TCN Resources: Difference between revisions
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|valign="top"|ground dwelling arthropods | |valign="top"|ground dwelling arthropods | ||
|valign="top"|.73M / 15,125 | |valign="top"|.73M / 15,125 | ||
|valign="top"|18 ( | |valign="top"|18 (5 PENs) ([https://www.idigbio.org/content/digitization-tcn-southwest-collections-arthropods-network-scan-collaborator-map Map]) | ||
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|valign="top"|[https://www.idigbio.org/wiki/index.php/Fossil_Insect_Collaborative:_A_Deep-Time_Approach_to_Studying_Diversification_and_Response_to_Environmental_Change Fossil Insect Collaborative (FIC)] | |valign="top"|[https://www.idigbio.org/wiki/index.php/Fossil_Insect_Collaborative:_A_Deep-Time_Approach_to_Studying_Diversification_and_Response_to_Environmental_Change Fossil Insect Collaborative (FIC)] | ||
Revision as of 12:15, 10 May 2018
How this resource might be useful
These resources are an at-a-glance introduction to existing Thematic Collections Networks and Partner to Existing Network (TCNs/PENs), including a contact (with their email) 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
The TCN Lead PI submits reports quarterly to iDigBio using our online form: Online Form for TCN Quarterly Reports. The TCN Lead PI collects info from all collaborators and compiles into one bi-monthly report.
iDigBio maintains an archive of all previously submitted bi-monthly reports.
TCN Report
TCNs/PENs At a Glance
| Row | Count Description | Count |
|---|---|---|
| 1 | Total funded individual collaborators committed to contributing data via their network (see exceptions in roles, non-data contributors, e.g., assisting data contributors, advisory, etc.) among the 20 TCNs and 23 PENs | 576 |
| 2 | + no data - outreach contributors role | 3 |
| 3 | + no data - in some sort of advisory role, e.g., FilteredPush, Specify, Symbiota, Notes From Nature, Citizen Science | 17 |
| 4 | + participating in unfunded contributor role (perhaps because they had digitized data/images ready) | 112 |
| 5 | ..... of which are foreign participants - among the 'unfunded contributor' above (Copenhagen, Oslo, Bergen, Uppsala, Buenos Aires, + 12 from Canada) | 18 |
| 6 | Total participants in the project whether funded or not (add rows 1, 2, 3 and 4) | 708 |
| 7 | Unique funded TCN/PEN (ADBC) institutions (tip: some institution have more than one TCN/PEN) | 304 |
| 8 | Unique overall institutions derived from row 6 (see Map & List) | 396 |
Collaborators funded includes PENs
TCNs/PENs Digitization Progress
| TCN | Date | Status | #Collaborators funded | #Funded datasets ingested | +Dataset volunteers | +Collaborators no data |
|---|---|---|---|---|---|---|
| Cretaceous World | 2016 - 2019 | active | 9 | 6 | 1 | |
| EPICC (includes 1 CSBR) | 2015 - 2019 | active | 8 | 5 | 1 | |
| Fossil Insects (FIC) | 2013 - 2017 | NCE | 9 | 5 | 2 | |
| Great Lakes Invasives (GLI) | 2014 - 2017 | NCE | 39 | 33 | 1 | 1 |
| InvertEBase | 2014 - 2018 | active | 8 | 6 | 6 | 1 |
| InvertNet | 2011 - 2015 | retired | 23 | 11 | ||
| LepNet | 2016 - 2020 | active | 27 | 34 | 4 | |
| Lichens & Bryophytes (LBCC) | 2011 - 2015 | NCE | 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 | NCE | 25 | 24 | 2 | 4 |
| oVert (*) | 2017 - 2021 | active | 51 | 2 | ||
| Paleoniches | 2012 - 2016 | NCE | 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 | 576 | 392 | 112 | 20 |
(Updated ~monthly :: March, 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 | 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 | 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 | 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 | 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 (1 PEN) (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 | 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 PEN) (Map) |
| The Key to the Cabinets (SERNEC - TCN) | 2014 - 2018 | Zack Murrell | Symbiota | plants | >3M | 93 (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 and other | fossil marine invertebrates | 1.6M/85k | 8 (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 (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) |
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 |