[ENH] Functions added to fetch the termURLs of diagnosis, assessment, sex and image modality

.github/workflows/test.yaml

@@ -32,6 +32,7 @@ jobs:
     - name: Pull Mistral Model
       run: |
         ollama pull mistral
+        ollama pull llama3
 
     - name: Run tests
       run: |
@@ -42,3 +43,4 @@ jobs:
       uses: coverallsapp/[email protected]
       with:
         github-token: ${{ secrets.GITHUB_TOKEN }}
+

.pre-commit-config.yaml

@@ -21,3 +21,4 @@ repos:
       - id: mypy
         args:
           - --ignore-missing-imports
+        additional_dependencies: ['types-requests']

app/LLM_extractions/extractions.py

@@ -29,7 +29,11 @@ class Parameters(BaseModel):
     min_age: Optional[str] = Field(
         description="minimum age (lower age limit) if specified", default=None
     )
-    sex: Optional[str] = Field(description="sex", default=None)
+    sex: Optional[str] = Field(
+        description="sex, only accepts 'male' or 'female' or 'other'",
+        default=None,
+        examples=["male", "female", "other"],
+    )
     diagnosis: Optional[str] = Field(description="diagnosis", default=None)
     is_control: Optional[bool] = Field(
         description="healthy control subjects", default=None
@@ -93,7 +97,26 @@ def extract_information(context: str) -> Optional[Union[dict, str, None]]:
 
         # Filter out keys where the value is None or 'None' (string)
         filtered_ordered_response = {
-            k: v
+            k: (
+                float(v)
+                if k in ["min_age", "max_age"] and v is not None
+                else (
+                    int(v)
+                    if k
+                    in [
+                        "min_num_phenotypic_sessions",
+                        "min_num_imaging_sessions",
+                    ]
+                    and v is not None
+                    else (
+                        v.lower()
+                        if isinstance(v, str)
+                        and k
+                        in ["diagnosis", "assessment", "image_modal", "sex"]
+                        else v
+                    )
+                )
+            )
             for k, v in ordered_response.items()
             if v is not None and v != "None"
         }

app/fetch_termURLs/__init__.py

@@ -0,0 +1,6 @@
+import os
+import sys
+
+sys.path.append(
+    os.path.dirname(os.path.realpath(__file__))
+)  # Fixes relative import error.

app/fetch_termURLs/abbreviations/__init__.py

@@ -0,0 +1,6 @@
+import os
+import sys
+
+sys.path.append(
+    os.path.dirname(os.path.realpath(__file__))
+)  # Fixes relative import error.

app/fetch_termURLs/abbreviations/abbreviations_assessment.py

@@ -0,0 +1,91 @@
+abbreviations_assessment = [
+    {
+        "label": "behavioral approach/inhibition systems",
+        "abbreviations": ["BIS"],
+    },
+    {"label": "Barratt Impulsiveness Scale", "abbreviations": ["BIS"]},
+    {"label": "DOSPERT", "abbreviations": ["DO", "DOTS", "DOS"]},
+    {
+        "label": "Positive and Negative Affect Scale",
+        "abbreviations": ["PANAS"],
+    },
+    {"label": "balloon analogue risk task", "abbreviations": ["BART"]},
+    {"label": "stop signal task", "abbreviations": ["SST", "SSTT"]},
+    {"label": "breath-holding", "abbreviations": ["BH"]},
+    {"label": "paired associate learning", "abbreviations": ["PAL", "PALA"]},
+    {"label": "paired associate recall", "abbreviations": ["PAIR"]},
+    {
+        "label": "spatial working memory task",
+        "abbreviations": ["SWM", "SWMT", "N-back"],
+    },
+    {
+        "label": "Wechsler Memory Scale Fourth Edition",
+        "abbreviations": ["WMS-IV"],
+    },
+    {"label": "letter number sequencing", "abbreviations": ["LNS", "LNSS"]},
+    {
+        "label": "Wechsler Adult Intelligence Scale - Revised",
+        "abbreviations": ["WAIS-R"],
+    },
+    {
+        "label": "n-back task",
+        "abbreviations": ["NVT", "N-Task", "NTB", "n-task"],
+    },
+    {
+        "label": "Scale for the Assessment of Negative Symptoms",
+        "abbreviations": ["SANS"],
+    },
+    {
+        "label": "Scale for the Assessment of Positive Symptoms",
+        "abbreviations": ["SAPS"],
+    },
+    {"label": "big five questionnaire", "abbreviations": ["NEO-FFI", "PAQ"]},
+    {"label": "Mini Mental State Examination", "abbreviations": ["MMSE"]},
+    {"label": "PEBL Perceptual Vigilance Task", "abbreviations": ["PVT"]},
+    {
+        "label": "Raven's Advanced Progressive Matrices",
+        "abbreviations": ["RAPM"],
+    },
+    {"label": "Kaufman Brief Intelligence Test", "abbreviations": ["KBIT"]},
+    {"label": "theory of mind task", "abbreviations": ["ToM", "TOMS"]},
+    {"label": "Stroop task", "abbreviations": ["ST"]},
+    {
+        "label": "Comprehensive Test of Phonological Processing",
+        "abbreviations": ["CTOPP"],
+    },
+    {"label": "Peabody Picture Vocabulary Test", "abbreviations": ["PPVT"]},
+    {
+        "label": "Wechsler Abbreviated Scale of Intelligence",
+        "abbreviations": ["WASI"],
+    },
+    {"label": "multisource interference task", "abbreviations": ["MIST"]},
+    {
+        "label": "Center for Epidemiologic Studies Depression Scale",
+        "abbreviations": ["CES-D"],
+    },
+    {"label": "Kirby Delay Discounting Task", "abbreviations": ["KD", "KDDT"]},
+    {
+        "label": "UPPS-P Impulsivity Scale",
+        "abbreviations": ["UPISS", "UPPS-PIS"],
+    },
+    {"label": "Zuckerman Sensation Seeking Scale", "abbreviations": ["SSS"]},
+    {"label": "Eriksen flanker task", "abbreviations": ["EF"]},
+    {"label": "Continuous Performance Task", "abbreviations": ["CPT", "CPCT"]},
+    {"label": "Emotion Regulation Questionnaire", "abbreviations": ["ERQ"]},
+    {"label": "Motor Screening Task", "abbreviations": ["MST"]},
+    {"label": "Reaction Time", "abbreviations": ["RT", "RTT"]},
+    {
+        "label": "Rapid Visual Information Processing",
+        "abbreviations": ["RVIP", "RVP"],
+    },
+    {"label": "Stockings of Cambridge Task", "abbreviations": ["SCAT"]},
+    {
+        "label": "Edinburgh Handedness Inventory",
+        "abbreviations": ["EHI", "EHII"],
+    },
+    {"label": "National Adult Reading Test", "abbreviations": ["NART", "NAT"]},
+    {
+        "label": "Structured Clinical Interview for Diagnostic and Statistical Manual of Mental Disorders (DSM-IV)",
+        "abbreviations": ["SCID"],
+    },
+]

app/fetch_termURLs/abbreviations/abbreviations_diagnosis.py

@@ -0,0 +1,36 @@
+abbreviations_diagnosis = [
+    {"label": "Schizophrenia", "abbreviations": ["SZ", "SP", "SZD"]},
+    {"label": "Bipolar disorder", "abbreviations": ["BD", "BPI"]},
+    {
+        "label": "Attention deficit hyperactivity disorder",
+        "abbreviations": ["ADHD", "ADHD-PI", "ADHD-C"],
+    },
+    {"label": "Separation anxiety", "abbreviations": ["SAD", "SAS"]},
+    {"label": "Generalized anxiety disorder", "abbreviations": ["GAD", "GAN"]},
+    {"label": "Social phobia", "abbreviations": ["SAD", "SPS", "SPH"]},
+    {"label": "Major depressive disorder", "abbreviations": ["MDD"]},
+    {
+        "label": "Autism spectrum disorder",
+        "abbreviations": ["ASD", "AS", "ASDs"],
+    },
+    {"label": "Overweight", "abbreviations": ["OW", "BW"]},
+    {"label": "Parkinson's disease", "abbreviations": ["PD", "PDx", "PDs"]},
+    {"label": "Traumatic brain injury", "abbreviations": ["TBI", "TBI-SCI"]},
+    {"label": "Obsessive-compulsive disorder", "abbreviations": ["OCD"]},
+    {"label": "Fibromyalgia", "abbreviations": ["FM"]},
+    {"label": "Visual impairment", "abbreviations": ["VI", "VIa", "VA"]},
+    {"label": "Depressive disorder", "abbreviations": ["MDD", "DD"]},
+    {"label": "Dysthymia", "abbreviations": ["DYSM", "DD"]},
+    {"label": "Mood disorder", "abbreviations": ["MDD", "MD"]},
+    {"label": "Dyslexia", "abbreviations": ["ID", "IDR", "DLX", "dys."]},
+    {"label": "Specific spelling disorder", "abbreviations": ["SSD"]},
+    {
+        "label": "Mental disorder",
+        "abbreviations": ["MD", "MDD", "BD", "PD", "MPD"],
+    },
+    {"label": "Anxiety disorder", "abbreviations": ["AD"]},
+    {"label": "Concussion injury of brain", "abbreviations": ["CI"]},
+    {"label": "Moderate depression", "abbreviations": ["MDD", "MODD"]},
+    {"label": "Mild depression", "abbreviations": ["MD"]},
+    {"label": "Aphasia", "abbreviations": ["AS", "AP", "Aphas."]},
+]

app/fetch_termURLs/abbreviations/abbreviations_image_modality.py

@@ -0,0 +1,8 @@
+abbreviations_image_modality = [
+    {"label": "Arterial Spin Labeling", "abbreviations": ["ASL"]},
+    {"label": "Diffusion Weighted", "abbreviations": ["DWI", "DW"]},
+    {"label": "Electroencephalogram", "abbreviations": ["EEG", "ECG"]},
+    {"label": "Flow Weighted", "abbreviations": ["FW"]},
+    {"label": "T1 Weighted", "abbreviations": ["T1W", "T1WI"]},
+    {"label": "T2 Weighted", "abbreviations": ["TW", "T2W"]},
+]

app/fetch_termURLs/abbreviations/abbreviations_sex.py

@@ -0,0 +1,5 @@
+abbreviations_sex = [
+    {"label": "male", "abbreviations": ["MALE", "M", "m"]},
+    {"label": "female", "abbreviations": ["WF", "F", "Fem.", "Female", "F."]},
+    {"label": "other", "abbreviations": ["OTH", "Oth", "OT"]},
+]