SGD December 2010: Difference between revisions

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A. Ontology Development Contributions:  
A. Ontology Development Contributions:  


1) K. Christie has been working on improving the ontology branches related to transcription, and the has_part relationship
1) K. Christie has been working on improving the ontology branches related to transcription, and the has_part relationship. She has added xx terms in MF and BP aspects.


2) K. Christie participates in OBO-Edit working group.
2) K. Christie participates in OBO-Edit working group.
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1) R. Balakrishnan has been working on generating inferences using PAINT
1) R. Balakrishnan has been working on generating inferences using PAINT
C. Evidence code ontology:
1) R. Balakrishnan and K. Christie are working with Michelle and Marcus on the ECO project.


==Annotation Outreach and User Advocacy Efforts==
==Annotation Outreach and User Advocacy Efforts==

Revision as of 16:11, 29 November 2010

Saccharomyces Genome Database Summary, 2010

Overview

Staff:

J. Michael Cherry, Eurie Hong, Rama Balakrishnan, Gail Binkley, Karen Christie, Maria Costanzo, Selina Dwight, Stacia Engel, Dianna Fisk, Jodi Hirschman, Ben Hitz, Cindy Krieger, Stuart Miyasato, Rob Nash, Julie Park, Marek Skrzypek, Shuai Weng, Edith Wong, Kalpana Karra, Craig Amundsen, Jo Chung, Esther Chan

Annotation Progress

Since October 2009 the following annotations have been added to SGD*
  • Note that these numbers count manually curated and high-throughput annotations only for ORFs that are Verified or Uncharacterized (Dubious ORFs are excluded), for RNA genes (ncRNA, rRNA, snRNA, snoRNA, or tRNA) and for genes encoded within transposable elements. It should also be noted these annotations may include both new annotations and updated annotations which replaced older ones.
GO Aspect Number of Annotations Added Number of genes updated Number of publications used
Biological Process 1560 845 743
Molecular Function 677 455 377
Cellular Component 687 458 317

State of GO annotations Genome wide

Type Counts as of November 29, 2010
GP with Any Annotation 6357
GPs with Manual annotation 6357
GP with Experimental and Computational Evidence 3554
GP with Computational Evidence 3554
GP with Curator Evidence (TAS, NAS, IC) 1615
GP with No Data (ND) 2310
All annotations 79378
Total Annotations with Experimental Evidence 37045
Total Annotations with Computational Evidence 35580
Annotations with Curator Evidence (TAS, NAS, IC) 3753
Annotations with No Data (ND) 4072

Methods and strategies for annotation

a. Literature curation: 100% of SGD’s effort is dedicated to manual curation based on the published literature for budding yeast gene and their products.

b. Computational annotation strategies: SGD does not employ automated methods to assign annotations, rather we absorb the computationally predicted annotations made by the UniProtKB GOA project for S. cerevisiae. The IEA annotations are loaded into the SGD database from the GOA gene association file after each release. In addition, SGD has incorporated computationally predicted annotations generated by the integrated bioinformatic analysis of high-throughput data from the Roth and Troyanskaya labs (Tian et. al., 2008, Huttenhower and Troyanskaya, 2008). All these annotations are included in the gene_association.sgd file, which represents a significant expansion of the types of evidence codes and data sources that are provided by SGD.

c. Priorities for annotation: The highest priority is to capture annotations where new information is available for an Uncharacterized gene product. These papers are identified during the literature triage process. In addition, we update older annotations and replace TAS evidence code with experimental evidence. SGD captures the date when the annotations for a gene were reviewed. Using this date reviewed, older annotations are checked for consistency with the current literature.

Presentations and Publications

Publications,_Talks,_Posters_2010-

Other Highlights

A. Ontology Development Contributions:

1) K. Christie has been working on improving the ontology branches related to transcription, and the has_part relationship. She has added xx terms in MF and BP aspects.

2) K. Christie participates in OBO-Edit working group.

3) SGD curators participate in the Annotation Jamboree. R. Balakrishnan, K. Christie, Julie Park participated in the Annotation Jamboree held in November 2010.

SGD's participation in Source Forge items:

B. Reference Genome Project:

1) R. Balakrishnan has been working on generating inferences using PAINT

C. Evidence code ontology:

1) R. Balakrishnan and K. Christie are working with Michelle and Marcus on the ECO project.

Annotation Outreach and User Advocacy Efforts

1) E. Hong is part of the rotation that answers user email from gohelp.

2) R. Balakrishnan, E. Wong and B. Hitz participate in the WebPresence and AmiGO Hub working groups.

3) B. Hitz, Gail Binkley and Stuart Miyasato are part of the software group