d eveloping s ynergies b etween l arge -s cale r esearch and g eodatabases : n eotoma a nd p al eon...

DEVELOPING SYNERGIES BETWEEN LARGE-SCALE

RESEARCH AND GEODATABASES: 

NEOTOMA AND PALEONSimon Goring, John W. Williams, Eric C. Grimm, Russell W. Graham, Chris J Paciorek, Andria Dawson, Jason McLachlan,

Brian Bills, Michael Anderson

Databases:Adapt or go extinct

Image Credit: Barry Mieny

Databases aren’t just boxes

Data input is critical

So is data access

Databases aren’t just boxes

Requirements change

Dishes

Databases aren’t just boxes

Requirements change

Databases must change

DishesSheets

Databases:Adapt or go extinct

Image Credit: Barry Mieny

Debugging Expand User Support

Tool Development Modify Structure

Databases:Adapt or go extinct

Debugging

Correct & Track Data ErrorsImprove Table RelationshipsStandardize Terminology

Databases:Adapt or go extinct

Expand User Support

Facilitate Data InputImprove User InterfaceImprove Search CapabilitiesCustomize Data Outputs

Databases:Adapt or go extinct

Tool Development

Facilitate Data InputImprove Data OutputProvide Multiple Platforms

Databases:Adapt or go extinct

Modify StructureSupport for New Data-TypesImprove Metadata

Databases:Adapt or go extinct

Image Credit: Barry Mieny

Debugging Expand User Support

Tool Development Modify Structure

Neotoma Paleoecological Database

Early collaboration in paleoclimatology/paleoclimate

North American Pollen Database

COHMAP Members. 1988. Science, 241.

Early collaboration in paleoclimatology/paleoclimate

European Pollen Database

North American Pollen Database

Neotoma

FAUNMAP

Ongoing but Periodic Contribution

How do you find user needs?

◦Community development◦Ongoing review◦Ongoing development

PalEON: Paleoecological Observatory Network

PalEON

◦ PaleoEcological Observatory Network

PresentForest Inventory & AnalysisFlux TowersWater Chemistry

HistoricalPublic Land Survey

Fort Climate Data

PastPollen

DendrochronologyIsotope Data

Freidlingstein et al. 2012

PalEON

◦ PaleoEcological Observatory Network

PresentForest Inventory & AnalysisFlux TowersWater Chemistry

HistoricalPublic Land Survey

Fort Climate Data

PastPollen

DendrochronologyIsotope Data

Freidlingstein et al. 2012

Cum

ula

tive La

nd

Flux

(PgC

)

PalEON

◦ PaleoEcological Observatory Network

PresentForest Inventory & AnalysisFlux TowersWater Chemistry

HistoricalPublic Land Survey

Fort Climate Data

PastPollen

DendrochronologyIsotope Data

Freidlingstein et al. 2012

Cum

ula

tive La

nd

Flux

(PgC

)

NeotomaAdaptation

Image Credit: Barry Mieny

Debugging Add Support

Develop New Tools Modify Structure

Debugging

◦ Age – Depth Models◦ Need to characterize uncertainty◦ Geochronology data limitations◦ Age model limitations◦ Improved API outputs

NeotomaAdaptation

Image Credit: Barry Mieny

Identify CriticalDevelopment

Add Support

Develop New Tools Modify Structure

Making Connections

Neotoma

Pollen Data

Pollen Data User

Data Generators

Making Connections

Neotoma

Pollen Data

Pollen Data User

Data Generators

Data Generators

Making Connections

Neotoma PalEON

neotomahttp://github.com/ropensci/netoma

NeotomaAdaptation

Image Credit: Barry Mieny

Identify Weaknesses Add Support

Develop New Tools Modify Structure

Written by

WorkerIs#

Surface Sample

Described by

Sediment lithology

Collected from

Published on

Site

Publication

Author Collector Analyst

Responsible for Collected by

Analyzed by

Count

In

For

Pollen VariableIs also a

Synonym of

Worker

Sampled from

Pollen Sample

Contact person

Worker is

Country Phone Fax EMailAddr

Site#

PolDiv1

SiteName SiteCode SiteExists

PolDiv2 PolDiv3

Elevation

Latitude Longitude

AreaOfSite

Has info on ICode

DepthAtLoc

SampDevice

E#

DescriptorEntLoc

HasAnLam

LocalVegSampDate

C14DepthAdj

DataSource DataForm UseStatus

Var# VarCode VarName

Thickness DepthCM

Sample#

Count

Lith# Descript

DepthTopCM DepthBotCM LoBoundary

Acc# Publ#

Stratigraphic Entity

Authority for

the name

Auth#

Contact#

Analyst#

Notes

Published in

Published in

AccVar#SynType

OrderAuthor#

Coll#

Site#

Pollen Entity

HVar#

Name

YearOfPubl

Sigle

AnalyDate Citation

Worker#Status

LastNameFirstName

InitialsSuffix

Title

Address

MHVar#

Notes

IceThickCM

Divided into

Annual LaminationSegment

Annual LaminationDepth

Dated sample

Sampled from

DepthTopCM DepthBotCM

Seg#

DepthCM Sample# Thickness CountTop CountBot

Thickness

Sampled from Synchronous EventDating Sample

Event

Classified as

DepthCM Event# Name Event AgeBP AgeUncertUp AgeUncertLo

PhysiographySurroundVeg

VegFormationIGCPtype

SiteDescript

Loss-on-ignition

Sampled from

Sample# DepthCM Thickness TempLo

LOILo TempHi LOIHi BulkDens

Section Core

CoreDiamCM DepthAtLoc

Subsection

Taken for Sample# DepthCM Thickness TempLo

Drive

Taken for DriveBotCM InfTopCM InfBotCM RecoveryCM

DriveTopCM DriveLabel Drive#

Sampled from Dating SampleGeochronological

Sample#

Method DepthCM Thickness MaterialDated

USeries

TL

AAR

C14FT

KAR

ESRPB210 AgeBP

ErrorLimits LabNumber

Notes

AgeBP ErrorLimits LabNumber

AgeBP ErrorLimits LabNumber

AgeBP ErrorLimits LabNumber

AgeBP ErrorLimits GrainSize LabNumber

AgeAD

AgeSDUp AgeSDLo GrThanAge

AgeBPErrorLimits

TaxonDatedLabNumber

AgeBPAgeSDUpAgeSDLo

GrThanAge

EnrichedLabNumber

DeltaC13

Basis

Notes

NeotomaAdaptation

Image Credit: Barry Mieny

Identify Weaknesses Add Support

Develop New Tools Modify Structure

Develop New Tools

◦API Development (Neotoma Side)

◦Package Development (PalEON Side)

Goring et al. neotoma: A Programmatic Interface to the Neotoma Paleoecological Database. Open Quaternary. submitted

NeotomaAdaptation

Image Credit: Barry Mieny

Identify Weaknesses Add Support

Develop New Tools Modify Structure