search

ioos / ioos_code_lab

Notebook demonstrations and examples
https://ioos.github.io/ioos_code_lab
MIT License
9 stars 11 forks source link

MBON Pole to Pole example #45

Open MathewBiddle opened 2 years ago

MathewBiddle commented 2 years ago

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?

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 It looks like that was last contributed to in 2017, so it might be out of date, but it could be worth exploring.

Access the data including the extended measurement or facts tables from OBIS API.

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).

See 279acdb

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

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

ocefpaf commented 1 year ago

@MathewBiddle does the notebook in #115 covers this? Can we close it?

MathewBiddle commented 1 year ago

I think this is still worth pursuing. The last link (https://marinebon.org/p2p/z_usa-pumphouse-nahantma.html) is created from this template https://github.com/marinebon/p2p/blob/master/_site_template.Rmd. Something that would be nice to explore is following that example, but pulling in other IOOS resources (gliders, hf-radar, sensors, models, etc.)