Publishing wetland data to KNB - Githubissues

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Publishing wetland data to KNB #96

Closed angelchen7 closed 1 month ago

angelchen7 commented 3 months ago

Summary

This wetland dataset lives in the Delta Sharepoint folder and hasn't been published yet. We need to get it into a data repository like KNB in order to be able to read the data reproducibly. The contact person is Chris Kwan.

Starting Tasks

[x] Camila: emailed them for the link to the data
[x] Get familiarized with the Sharepoint data itself
[x] Get familiarized with the KNB interface and understand what metadata I need for submission
[x] Email Chris to let him know we're moving forward with this and ask for the big-picture metadata (title of package, author, contact(s), short abstract, maybe methods)
[x] Upload data to KNB with the corresponding metadata
[x] Email Chris again
[x] Get the DOI and let the team know so they can change their scripts

Useful links

Learning Hub's KNB demo
Tidal Delta Natural Habitats Managed Wetlands shapefiles in Sharepoint (Infrastructure Group > Data Sets and Products > Recreation & Natural Spaces )

angelchen7 commented 2 months ago

Emailed Trinh and Chris

Finally got some bandwidth to handle this task! After looking over the data on Sharepoint, I emailed Trinh and Chris about moving this issue forward.

Hi Trinh and Chris!

Apologies for the delay, I wanted to touch base with you all to make sure the correct metadata gets submitted to the KNB repository. Could I get some information on the following details?

- Title (maybe "Map of modern (mid-2010s) habitat types in the Sacramento-San Joaquin Delta and Suisun Marsh intended for use in the Landscape Scenario Planning Tool"?)

- Abstract (around 100 words)

- Funding Information (NSF award(s) or custom funding information)

- Data Set Creators (Name, Organization, Position, Email, ORCID if applicable)

- Data Set Contacts (Name, Organization, Position, Email, ORCID if applicable)

- Date Range of Dataset

- Methods (For each procedure or “step” used to produce these data, describe the series of procedures. This should include any relevant descriptions of the procedures, details about software or instrumentation used, source data, and any quality control measures.)

- Sampling Study Extent (Describe the geographic area sampled, the sampling frequency, how sites were chosen, and the living organisms sampled to generate this dataset.)

- Sampling Description (Describe the sampling procedures used in this research project as you would describe the sampling procedures found in the methods section of a journal article for this project.)

It would be extremely helpful if these details can get filled in however much it can. 

I was able to glean some descriptions from the Modern_Habitat_LandExtend_2016.shp.xml that may serve as the methods. You can view them [here](https://docs.google.com/document/d/1ek4Io1zJhGz2leafx9ytNWVpxwu9-Uwu2Spkjy2thhg/edit?usp=sharing) and if it's appropriate, I can enter this information in as the Methods. 

Also, since the vector data contains multiple files, I am thinking of submitting relevant files together as a zip file. 

For example, I can submit a Modern_Habitat_LandExtend_2016.zip file that contains all the files starting with "Modern_Habitat_LandExtend_2016". Similarly, PM4.16.gdb.zip will contain the relevant Geodatabase files. 

If that's alright with you, I can submit both Modern_Habitat_LandExtend_2016.zip and PM4.16.gdb.zip together in the same submission. Otherwise, please let me know if I should submit them separately or if you would like me to do something else. 

Thank you so much for your patience!

angelchen7 commented 2 months ago

Chris' reply!

Hi Trinh and Chris!

Apologies for the delay, I wanted to touch base with you all to make sure the correct metadata gets submitted to the KNB repository. Could I get some information on the following details?

- Title (maybe "Map of modern (mid-2010s) habitat types in the Sacramento-San Joaquin Delta and Suisun Marsh intended for use in the Landscape Scenario Planning Tool"?) Please use your suggested title.

- Abstract (around 100 words) This is a map of natural habitats and managed wetlands in the in the Sacramento-San Joaquin Delta (Delta) and Suisun Marsh in the mid-2010’s. The historical tidal extent of the Delta were used as the boundaries, not the legal Delta. Natural habitats include Alkali season wetland complex, Dune Vegetation, Grassland, Riparian, Seasonal and Non-tidal wetland, tidal wetland, and vernal pool complex.

- Funding Information (NSF award(s) or custom funding information California Department of Fish and Wildlife, Delta Stewardship Council

- Data Set Creators (Name, Organization, Position, Email, ORCID if applicable) [megan.thompson@deltacouncil.ca.gov](mailto:megan.thompson@deltacouncil.ca.gov), Delta Stewardship Council, Environmental Scientist

- Data Set Contacts (Name, Organization, Position, Email, ORCID if applicable) [chris.kwan@deltacouncil.ca.gov](mailto:chris.kwan@deltacouncil.ca.gov), Delta Stewardship Council, Senior Environmental Scientist, https://orcid.org/0009-0006-7810-7301

- Date Range of Dataset 2016

- Methods (For each procedure or “step” used to produce these data, describe the series of procedures. This should include any relevant descriptions of the procedures, details about software or instrumentation used, source data, and any quality control measures.) Use what Angel wrote up

- Sampling Study Extent (Describe the geographic area sampled, the sampling frequency, how sites were chosen, and the living organisms sampled to generate this dataset.) Data were from the California Fish and Wildlife Vegetation Classification and Mapping Program which surveyed and sampled using remote sensing and field collection methods: https://wildlife.ca.gov/Data/VegCAMP

- Sampling Description (Describe the sampling procedures used in this research project as you would describe the sampling procedures found in the methods section of a journal article for this project.  Data were from the California Fish and Wildlife Vegetation Classification and Mapping Program which surveyed and sampled using remote sensing and field collection methods: https://wildlife.ca.gov/Data/VegCAMP

It would be extremely helpful if these details can get filled in however much it can. 

I was able to glean some descriptions from the Modern_Habitat_LandExtend_2016.shp.xml that may serve as the methods. You can view them [here](https://docs.google.com/document/d/1ek4Io1zJhGz2leafx9ytNWVpxwu9-Uwu2Spkjy2thhg/edit?usp=sharing) and if it's appropriate, I can enter this information in as the Methods. Please use thanks.

Also, since the vector data contains multiple files, I am thinking of submitting relevant files together as a zip file. Sounds good.

angelchen7 commented 2 months ago

More metadata from Chris

I emailed Chris to confirm and ask for the attribute definitions for the files and now I have a complete list of the definitions below:

PM4.16.gdb

- Shape_Length: Positive real numbers that are automatically generated describing length.
- Shape_Area: Positive real numbers that are automatically generated describing area in units squared.
- Acres: Number of acres represented by each polygon.
- Shape: The feature geometry.

Modern_Habitat_LandExtend_2016

- OBJECTID: Sequential unique whole numbers that are automatically generated.
- Source_cla: Plant species classification.
- Source_OID: Object Identification number.
- Source: Originator of data for each polygon attributed.
- Habitat_Ty: The type of habitat.
- Tidal: The tidal vs non-tidal status. 0 = Non-tidal, 1 = tidal
- Symb_class: Symbol classification of habitat.
- Crop2016: The crop type as mapped by LandIQ/DWR
- FMMP2016: The farmland classification as mapped by the Farmland Mapping and Monitoring Program of the California Department of Conservation  
- Managed: The managed wetland status.
- Shape_Leng: Automatically generated number defining length.
- Shape_Area: Positive real numbers that are automatically generated describing area in units squared.
- PM_LandTyp: Land type of Performance Measure.
- Acres: Number of acres represented by each polygon.
- geometry: The feature geometry.

angelchen7 commented 2 months ago

Submitted to KNB! 🎉

I finally got around to submitting to KNB and the submission link is here! https://knb.ecoinformatics.org/view/urn%3Auuid%3A723b0519-ed6c-473d-9b62-5479f3362135

I'm not sure who the KNB will contact (me or Chris) because I only put Chris' contact info in the Dataset Contacts section. So far, I'm not getting an email confirmation from KNB so perhaps they sent the autoreply confirmation to Chris instead..

angelchen7 commented 2 months ago

I can assign DOI on my own!

Found out that KNB allows me to publish with a DOI by clicking on the appropriate button (see screenshot). Before I do though, I'll need to email Chris on Monday to let him check over all the metadata first.

angelchen7 commented 2 months ago

Emailed Chris again

Just waiting back to hear from him before starting the process of assigning a DOI!

angelchen7 commented 1 month ago

Got approval to publish 🎉

Chris got back to me and approved the dataset for publication, so I went ahead and got a DOI number for it: https://doi.org/10.5063/F1PG1Q67

I'll be closing this issue...