TCN Resources: Difference between revisions
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|valign="top" align="center"|2015 - 2018 | |valign="top" align="center"|2015 - 2018 | ||
|valign="top"|[mailto:amiller7@illinois.edu Andrew Miller] | |valign="top"|[mailto:amiller7@illinois.edu Andrew Miller] | ||
|valign="top"| | |valign="top"|label imaging, creation of a voice data command center in Symbiota, crowd-sourcing of label data | ||
|valign="top"|Symbiota | |valign="top"|Symbiota | ||
|valign="top"|microfungi | |valign="top"|microfungi | ||
Revision as of 16:10, 15 October 2015
How this resource might be useful: These resources are an at-a-glance introduction to existing Thematic Collections Networks (TCNs), 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
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
ADBC Annual Report Info Sheet
Guidelines for Annual Reporting Requirements for Lead Proposal PIs and Collaborative Proposal PIs at iDigBio, TCN and PEN locations. ADBC Annual Report Info Sheet
TCN Bi-Monthly Reports to iDigBio
Reporting Process for TCNs:
Bi-Monthly:
- For iDigBio: TCN Lead PI submits reports bi-monthly using our online form: Online Form for TCN Bi-Monthly Reports
Collect info from all members and compile into one bi-monthly report.
Annually: (we provide this for your edification, note that no annual report is due to iDigBio from the TCNs)
- For NSF: Each institution that received funding will need to submit their own report. The TCN Lead PI submits a report of their own activities AND the whole TCN activities.
For further details see : NSF Annual Report Info Sheet
TCN Lightning Round Progress Reports at Summit 3, November 2013
Each TCN gave a succinct digitization progress report: https://www.idigbio.org/content/idigbio-summit-iii-0
Summit 4, October 2014
This page has recordings from most of the sessions, including the TCNs: Day 1 recordings
TCN Record Counts
| Count Description | Count |
|---|---|
| unique funded TCN/PEN (ADBC) institutions (tip: some institution have more than one TCN/PEN) | 250 |
| total collaborators committed to contributing data (see exceptions in roles below, e.g., assisting data contributors) among the 15 TCNs | 482 |
| participating in 'unfunded contributor' role (perhaps because they had digitized data/images ready) | 47 |
| outreach contributors (no data) | 2 |
| in some sort of advisory capacity, e.g., FilteredPush, Symbiota, Citizen Science (no data) | 8 |
| foreign participants - among the 'unfunded contributor' above (Copenhagen, Oslo, Bergen, Uppsala, + 2 from Canada) | 6 |
| TCN | Date | #Collaborators / Ingested so far | Specimen records ingested | Media ingested |
|---|---|---|---|---|
| EPICC | 2015 - 2019 | 7 / 0 | 0 | 0 |
| Fossil Insects (FIC) | 2013 - 2017 | 10 / 2 | 415,466 | 0 |
| Great Lakes Invasives (GLI) | 2014 - 2017 | 29 / 0 | 0 | 0 |
| InvertEBase | 2014 - 2018 | 7 / 0 | 0 | 0 |
| InvertNet | 2011 - 2015 | 15 / 10 | 8930 | 7636 |
| Lichens & Bryophytes (LBCC) | 2011 - 2015 | 91 / 79 | 3,809,038 | 1,926,820 |
| MaCC | 2012 - 2015 | 43 / 37 | 1,765,550 | 503,809 |
| Macroalgae | 2013 - 2017 | 49 / 11 | 210,140 | 210,858 |
| MiCC | 2015 - 2018 | 38 / 0 | 0 | 0 |
| NEVP | 2012 - 2016 | 24 / 11 | 364,212 | 315,104 |
| Paleoniches | 2012 - 2015 | 7 / 5 | 891,929 | 0 |
| SCAN | 2012 - 2015 | 30 / 32 | 1,750,940 | 161,341 |
| SERNEC | 2014 - 2018 | 92 / 4 | 179,361 | 0 |
| Tri-trophic (TTD) | 2011 - 2015 | 33 / 16 | 1,872,164 | 323,000 |
| VACS | 2013 - 2017 | 7 / 0 | 0 | 0 |
| TOTAL | 482 / 187 | 9,306,949 | 3,107,196 |
(Updated monthly :: Sep, 2015)
TCNs 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 | 16 (1 PEN) (Map) | |
| Tri-trophic (TTD)
(website) |
2011 - 2015 | 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 | 32 (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 | 76 (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 | 19 (2 PENS) (Map) |
| PaleoNICHES | 2012 - 2015 | Bruce Lieberman | specimen-by-specimen label data capture | Specify | fossils: arthropods, brachiopods, echinoderms, and mollusks | 650K / 3600 | 8 (2 PENs) (Map) |
| MacroFungi Collection Consortium (MaCC) | 2012 - 2015 | Barbara Thiers | label imaging, crowd-sourcing of label data | Symbiota | macrofungi | 1.39M / 1.3M | 38 (2 PENS) (Map) |
| Southwest 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 | 16 (3 PENs) (Map) |
| Fossil Insect Collaborative (FIC)
(website) |
2013 - 2017 | Dena Smith | Visionary Digital workflow, most specimen data already captured | Specify, EMu and other (for home institutions) - developing the iDigPaleo Portal for our main interface. | fossil insects | 500k/200k | 7 (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 | 1.73M | 29 (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 | invertebrates: insects, arachnids, mollusks | >2M | 7 (Map) |
| SERNEC | 2014 - 2018 | Zack Murrell | Symbiota | plants | >3M | 45 (Map) | |
| Microfungi Consortium MiCC | 2015 - 2018 | Andrew Miller | label imaging, creation of a voice data command center in Symbiota, crowd-sourcing of label data | Symbiota | microfungi | >1.2M | 38 (Map) |
| Fossil Marine Invertebrates EPICC | 2015 - 2019 | Charles Marshall | fossil marine invertebrates | 6 (Map) |
RDCNs and others at a Glance
| RDCN | Contact with Email | Methodology | Software | Organisms | # of Participants |
|---|---|---|---|---|---|
| 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) |
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 | aggregator / facilitator | plants | 9 | |
| Wisconsin Flora (WisFlora)
(website) |
Ken Cameron | aggregator / facilitator | algae, fungi, lichens, bryophytes and vascular plants | 26 |