DictyBase December 2017

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dictyBase, December 2017

1. Staff working on GOC tasks

PI: Rex Chisholm

Annotators: Petra Fey, Robert Dodson Developer: Siddhartha Basu

All dictyBase staff contribute to GO activities. This is currently a total of 3 FTE positions. We do not receive specific funding for the GO.

2. Annotation progress

The total annotations includes all, including IEAs from GOA. The non-IEA annotation numbers also include annotations that are not from dictyBase, mainly those from the PAINT project (40% and a few from INTACT and UniProt (3%), while dictyBase contributes 57%. The experimental annotations are nearly all assigned by dictyBase (98%) and the indicated annotation extensions have been exclusively annotated by dictyBase curators.

Dec 2016 Dec 2017  % Change
Total GO Annotations 68587 70697 +3.1%
Non-IEA annotations 31081 30841 -0.8% 1
EXP annotations 7428 7886 +6.2%
Annotation extensions 2 556 872 +57%

1 The slight decrease is due to improvemnts in PAINT annotations and deletion of several expired ISS annotations.

2 Not yet available in dictyBase, will be released in early 2018.

3. Methods and strategies for annotation

a. Literature curation: Gene Ontology annotation is integral to the curation process at dictyBase. Annotation of gene products to GO terms is done concurrently with curation of literature, strains, phenotypes, and general nomenclature. Both curators work to annotate gene products of the Dictyostelium genome. 85% is currently dedicated to manual annotations from the literature. 15% is dedicated to internal annotation consistency exercises, ontology development and GO working groups.

We use the Protein2GO tool from the EBI to annotate GO for Dictyostelium. We re-import annotations monthly from GOA back into dictyBase, including electronic annotations. We currently still append our GO annotations to RNAs and send the GAF file to the GO consortium. Protein2GO allows curators to add annotation extensions, which will be imported into an upgraded dictyBase within the next months.

b. Computational annotation strategies: Importing annotations monthly from GOA into dictyBase, including electronic annotations.

c. Priorities for annotation: Highest priority is curation of new literature. GO annotations are added during Dictyostelium literature curation, along with strain, phenotype, nomenclature and gene product information. We focus on new papers but go back to older papers when cited and containing important functional data for GO annotation.

4. Presentations and Publications

International Dicty Conference 2017, Geneva, Switzerland: dictyBase workshop including a special tutorial for Gene Ontology evidence codes and extensions.

5. Highlights

A. Ontology Development Contributions: Both dictyBase curators work to improve the GO with GO editors and other curators in the field, and contribute to discussions in the bi-weekly annotation calls and on GitHub. When necessary, they use GitHub to request new GO terms or improve exiting terms and GO structure. In the past year, we added 22 new GO terms. We also initiated restructuring the graphs for ‘sporulation‘ and helped separating ‘social behavior’ from the new term ‘social cooperation’, which we created to annotate Dictyostelium proteins. Finally we alerted the GO editors of inconsistencies regarding ‘modification’ and ‘processing’, which was addressed and relationships updated.

Petra participates in the GO signaling project, working on GPCR signaling with Pascale Gaudet. A workshop was held before the recent GO meeting where each signaling group reported their analyses. Petra noticed that ‘cAMP receptor activity’ was not a child of ‘G-protein coupled receptor activity’. After some discussion this was updated in the ontology. Also, a few terms have been targeted for elimination because of inconsistency and/or redundancy. For example ‘cAMP biosynthetic process’ terms were recently obsoleted and annotations from all groups needed to be rehoused, e.g. to  'adenylate cyclase-activating G protein coupled receptor signaling pathway', if appropriate. We inspected all annotations and updated terms as required.

...to be continued