Three-minute orientation
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OmniVira is a curated viral spillover and zoonotic evidence knowledgebase. Its principal unit is a structured, source-linked evidence record rather than a publication alone or a binary virus-host association.
What OmniVira provides
Searchable literature, OVE evidence records, standardized virus and host entities, geographic annotations, a source-traceable One Health outbreak context layer, and provenance back to the original scientific or official source.
What OmniVira does not provide
A clinical decision tool, a formal pathogen-risk score, a claim that every detected host is a reservoir, or a substitute for reading the original publication or official outbreak report.
How the records relate
From a publication to traceable evidence
During curation, one PubMed publication may generate zero, one, or multiple candidate evidence records. Public source-article counts include only publications linked to at least one publicly retrievable OVE record.
Worked example
How to read OVE7661
- Source
- PMID 38140677
- Evidence type
- Molecular Adaptation
- Key finding
- SARS-CoV-2 genomes from mink and farm workers carried F486L and N501T mutations associated with adaptation in mink.
- Traceability
- The OVE record links the structured finding to its supporting text, standardized entities, source article, and extraction metadata.
Public methods overview
How OmniVira is constructed
Literature inclusion and exclusion rules
Primary research with extractable evidence relevant to viral detection, isolation, serology, reservoirs, transmission, host range, experimental infection, receptor usage, molecular adaptation, and genomic evolution is prioritized.
Records already identified as retracted during screening; errata, corrections, and corrigenda; news, comments, editorials, and letters; datasets and audiovisual records; non-original publication types; records with a missing title; and records without an abstract are excluded from V2 evidence extraction. Excluded candidates and their reasons are retained in the screening history rather than silently discarded. If an included source is retracted later, its Article and OVE records are retained for provenance and prominently marked with the updated publication status.
Why citation-based supplementation is separate from daily retrieval
Citation-based supplementation is used to identify potentially important earlier studies that may not be recovered by a single keyword strategy. Because highly cited records contain more reviews, methods papers, software, and other out-of-scope material, they undergo stricter relevance screening before evidence extraction.
Controlled Evidence Ontology v2.1.0
Five categories and fourteen evidence types
A category is a high-level scientific domain. An evidence type is the controlled label assigned to an individual OVE record. Category names are never used as substitutes for a specific evidence type.
Evidence category
Zoonotic Surveillance
Evidence from surveillance, sampling, virus detection, virus isolation, serology, or reservoir-ecology studies that documents viral presence, exposure, or ecological maintenance in hosts or host-associated environments relevant to zoonotic and spillover research.
Scope. This category captures observation and surveillance evidence. It does not by itself prove a transmission event unless source-recipient movement is explicitly supported.
Virus Isolation Evidence that infectious virus was recovered, cultured, or isolated from a host, sample, tissue, vector, environmental material, or host-associated source.
Definition
Evidence that infectious virus was recovered, cultured, or isolated from a host, sample, tissue, vector, environmental material, or host-associated source.
Boundary and exclusion rule
Use only when recovery/culture/isolation of infectious virus or isolate is supported; otherwise use Viral Detection.
Required type-specific fields
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virus_name_rawRaw name of the virus, viral species, strain, subtype, or viral group recovered or cultured from the sample. -
source_host_or_sample_rawRaw name of the host species, host group, vector, environmental source, specimen source, or animal-human interface source from which infectious virus was isolated. -
isolation_outcomeReported outcome of virus isolation, including successful isolation, culture positivity, recovery of infectious virus, cytopathic effect, plaque formation, passage result, or comparable isolation result.
Recommended fields when explicitly supported
sample_type_raw,
isolation_system,
isolate_name_raw
Viral Detection Evidence that viral nucleic acid, antigen, viral material, or viral signal was detected in hosts, samples, vectors, or environments without necessarily demonstrating infectious-virus isolation.
Definition
Evidence that viral nucleic acid, antigen, viral material, or viral signal was detected in hosts, samples, vectors, or environments without necessarily demonstrating infectious-virus isolation.
Boundary and exclusion rule
Use for detection or surveillance signals without evidence of successful infectious-virus isolation.
Required type-specific fields
-
target_host_rawRaw name of the monitored or sampled animal host, host group, vector, environmental source, or animal-human interface source. -
virus_name_rawRaw name of the virus, viral species, strain, subtype, sequence group, or viral group detected, discovered, or analyzed in surveillance specimens. -
methodsMethods used to monitor, detect, identify, sequence, or analyze viral material in surveillance specimens.
Recommended fields when explicitly supported
geographic_location_raw,
sample_types,
sample_size_raw
Serological Evidence Evidence of antibody, neutralization, seropositivity, seroconversion, or related immune exposure to a virus in a host population or sampled group.
Definition
Evidence of antibody, neutralization, seropositivity, seroconversion, or related immune exposure to a virus in a host population or sampled group.
Boundary and exclusion rule
Use for exposure evidence based on antibodies or neutralization; do not treat serology alone as proof of active infection or transmission.
Required type-specific fields
-
virus_name_rawRaw name of the virus, viral species, strain, subtype, antigen, or viral group targeted by serological or antibody evidence. -
sampled_host_rawRaw name of the host species, host group, exposed population, or human/animal population from which serum or antibody evidence was obtained. -
methodsSerological, antibody, neutralization, or immunological method used to detect exposure or infection history. -
serological_result_rawRaw text reporting seroprevalence, antibody positivity, seropositive proportion, neutralizing antibody result, titer, seroconversion, or antibody detection outcome.
Recommended fields when explicitly supported
sample_types
Reservoir Ecology Evidence characterizing ecological reservoirs, maintenance hosts, host populations, vectors, or ecological conditions associated with viral persistence, circulation, or exposure.
Definition
Evidence characterizing ecological reservoirs, maintenance hosts, host populations, vectors, or ecological conditions associated with viral persistence, circulation, or exposure.
Boundary and exclusion rule
Use for ecological reservoir or maintenance-host evidence; use Viral Detection for simple positive sampling without reservoir interpretation.
Required type-specific fields
-
virus_name_rawRaw name of the virus, viral species, strain, subtype, or viral group involved in ecological, reservoir-host, maintenance, or natural-circulation evidence. -
target_host_rawRaw name of the target host, proposed reservoir host, maintenance host, host population, host community, vector, or ecological source studied for viral persistence or circulation. -
methodsMethods used for ecological, reservoir-host, maintenance, or natural-circulation analysis.
Recommended fields when explicitly supported
geographic_location_raw,
sample_types,
ecological_metrics
Evidence category
Transmission Evidence
Evidence that describes, infers, or investigates viral movement between source and recipient hosts, including spillover, outbreak-associated transmission, and cross-species transmission among non-human hosts.
Scope. Use this category when the evidence concerns a transmission relationship or event, not merely detection of the same virus in multiple hosts.
Spillover Event Evidence describing a naturally occurring or epidemiologically supported animal-to-human viral transmission event in which a non-human animal source, reservoir, vector, or animal-derived exposure is linked directly to infection in a human individual or population.
Definition
Evidence describing a naturally occurring or epidemiologically supported animal-to-human viral transmission event in which a non-human animal source, reservoir, vector, or animal-derived exposure is linked directly to infection in a human individual or population.
Boundary and exclusion rule
Use only for animal-to-human transmission with a non-human animal source and a human recipient. Human-to-animal spillback and natural transmission between different non-human animal species belong to Cross-species Transmission; controlled transmission experiments belong to Experimental Transmission. Co-detection, serology, phylogenetic relatedness, ecological association, or speculative spillover risk alone is insufficient.
Required type-specific fields
-
virus_name_rawRaw name of the virus, viral species, strain, subtype, or viral group involved in the animal-to-human transmission event. -
source_host_rawRaw name of the non-human animal source, reservoir, intermediate host, vector, or animal-derived exposure source in the animal-to-human transmission event. -
recipient_host_rawRaw name of the human recipient, case, exposed occupational group, or affected human population in the animal-to-human transmission event. -
transmission_directionDirection of the animal-to-human transmission event.
Recommended fields when explicitly supported
geographic_location_raw,
study_design,
methods
Outbreak Investigation Evidence from an outbreak, epidemic, cluster, or case investigation that links a virus to affected hosts, settings, source hypotheses, transmission context, or outbreak scale.
Definition
Evidence from an outbreak, epidemic, cluster, or case investigation that links a virus to affected hosts, settings, source hypotheses, transmission context, or outbreak scale.
Boundary and exclusion rule
Use for outbreak/case-cluster investigations; use Spillover Event only when animal-human transmission is specifically supported.
Required type-specific fields
-
virus_name_rawRaw name of the virus, viral pathogen, virus group, strain, subtype, or variant involved in the outbreak, epidemic, cluster, or case investigation. -
outbreak_host_rawRaw name of the host species, host group, population, or human/animal group in which the outbreak occurred or was investigated.
Recommended fields when explicitly supported
suspected_source_host_raw,
affected_host_raw,
transmission_direction,
outbreak_setting_raw,
geographic_location_raw,
outbreak_time_raw,
outbreak_scale_raw,
methods
Cross-species Transmission Evidence of naturally occurring or epidemiologically supported viral transmission from humans to non-human animals, or between different non-human animal species, including reverse zoonosis and directionally unresolved but well-supported cross-species host-pair transmission.
Definition
Evidence of naturally occurring or epidemiologically supported viral transmission from humans to non-human animals, or between different non-human animal species, including reverse zoonosis and directionally unresolved but well-supported cross-species host-pair transmission.
Boundary and exclusion rule
Use for human-to-animal spillback, transmission between different non-human animal species, or a well-supported interspecies host pair for which direction cannot be resolved. Animal-to-human transmission belongs to Spillover Event; controlled transmission experiments belong to Experimental Transmission. Same-species, human-to-human, susceptibility-only, receptor-only, co-detection, serology-only, phylogeny-only, or speculative host-jump statements are excluded.
Required type-specific fields
-
virus_name_rawRaw name of the virus, strain, isolate, subtype, variant, or viral group involved in human-to-animal spillback or transmission between different non-human animal species. -
source_host_rawRaw name of the human or non-human source host, donor population, reservoir, or source population from which cross-species transmission originated or was inferred. -
recipient_host_rawRaw name of the non-human animal recipient host, spillback host, host species, host group, or target population receiving or participating in the cross-species transmission. -
transmission_directionDirection or host-pair relationship of a human-to-animal or non-human animal cross-species transmission event.
Recommended fields when explicitly supported
geographic_location_raw,
study_design,
methods
Evidence category
Experimental Infection
Controlled experimental evidence evaluating host susceptibility, host range, pathogenicity, or transmission using defined viruses, hosts, model systems, challenge systems, or exposure designs.
Scope. Use this category for deliberate experimental systems rather than natural outbreaks or field surveillance.
Pathogenicity Experiment Controlled experimental evidence evaluating disease phenotype, pathogenicity, virulence, tissue damage, clinical outcome, or severity caused by a virus in a tested host system.
Definition
Controlled experimental evidence evaluating disease phenotype, pathogenicity, virulence, tissue damage, clinical outcome, or severity caused by a virus in a tested host system.
Boundary and exclusion rule
Use for controlled disease phenotype or virulence assessment; use Host Range Experiment when the question is host susceptibility rather than disease severity.
Required type-specific fields
-
virus_name_rawRaw name of the virus, strain, isolate, subtype, variant, mutant, or viral group used in the pathogenicity experiment. -
tested_host_rawRaw name of the experimentally infected, challenged, exposed, or tested host used to evaluate pathogenicity. -
experimental_systemExperimental system used to evaluate pathogenicity, such as an animal model, humanized animal model, organoid, ex vivo tissue system, or other controlled infection model. -
pathogenicity_outcomesReported pathogenicity-related outcomes, including clinical signs, disease phenotype, weight loss, morbidity, mortality, lesions, pathology, tissue damage, viral shedding, host response, or attenuation/severity findings. -
methodsExperimental, virological, pathological, clinical-scoring, viral-load, histological, imaging, immunological, or analytical methods used to evaluate pathogenicity.
Host Range Experiment Controlled experimental evidence testing whether a virus can infect, replicate in, enter, or otherwise establish susceptibility across one or more host species or host-derived systems.
Definition
Controlled experimental evidence testing whether a virus can infect, replicate in, enter, or otherwise establish susceptibility across one or more host species or host-derived systems.
Boundary and exclusion rule
Use for controlled susceptibility/host-range testing; use Experimental Transmission when source-to-recipient spread is tested.
Required type-specific fields
-
virus_name_rawRaw name of the virus, strain, isolate, subtype, variant, mutant, or viral group used in the host-range experiment. -
tested_host_rawRaw name of the host species, host group, animal model, cell-derived host context, organoid, tissue, or host system tested for susceptibility, permissiveness, infection, replication, or host range. -
experimental_systemExperimental system used to test host range, such as an animal challenge model, cell-culture system, organoid, ex vivo tissue, pseudovirus system, receptor-expression system, or other controlled host-range assay. -
methodsExperimental, virological, cell-culture, animal-challenge, receptor-entry, replication, pathology, sequencing, or analytical methods used in the host-range experiment.
Recommended fields when explicitly supported
virus_source_host_raw,
sample_types
Experimental Transmission Controlled experimental evidence testing transmission from a source host or source system to a recipient host or recipient system under defined exposure conditions.
Definition
Controlled experimental evidence testing transmission from a source host or source system to a recipient host or recipient system under defined exposure conditions.
Boundary and exclusion rule
Use only when a source-to-recipient transmission design is present under controlled experimental conditions.
Required type-specific fields
-
virus_name_rawRaw name of the virus, strain, isolate, subtype, variant, mutant, or viral group used in the experimental transmission study. -
source_host_rawRaw name of the donor, infected source, shedding source, inoculated source, vector source, or starting host in the experimental transmission setup. -
recipient_host_rawRaw name of the recipient, contact, exposed, sentinel, vector-exposed, or target host tested for acquisition of infection in the experimental transmission setup. -
experimental_systemControlled experimental system used to test transmission, such as animal transmission model, contact transmission model, aerosol model, vector transmission model, environmental exposure model, or co-housing model. -
transmission_outcomesReported transmission outcome categories or findings, such as recipient infection, contact transmission, aerosol transmission, vector-borne transmission, seroconversion, shedding in recipients, inefficient transmission, or no transmission. -
methodsExperimental, virological, serological, sequencing, epidemiological-model, animal-model, vector-assay, sampling, or analytical methods used to evaluate experimental transmission.
Evidence category
Functional Mechanism
Mechanistic evidence describing molecular or cellular determinants of viral host range, entry, receptor usage, tissue tropism, adaptation, replication, immune escape, or other functional processes relevant to spillover potential.
Scope. Use this category when the evidence explains mechanism. Do not use it for genomic association alone without a functional interpretation.
Receptor Usage Functional evidence identifying or testing viral receptor usage, receptor binding, entry factors, or host-cell entry determinants.
Definition
Functional evidence identifying or testing viral receptor usage, receptor binding, entry factors, or host-cell entry determinants.
Boundary and exclusion rule
Use for receptor or entry-factor evidence; use Molecular Adaptation when the main claim is adaptive mechanism rather than receptor identity alone.
Required type-specific fields
-
virus_name_rawRaw name of the virus, viral species, strain, subtype, variant, pseudovirus, or viral system involved in receptor-usage or cell-entry evidence. -
receptor_rawRaw name of the receptor, co-receptor, attachment factor, or receptor-like molecule explicitly implicated in viral binding, entry, tropism, or host-range compatibility. -
methodsMethods used to support receptor usage, receptor compatibility, viral binding, cell entry, or receptor-mediated host range.
Recommended fields when explicitly supported
host_factors,
tested_host_raw
Molecular Adaptation Evidence linking viral or host molecular features to adaptation, host range, receptor binding, replication, immune escape, tropism, virulence, or transmission fitness.
Definition
Evidence linking viral or host molecular features to adaptation, host range, receptor binding, replication, immune escape, tropism, virulence, or transmission fitness.
Boundary and exclusion rule
Use for adaptive molecular mechanisms; do not assign this type to neutral genomic variation without mechanistic relevance.
Required type-specific fields
-
virus_name_rawRaw name of the virus, viral strain, isolate, subtype, variant, mutant, lineage, or viral group involved in molecular adaptation evidence. -
mechanism_typesMolecular adaptation mechanism category supported by the evidence, such as receptor binding, receptor usage, host entry, replication adaptation, immune escape, tropism, virulence adaptation, host-range expansion, or transmission fitness.
Recommended fields when explicitly supported
genes_or_proteins,
mutations,
receptors,
host_factors
Evidence category
Genomic Evolution
Genomic, phylogenetic, evolutionary, recombination, or reassortment evidence that informs viral emergence, host switching, lineage movement, adaptation history, or generation of novel viral genotypes.
Scope. Use this category for sequence-based evolutionary evidence. Functional receptor or pathogenicity assays should be assigned to their mechanism or experimental categories.
Recombination or Reassortment Evidence that viral recombination or genome-segment reassortment generated or contributed to a viral genotype relevant to emergence, host range, or transmission.
Definition
Evidence that viral recombination or genome-segment reassortment generated or contributed to a viral genotype relevant to emergence, host range, or transmission.
Boundary and exclusion rule
Use when recombination or reassortment is the evidence focus, not merely when a genome sequence is reported.
Required type-specific fields
-
recombinant_or_reassortant_virus_name_rawRaw name of the recombinant, reassortant, mosaic, segment-exchange, or mixed-ancestry virus, strain, subtype, lineage, or viral group described in the evidence record. -
event_typeType of genomic exchange or mosaic event described by the evidence record.
Recommended fields when explicitly supported
parental_virus_a_raw,
parental_virus_b_raw,
parental_virus_names_raw,
genes_or_segments
Phylogenetic Evolution Phylogenetic or genomic-evolution evidence describing viral lineage relationships, host-associated evolution, divergence, adaptation, or evolutionary origin.
Definition
Phylogenetic or genomic-evolution evidence describing viral lineage relationships, host-associated evolution, divergence, adaptation, or evolutionary origin.
Boundary and exclusion rule
Use for phylogenetic/evolutionary inference; use Recombination or Reassortment when genome exchange is the central claim.
Required type-specific fields
-
virus_name_rawRaw name of the virus, viral species, strain, subtype, lineage, clade, genotype, or viral group involved in phylogenetic or genomic-evolution analysis. -
analysis_methodsEvolutionary, phylogenetic, phylodynamic, phylogeographic, comparative genomic, lineage, molecular-clock, or related sequence-analysis methods used to support the evidence.
Recommended fields when explicitly supported
host_raw,
genes_or_proteins
High-value boundary decisions
Transparent provenance
AI assistance and human-supervised curation
OmniVira uses AI to make evidence-scale curation feasible, but AI output, authority-based normalization, and curator approval are distinct states. The current beta contains active records at different stages of record-level review.
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AI-assisted
Screening and candidate extraction
LLMs support relevance triage, Evidence Type assignment, and initial field extraction.
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Validated
Schema and boundary checks
Required fields, controlled values, direction rules, duplicates, and source hashes are checked.
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Normalized
Authority and mapping resolution
Raw virus, host, and geographic mentions are mapped without discarding their original form.
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Human-supervised
Correction, approval, or exclusion
The Curation Console preserves reviewer decisions, reasons, changes, and audit history.
How AI-generated summaries differ from evidence records
Evidence-grounded Research Briefs are AI-assisted orientation summaries. They synthesize linked, publicly active OVE records as the factual basis and use the corresponding article titles and abstracts only for study context. They are not primary evidence records and do not replace source-level verification. WHO monitoring summaries are generated separately from WHO source reports. An OVE record, by contrast, has a controlled Evidence Type, supporting text, source PMID, structured fields, entity mappings, and an auditable curation state.
Reported claims, source status, and responsible interpretation
Evidence interpretation and publication status
An OmniVira Evidence (OVE) record represents a source-linked finding or claim reported in a scientific publication. Inclusion means that the structured claim can be traced to its cited source; it does not mean that OmniVira has independently reproduced or experimentally validated the underlying biological finding.
What curation verifies
Curation assesses whether an OVE faithfully represents a claim reported in the source text, whether required structured fields are supported, and whether source provenance is preserved.
What curation does not verify
OmniVira does not independently establish reproducibility, methodological validity, or the ultimate biological truth of every primary study. Individual findings should be interpreted together with the linked publication and its editorial history.
Publication-status monitoring
OmniVira checks source-publication status against official NCBI PubMed metadata when a record is imported and through a rolling re-check in the daily update workflow. Checks use PubMed publication types and linked comments/corrections relations rather than title keywords. A temporary retrieval failure never overwrites the last confirmed status; it is recorded for a later retry.
- Active
- No qualifying PubMed retraction or editorial concern was identified at the most recent successful check.
- Retracted
- The publication has been formally retracted. Its OVE records remain accessible for provenance, carry a prominent warning, and should not be treated as current supporting evidence without reviewing the retraction notice.
- Expression of Concern
- A journal or publisher has issued a formal concern that remains unresolved. This status is not equivalent to retraction and does not automatically mean that every reported finding is false.
- Corrected / Erratum
- PubMed links the publication to a correction, erratum, or corrected republication. Users should inspect the linked notice to determine which content changed.
- Updated / Other Editorial Notice
- PubMed records another update or editorial relation that may be relevant to interpretation.
- Unknown / Not Checked
- A current successful publication-status check is not yet available. This label is not evidence of an adverse publication state.
Retraction and Expression of Concern annotations describe the editorial state of the source; they do not constitute an automated verdict that a biological claim is true or false. Source Articles, linked OVE identifiers, status notices, check dates, and status-change history are retained to support audit and re-evaluation.
Controlled names with raw provenance
Virus, host, and country normalization
Authors use abbreviations, historical names, strain codes, informal host descriptions, and locations at different geographic levels. OmniVira preserves the raw wording and links it to a controlled entity only when the mapping is sufficiently supported.
ICTV family, genus, subgenus, and species form the authority backbone. OmniVira adds a curated virus/subtype display layer for named viruses, accepted abbreviations, and influenza HxNy subtypes without replacing the ICTV lineage.
Raw name → confirmed mapping → ICTV hierarchy → curated virus/subtypeTaxID and scientific lineage remain authoritative. English common names and images are readability aids. Cell systems are kept distinct and may link to their source organism. Host context is classified as Natural host, Experimental system, or Unclear.
Raw name → TaxID / lineage → public display name → host contextSpecific places and study sites remain available as raw geographic text. Country-level browsing uses canonical English country names and ISO-3 identifiers where a reliable country assignment can be made.
Raw location → country assignment → canonical country / ISO-3New entities, ambiguous or conflicting mappings, split names, and nonstandardizable phrases remain reviewable. A mapping is not silently promoted merely because an LLM suggests a plausible candidate.
An independent, versioned public-health annotation layer
WHO R&D Blueprint annotations
R&D means Research and Development. The WHO R&D Blueprint supports advance research, diagnostics, vaccines, therapeutics, and adaptable platform capacity for pathogens that may cause major epidemics or pandemics. It is a preparedness framework, not a ranking of zoonotic probability, transmissibility, disease severity, or pandemic risk.
Priority Pathogen
A specific pathogen that WHO identifies for prioritized epidemic or pandemic preparedness R&D. This is a WHO research-priority designation, not an OmniVira-derived zoonotic risk score.
Prototype Pathogen
A representative pathogen selected to establish research and product-development capacity that can be transferred to other known or future pathogens within a broader family or taxon. A prototype is not necessarily the “most dangerous” virus in that family.
Family-level preparedness
The entity belongs to a family included in WHO family-based preparedness or prioritization. Membership does not make every virus in that family a direct Priority or Prototype Pathogen.
Family-specific R&D Roadmap
The entity belongs to a family addressed by the WHO family-specific R&D roadmaps announced in 2026. This indicates roadmap coverage, not that the individual virus received the highest risk designation.
- Direct
- The WHO designation directly corresponds to the current OmniVira entity through an explicit WHO-to-ICTV-to-OmniVira crosswalk.
- Taxonomic coverage
- WHO designated a genus, subgenus, subtype group, or another upper taxon; this entity is a member of that taxon but is not itself presented as a direct designation.
- Family-level
- The entity is annotated only because it belongs to a WHO-designated family. Family membership is never converted into a direct Priority or Prototype designation.
- Not designated
- No current annotation of that designation type is linked to the entity under the displayed framework version. This is not evidence that WHO has assessed the virus as low risk.
WHO terminology and virus taxonomy change over time. OmniVira therefore retains the original WHO wording, source document, publication or effective date, framework year/version, current ICTV crosswalk target, relationship, and mapping note. A newer framework creates a new versioned annotation; older provenance is not silently overwritten. Ambiguous names, disease-level wording, genotype or serotype designations, and taxonomic revisions remain in curator review rather than being forced into a one-to-one virus mapping.
The 2024 WHO framework evaluated 28 viral families under the taxonomy used in the source report. In the current ICTV MSL41 crosswalk, the historical family Reoviridae is represented by Sedoreoviridae and Spinareoviridae. OmniVira therefore records 29 current-family crosswalk designations while preserving the original WHO framework and wording; this does not represent an additional family selected by WHO.
Choosing the right entry point
Search, browse, and interpret records
Before interpreting an OVE record
- Read the key finding as a structured summary, not as a replacement for the source text.
- Open Supporting text and confirm that it directly supports the relevant structured fields.
- Check the Evidence Category, Evidence Type, host context, and standardized entities together.
- Open the PMID or DOI before reusing a scientific claim.
How abstract highlighting should be read
Supporting-text highlights indicate the abstract sentence or sentence segment most closely aligned with an OVE record. Virus, host, and location underlines are matched primarily from raw extracted names so that later normalization changes do not break provenance. Approximate sentence matching can be used when extraction contains a close paraphrase or merges adjacent source statements.
Official reports outside the OVE ontology
One Health outbreak context
OmniVira integrates official outbreak context from WHO Disease Outbreak News and FAO EMPRES-i. This layer complements literature-derived OVE records but is not part of the Evidence ontology. It does not represent an OmniVira judgement of event truth, disease severity, spillover probability, or pandemic risk.
- WHO Disease Outbreak News
- Public-health narratives that may describe broad, evolving events involving human cases, animal sources, or zoonotic exposure.
- FAO EMPRES-i
- Animal-disease reports compiled from multiple official and verified sources. OmniVira presents a rolling seven-day virus-level summary rather than a public portal of individual FAO records.
- FAO weekly monitor
- Rows count reports newly published by FAO within the displayed seven-day window. They are not counts of infected animals or people.
Source attribution and event matching
WHO and FAO records remain stored with immutable revisions and official source identifiers. WHO narratives are displayed as contextual reports. FAO records are aggregated by standardized virus and report-publication date for the weekly monitor; countries, hosts, diagnostic states, raw names, and upstream attribution remain traceable in the internal audit layer.
Independent and derived sources
FAO EMPRES-i incorporates records from several sources, including WAHIS. Where FAO reports WAHIS as its upstream source, OmniVira preserves that lineage internally; it is not presented as a separately ingested WOAH record or an additional independent confirmation.
Source relationship status
Single source, Concordant, Partially concordant, Conflicting reports, and Under review describe relationships among official records. They are not confidence grades or risk scores.
How reported differences are handled
- Dates retain their meaningObservation, onset, report, publication, and end dates are stored separately and are not substituted for one another.
- Counts retain their denominator and time pointCase, death, susceptible-animal, and affected-premises counts from different reports are not automatically added.
- Diagnosis is not upgradedSuspected, confirmed, and denied reports remain distinct. A suspected report is never converted into confirmed status merely because another source exists.
- Coordinate precision is explicitExact coordinates, approximate coordinates, and administrative centroids are distinguished; a centroid is not shown as an exact outbreak site.
- Raw names remain availableVirus, host, and country names are linked to OmniVira standardized entities while each agency's original expression is preserved.
- Differences remain visibleWhen official reports cannot be reconciled, OmniVira displays “Reported differently across official sources” and retains the source-specific values.
Continuous but reviewable updating
Daily updates, versions, and quality control
The literature workflow is scheduled daily. A successful run updates the database activity date even when no eligible new publication is found, so “Last updated” describes execution of the update workflow rather than a guarantee of new records.
Daily statistics are organized by PubMed publication or indexing dates where specified, not simply by the time a row was inserted into OmniVira. Screening decisions, exclusion reasons, raw mappings, prompt and schema versions, extraction metadata, and curator actions are retained to support reassessment.
- Evidence ontology
- v2.1.0
- Documentation
- 2026.08.30
- Documentation reviewed
- 30 August 2026
- Latest recorded data update
- 11 October 2026
Reproducible reuse
Data availability and citation
The public website can be searched without login. Versioned bulk-download endpoints are still being prepared; until they are released, dataset requests can be submitted through the feedback channel.
Manuscript in preparation
The OmniVira database article is currently in preparation. The formal citation and DOI will be provided here when the article is published.
Responsible interpretation
Limitations and known sources of uncertainty
- Abstract-level coverage Evidence extraction may rely on PubMed abstracts when full text is unavailable, so methods and contextual qualifiers can be incomplete.
- Retrieval bias Coverage reflects the configured PubMed strategy and supplementation rules; relevant literature outside indexed or searchable sources may be missed.
- Extraction uncertainty LLMs can omit, merge, or misclassify findings. Supporting text and the source publication remain the verification standard.
- Taxonomic resolution An entity can be standardized at family, genus, species, virus, subtype, or another supported rank. Parent-level mapping does not imply species-level certainty.
- Association is not causation Detection, seropositivity, receptor compatibility, or phylogenetic similarity alone does not establish reservoir status or a transmission event.
- Counts are descriptive Evidence and source-article counts describe database coverage, not prevalence, effect size, evidence quality, or public-health risk.
- Active beta curation Records and mappings can change as curators review new evidence, resolve names, apply ontology revisions, or respond to corrections.
Shared vocabulary
Glossary, corrections, and feedback
- Evidence record
- One structured, traceable finding derived from a source publication and assigned an OVE identifier.
- Key finding
- A concise statement describing the scientific result represented by one OVE record.
- Supporting text
- The specific source sentence or close textual support for the structured finding and its core fields.
- Raw name
- A virus, host, or location expression preserved as it appeared in the source material.
- Standardized entity
- A controlled virus, host, or geographic record linked to one or more raw mentions.
- Spillover
- In OmniVira V2.1, a natural or epidemiologically supported non-human animal-to-human transmission event.
- Spillback
- Human-to-animal transmission, represented under Cross-species Transmission.
- Host context
- The role of a standardized host mention: Natural host, Experimental system, or Unclear.
To report an error, include the OVE identifier or PMID, the affected virus, host, country, Evidence Type or field, and the source text supporting the proposed correction. This makes the issue reproducible and shortens curator review.