Category Archives: Scholarly Life

USDA VIVO Compatibility with

Results of inquiry at re: USDA VIVO, which is a type of CRIS (Current Research Information Systems). More on VIVO online:

From: Jessel, Tanner – FS
Sent: Tuesday, December 20, 2016 5:29 PM
To: Marsh, Emily <emily.marsh>
Subject: RE: Message from the VIVO Contact Form

Thanks for the info –

Will pass this info along.

By the way, I have since learned that an ORCID was not a requirement of a publisher, but a requirement of the USGS –

One of our scientists was a co-author on a USGS paper.

Since we do not have ORCID for our FS researchers, the USGS dropped the requirement for non-USGS co-authors.

By the way, I do like the sound of “Dr. Jessel,” but I’m only a post-masters’ researcher right now, MSIS. 

Perhaps one day, though!


From: Marsh, Emily
Sent: Tuesday, December 20, 2016 2:13 PM
To: Jessel, Tanner – FS <tjessel>
Subject: RE: Message from the VIVO Contact Form


Hello Dr. Jessel:

Thank you for your interest in VIVO.

At this time, the USDA VIVO instance is not equipped for integration with ORCID identifiers. The implementation of new features is on hold until ARS can determine in what direction it wants the project to proceed.

We will keep your observation in mind when the project can more forward again.

Thanks again, Emily

Emily Marsh, Ph.D., MLS

Librarian | Digital Library Branch

National Agricultural Library

From: Tanner Jessel [mailto:tjessel]
Sent: Tuesday, December 20, 2016 4:32 PM
Subject: Message from the VIVO Contact Form

Message from the VIVO Contact Form

From: Tanner Jessel

Email Address: tjessel

IP address:

Comments: Hi, I’m a researcher in science communications with USDA FS Research and Development, Pacific Northwest Research Station, Communications and Applications Group. We have a researcher who is being required to register for an Open Researcher and Contributor ID (ORCID) as a condition of submitting a manuscript for publication to a scientific journal. I understand that VIVO can be integrated with ORCID. If it has not been done already, I am wondering if it is possible for you to integrate ORCID with USDA VIVO so that our researchers will have an ORCID that is linked to USDA Vivo. Instructions here: If it has already been done, can you advise on how our scientist might obtain her VIVO-linked ORCID? Thanks, Tanner

Thoughts on Importance of Online Portfolio Building

Hi Dr. Bishop and Prof. Dodsworth:

I have a postcard in the mail informing me that a selection has been made for GIS Stormwater Administrator that I applied and interviewed for (it wasn’t me).

In a lot of ways, it was a GIS librarian position; they needed traditional GIS analysis skills but also data management and data curation skills, along with education and outreach skills.

There were 20 well qualified applicants and I think it reflects well on SIS that I even got an interview.

However, in reflection I feel I should have brought printouts of work I have done to provide concrete evidence in response to the question, “how are your map making skills.”  I’ve been told to bring along examples to interviews in my geography classes – I’m not sure why I didn’t do that for this interview.

The next best thing to a printed map would be a robust online portfolio.  To be honest I’ve made tons of nice maps in my GIS classes, but getting the labs done is so mentally draining that I rarely re-visit them to present in an online portfolio.

I’m trying to do a better job about getting my work online.

However, I wanted to encourage you both as GIS instructors to try and build creating an online portfolio into your coursework.

I saw this example from the graduate certificate program I’m getting into at UWF –

In sum, I think it would be very helpful for students to have a GIS online portfolio as part of the normal coursework.



Blacklight UI for PostgreSQL and Solr – Google Group Discussion

A discussion thread I started in January, 2014:!topic/blacklight-development/Ax0840hBeUA


I’ve poked around a bit and did not see anything about support for geospatial search.
I became interested in Blacklight after visiting the Environment Australia Web site.
Their site is built on PostgreSQL relational database, and since it pertains to the environment, I thought they might have spatially explicit data.
They do have “Search by Region,” but it is just a linked list of regions.
Thanks for any tips,

I got a few responses asking for more information and potential use cases so I added (in July 2014):

My opinion is any geographic representation of a collection constitutes value-added.

I am interested building a functional SKOS ontology based on the relationships between EPA ecological regions and protected areas of the United States. There are a few hierarchical levels which the ontology could describe. There are also relationships between protected areas and each ecological region.

For example, Great Smoky Mountains National Park on the North Carolina and Tennessee belongs to two main ecological regions: Ridge and Valley (67) ,and Blue Ridge (66). A full accounting of Level III ecological regions is available at <>.

The Level III ecological regions can be further divided into Level IV ecoregions, a higher level of granularity, available at <>.

Using the Smokies again as the exemplar, new ecological sub-regions at the Level IV resolution emerge: High mountains (66i), Southern sedimentary ridges (66e), Limestome Valleys and Coves (66f), Southern Metasedimentary mountains (66g), Broad basins (66j), and Southern Dissected Ridges and Knobs (67i), Southern sandstone ridges (67h), Southern Shale Valley (67g).

These regions can be linked via an ontology to other protected areas, allowing environmental information resources to be grouped based on meaningful ecological relationships. For example, a search in an information retrieval system for “High Mountains (66i)” would retrieve results from relevant protected areas: Roane Mountain State Park, Pisgah National Forest, Cherokee National Forest, AND Great Smoky Mountains National Park, and perhaps any location built in to the ontology as a member of the given ecological region’s footprint. This represents a sophisticated query with minimal effort on behalf of the user.

Along with providing a framework for information retrieval via “regions” as the Australia site does, the ontology would have useful text mining and automated spatial metadata creation applications.

Potential use cases include:

I wanted to do a Masters thesis on the impact of an ontology on search and retrieval, but after discussing with my thesis coordinator who indicated this was more of a PhD level undertaking, I opted to instead pursue comprehensive exams as my exit strategy.

I still think this is a worthwhile area of research and I am happy to see the example you have shared, and that there are others interested in the topic.

Vascular Plants in ATBI Database Suitable for MaxEnt SDM Modeling

This afternoon I have established a few facts concerning plants in the Smokies.

The ATBI database (available to me on public server) has 432 vascular plant species for which there are 30 or more occurrence records.

This is out of 2001 entries – although the ATBI database reports “1643 species” for subkingdom Tracheobionta. So, 432/2001 is about 21% species that have 30 or more records.

The SEElab already has maps for 225 plant species. (SeeLab-Plants-Mod)

I combined the SEElab plant list (n=225) with the ATBI vascular plants list of more than 30 records (n=432), then filtered for unique records based on scientific name.

This yielded a total of 257 scientific names, suggesting there are 257 plant species from the ATBI database that have NOT been modeled by SEElab.

I have attached this data in the .csv file, “Vasc-Plant-Unique.” Perhaps this is the roughly 257 species Keith Langdon mentioned to me on the phone?

I don’t yet have access to the Nautilus supercomputer so initial runs would need to be done on a PC. I can make my documentation for running individual models on a PC by doing these first runs.

With the refined list of ~257 plant species, is there a preference for particular species or species assemblages?

If there is no preference for a particular plant species (out of those that have the requisite number of 30 or more records) I could just do some species modelling for Hemlock forests, as there is literature available for me to reference and it is interesting to look at potential community impacts from the HWA.

I’m having some trouble forwarding the .csv file to NPS staff (filtering, probably a security risk).

And, WordPress is not letting me upload any file other than a Microsoft .xls file. This is poor data management practice; I should archive a plain text or .csv file. So, my solution for the time being is that I believe I will paste the plain text here:

Saving the file on my local machine:


RecordNo,Kingdom,Class,Order,Family,Taxon,……,Data……………….,Type,Common Name 13413,,,,,Carex brunnescens sphaerostachya,,38,Specimens,Few flowered sedge 13432,,,,,Carex debilis variety,,75,Specimens, 13433,,,,,Carex digitalis,,43,Specimens,sedge 13449,,,,,Carex prasina,,30,Specimens,Drooping sedge 13456,,,,,Carex scabrata,,31,Specimens,Rough sedge 13460,,,,,Carex species,,291,Specimens, 13464,,,,,Carex swanii,,38,Specimens,Swan’s sedge 13471,,,,,Carex virescens,,31,Specimens,sedge 13513,,,,,Agrostis perennans,,42,Specimens,Upland bent 13522,,,,,Andropogon species,,71,Specimens, 13608,,,Ophioglossales,Ophioglossaceae,Botrychium biternatum,,58,Specimens,Southern grape fern 13610,,,,,Botrychium dissectum v. dissectum,,978,Specimens,”Cutleaf grapefern, dissectum” 13611,,,,,Botrychium dissectum v. obliquum,,155,Specimens,”Cutleaf grapefern, obliquum” 13617,,,,,Botrychium species,,38,Specimens, 13625,,,,,Asplenium rhizophyllum,,110,Specimens,Walking-fern spleenwort 13628,,,,,Asplenium trichomanes,,43,Specimens,Maiden-hair spleenwort 13630,,,,Blechnaceae,Woodwardia areolata,,126,Specimens,Netted chain fern 13633,,,,,Pteridium aquilinum,,1058,Specimens,Bracken fern 13634,,,,,Pteridium aquilinum subspecies,,78,Specimens, 13637,,,,,Pteridium aquilinum variety,,89,Specimens, 13638,,,,Dryopteridaceae,Athyrium asplenioides,,64,Specimens, 13639,,,,,Athyrium filix-femina angustum,,306,Specimens,Small northern lady fern 13640,,,,,Athyrium filix-femina asplenioides,,10129,Specimens,Southern lady fern 13648,,,,,Diplazium pycnocarpon,,66,Specimens,Glade fern 13652,,,,,Dryopteris cristata,,401,Specimens,”Crested wood fern,” 13656,,,,,Dryopteris species,,83,Specimens, 13658,,,,,Onoclea sensibilis,,43,Specimens,Sensitive fern 13665,,,,,Osmunda claytoniana,,42,Specimens,Interrupted fern 13666,,,,,Osmunda regalis,,66,Specimens,Royal fern 13669,,,,Polypodiaceae,Pleopeltis polypodioides,,63,Specimens,Resurrection fern 13671,,,,,Polypodium appalachianum,,3307,Specimens, 13768,,,,,Arisaema triphyllum triphyllum,,76,Specimens, 13772,,,Commelinales,Commelinaceae,Commelina communis,,39,Specimens,Common dayflower 13779,,,,,Tradescantia subaspera,,35,Specimens,Spiderwort 13788,,,,,Carex intumescens,,44,Specimens,Intumescent sedge 13794,,,,,Carex laxiflora v. laxiflora,,36,Specimens, 13802,,,,,Carex lurida,,30,Specimens,smaller hop sedge 13805,,,,,Carex nigromarginata,,42,Specimens,Black-margined sedge 13814,,,,,Arundinaria gigantea,,42,Specimens,Cane 13835,,,,,Spiranthes cernua,,38,Specimens,Nodding lady’s tresses 13839,,,,,Spiranthes species,,103,Specimens, 13843,,,,,Triphora trianthophora,,73,Specimens,Nodding Pogonia 13844,,,Liliales,Liliaceae,Trillium undulatum,,85,Specimens,Painted Trillium 13845,,,,,Trillium vaseyi,,35,Specimens,Vasey`s trillium 13863,,,,,Smilax species,,57,Specimens, 13876,,,,,Cypripedium acaule,,37,Specimens,Pink lady’s slipper 13881,,,,Typhaceae,Typha latifolia,,81,Specimens,wideleaf cattail 13887,,,,,Huperzia lucidula,,4103,Specimens,shining Club-moss 13908,,,,,Chaerophyllum tainturieri v. tainturieri,,10010,Specimens,wild chervil 13910,,,,,Cryptotaenia canadensis,,43,Specimens,Honewort 13924,,,,,Sanicula canadensis v. canadensis,,125,Specimens,Canada black snakeroot 13928,,,,,Sanicula smallii,,35,Specimens,small’s black snakeroot 13929,,,,,Sanicula species,,47,Specimens, 13931,,,,,Taenidia integerrima,,31,Specimens,Yellow pimpernel 13932,,,,,Thaspium barbinode,,30,Specimens,meadow-parsnip 13939,,,,,Cinna latifolia,,37,Specimens,woodreed 13944,,,,,Danthonia species,,44,Specimens, 13945,,,,,Danthonia spicata,,35,Specimens,Poverty grass 13950,,,,,Dichanthelium clandestinum,,41,Specimens,Deer-tongue witchgrass 13953,,,,,Dichanthelium dichotomum v. dichotomum,,36,Specimens, 13963,,,,,Dichanthelium species,,96,Specimens, 13976,,,,,Elymus riparius,,105,Specimens,wild rye 13993,,,,,Festuca subverticillata,,31,Specimens,Sheep`s-fescue 13995,,,,,Glyceria nubigena,,123,Specimens,Smoky Mountain Mannagrass 14003,,,,,Lolium arundinaceum,,76,Specimens, 14014,,,,,Muhlenbergia tenuiflora,,43,Specimens,Muhly 14026,,,,,Panicum species,,192,Specimens, 14042,,,,,Poa alsodes,,38,Specimens,wood bluegrass 14052,,,,,Poa species,,47,Specimens, 14055,,,,,Poaceae_genus species,,110,Specimens, 14058,,,,,Schizachyrium scoparium v. scoparium,,167,Specimens, 14087,,,,,Juncus effusus solutus,,37,Specimens,Soft rush 14093,,,,,Juncus tenuis,,103,Specimens,Larger path rush 14099,,,,,Luzula acuminata variety,,34,Specimens, 14110,,,,,Dioscorea quaternata,,221,Specimens,wild yam 14112,,,,,Dioscorea villosa,,47,Specimens, 14131,,,,,Allium tricoccum,,35,Specimens,”Ramps, wild leeks” 14135,,,,,Chamaelirium luteum,,50,Specimens,Fairy wand 14148,,,,,Erythronium umbilicatum umbilicatum,,154,Specimens, 14154,,,,,Lilium michauxii,,43,Specimens,Carolina lily 14157,,,,,Lilium superbum,,157,Specimens,Turk’s cap lily 14161,,,,,Maianthemum racemosum racemosum,,1292,Specimens, 14173,,,,,Polygonatum biflorum v. biflorum,,40,Specimens,Great Solomon’s seal 14175,,,,,Polygonatum biflorum variety,,126,Specimens, 14177,,,,,Polygonatum pubescens,,123,Specimens,hairy Solomon’s seal 14188,,,,,Trillium catesbaei,,78,Specimens,catesby’s trillium 14190,,,,,Trillium erectum,,122,Specimens,Wake robin 14191,,,,,Trillium grandiflorum,,34,Specimens,white trillium 14195,,,,,Trillium species,,80,Specimens, 14200,,,,,Galearis spectabilis,,58,Specimens,Showy orchis 14201,,,,,Goodyera pubescens,,292,Specimens,Downy rattlesnake-plantain 14202,,,,,Goodyera repens,,89,Specimens,Lesser rattlesnake-plantain 14285,,,Fagales,Betulaceae,Alnus serrulata,,111,Specimens,Common alder 14288,,,,,Thaspium trifoliatum variety,,45,Specimens, 14295,,,,,Aralia racemosa,,33,Specimens,wild spikenard 14297,,,,,Aralia spinosa,,53,Specimens,Devil’s walking stick 14298,,,,,Hedera helix,,402,Specimens,English Ivy 14299,,,,,Panax quinquefolius,,88,Specimens,Ginseng 14307,,,,,Hexastylis arifolia v. arifolia,,70,Specimens,Little brown jugs 14314,,,,,Ageratina altissima v. altissima,,119,Specimens,white snakeroot 14315,,,,,Ageratina altissima v. roanensis,,69,Specimens, 14321,,,,,Antennaria plantaginifolia,,46,Specimens,Plantain-leaved pussy toes 14335,,,,,Aster cordifolius,,44,Specimens, 14353,,,,,Aster species,,45,Specimens, 14359,,,,,Asteraceae_genus species,,137,Specimens,Aster family species 14366,,,,,Cacalia atriplicifolia,,33,Specimens, 14374,,,,,Chrysopsis mariana,,36,Specimens,Maryland golden aster 14387,,,,,Coreopsis major variety,,129,Specimens,wood Tickseed 14403,,,,,Erigeron pulchellus v. pulchellus,,33,Specimens,Robin’s-plantain 14406,,,,,Eupatorium album,,59,Specimens,white eupatorium 14409,,,,,Eupatorium fistulosum,,33,Specimens,Joe-Pye-weed 14411,,,,,Eupatorium maculatum,,32,Specimens,Joe-Pye-weed 14414,,,,,Eupatorium rotundifolium,,41,Specimens,Round-leaved snake-root 14418,,,,,Eupatorium species,,60,Specimens, 14424,,,,,Eurybia surculosa,,33,Specimens,Recurved aster 14426,,,,,Eutrochium purpureum v. pupureum,,42,Specimens, 14430,,,,,Gamochaeta purpureum,,33,Specimens,Purple Cudweed 14459,,,,,Iva annua,,153,Specimens,Iva 14469,,,,,Lactuca species,,32,Specimens, 14486,,,,,Polymnia laevigata,,2000,Specimens,Tennessee Leafcup 14492,,,,,Prenanthes species,,236,Specimens, 14493,,,,,Prenanthes trifoliolata,,36,Specimens,Lion’s foot 14506,,,,,Rugelia nudicaulis,,165,Specimens, 14508,,,,,Senecio anonymus,,43,Specimens,Yellow ragwort 14521,,,,,Solidago altissima v. altissima,,44,Specimens, 14523,,,,,Solidago arguta variety,,36,Specimens,Sharp-leaved goldenrod 14525,,,,,Solidago caesia,,42,Specimens,Curtis goldenrod 14546,,,,,Solidago species,,276,Specimens, 14547,,,,,Solidago speciosa v. rigidiuscula,,53,Specimens, 14552,,,,,Symphyotrichum concolor,,53,Specimens, 14570,,,,,Verbesina alternifolia,,57,Specimens,wingstem 14571,,,,,Verbesina occidentalis,,41,Specimens,wingstem 14582,,,,,Campanulastrum americanum,,33,Specimens, 14583,,,,,Lobelia cardinalis,,34,Specimens,Cardinal Flower 14584,,,,,Lobelia inflata,,68,Specimens,Indian tabacco 14595,,,Fagales,Fagaceae,Quercus montana,,408,Specimens,chestnut oak 14596,,,,,Quercus muehlenbergii,,31,Specimens,Yellow oak 14600,,,,,Quercus species,,72,Specimens, 14601,,,,,Quercus stellata,,39,Specimens,Post oak 14634,,,Geraniales,Balsaminaceae,Impatiens capensis,,71,Specimens,”Orange jewelweed, touch-me-not” 14636,,,,,Impatiens species,,44,Specimens, 14641,,,,,Geranium maculatum,,86,Specimens,wild geranium 14649,,,,,Oxalis stricta,,31,Specimens,Yellow wood-sorrel 14679,,,,,Silene virginica,,59,Specimens,Fire Pink 14682,,,,,Stellaria corei,,30,Specimens,Core’s chickweed 14700,,,Celastrales,Aquifoliaceae,Ilex ambigua,,36,Specimens, 14704,,,,,Ilex opaca v. opaca,,455,Specimens,American holly 14711,,,,,Euonymus americanus,,252,Specimens,American strawberry-bush 14718,,,,,Cornus amomum,,50,Specimens,Silky Dogwood 14721,,,,,Cornus species,,58,Specimens, 14724,,,,,Galax urceolata,,307,Specimens, 14726,,,,,Diervilla sessilifolia,,33,Specimens,Sessile-leaved bush-honey-suck 14731,,,,,Lonicera japonica,,45,Specimens,Japanese Honeysuckle 14744,,,,,Sambucus racemosa v. racemosa,,49,Specimens, 14755,,,,,Viburnum nudum v. cassinoides,,41,Specimens,wild raisin 14783,,,,,Lyonia ligustrina v. ligustrina,,73,Specimens,Maleberry 14788,,,,,Rhododendron calendulaceum,,335,Specimens,Flame Azalea 14793,,,,,Rhododendron minus,,1134,Specimens,small-leaved rhododendron 14798,,,,,Rhododendron species,,2610,Specimens, 14801,,,,,Vaccinium arboreum,,54,Specimens,Sparkleberry 14809,,,,,Vaccinium simulatum,,58,Specimens, 14810,,,,,Vaccinium species,,63,Specimens, 14817,,,,,Monotropa uniflora,,99,Specimens,Indian pipe 14848,,,,,Cercis canadensis v. canadensis,,242,Specimens,redbud 14851,,,,,Cladrastis kentukea,,202,Specimens,Yellowwood 14869,,,,,Desmodium species,,45,Specimens, 14874,,,,,Gleditsia triacanthos,,58,Specimens,Honeylocust 14883,,,,,Lespedeza cuneata,,160,Specimens,Cuneate bush-clover 14884,,,,,Lespedeza hirta,,37,Specimens,hairy Bush-clover 14888,,,,,Lespedeza species,,60,Specimens, 14906,,,Fagales,Betulaceae,Betula alleghaniensis v. alleghaniensis,,65,Specimens, 14909,,,,,Betula lutea,,32,Specimens,Yellow Birch 14910,,,,,Betula nigra,,44,Specimens,River Birch 14912,,,,,Betula species,,231,Specimens, 14918,,,,,Vitis species,,126,Specimens, 14937,,,,,Hydrangea radiata,,96,Specimens,white-leaf hydrangea 14940,,,,,Philadelphus hirsutus,,118,Specimens,small-flowered hairy mock-orange 14952,,,,,Amelanchier species,,116,Specimens, 14953,,,,,Amelanchier stolonifera,,36,Specimens,Running serviceberry 14958,,,,,Aruncus dioicus,,39,Specimens,Goats beard 14971,,,,,Crataegus species,,56,Specimens, 14980,,,,,Phacelia dubia v. dubia,,203,Specimens,small-flowered phacelia 14998,,,,Fagaceae,Castanea dentata,,868,Specimens,American chestnut 15006,,,,,Quercus imbricaria,,92,Specimens,shingle oak 15021,,,,,Carya ovata,,41,Specimens,Shagbark hickory 15023,,,,,Carya species,,184,Specimens, 15025,,,,,Juglans cinerea,,313,Specimens,butternut 15028,,,Lamiales,Boraginaceae,Cynoglossum virginianum v. virginianum,,45,Specimens,wild comfrey 15057,,,,,Lycopus virginicus,,31,Specimens,Virginia water-horehound 15079,,,,,Pycnanthemum species,,49,Specimens, 15081,,,,,Salvia lyrata,,31,Specimens,Lyre-leaved sage 15093,,,,,Stachys nuttallii,,61,Specimens, 15111,,,,,Calycanthus floridus v. glaucus,,67,Specimens, 15112,,,,,Calycanthus floridus variety,,195,Specimens,Sweetshrub 15114,,,,Lauraceae,Lindera.Plantae benzoin,,209,Specimens,Spicebush 15118,,,Magnoliales,Annonaceae,Asimina triloba,,82,Specimens,Paw-paw 15131,,,,Tiliaceae,Tilia americana v. americana,,118,Specimens,American basswood 15132,,,,,Tilia americana v. heterophylla,,789,Specimens,white Basswood 15133,,,,,Tilia americana variety,,178,Specimens, 15134,,,,,Tilia species,,94,Specimens,Basswood species 15143,,,,Onagraceae,Circaea alpina alpina,,47,Specimens, 15163,,,,Thymelaceae,Dirca palustris,,105,Specimens, 15174,,,,Papaveraceae,Sanguinaria canadensis,,91,Specimens,Bloodroot 15177,,,,,Plantago major,,86,Specimens,Plantain 15211,,,,,Polygonum sagittatum,,33,Specimens,tearthumb 15235,,,,,Caulophyllum thalictroides,,129,Specimens,Blue cohosh 15239,,,,,Podophyllum peltatum,,48,Specimens,May-apple 15246,,,,,Actaea podocarpa,,40,Specimens, 15248,,,,,Actaea racemosa v. racemosa,,117,Specimens, 15255,,,,,Cimicifuga racemosa,,31,Specimens, 15265,,,,,Hepatica nobilis v. acuta,,46,Specimens,Round-lobed hepatica 15275,,,,,Ranunculus hispidus,,34,Specimens,Carolina buttercup 15282,,,,,Thalictrum clavatum,,37,Specimens,Brook meadowrue 15290,,,,,Thalictrum species,,31,Specimens, 15309,,,Theales,Theaceae,Stewartia ovata,,32,Specimens,Mountain stewartia 15314,,,,,Morus rubra,,107,Specimens,red Mulberry 15319,,,,,Ulmus alata,,37,Specimens,winged elm 15320,,,,,Ulmus americana,,156,Specimens,American elm 15326,,,,,Pilea pumila,,35,Specimens,”Richweed, clearweed” 15336,,,,,Passiflora lutea,,44,Specimens,Yellow passion-flower 15338,,,,Violaceae,Hybanthus concolor,,62,Specimens,green violet 15342,,,,,Viola canadensis v. canadensis,,673,Specimens,Canadian violet 15344,,,,,Viola cucullata,,453,Specimens,Marsh blue violet 15346,,,,,Viola hirsutula,,238,Specimens,Southern wood violet 15348,,,,,Viola labradorica,,784,Specimens, 15349,,,,,Viola lanceolata,,200,Specimens,Lance-leaved violet 15352,,,,,Viola palmata,,85,Specimens,Three-lobed violet 15353,,,,,Viola pedata,,145,Specimens,Birds foot violet 15357,,,,,Geum canadense,,33,Specimens,white Avens 15373,,,,,Physocarpus opulifolius v. opulifolius,,30,Specimens,Ninebark 15382,,,,,Prunus americana,,42,Specimens,wild plum 15391,,,,,Prunus serotina v. serotina,,1257,Specimens,Black cherry 15413,,,,,Rubus flagellaris,,40,Specimens,Northern Dewberry 15419,,,,,Rubus phoenicolasius,,93,Specimens,wineberry 15420,,,,,Rubus species,,430,Specimens, 15430,,,,Saxifragaceae,Astilbe biternata,,38,Specimens,false goats beard 15433,,,,,Heuchera americana,,38,Specimens,Alumroot 15442,,,,,Mitella diphylla,,41,Specimens,Bishops cap 15443,,,,,Parnassia asarifolia,,108,Specimens,grass-of-Parnassus 15449,,,,,Tiarella cordifolia,,233,Specimens, 15459,,,,,Galium circaezans v. circaezans,,76,Specimens,wild Licorice 15465,,,,,Galium pilosum variety,,30,Specimens, 15466,,,,,Galium species,,75,Specimens, 15474,,,,,Houstonia purpurea v. purpurea,,65,Specimens,woodland bluets 15475,,,,,Houstonia purpurea variety,,97,Specimens, 15480,,,,,Mitchella repens,,359,Specimens,Partridgeberry 15493,,,,,Salix nigra,,52,Specimens,Black willow 15494,,,,,Salix sericea,,39,Specimens,Silky willow 15498,,,,,Phoradendron leucarpum,,55,Specimens, 15501,,,,,Acer negundo,,41,Specimens,Box-elder 15506,,,,,Acer rubrum v. rubrum,,92,Specimens,Trident maple 15508,,,,,Acer rubrum variety,,9526,Specimens, 15516,,,,,Rhus copallinum variety,,102,Specimens, 15517,,,,,Rhus glabra,,34,Specimens,Smooth Sumac 15521,,,,,Toxicodendron radicans radicans,,274,Specimens,Poison ivy 15529,,,,Simaroubaceae,Ailanthus altissima,,37,Specimens,tree-Of-Heaven


Presentation – Geocoding in Geographic Information Retrieval Systems

I presented this paper at the Geographic Information Systems II (GIS II) session at the 2014 Geography Symposium (See UT Geography Symposium Program 2014)

I represented The University of Tennessee School of Information Sciences at this interdisciplinary conference themed “Mapping outside the lines: Geography as a nexus for interdisciplinary and collaborative research.”

Tanner Jessel, School of Information Sciences, University of Tennessee. “Geocoding in Geographic Information Retrieval Systems.”

Information with a geographic component is among the most valuable and sought after types of information. However, the majority of geographical information exists as indirectly referenced locational information within unstructured text. Even among well-annotated, spatially explicit datasets, existing metadata can be of sparse, inconsistent, or otherwise of poor quality due to time and budgetary constraints. For these reasons, automated annotation of spatially explicit coordinates, a process known as geocoding, is an active area of research in geographic infor- mation science. Research concerning geocoding represents a long-term effort with a body of knowledge that has grown across several decades. Unfortunately, funding cycles are not always long-term, and some groundbreaking technologies and tools are no longer available. The present article attempts to synthesize the current state-of-the art of geocoding and presents a “toolkit” of resources used across the literature to accomplish geocoding, with an emphasis on applications for geographic information retrieval.

Big Data and Environmental Information

Environmental information gathered by modern computational methods has all the hallmarks of “Big Data” including volume, variety, and velocity. This includes information collected by remote sensing from earth observing satellites, information collected by terrestrial, freshwater, and marine sensor networks, and data collected with portable devices such as radio telemetry or global positioning satellite transponders. Even small animals can be paired with “passive integrated transponders” that transform an organism into a data point – and tissue samples and specimens can be taken back to the lab, herbarium, or other natural history collection, with further analysis and data generation and curation done at the molecular and genetic level.

The volume of data available to be collected from the environment approaches infinity, with complex edges like a fractal.  In fact, the National Ecological Observation Network states the defining characteristic of ecological data is complexity.  The complex interactions between elements of the environment, such as distributions of species, interactions between species, and interactions between biotic and abiotic factors, generate a wealth of data points.  A February 3, 2014 article entitled “Ecologists urged to avail themselves of big data in studies” suggests advances in data science and computational methods require a new generation of ecologists  who can work with “big datasets at large scale” to mesh together both large and small datasets to better understand the complex dynamics of the natural world.

An adage in the wildlife biology field is to “know your stats and know your critters.” However, a 2012 paper by Strasser and Hampton concerning undergraduate training in data management for ecology students suggests that knowledge of data management tools and methods is lacking in undergraduate curriculum.  At the University of Tennessee, students of the Environmental Studies Program are encouraged to take an “Environmental Information Science” course available through the College of Communication’s undergraduate minor in Information Science and Technology.  Graduate level training is available from the University of New Mexico’s Environmental Information Management Institute, and the University of Tennessee offers a course in “Environmental Informatics.”

These course offerings are needed. In addition to “knowing the stats” and “knowing the critters,” students of ecology are increasingly expected to work with large datasets.  Further, working with data that has already been collected is in fact less costly than collecting new data. Collected data becomes increasingly valuable, and personnel who can effectively manage and safeguard the investment in research effort offer a new skillset to the field of ecology beyond skills in quantitative analysis or biology.  In “The Age of Big Data,” Steve Lohr wrote that the U.S. would need shy of 200,000 workers with skill in data analysis, and 1.5 million well versed in data management.

The need for data literacy in the environmental domain is underscored by the variety of applications, what the President’s Council of Advisors for Science and Technology in 2011 called “extreme heterogeneity of the data.” Along with remote-sensed data and ongoing field collection of data, museum collections hold millions of specimens.  Many sites are in the process of digitizing their holdings for greater access.  The U.S. Geological Survey’s Biological Information Serving Our Nation Program provides federated access to over 256 museum and herbarium collections, for a total of over 100 million occurrence records.  Taken together, these records can provide new opportunities for inquiry in biodiversity science:  with increased data access comes increased opportunities to conduct data-driven investigations.

The extreme volume, variety, and velocity of data necessitates a suite of tools to collect, curate, and visualize environmental information.  Professional organizations such as Earth Science Information Providers or the Organization for Fish and Wildlife Information Managers or DataONE Users Group offer continual training in data management.  Tutorials and methods abound on the Web.

A basic problem for any data scientist working with ecological data might be to curate his or her own collection of tools.  DataONE addressed this by creating an online database of tools and software, which contains several hundred examples of computer tools that range across the data life cycle, from planning, to collecting, assuring quality, describing, preserving, discovering, integrating, and analyzing.  The database includes brief descriptions and a rudimentary controlled vocabulary.  It is searchable.  Unfortunately the end user cannot modify the database and is forced to rely on website manager to update the site in case of expired links, and the end user cannot add new tools that emerge.

Here, a solution is proposed by integrating the database into a collection of online bookmarks, and expanding on the collection with new tools and best practices.  Categories closely follow the DataONE Tools and Software Database, and include the following: Biodiversity, Databases, GIS, Metadata, Repository, Visualization. As the material is available online, feeds are presented in Table 1.


Table 1. XML Feeds of Annotated Bibliography    

Note: PDF version of Assignment 1 online:  IS-592-ASSN1-JesselT

Related presentation in “Big Data in Ecology: Volume, Variety and Velocity in Environmental Information.

Identifying Library & Information Science Graduate Student Competencies

Hi Dr. Mehra,

I read in the latest issue of Interface with interest:

His article co-authored with Dr. Vandana Singh entitled “Strengths and weaknesses of the information technology curriculum in library and information science graduate programs” has been published in the Journal of Librarianship and Information Science, 45(3).

The idea of matching course content with employer expectations has interested me since starting at SIS.

Personally I have taken a variety of courses outside SIS / CCI to develop the skillset I need for my own career goal as a professional data manager working with environmental data.

In reading your paper, I was particularly interested in your methods concerning the WebJunction competencies available online at <>.

For future research, I would like to suggest collecting job descriptions from job listings to synthesize employer expectations, as opposed to lists of competencies put together by any single organization. I’ve noticed job listings often have "required" and "desirable" qualifications.

My guess is this approach would yield an interdisciplinary, "state of the art" view expanding on WebJunction’s competencies focused on libraries. This approach might also impact your final recommendations, which I was disappointed to see did not include computer programming proficiency. Programming and data visualization skills frequently appear in job listings for my specific realm of interest, which is one reason I and two other SIS students in my cohort are taking "Introduction to Programming for Scientists and Engineers" in the College of Engineering in the Spring 2014 Semester, along with free online courses in programming. I do not believe that computer programming skills for data management tasks like quality assurance / quality control are skills that can presently be acquired through SIS or CCI coursework, which poses a problem for accumulating skills for the workplace while also accumulating credits towards the major.

Expanding on the e-portfolio concept, I recently began a tumblr blog to capture job listings that interest me. Along with tips on developing IT skills, I cut out the "qualifications" section for jobs I can imagine myself enjoying. This keeps me focused on developing the skills I need for work I would enjoy. The result is my "Data Pro" tumblr:

You might be able to do something similar (collect and analyze minimal / desired qualifications) for job listings from sources like,, or other appropriate job boards. I think this approach would be particularly valuable for building curriculum pertaining to information management for STEM fields.

Anyway I am glad you and Dr. Singh are looking at this issue in LIS education. I hope your research will help SIS continue to develop curriculum that keeps pace with what prospective employers need.



Tanner Jessel
Graduate Research Assistant:
Data Observation Network for Earth (DataONE)

Center for Information and Communication Studies
The University of Tennessee
Mail: 1345 Circle Park Drive, Suite 420

GIS Training / ESRI Online Courses of Interest

With the upcoming winter break, I noticed UT offers some self-paced virtual training and has a course list online at <>

Looking over the courses offered, I noticed a few I’m interested in that could be useful for my career goals as a data manager for a natural resources organization.

I’m not sure how long each module would take, but I would like to work on a few over the break if it’s possible to work on several in one month.

I saw that course codes are needed and the instructions are to contact the Geospatial Data Librarian.

ESRI Training Courses of Interest:

Basics of the Geodatabase Data Model

Getting Started with the Geodatabase

Archiving Data in a Multiuser Geodatabase

Creating and Editing Geodatabase Features with ArcGIS Desktop (for ArcEditor and ArcInfo)

Creating and Integrating Data for Natural Resource Applications

Basics of Python (for ArcGIS 10)

Python Scripting for Geoprocessing Workflows (for ArcGIS 10)

I’m also not sure how many of these are identical to modules in other ESRI resources, like the GIS workbooks or ArcGIS 10.1 tutorial CDs. However, my home computer does not have an optical drive, so it would be useful to download data directly even if the data is identical to what is found on the CDs.

Role of Dataset in Scholarly Publishing – Final Paper Feedback

From: Tenopir, Carol
Date: Fri, Aug 9, 2013 at 6:53 PM
Subject: RE: Jessel IS590 Research Paper
To: Tanner Jessel

Tanner: Attached is your final paper with my comments and your grade on the paper. Below is a summary of your grades for each assignment and final grade. I had a great time with you all in London and enjoyed reading your journals and papers. Have a good fall semester!

· Attendance and participation – (25%) Grade: A. We appreciated your insights and active questions throughout the two week experience. You added a lot to the course.

· Daily Journal –(25%) I loved your blog entries! Hope you follow up on some of the things you’ve made notes on, for example looking into Scielo some more and following up with some of the folks you met.

· Course Paper – (50%) Grade: A see comments on paper

Final Grade in Course: A. Great work!

Carol Tenopir
Chancellor’s Professor, School of Information Sciences
Director of Research and Director of the
Center for Information and Communication Studies
College of Communication and Information
University of Tennessee
1340 Circle Park Drive, 423 Communications Bldg
Knoxville, TN 37996-0341
Office: 865 9747911


Knoxville REI “Flagship Presence” Proposed for Standard Knitting Mill Site

Here is an e-mail I sent to REI – South retail director Gail Kirkland.  The original e-mail contained hyperlinks – I’ve added a few here as well.  Also – I quoted 20 miles as the total mileage for the Urban Wilderness.  I was wrong – it’s over 40 miles of trail just outside downtown Knoxville.

From: Tanner Jessel
Date: Sat, Aug 17, 2013 at 4:14 PM
Subject: Re: Knoxville location
To: Gail Kirkland
Cc: Madeline Rogero, Nick Della Volpe

Hello Gail,

Thanks for taking the time to write on a weekend.

I realize you are busy so I appreciate it.

I’m a fan of spatial data analysis so I appreciate your reasons for choosing Papermill Plaza. But I think Knoxville is a place that has some other variables at play that may not have appeared in your analysis – and I’d appreciate your considering an idea I had for REI.

The reason I wanted to talk to you is I admire REI for restoring historic properties like the Old Mill in Bend Oregon and Traction Powerhouse in Denver.

I think a similar opportunity exists in Knoxville at the former Standard Knitting Mill – a historic textile mill built in the 40s that earned Knoxville the title “the underwear capital of the world.”

Today, Knoxville’s trying to establish itself as an outdoor recreation mecca with urban trails and corridors including an “urban wildernesss“- a network of trails totaling 20 miles on 1,000 acres just across the river from downtown.

Apart from being a 10 minute drive further east for the lucrative West Knoxville market, the knitting mill has the characteristics of Papermill Plaza – plus some unique features you may not have considered.

First, it’s on the way to the Smokies for most residents of all points West headed there. Second, it’s 20 minutes west from Bass Pro Shops and exit 407 in Sevierville. It’s easily integrated into the existing downtown Knoxville shopping scene via a free trolley system – perhaps an “Outdoor Adventure Express” linking the location to Knoxville’s Waterfront. It’s right on the greenway and creek that could one day be a blueway. It’s a short hop from the “Outdoor Knoxville Adventure Center” and University of Tennessee campus – also served by the free trolley system.

It’s big, highly visible off the interstate with two nearby interchanges, and has some development incentives as it’s in an “empowerment zone” with available tax increment financing.

It’s so big (over 400,000 square feet), you could have an indoor whitewater kayak circuit for people to test out equipment. So big you could install an indoor mountain bike course for teaching and trying out equipment, or synthetic ski slopes or climbing walls. Think of the U.S. National Whitewater Center (albeit on a smaller scale) and the mountain biking trails around the Denver store.

I know a big part of REI’s mission is education. I also know for REI and other outfitters to continue doing business – you need to engage young people and create a culture of outdoor enthusiasm to drive purchases of outdoor gear. At this space I’m suggesting for you, you have the room and amenities (greenway, urban wilderness, creek) to do a great outreach – plus the opportunity to lure visitors from exit 407 and serve as a launching point for Smokies excursions, or even guided trips into the Urban Wilderness.

Knoxville is pushing hard for this “outdoor adventure” identity and I think that local policy makers would want to support you on an idea like this. It’d just take a brand like REI to make it possible.

In conclusion I’d really like you to look at making something more than a retail experience in Knoxville- please look at making a retail destination – a regional landmark that draws people in to both the store and the outdoor lifestyle. Bass Pro shops is a real “pro” at that – their store at Exit 407 20 minutes east of Knoxville has an aquarium with indoor waterfall. I know that’s not exactly REI’s style, but you have an opportunity here to make something that is a regional destination, aligned with the City’s aspirations to be a regional outdoor recreation destination.

Thanks for hearing me out. I respect that you’re locked into a lease, but if the store does well and you’re open to having a “flagship” presence in the Knoxville area similar to your Denver “flagship” store, I believe the local membership and community would wholeheartedly – and I’ll even venture to guess financially via incentives or perhaps partnerships – support you.

I’m CC’ing Knoxville Mayor Madeline Rogero and 4th District City Councilman Nick Della Volpe on this suggestion. They are familiar with me from my work on the Greenways Commission.

Thanks again and have a great weekend,