A controlled vocabulary for studies with pathogen and biomarker shedding information (published at BioPortal: https://bioportal.bioontology.org/ontologies/SHEDDING-HUB)
The Shedding Hub Vocabulary is a SKOS-based controlled vocabulary designed for standardizing terminology used in studies involving pathogen and biomarker shedding. It provides a structured framework for describing analytes, specimen types, measurement units, reference events, and participant attributes.
@prefix dcat: <http://www.w3.org/ns/dcat#> .
@prefix dct: <http://purl.org/dc/terms/> .
@prefix owl: <http://www.w3.org/2002/07/owl#> .
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix schema: <http://schema.org/> .
@prefix shv: <https://shedding-hub.github.io/vocab#> .
@prefix skos: <http://www.w3.org/2004/02/skos/core#> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .URI: shv:analyte
Label: Analyte
Created: 2025-05-20
URI: shv:doi
Label: Digital object identifier
Definition: Digital object identifier (doi) for the source publication, study, or data repository
Created: 2025-05-20
URI: shv:participants
Label: Partifipants or subjects
Definition: Participants include patients who enrolled after disease confirmation or participants in a prospective study or human challenging study
Created: 2025-05-20
URI: shv:title
Label: Title
Definition: Title of the source publication, study, or data repository.
Created: 2025-05-20
URI: shv:url
Label: Access URL
Definition: Url for the source publication, study, or data repository
Created: 2025-05-20
URI: shv:biomarker
Label: Biomarker or pathogen being measured
Created: 2025-05-20
URI: shv:crAssphage
Label: Cross-assembly phage
Created: 2025-05-20
URI: shv:mtDNA
Label: Mitochondrial DNA (mtDNA)
Created: 2025-05-20
URI: shv:PMMoV
Label: Pepper mild mottle virus (PMMoV)
Created: 2025-05-20
URI: shv:SARS
Label: Severe acute respiratory syndrome (SARS) virus
Created: 2025-05-20
URI: shv:SARS-CoV-2
Label: Severe acute respiratory syndrome coronavirus 2 (SARS‑CoV‑2) virus
Created: 2025-05-20
URI: shv:gene_target
Label: PCR gene target
Definition: In PCR (Polymerase Chain Reaction), the specific gene or DNA sequence that is targeted for amplification
Created: 2025-05-20
URI: shv:specimen
Label: Specimen type or specimen types for combined samples
Created: 2025-05-20
URI: shv:bronchoalveolar_lavage_fluid
Label: Bronchoalveolar lavage fluid sample
Created: 2025-05-20
URI: shv:nasopharyngeal_swab
Label: Nasopharyngeal swab sample
Created: 2025-05-20
URI: shv:oropharyngeal_swab
Label: Oropharyngeal swab or throat swab sample
Created: 2025-05-20
URI: shv:rectal_swab
Label: Rectal swab sample
Created: 2025-05-20
URI: shv:unit
Label: Unit in which measurements are reported
Created: 2025-05-20
URI: shv:cycle_threshold
Label: Cycle threshold
Created: 2025-05-20
URI: shv:gc_dry_gram
Label: gene copies/dry gram
Created: 2025-05-20
URI: shv:gc_wet_gram
Label: gene copies/wet gram
Created: 2025-05-20
URI: shv:pfu_mL
Label: plaque-forming unit (pfu)/mL
Created: 2025-05-20
URI: shv:attributes
Label: Participant's attributes (such as demographics, comorbidities, and clinical characteristics)
Created: 2025-05-20
URI: shv:age
Label: Age of the participant in years
Created: 2025-05-20
URI: shv:ethnicity
Label: Ethnicity of the participant
Created: 2025-05-20
URI: shv:hispanic
Label: If the participant is hispanic
Created: 2025-05-20
URI: shv:not_hispanic
Label: If the participant is not hispanic
Created: 2025-05-20
URI: shv:race
Label: Race of the participant
Created: 2025-05-20
URI: shv:race_other
Label: If the participant is other than Asian, Black, and White.
Created: 2025-05-20
URI: shv:sex
Label: Sex of the participant at birth
Created: 2025-05-20
URI: shv:female
Label: If the participant at birth is female
Created: 2025-05-20
URI: shv:male
Label: If the participant at birth is male
Created: 2025-05-20
URI: shv:variant
Label: Pathogen variant for the participant
Created: 2025-05-20
URI: shv:vaccinated
Label: If the participant was vaccinated against the pathogen.
Created: 2025-05-20
URI: shv:measurements
Label: Measurements of samples collected from the participant
Created: 2025-05-20
URI: shv:sample_id
Label: Unique sample identifier
Definition: Unique sample identifier in case multiple measurements are reported for the same sample
Created: 2025-05-20
URI: shv:time
Label: Sample collection time
Definition: Time of sample collection since the reference event (e.g., symptom onset)
Created: 2025-05-20
URI: shv:value
Label: Measurement value for the analyte
Created: 2025-05-20