TCN Resources: Difference between revisions
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|valign="top"|[https://www.idigbio.org/wiki/index.php/TCN:_Collaborative_Research:_Digitization_and_Enrichment_of_U.S._Herbarium_Data_from_Tropical_Africa_to_Enable_Urgent_Quantitative_Conservation_Assessments African Plants | |valign="top"|[https://www.idigbio.org/wiki/index.php/TCN:_Collaborative_Research:_Digitization_and_Enrichment_of_U.S._Herbarium_Data_from_Tropical_Africa_to_Enable_Urgent_Quantitative_Conservation_Assessments Tropical African Plants (TAP) TCN (Collaborative Research: Digitization and Enrichment of U.S. Herbarium Data from Tropical Africa to Enable Urgent Quantitative Conservation Assessments)] | ||
([https://african-plants.org/portal/index.php/ Portal website]), | ([https://african-plants.org/portal/index.php/ Portal website]), | ||
|valign="top" align="center"|2022 - 2026 | |valign="top" align="center"|2022 - 2026 | ||
Latest revision as of 10:28, 5 September 2024
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) | 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 | 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) | 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) | 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) | 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 | 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 |