| Domain | Recommended identifier/ontology term | Meaning/use | Evidence caveat |
|---|---|---|---|
| Disease | MONDO: verify in source ontology | Preferred disease ontology anchor for anencephaly in cross-resource integration | Exact MONDO ID not confirmed from retrieved context; verify before database ingestion (pqac-00000000) |
| Disease | Orphanet: anencephaly — verify in source ontology | Rare-disease registry identifier for disease-level aggregation | Exact Orphanet code not confirmed in retrieved context; verify in Orphanet (pqac-00000000) |
| Disease | ICD-10: Q00.0 Anencephaly | Billing/classification code for congenital CNS malformation | Commonly used code; not directly confirmed in retrieved context, so verify against current ICD release (pqac-00000000) |
| Disease | ICD-11: verify in source ontology | International classification term for contemporary coding/interoperability | Exact ICD-11 stem code not confirmed from retrieved context; verify in WHO browser (pqac-00000000) |
| Disease | MeSH: Anencephaly (verify descriptor ID) | Literature indexing term for PubMed/biomedical retrieval | Descriptor name is standard; exact MeSH unique ID not confirmed here (pqac-00000000) |
| Disease concept | Open neural tube defect | High-level grouping used for etiologic and mechanistic aggregation | Much mechanistic evidence is NTD-wide rather than anencephaly-specific (pqac-00000004, pqac-00000006) |
| Phenotype (HPO) | HP:0002323 Anencephaly | Core phenotype/disease-defining cranial neural tube closure defect | Primary phenotype; use as top phenotype assertion (pqac-00000000, pqac-00000005) |
| Phenotype (HPO) | HP:0000248 Microcephaly or verify more specific cranial-abnormality term | Differential/related cranial size abnormality in prenatal imaging/pathology context | Mentioned mainly for differential diagnosis; exact best-fit term should be curated (pqac-00000002) |
| Phenotype (HPO) | HP:0001363 Craniorachischisis | Associated severe open NTD phenotype/subclassification when present | Not present in all cases; use only where explicitly documented (pqac-00000000, pqac-00000005) |
| Phenotype (HPO) | HP:0000238 Hydrocephalus / verify relevance | Potential associated CNS phenotype in broader NTD contexts | Association is broader NTD-wide; not core to isolated anencephaly (pqac-00000004) |
| Prenatal imaging sign | “Mickey Mouse” sign — verify ontology mapping | Useful prenatal ultrasound annotation for first-trimester detection | Imaging descriptor, not a standard disease ontology term (pqac-00000003) |
| Anatomy (UBERON) | UBERON:0000955 brain | Primary malformed/absent organ structure | Central anatomic entity for disease localization (pqac-00000000) |
| Anatomy (UBERON) | UBERON:0003129 calvaria | Absent/partially absent calvarium is part of defining morphology | Verify exact UBERON term label/version in target pipeline (pqac-00000000) |
| Anatomy (UBERON) | UBERON:0001049 neural tube | Embryonic structure whose cranial closure failure causes disease | Core developmental anatomy term (pqac-00000001, pqac-00000005) |
| Anatomy (UBERON) | UBERON:0001891 surface ectoderm / verify | Relevant tissue in neurulation and some model mechanisms | Stronger support from model systems than direct human pathology (pqac-00000004) |
| Cell type (CL) | CL:0000031 neuroepithelial cell / verify | Principal embryonic cell population participating in neurulation | Exact CL mapping should be checked in target ontology version (pqac-00000004, pqac-00000006) |
| Cell type (CL) | Neural fold cells — verify CL term | Developmentally relevant cells for cranial neural tube elevation/fusion | Often described anatomically/developmentally rather than by stable CL code (pqac-00000001, pqac-00000004) |
| Biological process (GO) | GO:0001841 neural tube formation | Broad developmental process disrupted in anencephaly | High-confidence process-level annotation (pqac-00000001, pqac-00000004) |
| Biological process (GO) | GO:0001838 embryonic epithelial tube formation / verify specificity | Supports morphogenetic framing of neurulation failure | Use if broader developmental annotation is desired; may be less specific (pqac-00000004) |
| Biological process (GO) | GO:0035252 planar cell polarity pathway involved in neural tube closure / verify | Mechanistically relevant pathway implicated by human and animal studies | Exact GO child term should be verified; evidence mostly NTD-wide (pqac-00000001, pqac-00000006) |
| Biological process (GO) | Convergent extension — verify GO term | Key morphogenetic mechanism downstream of PCP/Wnt signaling | Strong mechanistic support, but usually broader NTD rather than isolated anencephaly (pqac-00000006) |
| Pathway | Non-canonical Wnt/planar cell polarity signaling | Important pathway for neurulation genes such as VANGL/CELSR | Pathway evidence is robust but not specific to every anencephaly case (pqac-00000001, pqac-00000006) |
| Gene-level annotation | MTHFR | Folate metabolism susceptibility gene frequently discussed in risk/prevention context | Association often based on polymorphism/risk studies, not monogenic causation (pqac-00000000, pqac-00000001) |
| Gene-level annotation | PDGFRA | Candidate/causal-susceptibility gene with rare damaging variants reported in anencephaly | Variant evidence comes from sequencing cohorts and likely oligogenic models (pqac-00000005) |
| Gene-level annotation | VANGL1 / VANGL2 / CELSR1 | PCP pathway genes implicated in neurulation defects | Often stronger in NTD-wide aggregation and model systems than isolated anencephaly-only cohorts (pqac-00000000, pqac-00000001, pqac-00000006) |
| Chemical (CHEBI) | CHEBI:27470 folic acid | Prevention exposure/intervention and nutrient ontology anchor | Central preventive chemical entity; exact CHEBI version should be checked (pqac-00000008, pqac-00000009) |
| Chemical (CHEBI) | folate / tetrahydrofolate derivatives — verify CHEBI term | Nutrient class for one-carbon metabolism annotations | Multiple related CHEBI entities exist; choose level appropriate to data model (pqac-00000008, pqac-00000009) |
| Chemical (CHEBI) | 5-methyltetrahydrofolate (5-MTHF) — verify CHEBI term | Alternative supplemental folate form discussed in recent literature | Evidence for equivalence to folic acid in prevention remains insufficient (pqac-00000008, pqac-00000009) |
| Exposure/risk | Valproic acid — map to CHEBI/Drug ontology in implementation | Major teratogenic exposure/risk factor to capture in exposure model | Evidence is NTD-wide; not unique to anencephaly (pqac-00000001, pqac-00000006) |
| Exposure/risk | Maternal diabetes / obesity / hyperthermia | Key maternal risk factor concepts for epidemiology and prevention annotations | These are clinical exposure concepts rather than disease ontology IDs here (pqac-00000001, pqac-00000006) |
| Intervention (NCIT) | NCIT: folic acid supplementation — verify exact NCIT code | Primary prevention intervention for at-risk or general reproductive-age populations | Exact NCIT code not confirmed; term should be checked in NCIt browser (pqac-00000008, pqac-00000009) |
| Intervention (NCIT) | Prenatal ultrasonography — verify exact NCIT code | Main diagnostic/screening intervention, especially first trimester | Exact NCIT code not confirmed; disease detection evidence strong (pqac-00000000, pqac-00000002) |
| Intervention (NCIT) | Maternal serum alpha-fetoprotein measurement — verify exact NCIT code | Ancillary prenatal screening biomarker test | Less specific than ultrasound; exact NCIT code should be verified (pqac-00000000) |
| Intervention (NCIT) | Pregnancy termination counseling/management — verify exact NCIT concept | Real-world management consequence after prenatal diagnosis of lethal anomaly | Sensitive management domain; terminology should follow local governance and ontology policy (pqac-00000002) |
| Public health | Mandatory folic acid food fortification | Population-level primary prevention implementation concept | Strong NTD-prevention evidence, but policy effect is usually reported for combined spina bifida/anencephaly burden (pqac-00000001, pqac-00000008) |
| Data provenance | Aggregated disease-level resource | Most current information comes from literature reviews, sequencing cohorts, and public-health studies rather than individual-patient EHR data | Distinguish curated disease knowledge from case-level records in KB design (pqac-00000000, pqac-00000005, pqac-00000008) |


*Table: This table provides a compact, database-oriented set of recommended identifiers and ontology terms for representing anencephaly across disease, phenotype, anatomy, mechanism, exposure, and intervention domains. It also flags where exact codes should be verified rather than assumed, which is important for safe knowledge-base population.*