corey-cox
body: ```suggestion
output_dir: output/
```
Let's just keep everything in the output directory that Patrick set up with `make`. As I mentioned, this is safe from accidental commits to git, too.
created_at: 2025-05-16T18:25:54Z
author_association: COLLABORATOR
diff_hunk: @@ -0,0 +1,67 @@
+# Harmonica
+Annotate data with ontology terms.
+
+## Prerequisites
+The prerequisites to run the script are maintained within the `pyproject.toml` file. To update your virtual environment run `poetry install`.
+
+## Usage
+### Python
+```
+python harmonize.py annotate \
+    --config ../config/config.yml \
+    --input_file ../toy_data/raw_data_conditions/conditions_simple.tsv \
+    --output_dir tmp/output/ \
path: harmonica/README.md
user: login: amc-corey-cox
body: Is this the right location? Are we running `harmonica` from it's own directory?
created_at: 2025-05-16T18:26:36Z
author_association: COLLABORATOR
diff_hunk: @@ -0,0 +1,67 @@
+# Harmonica
+Annotate data with ontology terms.
+
+## Prerequisites
+The prerequisites to run the script are maintained within the `pyproject.toml` file. To update your virtual environment run `poetry install`.
+
+## Usage
+### Python
+```
+python harmonize.py annotate \
+    --config ../config/config.yml \
+    --input_file ../toy_data/raw_data_conditions/conditions_simple.tsv \
+    --output_dir tmp/output/ \
path: harmonica/README.md
user: login: twhetzel
body: Yes, currently. I followed the pattern for the `simple_clean`, which is at the same level, but these seem like they should be under `src`. Can you let me know what location you prefer? 
created_at: 2025-05-16T18:34:33Z
author_association: COLLABORATOR

PR comments:
user: login: twhetzel
created_at: 2025-05-16T18:32:44Z
body: Thanks for reviewing @amc-corey-cox! Yes, I anticipated those types of comments for repo structural items, ie directory locations. 
author_association: COLLABORATOR
user: login: amc-corey-cox
created_at: 2025-05-19T16:14:59Z
body: I'm merging this so we don't get out of sync. We can worry about the nitpicks later if we care.
author_association: COLLABORATOR