Biotic submission options

[odontaster]

I have been looking at the way the Biotic files are submitted and reduced the submissions to two main types:

• Catch with weight, Biology with Length Distribution: only total weight and subsampled weight per species is reported in Catch. The subsample length distribution and other measured parameters are reported in Biology. In most cases the information in Biology is not fully related to the information provided in Catch: numbers reported in Biology for a certain species, haul, category etc, are most times less to the numbers reported in Catch for that same species, haul, category etc . Heras Dk is an exception to this, they report same numbers in Biology as those for the subsample in Catch. This is the preferred reporting way for StoX users.
• Catch with Length Distribution: the Length distribution and weight at length are reported in Catch. Subsampling and categorization can happen or not. The information contained in Biology does not refer necessarily to all the sample or subsample. This makes sense as length distribution is reported in catch, so whatever reported in Biology, although it will have length information, does not have to be the full subsample. This is the preferred reporting way for non-StoX users.

[odontaster]

I would have a couple of suggestions to be discussed:

• Adopt the Catch with Length Distribution submission for all. It will allow to set up better checks on submission than the current flexible way. It will hopefully not mean a lot of extra work for anyone.
• Try to simplify Catch format: several fields seem redundant in the way they are being used right now (CatchSpeciesSex, CatchSpeciesCatWeight and CatchWeightUnit), they could be removed from the format. Furthermore, if one single submission way is adopted, length fields in catc could be made mandatory. Right now the format is flexible but also confussing to follow.

[HjalteParner]

To also address

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[odontaster]

Subgroup met last month, find minutes here: https://community.ices.dk/ExpertGroups/WGAcousticGov/2023%20Meeting%20Documents/04.%20Working%20documents/Biotic%20format%20subgroup

Next steps, as suggested by Susan:

Maybe we now need to digest a little and then try to divide them into:

-those that can be solved in the DB (without breaking good DB practice such as not storing derived data in the db)

-those that can be solved between Db and Stox (or in StoX) Here I am thinking of the mean weight at length issue for one – adding a building block in the StoX library for calculating “individual weights” from total weight of length class could potentially be better than uploading the calculated mean weight for unweighed fish in the biology section of DB.

-Those that will have to be solved by changing practice at the institutes (or continue manipulating data to fit the further workflow in Db and StoX).

[odontaster]

Subgroup met again in late November 2023. Main points:

• Hope to solve CEFAS reporting issues with new StoX update
• ICES secretariat action: to check whether catch number < biology numbers, consistency report
• ICES secretariat action: look into if catch species category in catch and biology could be made optional

Next steps:

• Review of format document
• Draft of user handbook to explain main sampling procedures/submission options

ICES secretariat team need some time for this, probably to be presented in WGACOUSTIC 2024 Q2 at least.

[odontaster]

I am working on the review of the documentation. Intersessionally I will ask the feedback of the biotic subgroup if that is ok, so we have something ready for approval or review by the whole group for the Q2 meeting.

[HjalteParner]

Will be process in Q3

[odontaster]

Please review and comment the format file and the extract of the documentation here: https://community.ices.dk/ExpertGroups/WGAcousticGov/2024%20Meeting%20Documents/04.%20Working%20documents/Biotic%20format%20and%20examples%20work

[odontaster]

https://github.com/SMLusseau

[odontaster]

@SMLusseau

[odontaster]

@arnejohannesholmin

[elorsepp]

Please comment on the files by 07.10.2024!!! (Hjalte, this is seventh of the October) https://community.ices.dk/ExpertGroups/WGAcousticGov/2024%20Meeting%20Documents/04.%20Working%20documents/Biotic%20format%20and%20examples%20work