Specimen Cataloging at The New York Botanical Garden Using KE Software’s Electronic Museum (EMu) Anthony Kirchgessner Bioinformatics 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 –Bibliographic data, including published works as well as manuscripts, letters and other unpublished artifacts.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
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
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!)
Pouzarella squamifolia Crinipellis squamifolia Entoloma squamifolium Marasmius squamifolius Rhodophyllus squamifolius One species can be known by many names Synonymy
Pouzarella squamifolia Crinipellis squamifolia Entoloma squamifolium Marasmius squamifolius Rhodophyllus squamifolius 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?
Geographic Information in EMu Sites Module 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
Geographic Information in EMu Sites Module 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 EMu Mapping Current Issues: – minor changes to display – add the Americas Base Map as a layer
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
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 Herbariorum Parties Module
Specimen Digitization and Enhancements to the Multimedia Module Melissa Tulig Bioinformatics Manager New York Botanical Garden
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 Log Multimedia files are in sub-directories of: /u01/emu/nybglive/multimedia 404 pending files. ERROR: No catalogue record has Barcode 810361 pending/v-245-00810361.jpg => fail/v-245-00810361.jpg pending/v-245-00810361.sid => fail/v-245-00810361.sid ######## Inserting 198 records into emultimedia... Rebuild / Load report --------------------- Number of erroneous records = 0 Number of records inserted = 198 ######## Add multimedia IRN 100200 to Catalogue IRN 244412 tmp/v-245-00189634.jpg => multimedia/100/200/v-245-00189634.jpg tmp/v-245-00189634.thumb.jpg => multimedia/100/200/v-245- 00189634.thumb.jpg tmp/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 IRN MulIdentifierMulTitleDetSubject_tab etaxonomy102154http://mobot.org/cgTROPICOSLecythis peruviana etaxonomy102154http://www.ipni.orgIPNILecythis peruviana etaxonomy102154http://ncbi.nlm.nihGenBankLecythis peruviana ebibliography7859http://opac.nybg.orCATALPAFlora Neotropica eparties435863http://sciweb.nybg.NYBG CuratorScott Mori
Example CSV File for Data Import irnMulTitleMulDescriptionMulCreator Ref_tab DetSubject_tab 29384Type specimenType of Poa montana29830Poaceae 98876Cariniana barkSlash of the reddish bark578Brazil 7765Herbarium specimen Penstemon versicolor2983Scrophulariaceae 9800Brian M. Boom1989 photo of B. M. Boom in Peru 4550Brian Boom 987A new species of Gleasonia 1985 publication of Gleasonia 28376Rubiaceae Gleasonia