Difference between revisions of "DictyBase Nov2011"

From GO Wiki
Jump to: navigation, search
m (Literature curation)
m (Staff)
Line 13: Line 13:
 
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.  
 
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 RELEASE 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.  
+
We have recently moved to store GO annotations in Chado. '''SIDD PLEASE 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 For example, we deleted all our ISS annotations to InterPro because most were outdated and invalid; we fixed many 'with' IDs that were incorrect because free text introduced many mistakes; we mapped our internal references to GO references, for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 always tremendously helpful!
 
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 For example, we deleted all our ISS annotations to InterPro because most were outdated and invalid; we fixed many 'with' IDs that were incorrect because free text introduced many mistakes; we mapped our internal references to GO references, for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 always tremendously helpful!
Line 29: Line 29:
 
Petra, Robert  and Siddhartha are working with Arun Rangarajan  and Kimberly Van Auken towards semi-automatic CC annotations using textpresso.
 
Petra, Robert  and Siddhartha are working with Arun Rangarajan  and Kimberly Van Auken towards semi-automatic CC annotations using textpresso.
  
Siddhartha is part of the Software group and is working with Tony Sawford on the pipeline to import our annotations from the EBI '''SIDD RELEASE CHANGE/ADD'''
+
Siddhartha is part of the Software group and is working with Tony Sawford on the pipeline to import our annotations from the EBI '''SIDD PLEASE 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. fasciculatum and P. pallidum websites is imminent. We are panning to automatically annotate 1:1 orthologs in these species.
 
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. fasciculatum and P. pallidum websites is imminent. We are panning to automatically annotate 1:1 orthologs in these species.
 
  
 
= Annotation Progress=
 
= Annotation Progress=

Revision as of 15:31, 3 November 2011

IN PROGRESS!!

dictyBase Statement of Year 2011 objectives (March 1, 2011 – February 29, 2012)

Staff

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 PLEASE 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 always 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 [1]

We are starting to use 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 currently establishing a pipeline that will run full text search on GO cellular component terms and provide curators suggestions for annotation. A set of uncurated 2010 Dicty papers has been selected for a pilot run of the CC pipeline. Wormbase is currently also working on 'cloning' the curation interface for dictyBase curators, so annotations can be approved, rejected or modified once the pipeline is run. This will increase efficiency of GO curation by reducing time curators spend on literature mining.

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.

Petra, Robert and Siddhartha are working with Arun Rangarajan and Kimberly Van Auken towards semi-automatic CC annotations using textpresso.

Siddhartha is part of the Software group and is working with Tony Sawford on the pipeline to import our annotations from the EBI SIDD PLEASE 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. fasciculatum and P. pallidum websites is imminent. We are panning to automatically annotate 1:1 orthologs in these species.

Annotation Progress

Table 1: Number of Annotations

09/2010 03/2011 % Change
Total number of annotations 31109 31604 +2 %
Function 13240 13278 + 0.3%
Process 9980 10001 + 0.2%
Component 7889 8325 +5%


Table 2: Number of non-IEA Annotations

09/2010 03/2011 % Change
Total number of annotations 20410 20985 +2%
Function 6878 6959 + 1%
Process 7304 7358 + 0.7%
Component 6228 6668 + 7%

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.

Literature curation

In addition to gene product, strain and phenotype annotation, dictyBase curators extract GO annotations from Dictyostelium publications.

Using of textpresso to annotate cellular components is imminent. Extension of the textpresso pipeline to capture GO molecular functions is currently under development by WormBase.

Automated methods

IEAs are 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. THIS IS SO FAR UNCHANGED - SHOULD I WRITE HERE THAT BOB IS TRAINING?