DictyBase December 2016

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Mod NamedictyBaseDecember , 2016

Overview:

1. Staff:

PI: Rex Chisholm

Annotators: Petra Fey*, Robert Dodson

Developer: Siddhartha Basu


* funded

All dictyBase staff contribute to GO activities. This is currently a total of 3 FTE positions. Of these we receive sufficient funding from the GO grant to support 0.45 FTEs.


2. Annotation Progress

The total and non-IEA annotation numbers include annotations that are not from dictyBase, with most of these from the PAINT project and a few from INTACT and SwissProt. At this point we cannot easily query them by source; however, the experimental annotations are nearly all from dictyBase and the indicated annotation extensions have been exclusively annotated by dictyBase curators (Table 3).


Table 1: Number of Annotations


Dec2015 Dec2016 % Change
Total number of annotations 69130 68587 - 0.8%
Function 22915 23971 + 4.6%
Process 24209 21283 - 12% *
Component 22006 23333 + 6%

Table 2: Number of non-IEA Annotations


Dec2015 Dec2016 % Change
Total number of annotations 29547 31081 + 5.2%
Function 7572 8777 + 15.9%
Process 13267 12068 - 9% *
Component 8708 10236 + 17.5%

Table 3: Additional Numbers


Dec2015 Dec2016 % Change
Total EXP annotations 7049 7428 + 5.4%
Annotation extensions 367 928 + 153% **

* Nearly 3,000 process annotations from a single paper using the RCA evidence code have been deleted, prompted by researcher request and new internal giudelines for high throuput annotations; improving annotation quality.


** Not yet available in the current dictyBase, will be release in 2017.


3. Methods and strategies for annotation

(please note % effort on literature curation vs. computational annotation methods)


  1. 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. 95% is currently dedicated to manual annotations from the literature.

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 year.


  1. Computational annotation strategies: Importing annotations monthly from GOA into dictyBase, including electronic annotations.
  1. Priorities for annotation: Highest priority is literture curation. 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


a. Basu S, Fey P, Jimenez-Morales D, Dodson RJ, Chisholm RL.dictyBase 2015: Expanding data and annotations in a new software environment. Genesis. 2015 Aug;53(8):523-34.


b. Poster at the International Biocurator Meeting in Geneva, April, 2016. The Future of Curation at dictyBase, P. Fey, S. Basu, R. Dodson, R. Chisholm; A large part showed annotation extension representation in the new dictyBase environment.


5, Other 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 TermGenie or GitHub to create new GO terms or improve exiting terms and GO structure.

In the past year, we added 10 new GO terms. Some of these new terms involved renaming and/or updating 5 existing terms, and one resulted from restructuring the graph for ‘fruiting body development‘. One additional issue involves taxon restrictions to ‘social behavior’, which is still under discussion. All dictyBase issues can be viewed here:

https://github.com/geneontology/go-ontology/issues?q=is%3Aclosed+label%3AdictyBase

B. Annotation Outreach and User Advocacy Efforts:

Petra contributes to the GO Help Desk and provides all GO help to dictyBase users as needed.

C. Other Highlights:

Petra attended 2 LEGO workshops at recent GO meetings and modeled Dicty annotations with David, Kimberly and Paul in fall 2016. Curators will now regularly add LEGO models for Dicty data. With the emergence of LEGO annotations in OWL format we have therefore started exploring options for storing our GO annotations in a graph database in the near future. As documented here https://github.com/geneontology/noctua-models#availability , first we will convert our GAF to owl format and then store those owl files in a suitable graph database.