PUBLICATION
COMICS: Cartoon Visualization of Omics Data in Spatial Context using Anatomical Ontologies
- Authors
- Travin, D., Popov, I., Guler, A.T., Medvedev, D., van der Plas-Duivesteijn, S., Varela, M., Kolder, I.C.R.M., Meijer, A.H., Spaink, H.P., Palmblad, M.
- ID
- ZDB-PUB-171031-3
- Date
- 2017
- Source
- Journal of Proteome Research 17(1): 739-744 (Journal)
- Registered Authors
- Meijer, Annemarie H., Spaink, Herman P., Varela, Monica
- Keywords
- none
- MeSH Terms
-
- Animals
- Biological Ontologies
- Carps
- Data Display*
- Mice
- Terminology as Topic
- User-Computer Interface
- Zebrafish
- PubMed
- 29083911 Full text @ J. Proteome Res.
Citation
Travin, D., Popov, I., Guler, A.T., Medvedev, D., van der Plas-Duivesteijn, S., Varela, M., Kolder, I.C.R.M., Meijer, A.H., Spaink, H.P., Palmblad, M. (2017) COMICS: Cartoon Visualization of Omics Data in Spatial Context using Anatomical Ontologies. Journal of Proteome Research. 17(1):739-744.
Abstract
COMICS is an interactive and open-access Web platform for integration and visualization of molecular expression data in anatomograms of zebrafish, carp and mouse model systems. Anatomical ontologies are used to map omics data across experiments and between an experiment and a particular visualization in a data dependent manner. COMICS is built on top of several existing resources. Zebrafish and mouse anatomical ontologies with their controlled vocabulary (CV) and defined hierarchy are used with the ontoCAT R package to aggregate data for comparison and visualization. Libraries from the QGIS geographical information system are used with the R packages "maps" and "maptools" to visualize and interact with molecular expression data in anatomical drawings of zebrafish and carp model systems. COMICS allows users to upload their own data from omics experiments, using any gene or protein nomenclature they wish, as long as CV terms are used to define anatomical regions or developmental stages. Common nomenclatures such as the ZFIN gene names and UniProt accessions are provided as additional support. COMICS can be used to generate publication-quality visualization of gene and protein expression across experiments. Unlike previous tools that have used anatomical ontologies to interpret imaging data in several animal models, including zebrafish, COMICS is designed to take spatially resolved data generated by dissection or fractionation and display this data in visually clear anatomical representations rather than large data tables. COMICS is optimized for ease-of-use, with a minimalistic web interface and automatic selection of the appropriate visual representation depending on the input data.
Genes / Markers
Expression
Phenotype
Mutations / Transgenics
Human Disease / Model
Sequence Targeting Reagents
Fish
Orthology
Engineered Foreign Genes
Mapping