ADBC Summit 2017: Difference between revisions

From iDigBio
Jump to navigation Jump to search
Line 491: Line 491:
The [[Integrating Collections and Ecological Research|ICER Working Group]] (Integrating Collections and Ecological Research), along with [https://bcon.aibs.org/ BCoN], will present a half-day workshop centered around ecologists who incorporate collections data in their scientific research and sharing a potential model program for integrating collections data in conservation efforts. Speakers invited will give talks representing community examples of museum specimen data integrated with other biodiversity data to enhance and inform efforts to address key ecological questions and support conservation efforts.
The [[Integrating Collections and Ecological Research|ICER Working Group]] (Integrating Collections and Ecological Research), along with [https://bcon.aibs.org/ BCoN], will present a half-day workshop centered around ecologists who incorporate collections data in their scientific research and sharing a potential model program for integrating collections data in conservation efforts. Speakers invited will give talks representing community examples of museum specimen data integrated with other biodiversity data to enhance and inform efforts to address key ecological questions and support conservation efforts.
| '''Changes/Improvements to the [https://www.idigbio.org/portal iDigBio Portal]''' (Joanna McCaffrey, Shari Ellis, Richard Garand)
| '''Changes/Improvements to the [https://www.idigbio.org/portal iDigBio Portal]''' (Joanna McCaffrey, Shari Ellis, Richard Garand)
| '''Rapid digitization of incoming insect material''' (Neil Cobb, Crystal Maier, Jen Zaspel)
| '''Rapid digitization of incoming insect material  
'''Goal:''' Develop workflow(s) for rapidly digitizing material from “collecting events”, especially where a large amount of material is brought into the collection from inventories.  The workflow would be database neutral (Arctos [Derek], EMu [Crystal], institutional [Chris], Specify [Andrew], Symbiota [ Neil for now]), it would be scalable from small to large institutions, and it would be cross-phyla functional (e.g., plants/herbaria, insects/museums). 
'''Rationale:''' There are an estimated 256 million specimens in US collections, we are currently digitizing 2.5 million per year, which is the same amount of new material that is added to collections per year.  Thus, we are currently running in place and we need to implement workflows that will help us at least double our current rate of digitization.  Several collections have already developed workflows that greatly increase the rate of digitizing new specimens that need to be integrated into the collection from surveys and inventories https://vimeo.com/184611446.
'''Action Items:''' Provide workflows that can be shared by all museums.  This may involve options that take into consideration the type of specimens, the size of the museum, and the size and diversity of material.  We will initially share drafts via dropbox. During this meeting we will produce a first draft and if there is time left we will outline a strategy to overcome the top 10 challenges in digitizing arthropods.
''' (Neil Cobb, Crystal Maier, Jen Zaspel)
|-
|-
| 10:10-10:25
| 10:10-10:25

Revision as of 17:54, 23 October 2017


Digitizing the Past and Present for the Future
Summit-Banner-2017.png
ADBC Summit VII Quick Links
Calendar Announcement
PDF Program
Online Agenda

Join the leading researchers and professionals striving to digitize our nation's Natural History Collections! The annual ADBC Summit brings together representatives from TCNs, PENs, NSF, iDigBio, and other initiatives related to the U.S. National Science Foundation’s Advancing Digitization of Biodiversity Collections (ADBC) program. The Summit inspires collaboration and focuses discussions on shared goals, challenges, and opportunities.

General Information

Maps & Dining Information

Note: There is a restaurant in the Hilton. On maps, it is listed as "Albert's." It is now a "Shula's Steakhouse."

Area Information

Ground Transportation Options

Wireless Service

Wireless access for onsite iDigBio participants is provided by the University of Florida. Refer to iDigBio's Wireless Network Service wiki page for more information on how to connect.

Remote Access

To the extent possible, the Summit sessions will be broadcast and recorded using Adobe Connect. If you wish to listen to the meeting remotely:

  1. First, read the iDigBio Web Conferencing Wiki Page to get you started.
  2. Connect to the meeting:

Summit Program

We are in the process of preparing an interactive PDF program for the Summit. Check back here for a download link as the meeting gets closer. Note that we also plan to print a one-page, double-sided reference agenda for distribution at the Summit.

Agenda

Monday, October 30, 2017 thru Tuesday, October 31, 2017 -- Data Carpentry

Time Location/Information
9:00-4:30 Data Carpentry Workshop

The UF Carpentries Club and iDigBio are offering a two day Data Carpentry Workshop to help participants in the 2017 ADBC Summit and the UF community get started learning R and common data management tools such as the spreadsheets, OpenRefine, and SQL. Need to learn some programming for a class? Have data you're scared to work with in Excel? Want to collaborate effectively with your peers? We were there once too. Come start learning with us! Visit the workshop website to learn more: https://idigbio.github.io/2017-10-30-iDigBio-Summit-UFII/

The workshop will be held at the UF Informatics Institute, which has generously volunteered space and resources for this workshop. iDigBio is providing staff support. All of the organizers, instructors, and helpers are volunteering their time to help ADBC, UF, and you!

Register at: http://reg.conferences.dce.ufl.edu/SSP/1400065271

Wednesday, November 1, 2017 -- Florida Museum Collections Tours

Time Location/Information
2:00-5:00

Wednesday, November 1, 2017 -- Pre-Summit Meetings

Time Harn Galleria Harn Chandler Auditorium Harn Classroom 1 Harn Classroom 2 Powell Classroom McGuire Classroom McGuire Director's Conference Room
Morning Breakfast on your own
8:00-10:00 Unavailable Unavailable Unavailable Unavailable Unavailable iDigBio-GBIF Whiteboarding Session on Worldwide Collections-Level Data (closed session) Open meeting space
10:00-10:30 Unavailable Unavailable Unavailable Unavailable Unavailable Setup Open meeting space
10:30-12:00 Unavailable Unavailable Unavailable Unavailable Unavailable Orientation - Welcome to ADBC (David Jennings, Joanna McCaffrey)

Join us for an iDigBio and ADBC orientation session where we will present information-fit-for-use about the following:

  1. What ADBC and iDigBio are about, the acronyms, the scope
  2. How you can fire up your involvement by participating in interest and working groups, community surveys, and useful website content
  3. How to get specimen data to us, the first time and with every update
  4. Ways to interact with us - listservs, meet the staff
  5. Forum for suggestions to make all of this better

Everyone is welcome! Come to learn, to refresh, to meet your fellow digitizers!

Open meeting space
12:00-1:00 Lunch on your own
12:30-1:00 Unavailable Unavailable Unavailable Unavailable Setup Setup Setup
1:00-4:30 Unavailable Unavailable Unavailable Unavailable Open meeting space oVert TCN Kickoff Meeting IDigBio External Advisory Board (closed session)
4:30-5:00 Unavailable Unavailable Unavailable Unavailable Cleanup Cleanup Cleanup
Evening Dinner on your own
6:30-9:30 Informal welcome and meet & greet with iDigBio staff in the No Name Lounge inside the Hilton

Thursday, November 2, 2017 -- Summit Day 1

Time Harn Galleria Harn Chandler Auditorium Harn Classroom 1 Harn Classroom 2 Powell Classroom McGuire Classroom McGuire Director's Conference Room
Morning Breakfast on your own
8:00-9:00 Setup Setup Unavailable Unavailable Unavailable Review of iDigBio in supporting Thematic Collection Networks

iDigBio External Advisory Board (EAB) October 23, 2017 Since 2011, the NSF-ADBC program has funded 19 Thematic Collection Networks (TCNs) and 24 Partners to Existing Networks (PENs). The role of TCNs is to mobilize a community of museums and herbaria to provide specimen related data and media to iDigBio. Additionally, they collaborate with each other and iDigBio to promote the use of digitization products for research and education. As part of its role in advising iDigBio, the External Advisory Board (EAB) wants to better understand the relationship between iDigBio and the TCNs in order to assess how iDigBio is meeting community needs. The description and makeup of the EAB can be found here https://www.idigbio.org/wiki/index.php/IDigBio_External_Advisory_Board.

Every year the EAB meets with iDigBio and NSF at the ADBC Summit. For the upcoming 2017 meeting in Gainesville the EAB would like to meet with TCN leaders to discuss the role of iDigBio in supporting TCN activities. The meeting will be held 8-9AM on Thursday morning (Nov 2) in the McGuire Classroom in the Florida Museum. There will be someone posted outside the museum to help people gain access to the meeting room and you can text Neil Cobb 928-607-4075.

To help frame the discussion for the meeting the EAB is interested in having TCN leaders consider two broad questions: 1) How much and in what form do TCNs currently interact with iDigBio; and 2) What services would be of greatest benefit to the TCN – including their individual participating institutions – sustain their digitization and sharing of information into the future. Below are more specific issues to consider for the meeting, feel free to bring your own to the meeting. 1. iDigBio provides services that can be categorized in four areas, which of these areas do you interact with iDigBio and do they meet your expectations? 1) Digitization workforce training, 2) Informatics/Website/database, 3) Promoting Research use of data, and 4) Education/outreach. Are there other services not included in the ones above? Do TCNs contribute to ADBC beyond providing TCN data? 2. iDigBio provides a number of specific resources on the website; to what degree do TCNs use these resources, for example the data usage stats and data compliance reports. 3. Is your TCN able to access and link to all necessary and relevant databases and information systems (at a national or international scale)? If not, are there services that iDigBio could develop to assist with such linkages? 4. What are the 2-3 major challenges you face regarding the future of your TCN’s digitization, collaboration, or data sharing efforts over the next five years? 5. What would you like iDigBio to do to help you address these concerns, and to help you or TCNs in general sustain a viable digitization and data sharing program? 6. What do you foresee as the most important barriers to having iDigBio provide the services you need? 7. Among all of the ideas discussed, what are the top three opportunities for iDigBio to help the greatest number of TCNs, and their member institutions to maintain viable digitization and data sharing programs? 8. What are the plans for sustaining your TCN after ADBC funding ends?

(Neil Cobb)

Open meeting space
9:00-9:30 Arrival, Summit check-in, coffee, networking Networking, getting settled Unavailable Unavailable Unavailable   Open meeting space
9:30-10:35 Unavailable
9:30-9:45 Opening & Welcome (Larry Page)
9:45-9:55 Logistics (David Jennings)
9:55-10:10 ADBC Program Update (Reed Beaman)
10:10-10:20 2017 TCNs
  • oVert - David Blackburn
  • SoRo - Ryan Allen
10:20-10:35 2016 TCNs
  • Cretaceous World - Bruce Lieberman
  • LepNet - Neil Cobb
  • Mid-Atlantic Megalopolis (MAM) - Anne Barber
 Unavailable Unavailable Unavailable   Open meeting space
10:35-10:55 Morning break   Unavailable Unavailable Unavailable    
10:55-12:10 Unavailable
10:55-11:05 2015 TCNs
  • Microfungi (MiCC) - Andy Miller
  • Fossil Marine Invertebrates (EPICC) - Erica Clites
11:05-11:20 2014 TCNs
  • Great Lakes Aquatic Invasives (GLI) - Rich Rabeler
  • InvertEBase - Petra Sierwald
  • Key to the Cabinets (SERNEC) - Michael Denslow
11:20-11:35 2013 TCNs
  • Fossil Insect Collaborative (FIC) - Talia Karim
  • Vouchered Animal Communication Signals (VACS) - Mike Webster
  • Macroalgal Herbarium Consortium - Chris Neefus
11:35-11:55 2012 TCNs
  • New England Vascular Plants (NEVP) - Patrick Sweeney
  • Paleoniches - Bruce Lieberman
  • Macrofungi Collection Consortium (MaCC)
  • Symbiota Collections of Arthropods Network (SCAN) - Neil Cobb
11:55-12:10 2011 TCNs
  • InvertNet - Jen Zaspel
  • Tri-Trophic Associations (TTD)
  • North American Lichens and Bryophytes (LBCC) - Tom Nash
 Unavailable Unavailable Unavailable   Open meeting space
12:10-1:15 Unavailable   Box lunch provided Setup   Open meeting space
1:15-2:30 Unavailable Group Discussion: Data Integration, attribution and interoperability (Andy Bentley, Robert Gropp)

Collections, aggregators, data re-packagers, publishers, researchers, and external user groups form a complex web of data connections and pipelines. This forms the natural history infrastructure essential for collections use by an ever increasing and diverse external user community. We have made great strides in developing the individual actors within this system and we are now well poised to utilize these capabilities to address big picture questions. We need to continue work on the individual aspects, but the focus now needs to be on integration of the functionality provided by the actors involved in the pipeline to facilitate the transfer of data between them with as few human interventions as possible. In order for the system to function efficiently and to the benefit of all parties, information, data, and resources need not only to be integrated efficiently but flow in the reverse direction (attribution) to facilitate collections advocacy and sustainability. For instance, there are benefits to collections from inclusion into aggregators and subsequent use by researchers and publishers that are not being realized. The Biodiversity Collections Network (BCoN) is planning a program of workshops in conjunction with other groups to perform a needs assessment to identify gaps and problems in the data pipeline and explore future steps in coordinating efforts, providing solutions and standardizing tools and methods. This talk will explore this landscape and highlight BCoN’s efforts in this regard while soliciting participation from actors in the pipeline and the community at large.

        Open meeting space
2:30-3:00 Unavailable   Afternoon break     Open meeting space
3:00-4:15 Unavailable Meeting of the Symbiota Working Group (Neil Cobb, Andy Miller)
1. The role of Symbiota in the ecosystem of biodiversity informatics platforms (Neil Cobb)

2. Symbiota Tools & Restructuring: Genetic Linking and new GenBank Sequence Submission Tool (Andy Miller) NfN loader (Herrick Brown & Michael Denslow) CoGe plugin (Herrick Brown and Michael Denslow) iPlant Image Processor (Herrick Brown and Michael Denslow) Skeletal Data Entry (Herrick Brown and Michael Denslow) Symbiota2 – (Ben Brandt) Spatial Module (Ben Brandt) Phenology Tracker (Will Pearse and Ben Brandt) Phylogenetics Module (Will Pearse and Ben Brandt)
3. Extending the functions of Symbiota - Examples: FieldGuide Computer Vision– LepSnap, CVBatch & CVWidget (Andre Poremski) Oregon Flora Project – focus on regional management & conservation (Ben Brandt with Linda Hardison virtual) Documenting the Ethnobiology of Mexico and Central America (DEMCA) (Jonathan or Ben Brandt) Education & Outreach (Anne Basham) SeedTrack – From seed to seed: tracking seed types in restoration treatments (Neil Cobb) Education & Outreach (Anne Basham)
4. Areas in Symbiota that need attention (Neil Cobb & Ben Brandt) Data entry form, Data search fields Best practices for sharing needs and providing solutions (Neil Cobb)
5. Open Discussion Time permitting

WeDigBio Planning Meeting (Austin Mast)

After a brief introduction to the annual Worldwide Engagement for Digitizing Biocollections (WeDigBio) event, participants will brainstorm new innovations for WeDigBio 2018, including the development of a virtual science festival (e.g., on the Sococo platform) and virtual reality collections tours and field experiences.

Legal Issues with Collections (Linda S. Ford)

As biodiversity collections are increasingly available online, they will be under increasing scrutiny. The Nagoya Protocol – a supplementary agreement to the Convention on Biological Diversity – has important implications for the conduct of U.S. biological collections, especially those whose data are available digitally. Knowledge of the protocol is not widespread among researchers or institutions. This session will discuss legal concerns associated with digitized collections and mitigating these issues using digital means. Compliance with the Nagoya Protocol will be a test case to evaluate how institutions must respond to requirements for increased transparency and digital tracking.

Open meeting space Meeting of the iDigBio student group Open meeting space
4:15-4:30 Unavailable Transition to Auditorium for wrap-up Cleanup Cleanup Cleanup Cleanup Cleanup
4:30-5:00 Unavailable Day 1 Wrap-up Unavailable Unavailable Unavailable Unavailable Unavailable
5:00-6:30 Unavailable Unavailable Unavailable Unavailable iDigBio meeting with NSF (closed session) Unavailable Unavailable
6:30-9:30 Evening program at the Florida Museum of Natural History (Powell Hall)
6:30-7:30 Arrival, heavy hors d'oeuvres, cash bar
7:30-7:40 Welcome by Roland Roberts, NSF Program Director and BIO Centers Science Advisor
7:40-8:00 Presentation about the Florida Museum's 100-year Anniversary by David Reed, Florida Museum Natural History Department Chair
8:00-9:30 Museum exhibits open for your enjoyment

Friday, November 3, 2017 -- Summit Day 2

Time Harn Galleria Harn Chandler Auditorium Harn Classroom 1 Harn Classroom 2 Powell Classroom McGuire Classroom McGuire Director's Conference Room
Morning Breakfast on your own
8:00-9:00 Setup Setup Unavailable Unavailable Setup Setup Open meeting space
9:00-9:30 Arrival, Summit check-in, coffee, networking   Unavailable Unavailable     Open meeting space
9:30-10:10 Unavailable DemoCamp (Matt Collins, Alex Thompson)

Live demos and talks of community-contributed software.

9:30-10:00 GUODA/iDigBio JupyterHub (Matt Collins)
Unavailable Unavailable ICER Working Group workshop on collections data in ecological and conservation research (Deborah Paul, Anna Monfils)

The ICER Working Group (Integrating Collections and Ecological Research), along with BCoN, will present a half-day workshop centered around ecologists who incorporate collections data in their scientific research and sharing a potential model program for integrating collections data in conservation efforts. Speakers invited will give talks representing community examples of museum specimen data integrated with other biodiversity data to enhance and inform efforts to address key ecological questions and support conservation efforts.

Changes/Improvements to the iDigBio Portal (Joanna McCaffrey, Shari Ellis, Richard Garand) Rapid digitization of incoming insect material

Goal: Develop workflow(s) for rapidly digitizing material from “collecting events”, especially where a large amount of material is brought into the collection from inventories. The workflow would be database neutral (Arctos [Derek], EMu [Crystal], institutional [Chris], Specify [Andrew], Symbiota [ Neil for now]), it would be scalable from small to large institutions, and it would be cross-phyla functional (e.g., plants/herbaria, insects/museums). Rationale: There are an estimated 256 million specimens in US collections, we are currently digitizing 2.5 million per year, which is the same amount of new material that is added to collections per year. Thus, we are currently running in place and we need to implement workflows that will help us at least double our current rate of digitization. Several collections have already developed workflows that greatly increase the rate of digitizing new specimens that need to be integrated into the collection from surveys and inventories https://vimeo.com/184611446. Action Items: Provide workflows that can be shared by all museums. This may involve options that take into consideration the type of specimens, the size of the museum, and the size and diversity of material. We will initially share drafts via dropbox. During this meeting we will produce a first draft and if there is time left we will outline a strategy to overcome the top 10 challenges in digitizing arthropods. (Neil Cobb, Crystal Maier, Jen Zaspel)

10:10-10:25 Morning break   Unavailable Unavailable     Open meeting space
10:25-12:30 Unavailable DemoCamp (continued)
10:30-11:00 MorphoSource (Julie Winchester)
11:00-11:30 TaxonWorks (Matt Yoder)
11:30-12:00 OntoPilot (Brain Stucky)
12:00-12:30 Index Herbariorum (Barbara Thiers)
Unavailable Unavailable ICER Working Group workshop (continued) iDigPaleo meeting iDigPaleo (Talia Karim)

This session will focus on current and future developments for iDigPaleo and how you can utilize the portal for your education and outreach needs. iDigPaleo was build as a proof of concept E&O portal for the Fossil Insect Collaborative. It currently hosts data for the FIC-TCN and the CW-TCN, with several other projects to be added this fall. Bring your ideas for the future of this portal (including any ideas you might have for a new name!).

Open meeting space
12:30-1:30 Unavailable   Box lunch provided     Open meeting space
1:30-3:15 Unavailable Building a Local Carpentries Community (Matt Collins, Deborah Paul)

The capacity to manage, manipulate, and analyze data is important to modern research programs. Ensuring research staff and students have access to the education and learning opportunities to maintain their development is the role of PIs, program heads, and institutional directors. Peer teaching and learning communities provide a learner-lead environment that is easy to foster and support in parallel with formal structures like academic curricula and professional development. We will describe our experiences at UF and FSU developing a community centered around the Data and Software Carpentry organizations to advance the informatics capacity of our organizations.

Broadening Participation & Biodiversity Literacy in Undergraduate Education (BLUE) (Anna Monfils, Molly Phillips, Libby Ellwood)

This session is an introduction and invitation to participate in two new initiatives related to biodiversity education: Biodiversity Literacy in Undergraduate Education (BLUE) a newly funded RCN-UBE, and the Broadening Participation in Biodiversity Sciences Working Group. Following a brief presentation on the two project’s upcoming activities and opportunities, facilitators will lead participants in a discussion focusing on the following: 1) What core data skills do all undergraduate biology students need to access and interpret data from digital natural history collection archives? 2) What resources are currently available for introductory biology instructors wanting to use collections based digital data in the classroom? and 3) What resources are available to biodiversity scientists seeking to broaden participation of underrepresented groups in the biodiversity sciences.

iDigBio brainstorming session with TCNs

iDigBio would like to brainstorm with the TCNs about the IAC meetings, bi-monthly reports, etc. The goal is to make these more effective and beneficial for all. This can also be a forum to brainstorm about other topics related to interaction among iDigBio and the TCNs.

Specify meeting (Andy Bentley)

The Specify Project and the biological collections it serves are approaching a fork in the road. After 30 years of underwriting biological collections software as a “public good” we have a strong indication that the US NSF will no longer bear the sole responsibility for funding at the level which has sustained the core software development activities of the Specify Project. We have been encouraged to develop a collections community-supported business model to sustain collections database innovation, and software maintenance, as well as related help desk, cloud hosting, and analytical data services. This session will be a drop in session that will include a short status update of Specify, a quick overview of key features, and discussion of our future vision. There will be time for Q & A and help desk problem solving/support and an opportunity to discuss TCN issues with Specify.


Open meeting space Open meeting space
3:15-3:30 Unavailable Transition to Auditorium for wrap-up Afternoon break Cleanup Cleanup Cleanup
3:30-4:00 Unavailable Summit Wrap-up Cleanup Cleanup Unavailable Unavailable Unavailable
4:00-5:45 Natural History Seminar at the Harn Chandler Auditorium in collaboration with the Florida Museum's Department of Natural History, iDigBio, myFOSSIL, and the Paleontological Society
4:00-4:30 Arrival, refreshments
4:30-5:00 "The Digital Atlas of Ancient Life" presented by Dr. Jonathan Hendricks of the Paleontological Research Institution (Ithaca, NY)
5:00-5:15 Questions & answers
5:15-5:45 Chat, departure
5:45pm-6:00pm Unavailable Cleanup Unavailable Unavailable Unavailable Unavailable Unavailable
Evening Dinner on your own
7:00-9:00 Drink with the Extinct at the Florida Museum (optional activity)

Separate registration and payment is required, but a discount code will be available for Summit participants (contact us for details). Registration for this event opens Monday, September 25. Event details are available on the Florida Museum's website.

Saturday, November 4, 2017 -- Optional Activities & Field Trip

Self-Guided Activities

Guided Field Trip

Sweetwater Wetlands Preserve

Report and Evaluation

Photos

Recordings

Retrieved from "http://www.idigbio.org/wiki/index.php?title=ADBC_Summit_2017&oldid=25852"