Updates

December 2, 2015

 

Best Practice Guide for Data Gap Analysis for Biodiversity Stakeholders

 

April 5, 2015

We continue to grow in both records and participating musueums.  We started with 10 institutional collections and have increased to 26 collections.  We are hosting two observational datasets (Moth observation database and Scarab Central).  We now serve over 1 million records and all of our data that are not served to iDigBio via another portal are havested bi-weekly by iDigBio through our Darwin Core archives..

 

July 30, 2014

SCAN mentioned in Wired Magazine!

SCAN was mentioned (and linked) in a article by Gwen Pearson of Wirde Magazine.  The article discusses the physics behind brightly-metalic colored beetles and quotes Chris Grinter of SCAN partner Denver Museum of Nature & Science.

 

February 12, 2014

We have the current Symbiota guide for entering data, searching data, and editing data on this website. 

There are a number of goals that we have all agreed upon, but if I had to boil it down to the two most important goals at this point in the project they would be recording specimens that are identified to species and all records georeferenced.  Meeting these two goals will provide us with the opportunity for promoting future funding.  Whether the data goes directly into Symbiota or a local periodical snapshot of a local database, the data is not that usable until it is in the SCAN database.

We are still a few months away from having good options for images.

Until then it would be helpful for museums to document QA/QC procedures that work for your museum and documenting working protocols for georeferencing and obtaining identifications. For example at NAU we have decided on a one-minute rule for undergraduates to georeference specimen records, and if the location is a town then we just use the centroid and it falls within the one-minute rule.  If a geographic locality is more nebulous (e.g., south slope of Huachuca Mtns) then they move on and it becomes one of the records that is batch geolocated by one or more experts.  If the format of your specimen record is not exactly alike (e.g. USA vs United States vs United States of America) then specimens from same location will not show up in the same batch for georeferencing.  It might be useful therefore to utilize some reasonable standards rather than always adhere to strict verbatim recording rules.  In March I would like to start compiling material for the annual report and these would be useful to have for each museum.

Primary research uses of the data will be species distribution modeling and taxonomy, while historical ecology, and community ecology might be farther down the road.  Species distribution modeling can help identify cryptic species as well as describe present niche space using both climate and environmental data.  Niche modeling can provide understanding of past and future distributions.  There is also clear potential for predicting a biodiversity patterns for a variety of taxa.  The amount of data already coming out of SCAN affords several possibilities for modeling projects. 

One SCAN modeling project is being launched.  Aaron Smith in collaboration with Quentin Wheeler and Nico Franz received NSF funding to revise the genus Eleodes.  An unfunded broader impact of that grant will allow Aaron to work with Joe smith and others to model a Tenebrionid mimicry ring involving an Eleodes species.  Joe Smith is will take the lead on the modeling and allow us to develop projections for future distributions that in turn will raise a number of interesting questions concerning biogeographic dynamics of the species involved in the ring.  I have attached a publication where Joe incorporporated niche modeling

But one does not have to put the data into a model to make use of it.  When I work out I typically download SCAN data on my iPad for various taxa into several mapping/GIS programs to just look at patterns.  For most places (with Verizon coverage) I can also stop anywhere and see what species have been recorded near that location.  It is also a humbling reminder how few records we really have for even common species.   

You may have noticed there are museums on SCAN Symbiota that are not part of the original SCAN project http://symbiota1.acis.ufl.edu/scan/portal/collections/index.php .  Although the focus continues to be what was in the proposal, we are opening the door and using the SCAN Symbiota portal to include other collections.  The purpose is to promote the use of Symbiota by other groups and we will see how things progress. 

Nico is developing the first SCAN taxonomic key using Curculionidae, hopefully there will be at least one product that uses all the features of Symbiota that the botanists have developed.

 

SCAN UPDATE,  June 2013

I hope everyone turned in their annual reports to NSF .  It has been several months since my last update to the larger group, I apologize that several Adobe Connect virtual meetings failed to materialize in the spring.  

Top Five Action Items for the Summer (besides continuing to catalog specimen data)

1.  Review & Clean up data.  Please go through your records in SCAN, make sure everything looks good.

2.  Taxonomic Authority Files.  We still need help a importing and managing the taxonomic thesaurus taxonomy tables.

3.  July will be “SCAN Imaging Month”. We will kick-off implementing production mode for imaging.  I will send out a separate email to museums doing high-resolution imaging.

4.  Filtered Push beta testing

5.  Host several Adobe Connect meetings on Symbiota, imaging, georeferencing (something that did not happen in the spring).

 

SCAN Symbiota Portal

The SCAN portal continues to grow daily by ~1,000 records per day, we could very well be over a half-million records by September.  We have added “Summary Statistics” capability that allows people to look at records for families and countries quickly.  It provides statistics on the number of records with species-level designations and the number of records that are georeferenced.  It is similar to what you can view by “Search Collections” except it allows you to view statistics for two or more collections.  The additional capability we have in “Summary Statistics” will be applied to “Search Collections” summary statistics (e.g., download summary data as a CSV).  Below are the top 10 taxa to date.  We are doing well for the top five priority groups (Acrididae, Formicidae, Carabidae, Tenebrionidae, and Araneae).

Family

SpecimenCount

Araneae

81,432

Scarabaeidae

64,913

Acrididae

48,080

Carabidae

35,462

Formicidae

31,487

Tenebrionidae

15,134

Curculionidae

12,015

Crabronidae

5,054

Meloidae

3,347

Vespidae

3,298

 

SCAN Broader Impact Taxa

We will continue to ingest/display data from other museums; the latest addition is the entomology collection at the Utah Department of Agriculture and Food.  Caressa and Clint from UDAF have been added to the list.  We will continue to ingest taxa not targeted in the SCAN-ADBC project. If you know of a museum that would be interested please let me know and we can work with them.  If you have NPS projects that involve digitization we have found that it is easy to export NPS ICMS data into SCAN.  I will personally promote digitization of Lepidoptera and Apoideae, two groups we talked about as focal taxa several years ago.  At NAU we have already used five different resources to digitize other taxa that do not use SCAN funding.

1. Build digitization into project cost

2. Museum operating costs

3. Internal institutional grants

4. Student research credit

5. Invite colleagues to use SCAN (provide free support).

PEN Proposals

Harvard’s PEN proposal was funded, and starting in September they will begin entering up to 90,000 records of ant data for the Southwest along with lots of images.  Below is the proposal summary. 

PEN: Digitization: Facilitating a Shared Image library and Occurrence Databased for Ants of the Southwest

Intellectual merit. The Museum of Comparative Zoology (MCZ) proposes to enhance the Southwest Collections of Arthropods Network (SCAN) Thematic Collection Network (TCN) by expanding and upgrading the representation of ants (a SCAN focal group) from the southwestern USA.  The MCZ will develop a complete online image library of Formicidae from the southwestern states (AZ, UT, CO, NM).  This will facilitate identification of ants, especially those in the collections of the SCAN TCN.  It will include images of MCZ type specimens and annotated images of exemplar specimens from the MCZ collection for all species known to occur in the region.  All types will be databased, geo-referenced, imaged and barcoded.  All MCZ specimens will be barcoded and exemplars for each species imaged.  To facilitate identifications, key morphological characters essential for species diagnosis will be illustrated along with brief explanatory comments.  This field guide approach will create an effective interface for the general public as well as the scientific community. The result will improve the ability of the SCAN TCN member institutions to correctly identify ant specimens in their collections to genus and species. The MCZ will also supplement the image library with occurrence data for approximately 90,000 terrestrial ants collected over the last 20-25 years in Arizona, New Mexico, Utah, Colorado and Texas, and this will facilitate the creation of distribution maps for each taxon. The MCZ has a world-class collection of ants from the region, representing about 90% of the approximately 422 species known from the four corners states (AZ, CO, UT, NM), and 50% of the species are represented by type material.  More than 1,500,000 specimens of historical importance are present in the MCZ, and the collection data from these specimens provide information about species distributions going back to the early 1900’s.  Digital collection records for 90,000 ants will augment the 60,000 specimen records of ants that the SCAN project is already scheduled to produce, thus contributing to the long term goal of using occurrence data for ecological modeling to gain a better understanding of the effects of climate change in the region.

Broader impacts. The image library and enlarged database of collection records produced by this research will be a resource available to SCAN and to the general public, and the creation of these resources will involve the training of graduate students, undergraduates and volunteers in museum databasing and curation. This research will enhance our understanding of biodiversity in the American Southwest, and help guide conservation strategies in the face of climate change.  Ants are of wide interest to the general public, and the activities described here will be featured in public presentations and outreach. In particular, the broader impacts of this project will focus on the Navajo Nation, a sovereign region comprising over 30,000 square miles located at the heart of the target area.  With support from the Christensen Fund, researchers from the MCZ have studied the ant fauna of the Navajo Reservation for the last four summers (http://www.navajonature.org/).  In collaboration with the Dine Environmental Institute and with permits from the Navajo Nation Fish and Wildlife, and working with Navajo scientists and student interns, more than 15,000 ants have already been collected from about 80 different localities on the reservation. Specimens collected from this study are among those whose records will be incorporated into the SCAN database.  With help from the Encyclopedia of Life (EOL), these data will be used to develop Navajo-friendly educational resources including a field guide to the ants of the Nation.

 

SCAN Announcement, May 2013

Hi,

I  inviting you and/or your colleagues to speak during one of the arthropod biodiversity sessions I am organizing for the next regional Biennial Conference that is scheduled for next September 16-19.   I want to solicit a wide range of talks that range from systematics to ecology and they do not need to have a Colorado Plateau focus as long as they are relevant in some way.  I have attached the list of talks and abstracts from the last meeting in 2011, which was the first meeting that had “Bug-Specific” sessions.  I am doing this in large part because I want everyone, including land managers, to appreciate or at least realize that arthropods do matter and people are doing interesting work.  This conference is usually dominated by vertebrates and vascular plants, which is great, but I think it is time to expand the taxonomic scope.

I have already received initial verbal confirmation that you can participate in the conference.  As of yet there is no financial support for speakers, and the best I may be able to do is to reduce or eliminate registration costs.  If it helps you tap funds from your institution I would be happy to send you a personal invitation to participate.  If you know of anyone else that would like to attend this conference feel free to forward this email.

Please let me know if you can participate and provide me with a provisional title.  I need commitments by Friday, May 31.  It is ok if you decide by July/early August that you cannot participate. 

Thanks,

Neil

SCAN Update  February 9, 2013

I have added Christy Bills, Joe Wilson, and Greg Setliff to the list.  Christy has set up the Natural History Museum of Utah collection on SCAN and has started entering specimen data.  Joe Wilson is a faculty member at Utah State who is interested in utilizing occurrence data in niche models.  Greg Setliff (Kutztown University) is starting to add weevil data to the Symbiota database.

Attached is the current Symbiota guide for entering data, searching data, and editing data.  We will put out more specific guides for searching and editing data.  Feel free to edit this draft and send back to me.

There are a number of agreed upon goals, but if I had to boil it down to the two most important goals at this point in the project they would be recording specimens that are identified to species and having all records georeferenced.  Meeting these two goals will provide us with the opportunity for promoting future funding.  Whether the data goes directly into Symbiota or a local periodical snapshot of a local database, the data is not that usable until it is in the SCAN database.

We are still a few months away from having good options for suggesting standards for acquiring and serving images.

Until then it would be helpful for museums to document QA/QC procedures that work for your museum and documenting working protocols for georeferencing and obtaining identifications. For example at NAU we have decided on a one-minute rule for undergraduates to georeference specimen records, and if the location is a town then we just use the centroid and it falls within the one-minute rule.  If a geographic locality is more nebulous (e.g., south slope of Huachuca Mtns) then they move on and it becomes one of the records that is batch geolocated by one or more experts.  If the format of your specimen records from the same locality is not exactly alike (e.g. USA vs United States vs United States of America) then specimens from same location will not show up in the same batch for georeferencing.  It might be useful therefore to utilize some reasonable standards rather than always adhere to strict verbatim recording rules.  In March I would like to start compiling material for the annual report and these would be useful to have for each museum.

Many thanks to Chris Grinter at DMNS for identifying a number of needs and fixes with Symbiota, which has been developed primarily for plan-based data and so there were several functions that needed to be worked on.  And many thanks to Ed Gilbert for being so accommodating in implementing the changes.

Primary research uses of the data will be species distribution modeling and taxonomy, while historical ecology, and community ecology might be farther down the road.  The amount of data already coming out of SCAN affords several possibilities for modeling projects.  One SCAN modeling project is being launched.  Aaron Smith in collaboration with Quentin Wheeler and Nico Franz received NSF funding to revise two subgenera of Eleodes.  An unfunded broader impact of that grant will allow Aaron to work with Joe Wilson and others to model a tenebrionid mimicry ring involving an Eleodes species.  Joe will take the lead on the modeling and allow us to develop projections for future distributions that in turn will raise a number of interesting questions concerning biogeographic dynamics of the species involved in the ring.  I have attached a publication where Joe incorporated niche modeling in his studies of mutillids.

But one does not have to put the data into a model to make use of it.  When I work out I typically download SCAN data on my iPad for various taxa into several mapping/GIS programs to just look at patterns.  For most places (with Verizon coverage) I can also stop to see what species have been recorded near that location.  It is also a humbling reminder how few records we really have for even common species.   

You may have noticed there are museums on SCAN Symbiota that are not part of the original SCAN project http://symbiota1.acis.ufl.edu/scan/portal/collections/index.php .  Although the focus continues to be what was in the proposal, we are opening the door and using the SCAN Symbiota portal to include other collections.  The purpose is to promote the use of Symbiota by other groups and we will see how things progress. 

Nico is developing the first SCAN taxonomic key using Curculionidae, hopefully there will be at least one product that uses all the features of Symbiota that the botanists have developed.

I would like to call a virtual meeting during the week of March 4-8, please fill out the doodle poll at http://doodle.com/87wudrppuvhvx993.  It will be through AdobeConnect, and I will request monthly virtual meetings at least through June, when our first annual report is due.

 

SCAN Update

November, 11, 2012 7:22 PM

We just added two key links on the SCAN Symbiota data portal.  One link goes to the Symbiota home page http://symbiota.org/tiki/tiki-index.php and the other goes to Symbiota help pages http://symbiota.org/tiki/tiki-index.php?page=HelpPages .  Symbiota not only serves as a way to enter and edit data for most SCAN museums, but it also is a great way to query and visualize data.  It would be extremely advantageous for anyone working with SCAN data to view all the Symbiota tutorials.  It would also be useful to visit SEINet and other Symbiota portals to get a sense of how other projects are developing.

The success of the Southwest Collections of Arthropods Network, or SCAN, hinges on the ability its 10 far-flung partner organizations to effectively collaborate and share information across the network. New technologies make sharing information and group communication cheaper and easier than ever before in human history. Because network partners are at diverse institutions that use a range of specific technologies, communications solutions that are easily available to each organization and require no or limited cost offer the best opportunity for successful communication. The range of possible communication solutions include the following:

(1.) Skype: This service allows users to communicate with peers by voice, video, and instant messaging over the Internet. Calls to other users within the Skype service are free of charge, while calls to landline telephones and cell phones are charged to a user account system on a pay-as-you-go basis. Additional features include file transfer and video conferencing. Skype is suitable for use with small groups.
Basic Skype service is free. Skype Premium, which costs $60/year, allows users to participate in group video calling and screen sharing, access live chat customer support, and call one other country on an unlimited basis.
(2.) Blackboard Collaborate: Northern Arizona University uses Blackboard Collaborate as its web conferencing and e-learning platform. Features include two-way audio, multi-point video, interactive whiteboard, application and desktop sharing, rich media, breakout rooms, and session recording. SCAN is able to use this service at no charge, unless landlines are used. Collaborate can accommodate meetings or workshops that involve up to 200 people. To avoid phone charges, Collaborate requires the use of a microphone and camera.
(3.) Adobe Connect: Adobe Connect is the web conferencing and e-learning platform used by iDigBio, which will host a meeting or webinar for any TCN for free. Features include two-way audio, multi-point video, interactive whiteboard, application and desktop sharing, rich media, breakout rooms, and session recording.
(4.) Google Calendar: This is a free service that allows users to create and manage online personal or group calendars. Users can share their schedules, invite others to events and meetings, access their calendars remotely, and receive meeting reminders via email or text. This service requires users to have or create a Google account. For SCAN, Google Calendar could be particularly useful in scheduling meetings with network participants.
The group Google calendar for SCAN is available on the SCAN website.
(5.) Google Drive: Google Drive is a free, web-based data storage service and document editing suite offered by Google. It allows users to create and edit documents online while collaborating in real-time with other users. Users get 5 GB of cloud storage at no change; additional storage is fee based and available at up to 16 TB.

Communications Tools for NAU Staff
(1.) Outlook Calendar: Outlook Calendar is the calendar and scheduling component of MS Outlook email software, the system used by Northern Arizona University. Outlook Calendar allows users to create and invite others to meetings and events, create tasks, and schedule appointments. Outlook Calendar is very useful for scheduling meetings with NAU colleagues.

 

SCAN Update October 28, 2012

Sorry, here is a long-awaited update.  I have divided the update into categories.  I assume everyone is in a similar situation as I am in and you have been immersed in all those wonderful academic activities since late August.  Starting next week we will ramp back up at NAU and probably peak over the break in terms of coordinating SCAN and getting NAU work accomplished.

Priorities     The priority for everyone should be to 1) curate collections in preparation for digitization (i.e., increase profiling status), and 2) catalog (i.e. label data) specimens with a focus on the highest priority taxa.  Imaging exemplars will ramp up next summer.  Let me know if this is a problem or if you are having problems getting started.

Cataloging     We will have a compiled a Symbiota cataloging protocol and other resources by the end of November on the SCANBUGS website.  I am confident that people entering data now are capturing the correct information, this protocol will be of help to future digitizers.  Below is the priority list of taxa to digitize for the SCAN project.  The five high-priority groups are still the same (Tenebrionidae, Carabidae, Formicidae, Acrididae, Araneae).  The Symbiota site includes taxa from non-target groups and we have put up some NPS records (CPMAB-NPS).  Feel free to add non-SCAN taxa using other project funds.  For example, in addition to NPS data we will be inputting bee data from another NAU project over the break.  We do need to make sure the priority taxa are covered. 

Priority

Taxon

1

Tenebrionidae

1

Zopheridae (teneb-related)

1

Carabidae

1

Formicidae

1

Acrididae

1

Spiders (ground-dwelling represented)

2

Other non-mite arachnids

2

Curculionidae

2

Mutillidae

2

Elateridae

2

Myrmeleontidae

2

Romaleidae

2

Tetrigidae

2

Stenopelmatidae

2

Gryllidae

2

Tridactylidae

2

Mogoplistidae

2

Polyphagidae

2

Rhaphidophoridae

2

Staphylinidae

2

Bradynobaenidae

2

Tiphiidae

2

Lygaeoidea

2

Scarabaeoidea

2

Trogidae

2

Dermestidae

2

Ptiliidae

2

Lathridiidae

2

Cryptophagidae

2

Nitidulidae

2

Histeridae

2

Leiodidae

2

Silphidae

2

Isopoda

2

Myriapoda

Databases  Everyone is set up with the database(s) they will use and has either submitted initial bulk legacy data or they are very close.  We have over 100,000 records entered and ASU, CSU, UA, and NAU are all entering new data into the SCAN Symbiota portal.  James has Specify up and running at TTU and BYU is using Specify as well.  KE-Emu is developing a link with Filtered Push so that should make DMNS happy. 

Imaging Systems     TTU, DMNS, and NMSU should all have their imaging systems set up and have started playing.  UCB is still waiting to purchase the system (Deane?).  All of our how-to-videos are loaded on our new website.  Because the new website is in a content management system (CMS) we might lose functionality periodically.

PEN Proposals     Both BYU and Harvard submitted proposals to the ADBC program.  There were 14 TCN and 8 PEN proposals submitted to NSF this year. BYU proposes to digitize the four main insect taxa (Tenebrionidae, Carabidae, Formicidae, and Acrididae).  The Harvard proposal is focused on southwestern ants.  If both are funded we will almost double the number of ant records and significantly increase records in the other three high-priority insect families.

Websites     The primary SCAN website is http://symbiota1.acis.ufl.edu/scan/portal/index.php the site where you can look at all the records Ed has ingested through Symbiota.  The project website http://www.scanbugs.org/ is still a shell.  We will convert it to either a drupal site or a more generic content management system site. 

iDigBio      The second iDigBio Summit took place this past week, and was very successful, all seven TCNs were represented and there was wonderful sharing of information.  The iDigBio staff has been compiling a lot of useful protocols and other information.  I would urge people to visit the iDigBio website, it has a lot of great information https://www.idigbio.org/ .  You may have to spend an hour just exploring the site before you can reliably find information, they are going to develop a new structure to the site soon and that should help with navigation.  They are putting up a lot of information regularly, especially from the working groups.  Below are the current working groups and SCAN representatives. https://www.idigbio.org/wiki/index.php/IDigBio_Working_Groups#Public_Participation_in_Digitization

Taxonomic Authority Files & Minimum Information Standards, Authority Files, & Semantics (MISC)

Nico Franz (ASU)     Paul Morris (Filtered Push)

Optical Character Recognition (OCR)

Ed Gilbert (Symbiota)

Public Participation in Digitization Education/Outreach

Melody Basham (ASU)

Developing Robust Object to Image to Data (DROID2)_

The Pinned Specimens in Trays and Drawers Working Group

Nico Franz (ASU), Ed Riley (TAMU), John Oswald (TAMU)

Georeferencing

Paul Heinrich (NAU), Jacob Higgins (NAU)

Cyberinfrastructure

Paul Heinrich (NAU), Ed Gilbert (Symbiota)

Automated Specimen Identification (pending approval working group)

Neil Cobb (NAU)

 

SCAN Update   8/30/2012

Hi Everyone,

First, I have added Naomi Pierce, Gary Alpert, Stefan Cover, and Linda Ford from the Museum of Comparative Zoology at Harvard.  Along with Jim Hanken, they will be submitting a PEN proposal as will Shawn Clark and Riley Nelson from BYU.  The Harvard proposal will be restricted to southwestern ants and they should double the ant occurrence data we have projected for the SCAN.  If you have not seen Harvard’s Navajo Nature Ant website it is a very nice “Broader Impacts” outreach project that is worth perusing http://navajonature.org/ants/navajo-ants.html .  I am really grateful to both BYU and Harvard for joining the network.

Second, thanks to Nico for incorporating my request in with his request. However, the list Nico presented was an earlier list, some of these taxa were removed after we reprioritized.  The current list is in the the attachment “SCAN-Timelines Personnel Taxonomists”.  If we keep lower priority groups that are very large (e.g., Cerambycidae, Sphecidae [really meant Sphecoidea], and Buprestidae) I know we will lose continuity.  In the first spreadsheet in “SCAN-Timelines Personnel Taxonomists”   I prioritized taxa at NAU with regard to when we plan to start digitization, and the key groups are all scheduled in the first two years (with the exception of Scarabaeiodea).  In this same sheet I also list taxa that were next in line (based on an informal perusal of pitfall data), but I put question marks in the Timeline.

I apologize for the confusion, I should have made sure everyone had updated taxa lists.  I am behind on a couple of SCAN activities and unfortunately I have to attend to other business in the next month, so I will not get back into SCAN fully until October.  But by then we will have populated the project website http://perceval.bio.nau.edu/scanbugs/index.html and the data portal is already growing http://symbiota1.acis.ufl.edu/scan/portal/index.php .

As I mentioned at the meeting as long as people start digitizing the key groups we will have time to resolve other taxa.  Those key groups are Carabidae, Tenebrionidae, Formicidae, Acrididae, and of course spiders.  I have highlighted taxa in Nico’s list with yellow that I removed last fall, and below I have list names that are in my list but not in Nico’s list.  I will send out a separate email to anyone that wants to participate in a discussion about resolving these groups, but please let me know in the next week.    

Thanks,  Neil