Upload
amato
View
15
Download
0
Tags:
Embed Size (px)
DESCRIPTION
Data and Metadata Standards in Zoomorphology : A Call to Action. Lars Vogt. The Evolution of Scientific Standards A Historical Perspective. - PowerPoint PPT Presentation
Citation preview
Data and Metadata Standards inZoomorphology: A Call to Action
Lars Vogt
Universität BonnL. VogtStandardization in Zoomorphology
The Evolution of Scientific Standards
A Historical Perspective
Vogt (submitted) On Standards in Science: In Pursuit of Truth-to-Nature and Objectivity. In: Special Issue “Data platforms in integrative biodiversity research. Ecological Informatics.
All Scientific Standards depend on some
Epistemic Virtue
Universität BonnL. VogtStandardization in Zoomorphology
One can distinguish two types of general Epistemic
Virtues:
Truth-to-NatureScientific Objectivity
Universität BonnL. VogtStandardization in Zoomorphology
Truth-to-Nature
Truth-SeekingMethods
Universität BonnL. VogtStandardization in Zoomorphology
These are Standards of
Justification of Scientific Reasoning
Provide Demarcation CriteriaScience vs Believe
Universität BonnL. VogtStandardization in Zoomorphology
Classic Methods & Criteria
Plato
Universität BonnL. VogtStandardization in Zoomorphology
Essentialism
Syllogistic Demonstration
Aristotle
Classic Methods & Criteria
Plato
Universität BonnL. VogtStandardization in Zoomorphology
Essentialism
Syllogistic Demonstration
Aristotle
Standard is set bygeneral Principles of Logical Coherence
Leonardo da Vinci
Renaissance &“Scientific Revolution”
Francis Bacon
Universität BonnL. VogtStandardization in Zoomorphology
Laboratory Method&
Induction
Leonardo da Vinci
Renaissance &“Scientific Revolution”
Francis Bacon
Universität BonnL. VogtStandardization in Zoomorphology
Laboratory Method&
Induction
Standard is set bygeneral Principles of
Empirical Grounding
Modern Criteria of Testability
Rudolf Carnap
Universität BonnL. VogtStandardization in Zoomorphology
Verification PrincipleInduction
Modern Criteria of Testability
Universität BonnL. VogtStandardization in Zoomorphology
Falsificationism
DeductionKarl Popper
Modern Criteria of Testability
Universität BonnL. VogtStandardization in Zoomorphology
Falsificationism
DeductionKarl Popper
Standard is set by moresophisticated Theories of
Empirical Grounding(e.g. Carnap) or
Logical Coherence(e.g. Popper)
Modern Criteria of Testability
Universität BonnL. VogtStandardization in Zoomorphology
Falsificationism
DeductionKarl Popper
Standard is set by moresophisticated Theories of
Empirical Grounding(e.g. Carnap) or
Logical Coherence(e.g. Popper)
These Standards
DO NOT interest
Us Today!
Scientific Objectivity
‘Objectifying’ Methods
Universität BonnL. VogtStandardization in Zoomorphology
These are Standards of
Data Production
Provide Criteria forData Quality & Documentation
Universität BonnL. VogtStandardization in Zoomorphology
These are Standards of
Data Production
Provide Criteria forData Quality & Documentation
Universität BonnL. VogtStandardization in Zoomorphology
Reproducibility& operational Transparency
“Scientific Revolution” Methods & Criteria
Royal Society
Universität BonnL. VogtStandardization in Zoomorphology
“Gentleman’s”Objectivity
“Scientific Revolution” Methods & Criteria
Royal Society
Universität BonnL. VogtStandardization in Zoomorphology
“Gentleman’s”Objectivity
Experiment as Demonstration
“Scientific Revolution” Methods & Criteria
Royal Society
Universität BonnL. VogtStandardization in Zoomorphology
“Gentleman’s”Objectivity
Experiment as Demonstration
Standard is set bythe Verdict of
the eye wittnessing Gentlemen
Modern Methods & Criteria
Philosophical Transactions
Universität BonnL. VogtStandardization in Zoomorphology
Reproducibilityoperational
Transparency
Modern Methods & Criteria
Philosophical Transactions
Universität BonnL. VogtStandardization in Zoomorphology
Reproducibilityoperational
Transparency
Standard is set byEditors andReviewers
Modern Methods & Criteria
Philosophical Transactions
Universität BonnL. VogtStandardization in Zoomorphology
Reproducibilityoperational
Transparency
Standard is set byEditors andReviewersCurrent Status in
Morphology
Standards based on Convention
internationally standardized
Measurement Units
Universität BonnL. VogtStandardization in Zoomorphology
Standards based on Technology:
PhotographyHistology
Immunohistology
Universität BonnL. VogtStandardization in Zoomorphology
Daston & Galison (1992) The image of objectivity. Representations 40, 81-128.
see also Procedural Objectivity sensu Heintz (2000) Die Innenwelt der Mathematik. Zur Kultur und Praxis einer beweisenden Disziplin. Wien, Springer.
*
Standards based on Technology:
PhotographyHistology
Immunohistology
Universität BonnL. VogtStandardization in Zoomorphology
MechanicalObjectivity*
Daston & Galison (1992) The image of objectivity. Representations 40, 81-128.
see also Procedural Objectivity sensu Heintz (2000) Die Innenwelt der Mathematik. Zur Kultur und Praxis einer beweisenden Disziplin. Wien, Springer.
*
Universität BonnL. VogtStandardization in Zoomorphology
Are these Standardsstill sufficient
today?
“Web of Things”
CommunicabilitySemantic
TransparencyCompatibilityInternet &
Databases
Universität BonnL. VogtStandardization in Zoomorphology
“Web of Things”
CommunicabilitySemantic
TransparencyCompatibilityInternet &
Databases
Universität BonnL. VogtStandardization in Zoomorphology
Data Repositories
“Web of Things”
CommunicabilitySemantic
TransparencyCompatibilityInternet &
Databases
Universität BonnL. VogtStandardization in Zoomorphology
Data RepositoriesRequire highly
formalized Rules,Conventions & Formats
Universität BonnL. VogtStandardization in Zoomorphology
From a Presentation from Bendix et al. 2011: Introduction to the Workshop “Data repositories in environmental sciences – concepts, definitions, technical solutions and user requirements”
Universität BonnL. VogtStandardization in Zoomorphology
From a Presentation from Bach K 2011: A comparative evaluation on technical solutions of long-term data repositories related to biodiversity
Data Repositories
Universität BonnL. VogtStandardization in Zoomorphology
Do we really need more Standards in
Zoomorphology?
Universität BonnL. VogtStandardization in Zoomorphology
From a Presentation from Enke N & Gemeinholzer B 2011: The user’s view on data sharing
Data Harvesters
Universität BonnL. VogtStandardization in Zoomorphology
Data Harvesters
… benefit fromData and Metadata
Standards
Universität BonnL. VogtStandardization in Zoomorphology
Data Harvesters
… benefit fromData and Metadata
Standards
Universität BonnL. VogtStandardization in Zoomorphology
Commonly accepted Morphological Data and
Metadata Standards would increase Visibility of
Morphology
Universität BonnL. VogtStandardization in Zoomorphology
The Global View
What drives Progress in Science?
…in its early days mainly Experimentation & Theory
Hey, T. et al. (2009) The Fourth Paradigm: Data-Intensive Scientific Discovery. Microsoft Research, 284pp.
Universität BonnL. VogtStandardization in Zoomorphology
What drives Progress in Science?
…in its early days mainly Experimentation & Theory
Hey, T. et al. (2009) The Fourth Paradigm: Data-Intensive Scientific Discovery. Microsoft Research, 284pp.
With the advent of Computers also Simulation…
Universität BonnL. VogtStandardization in Zoomorphology
What drives Progress in Science?
…in its early days mainly Experimentation & Theory
Hey, T. et al. (2009) The Fourth Paradigm: Data-Intensive Scientific Discovery. Microsoft Research, 284pp.
With the advent of Computers also Simulation…
…and today, with Databases, Semantic Tools (e.g. Ontologies) and high-throughput Technologies also
Data Exploration.
Universität BonnL. VogtStandardization in Zoomorphology
Data-driven Science
“Web of Things”
Semantic Web
Databases
Ontologies
Universität BonnL. VogtStandardization in Zoomorphology
“Web of Things”
Semantic Web
Databases
Ontologies
Universität BonnL. VogtStandardization in Zoomorphology
Data-driven Science
“Web of Things”
Semantic Web
Databases
Ontologies
Universität BonnL. VogtStandardization in Zoomorphology
Data-driven Science
Intelligent Systems and Tools for
Data Exploration
Universität BonnL. VogtStandardization in Zoomorphology
Gray, J. (2009) Jim Gray on eScience: A Transformed Scientific Method. In: Hey
et al. (eds.) The Fourth Paradigm: Data-Intensive Scientific Discovery. Microsoft Research, xvii-xxxi.
Universität BonnL. VogtStandardization in Zoomorphology
Gray, J. (2009) Jim Gray on eScience: A Transformed Scientific Method. In: Hey
et al. (eds.) The Fourth Paradigm: Data-Intensive Scientific Discovery. Microsoft Research, xvii-xxxi.
The currentMorphological Record
Universität BonnL. VogtStandardization in Zoomorphology
Gray, J. (2009) Jim Gray on eScience: A Transformed Scientific Method. In: Hey
et al. (eds.) The Fourth Paradigm: Data-Intensive Scientific Discovery. Microsoft Research, xvii-xxxi.
Utilizing the Semantic Web
&Data Repositories
Universität BonnL. VogtStandardization in Zoomorphology
Gray, J. (2009) Jim Gray on eScience: A Transformed Scientific Method. In: Hey
et al. (eds.) The Fourth Paradigm: Data-Intensive Scientific Discovery. Microsoft Research, xvii-xxxi.
eScience
Universität BonnL. VogtStandardization in Zoomorphology
Data Integration
Wiley, H.S. (2011): Integrating Multiple Types of Data for Signaling Research: Challenges and Opportunities. Science Signaling 4: 160.
Universität BonnL. VogtStandardization in Zoomorphology
Data Integration
Wiley, H.S. (2011): Integrating Multiple Types of Data for Signaling Research: Challenges and Opportunities. Science Signaling 4: 160.
Next obvious Step:Integration of Morphology
Data Visualization
Universität BonnL. VogtStandardization in Zoomorphology
Data Visualization
Universität BonnL. VogtStandardization in Zoomorphology
Data Visualization
Universität BonnL. VogtStandardization in Zoomorphology
Fox, P. & Hendler, J. (2011) Changing the Equation on Scientific Data Visualization. Science 331(6018): 705-708.
Rowe, T. & Frank, L.R. (2011) The disappearing third dimension. Science 331(6018): 712-714.
Universität BonnL. VogtStandardization in Zoomorphology
Integrating theScientific Record
Publications &
Databases
Penev et al. (2009): Data publication and dissemination of interactive keys
under the open access model – ZooKeys working example. ZooKeys 21: 1-17.
Publications & Databases
Universität BonnL. VogtStandardization in Zoomorphology
Universität BonnL. VogtStandardization in Zoomorphology
Semantic Tools
Ontologies
Universität BonnL. VogtStandardization in Zoomorphology
Semantic Tools
OntologiesOntologieshighly formalized controlled
defined Vocabularies
Universität BonnL. VogtStandardization in Zoomorphology
Semantic Enhancement
Universität BonnL. VogtStandardization in Zoomorphology
Ontologies & Data Annotation
Dadzie, A.-S. & Burger, A. (2005) Providing visualisation support for the analysis of anatomy ontology data. BMC Bioinformatics 6: 74.
Universität BonnL. VogtStandardization in Zoomorphology
Ontologies & Data Annotation
Washington et al. (2009) Linking human diseases to animal models using ontology-based phenotype annotation. PLoS Biology 7: 11.
Universität BonnL. VogtStandardization in Zoomorphology
Ontologies & Data Annotation
Kuß et al. (2008) Ontology-based visualization of hierarchical neuroanatomical structures. In: Botha et al. (eds.) Eurographics Workshop on Visual Computing for Biomedicine. The Eurographics Association: 6-16.
Universität BonnL. VogtStandardization in Zoomorphology
Ontologies & Data Annotation
Kuß et al. (2008) Ontology-based visualization of hierarchical neuroanatomical structures. In: Botha et al. (eds.) Eurographics Workshop on Visual Computing for Biomedicine. The Eurographics Association: 6-16.
EmpiricalGrounding
Universität BonnL. VogtStandardization in Zoomorphology
Ontologies & Data Annotation
Kuß et al. (2008) Ontology-based visualization of hierarchical neuroanatomical structures. In: Botha et al. (eds.) Eurographics Workshop on Visual Computing for Biomedicine. The Eurographics Association: 6-16.
MorphologicalData
EmpiricalGrounding
Universität BonnL. VogtStandardization in Zoomorphology
Ontologies & Data Annotation
Kuß et al. (2008) Ontology-based visualization of hierarchical neuroanatomical structures. In: Botha et al. (eds.) Eurographics Workshop on Visual Computing for Biomedicine. The Eurographics Association: 6-16.
User
MorphologicalData
EmpiricalGrounding
Universität BonnL. VogtStandardization in Zoomorphology
Ontologies & Data Annotation
Kuß et al. (2008) Ontology-based visualization of hierarchical neuroanatomical structures. In: Botha et al. (eds.) Eurographics Workshop on Visual Computing for Biomedicine. The Eurographics Association: 6-16.
User
MorphologicalData
EmpiricalGrounding
Universität BonnL. VogtStandardization in Zoomorphology
If the MorphologicalCommunity wants to
participate in eScience,we have to develop
the appropriate
Data and MetadataStandards
Universität BonnL. VogtStandardization in Zoomorphology
What is the Difference between Data and
Metadata?
Universität BonnL. VogtStandardization in Zoomorphology
Data
ObjectThing orProcess
ObserverPerson orInstrument
Representation
SomeContent
General Scheme of a Scientific Study
SomeContent
Universität BonnL. VogtStandardization in Zoomorphology
ObjectThing orProcess
ObserverPerson orInstrument
Representation
SomeContent
General Scheme of a Scientific Study
SomeContent
Universität BonnL. VogtStandardization in Zoomorphology
Data
Morphology is about theForm & Existence
of Biological Material Entities
Universität BonnL. VogtStandardization in Zoomorphology
Data are Descriptions aboutthe Existence of Organisms, their supramolecular parts
and the material and topological Properties of them
Morphological Data
Composition, Form, Consistency, relative Position, Orientation, etc.
Universität BonnL. VogtStandardization in Zoomorphology
Universität BonnL. VogtStandardization in Zoomorphology
Metadata
ObjectThing orProcess
ObserverPerson orInstrument
Representation
SomeContentSome
Content
Universität BonnL. VogtStandardization in Zoomorphology
Transparent & Reproducible
ObjectThing orProcess
ObserverPerson orInstrument
Representation
SomeContentSome
Content
Universität BonnL. VogtStandardization in Zoomorphology
Transparent & Reproducible
requires
DOCUMENTATION
Documentation of…
…all that is required for a Third Person to re-produce the same Content (i.e. Data).
All relevant information regarding the Object of Study and the Methods
applied and Instruments used during Data Production.
Universität BonnL. VogtStandardization in Zoomorphology
Documentation of…
…all that is required for a Third Person to re-produce the same Content (i.e. Data).
All relevant information regarding the Object of Study and the Methods
applied and Instruments used during Data Production.
Universität BonnL. VogtStandardization in Zoomorphology
Metadata
Observer
Object Representation
Thing orProcess
Person orInstrument
SomeContent
What, where, when, etc.
Methods,Instruments,
etc.What, where,
when, etc.What, where,
when, etc.
Methods,Instruments,
etc.What, where,
when, etc.
Universität BonnL. VogtStandardization in Zoomorphology
Metadata
Transparent & Reproducible
Observer
Object Representation
Thing orProcess
Person orInstrument
SomeContent
What, where, when, etc.
Methods,Instruments,
etc.What, where,
when, etc.What, where,
when, etc.
Methods,Instruments,
etc.What, where,
when, etc.
Universität BonnL. VogtStandardization in Zoomorphology
Transparent & Reproducible
Metadata
CommunicableTransparent & Reproducible
Observer
Object Representation
Thing orProcess
Person orInstrument
SomeContent
What, where, when, etc.
Methods,Instruments,
etc.What, where,
when, etc.What, where,
when, etc.
Methods,Instruments,
etc.What, where,
when, etc.
Universität BonnL. VogtStandardization in Zoomorphology
Transparent & Reproducible
Metadata
Communicable
requires
STANDARDIZATION
Transparent & Reproducible
Universität BonnL. VogtStandardization in Zoomorphology
How to develop aMetadata Standard
Developing Metadata Standards – an Example:
OMICS (Genomics, Transcriptonics, Proteomics, Metabolomics)
Universität BonnL. VogtStandardization in Zoomorphology
Commonly accepted Reporting Structure is required that specifies which Annotations should be included
Minimum Information Checklists
Brazma et al. (2001): Minimum information about a microarray experiment (MIAME) – towards tandards for microarray data. Nature 29: 365-371.
Developing Metadata Standards – an Example:
OMICS (Genomics, Transcriptonics, Proteomics, Metabolomics)
Universität BonnL. VogtStandardization in Zoomorphology
Commonly accepted Reporting Structure is required that specifies which Annotations should be included
Minimum Information Checklists
Brazma et al. (2001): Minimum information about a microarray experiment (MIAME) – towards tandards for microarray data. Nature 29: 365-371.
First Step towards Standardization…
Universität BonnL. VogtStandardization in Zoomorphology
What does a Modern METADATA Standard
account for?
Universität BonnL. VogtStandardization in Zoomorphology
Content Standard Reproducibility &
Operational TransparencyWhat is relevant Content ?
Universität BonnL. VogtStandardization in Zoomorphology
Vogt (submitted) On Standards in Science: In Pursuit of Truth-to-Nature and Objectivity. In: Special Issue “Data platforms in integrative biodiversity research. Ecological Informatics.
Insufficient!
Vogt (2009) The future role of bio-ontologies for developing a general data standard in biology: chance and challenge for zoo-morphology. Zoomorphology 128(3), 201-217.
Content Standard Reproducibility &
Operational TransparencyWhat is relevant Content ?
Universität BonnL. VogtStandardization in Zoomorphology
Vogt (submitted) On Standards in Science: In Pursuit of Truth-to-Nature and Objectivity. In: Special Issue “Data platforms in integrative biodiversity research. Ecological Informatics.
Vogt (2009) The future role of bio-ontologies for developing a general data standard in biology: chance and challenge for zoo-morphology. Zoomorphology 128(3), 201-217.
Universität BonnL. VogtStandardization in Zoomorphology
Vogt (submitted) On Standards in Science: In Pursuit of Truth-to-Nature and Objectivity. In: Special Issue “Data platforms in integrative biodiversity research. Ecological Informatics.
Vogt (2009) The future role of bio-ontologies for developing a general data standard in biology: chance and challenge for zoo-morphology. Zoomorphology 128(3), 201-217.
Universität BonnL. VogtStandardization in Zoomorphology
Concept Standard Semantic Transparency
What does a Concept/Term mean ?
Vogt (submitted) On Standards in Science: In Pursuit of Truth-to-Nature and Objectivity. In: Special Issue “Data platforms in integrative biodiversity research. Ecological Informatics.
Vogt (2009) The future role of bio-ontologies for developing a general data standard in biology: chance and challenge for zoo-morphology. Zoomorphology 128(3), 201-217.
Universität BonnL. VogtStandardization in Zoomorphology
Vogt (submitted) On Standards in Science: In Pursuit of Truth-to-Nature and Objectivity. In: Special Issue “Data platforms in integrative biodiversity research. Ecological Informatics.
Vogt (2009) The future role of bio-ontologies for developing a general data standard in biology: chance and challenge for zoo-morphology. Zoomorphology 128(3), 201-217.
Universität BonnL. VogtStandardization in Zoomorphology
Format Standard Compatibility &
Computer ParsabilityWhat Syntax for Content
Transmission?
Vogt (submitted) On Standards in Science: In Pursuit of Truth-to-Nature and Objectivity. In: Special Issue “Data platforms in integrative biodiversity research. Ecological Informatics.
Vogt (2009) The future role of bio-ontologies for developing a general data standard in biology: chance and challenge for zoo-morphology. Zoomorphology 128(3), 201-217.
Universität BonnL. VogtStandardization in Zoomorphology
Vogt (submitted) On Standards in Science: In Pursuit of Truth-to-Nature and Objectivity. In: Special Issue “Data platforms in integrative biodiversity research. Ecological Informatics.
Vogt (2009) The future role of bio-ontologies for developing a general data standard in biology: chance and challenge for zoo-morphology. Zoomorphology 128(3), 201-217.
Universität BonnL. VogtStandardization in Zoomorphology
Nomenclatural Standard Communicability
Which Symbol/Word refers to which Concept?
Universität BonnL. VogtStandardization in Zoomorphology
Universität BonnL. VogtStandardization in Zoomorphology
But what aboutDATA Standards
in Zoomorphology?
Data are Descriptions aboutthe Existence of Organisms, their supramolecular Parts
and the material and topological Properties of them
Morphological Data
Universität BonnL. VogtStandardization in Zoomorphology
Data are Descriptions aboutthe Existence of Organisms, their supramolecular Parts
and the material and topological Properties of them
Data are Descriptions aboutthe Existence of Organisms, their supramolecular Parts
and the material and topological Properties of them
Morphological Data
Universität BonnL. VogtStandardization in Zoomorphology
Data are Descriptions aboutthe Existence of Organisms, their supramolecular Parts
and the material and topological Properties of them
Terminology
Problem equivalent structures possess different denotations
Problems with Morphological Terminology
differing structures possess identical denotations
Universität BonnL. VogtStandardization in Zoomorphology
Problems with Morphological Terminology
Universität BonnL. VogtStandardization in Zoomorphology
Reason some terms are based on homology hypotheses
some terms refer to functions, some to development, others to forms
taxon-specific terminologies
continuous change of meaning of a term
individual preferences
(which at their turn are based on morphological descriptions)
Universität BonnL. VogtStandardization in Morphology
Vogt (2008) Learning from Linnaeus: towards developing the foundation for a general structure concept for morphology. Zootaxa 1950, 123-152.
Vogt (2009) The future role of bio-ontologies for developing a general data standard in biology: chance and challenge for zoo-morphology. Zoomorphology 128, 3: 201-217.
Vogt et al. (2010) The linguistic problem of morphology: structure versus homology and the standardization of morphological data. Cladistics 26, 3: 301-325.
*
The Linguistic Problem of Morphology*
(Definitions free of homology assumptions)
Lack of commonly accepted, standardized and taxon- independent morphological terminology
commonly accepted, standardized and formalized method of description
Universität BonnL. VogtStandardization in Morphology
Vogt (2008) Learning from Linnaeus: towards developing the foundation for a general structure concept for morphology. Zootaxa 1950, 123-152.
Vogt (2009) The future role of bio-ontologies for developing a general data standard in biology: chance and challenge for zoo-morphology. Zoomorphology 128, 3: 201-217.
Vogt et al. (2010) The linguistic problem of morphology: structure versus homology and the standardization of morphological data. Cladistics 26, 3: 301-325.
*
The Linguistic Problem of Morphology*
(Definitions free of homology assumptions)
Lack of commonly accepted, standardized and taxon- independent morphological terminology
commonly accepted, standardized and formalized method of description
Reference System of Biology(Inventory & Data Management)
Important for allsupra-molecular biological
Data
Universität BonnL. VogtStandardization in Morphology
Vogt (2008) Learning from Linnaeus: towards developing the foundation for a general structure concept for morphology. Zootaxa 1950, 123-152.
Vogt (2009) The future role of bio-ontologies for developing a general data standard in biology: chance and challenge for zoo-morphology. Zoomorphology 128, 3: 201-217.
Vogt et al. (2010) The linguistic problem of morphology: structure versus homology and the standardization of morphological data. Cladistics 26, 3: 301-325.
*
The Linguistic Problem of Morphology*
(Definitions free of homology assumptions)
Lack of commonly accepted, standardized and taxon- independent morphological terminology
commonly accepted, standardized and formalized method of description
Reference System of Biology(Inventory & Data Management)
Important for allsupra-molecular biological
Data
Meaning &
Reference of
Terms is
problematic
Universität BonnL. VogtStandardization in Zoomorphology
2 underlying General Problems
1
Universität BonnL. VogtStandardization in Zoomorphology
Language & Epistemology
Terms as TextualRepresentationsof Real Entities
Observer
Object Representation
Universität BonnL. VogtStandardization in Zoomorphology
Real Entitiesobjects, processes,
qualities, states
textual/graphical Representational
Artifactsof Real Entities
Cognitive Representations
of Real Entities
Vogt (in press) Sings and Terminology – Science caught between language and perception. BIONOMINA.
Observer
Object Representation
Universität BonnL. VogtStandardization in Zoomorphology
Real Entitiesobjects, processes,
qualities, states
textual/graphical Representational
Artifactsof Real Entities
Cognitive Representations
of Real Entities
Observation, Measurement
Vogt (in press) Sings and Terminology – Science caught between language and perception. BIONOMINA.
Observer
Object Representation
Universität BonnL. VogtStandardization in Zoomorphology
Real Entitiesobjects, processes,
qualities, states
textual/graphical Representational
Artifactsof Real Entities
Cognitive Representations
of Real Entities
Observation, Measurement
Vogt (in press) Sings and Terminology – Science caught between language and perception. BIONOMINA.
Observer
Object Representation
Universität BonnL. VogtStandardization in Zoomorphology
Real Entitiesobjects, processes,
qualities, states
textual/graphical Representational
Artifactsof Real Entities
Cognitive Representations
of Real Entities
Observation, Measurement
Communication
Vogt (in press) Sings and Terminology – Science caught between language and perception. BIONOMINA.
Observer
Object Representation
Universität BonnL. VogtStandardization in Zoomorphology
Real Entitiesobjects, processes,
qualities, states
textual/graphical Representational
Artifactsof Real Entities
Cognitive Representations
of Real Entities
Communication
Vogt (in press) Sings and Terminology – Science caught between language and perception. BIONOMINA.
Observer
Object Representation
Universität BonnL. VogtStandardization in Zoomorphology
Real Entitiesobjects, processes,
qualities, states
textual/graphical Representational
Artifactsof Real Entities
Cognitive Representations
of Real Entities
Communication
Vogt (in press) Sings and Terminology – Science caught between language and perception. BIONOMINA.
Observer
Object Representation
Universität BonnL. VogtStandardization in Zoomorphology
Real Entitiesobjects, processes,
qualities, states
textual/graphical Representational
Artifactsof Real Entities
Cognitive Representations
of Real Entities
Communication
Vogt (in press) Sings and Terminology – Science caught between language and perception. BIONOMINA.
Observer
Object Representation
Universität BonnL. VogtStandardization in Zoomorphology
Real Entitiesobjects, processes,
qualities, states
textual/graphical Representational
Artifactsof Real Entities
Cognitive Representations
of Real Entities
Communication
Vogt (in press) Sings and Terminology – Science caught between language and perception. BIONOMINA.
Observer
Object Representation
Universität BonnL. VogtStandardization in Zoomorphology
Real Entitiesobjects, processes,
qualities, states
textual/graphical Representational
Artifactsof Real Entities
Cognitive Representations
of Real Entities
CommunicationReference
Vogt (in press) Sings and Terminology – Science caught between language and perception. BIONOMINA.
Observer
Object Representation
Universität BonnL. VogtStandardization in Zoomorphology
Real Entitiesobjects, processes,
qualities, states
textual/graphical Representational
Artifactsof Real Entities
Cognitive Representations
of Real Entities
CommunicationReference
Vogt (in press) Sings and Terminology – Science caught between language and perception. BIONOMINA.
Observer
Object Representation
Universität BonnL. VogtStandardization in Zoomorphology
Real Entitiesobjects, processes,
qualities, states
textual/graphical Representational
Artifactsof Real Entities
Cognitive Representations
of Real Entities
CommunicationReference
Vogt (in press) Sings and Terminology – Science caught between language and perception. BIONOMINA.
?
Observer
Object Representation
Universität BonnL. VogtStandardization in Zoomorphology
Real Entitiesobjects, processes,
qualities, states
textual/graphical Representational
Artifactsof Real Entities
Cognitive Representations
of Real Entities
Communication
indirect Reference
Vogt (in press) Sings and Terminology – Science caught between language and perception. BIONOMINA.
Universität BonnL. VogtStandardization in Zoomorphology
Are there differences regarding Reference
between differentTypes of Terms?
Universität BonnL. VogtStandardization in Zoomorphology
Proper Names&
Unambiguous Reference
Vogt (in press) Sings and Terminology – Science caught between language and perception. BIONOMINA.
Vogt (submitted) On Standards in Science: In Pursuit of Truth-to-Nature and Objectivity. In: Special Issue “Data platforms in integrative biodiversity research. Ecological Informatics
Communication about individual Entities (i.e. Particulars)
Object Representation
Universität BonnL. VogtStandardization in Zoomorphology
Real Entitiesobjects, processes,
qualities, states
textual/graphical Representational
Artifactsof Real Entities
Vogt (in press) Sings and Terminology – Science caught between language and perception. BIONOMINA.
Vogt (submitted) On Standards in Science: In Pursuit of Truth-to-Nature and Objectivity. In: Special Issue “Data platforms in integrative biodiversity research. Ecological Informatics
Communication about individual Entities (i.e. Particulars)
Object Representation
Universität BonnL. VogtStandardization in Zoomorphology
Real Entitiesobjects, processes,
qualities, states
textual/graphical Representational
Artifactsof Real Entities
Vogt (in press) Sings and Terminology – Science caught between language and perception. BIONOMINA.
Vogt (submitted) On Standards in Science: In Pursuit of Truth-to-Nature and Objectivity. In: Special Issue “Data platforms in integrative biodiversity research. Ecological Informatics
Communication about individual Entities (i.e. Particulars)
Object Representation
Universität BonnL. VogtStandardization in Zoomorphology
Real Entitiesobjects, processes,
qualities, states
textual/graphical Representational
Artifactsof Real Entities
Vogt (in press) Sings and Terminology – Science caught between language and perception. BIONOMINA.
Vogt (submitted) On Standards in Science: In Pursuit of Truth-to-Nature and Objectivity. In: Special Issue “Data platforms in integrative biodiversity research. Ecological Informatics
Communication about individual Entities (i.e. Particulars)
Object Representation
Universität BonnL. VogtStandardization in Zoomorphology
Real Entitiesobjects, processes,
qualities, states
textual/graphical Representational
Artifactsof Real Entities
Communication
Vogt (in press) Sings and Terminology – Science caught between language and perception. BIONOMINA.
Vogt (submitted) On Standards in Science: In Pursuit of Truth-to-Nature and Objectivity. In: Special Issue “Data platforms in integrative biodiversity research. Ecological Informatics
Communication about individual Entities (i.e. Particulars)
Object Representation
Universität BonnL. VogtStandardization in Zoomorphology
Real Entitiesobjects, processes,
qualities, states
textual/graphical Representational
Artifactsof Real Entities
Communication
SupermanDC-Comic
Hero
Vogt (in press) Sings and Terminology – Science caught between language and perception. BIONOMINA.
Vogt (submitted) On Standards in Science: In Pursuit of Truth-to-Nature and Objectivity. In: Special Issue “Data platforms in integrative biodiversity research. Ecological Informatics
Communication about individual Entities (i.e. Particulars)
Object Representation
Universität BonnL. VogtStandardization in Zoomorphology
Real Entitiesobjects, processes,
qualities, states
textual/graphical Representational
Artifactsof Real Entities
Communication
‘Superman’
SupermanDC-Comic
Hero
Vogt (in press) Sings and Terminology – Science caught between language and perception. BIONOMINA.
Vogt (submitted) On Standards in Science: In Pursuit of Truth-to-Nature and Objectivity. In: Special Issue “Data platforms in integrative biodiversity research. Ecological Informatics
Communication about individual Entities (i.e. Particulars)
Object Representation
Universität BonnL. VogtStandardization in Zoomorphology
Real Entitiesobjects, processes,
qualities, states
textual/graphical Representational
Artifactsof Real Entities
Communicationdirect Referencethrough Ostensive
Definitions
‘Superman’
SupermanDC-Comic
Hero
Vogt (in press) Sings and Terminology – Science caught between language and perception. BIONOMINA.
Vogt (submitted) On Standards in Science: In Pursuit of Truth-to-Nature and Objectivity. In: Special Issue “Data platforms in integrative biodiversity research. Ecological Informatics
Communication about individual Entities (i.e. Particulars)
Object Representation
Universität BonnL. VogtStandardization in Zoomorphology
Real Entitiesobjects, processes,
qualities, states
textual/graphical Representational
Artifactsof Real Entities
Communication
e.g.
Pointing and Calling the Name
Name Label on a Photograph
Taxon Name Label on a Type Specimen
Vogt (in press) Sings and Terminology – Science caught between language and perception. BIONOMINA.
Vogt (submitted) On Standards in Science: In Pursuit of Truth-to-Nature and Objectivity. In: Special Issue “Data platforms in integrative biodiversity research. Ecological Informatics
Communication about individual Entities (i.e. Particulars)
Object Representation
Universität BonnL. VogtStandardization in Zoomorphology
Real Entitiesobjects, processes,
qualities, states
textual/graphical Representational
Artifactsof Real Entities
Communication
In the Internet:
Unique Persistent Identifiers,e.g. DOIs, LSIDs, GUIDs…
Universität BonnL. VogtStandardization in Zoomorphology
General Terms&
Reference
Communication about general Types of Entities (i.e. Universals/Classes)
Object Representation
Universität BonnL. VogtStandardization in Zoomorphology
Real Entitiesobjects, processes,
qualities, states
textual/graphical Representational
Artifactsof Real Entities
Communication about general Types of Entities (i.e. Universals/Classes)
Object Representation
Universität BonnL. VogtStandardization in Zoomorphology
Real Entitiesobjects, processes,
qualities, states
textual/graphical Representational
Artifactsof Real Entities
Communication about general Types of Entities (i.e. Universals/Classes)
Object Representation
Universität BonnL. VogtStandardization in Zoomorphology
Real Entitiesobjects, processes,
qualities, states
textual/graphical Representational
Artifactsof Real Entities
Communication
Communication about general Types of Entities (i.e. Universals/Classes)
Object Representation
Universität BonnL. VogtStandardization in Zoomorphology
Real Entitiesobjects, processes,
qualities, states
textual/graphical Representational
Artifactsof Real Entities
Communication
NO direct Reference
Communication about general Types of Entities (i.e. Universals/Classes)
Object Representation
Universität BonnL. VogtStandardization in Zoomorphology
Real Entitiesobjects, processes,
qualities, states
textual/graphical Representational
Artifactsof Real Entities
Communication
NO direct Reference
Reference requires
Definition of essential Properties
Aristotelian Definitions
2
Universität BonnL. VogtStandardization in Zoomorphology
Dealing with Complexity
Terminology and the Organization of Morphological
Knowledge
2 Basic Typesof organizational
Hierarchies:
TaxonomiesPartonomies
Universität BonnL. VogtStandardization in Zoomorphology
Taxonomy: by Subsumption (Class-Subclass Hierarchy)
Aristotelian Definition
necessary propertydefinition of parent classinherited definition part
sufficient propertyessence of the groupdistinguishing definition part
genus
differentia
Universität BonnL. VogtStandardization in Zoomorphology
Topological Aspectsintrinsic material and topological properties
Morphological Terminology: Taxonomy
Morphological Terminology distinguishes more general from more specialized Types/Kinds
e.g. ‘Neuron’ is_a type of ‘Cell’
Universität BonnL. VogtStandardization in Zoomorphology
Partonomy: by Parthood (Part-Whole Hierarchy)
Universität BonnL. VogtStandardization in Zoomorphology
Parts are related to their
Wholesthrough
direct proper Parthood relations
Topological Aspectsintrinsic material and topological properties
Individual Partonomy of a particular Specimen
Universität BonnL. VogtStandardization in Zoomorphology
Parts of parts of an Organism
e.g. ‘Head’ is_part_of ‘Body’
Topological Aspectsintrinsic material and topological properties
Universität BonnL. VogtStandardization in Zoomorphology
General Levels of Organization: Partonomy
Vogt (2010) Spatio-structural granularity of biological material entities. BMC Bioinformatics 11, 289.
molecular level
cellular level
multicellular level
part-of relations
part-of relations
These two types of Hierarchies can be applied in various ways
due to theinherent Complexity
of Biological Material Entities
Universität BonnL. VogtStandardization in Zoomorphology
We can do the same forFunctional
Aspects of Biological Material Entities
Functional Terminology: Taxonomy
Functional Organization: Partonomy
Universität BonnL. VogtStandardization in Zoomorphology
We can do the same forFunctional
Aspects of Biological Material Entities
Functional Terminology: Taxonomy
Functional Organization: Partonomy
Universität BonnL. VogtStandardization in Zoomorphology
Formin relation to
causal Processes
…and forDevelopmental
Aspects of Biological Material Entities
Developmental Terminology: Taxonomy
Developmental Organization: Partonomy
Universität BonnL. VogtStandardization in Zoomorphology
…and forDevelopmental
Aspects of Biological Material Entities
Developmental Terminology: Taxonomy
Developmental Organization: Partonomy
Universität BonnL. VogtStandardization in Zoomorphology
Formin relation to
causal Processes involved in
Growth/Change of Form
…and forEvolutionary
Aspects of Biological Material Entities
Homology based Terminology: Taxonomy
Lineage Organization: PartonomyPhylogeny, Genealogy, Gene-trees, etc.
Universität BonnL. VogtStandardization in Zoomorphology
…and forEvolutionary
Aspects of Biological Material Entities
Homology based Terminology: Taxonomy
Lineage Organization: PartonomyPhylogeny, Genealogy, Gene-trees, etc.
Universität BonnL. VogtStandardization in Zoomorphology
Formin relation to
Past Processes
Classificatory AspectsDifferent properties have been used
Classification of Taxa: Taxonomy
Universität BonnL. VogtStandardization in Zoomorphology
Classificatory AspectsDifferent properties have been used
Classification of Taxa: Taxonomy
Universität BonnL. VogtStandardization in Zoomorphology
Conclusion for StandardizationWe should take it
Step-by-Step, distinguish the different aspects and
first focus on the Basics: intrinsic Material and
Topological Properties
Universität BonnL. VogtStandardization in Zoomorphology
Ontologies&
Morphological Standards
Universität BonnL. VogtStandardization in Zoomorphology
Universität BonnL. VogtStandardization in Zoomorphology
Problems withcurrently available
Anatomy Ontologies
Conceptual Shortcomings*is a Synapse a cell-part or a cell aggregate or a…?
Lack of Framework for Integrating different Perspectives* anatomy, function, development, evolution
Problems of many Anatomy OntologiesModel-Organism and Vertebrate centered
Vogt (2010) Spatio-structural granularity of biological material entities. BMC Bioinformatics 11, 289. Vogt et al. (2011) Top-level categories of constitutively organized material entities. PLoS ONE 6(4): e18794
*
Not applicable in a broad taxonomic Approachtry to define Organ for all Metazoa…
Irrealistic basic Assumptions*
Universität BonnL. VogtStandardization in Morphology
Conceptual Shortcomings*is a Synapse a cell-part or a cell aggregate or a…?
Lack of Framework for Integrating different Perspectives* anatomy, function, development, evolution
Problems of many Anatomy OntologiesModel-Organism and Vertebrate centered
Vogt (2010) Spatio-structural granularity of biological material entities. BMC Bioinformatics 11, 289. Vogt et al. (2011) Top-level categories of constitutively organized material entities. PLoS ONE 6(4): e18794
*
Not applicable in a broad taxonomic Approachtry to define Organ for all Metazoa…
Irrealistic basic Assumptions*Presupposition of most
Anatomy Ontologies
Universität BonnL. VogtStandardization in Morphology
Conceptual Shortcomings*is a Synapse a cell-part or a cell aggregate or a…?
Lack of Framework for Integrating different Perspectives* anatomy, function, development, evolution
Problems of many Anatomy OntologiesModel-Organism and Vertebrate centered
Vogt (2010) Spatio-structural granularity of biological material entities. BMC Bioinformatics 11, 289. Vogt et al. (2011) Top-level categories of constitutively organized material entities. PLoS ONE 6(4): e18794
*
Not applicable in a broad taxonomic Approachtry to define Organ for all Metazoa…
Irrealistic basic Assumptions*Reality of most
biological Objects
Universität BonnL. VogtStandardization in Morphology
Conceptual Shortcomings*is a Synapse a cell-part or a cell aggregate or a…?
Lack of Framework for Integrating different Perspectives* anatomy, function, development, evolution
Problems of many Anatomy OntologiesModel-Organism and Vertebrate centered
Vogt (2010) Spatio-structural granularity of biological material entities. BMC Bioinformatics 11, 289. Vogt et al. (2011) Top-level categories of constitutively organized material entities. PLoS ONE 6(4): e18794
*
Not applicable in a broad taxonomic Approachtry to define Organ for all Metazoa…
Irrealistic basic Assumptions*Reality of most
biological Objects
We need an
Anatomy
Reference
Ontology
Universität BonnL. VogtStandardization in Morphology
Universität BonnL. VogtStandardization in Zoomorphology
Basic Principles for a Cross-SpeciesMorphologicalTerminology
1. Use of Aristotelian Definitions (Class-Subclass Hierarchy)
Definition Neuron:A Neuron is a Cell that…
Universität BonnL. VogtStandardization in Zoomorphology
1. Use of Aristotelian Definitions (Class-Subclass Hierarchy)
Universität BonnL. VogtStandardization in Zoomorphology
2. Taxon-Independent: Definitions contain NO Reference to a specific Taxon
1. Use of Aristotelian Definitions (Class-Subclass Hierarchy)
Universität BonnL. VogtStandardization in Zoomorphology
2. Taxon-Independent: Definitions contain NO Reference to a specific Taxon
3. Homology-Free: Definitions contain NO Assumptions about underlying Putative Homology
Call to Action
Universität BonnL. VogtStandardization in Zoomorphology
Call to Action
Universität BonnL. VogtStandardization in Zoomorphology
officially supported by
oomorphological tandards onsortium
ZSC
Call to Action
Universität BonnL. VogtStandardization in Zoomorphology
officially supported by
oomorphological tandards onsortium
ZSC
Thank You for Your Attention !
Universität BonnL. VogtStandardization in Zoomorphology
oomorphological tandards onsortium
ZSC Goal
Promote Mechanism that
• Standardize the Description of Anatomical Structures
• Exchange and Integrate Morphological Data & Metadata
• Develop and Establish a General Morphological Data & Metadata Report Standard
• Develop Minimum Information Checklists
Universität BonnL. VogtStandardization in Zoomorphology
oomorphological tandards onsortium
ZSC Organization
• Open Membership
• International Working Body
• Collaboration with Societies & Journals