dictyBase Statement of Year 2011 objectives (March 1, 2011 – February 29, 2012)
PI: Rex Chisholm
Annotators: Petra Fey, Pascale Gaudet, Robert Dodson
Developers: Siddhartha Basu, Yulia Bushmanova (until July 2011)
All dictyBase staff contributes to GO activities. This is a total of 5 FTE positions. Of these we receive sufficient funding from the GO grant to support about 1.05 FTEs. IS THIS STILL TRUE?
Annotation. 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 until June 2011, sequences. All curators work to annotate gene products of the Dictyostelium genome.
We have recently moved to store GO annotations in Chado. SIDD PELEASE ADD ANOTHER SENTENCE OR 2 HERE! This move made our own GO annotation tool obsolete, which coincided with a curator focus on gene model curation until June 2011. Because of our small staff, we decided to make use of the Protein2GO tool at EBI, and GO annotations with that tool have started in August 2011.
The process of moving to use the Protein2GO tool required changes and 'cleanup' on many levels. For example, we deleted all our ISS annotations to InterPro because most were outdated and invalid; we fixed many 'with' IDs that were incorrect because free text introduced many mistakes; we mapped our internal references to GO references, for which one had to be added and others needed to be widened/changed. Countless smaller issues arose, and Emily Dimmer and Tony Sawford from the EBI have been and are tremendously helpful!
Reference Genome Project. PASCALE, DOES THIS NEED UPDATE? Pascale is manager for the Reference Genome project. All dictyBase curators annotate reference genome genes and are up-to-date with the selected orthologs. A paper describing the project has been published earlier this year: Mi et al 2010. PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium. NAR Database issue 
Other dictyBase contributions to GO:
All dictyBase curators work to improve the GO with GO editors and other curators in the field, and contribute to discussion on the GO email list and Source Forge. Pascale is a member of the Reference Genome, AmiGO/web presence, GO Evidence Code and Ontology development working groups. In the course of the Reference Genome Project, Pascale works with Suzi Lewis, Kara Dolinski and Paul Thomas (Panther) to develop a tree-based orthology inference system for the Reference Genome project. Currently there is a lot of effort in the development of the software tool, PAINT that will be used to make the tree-based annotations. PASCALE, PLEASE UPDATE
Petra is a member of the Newsletter group, and the Reference Genome annotation group, and has prepared dictyBase annotation to be annotated with Protein2GO with the help of Emily Dimmer.
Siddhartha is part of the Software group and is working with Tony Sawford on the pipeline to import our annotations from the EBI SIDD PELEASE CHANGE/ADD
Other species related to Dictyostelium discoideum, including D. purpureum and D. fasciculatum have been completed. dictyBase created the multi genome environment and now contains a D. purpureum website and the release of the D. fasciculatim and P. pallidum websites is imminent.
Table 1: Number of Annotations
|Total number of annotations||30762||31109||+1 %|
Table 2: Number of non-IEA Annotations
|Total number of annotations||19998||20410||+2%|
Methods and strategies for annotation
(please note % effort on literature curation vs. computational annotation methods)
Literature and other manual curation represent nearly 100% of the curation activities at dictyBase.
In addition to gene product, strain and phenotype annotation, dictyBase curators extract GO annotations from Dictyostelium publications.
We began collaborating with WormBase in using Textpresso to suggest GO terms for annotation to cellular component terms (Van Auken et al., 2009, BMC Bioinformatics 2009, 10:228). This tool has been trained to evaluate the semantic context of GO terms to enrich for terms in sections of the papers describing methods or results, providing a high recall rate for experimentally supported GO annotations. We are establishing a pipeline that will run full text search on GO cellular component terms and provide curators suggestions for annotation. The curation interface will show the gene name, the suggested GO term, and the relevant sentence from the paper leading to the annotation, allowing the curator to accept or reject the annotation. Extension of the tool to capture GO molecular functions is currently under development by WormBase. This will increase efficiency of GO curation by reducing time curators spend on literature mining.
Curation of previously unidentified genes and gene products
In addition to genes that have been characterized in the literature, dictyBase curators are annotating gene products that have EST coverage and/or contain conserved functional domains. Gene products of this type are annotated with the ISS and ND evidence codes as there is no published data available.
IEAs imported from GOA: include InterPro2GO and SPKW2GO and assigned to the respective gene products.
Quality control measures
dictyBase curators work closely to ensure that annotations are consistent between curators and conform to the guidelines set in the annotation documentation. We also have a set of internal guidelines recorded in the dictyBase Standard Operating Procedures (http://wiki.dictybase.org/dictywiki/index.php/Standard_Operating_Procedures) to which curators adhere. The three curators discuss consistency issues as they arise and decisions are recorded in the Standard Operating Procedures.