RDBES: BiologicalMeasurementType 2 new codes

[HenrikK-N]

Hi RMG. The Core Group support the herring benchmark, who request the following new codes to be added to the code type BiologicalMeasurementType:

Code Description VertebraCount Number of Vertebrae HatchMonth The month (1 to 12) of hatching

These codes are historical used for identification of herring stocks, and are therefore essential for doing the right splitting of the historical herring data. It is also relevant to have the original measurements, as it has been up for discussions previously.

[Osanna123]

VertebraCount - ok HatchMonth, we need a bit more info on this - the parameter seems like an estimate from the larvae age. Is that recorded?

[MariaMakri]

I think that hatching month, is used as a more accurate metric to distinguish among autumn, spring or winter-spawning herring stocks.

With a little research, I think that it might refer to hatching month as estimated by inspection of the larval otolith microstructure in adult herring.

Here the first paper describes the methodology used to classify different hatch types (autumn, spring..): file:///D:/OneDrive%20-%20International%20Council%20for%20the%20Exploration%20of%20the%20Sea%20(ICES)/Profile/Downloads/Application_and_validation_of_otolith_microstructu.pdf

Here, they identify hatching type on a month level. https://academic.oup.com/icesjms/article/80/1/173/6969398

There is an otolith morphometry information code in BiologicalMeasurementType that I am not sure what information it includes.

I have sent an email to Kirsten Birch Håkansson and await for her response.

[MariaMakri]

This is her answer:

I spoke with my colleague Julie, she is our expert in anything otolith related, and she confirmed that they look at the part of the otolith laid down during the larval stage to determine with month the fish has been hated.

The information is used to determine which stock the herring belong to (Western Baltic Spring spawners or North sea autumn spawner herring) and split the commercial catch and survey indices per stock.

[MariaMakri]

Add a proper description (ask Julie) and add reference to long description.

[MariaMakri]

I have asked Julie for a description and this was her answer

HatchMonth, even though it can be 4, 9 or 12 does not refer specifically to the month of hatch as those called 4 can be hatched in “Spring”, so not necessarily April, but could be from late March and into May. It is the same for 9 (“Autumn”) and 12 (“Winter”). I think it would be better to refer to the code as HatchType.

For the long description: Hatching season of herring stocks, as estimated by visual inspection of season-specific daily increment pattern of the otolith microstructure laid down during the larval and post-larval period (Clausen et al. 2007).

So, she suggested that we use these as the accepted values of this code:

4-Spring 9-Autumn 12-Winter

[cekv]

@MariaMakri to Suggest "Hatching season" to Julie, then take this up with the RDBS core group to accept the suggestions from Julie. The codes can be either number (could include letters, i.e HS4, etc) or season, not both. The description can be more explorative. RMG has no strong position on the code.

[cekv]

@MariaMakri to send an email to @HenrikK-N with details to present to RDBES core group for confirmation

[MariaMakri]

There is some updates on the HatchSeason Code for biologicalMeasurementType.

So, Kirsten Hachansson asked WGHAWG for feedback and they agreed on HatchSeason and the following values as accepted. Then they think that a shorter description is sufficient and a new code to be added to SampleType : otolithMicrostructureLarval (Daily increment pattern of the Otolith microstructure laid down during the larval and post-larval period)

These will be discussed tommorrow (24th of Jan) in the Core group.

I am thinking of recommending something else, because it seems to me that adding otolithLarvalMicrostructure to SampleType is not exactly fit, since SampleType contains more general samples like 'scale' etc. and there is already an otolith code. //vocab.ices.dk/?ref=1507

As I understand from Kristen's answer, there are two methods for estimating Hatching Season of herring stocks; by visual inspection of the otolith microstructure layed during the larval period and by the otolith shape.

Another recommendation would be to specify the hatchSeason code as HatchSeasonMicro with a description of the method used (Hatching season of herring stocks estimated by inspection of the Daily increment pattern of the Otolith microstructure laid down during the larval and post-larval period), and use otolith as the SampleType.

I would like your view on this, do you think that it would be fine to add the otolith microstructure code in the Sample type, or specify two different Hatchseason codes based on the method used, while using otolith as the sample type.

[odontaster]

Hi @MariaMakri , I will resume here the options I see:

• Biological measurement: HatchSeason, SampleType: otolith, METOA: this and this (microstructure and shape or whatever they need). For me this would be the best option, we might have to create new methods.
• Biological measurement: HatchSeasonMicro +HatchSeasonShape (if they need it) and Sampletype: otolith. This is suboptimal because you are adding some method in the measurement, but could be ok if its difficult to add the METOA required.

I am with you that otolithMicrostructureLarval in SampleType does not fit. It is adding a level of detail that is not refelcted in any of the other codes in this CodeType. I could consider subdividing otolith into the two parts: otolithAdult and otolithLarval (apparently these are distinguishable in an adult otolith). But this is a bit overcomplicating things, mainly if they do not foresee to use the otolithLarval for any other Measurement. The same thing should be easily inferred with the combination of Measurement and Method with code otholit as SampleType.

Hope that helps

[MariaMakri]

At today's RDBES core group meeting, the following were discussed:

1. First of all, I asked and it seems that the information on the methodology used for the estimation of Hatch Season is important and needs to be included in some way for the purpose of this data call.

2. The option to include two codes for different methods in the METOA code type seemed the most reasonable after looking at the possibilities. Although the METOA code type is composed of more general methods, it seems that there is one more specific method, described in a paper, which is referenced in the description.

   https://vocab.ices.dk/

   

We said we will discuss with Kirsten what those codes could be, but any input on the codes would be great, if you agree on this .

[odontaster]

@MariaMakri it seems ok to me. I see variable detail level in METOA. If you can suggest codes that fit into METOA codes and a simple yet specific description with available reference, that should be ok. @Osanna123 @cekv @pcrjoana @neil-ices-dk any opossition to this?

[cekv]

@MariaMakri I think I would agree with @odontaster about option 1, if the codes fit into METOA.

[MariaMakri]

My suggestion for codes: MIC-OT-L is a code that fits quite well I think to the rest of the codes in METOA, since there are other codes for microscopic analysis that follow a similar pattern: Microscope-base reflected light https://vocab.ices.dk/?codeguid=16a4e745-a505-464b-89d1-57f019dcb213 Microscope - light microscope https://vocab.ices.dk/?codeguid=9f3f167e-664c-41c1-bbee-524997cd6aa6

MIC-OT-S, Description: Microscopic (?) analysis of otolith shape ?

Kirsten's email:

Looking at the other MIC codes in METOA these are very much related to type of microscope used, so may something more like below where the focus is on what the analysis is.

OTO-MS-L-MIC – OTOlith MicroStructure Larval (inspected with) MICroscope Description: Microscopic inspection of otolith microstructure laid down during the larval and post larval period (Clausen et al., 2007).

Then the code for otolith shape analysis could then be

OTO-SHA-ANA - OTOlith SHApe Analysis. Description: Otolith shape analysis – unspecified (This is very unspecific, but Otolith shape analysis methods are very diverse and used for multiple species, e.g. herring and cod. If more specifics are need then it could be by expanding the code with a -XXX later on of needed)

[MariaMakri]

@MariaMakri and @pcrjoana to communicate with the core group. Check whether the level of detail is needed in the specific context.

@pcrjoana to check if there is a place for hatchseason in smartdots.

[Osanna123]

If we can not avoid using the METOA, to align it with the other methods, i suggest something in line with: HATS-OSH Hatching season estimation by otolith shape analysis HATS-OLAM Hatching season estimation from the microscopic inspection of otolith microstructure laid down during the larval and post larval period (Clausen et al., 2007).

[pcrjoana]

Suggestion after meeting RDBES core group: having a general code for microscope (MIC) and a code for morphometric shape analysis. Shape analysis is a computer method used to compare shapes (i.e. it's an actual thing).

More on morphometric shape analysis: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0121102

[MariaMakri]

Also, it was discussed to create a code list for seasons (Summer,Autumn, Spring, Winter). There are already some codes that could be used: https://vocab.ices.dk/?codetypeguid=69e5d7fa-649f-4f07-b866-f5a7ee647f86 https://vocab.ices.dk/?codetypeguid=f5c324a3-1116-4ae4-a319-6bd385bb8694

[MariaMakri]

There is already a light microscope code to use, tell them about that. Add morphometric analysis code.

Add a 'season' code type.

[MariaMakri]

I talked with Nuno in the core group. He said that morphometric is broader than shape analysis (morphometrics can include both shape and other metrics like length etc), so it would be nice to have shape, as it is more specific.

[MariaMakri]

Kirsten said they can use the MIC codes that already are there. To ask @Osanna123 Anna about morphometrics code to METOA

[MariaMakri]

Agreed with Anna on the following code in the METOA code type:

MMA: Morphometric analysis-unspecified

This is because there are many different metrics related to morphometric analyses (shape, size length) and many methodologies to measure them) so we will add a code as general as possible.

The code had been added.