Table 3 Data standard field definitions (part 3): detection methods and parasite identification.

Detection target

String

✓

The taxonomic identity of the parasite being screened for in the sample. This will often be coarser than the identity of a specific parasite identified in the sample: for example, in a study screening for novel bat coronaviruses, the entire family Coronaviridae might be the target; in a parasite dissection, the targets might be Acanthocephala, Cestoda, Nematoda, and Trematoda. For deep sequencing approaches (e.g., metagenomic and metatranscriptomic viral discovery), researchers should report each alignment target used as a new “test” to maximize reporting of negative data, or alternatively, select a subset that reflect specific study objectives and the focus of analysis (e.g., specific viral families). Equivalent to dwc:associatedOccurrences.

Detection method

String

✓

The type of test performed to detect the parasite or parasite-specific antibody (e.g., “PCR”, “ELISA”).

Forward primer sequence

String

The sequence of the forward primer used for parasite detection (e.g., for a pan-coronavirus primer: 5’ CDCAYGARTTYTGYTCNCARC 3’). (Strongly encouraged if applicable, e.g., for PCR.)

Reverse primer sequence

String

The sequence of the reverse primer used for parasite detection (e.g., 5’ RHGGRTANGCRTCWATDGC 3’). (Strongly encouraged if applicable, e.g., for PCR.)

Gene target

String

The parasite gene targeted by the primer (e.g., “RdRp”, e.g., for PCR.).

Primer citation

String

Citation(s) for the primer(s) (ideally doi, or other permanent identifier for a work, e.g. PMID).

Probe target

String

Antibody or antigen targeted for detection. (Strongly encouraged if applicable, e.g., for ELISA.)

Probe type

String

Antibody or antigen used for detection. (Strongly encouraged if applicable, e.g., for ELISA.)

Probe citation

String

Citation(s) for the probe(s) (ideally doi, or other permanent identifier for a work, e.g. PMID).

Detection outcome

String

✓

The test result (i.e., “positive”, “negative”, or “inconclusive”). To avoid ambiguity, these specific values are suggested over numeric values (“0” or “1”). Equivalent to dwc:occurrenceStatus.

Detection measurement

Number

Any numeric measurement of parasite detection that is more detailed than simple positive or negative results (e.g., viral titer, parasite counts, sequence reads).

Detection measurement units

String

Units for quantitative measurements of parasite intensity or test results (e.g., “Ct”, “TCID50/mL”, or “parasite count”).

Parasite identification

String

✓

The identity of a parasite detected by the test, if any, reported to the lowest possible taxonomic level, either as a Linnaean binomial classification or within the convention of a relevant taxonomic authority (e.g., “Borrelia burgdorferi” or “Zika virus”). Parasite identification may be more specific than detection target.

Parasite ID

String

A researcher-generated unique ID for an individual parasite (primarily useful in nested cases where this ID is used as an animal ID in another row, such as pathogen testing of a blood-feeding arthropod removed from a vertebrate host).

Parasite life stage

String

The life stage of the parasite from which the sample was collected (as appropriate for the organism) (e.g., “juvenile”, “adult”).

GenBank accession

String

The GenBank accession for any parasite genetic sequence(s). Accession numbers or other identifiers for related data stored on another platform should be added in a different field (e.g. GISAID Accession, ImmPort Accession). Equivalent to dwc:otherCatalogNumbers.