Transcript PowerPoint Presentation - Overview of Mandala Database System

An Introduction to the
Mandala Database
System
Kevin C. Holston, NRM
[email protected]
Gail E. Kampmeier
Illinois Natural History Survey
Center for Ecological Entomology
[email protected]
The History of Mandala
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Begun in 1995 for therevid
(fly) NSF PEET* project
Uses FileMaker® Pro 7/8
Relational
 Works on Macintosh & Windows OS
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Extensible, adaptable, & evolving
Fully operational demo available by request
*U.S. National Science Foundation Partnerships for Enhancing Expertise in Taxonomy DEB 95-21925 & 99-77958
What is Mandala?
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Cross-platform database system supporting
data acquisition & management for
systematics & biodiversity studies
Specimens
Taxonomic
Names
Literature
Illustrations
Most
functions are
accessed
from 3 or 4
tables dealing
with:
TAXA,
SPECIMENs,
ILLUS (images),
& LITERATURE
MANDALA: Attributes, Features
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handles specimen and batch sample data
handles specimens from multiple institutions
generates output for labels
captures determination and deposit history as well as
ecological/behavioral data
remote access for data entry and searches (through FileMaker
server)
extensive help files (context sensitive help – overview of database
structure available during database use)
tracks development (version and field) changes
separates ”people” table, separates ”locality” from ”event”
accomodates detailed and precise nomenclatural data
provided as an open source system, non-commercial license
available
Developments: 2005
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A major overhaul of Mandala
 Renaming of all fields, layouts, value lists, scripts, and relationships
with uniform conventions;
 Reduction of the number of files from 27 to 23 & their functionality
absorbed elsewhere;
 Review of all fields, layouts, value lists, scripts, & relationships, and
pruning of vestigial appendages;
 Redesign of layouts with a new color scheme & addition of a tabbed
interface where appropriate;
 Addition of scripts to Mandala 6 (compatible with FMP 5/6) to
facilitate import of data from earlier versions;
 Revision of the context sensitive HELP file.
Current Functions and Use
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The major overhaul in 2005 consolidated separately evolving
functionalities in a single version
 “Original” Mandala, optimized for often retroactive data entry of
intensive specimen-based systematics studies on a specialized
group of organisms for whom the nomenclature will be well, if
not fully documented;
 “Bioinventory” Mandala, optimized for proactive data entry of
bulk samples distributed to specialists as loans for
identification, along with the generation of multiple specimen
records based on a model record & the ability to print or export
labels;
 “BioBlitz” Mandala, simplified data entry with reports based on
common taxonomic categories for public consumption & a
running total of taxa. Updated for the Busey Woods BioBlitz in
June.
Audience and Planned
Development
Audience
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mostly entomologists
systematics and biodiversity surveys and projects –
Therevid PEET, aplacophorans and lichens. Bishop
Museum (Fiji). Illinois “Bioblitz” (001 and 2005).
entomological collections management: CNCI, Ottawa –
Pat Bouchard, Jeff Skevington.
Planned Development
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DiGIR for MANDALA – 2007.
web searchable protocols available via PHP before end
of year (2006) – instant web publishing for Fiji database.
EndNote from literature to be implemented (2007).
Data Entry & Viewing Options
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Buttons allow you to
navigate from a
central point for data
entry.
Customize* this
screen to rename,
show, or remove
BioBlitz navigation,
bulk sample
features, custom
localities & collection
events.
Quit Mandala &
FileMaker from here.
Enter Specimen Data
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Enter basic
information about
a specimen:
 Unique ID
 Verbatim
label(s)
 Life history
 Curatorial info
Link to locality,
collecting event &
taxon ID
Navigate via
tabbed interface
for additional data
entry options
Enter Taxonomic Names
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Document all ranks
& status of
taxonomic names
Minimum
information:
 Rank
 Taxonomic
epithet alone or if
required, in
combination
 Status (Valid,
Invalid,
Unregulated)
Types, history, &
classification
Links to literature
Resource: People
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The PEOPLE table is used
to reference, via the
PeopleID, all the
information stored about a
person, give the flexibility
of constructing that
person’s name in various
ways, & determine of the
various ways a name is
presented, which is the
senior synonym.
This table is referenced for
authors of literature;
authorities of taxa;
illustrators & copyright
holders; and determiners,
borrowers, lenders, &
collectors of specimens.
Collection Labels
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In retrospective capture of
specimen data, often from
museum specimens that
may be over 100 years
old & with incomplete or
difficult to interpret data, it
is more efficient to split
the labor of recording the
verbatim label(s) in
SPECIMEN, which does
not require much training,
from their interpretation in
the LOCALITY &
COLLEVENT tables.
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In prospective data entry of
information for specimens or
bulk samples, it is more likely
that labels will be generated
from the information entered &
that it will not need much
additional interpretation, e.g.,
latitude, longitude, elevation, &
more complete locality &
collecting data will be available.
Recording Serial Localities
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Because serial localities are
most often used with
retrospective data capture with
greater interpretation needs,
features were added to aid in
this task:
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Translating elevation in feet to
meters
Calculating displacement from
a known lat/long by distance in
km & one of 16 compass
directions.
Translating miles to kilometers
(on Political Locality &
Regions & Features tabs)
With either serial or non-serial locality records, you can generate a new
collecting event based on the locality record. Serial localities automatically
generate serial CollEvents; non-serial localities generate non-serial CEVs
Collecting Event
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Collecting events
include the collecting
method, collectors,
collection date range,
abiotic conditions at the
time of collection, & a
localityID.
Serial collecting event
records could be
unique references to
both the locality &
event, but because
non-serial collecting
eventIDs may NOT be
unique, a combination
of the LocCollEventID
is used as the key.
Loans
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When you click on the pencil
icon, you create DEPOSIT
record based on the sampleID,
but also reflecting taxa in a loan
that may be accumulated by
loan.
Fill in information in relevant
white fields & when you are
ready to ship the loan, fill in the
details (see shipping details
button) & print out the loan form
(click see Loan Form button).
Sample Loan
Form
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Note that this loan form lists
taxa from one or more
sampleIDs that have
accumulated under a single
loan number.
You can see this form as it
will print, print this form, or
return to the data entry
screen using the icons in the
upper right (these will not
print).
Track GenBank Accessions
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List identifier, gene or other sequence deposited,
associated specimen, URL to record in GenBank or
other repository, & related information.
Click on globe icon to open your browser & go to URL
Digital Archiving of Images
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Store images or other
documents or links to
these to the ILLUS
table.
Give detailed
description of method,
medium, background,
copyright, view, stage,
etc.
Detail archiving of both
digital & physical
images.
Enter Literature Citations
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Enter all types of literature
Link to journals, URL
Translate titles from nontarget language
Give location & level of
curation of the literature
Sample citations prebuilt by
citation type
Dissect the Literature
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Not likely the first task you will undertake in Mandala, mining the
literature & linking it to taxa are activities associated with maturing
databases with a specific taxonomic or geographic focus.
Help Resources
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A variety of help
resources are built into
Mandala, from general,
file, and field contextsensitive help, to
explanations of the icons
& terms used in Mandala,
to links to online
gazetteers, taxonomic
name servers, & an index
to codens used for many
museums & collections.
Glossary of Icons & Terms
Integrated Help
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File/Table & field context sensitive Help. Click ?
Icon in table or while in field for which you want
information.
Document Structural
Changes
END OF PRESENTATION
Gail E. Kampmeier
Illinois Natural History Survey
Center for Ecological Entomology
[email protected]
[email protected]
Thank you for your attention.