Finding Field Station Data Workshop

This wiki provides information about the virtual mini-workshop Finding Field Station Data for Research Use. Link to this wiki using bit.ly/obfs-idigbio-2020.

General Information

When: September 29, 2020 from 1:00-3:00 PM Eastern
Where: Zoom
Cost: Free
Organizers: Erica Krimmel, Gil Nelson, Cat Chapman, David Jennings, Molly Phillips
Registration (required): https://ufl.zoom.us/meeting/register/tJ0qf--hpzMqHtKxz7apfRhYbZF415bGXYRU

This workshop will follow iDigBio's Code of Conduct.

Goals & Outcomes

The discovery and use of digital field station data for place-based biodiversity research as well as species discovery within a station’s boundaries and service area are essential contributions. Although many field stations curate their own biological collections, at least some of which have been digitized and made available online, field stations have traditionally served as important specimen collecting localities for a variety of researchers across taxonomies, resulting in a potential plethora of station-relevant digital data curated by non-station universities and museums. The rapidly expanding online availability of these data, motivated in large part by the U.S. National Science Foundation’s Advancing Digitization of Biodiversity Collections program, has made these data readily available to station scientists. As the U.S. center for enabling and facilitating specimen data digitization and mobilization, iDigBio’s portal (http://portal.idigbio.org/) serves approximately 124 million transcribed specimen records and 35 million associated media records. This virtual mini-workshop will teach participants how to find and download records that are relevant to a specific field station and its surroundings, as well as how these records might be used to augment existing station data.

Logistics

Participation is free but registration is required. Workshop will be held on Zoom from 1-3pm Eastern on September 29, 2020. Participants will receive the Zoom link when they register.

• Recording policy: By attending iDigBio’s online events, you accept that the event will be recorded and posted for later asynchronous viewing.
• We recommend using the desktop client for Zoom (learn more here) vs. Zoom in your browser.
• Having dual monitors will make it easier for you to follow along with the workshop demos, but is not necessary.
• Tips for being a participant in Zoom: https://bit.ly/2wV6j2v
• Post-workshop feedback survey for participants

Agenda

1:00 PM EDT	Workshop introduction (Gil Nelson)
1:05 PM EDT	Overview of the iDigBio Portal (Erica Krimmel)
	Searching by geospatial bounding box
1:15 PM EDT	Demo (Gil Nelson)
1:20 PM EDT	Discovery time in Zoom breakout rooms
	Searching by text locality string
1:35 PM EDT	Demo (Cat Chapman)
1:40 PM EDT	Discovery time in Zoom breakout rooms
	break from 1:55 - 2:05
	Searching by other facets of the data
2:05 PM EDT	Demo (Molly Phillips)
2:10 PM EDT	Discovery time in Zoom breakout rooms
	Searching programmatically
2:25 PM EDT	Demo 4: Search via the API (Erica Krimmel)
	Workshop wrap-up
2:35 PM EDT	How to get data to iDigBio (Cat Chapman)
2:45 PM EDT	Additional resources, remaining Q&A, discussion

Links for searches used in demos

Searching by geospatial bounding box

• Georeferenced specimens collected within a bounding box around Tall Timbers Research Station, http://portal.idigbio.org/portal/search?rq={"geopoint":{"type":"geo_bounding_box","top_left":{"lat":30.9246106,"lon":-84.5494079},"bottom_right":{"lat":30.5315108,"lon":-83.9094543}}}

Searching by text locality string

• Specimens collected at Lockett Meadow using a keyword search in the locality field, http://portal.idigbio.org/portal/search?rq={"locality":"lockett"}
• Specimens collected at Lockett Meadow using a fulltext search across all fields, http://portal.idigbio.org/portal/search?rq={"data":{"type":"fulltext","value":"lockett meadow"}}

Searching by other facets of the data

• Specimens collected by Scott V. Edwards using a keyword search in the collector field, http://portal.idigbio.org/portal/search?rq={"collector":"edwards"}
• Specimens collected by Scott V. Edwards using a keyword search in the collector field, and narrowing the results by filtering on those where the class is Aves, http://portal.idigbio.org/portal/search?rq={"collector":"edwards","class":"aves"}
• Specimens collected by Scott V. Edwards using a keyword search in the collector field, and narrowing the results by filtering on those where the class is Aves and the collecting date is after January 1st, 1987, http://portal.idigbio.org/portal/search?rq={"collector":"edwards","class":"aves","datecollected": {"type":"range","gte":"1987-01-01"}}
• Specimens identified with a scientific name of Lepomis macrochirus, http://portal.idigbio.org/portal/search?rq={"scientificname":"Lepomis macrochirus"}
• Specimens identified with a scientific name of Lepomis macrochirus or Lepomis miniatus',http://portal.idigbio.org/portal/search?rq={"scientificname":["Lepomis macrochirus","Lepomis miniatus"}]
• Specimens in the genus Lepomis and species machrochirus,http://portal.idigbio.org/portal/search?rq={"genus":"Lepomis","specificepithet":"macrochirus"}

Searching programmatically

• Specimens in the genus Acer viewed as raw results from the search API, https://search.idigbio.org/v2/search/records?rq={"genus":"acer"}
• Specimens in the genus Lepomis and species machrochirus viewed as raw results from the search API, https://search.idigbio.org/v2/search/records?rq={"genus":"lepomis","specificepithet":"macrochirus"}

Reports and Resources

• iDigBio Field Station Interest Group
• Slides from OBFS 2020 Lightning Talk
• Presentation from SPNHC 2019, If a small collection exists in the forest, does anybody know it's there? Research value and digitization progress of field station collections
• iDigBio workshop at OBFS 2018
• iDigBio workshop at OBFS 2016 (this overview of iDigBio from OBFS 2016 may be particularly helpful for those unfamiliar with us!)
• iDigBio workshop at OBFS 2015