TCN Resources

How this resource might be useful

These resources are an at-a-glance introduction to Thematic Collections Networks and Partner to Existing Network (TCNs/PENs), including a contact who has volunteered to answer questions for each project, and some rudimentary information about the organisms in their proposal. This information may be useful to anyone writing a proposal, interested to see what others are doing, with what digitization technology; or who has recently received funding and is looking for digitization tips and advice from like-minded people.

Brief background

NSF's Advancing Digitization of Biological Collections (ADBC) initiative is funding iDigBio to be the hub to serve the digitized collections from TCNs projects (networks of institutions organized around a theme). Sometimes the theme includes a research question. RDCNs ('Regional' Digitization Collections Networks, managed by Collections in Support of Biological Research (CSBR)) are like a TCN, but not so closely tied managerially to iDigBio and the TCNs. As the hub, iDigBio seeks to serve all digitized specimens, not only those created by the ADBC program.

References

• Intro to iDigBio (from SPNHC 2013) https://www.idigbio.org/sites/default/files/workshop-presentations/spnhc2013/SPNHC_IntroToiDigBioJM.pdf
• Each TCN gave a succinct digitization progress report at iDigBio Summit III (November 2013): https://www.idigbio.org/content/idigbio-summit-iii-0
• This page has recordings from most of the sessions at iDigBio Summit IV, including the TCNs: Day 1 recordings

Information about ADBC

Anyone seeking information about ADBC, its grand challenges, or how to get involved in this funding stream should look on the NSF website for the solicitations:

• ADBC: http://www.nsf.gov/pubs/2015/nsf15576/nsf15576.htm
• CSBR: http://www.nsf.gov/pubs/2015/nsf15577/nsf15577.htm

For details about writing a proposal to the NSF ADBC program for digitization funding, see here

Annual/Final Reports to NSF

Each institution that received funding will need to submit their own report to NSF. The TCN Lead PI submits a report of their own activities AND the activities of the entire TCN. For more information, see the Guidelines for Annual Reporting Requirements.

"The Program expects the final report to be the same as the annual report for the last year of funding. As a result, it is expected that the format of previous annual reports will be followed. The lead PI (or his/her designee) collects all the reports from collaborators and prepares a high level picture of the accomplishments of the network. Each collaborating PI submits their individual report highlighting their own accomplishments as it relates to their part of the award and the personnel (students etc.) working with them. Collaborators attach the integrated report as a PDF. Because the integrated report focuses on high level network accomplishments, it is inappropriate for collaborators to refer to it in their reports (such as, see details in attachment) rather than explicitly stating their own accomplishments.”

TCN Quarterly Reports to iDigBio

Prior to each TCN Advisory Meeting, TCNs are asked to complete a quarterly progress report in the following areas:

• Progress in Digitization Efforts
• Best Practices, Standards, and Lessons Learned
• Identified Gaps in Digitization Areas and Technology
• Opportunities to Enhance Training Efforts
• Collaborations with other TCNs, Institutions, and/or Organizations
• Opportunities and Strategies for Sustainability
• Education, Outreach, Diversity, & Inclusion (EODI) Activities
• Information About Your Website and/or Portal Usage
• Other Activities and/or Progress

The TCN Lead PI or Project Manager collects information from all collaborators and compiles them into one overall progress report for the TCN. The TCN Lead PI or Project Manager then submits the quarterly reports via an email to Cat Chapman. iDigBio maintains an archive of previously submitted reports is available on the TCN Advisory Committee (IAC) wiki page.

We have created a template for the reports that TCN Lead PIs or Project Managers are welcome to use. This link will prompt you to make a copy of the template document to your own Google Drive account, where you may fill it out with the required information before sending it to us. If you do not have a Google Drive account, or do not wish to use it, you may use this link to access the template for downloading to your PC (after accessing the link, click File, then Download, and choose your desired filetype, preferably .docx).

You may contact Cat Chapman for further information about report submission using her contact page.

TCN Report

TCNs/PENs At a Glance

Row	Count Description	Count
1	Known U.S. Collections	1,590
2	ADBC Funded Collections	925
3	ADBC Funded Institutions	317
4	ADBC Collections Providing Data	663
6	Total ADBC Specimen Records	65,264,004

Collaborators funded includes PENs
Table is manually entered based on the data at: https://idigbio.shinyapps.io/golden-bower/

TCNs/PENs Digitization Progress

TCN	Date	Status	#Collaborators funded	#Funded datasets ingested	+Dataset volunteers	+Collaborators no data
Tropical African Plants (TAP)	2022 - 2026	active	7	11	24
Endless Forms	2018 - 2021	active	6
Pteridological Collections Consortium (PCC)	2018 - 2021	active	9
Capturing California's Flowers (CAP)	2018 - 2022	active	19
Cretaceous World	2016 - 2019	active	9	6		1
EPICC (includes 1 CSBR)	2015 - 2019	active	8	6	1
Fossil Insects (FIC)	2013 - 2017	NCE	9	5	2
Great Lakes Invasives (GLI)	2014 - 2017	retired	39	33	1	1
InvertEBase	2014 - 2018	active	9	6	6	1
InvertNet	2011 - 2015	retired	23	11
LepNet	2016 - 2020	active	27	34	4
Lichens & Bryophytes (LBCC)	2011 - 2015	retired	71	67	28
MaCC	2012 - 2015	retired	34	32	8	2
Macroalgae	2013 - 2017	NCE	50	33
MAM	2016 - 2019	active	12	7	1	1
MiCC	2015 - 2018	active	33	23	20	1
NEVP	2012 - 2016	retired	25	24	2	4
oVert (*)	2017 - 2021	active	51			2
Paleoniches	2012 - 2016	retired	8	7		1
SCAN	2012 - 2015	NCE	19	18	28	0
SERNEC	2014 - 2018	active	95	36	5	4
SoRo	2017 - 2021	active	19	10	3	1
Tri-trophic (TTD)	2011 - 2015	retired	29	29	3	1
VACS	2013 - 2017	NCE	7	6
TOTAL			613	393	112	20

(Updated ~monthly :: May, 2018)
NCE = NSF no cost extension

• = we have ingested 44 datasets from oVert's TCN, but we are still working on the media protocol, so the ingested counts are not available yet

TCN List at a Glance

Below is a table of individual TCN project information. RDCNs are added below for completeness since they work closely with thematic networks. For more iDigBio TCN info, see the master map for which institutions are in the project: https://www.idigbio.org/content/collaborating-institutions, and see each institution's map (links found below) for project details of the TCN. For a complete list of data publishers see: https://www.idigbio.org/portal/publishers

Note: the number of anticipated collaborators, specimens and images to be digitized is approximate, and based on the text in the proposal.

TCN	Date	Contact with Email	Digitization Methodology	Software Interface to iDigBio	Organisms	# of Specimens/Images	# of Collaborators
InvertNet (website)	2011 - 2015 Final	Christopher Dietrich	robotic scanning of vials, slides and drawers, crowd-sourcing of label data from images		arthropods	56.1M / .89M	23 (1 PEN) (Map)
Tri-trophic (TTD) (website)	2011 - 2015 Final	Katja Seltmann Toby Schuh (insects), Rob Naczi (plants)	imaging herbarium sheets with the Photo eBox Plus and direct transcription of insect labels into a database without imaging.	Arthropod Easy Capture, Symbiota, several other institutional databases including Specify	insects (Hemiptera, Hymenoptera) and vascular plants	1.2M (insects) 1.2M (plants) / 611,000	29 (Map)
Lichens & Bryophytes (LBCC) (lichen website), (bryophyte website)	2011 - 2015 Final	Corinna Gries, Tom Nash‎‎, Ed Gilbert‎	label imaging, using OCR for data capture workflow	Symbiota	lichens & bryophytes	2.3M / 2.3M	71 (4 PENs) (Map)
New England Vascular Plants (NEVP) (TCN website), (CNH website)	2012 - 2016 Final	Patrick Sweeney	robotic scanning apparatus for herbarium sheets, specimen-by-specimen label data capture	Symbiota, EMu	vascular plants	1.29M / 1.29M	25 (2 PENs) (Map)
PaleoNICHES (TCN website)	2012 - 2015 Final	Bruce Lieberman	specimen-by-specimen label data capture	Specify	fossils: arthropods, brachiopods, echinoderms, mollusks, cnidarians, vertebrates	930K / 4K	7 (3 PENs) (Map)
MacroFungi Collection Consortium (MaCC) (TCN website),(mycoportal website)	2012 - 2017 Final	Barbara Thiers	label imaging, crowd-sourcing of label data	Symbiota	macrofungi	1.39M / 1.3M	34 (2 PENs) (Map)
Symbiota Collections of Arthropods (SCAN) (TCN website), (website)	2012 - 2015	Neil Cobb	Visionary Digital workflow, specimen-by-specimen label data capture, plus ~16K specimen image suites (~40K images)	Symbiota	ground dwelling arthropods	.73M / 15,125	18 (5 PENs) (Map)
Fossil Insect Collaborative (FIC) (website)	2013 - 2017	Talia Karim	Imaging specimens using standard macrophotographic techniques including focus stacking, data capture via hand keystroke and voice recognition	Specify, EMu and other (for home institutions) - developing the iDigPaleo Portal for our main interface.	fossil insects	500k/200k	8 (2 PENs) (Map)
Vouchered Animal Communication Signals (VACS)	2013 - 2017	Michael Webster	digitizing analog sound recordings, imaging specimens & labels		birds, frogs, fish and insects	58,374 / 22,939	7 (Map)
Macroalgal Herbarium Consortium (MHC) (website)	2013 - 2017	Chris Neefus	imaging herbarium sheets with the Photo eBox Plus	Symbiota	macroalgae	1.14M / 1.14M	50 (Map)
Great Lakes Invasives (website)	2014 - 2017 Final	Ken Cameron	imaging herbarium sheets and animal specimen lots with the Photo eBox Plus	Symbiota	fish, clams, snails, mussels, algae, plants	>637K plants, >102K fish lots, >44K mollusk lots	41 (Map)
InvertEBase	2014 - 2018	Petra Sierwald	development of various workflows: data capture from labels; data capture from label images; data capture via voice recognition and OCR	Symbiota, Arctos	invertebrates: insects, arachnids, mollusks	>2M	7 (2 PENs) (Map)
The Key to the Cabinets (SERNEC - TCN)	2014 - 2018	Zack Murrell		Symbiota	plants	>3M	93 (1 PEN) (Map)
Microfungi Collections Consortium (MiCC) (TCN website),(mycoportal website)	2015 - 2018	Andrew Miller	label imaging, creation of a voice data command center in Symbiota, crowd-sourcing of label data, batch georeferencing	Symbiota	microfungi	>1.2M/1.3M	40 (Map)
Fossil Marine Invertebrates EPICC (website)	2015 - 2019	Charles Marshall	specimen-by-specimen label data capture, imaging exemplar specimens and historic labels, collaborative georeferencing	Specify, EMu, FileMaker, and other	fossil marine invertebrates	1.6M/85k	8 (1 PEN) (Map)
Cretaceous World	2016 - 2019	Bruce Lieberman	specimen-by-specimen label data capture	Specify	fossils: arthropods, brachiopods, echinoderms, mollusks, cnidarians, vertebrates	164K/1.6K	8 (Map)
LepNet	2016 - 2020	Neil Cobb	specimen-by-specimen label data capture; LepSnap	Symbiota	insects: Lepidoptera	2M/214K	27 (Map)
The Mid-Atlantic Megalopolis MAM	2016 - 2019	Cynthia Skema	imaging herbarium sheets, specimen-by-specimen label data capture	Symbiota	vascular plants	700K/700K	11 (1 PEN) (Map)
oVert: Open Exploration of Vertebrate Diversity in 3D	2017 - 2021	David Blackburn or Ed Stanley	capturing 3D phenotypes using CT-scanning	via MorphoSource	vertebrates		18 (Map)
Using Herbarium Data to Document Plant Niches in the High Peaks and High Plains of the Southern Rockies - Past, Present, and Future (SoRo)	2017 - 2021	Erin Tripp		Symbiota	vascular plants		20 (Map)
Digitizing "Endless Forms": Facilitating Research on Imperiled Plants with Extreme Morphologies	2018 - 2021	Matthew Pace			plants
The Pteridological Collections Consortium: An integrative Approach to Pteridophyte Diversity Over the Last 420 Million Years	2018 - 2021	Carl Rothfels		Symbiota	pteridophytes
Capturing California's Flowers: Using Digital Images to Investigate Phenological Change in a Biodiversity Hotspot	2018 - 2022	Jenn Yost		Symbiota	plants
Enhancing Access to Taxonomic and Biogeographical Data to Stem the Tide of Extinction of the Highly Imperiled Pacific Island Land Snails	2019 - 2023	Norine Yeung		Symbiota	mollusks
American Crossroads: Digitizing the Vascular Flora of the South-Central United States	2019 - 2023	Peter Fritsch		Symbiota	plants
Digitizing Collections to Trace Parasite-Host Associations and Predict the Spread of Vector-Borne Disease	2019 - 2022	Stephen Cameron		Symbiota	parasitic arthropods
Documenting Marine Biodiversity through Digitization of Invertebrate Collections (DigIn)	2020 - 2024	Regina Wetzer		Symbiota	marine invertebrates
Mobilizing Millions of Marine Mollusks of the Eastern Seaboard	2020 - 2024	Rudiger Bieler		Symbiota	marine mollusks
Building a Global Consortium of Bryophytes and Lichens: Keystones of Cryptobiotic Communities	2020 - 2024	Jessica Budke		Symbiota	bryophytes and lichens
Tropical African Plants (TAP) TCN (Collaborative Research: Digitization and Enrichment of U.S. Herbarium Data from Tropical Africa to Enable Urgent Quantitative Conservation Assessments) (Portal website),	2022 - 2026	A. Townsend Peterson		Symbiota	primary biodiversity records of plants from African countries

RDCNs and others at a Glance

RDCN	Contact with Email	Methodology	Software	Organisms	# of Participants
Unlocking the Fossil Cabinet: Improving Conservation and Accessibility of Invertebrate Paleontology Collections at the Natural History Museum of Los Angeles (CSBR website)	Austin Hendy	single site	EMu	fossil invertebrates	1
VertNet (website)	Dave Bloom	aggregator / facilitator		mammals, birds, fish, herps	63 institutions, 179 collections: mammals (46), birds (47), fish (26), herps (44), paleo (8), tissue (4), special (4) (as of 12Aug2014)
Consortium of California Herbaria (CCH) (website)	TBA - used to be David Baxter	aggregator / facilitator	custom	vascular plants	32
Fishnet2 Collaborative Georeferencing	Hank Bart, Jr.	georeferencing		fish
Mississippi Herbaria Consortium (Magnolia grandiFLORA)	Lucile McCook	aggregator / facilitator	Silver Biology, Specify	plants	8
Consortium of Pacific Northwest Herbaria (website)	Ben Legler	aggregator / facilitator		plants	57
Texas Oklahoma Regional Consortia of Herbaria (TORCH) (website)	Wayne Elisens-retired Bruce Hoagland	aggregator / facilitator		plants	9
Wisconsin Flora (WisFlora) (website)	Ken Cameron	aggregator / facilitator		algae, fungi, lichens, bryophytes and vascular plants	26

TCN Social Media Resources

TCN Blogs

• TTD blog

TCN Facebook

• TTD
• Microfungi

TCN Twitter

• EPICC

Other resources

• Project Management Resources