Table 3.
Issues related to the lack of controlled vocabulary / harmonization in terminology or field formats of the Comet assay data. Most of them can be resolved with the implementation of field format constrains and picklists based on domain-specific ontologies.
| Fields name | Findability related issue | Reccomended solution |
Examples | |
|---|---|---|---|---|
| Picklist/autocomplete | Constrain num/textual | |||
| Nanomaterial type/nanomaterial | Lack of controlled vocabulary | yes | SiO2 Silica Silicon dioxide |
|
| Endpoint | Lack of controlled vocabulary | yes | (in vitro) Genotoxicity Genotox DNA strand breaks % DNA in tail OTM NET FPG SITES FPG INCUBATION Not reported |
|
| Assay/Assay name | Lack of controlled vocabulary | yes | COMET Comet assay OxiSelect Comet assay Comet assay in BEAS 2B cells Comet FPG |
|
| Protocol | Lack of controlled vocabulary | yes | COMET COMET-SB COMET- Net Fpg DNA Strand breaks |
|
| Cell type/Cell line | Lack of controlled vocabulary | yes | BEAS 2B BEAS-2B BEAS2B |
|
| Cell pass/Cell passage | Field format | Numerical | 30 p49 P32 + 9 |
|
| Seeding | Field format | Numerical | 10,000 2x105 Not reported |
|
| Results (units) mean or median (SD) | Lack of controlled vocabulary /field format | yes (units) | Numerical (results, SD) | % of dna in tail No fpg % Tail DNA No fpg OTM |
| Treatment | Lack of controlled vocabulary | yes | In vitro stimulation Pos/neg control sample none |
|
| Exposure time /incubation time and units | Lack of controlled vocabulary/ field format |
yes (units) | Numerical (exposure) | 3 h, 24 h Hours, mins |
| Concentration and unit | Lack of controlled vocabulary / field format |
yes (units) | Numerical (concentration) | ug/cm2 or µg/cm2 (mg mL−1) µg/ml or µg/mL |
| Medium | Lack of controlled vocabulary | yes | Textual | DMEM, Dulbecco's modified Eagle medium |