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ioos / marine_life_data_network

Planning efforts relevant to IOOS Marine Life and IOOS DMAC.
https://ioos.github.io/marine_life_data_network/
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New Task: Identify AphiaIDs that align with groups in bio/eco variables #70

Closed laurabrenskelle closed 2 months ago

laurabrenskelle commented 5 months ago

Who is requesting this?

@ioos/marine-life

What is being requested?

Identify AphiaIDs that align with the taxonomic groups (if possible) listed in the bio/eco variables so data can be appropriately filtered to include all necessary taxa.

What is the requested deadline and why?

No response

What is the current status quo (i.e., what happens if this does not get done)?

Some of these variable names are taxonomically ambiguous so if the GOOS and U.S. IOOS community can agree on taxonomic definitions of the scope of these variables, that would help with further defining these variables and doing analyses.

What indicates this is done (i.e., how do we know this is complete)?

We will add a finalized list of AphiaIDs for the variables to the readme. These definitions are open for community discussion, and changes can be made if taxa are included or excluded inappropriately.

Provide a description or any other important information.

I will be doing this with a global scope, with the understanding that some taxa do not occur in the U.S. coastal region. A global definition of what these groups are seems most appropriate and usable by the community, as data can be filtered spatially.

laurabrenskelle commented 5 months ago

So far, these are the groups I have defined:

Marine Mammals

Seagrasses

Sea turtles

Hard corals

Sea birds (this is partial and incomplete; this group is more involved for a variety of reasons)

Remaining: phytoplankton, zooplankton, (marine) fish, mangroves, macroalgae

MathewBiddle commented 5 months ago

Zooplankton could be copepoda https://www.marinespecies.org/aphia.php?p=taxdetails&id=1080

MathewBiddle commented 5 months ago

Could worms help us do some of this filtering. Its constraints are marine, right?

laurabrenskelle commented 5 months ago

@MathewBiddle I discussed this with a colleague who studied marine invertebrates, and she basically said that zooplankton are "the animal component of the planktonic environment". Lots of animals across biological taxonomy have planktonic lifestyles for part or all of their lives. Apparently some copepods are planktonic, but not all. I think it is basically the same idea for phytoplankton.

I think it will take more conversations with the observing communities who work with these organisms and the data because a taxonomic definition in the form of a list of AphiaIDs for these two groups may not be possible because it depends on the life stage of the organism in a lot of cases. It's an interesting problem. I wonder if plankton observations focus on particular taxa to make this easier? Or if it is just a measure of organisms per volume? Some questions for us to ask in the future.

MathewBiddle commented 5 months ago

Great points! I forgot about life stages (thinking crab larvae in all the bottle samples I collected years ago). Well this is a little disheartening.

I agree that we need the GOOS EOV community to weigh in on phyto/zooplankton.

bbest commented 3 months ago

Hi @laurabrenskelle and @MathewBiddle,

This is a great topic and I'd love to help out. I'm noticing this interesting listing in the OBIS manual:

8 Dataset Examples: ENV-DATA | The OBIS manual

Contents

Special data types:

The example for Zooplankton biomass & diversity limits itself to a ZooScan dataset and references Best practices and recommendations for plankton imaging data management: Ensuring effective data flow towards European data infrastructures. Version 1., which does reference Biological entity life stage necessary to differentiate adult from larval zooplankton stages of species like crabs:

  • measurementValueID: Use collections SeaVoX Device Catalogue L22 and Biological entity life stage terms S11
MathewBiddle commented 3 months ago

add the final list as a checklist to https://www.checklistbank.org/

laurabrenskelle commented 3 months ago

Once these lists reach a community consensus, it could be interesting to approach the developers of robis or other occurrence-grabbing programming packages to see if they could build in these queries to allow users to easily query for the most up-to-date OBIS occurrences for these taxonomic groups with a simple function.

MathewBiddle commented 2 months ago

@laurabrenskelle can you take a look at what it means to create and maintain a checklist at https://www.checklistbank.org/?

It would be nice to have an authoritative resource we can support and evolve over time.

laurabrenskelle commented 2 months ago

I looked into this, and Checklistbank does not have the functionality to create a custom list of species that you can then share with others. It is just a taxon matching tool using versions of taxonomic databases that are stored in Checklistbank. I am going to make a folder in this GH repo with different files for our lists by taxon instead.

laurabrenskelle commented 2 months ago

I added files for fish, hard corals, marine mammals, sea turtles, and seagrasses. The fish definitions are relying on the scope of OBIS/WoRMS to "filter" the data for marine species only.

If this is acceptable, we could do the same for birds? I am not sure how WoRMS handles birds/what species it considers "marine" vs. not.

MathewBiddle commented 2 months ago

That seems like a reasonable approach for now. I'd say go ahead and do the same for birds. If folks don't like it we can make it better with their contributions.

Feel free to send in another PR for birds and set it to close this issue. I think we have a good starting point to build something on top of.

MathewBiddle commented 2 months ago

The lists can now be found at https://github.com/ioos/marine_life_data_network/tree/main/eov_taxonomy

laurabrenskelle commented 1 month ago

https://github.com/iodepo/odis-arch/issues/465