Skill UI

This skill performs the crucial ETL process of mapping OpenMed-extracted, terminology-coded clinical facts (conditions, drugs, measurements) into the OMOP Common Data Model (CDM) v5.4 tables. It is used downstream after entity extraction and source coding, transforming raw NLP findings into standardized, OMOP-conformant records for OHDSI analytics.

This skill facilitates the extraction of population-scale (cohort-level) clinical text from Electronic Health Records (EHR) or FHIR data warehouses using the FHIR Bulk Data Access ($export) operation. It manages the asynchronous job kickoff, polling, and downloading of NDJSON files. The resulting data stream is designed to be fed in batches into OpenMed for mandatory de-identification and Named Entity Recognition (NER) analysis.

This skill extracts critical patient metadata (PHI) from DICOM headers using pydicom, and recursively pulls structured report narrative text from DICOM-SR content trees. It is essential for ingesting medical images into NLP pipelines, enabling subsequent de-identification and clinical text analysis.

This skill automatically detects and extracts tabular laboratory panels from diverse sources, including scanned images, photos, and delimited files (CSV/TSV). It converts complex visual data into clean, structured rows, capturing the test name, measured value, unit, reference range, and abnormal flag. It is essential for preparing medical data for subsequent standardization using LOINC and UCUM, and for mapping into FHIR resources.

This skill replaces detected Protected Health Information (PHI) in clinical notes with realistic, type-matched synthetic surrogates. Unlike simple redaction, surrogates maintain the natural readability and structure of the text, ensuring the data remains parseable for downstream NLP tasks, QA, or human review. It supports consistent, reproducible fake identities and allows custom identifier generation for proprietary formats.

This skill resolves entities extracted by OpenMed (e.g., Disease, Drug) to standardized Concept Unique Identifiers (CUIs) within the UMLS Metathesaurus. It is essential for cross-vocabulary normalization, allowing users to unify concepts (like SNOMED CT, ICD-10, RxNorm) to a single canonical CUI. Crucially, the process relies entirely on the user's own UTS API key, ensuring that the Metathesaurus content is never bundled or cached.

This skill maps free-text laboratory and clinical observation names to standardized LOINC codes. It resolves ambiguous terms by considering the full six-axis model: Component, Property, Time, System (specimen), Scale, and Method. It integrates with FHIR terminology services to ensure accuracy, supporting US Core Laboratory Results and UCUM units.

This skill implements an advanced reference pattern for integrating with Monitoring Control Platform (MCP) servers. It ensures accurate data retrieval by first reading a domain-specific 'gotchas' reference file, mitigating query failures caused by complex server behaviors, pagination limits, or subtle API quirks. It analyzes issue data, groups errors by root cause, and generates a structured, actionable markdown report for improved system health visibility.

This skill programmatically searches and fetches biomedical literature from PubMed and PMC using NCBI E-utilities (ESearch, EFetch, ESummary). It allows users to gather large corpora of abstracts, full texts, and metadata related to specific conditions, drugs, or genes. Ideal for building evidence bases, performing biomedical Named Entity Recognition (NER), or summarizing scientific findings.

This skill standardizes free-text medication mentions extracted by OpenMed to RxNorm RxCUIs using the public RxNav API. It resolves complex relationships between brand names, generic ingredients, strengths, and dose forms, providing a stable, canonical code. Ideal for clinical interoperability, data analytics, de-duplication, and building US Core Medication resources.

This skill decodes complex pipe-delimited HL7 v2.x messages (including ADT, ORU, MDM) into structured segments and fields. It is essential for ingesting HL7 feeds from interface engines, allowing users to surface embedded clinical narratives (OBX-5 and NTE-3) for subsequent Natural Language Processing (NLP) analysis. It also provides segment-aware de-identification capabilities to redact PHI while preserving the native HL7 message structure.

A comprehensive, multi-phase workflow guide for authorized reverse engineering of complex network protocols. Ideal for analyzing proprietary formats such as custom TCP/UDP binary protocols, Protobuf, gRPC, WebSocket frames, and reconstructing state machines from raw PCAP data. This guide covers data collection, field layout restoration, serialization recovery, and secure replaying.