| Category | Suggested ontology | Term label | Term ID | Evidence-supported rationale |
|---|---|---|---|---|
| Disease | MONDO | anti-NMDA receptor encephalitis | MONDO_0021081 | OpenTargets identifies the disease as anti-NMDA receptor encephalitis with MONDO_0021081, matching the requested disease concept (pqac-00000000). |
| Anatomy | UBERON | brain | UBERON:0000955 | Anti-NMDAR encephalitis is a CNS autoimmune encephalitis with neuropsychiatric, seizure, and cognitive manifestations indicating primary brain involvement (pqac-00000001, pqac-00000011). |
| Anatomy | UBERON | hippocampus | UBERON:0001954 | Mechanistic studies describe impaired hippocampal synaptic activity/plasticity and hippocampal binding of patient antibodies, supporting hippocampal involvement (pqac-00000011, pqac-00000019). |
| Anatomy | UBERON | cerebrospinal fluid | UBERON:0001359 | CSF is the preferred compartment for antibody detection and frequently shows pleocytosis or oligoclonal bands in this disease (pqac-00000006, pqac-00000007). |
| Anatomy | UBERON | blood-brain barrier | UBERON:0013702 | BBB dysfunction is implicated because the BBB is described as crucial for antibody and immune-cell trafficking into and out of the CNS (pqac-00000011, pqac-00000024). |
| Anatomy | UBERON | ovary | UBERON:0000992 | Ovarian teratoma is the major tumor trigger, especially in female patients, supporting ovary as a key associated anatomical site (pqac-00000007, pqac-00000012). |
| Cell type | CL | B cell | CL:0000236 | CNS B-cell expansion and intrathecal antibody production are described in anti-NMDAR encephalitis, making B cells a central disease-relevant cell type (pqac-00000011, pqac-00000023). |
| Cell type | CL | plasma cell | CL:0000786 | Intrathecal plasma cells are a reported source of GluN1 autoantibodies in mechanistic studies (pqac-00000020, pqac-00000023). |
| Cell type | CL | neuron | CL:0000540 | Patient antibodies bind neuronal surface NMDARs and alter synaptic receptor density and function, implicating neurons as the primary target cell type (pqac-00000018, pqac-00000022). |
| Subcellular | GO | synapse | GO:0045202 | Anti-NMDAR antibodies reduce synaptic NMDAR density and disrupt synaptic plasticity, so synapse is a core affected compartment (pqac-00000020, pqac-00000024). |
| Subcellular | GO | plasma membrane | GO:0005886 | The pathogenic antibodies bind cell-surface NMDARs and decrease surface receptor density/localization (pqac-00000022, pqac-00000024). |
| Subcellular | GO | recycling endosome | GO:0055037 | Internalized receptors preferentially traffic to Rab11-positive recycling endosomes in mechanistic studies (pqac-00000018). |
| Phenotype | HPO | Psychiatric symptoms | HP:0000708 | Psychiatric/behavioral symptoms are among the most common presenting features, affecting about 90% of teenagers/adults in review data (pqac-00000033). |
| Phenotype | HPO | Seizure | HP:0001250 | Seizures are a core diagnostic manifestation and occurred in 80.9% of a 220-patient cohort and 67% of a 106-patient cohort (pqac-00000036, pqac-00000035). |
| Phenotype | HPO | Dyskinesia | HP:0100660 | Movement disorder, especially orolingual-facial dyskinesia, is characteristic of anti-NMDAR encephalitis (pqac-00000033). |
| Phenotype | HPO | Autonomic dysfunction | HP:0002271 | Autonomic dysfunction is included in diagnostic criteria and includes instability of temperature, salivation, blood pressure, heart rate, and continence (pqac-00000033, pqac-00000038). |
| Phenotype | HPO | Central hypoventilation | HP:0007110 | Central hypoventilation is a recognized core manifestation linked to ICU care and worse prognosis (pqac-00000033, pqac-00000038). |
| Phenotype | HPO | Memory impairment | HP:0002354 | Memory deficits are frequent in the acute syndrome and remain a major long-term deficit domain in survivors (pqac-00000034, pqac-00000036). |
| Phenotype | HPO | Language impairment | HP:0002465 | Language scores remain persistently reduced in long-term follow-up and speech dysfunction is a core diagnostic domain (pqac-00000034, pqac-00000038). |
| Phenotype | HPO | Mutism | HP:0002300 | Speech dysfunction in anti-NMDAR encephalitis includes verbal reduction and mutism in clinical criteria/reviews (pqac-00000033). |
| Phenotype | HPO | Cerebrospinal fluid pleocytosis | HP:0012675 | CSF pleocytosis is common, with reported frequencies ranging from 47% to 91% across cohorts (pqac-00000006, pqac-00000013). |
| Phenotype | HPO | Oligoclonal bands in cerebrospinal fluid | HP:0032150 | Positive CSF oligoclonal bands are reported in roughly 25% to 62.6% of cases across studies (pqac-00000006, pqac-00000007). |
| Phenotype | HPO | Abnormality of EEG | HP:0002353 | EEG is abnormal in most patients and supports diagnosis when antibody results are pending (pqac-00000007, pqac-00000013). |
| Phenotype | HPO | Delta brush EEG pattern | ID not retrieved | Extreme delta brush is a disease-associated EEG pattern specifically highlighted in anti-NMDAR encephalitis diagnostic discussions (pqac-00000006, pqac-00000015). |
| Process | GO | receptor internalization | GO:0031623 | Patient antibodies cause NMDAR loss primarily through receptor crosslinking and internalization rather than agonist activation (pqac-00000018, pqac-00000021). |
| Process | GO | regulation of synaptic plasticity | GO:0048167 | Loss of synaptic NMDARs impairs long-term potentiation and broader synaptic plasticity in passive-transfer studies (pqac-00000019, pqac-00000020). |
| Process | GO | trans-synaptic signaling | GO:0099537 | Reduced synaptic receptor density and altered hippocampal signaling support disruption of synaptic communication pathways (pqac-00000011, pqac-00000024). |
| Process | GO | B cell mediated immunity | GO:0019724 | Disease pathogenesis involves autoreactive B cells and intrathecal antibody-producing cells targeting GluN1 (pqac-00000011, pqac-00000023). |
| Process | GO | immunoglobulin production | GO:0002377 | Intrathecal synthesis of anti-GluN1 antibodies by B cells/plasma cells is part of the proposed pathogenic cascade (pqac-00000020, pqac-00000023). |
| Process | GO | blood-brain barrier maintenance | GO:1990961 | BBB dysfunction is repeatedly proposed as enabling entry/exit of antibodies and immune cells in anti-NMDAR encephalitis (pqac-00000011, pqac-00000024). |
| Treatment | MAXO | corticosteroid therapy | ID not retrieved | High-dose corticosteroids are standard first-line immunotherapy in anti-NMDAR encephalitis management algorithms (pqac-00000001, pqac-00000014). |
| Treatment | CHEBI | methylprednisolone | CHEBI:6888 | IV methylprednisolone is explicitly listed as a first-line treatment option and regimen in the treatment table (pqac-00000014, pqac-00000016). |
| Treatment | MAXO | intravenous immunoglobulin therapy | ID not retrieved | IVIG is a standard first-line immunotherapy and commonly combined with steroids in clinical practice (pqac-00000001, pqac-00000014). |
| Treatment | CHEBI | immunoglobulin | CHEBI:59132 | IVIG is directly listed in treatment recommendations and Table 2 for anti-NMDAR encephalitis (pqac-00000014, pqac-00000016). |
| Treatment | MAXO | plasma exchange therapy | ID not retrieved | Plasma exchange/PLEX is a recommended first-line therapy for acute disease (pqac-00000001, pqac-00000014). |
| Treatment | MAXO | rituximab therapy | ID not retrieved | Rituximab is the best-established second-line escalation therapy for refractory disease and relapse prevention (pqac-00000001, pqac-00000014). |
| Treatment | CHEBI | rituximab | CHEBI:64357 | Rituximab is specifically named in the treatment table as second-line immunotherapy (pqac-00000014, pqac-00000016). |
| Treatment | MAXO | cyclophosphamide therapy | ID not retrieved | Cyclophosphamide is a recommended second-line agent for refractory anti-NMDAR encephalitis (pqac-00000001, pqac-00000014). |
| Treatment | CHEBI | cyclophosphamide | CHEBI:4027 | Cyclophosphamide appears in the treatment table as a second-line immunotherapy option (pqac-00000014, pqac-00000016). |
| Treatment | MAXO | tocilizumab therapy | ID not retrieved | Tocilizumab is described as a complementary option in refractory cases beyond standard second-line therapy (pqac-00000001, pqac-00000016). |
| Treatment | CHEBI | tocilizumab | CHEBI:71416 | Tocilizumab is included among escalation/refractory therapies in the visualized treatment table (pqac-00000016, pqac-00000017). |
| Treatment | MAXO | bortezomib therapy | ID not retrieved | Bortezomib is considered in refractory cases when standard escalation is insufficient (pqac-00000001, pqac-00000016). |
| Treatment | CHEBI | bortezomib | CHEBI:52717 | Bortezomib is listed among additional escalation therapies in the treatment table (pqac-00000017). |
| Treatment | MAXO | mycophenolate mofetil therapy | ID not retrieved | Mycophenolate mofetil is used as prolonged/maintenance immunotherapy in some cohorts and tables (pqac-00000003, pqac-00000017). |
| Treatment | CHEBI | mycophenolate mofetil | CHEBI:31824 | MMF is specifically listed as a maintenance therapy and was used >1 year in a large Chinese cohort (pqac-00000003, pqac-00000017). |
| Treatment | MAXO | azathioprine therapy | ID not retrieved | Azathioprine is used as long-term maintenance immunotherapy in some patients after the acute phase (pqac-00000003, pqac-00000017). |
| Treatment | CHEBI | azathioprine | CHEBI:22636 | Azathioprine is named in the treatment table and in long-term immunotherapy descriptions (pqac-00000003, pqac-00000017). |
| Treatment | MAXO | tumor resection | ID not retrieved | Treatment guidance emphasizes teratoma removal alongside immunotherapy when an ovarian teratoma is present (pqac-00000001, pqac-00000014). |
| Treatment | MAXO | tumor screening | ID not retrieved | All patients should be screened at least once for neoplasm, and female patients may need serial pelvic imaging because ovarian teratoma is a common trigger (pqac-00000001, pqac-00000007). |


*Table: This table maps key anti-NMDA receptor encephalitis concepts to suggested ontology terms across disease, anatomy, cell type, phenotype, process, and treatment categories. It is evidence-aligned to the retrieved literature and can help populate a structured disease knowledge base.*