Skill UI

This skill transforms raw genomic identifiers (VCF, HGVS, rsID) into highly annotated, consequence-predicted records. It utilizes powerful, open-source tools like Ensembl VEP and gnomAD to predict variant consequences (e.g., missense, nonsense), map coordinates, and attach population allele frequencies. Furthermore, it links these molecular findings to clinical and phenotype context extracted by OpenMed, forming a comprehensive research record.

This skill scaffolds a gold-standard annotation project tailored for evaluating clinical NER and de-identification models (OpenMed). It guides users through defining label schemas, writing rigorous guidelines, configuring annotation tools (like BRAT/Label Studio), generating synthetic clinical text, and creating disciplined, non-leaking train/dev/test splits. It ensures that all committed data are synthetic fixtures for reproducible evaluation.

Provides decision support for mapping diagnoses and procedures extracted by OpenMed to standardized ICD-10-CM and ICD-10-PCS codes. This skill suggests candidate codes along with detailed clinical rationale, helping human coders narrow down options, route findings to specific chapters, and pre-fill encounter records. Note that the output is advisory and requires mandatory validation by a certified medical coder.

This tool de-identifies sensitive free-text columns (e.g., names, dates, identifiers) in local structured datasets (CSV, JSONL, Parquet) using advanced OpenMed models. It ensures strict privacy by generating a completely redacted dataset and a separate PHI-free aggregate summary, allowing for secure data sharing and analysis without compromising source privacy or logging sensitive values.

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 utility separates clinical entity extraction from clinical coding. It processes de-identified text, utilizing OpenMed to identify key clinical spans. These spans are then programmatically mapped into structured FHIR R4 resources (like Condition, Observation, and MedicationStatement) and assembled into a Bundle. This process ensures deterministic, standardized data output suitable for interoperability and medical record structuring.

This skill facilitates the ingestion of unstructured clinical notes and reports from FHIR R4 EHR APIs (e.g., Epic, Cerner). It handles complex tasks including paginating large search results, decoding base64 attachments (PDF, text), and extracting narrative content. The extracted text is then passed to the OpenMed pipeline for HIPAA-compliant de-identification and subsequent NLP analysis, enabling structured data insights from raw clinical records.

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 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.