Animal GO-terms

[PavlSi]

GOMAP-singularity version
v1.3.4

GOMAP-singularity step questions is related to
mixmeth?

Question
Hello,
we have run GOMAP-singularity on barley Morex genome and supposedly it ran well. But in the resulting annotation, there are GO-term IDs that when assigned with a name (using 'get_names' R function), relate to animals. For example there were:
GO:0048513 | animal organ development | biological_process
GO:0009887 | animal organ morphogenesis | biological_process
and more.

How is this possible when using only plant databases for the GO-annotation? Could we have done something wrong?
Would you have any idea what might be the problem here, if this is indeed not normal?

Also additionally, is it possible to get the GO-term names right from GOMAP or does it work only with IDs?

[wkpalan]

How is this possible when using only plant databases for the GO-annotation? Could we have done something wrong?

@PavlSi, your use of GOMAP was correct. You did not do anything wrong.

When GOMAP was designed it was intentional to allow for the annotation of all possible GO terms, and this includes GO terms that could be annotated to other kingdoms. The source data includes annotations from tools that might annotate non-plant GO terms. The intention was to leave the animal terms to enable identification of parallel pathways and gene networks in plants which could be performing different functions in other kingdoms such as animals and fungi. It would require some manual curation for the cleaning of dataset.

I would not advise using the GOMAP annotations for quality check of assembled genomes or transcriptomes. GOMAP annotations might be better for use to analyze different gene functions using GO categories based on high-coverage annotations, and enrichment analysis of high-throughput "omics" studies.

1. Cleanup of the GOMAP could be performed by the following scripts
   https://datacommons.cyverse.org/browse/iplant/home/shared/commons_repo/curated/Carolyn_Lawrence_Dill_GOMAP_Maize_MaizeGDB_B73_NAM_5.0_December_2021.r1/2_cleanup
2. Possible to use the plant GO subset and filter for terms in that
   http://geneontology.org/docs/download-ontology/#subsets

@LeilaFattel might be able to add more suggestions as they are working on specific methods for cleaning plant-specific terms.

Also additionally, is it possible to get the GO-term names right from GOMAP or does it work only with IDs?

GOMAP outputs the annotations in GAF 2.1 format and that does not include term names (http://geneontology.org/docs/go-annotation-file-gaf-format-2.1/).