Implementation of KE EMu at The New York Botanical Garden Barbara Thiers Anthony Kirchgessner...

Implementation of KE EMu at The New York Botanical Garden

Barbara ThiersAnthony Kirchgessner

Shannon DominickEmily AshleyMelissa Tulig

Specimen Cataloging at The New York Botanical Garden

Using KE Software’s Electronic Museum (EMu)

Anthony KirchgessnerBioinformatics Manager

New York Botanical Garden

NY Data in EMu

• 2003 - EMu purchased

• 2004 - Data transferred

• 2005 - New web interface completed

Goals of Herbarium Specimen Databasing

• to make specimen data available electronically for use in biodiversity research projects by NYBG staff and scientists around the world

• to reduce handling of specimens by supplying data transcription and images for uses that do not require direct examination of specimens

• to reunite data elements (e.g., photographs and drawings, manuscripts, published works, microscopic preparations, gene sequences) derived from a specimen with the catalog record for that specimen

EMu Overview

• Pulls together disparate data elements residing in many physical locations– Individual scientists’ specimen databases.

– Institutional databases (frozen DNA samples, economic botany data, pharmaceutical specimen extract data, etc.).

– Bibliographic data, including published works as well as manuscripts, letters and other unpublished artifacts.

Database Management

• Preparation of documents that standardize data entry, a procedural or best-practices document, will greatly reduce the amount of data cleanup that is necessary.

• Non-standardization of data entry can serve as an enormous strain on resources later on.

• Standardization is impressed on catalogers during a training phase.

Data Sharing

• Specimen data downloads from NYBG website.

• DiGIR-formatted data are exported from EMu, but...

• DiGIR fields within EMu would make this much easier.

Internet Access of EMu

• Specimen data now available online: http://sciweb.nybg.org/science2/VirtualHerbarium.asp

• Features include checklists, downloads of data, maps.

http://sciweb.nybg.org/science2/VirtualHerbarium.asp

Web Interface Development

• NY hired a consultant to develop the php code and database/web interface.

• Collaboration with KE staff was essential for our success.

http://sciweb.nybg.org/science2/VirtualHerbarium.asp

KE EMu Taxonomy Module

Implementation of the module and web capabilities at the New York Botanical

Garden

Shannon DominickFungi Type Specimen ProjectNew York Botanical Garden

• Nomenclatural, taxonomic data present only in as much as it is part of specimen data

• Nomenclatural, taxonomic data present only in as much as it is part of specimen data

• Curator’s nomenclatural or taxonomic data in separate databases - research difficult to integrate with the specimen catalogue

• Taxonomy Module presents very new capabilities for the herbarium specimen database

• Taxonomy Module presents very new capabilities for the herbarium specimen database

• We are exploring how this data can be used to add value to our specimen catalogues

‘Vital Statistics’

• Taxonomy Module– Very little customization

– Want several changes but would like to work with other institutions

• Web Interface– Very customized

– Pages built from the KE Custom Interface objects (Extractors! Yeah!)

Web Access To Taxonomy Record Data

Web Access To Taxonomy Record Data

MIGRATED DATA

The Taxonomy Module changes this...

What new nomenclatural and taxonomic data do we want to capture?

How do we present these data online?

Pouzarella squamifolia

Crinipellis squamifolia

Entoloma squamifolium

Marasmius squamifolius

Rhodophyllus squamifolius

Synonymy






• One species can be known by many names

Synonymy






• One species can be known by many names• All synonyms are rarely present with a herbarium specimen

Synonymy

Current Name

Description of taxonomic features

Images of identifying taxonomic traits

How do the new Taxonomy pages look with the data incorporated?

How will this data be accessed from the web interface?

Taxonomy Module SearchQuery Page for Types

Can Search:• Scientific name

• Synonyms of name entered

• Higher classification data

• Common names

• Citations

Geographic Information and an Index of Herbaria in KE EMu

Emily AshleyBioinformatics Manager


Geographic Information in EMuSites Module

Recent Issues:

– new fields added for georeferencing


Recent Issues:

– new fields added for georeferencing

– removing endangered species localities


Current Issues:

– editing sites attached to many collection events can be problematic

– retrospective cataloguing means usually need to create new sites for each catalogue record


Solutions:

– merge sites and collection events into the catalogue module

– request new tool for updating coordinates and related information

– request new “field book” record type

Geographic Information in EMuMapping

Current Issues:

– minor changes to display

– add the Americas Base Map as a layer

The Americas Base Map

What is it?

– a detailed directory of 3,220+ public herbaria of the world and the 9,775+ staff members associated with them

– published in book format and online

– ~7000 hits a month

Index Herbariorum

Changes:

– two new record types added to Parties: IH person & IH herbarium

– various new fields added

Index HerbariorumParties Module

Current Issues:– entire parties module not editable by

users other than admin.– leads to an enormous amount of

data“clean up”

Solution:– need record level security!

Index HerbariorumParties Module

Specimen Digitization and Enhancements to the Multimedia

Module

Melissa TuligBioinformatics Manager


• FTP image files to a specified location on the EMu server

• Run Image Import from Admin tasks

• New multimedia records are created for each image file

• Attachments are automatically made to the Catalogue module by barcode number

Image Import Feature

Image LogMultimedia files are in sub-directories of: /u01/emu/nybglive/multimedia

404 pending files.

ERROR: No catalogue record has Barcode 810361pending/v-245-00810361.jpg => fail/v-245-00810361.jpgpending/v-245-00810361.sid => fail/v-245-00810361.sid

########Inserting 198 records into emultimedia... Rebuild / Load report ---------------------

Number of erroneous records = 0Number of records inserted = 198########

Add multimedia IRN 100200 to Catalogue IRN 244412tmp/v-245-00189634.jpg => multimedia/100/200/v-245-00189634.jpgtmp/v-245-00189634.thumb.jpg => multimedia/100/200/v-245-00189634.thumb.jpgtmp/v-245-00189634.sid => multimedia/100/200/v-245-00189634.sid

Image Import Issues

• Only works with files in a very specific format

v-136-00215458.jpg

• Only attaches images to the Catalogue module

• Multimedia records created are mostly blank

New CSV Import

Two Purposes:

1. Hyperlink import for creating new Multimedia records

2. Data import for updating existing Multimedia records

Example CSV File for Hyperlink Import

Module Module

IRN

MulIdentifier MulTitle DetSubject_tab

etaxonomy 102154 http://mobot.org/cg TROPICOS Lecythis peruviana

etaxonomy 102154 http://www.ipni.org IPNI Lecythis peruviana

etaxonomy 102154 http://ncbi.nlm.nih GenBank Lecythis peruviana

ebibliography 7859 http://opac.nybg.or CATALPA Flora Neotropica

eparties 435863 http://sciweb.nybg. NYBG Curator Scott Mori

Example CSV File for Data Import

irn MulTitle MulDescription MulCreator

Ref_tab

DetSubject_tab

29384 Type specimen Type of Poa montana 29830 Poaceae

98876 Cariniana bark Slash of the reddish bark 578 Brazil

7765 Herbarium specimen

Penstemon versicolor 2983 Scrophulariaceae

9800 Brian M. Boom 1989 photo of B. M. Boom in Peru

4550 Brian Boom

987 A new species of Gleasonia

1985 publication of Gleasonia

28376 Rubiaceae

Gleasonia

EMu at NYBG

• Specimen catalog & associated authority files

• Transactions• Index Herbariorum• Index to American Botanical Literature• Economic botany data• Type images• Next?

Contact

• Barbara Thiers ([email protected])

• Tony Kirchgessner ([email protected])

• Shannon Dominick ([email protected])

• Emily Ashley ([email protected])

• Melissa Tulig ([email protected])

Implementation of KE EMu at The New York Botanical Garden Barbara Thiers Anthony Kirchgessner...

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