Proposal to change source_mat_id definition

[cpavloud]

@09012000-tosca @melanthia New definition: A unique identifier assigned to a material sample according to EMO BON Handbook. This ID should be formatted as indicated in the EMO BON Handbook. This identifier will characterize the sample during nucleic acid extraction, and subsequent sequencing or biobanking and data publication. There are two columns for the material sample ID - This one, which is formulated via an equation and which you cannot edit. We did this to avoid mistakes in this ID, which is THE crucial key to keep all EMO BON metadata together. To create a new value in a new row when you have a new sampling event to add to the logsheets, you can simply drag-drop from the cell above. - The next one (see below), which is the value that you can enter yourself. Please try to follow the recommendation anyway, but in any case make sure that this ID and that written on the sample containers are the same as each other. This identifier consists of 5 terms: 1) Project (“EMOBON”) 2) Sampling Site ID; that is the Observatory ID (for example “SMN99”) supplemented with the sampling site indicator (“Wa” for water column, “So” for soft substrates and “Ha” for hard substrates) 3) Sampling Campaign Date formated as YYMMDD for Wa and So (for example, “220315” would be the campaign on 15 March 2022) and as YYMMDDYYMMDD for Ha, i.e. including the deployment and retrieval dates 4) Size fraction (Wa: “3um” / “0.2um” / “20um” / “200um”) or organisms collected (So: “micro” for microorganisms, “meio” for meiobenthos and “macro” for macrobenthos) or ARMS fraction (Ha: “SF40” for sessile fraction sieved through 0.04mm, “MF500” for motile fraction sieved through 0.5 mm, “MF100” for motile fraction sieved through 0.1 mm) 5) Replicate number (1-4). For labelling the negative control, this term will be replaced by the notation “blank” (for the case of a single blank of a particular sample) or "blank 1/2" (for the case of multiple blanks). All terms must be separated by "".

More info: A unique identifier assigned to a material sample according to EMO BON Handbook. This ID should be formatted as indicated in the EMO BON Handbook. This identifier will characterize the sample during nucleic acid extraction, and subsequent sequencing or biobanking and data publication. There are two columns for the material sample ID

• This one, which is formulated via an equation and which you cannot edit. We did this to avoid mistakes in this ID, which is THE crucial key to keep all EMO BON metadata together. To create a new value in a new row when you have a new sampling event to add to the logsheets, you can simply drag-drop from the cell above.
• The next one (see below), which is the value that you can enter yourself. Please try to follow the recommendation anyway, but in any case make sure that this ID and that written on the sample containers are the same as each other. This identifier consists of 5 terms: 1) Project (“EMOBON”) 2) Sampling Site ID; that is the Observatory ID (for example “SMN99”) supplemented with the sampling site indicator (“Wa” for water column, “So” for soft substrates and “Ha” for hard substrates) 3) Sampling Campaign Date formated as YYMMDD for Wa and So (for example, “220315” would be the campaign on 15 March 2022) and as YYMMDDYYMMDD for Ha, i.e. including the deployment and retrieval dates 4) Size fraction (Wa: “3um” / “0.2um” / “20um” / “200um”) or organisms collected (So: “micro” for microorganisms, “meio” for meiobenthos and “macro” for macrobenthos) or ARMS fraction (Ha: “SF40” for sessile fraction sieved through 0.04mm, “MF500” for motile fraction sieved through 0.5 mm, “MF100” for motile fraction sieved through 0.1 mm) 5) Replicate number (1-4). For labelling the negative control, this term will be replaced by the notation “blank” (for the case of a single blank of a particular sample) or "blank 1/2" (for the case of multiple blanks). All terms must be separated by "".

[laurianvm]

Is this the same issue as #5?

[cpavloud]

I have corrected issue https://github.com/emo-bon/observatory-profile/issues/5 (the devil of copy pasting...)

[kmexter]

I am not sure what we are supposed to do for this issue, @cpavloud ?

[cpavloud]

We wanted to update the source_mat_id definition, no?

[kmexter]

ah yes, we did. HQ can do that now that all logsheets have a new definitions tab (if not done already)

[melinalou]

This change has not yet been made. Could you please help me find all the issues with definitions that need to be changed to do this on all the log sheets at once? By now I can see only this, source_mat_id.(I have already change the n_alkanes and the size_frac_up/low.

[melinalou]

The definition of source_mat_id has also changed.

[kmexter]

OK, the only thing left to do is check the Handbook - apparently in the handbook the examples are _(1) for replicates, not _1. If that is the case, the Handbook should be updated