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October 14th, 2020:  Serving the U.S. Geological Survey’s geochronological data, Rocky Mountain Science Exchange, and CDI Pop-Up Lab

The Community for Data Integration (CDI) meetings are held the 2nd Wednesday of each month from 11:00 a.m. to 12:30 p.m. Eastern Time.


Meeting Recording and Slides

These are the publicly available materials.

Log in to view all the meeting resources. If you would like to become a member of CDI, join at https://listserv.usgs.gov/mailman/listinfo/cdi-all.

 

Agenda (in Eastern time)

Times are approximate.

11:00 am Welcome and Opening Announcements - Leslie Hsu and Kevin T. Gallagher

11:15 am Collaboration Area Announcements

11:25 am Serving the U.S. Geological Survey’s geochronological data - Leah Morgan and Amy Gilmer, USGS

11:50 am Rocky Mountain Region Science Exchange - Alicia Torregrosa, USGS

12:10 pm CDI Pop-up Lab

Using Git - an interview - Richie Erickson, USGS

Remote Sensing Forest Classification for Timber Appraisal - Joe Adams, USGS

12:30 pm  Adjourn

Highlights

  1. CDI FY2021 Statements of Interest are due Friday, October 16th, at 5pm Eastern.
  2. Don't miss the SOI Lightning Presentation Session on Thursday, October 22nd, at 2pm Eastern.

Notes

  1. Welcome and Opening Announcements - Leslie Hsu and Kevin T. Gallagher
    1. Update on meeting the CDI community
      1. Used the entire CDI email list to look at job titles and expertise terms
      2. (see recording for word cloud)
    2. Kevin Gallagher
      1. Deadline for Statements of Interest for FY2021 are due this Friday, October 16, 5pm Eastern
      2. RFP themes are fire science and coastal resilience, but proposals with any topic are accepted
      3. SOI Lightning Presentation Session: Thursday, October 22, 2pm Eastern
      4. Join the comment and voting period, starting October 20
  2. Collaboration Area Announcements
    1. See full details on slides/recording, and on the collaboration area wiki page
    2. Software Development
      1. Next meeting 10/22, focusing on Agile, with presentations from Michelle Guy and Sophie Hou
    3. Data Visualization
      1. Next meeting 10/29, Data sketches with Nadieh Bremer
      2. See wiki for more info
    4. Usability
      1. Next meeting 10/21, FY21 planning
      2. Survey
    5. eDNA
      1. GeDWG 4th annual workshop has been announced (see eDNA wiki page)
      2. See wiki page for forum discussions and Mendeley group
    6. EarthMap
      1. Released survey (RFI), looking for examples of the kind of work EarthMap represents
      2. NTK blog post went out yesterday
    7. Data Management Working Group
      1. Next meeting 11/9, BCO-DMO speakers on capturing provenance of data curation; frictionless data (more here)
    8. Risk CoP
      1. Annual Risk RFP is now open (more info here)
        1. 11/20 deadline for letter of intent
        2. 1/15 deadline for full proposal
        3. Theme: concurrent disruptions
      2. Next meeting 10/15, FY21 RFP Information session; using CoSMos for determining costs and benefits of adaptation strategies
    9. DevOps
      1. Next meeting 12/1, General Dynamics IT Division
  3. Serving the U.S. Geological Survey’s geochronological data - Leah Morgan and Amy Gilmer, USGS
    1. Project goal is to bring together and serve USGS geochronological data
    2. National Geochronological Database (NGDB) was last updated in the 90's. There is currently no central, integrated source for this data and new data.
    3. To serve this data, project team is:
      1. Working with collaborators to build a database in a Post-Gres SQL structure
      2. Populating the database with useful data
      3. 3 parallel approaches:
        1. Migrate data from old NGDB database
        2. NAGT USGS intern will manually input data from published literature, first with scientists nearing retirement
        3. Work with University of Kansas and geochron.org to build APIs to automatically populate data (new data releases as posted to SB)
    4. Database schema model built by Andy Park at Eastern Energy Resources Science Center (see slide)
    5. Schema captures info about each sample (material type, location information, temporal information, etc.)
    6. Schema also captures info about analysis/techniques
    7. Application
      1. Integrating data with the National Cooperative Geologic Mapping Programs Intermountain West Geologic Framework project
      2. Having geochronological data is essential to making comprehensive compilation work
      3. Integration of geochronology with geologic mapping
      4. Geochronological data with critical mineral studies (how it formed, looking for additional resources)
  4. Rocky Mountain Region Science Exchange - Alicia Torregrosa, USGS
    1. Objectives for the Rocky Mountain Science Exchange are exchange of knowledge, cross-center collaboration. 2020 goals were focused on drought, EarthMap and the creation of this new culture, and creating an online presence. 
    2. RMR Science Exchange 
      1. Held entirely on Teams 
      2. 216 attendees and 37 science talks 
      3. SharePoint site has all recordings 
      4. ArcGIS online spatial catalog linked by StoryMap to participant entries 
      5. Internal access only 
    3. Content 
      1. EarthMap set the stage 
        1. Provided background information 
        2. Included Office of Science Quality and Integrity initiatives 
        3. Lightning talks and panel discussions focused on themes of EarthMap and drivers of landscape change 
      2. Colorado River Basin use case presentations (EarthMap pilot project) 
        1. These types of use cases are being solicited by EarthMap - submit if you have a use case. 
        2. This pilot evaluates and predicts impacts of severe drought on earth system components. 
      3. One objective was to gauge knowledge of EarthMap - participants in the workshop had a stronger understanding after workshop ended. 
  5. CDI Pop-up Lab
    1. Using Git - an interview - Richie Erickson, USGS
      1. (see slide for full details) 
      2. Git helps with version control (what got changed, when, and by who) 
      3. Allows code to be put in the cloud 
      4. Git is an open source tool that is free; there are also commercial vendors like GitLab 
      5. Git project homepage has several nice video tutorials. Software carpentry also has nice tutorials. 
      6. Richie has also gathered tutorials as a part of a CDI project. Come to the December CDI monthly meeting to learn more. 
      7. CDI calls are a great spot to see what others are using. 
    2. Remote Sensing Forest Classification for Timber Appraisal - Joe Adams, USGS
      1. (see slide for full details) 
      2. Pain point: appraising land that has timber on it. 
      3. FRASS (forest resource analysis system software)  
      4. PoTree Viewer: https://uas.usgs.gov/outgoing/Visualizations/Warm_Springs_Stand_of_Trees_Test/ 
      5. Trimble presentation tomorrow

Questions & Answers

  1. Does the interaction with the National Geologic Map Database allow the Geolex data (geologic fm names) to join the geochron data?
    1. No, we have not integrated.
  2. Was there anything that was new or difficult ot fit into the schema based on newer ScienceBase Data releaseas?
    1. Flexible approach - schema will need to add info later
    2. Varying levels of info in new data vs old data
    3. Several levels of geochronological data; age for one sample or one formation (parent child relationships can incorporate all these data)
  3. Will guidance be released?
    1. Working with geochronologists who are actively collecting data - schema reflects data release structure. Will provide documentation to capture that information
  4. Do you have a tentative timeline for rolling out a publicly-accessible version?
    1. No timeline as of now.
  5. Are you keeping a link to the ScienceBase item in your database so if someone wants to get back to the original data they will be able to do so?
    1. Yes. Also keeping links for older publications that have been incorporated but do not have a ScienceBase data release
  6. Who can I contact at KSU (?) about the SB harvesting scripts?
    1. Working with Noah McClean in the geology department and Jason Ash
  7. Updates on the geochronological database effort?
    1. Contact Leah Morgan or Amy Gilmer
    2. Within next year, hope to have an interface begun through the National Geologic Mapping Database project
  8. Do we have access to the EarthMap SharePoint site and the primer video? If so, can we share the link in this chat or are the slides available some place?
    1. Yes. https://atthecore.usgs.gov/special-groups/earth-monitoring-analyses-and-prediction-earthmap
    2. RMR SharePoint: https://doimspp.sharepoint.com/sites/gs-rmr-scienceexchange487
  9. Do you have any tips for holding a large virtual meeting?
    1. Much more work than you think. Did not bring on IT support soon enough. Made heavy use of OneNote. ArcGIS Online and the Power Flow in O365 were useful. Did lots of dry runs to get everything working correctly. Challenge with overloaded Microsoft servers, so were encouraged to record the presentations with another program like Camtasia. The screen capture did not always work.
  10. Can you quickly cover using Git vs Jupyter? Pros/cons?
    1. Two different things. Git keeps track of code, can use with any plain text code. Jupyter is an interactive way to work with code. Jupyter = Microsoft Word; Git = SharePoint. Jupyter is part of the conda project, and they have their own way of sharing things.
  11. Is there a write-up anywhere of this RFP / need?ere a write-up anywhere of this RFP / need?
    1. Joe's post: https://teams.microsoft.com/l/message/19:41d7e1c2ef45473fb287943929badb54@thread.skype/1601482340361?tenantId=0693b5ba-4b18-4d7b-9341-f32f400a5494&groupId=8d63facc-9fdc-4c6e-9a32-9a4172553b46&parentMessageId=1601482340361&teamName=GS-CDI-CommunityForDataIntegration&channelName=Questions%20and%20Answers&createdTime=1601482340361
  12. Trimble link
    1. https://go2.trimble.com/2020-10-15-GEO-WB-eCognition_LandingPage-Registration.html