R/ConceptSetTargets.R
getConceptSetTargets.RdGet the concept set targets included in the concept sets
getConceptSetTargets()A data frame with one row per concept set, and the following columns:
id: A unique identifier. Use this when feeding the results in evaluateConceptSets().
name: The name of the clinical idea for which to generate the concept set.
definition: A long free-text definition of the clinical idea, including the intended use of the concept set.
closestConceptId: The concept ID of the concept that most closely matched the clinical idea.
closestConceptName: The name of the concept that most closely matched the clinical idea.
getConceptSetTargets()
#> id name
#> 1 C01 Systemic Lupus Erythematosus
#> 2 C02 Rheumatoid Arthritis
#> 3 C03 Diabetic Macular Edema
#> 4 C04 Deep-Vein Thrombosis
#> 5 C06 Posterior Uveitis
#> 6 C07 Systemic Sclerosis
#> definition
#> 1 Build a concept set for Systemic Lupus Erythematosus — systemic form that captures current, clinically active disease for use in a phenotype for clinically active, prevalent SLE supporting comparative-effectiveness work. The concept set must reflect explicit systemic SLE diagnoses (including “SLE with organ involvement”). The motivating question is generalized as: among patients with active systemic SLE, what are 12-month outcomes (e.g., steroid burden, inadequate response) after initiating Drug A versus Drug B?\n\n---\n\n### Clinical Case Definition\n\nA chronic, systemic autoimmune disease characterized by multisystem involvement and immunologic abnormalities consistent with SLE (e.g., anti-dsDNA and/or anti-Sm antibodies, hypocomplementemia). In routine care, SLE is managed primarily by rheumatology and treated with antimalarials, immunosuppressants, biologics, and judicious glucocorticoids.\n\n### Diagnostic Criteria (for context; not encoded in this concept set)\n\nSerology: ANA (entry), anti-dsDNA and/or anti-Sm positivity; low C3/C4. Organ involvement: renal (proteinuria, biopsy-proven LN), hematologic, mucocutaneous, musculoskeletal, neuropsychiatric, serositis. Classification frameworks (e.g., 2019 EULAR/ACR) inform measurement concept sets but are not used to gate diagnosis codes here.\n\n### Presentation & Course\n\nRelapsing-remitting with flares and remissions; severity ranges from mild mucocutaneous/arthralgia to life-threatening organ disease (e.g., nephritis). Long-term morbidity is strongly influenced by cumulative glucocorticoid exposure.\n\n### Common Treatments/Management\n\nHydroxychloroquine, azathioprine, mycophenolate, methotrexate, cyclophosphamide; calcineurin inhibitors (e.g., tacrolimus; voclosporin for LN); biologics (belimumab, anifrolumab); off-label rituximab; systemic glucocorticoids (oral and pulse). These support phenotype confirmation but are not part of this diagnosis concept set.\n\n---\n\n### Clinical Scope and Granularity\n\n* **Disease entity:** Chronic, systemic autoimmune disease with a relapsing–remitting course; typical features include mucocutaneous, musculoskeletal, hematologic, renal, neuropsychiatric, and serosal involvement, with immunologic abnormalities consistent with SLE. \n* **Temporality:** The phenotype should identify patients with currently active systemic SLE. Both newly diagnosed (incident) and existing (prevalent) cases are in scope, provided there is evidence of disease activity. Historical disease in remission is out of scope. \n* **Severity & acuity:** All severities —from mild to life-threatening organ disease—are in scope when the diagnosis explicitly denotes active systemic SLE. \n* **Manifestations:** Organ/system involvement that is linked to SLE. \n* **Etiology:** Primary systemic SLE only; other etiologies (for example, drug-induced) are not within the scope. \n* **Population:** Adult (18 and above).\n\n---\n\n### Related, differential or comorbid conditions that are not sufficient for inclusion:\n\n* Cutaneous lupus erythematosus (discoid, subacute cutaneous) without systemic SLE. \n* Drug-induced lupus; neonatal lupus. \n* Antiphospholipid syndrome without SLE. \n* Undifferentiated or mixed connective tissue disease; systemic sclerosis; dermatomyositis/polymyositis; Sjögren’s syndrome; rheumatoid arthritis. \n* Organ-specific diagnoses (e.g., nephritis, serositis, cytopenias, CNS vasculitis) without explicit SLE linkage. \n* Non-SLE “lupus” such as lupus vulgaris. \n* Antiphospholipid syndrome (APS) without SLE. \n* Fibromyalgia.\n\n---\n\n### Synonyms\n\n* Systemic lupus erythematosus \n* SLE \n* Systemic lupus \n* Disseminated lupus erythematosus (historic) \n* SLE with organ involvement (e.g., “SLE with nephritis”)
#> 2 Build a diagnosis concept set for *Rheumatoid Arthritis (RA)—adult, systemic form* that captures prevalent, established disease with high clinical validity. Include RA diagnoses and RA-linked extra-articular manifestations. This concept set will support an observational study that aims to answer the following research question:\n\nAmongst patients who are diagnosed with **\\[Rheumatoid Arthritis\\]**, what are the patient’s characteristics from their medical history (including demographics, comorbidities, HCRU, and total costs).\n\nThe concept set will be used in the phenotype of patients with *Rheumatoid Arthritis (RA) as the target cohort in this research question.*\n\n**Clinical case definition:** A chronic, systemic autoimmune and inflammatory disease primarily characterized by persistent synovitis of diarthrodial joints, often symmetrical. The disease trajectory involves inflammation of the synovial membrane, leading to potential cartilage destruction, bone erosions, and joint deformity. Systemic features include the production of autoantibodies (Rheumatoid Factor (RF) and anti-citrullinated peptide antibodies (ACPA)).\n\n**Diagnostic Criteria:** Diagnosis is based on established clinical criteria (e.g., ACR/EULAR 2010 criteria), which consider the pattern of joint involvement, serology (RF/ACPA), acute phase reactants (ESR/CRP), and duration of symptoms. In RWD, we rely on the clinician's recorded diagnosis based on these criteria.\n\n**Presentation and Course:** Presentation typically involves insidious onset of pain, stiffness (especially morning stiffness), and swelling in multiple joints (polyarthritis), commonly affecting the small joints of the hands and feet. The course is typically chronic and progressive without adequate treatment, characterized by flares and potential remission.\n\n**Differential Diagnoses: (Conditions to be distinguished and not considered inclusive)**\n\n* Psoriatic Arthritis (PsA) \n* Ankylosing Spondylitis (AS) and other spondyloarthropathies \n* Systemic Lupus Erythematosus (SLE) \n* Gout and Pseudogout (Crystal arthropathies) \n* Polymyalgia Rheumatica (PMR) \n* Osteoarthritis (OA) \n* Juvenile Idiopathic Arthritis (JIA) \n* viral arthritis (e.g., from Parvovirus B19, Hepatitis C) \n* undifferentiated inflammatory arthritis\n\n**Common Treatments/Management**: Conventional synthetic DMARDs (e.g., Methotrexate), biologic DMARDs (e.g., TNF inhibitors), targeted synthetic DMARDs (e.g., JAK inhibitors), systemic glucocorticoids.\n\n**Clinical Scope and Granularity**\n\n* **Disease entity:** Chronic, systemic autoimmune inflammatory polyarthritis characterized by persistent, often symmetrical synovitis of diarthrodial joints with risk of cartilage loss, bone erosions, and deformity; commonly presents with insidious polyarticular pain, swelling, and morning stiffness; may include autoantibodies (RF/ACPA) and flares/remission over a chronic course. \n* **Temporality:** Prevalent/established RA. “History of RA” is in scope only when it reflects an ongoing established diagnosis, not a resolved remote event. \n* **Severity & acuity:** Include all severities (mild to severe) and states (active disease or remission). \n* **Manifestations:** Extra-articular disease that is explicitly linked to RA (e.g., rheumatoid lung disease, rheumatoid vasculitis, Felty’s syndrome) is RA. \n* **Etiology:** Autoimmune inflammatory arthritis; irrespective of seropositivity. non-inflammatory arthropathies are not in scope. \n* **Population:** **Adults**; pediatric entities (JIA, juvenile RA, Still’s disease) are out of scope.\n\n**Related, differential conditions or comorbidities that are not sufficient for inclusion**\n\n* Psoriatic arthritis; ankylosing spondylitis and other spondyloarthropathies; reactive and enteropathic arthritis. \n* Systemic lupus erythematosus; systemic sclerosis; Sjögren’s; dermatomyositis/polymyositis; undifferentiated/mixed connective tissue disease. \n* Gout; calcium pyrophosphate disease (pseudogout/CPPD). \n* Polymyalgia rheumatica. \n* Osteoarthritis. \n* Any other arthralgia or unspecified arthritis.\n\n**Synonyms**\n\n* Rheumatoid arthritis \n* Rheumatoid polyarthritis \n* Seropositive rheumatoid arthritis \n* Seronegative rheumatoid arthritis \n* Felty’s syndrome (RA with splenomegaly and neutropenia)
#> 3 Construct a diagnosis concept set for *Diabetic Macular Edema (DME)*—macular thickening and/or intra-/sub-retinal fluid explicitly attributable to diabetes mellitus—to support a treatment-anchored phenotype. The set must capture *current, clinically active* DME.\n\nThis concept set will support an observational study that aims to answer the following research question:\n\nAmong adult diabetic patients on drug-a anti-diabetic medication what is the incidence rate of developing *Diabetic Macular Edema (DME)*.\n\nThe concept set will be used in the phenotype of the outcome *Diabetic Macular Edema (DME)*.\n\n**Clinical case definition:** Retinal thickening and/or intra/sub-retinal fluid in the macula due to diabetes mellitus (type 1 or 2). Diagnostic criteria is confirmed through OCT evidence of macular thickening and/or intra/sub-retinal fluid.\n\n**Presentation & Course:** Blurred vision, metamorphopsia; may be asymptomatic early. Often chronic, managed with anti-VEGF, steroids, and/or focal/grid laser; treat-and-extend or PRN patterns are common.\n\n**Differential Diagnoses (Conditions to be distinguished and not considered inclusive)**\n\n* Neovascular age-related macular degeneration (nAMD) \n* Retinal vein occlusions (CRVO/BRVO) with macular edema \n* Polypoidal choroidal vasculopathy; myopic CNV \n* Post-operative cystoid macular edema (Irvine–Gass) \n* Uveitic cystoid macular edema \n* Unspecified macular edema without diabetic attribution\n\n**Common Treatments/Management:** Intravitreal anti-VEGF; intravitreal/periocular corticosteroids (dexamethasone, fluocinolone implants); focal/grid macular laser; serial OCT monitoring.\n\n**Clinical Scope and Granularity**\n\n* **Disease entity:** Diabetes-attributable macular edema characterized by retinal thickening and/or intra/sub-retinal fluid at the macula; typical presentation includes blurred vision and metamorphopsia. Clinical confirmation commonly relies on OCT; management includes intravitreal anti-VEGF, corticosteroid implants, and/or focal/grid laser. \n* **Temporality:** Incidence and **current** disease; historical or resolved disease alone is out of scope. \n* **Severity & acuity:** All severities (center-involved or non-center-involved; unilateral or bilateral) are in scope when DME is explicitly diagnosed. \n* **Manifestations:** Diabetic retinopathy that is explicitly linked to macular edema. Both laterality or “center-involved” are within scope. \n* **Etiology:** Restrict to DME due to type 1 or type 2 diabetes; macular edema from other causes (post-operative, uveitic, retinal vein occlusion, neovascular AMD, myopic/PCV CNV) are not within scope. \n* **Population:** Adults with diabetes; pediatric use is not targeted by this concept set.\n\n**Related, differential conditions or comorbidities that are not sufficient for inclusion**\n\n* Neovascular age-related macular degeneration. \n* Retinal vein occlusions (CRVO/BRVO) with macular edema. \n* Polypoidal choroidal vasculopathy; myopic choroidal neovascularization. \n* Post-operative cystoid macular edema (Irvine–Gass); uveitic cystoid macular edema. \n* Unspecified macular edema without diabetic linkage. \n* Diabetic retinopathy without macular edema.\n\n**Synonyms**\n\n* Diabetic macular edema (DME) \n* Diabetic retinopathy with macular edema \n* Diabetic maculopathy with macular edema/ “with macular edema” modifiers \n* Center-involved DME (CI-DME) \n* Clinically significant macular edema (CSME) — when explicitly diabetic
#> 4 Develop a diagnosis concept set for *Acute Proximal Lower-Extremity Deep-Vein Thrombosis (LE-DVT)*—an incident, clinically acute thrombus in popliteal or more proximal deep veins—to support a cancer-associated thrombosis phenotype. The set must represent current, incident proximal LE-DVT (including incidental events).\n\nThis concept set will support an observational study that aims to answer the following research question: Among adults with active malignancy receiving therapeutic anticoagulation, what is the comparative effectiveness of drug A to prevent *Lower-Extremity Deep-Vein Thrombosis*.\n\nThe concept set will be used in the phenotype of the outcome *Lower-Extremity Deep-Vein Thrombosis*.\n\n**Clinical case definition:** An acute thrombus in the proximal deep veins of the lower extremity—popliteal, femoral (common/superficial), deep femoral, iliac, or inferior vena cava segments—presenting symptomatically (e.g., unilateral leg swelling/pain) or incidentally on imaging in a patient with active malignancy.\n\n**Diagnostic criteria (objective confirmation).**\n\n* Compression duplex ultrasound documenting non-compressibility/intraluminal thrombus in proximal segments; or \n* CT/MR venography confirming proximal LE thrombus. (Imaging evidence is captured by procedure codes in the phenotype but not embedded inside this condition concept set.)\n\n**Presentation & course (typical).** Acute onset limb swelling, pain, warmth; occasionally asymptomatic if discovered during cancer imaging. Risk of extension/embolization without treatment.\n\n**Differential diagnoses (Conditions to be distinguished and not considered inclusive).** Isolated distal calf DVT (peroneal/posterior/anterior tibial, muscular veins), superficial thrombophlebitis, chronic post-thrombotic changes, lympema/venous insufficiency, cellulitis, Baker cyst.\n\n**Common treatments/management (positive proxies).** Therapeutic-intensity DOACs (apixaban/rivaroxaban/edoxaban) or LMWH, less commonly VKA; in select cases thrombectomy/thrombolysis/IVC filter. (Treatment will be enforced by phenotype logic; do not add drug codes to this condition concept set.)\n\n**Clinical Scope and Granularity**\n\n* **Disease entity:** Acute thrombus in proximal lower-extremity deep veins—popliteal, femoral (common/superficial), deep femoral, iliac, or IVC—typically presenting with unilateral leg swelling, pain, warmth; may be incidentally detected on imaging in oncology care. Objective confirmation usually by compression duplex ultrasound or CT/MR venography. \n* **Temporality:** Incident/current event only; remote or resolved events are out of scope. \n* **Severity & acuity:** All acute severities are in scope, including iliofemoral extension and IVC involvement when proximal LE origin is explicit. \n* **Etiology:** Any cause (including cancer-associated or postoperative) provided location is proximal LE; pregnancy-related VTE is not within scope. \n* **Anatomy:** Deep and proximal veins only (ex. thrombophlebitis is not in scope). \n* **Population:** adults or pediatrics. \n* **Ambiguity tolerance:** Prefer site-specific proximal terms; avoid broad/unspecified venous thrombosis labels unless clearly proximal LE.\n\n**Related, differential conditions or comorbidities that are not sufficient for inclusion**\n\n* Distal calf DVT (peroneal/posterior/anterior tibial, muscular veins). \n* Superficial vein thrombosis (e.g., great saphenous). \n* Chronic post-thrombotic changes; lymphedema; venous insufficiency; cellulitis; Baker cyst. \n* Upper-extremity DVT; pulmonary embolism.\n\n**Synonyms**\n\n* Proximal lower-extremity DVT \n* Iliofemoral DVT \n* Femoral vein thrombosis \n* Popliteal vein thrombosis \n* Iliac vein thrombosis \n* Lower-limb DVT—proximal
#> 5 Develop a diagnosis concept set for *active, non-infectious posterior-segment uveitis*—encompassing intermediate uveitis, posterior uveitis, and panuveitis—to support a phenotype used in comparative effectiveness work (e.g., Drug A vs Drug B). The set must capture current, clinically active disease at or immediately preceding initiation of systemic therapy. The research aim is to compare time to treatment failure and steroid dependence after treatment start for patients with posterior uveitis.\n\nThis concept set will support an observational study that aims to answer the following research question: Among adults with *non-infectious posterior-segment uveitis*, what is the comparative effectiveness of drug A to prevent steroid dependency, compared to drug B.\n\nThe concept set will be used in the phenotype of patients with *non-infectious posterior-segment uveitis as the target cohort in this research question.*\n\n**Clinical case definition:** Inflammation of the uveal tract with posterior-segment involvement—intermediate uveitis, posterior uveitis, or panuveitis—that is Non-Infectious (autoimmune/autoinflammatory; idiopathic or associated with systemic disease) and clinically active.\n\n**Diagnostic criteria:**\n\n* Ophthalmic exam consistent with posterior-segment inflammation: vitreous cells/haze, “snowballs/snowbanking” (intermediate), chorioretinitis/retinitis, retinal vasculitis, optic disc edema; activity graded per SUN where available. \n* Imaging support when present: OCT (CME), FFA (leakage/vasculitis), ± ICGA/ultrawidefield angiography. \n* Exclusion of infection and masquerade by appropriate work-up.\n\n**Presentation and course:** Chronic or recurrent disease with active flares; may be sight-threatening; often steroid-responsive but steroid-dependent without additional IMT.\n\n**Differential diagnoses (Conditions to be distinguished and not considered inclusive):** Infectious uveitis (e.g., toxoplasma, HSV/VZV/CMV retinitis, TB, syphilis), intraocular lymphoma/other masquerades, isolated anterior uveitis, scleritis/episcleritis, non-inflammatory mimics.\n\n**Common treatments/management:** High-dose systemic corticosteroids; steroid-sparing IMT (methotrexate, mycophenolate, azathioprine, cyclosporine, tacrolimus); biologics (adalimumab). *Therapies are not part of this concept set.* \nClinical Scope and Granularity:\n\n* **Disease entity:** immune-mediated, non-infectious inflammation of the uveal tract with posterior-segment involvement (intermediate, posterior, panuveitis); may be chronic/recurrent and sight-threatening. \n* **Typical presentation:** vitreous cells/haze; “snowballs/snowbanking” (intermediate); chorioretinitis/retinitis; retinal vasculitis; optic disc edema. Imaging may show CME on OCT and leakage/vasculitis on angiography. \n* **Temporality:** prevalent/current active episodes at or immediately before a systemic treatment would start. \n* **Severity/acuity:** all severities in scope, including steroid-dependent or refractory disease. \n* **Manifestations:** may manifest with posterior-segment findings that are linked to uveitis. \n* **Etiology:** non-infectious (idiopathic or associated with systemic autoimmune/autoinflammatory disease). \n* **Population:** All patients.\n\n\n**Related, differential conditions or comorbidities that are not sufficient for inclusion**\n\n* Infectious posterior uveitides (toxoplasma; HSV/VZV/CMV; tuberculosis; syphilis). \n* Intraocular lymphoma and other masquerade entities. \n* Anterior uveitis, episcleritis/scleritis, non-inflammatory mimics. \n* Organ-specific findings such as cystoid macular edema or retinal vasculitis without an explicit uveitis diagnosis.\n\n**Synonyms**\n\n* Intermediate uveitis; pars planitis; posterior uveitis; panuveitis; posterior cyclitis. \n* Retinochoroiditis/choroiditis (non-infectious context). \n* Named non-infectious posterior/panuveitis entities: birdshot chorioretinopathy; Vogt–Koyanagi–Harada–associated uveitis; sympathetic ophthalmia; sarcoid-associated uveitis; Behçet-associated posterior uveitis.
#> 6 This concept set will identify Systemic Sclerosis (SSc; systemic scleroderma)—a systemic, not localized, autoimmune fibrosing vasculopathy. The set must represent current, active systemic disease. This concept set will support an observational study that aims to answer the following research objective:\n\n*The study aims to explore treatment utilization among patients newly diagnosed with systemic sclerosis in real-world data.*\n\nThe concept set will be used to phenotype patients with *systemic sclerosis as the target cohort in this research question.*\n\n**Clinical case definition:** Systemic Sclerosis (SSc), also known as systemic scleroderma, is a complex, chronic autoimmune disorder characterized by three hallmark features: immune dysregulation (autoimmunity and inflammation), microvasculopathy (vascular injury and remodeling), and progressive fibrosis (excessive collagen deposition) affecting the skin and internal organs (e.g., lungs, gastrointestinal tract, heart, kidneys).\n\n**Diagnostic Criteria:** Diagnosis is clinical, often informed by the 2013 ACR/EULAR classification criteria (score ≥9). Key elements include skin thickening proximal to the MCP joints (sufficient criterion), Raynaud’s phenomenon, digital tip lesions, telangiectasias, abnormal nailfold capillaries, pulmonary arterial hypertension (PAH) and/or interstitial lung disease (ILD), and SSc-specific autoantibodies (Anti-Scl-70/Topoisomerase I, Anti-centromere, Anti-RNA polymerase III).\n\n**Presentation and Course:** The presentation is heterogeneous and the course is chronic and lifelong. It is categorized based on skin involvement:\n\n* **Diffuse Cutaneous SSc (dcSSc):** Extensive skin thickening, higher risk of early ILD and renal crisis. \n* **Limited Cutaneous SSc (lcSSc):** Skin thickening restricted distally. Includes CREST syndrome. \n* **SSc sine scleroderma:** Internal organ involvement without skin thickening.\n\n**Differential Diagnoses (Conditions to be distinguished and not considered inclusive):** Undifferentiated Connective Tissue Disease (UCTD), Mixed Connective Tissue Disease (MCTD), Isolated Raynaud’s phenomenon, and various scleroderma mimics (see Exclusions).\n\n**Common Treatments/Management:** Management is typically overseen by a Rheumatologist. Treatments include immunosuppression (e.g., Mycophenolate Mofetil, Cyclophosphamide) and targeted therapies for ILD (Nintedanib, Tocilizumab, Rituximab). \n**Clinical Scope**\n\n* **Disease entity:** Chronic autoimmune disorder with immune dysregulation, microvasculopathy, and progressive fibrosis affecting skin and internal organs (lungs, GI tract, heart, kidneys). Diagnosis is clinical; 2013 ACR/EULAR elements include proximal skin thickening (sufficient criterion), Raynaud’s phenomenon, digital ischemic lesions, telangiectasias, abnormal nailfold capillaries, PAH and/or ILD, and SSc-specific autoantibodies (anti–Scl-70, anticentromere, anti–RNA polymerase III). \n* **Subtypes:** Diffuse cutaneous (dcSSc), limited cutaneous (lcSSc, includes CREST), and SSc sine scleroderma (internal organ involvement without skin thickening) all are within scope. \n* **Temporality:** capture prevalent established, and active current disease. \n* **Severity & acuity:** Include full spectrum from mild to life-threatening, acute manifestations and chronic progression. \n* **Manifestations:** Multisystem involvement is in scope **when explicitly linked to SSc** (e.g., SSc-ILD, SSc-PAH). \n* **Etiology:** Autoimmune/idiopathic SSc only. \n* **Population:** all population\n\n**Related, differential conditions or comorbidities that are not sufficient for inclusion**\n\n* **Localized scleroderma (critical exclusion):** morphea (generalized/plaque/guttate), linear scleroderma, en coup de sabre. \n* **Mimics/fibrosing conditions:** eosinophilic fasciitis, scleredema, scleromyxedema, nephrogenic systemic fibrosis. \n* **Induced scleroderma:** drug-induced (e.g., bleomycin, taxanes) or environmental/occupational (silica, vinyl chloride, toxic oil). \n* **Other/overlap:** GVHD with sclerodermatous features; MCTD or UCTD unless “systemic sclerosis” is explicitly stated; isolated Raynaud’s, acrosclerosis, or sclerodactyly.\n\n**Synonyms**\n\n* Systemic scleroderma; Progressive systemic sclerosis (PSS); CREST syndrome (limited cutaneous SSc Calcinosis, Raynaud's phenomenon, Esophageal dysmotility, Sclerodactyly, and Telangiectasias).
#> closestConceptId closestConceptName
#> 1 257628 Systemic lupus erythematosus
#> 2 80809 Rheumatoid arthritis
#> 3 380097 Macular edema due to diabetes mellitus
#> 4 4133004 Deep venous thrombosis
#> 5 4183040 Posterior uveitis
#> 6 134442 Systemic sclerosis