jdeck88
commented
7 months ago Attached is the proposed template to this point. template.xlsx
New terms highlighted in yellow
Open jdeck88 opened 7 months ago
jdeck88
commented
7 months ago Attached is the proposed template to this point. template.xlsx
New terms highlighted in yellow
Pulling in discussion about requested terms here:
Rob Ellis: But – method of DNA extraction this is quite varied, and not sure what to put here (for example there are hundreds of types of kits that can be purchased off the shelf, each with subtly different protocols – in theory each could be used). There are two thoughts, in the first instance all of our samples have come from one group in Ireland processing all samples, so is one method (so info not even needed). But the idea is quickly to go more groups around the world to start using it the array themselves, therefore having this open is very useful. I am not a molecular biologist, so really not best placed to comment on the importance of this information – or the range of options we should include (or if it even matters).
JBD: keeping this.
Rob Ellis:Analysis date this is standard date format (as you have for experiment start date etc), and is when the samples are analysed on the array. Important because people could have historic samples that have sat in freezer for >5 years, and come back to them, vs ones processed immediately after sampling. Hence collection date and analysis date.
JBD: keeping this.
Rob Ellis: Service provider again, we use one in Ireland, but there are at least 5 in UK alone, and many worldwide. I can ask Thermo for a list, or we could leave open (if that’s possible), or just remove if too complicated. The issue here is the provider we use is now very experienced with the array, but another may not be and therefore they may not get such good data?
JBD Can use diagnosticsLab (already a field)
Rob Ellis:Associated experimental data derived data URI could be fine. I’ve never used it to my knowledge, but do put associated data on other repositories (so would get a DOI – would that work the same?).
JBD: I added a field called derivedDataDescription. This can be used for this.
Experimental location this is where it might get tricky, as we have where mussels are collected (lat long I presume), but then if have animals from multiple locations brought to a research facility then where an experiment takes place would be an alternative location (lat long would be fine, but good to link to an institution – maybe postcode?).
Keeping this.
Experimental duration I think start and end date could be totally fine
JBD: Removing
Rob Ellis:Experimental protocol I’ve never used IRI or any protocol website/repository. Happy if this is best practice, but wonder if others would then just omit (and if that’s an issue).
JBD: Keeping this.. the IRI is just a suggestion... it can be a text based description also
Rob Ellis:Exposure condition as above, this could almost be infinite. I come at it as a physiologist running environmental challenges. The idea is any info we have on performance of individual in a condition, could allow pretty complex analysis. But may just result in complexity/mess.
JBD: You can use measurementRemarks for this.
Rob Ellis:Thinking over many of these points, I may be overcomplicating. Perhaps best is just to simply remove all experiment info, but just ensure researcher and contact info is there. There could be a field asking a question – were these animals analysed collected directly from the field or included in field/laboratory experiment/manipulation. And then a second question is there associated data experimental data of this individual (Y/N) with DOI/URI for the data – with n concern on data type at this level.