GoMapMan

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GoMapMan is an open web-accessible resource for gene functional annotations in the plant sciences. It was developed to facilitate improvement, consolidation and visualization of gene annotations across several plant species. GoMapMan is based on the plant specific MapMan ontology, organized in the form of a hierarchical tree of biological concepts, which describe gene functions.

Three GoMapMan subsets exist:

  • Protein GoMapMan: Protein-coding genes of various plants described with MapMan ontology terms, grouped according to various implemented orthologue groups.
  • Metabolite GoMapMan: Plant metabolites functionally annotated with MapMan ontology terms.
  • SmallRNA GoMapMan: Plant small RNA's functionally annotated with MapMan ontology terms. Currently only available for potato.

For more information see the help section of the corresponding GoMapMan subset.

The web interface to the database allows for browsing and searching, and for authorized users curation of gene. metabolite or small RNA positions in the ontology. In addition to gene placement in the ontology, genes are linked with several external databases. The data and ontologies can be exported in the formats suitable for direct use with other tools (namely MapMan, GSEA, BioMine or SEGS).

Contact: gomapman@nib.si

Tutorials available on YouTube:

Tutorial1Tutorial2

Citing GoMapMan:
Ramšak Ž, Baebler Š, Rotter A, Korbar M, Mozetič I, Usadel B and Gruden K. (2014). GoMapMan: integration, consolidation and visualization of plant gene annotations within the MapMan ontology. Nucleic Acids Research, 42(D1): D1167-D1175, doi: 10.1093/nar/gkt1056.

GoMapMan was developed by the National Institute of Biology and Jožef Stefan Institute, Slovenia, and partly supported by the Slovenian Research Agency (Grants J4-2228, P2-0103). GoMapMan is released under the Creative Commons Attribution NonCommercial ShareAlike license.