Literature DB >> 23508988

The need for data standards in zoomorphology.

Lars Vogt1, Michael Nickel, Ronald A Jenner, Andrew R Deans.   

Abstract

eScience is a new approach to research that focuses on data mining and exploration rather than data generation or simulation. This new approach is arguably a driving force for scientific progress and requires data to be openly available, easily accessible via the Internet, and compatible with each other. eScience relies on modern standards for the reporting and documentation of data and metadata. Here, we suggest necessary components (i.e., content, concept, nomenclature, format) of such standards in the context of zoomorphology. We document the need for using data repositories to prevent data loss and how publication practice is currently changing, with the emergence of dynamic publications and the publication of digital datasets. Subsequently, we demonstrate that in zoomorphology the scientific record is still limited to published literature and that zoomorphological data are usually not accessible through data repositories. The underlying problem is that zoomorphology lacks the standards for data and metadata. As a consequence, zoomorphology cannot participate in eScience. We argue that the standardization of morphological data requires i) a standardized framework for terminologies for anatomy and ii) a formalized method of description that allows computer-parsable morphological data to be communicable, compatible, and comparable. The role of controlled vocabularies (e.g., ontologies) for developing respective terminologies and methods of description is discussed, especially in the context of data annotation and semantic enhancement of publications. Finally, we introduce the International Consortium for Zoomorphology Standards, a working group that is open to everyone and whose aim is to stimulate and synthesize dialog about standards. It is the Consortium's ultimate goal to assist the zoomorphology community in developing modern data and metadata standards, including anatomy ontologies, thereby facilitating the participation of zoomorphology in eScience.
Copyright © 2013 Wiley Periodicals, Inc.

Mesh:

Year:  2013        PMID: 23508988     DOI: 10.1002/jmor.20138

Source DB:  PubMed          Journal:  J Morphol        ISSN: 0022-2887            Impact factor:   1.804


  8 in total

1.  Folding wings like a cockroach: a review of transverse wing folding ensign wasps (Hymenoptera: Evaniidae: Afrevania and Trissevania).

Authors:  István Mikó; Robert S Copeland; James P Balhoff; Matthew J Yoder; Andrew R Deans
Journal:  PLoS One       Date:  2014-05-02       Impact factor: 3.240

2.  Finding our way through phenotypes.

Authors:  Andrew R Deans; Suzanna E Lewis; Eva Huala; Salvatore S Anzaldo; Michael Ashburner; James P Balhoff; David C Blackburn; Judith A Blake; J Gordon Burleigh; Bruno Chanet; Laurel D Cooper; Mélanie Courtot; Sándor Csösz; Hong Cui; Wasila Dahdul; Sandip Das; T Alexander Dececchi; Agnes Dettai; Rui Diogo; Robert E Druzinsky; Michel Dumontier; Nico M Franz; Frank Friedrich; George V Gkoutos; Melissa Haendel; Luke J Harmon; Terry F Hayamizu; Yongqun He; Heather M Hines; Nizar Ibrahim; Laura M Jackson; Pankaj Jaiswal; Christina James-Zorn; Sebastian Köhler; Guillaume Lecointre; Hilmar Lapp; Carolyn J Lawrence; Nicolas Le Novère; John G Lundberg; James Macklin; Austin R Mast; Peter E Midford; István Mikó; Christopher J Mungall; Anika Oellrich; David Osumi-Sutherland; Helen Parkinson; Martín J Ramírez; Stefan Richter; Peter N Robinson; Alan Ruttenberg; Katja S Schulz; Erik Segerdell; Katja C Seltmann; Michael J Sharkey; Aaron D Smith; Barry Smith; Chelsea D Specht; R Burke Squires; Robert W Thacker; Anne Thessen; Jose Fernandez-Triana; Mauno Vihinen; Peter D Vize; Lars Vogt; Christine E Wall; Ramona L Walls; Monte Westerfeld; Robert A Wharton; Christian S Wirkner; James B Woolley; Matthew J Yoder; Aaron M Zorn; Paula Mabee
Journal:  PLoS Biol       Date:  2015-01-06       Impact factor: 8.029

3.  Organizing phenotypic data-a semantic data model for anatomy.

Authors:  Lars Vogt
Journal:  J Biomed Semantics       Date:  2019-06-20

4.  Levels and building blocks-toward a domain granularity framework for the life sciences.

Authors:  Lars Vogt
Journal:  J Biomed Semantics       Date:  2019-01-28

5.  SOCCOMAS: a FAIR web content management system that uses knowledge graphs and that is based on semantic programming.

Authors:  Lars Vogt; Roman Baum; Philipp Bhatty; Christian Köhler; Sandra Meid; Björn Quast; Peter Grobe
Journal:  Database (Oxford)       Date:  2019-01-01       Impact factor: 3.451

6.  Anatomy and the type concept in biology show that ontologies must be adapted to the diagnostic needs of research.

Authors:  Lars Vogt; István Mikó; Thomas Bartolomaeus
Journal:  J Biomed Semantics       Date:  2022-06-27

7.  High-precision morphology: bifocal 4D-microscopy enables the comparison of detailed cell lineages of two chordate species separated for more than 525 million years.

Authors:  Thomas Stach; Chiara Anselmi
Journal:  BMC Biol       Date:  2015-12-23       Impact factor: 7.431

8.  Data Sources for Trait Databases: Comparing the Phenomic Content of Monographs and Evolutionary Matrices.

Authors:  T Alex Dececchi; Paula M Mabee; David C Blackburn
Journal:  PLoS One       Date:  2016-05-18       Impact factor: 3.240

  8 in total

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