Structured Terminologies and Ontologies in the Biological Domain: SDD

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Structured Terminologies and Ontologies in the
Biological Domain SDD

• Bob Morris
• And
• P. Bryan Heidorn

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Structure of Descriptive Data SDD

• Taxonomic Databases Working Group
• International Union of Biological Sciences
• Support from NSF, Betty and Gordon Moore
  Foundation, Institute for Museum and Library
  Services

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Structure of Descriptive Data

• Started 1998 at the TDWG meeting in Reading.
• Harvard in Oct 1999 it was agreed that the
  subgroup should attempt to analyze the
  requirements for a new interoperability standard
  for descriptive data.
• Version 1.0 approved as standard in 2005 after St
  Petersburg

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SDD

• The metaformat for the standard will be based on
  XML and XML-schema.
• It is hoped that this standard will reach
  universal recognition to become at some point a
  successor to existing standards like DELTA,
  NEXUS, or XDF.

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Unified Biosciences Information Framework (UBIF)

• UBIF is an attempt to define a common foundation
  for several TDWG/GBIF standards like SDD (see SDD
  WIKI), ABCD (see ABCD content schema homepage) or
  TaxonConceptNames (see Taxonomic Concept Transfer
  Schema WIKI).

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SDD Creation

• Lucid Export/Import
• Electronic Field Guide Project
• OpenKey (converted by EFG)
• Transformation of Legacy Text
• AMNH Legacy Lit Project, (PartsCompositionHierarc
  hy)
• UBIO - LIF format to SDD evaluation

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SDD XML Sample Overview
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Main Elements of SDD

• TechnicalMatadata
• Matadata
• TaxonNames
• ClassHierarchy
• Specimens
• Agents

• Publications
• Geograpy
• MediaResources
• MeasurementUnits
• Audience
• Others
• Descriptions

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Descriptions

• DescriptiveTeminology
• NaturalLanguageDescriptions
• CodedDescriptions
• IdentificationKeys

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Two Examples

• EFG Butterflies
• Designed by field naturalists
• OpenKey Prairie plants and Trees with shared
  terminologies
• Content by taxonomists

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Ithomid Butterflies Godyris zygia (male dorsal)
http//www.cs.umb.edu/whaber/Monte/Ithomid/Imf/Go
dy-zava-md-550.jpg
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Character matrix
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Coded Descriptions

• zavaleta"/
• Male
• CategoricalData.

Bebugref for humans only. Added programmatically
This is a reference to the taxon name space
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Flashback to TaxonName section

• zavaleta
• sp
• .
• Godyris zavaleta
• sp

Identification
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Character matrix
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Categorical Data
Again from the Terminology

• wing ventral with line of spots"
• OrSet
• along margin)"/
• .

One of several possible STATES
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Character Definition

• margin of hind wing ventral with line of
  spots
• debugkey"Yes"/
• debugkey"No"/

Character ID
Legal States Reference
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Categorical Data
Again from the Terminology

• wing ventral with line of spots"
• OrSet
• along margin)"/
• .

One of several possible STATES
Modifier (Qualification)
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Character matrix
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Quantitative Characteristics

• length"
• mmiation

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OpenKey

• One Terminology across multiple description sets
• Trees of Chapel Hill, NC Area
• Illinois Bioindicator Prairie Plants
• The terminology http//www.ibiblio.org/openkey/glo
  ssary/Character_and_Character_State_Definitions2.p
  df

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Several Hundred Characteristics and over 1000
states

• Growth Habit
• Aquatic-emergent ? Growing in water with stem and
  leaves extending above the surface. (Compare with
  aquatic-floating and aquatic-submerged.)
• Aquatic-floating ? Growing in water with leaves
  floating on the surface. (Compare with
  aquatic-emergent and aquatic-submerged.)
• Aquatic-submerged ? Growing in water with stem
  and leaves beneath the surface. (Compare with
  aquatic-emergent and aquatic-floating.)
• Broadleaf herbaceous ? Herbaceous with relatively
  broad leaves, thus differing from the long,
  narrow leaves of grasses (Poaceae) and other
  grass-like plants . (Compare with grass-like
  herbaceous.)
• Epiphytic ? Physically supported in its entirety
  by another plant through all or the major part of
  its life, but not drawing direct nutrition from
  the host plant. (Compare with parasitic.) KP,
  p. 44, modified

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Legacy Conversion through Machine Learning
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Fig 6.1 MARTT System Architecture and Data Flow
(Cui, Dec 2004)
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Knowledge Component

• Domain knowledge is extracted from marked-up
  semi-structured floras FNA and FOC
• Knowledge component is queried by markup system
  when marking up less structured collections FNCT
• Queries
• What are the probable classes for this set of
  terms?
• What is the probability for element A to occur n
  positions relative to element B?
• What is the probability for element A and B
  co-occurrence in one description?
• Experiments show the knowledge component helps to
  improve markup performance

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Baptisia HTML
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Baptisia leucantha
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Prairie Plant SDD XML
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Shared Character and State Terminology

• shape
• debugkey"fan-shaped"/
• debugkey"acicular"/
• debugkey"awl-shaped"/
• debugkey"clawed"/
• debugkey"cordate"/
• debugkey"spurred"/

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Baptisia leucophae

• Coded description 2831
• OrSet

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Prairie Plant SDD XML
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Taxonomy

• xonomicTree"
• Genera
• true

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Genus Baptisia

• leucantha"/
• leucophaea"/

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Prairie Plant SDD XML
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• leucantha"/
• Discussion Species is tall
  and widely branched. Leavessmooth, shiny leaves,
  trifoliolate, petioled 1-2 cm except of
  uppermost leaflets petioluted ca. 0.5-1 mm,
  elliptic-obovate to oblanceolate, 2-6 (-8) cm
  long, (1.5-) 2-4.5 r (ratio) leaves are normally
  2 to 4.5 times longer than they are wide
  stipules small, caducous FlowersHolds flowering
  stem upright,has bright white flowers. Raceme(s)
  elongate (-short), with numerous (-few) flowers
  bracts caducous bracteoles lacking pedicels
  3-10 mm long. Calyx 7-8 mm long,glabrous, lobes
  shorter than tube corolla white, 2-2.5 cm long
  ovules (12-) 20. Stems0.5-2.0 dm tall or long,
  erect or divaricate, glabrous, commonly glaucous.
  Roots Seeds
• Special diagnostic
  characters Itaposs large white flowers,
  deciduous bracts and stipules, and apically
  truncate, abruptly beaked pods distinquish it
  from other species.

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Credits

• Bob Morris, U Mass
• Jacob Asiedu, U Mass
• OpenKey Team

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Additional Information

• Electronicfieldguide project http//efg.cs.umb.edu
  /
• OpenKey httpwww.isrl.uiuc.edu/openkey
• SDD wiki http//wiki.cs.umb.edu/twiki/bin/view/SDD
  /WebHome