Table 3.
Summary of the NanoPUZZLES business rules.
| business rule no. | short description |
| 1 | A new “investigation” (corresponding to a new dataset comprising a single Investigation file, a set of Study, Assay and Material files and any “external” files if applicable) should be created for each reference (e.g., journal article), unless that reference specifically states that additional information regarding experiments on the same original nanomaterial samples was reported in another reference. |
| 2 | The “Factor Value […]” columns in the Study file refer to those values which are applicable to the sample prepared immediately prior to application of an assay protocol. |
| 3 | If the entry for a “Characteristics […]”, “Factor Value […]” or “Parameter Value […]” column corresponds to multiple components (e.g., mixtures), record this as a semicolon (“;”) delimited list of the separate components. |
| 4 | If the entry for a “Characteristics […]”, “Factor Value […]” or “Parameter Value […]” column corresponds to multiple components, record the entries in corresponding columns as a semicolon (“;”) delimited list with the entries in the corresponding order. |
| 5 | Any intrinsic chemical composition information associated with a nanomaterial sample (as originally sourced) should be recorded using a Material file even if it is determined/confirmed using assay measurements reported in the publication from which the data were extracted. |
| 6 | Any suspension medium associated with the nanomaterial sample (as originally sourced) should only be described using a Material file “Material Description” column. |
| 7 | Any impurities should be described using entries in the relevant Material file “Characteristics [….]” columns. |
| 8 | Any original nanomaterial components, which are neither a suspension medium nor described as “impurities” in the reference from which the data are extracted, should be described using separate rows of the Material file as per the generic ISA-TAB-Nano specification. |
| 9 | All “Sample Name” values for “true samples” should have the following form: “s_[Study Identifier]_[x]”, e.g., “s_[Study Identifier]_1”a |
| 10 | Assay file “Measurement Value […]” column entries which correspond to concentration-response curve statistics, or similarly derived measures, should be associated with a “derived sample” identifier rather than a “true sample” identifier. |
| 11 | Imprecisely reported experimental variables should be reported using “Factor Value [statistic(original factor name)]” columns created “on-the-fly”. |
| 12 | Imprecisely reported measurement values should be reported using “Measurement Value [statistic(measurement name)]” columns created “on-the-fly”. |
| 13 | “Comment […]” columns (rows) can be added without restriction to a Study, Assay, Material (Investigation) file as long as they are appropriately positioned and as long as each new “Comment […]” column (row) has a unique name for a given file. |
| 14 | All “statistic” names must be entered in the corresponding Investigation file template “Comment [Statistic name]” row. |
| 15 | When linking to terms from ontologies, the “preferred name” should be selected and the full ID entered in the corresponding “Term Accession Number” field. |
| 16 | “Factor Value […]” column entries are allowed to be constant. |
| 17 | Only “Parameter Value […]” column entries associated with a given “Protocol REF” column entry in a Study or Assay file need to be constant. |
| 18 | Images should be linked to assay measurements using a new “ImageLink” file type, if the generic ISA-TAB-Nano approach cannot be applied. |
| 19 | Any nanomaterial structure representation files, which are not associated with specific Assay file “Measurement Value […]” entries, should be linked to the corresponding Material file using ZIP archives specified in the appropriate “Material Data File” column entry. |
| 20 | Empty “Factor Value […]”, “Parameter Value […]” or “Measurement Value […]” columns in Study or Assay files can be deleted without having to update the corresponding Investigation file “Study Protocol Parameters Name”, “Study Factor Name”, or “Study Assay Measurement Name” fields. |
| 21 | Non-applicable columns should be populated with “N/A” where this conveys information. |
| 22 | “Measurement Value [statistic(measurement name)]” columns in the templates which use a label of the form “[TO DO:…]” for the statistic or measurement name must either be updated, based on the kind of statistic and/or measurement name indicated by the label(s), or deleted. |
aHere, the “[Study Identifier]” [37] is unique to the corresponding Study file and “[x]” denotes a numeric value which is specific to a given “true sample”, meaning a prepared sample corresponding to a specific set of experimental conditions, in contrast to the “derived sample” concept introduced in NanoPUZZLES business rule no. 10.