MBON Pole to Pole example

[MathewBiddle]

• [ ] What is language(s) for used in the example? R , maybe Python?
• [ ] Is it focused on a particular module/software or an IOOS data service? IOOS data service
• [ ] Can you provide a minimum example of the expected code and results in a notebook?

Please provide a detailed description of the suggested example below: I'm not quite sure yet what we want to show, but MBON Pole to Pole has a bunch of data in OBIS. Maybe we can use the OBIS API to grab the data?

I'll investigate more and update when we have a better idea of where to take this.

[ocefpaf]

Are you planning on exploring the API with Python or using the existing R library?

[MathewBiddle]

I surveyed a small group and got a split response 50/50. Using the existing R library would probably be a more effective use of our time, and more applicable to the biology folks.

I did find pyobis. It looks like that was last contributed to in 2017, so it might be out of date, but it could be worth exploring/

[ocefpaf]

Agreed. We would do better by teaching folks how to call Python from R and vice-versa.

[MathewBiddle]

Add on: access the data including the extended measurement or facts tables from OBIS API.

[MathewBiddle]

In the API occurrence endpoint the mof parameter (true/false) has been added which determines if MeasurementOrFact records are included in the results or not. In addition, filters have been added to find data with specific measurement types, values or units. For now this is a simple text search and does not yet take into account relationships between vocabulary terms.   For example, this request finds mollusc occurrences with biomass measurements: https://api.obis.org/occurrence?scientificname=Mollusca&measurementtype=biomass&mof=true   To get MeasurementOrFact support in the R package, please install the latest version from GitHub (version 2.2.0 or above).

[MathewBiddle]

See https://github.com/ioos/notebooks_demos/pull/370/commits/279acdbbef43e5f304823975fa355336994692be

[MathewBiddle]

Some additional information about the obis api. Here is a list of all the measurements or facts currently in OBIS: https://reports.obis.org/moftypes/

If you are interested in seeing which dataset have a particular measurement you can get that from the API using the measurementTypeID- here is an example: https://api.obis.org/dataset?measurementtypeid=http://vocab.nerc.ac.uk/collection/P01/current/SDBIOL05/

You can also search using the measurementType: https://api.obis.org/dataset?measurementtype=weight

[MathewBiddle]

Maybe bring in seascapes data as well: https://github.com/eqmh/ERDDAP-extractions/blob/master/seascape_example.R

similarly: https://github.com/marinebon/p2p/blob/2557dc03abe8e5779f5392586eb470232f8aa604/_site_template.Rmd#L142-L178

See https://marinebon.org/p2p/z_usa-pumphouse-nahantma.html for example

[MathewBiddle]

moved to code lab. closing.