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Linking of Digital Images to Phylogenetic Data Matrices Using a Morphological Ontology

Images are paramount in documentation of morphological data. Production and reproduction costs have traditionally limited how many illustrations taxonomy could afford to publish, and much comparative knowledge continues to be lost as generations turn over. Now digital images are cheaply produced and... Full description

Journal Title: Systematic biology 2007-04, Vol.56 (2), p.283-294
Main Author: Ramírez, Martín J.
Other Authors: Coddington, Jonathan A. , Maddison, Wayne P. , Midford, Peter E. , Prendini, Lorenzo , Miller, Jeremy , Griswold, Charles E. , Hormiga, Gustavo , Sierwald, Petra , Scharff, Nikolaj , Benjamin, Suresh P. , Wheeler, Ward C. , Page, Rod
Format: Electronic Article Electronic Article
Language: English
Subjects:
Quelle: Alma/SFX Local Collection
Publisher: England: Society of Systematic Zoology
ID: ISSN: 1063-5157
Link: https://www.ncbi.nlm.nih.gov/pubmed/17464883
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recordid: cdi_smithsonian_dspace_oai_repository_si_edu_10088_5426
title: Linking of Digital Images to Phylogenetic Data Matrices Using a Morphological Ontology
format: Article
creator:
  • Ramírez, Martín J.
  • Coddington, Jonathan A.
  • Maddison, Wayne P.
  • Midford, Peter E.
  • Prendini, Lorenzo
  • Miller, Jeremy
  • Griswold, Charles E.
  • Hormiga, Gustavo
  • Sierwald, Petra
  • Scharff, Nikolaj
  • Benjamin, Suresh P.
  • Wheeler, Ward C.
  • Page, Rod
subjects:
  • Anatomy
  • Anatomy, Comparative - methods
  • Animals
  • Araneae
  • AToL
  • Bioinformatics
  • Classification - methods
  • Computational Biology
  • Data collection
  • Databases
  • Databases, Factual
  • Datasets
  • digital images
  • Documentation
  • Domain ontologies
  • Evolutionary biology
  • Hypotheses
  • Hypothesis testing
  • Identifiers
  • Image databases
  • Image Processing, Computer-Assisted
  • Metadata
  • morphology
  • ontology
  • Phylogenetics
  • Phylogeny
  • Scanning electron microscopy
  • Software
  • Spiders
  • systematics
  • Taxa
  • Taxonomy
ispartof: Systematic biology, 2007-04, Vol.56 (2), p.283-294
description: Images are paramount in documentation of morphological data. Production and reproduction costs have traditionally limited how many illustrations taxonomy could afford to publish, and much comparative knowledge continues to be lost as generations turn over. Now digital images are cheaply produced and easily disseminated electronically but pose problems in maintenance, curation, sharing, and use, particularly in long-term data sets involving multiple collaborators and institutions. We propose an efficient linkage of images to phylogenetic data sets via an ontology of morphological terms; an underlying, fine-grained database of specimens, images, and associated metadata; fixation of the meaning of morphological terms (homolog names) by ostensive references to particular taxa; and formalization of images as standard views. The ontology provides the intellectual structure and fundamental design of the relationships and enables intelligent queries to populate phylogenetic data sets with images. The database itself documents primary morphological observations, their vouchers, and associated metadata, rather than the conventional data set cell, and thereby facilitates data maintenance despite character redefinition or specimen reidentification. It minimizes reexamination of specimens, loss of information or data quality, and echoes the data models of web-based repositories for images, specimens, and taxonomic names. Confusion and ambiguity in the meanings of technical morphological terms are reduced by ostensive definitions pointing to features in particular taxa, which may serve as reference for globally unique identifiers of characters. Finally, the concept of standard views (an image illustrating one or more homologs in a specific sex and life stage, in a specific orientation, using a specific device and preparation technique) enables efficient, dynamic linkage of images to the data set and automatic population of matrix cells with images independently of scoring decisions.
language: eng
source: Alma/SFX Local Collection
identifier: ISSN: 1063-5157
fulltext: fulltext
issn:
  • 1063-5157
  • 1076-836X
url: Link


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titleLinking of Digital Images to Phylogenetic Data Matrices Using a Morphological Ontology
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descriptionImages are paramount in documentation of morphological data. Production and reproduction costs have traditionally limited how many illustrations taxonomy could afford to publish, and much comparative knowledge continues to be lost as generations turn over. Now digital images are cheaply produced and easily disseminated electronically but pose problems in maintenance, curation, sharing, and use, particularly in long-term data sets involving multiple collaborators and institutions. We propose an efficient linkage of images to phylogenetic data sets via an ontology of morphological terms; an underlying, fine-grained database of specimens, images, and associated metadata; fixation of the meaning of morphological terms (homolog names) by ostensive references to particular taxa; and formalization of images as standard views. The ontology provides the intellectual structure and fundamental design of the relationships and enables intelligent queries to populate phylogenetic data sets with images. The database itself documents primary morphological observations, their vouchers, and associated metadata, rather than the conventional data set cell, and thereby facilitates data maintenance despite character redefinition or specimen reidentification. It minimizes reexamination of specimens, loss of information or data quality, and echoes the data models of web-based repositories for images, specimens, and taxonomic names. Confusion and ambiguity in the meanings of technical morphological terms are reduced by ostensive definitions pointing to features in particular taxa, which may serve as reference for globally unique identifiers of characters. Finally, the concept of standard views (an image illustrating one or more homologs in a specific sex and life stage, in a specific orientation, using a specific device and preparation technique) enables efficient, dynamic linkage of images to the data set and automatic population of matrix cells with images independently of scoring decisions.
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subjectAnatomy ; Anatomy, Comparative - methods ; Animals ; Araneae ; AToL ; Bioinformatics ; Classification - methods ; Computational Biology ; Data collection ; Databases ; Databases, Factual ; Datasets ; digital images ; Documentation ; Domain ontologies ; Evolutionary biology ; Hypotheses ; Hypothesis testing ; Identifiers ; Image databases ; Image Processing, Computer-Assisted ; Metadata ; morphology ; ontology ; Phylogenetics ; Phylogeny ; Scanning electron microscopy ; Software ; Spiders ; systematics ; Taxa ; Taxonomy
ispartofSystematic biology, 2007-04, Vol.56 (2), p.283-294
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descriptionImages are paramount in documentation of morphological data. Production and reproduction costs have traditionally limited how many illustrations taxonomy could afford to publish, and much comparative knowledge continues to be lost as generations turn over. Now digital images are cheaply produced and easily disseminated electronically but pose problems in maintenance, curation, sharing, and use, particularly in long-term data sets involving multiple collaborators and institutions. We propose an efficient linkage of images to phylogenetic data sets via an ontology of morphological terms; an underlying, fine-grained database of specimens, images, and associated metadata; fixation of the meaning of morphological terms (homolog names) by ostensive references to particular taxa; and formalization of images as standard views. The ontology provides the intellectual structure and fundamental design of the relationships and enables intelligent queries to populate phylogenetic data sets with images. The database itself documents primary morphological observations, their vouchers, and associated metadata, rather than the conventional data set cell, and thereby facilitates data maintenance despite character redefinition or specimen reidentification. It minimizes reexamination of specimens, loss of information or data quality, and echoes the data models of web-based repositories for images, specimens, and taxonomic names. Confusion and ambiguity in the meanings of technical morphological terms are reduced by ostensive definitions pointing to features in particular taxa, which may serve as reference for globally unique identifiers of characters. Finally, the concept of standard views (an image illustrating one or more homologs in a specific sex and life stage, in a specific orientation, using a specific device and preparation technique) enables efficient, dynamic linkage of images to the data set and automatic population of matrix cells with images independently of scoring decisions.
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3Midford, Peter E.
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5Miller, Jeremy
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0Ramirez, Martin J., Coddington, Jonathan A., Maddison, Wayne P., Midford, Peter E., Prendini, Lorenzo, Miller, Jeremy, Griswold, Charles E., Hormiga, Gustavo, Sierwald, Petra, and Scharff, Nikolaj. 2007. " Linking of Digital Images to Phylogenetic Data Matrices Using a Morphological Ontology ." Systematic Biology . 56 (2):283-294. https://doi.org/10.1080/10635150701313848
11063-5157
210.1080/10635150701313848
359931
4Systematic Biology
5http://hdl.handle.net/10088/5426
abstractImages are paramount in documentation of morphological data. Production and reproduction costs have traditionally limited how many illustrations taxonomy could afford to publish, and much comparative knowledge continues to be lost as generations turn over. Now digital images are cheaply produced and easily disseminated electronically but pose problems in maintenance, curation, sharing, and use, particularly in long-term data sets involving multiple collaborators and institutions. We propose an efficient linkage of images to phylogenetic data sets via an ontology of morphological terms; an underlying, fine-grained database of specimens, images, and associated metadata; fixation of the meaning of morphological terms (homolog names) by ostensive references to particular taxa; and formalization of images as standard views. The ontology provides the intellectual structure and fundamental design of the relationships and enables intelligent queries to populate phylogenetic data sets with images. The database itself documents primary morphological observations, their vouchers, and associated metadata, rather than the conventional data set cell, and thereby facilitates data maintenance despite character redefinition or specimen reidentification. It minimizes reexamination of specimens, loss of information or data quality, and echoes the data models of web-based repositories for images, specimens, and taxonomic names. Confusion and ambiguity in the meanings of technical morphological terms are reduced by ostensive definitions pointing to features in particular taxa, which may serve as reference for globally unique identifiers of characters. Finally, the concept of standard views (an image illustrating one or more homologs in a specific sex and life stage, in a specific orientation, using a specific device and preparation technique) enables efficient, dynamic linkage of images to the data set and automatic population of matrix cells with images independently of scoring decisions.
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