Table 1.

Summary of challenges with the generic ISA-TAB-Nano specification which were addressed in the current work.

no.	challenge	Applicable, in principle, to any format rather than being specific to ISA-TAB or ISA-TAB-Nano?	Applicable to ISA-TAB?	Applicable to ISA-TAB-Nano?
1	Standardised reporting of stepwise sample preparation needs to be established.	×	×	×
2	Ambiguity exists regarding where different kinds of information should be recorded.	—	×	×
3	Standardised recording of imprecisely reported experimental variables and measurements is required.	×	×	×
4	Ambiguity exists regarding the creation of “Comment […]” fields.	×	×	×
5	Statistical terms need to be clearly defined.	×	×a	×a
6	Ambiguity exists regarding how to link to terms from ontologies.	—	—	×
7	Ambiguity exists regarding whether or not “Parameter Value” or “Factor Value” column entries must be constant or not constant respectively.	—	×	×
8	Linking to images reported in publications is challenging.	×	×	×
9	Standardised reporting of multiple component “characteristics”, “factors”, and “parameters” (e.g. mixtures) needs to be established.	—	×	×
10	A standardised means of linking multiple “external” files to a given Material file is required.	—	—	×
11	Greater clarity regarding the existence of “unused” factors, parameters and measurement names in the Investigation file is required.	—	×a	×
12	A standardised approach for dealing with “non-applicable” metadata is required.	×	×	×
13	The concept of an “investigation” should be more tightly defined for the purpose of collecting data from the literature.	—	—	×
14	Clearly defined minimum information criteria are required.	×	×	×

^aIt should be noted that ISA-TAB is not designed to record experimental measurements in Assay files, i.e., the “Measurement Value [statistic(measurement name)]” Assay file columns and the corresponding Investigation file “Study Assay Measurement Name” field are an ISA-TAB-Nano extension [17,37,39]. However, regarding the issue of clearly defining statistical terms (challenge no. 5), ISA-TAB datasets may include “external” data files (i.e., “external” to the basic Investigation, Study and Assay file types) such as “data matrix” files which may include statistical terms such as “p-value” [36,43]. Standardisation of statistical terms may be achieved via using terms from the STATistics Ontology (STATO) [44]. The challenge noted here (challenge no. 5) regarding clearly defining statistical terms concerns how to appropriately create links to ontologies for these terms in ISA-TAB-Nano datasets.