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Publication Detail
DMDD Project: Curation and visualisation of 3D image data for mutant phenotypes
  • Publication Type:
  • Authors:
    Wilson R, rose J, Geyer S, Reissig L, Szumska D, Cook AC, Weninger W, Mazzeo C, White J, Prin F, Mohun T
  • Presented date:
  • Presented at:
    Biocuration 2016
  • Location:
The Deciphering the Mechanisms of Developmental Disorders (DMDD) consortium is a research programme characterising mouse lines carrying a targeted mutation that show embryonic and perinatal lethality when the mutation is homozygous. One of the goals of the project is to identify lines useful to developmental biologists and clinicians as animal models for investigating the basis of human developmental disorders. Approximately a third of all mouse strains that carry a null mutation show homozygous recessive embryonic or perinatal lethality, and among this group at least 60% show structural defects in one or more organ system that can be identified in histological sections by conventional microscopy. The DMDD project studies embryos that survive to at least mid gestation using a combination of comprehensive high resolution episcopic microscopy (HREM) for 3D imaging, and tissue histology to identify abnormalities in developing organ and placental structures. The images we collect are screened systematically for morphological defects by a team of developmental biologists and anatomists. The mutant phenotypes observed are recorded by using terms from the Mammalian Phenotype Ontology, or our own controlled vocabulary that enables us to document phenotypes in a systematic fashion prior to representation of the phenotype in the ontology. For 3D image datasets we capture the location at which the phenotype was observed through a plugin we developed for the open source image processing and visualisation software package Osirix. This plugin allows curators to export, import and merge sets of ontology terms and comments associated with points in 3D space, which makes it possible to carry out phenotype annotation at several sites. The image data and the phenotypes we have scored are available through the project website (http://dmdd.org.uk). The search function of the website enables end users to navigate directly to the 3D location within the image data that is the basis of the curated phenotype statement, and the stackviewer interface that displays the image also allows this section to be compared to similar ones from other embryos.
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