SGD December 2016

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Overview:

1. Staff:

PI: Mike Cherry

Biocurators: Rob Nash (0.5 FTE), Edith Wong (0.15 FTE), Stacia Engel (0.25 FTE)

Developers: Shuai Weng (0.25 FTE), Kalpana Karra (0.1 FTE)

Systems Administrators: Stuart Miyasato (0.5 FTE), Matt Simison (0.25 FTE)


Total 2 FTE funded by GOC NIHGRI grant


2. Annotation Progress

Total annotations by end of 2015 Annotations added 2016
Genes with manual annotations 20641 677
Papers with manual annotations 14509 342
Manual annotations 44460 1146
Genes with HTP annotations 5091 1229
Papers with HTP annotations 121 1
HTP annotations 5797 1400

3. Methods and strategies for annotation

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


  1. Literature curation: 95%

Literature curation continues to be the major focus of our annotation efforts.


  1. Computational annotation strategies: 5%

1. Yeast genes manually curated by other groups are brought in electronically from GOA with their associated evidence codes and the originating group acknowledged in the source.


2. Electronic annotations for yeast genes based on GO mapping to InterPro, Enzyme Commission and Swiss-Prot keywords, are brought in electronically with IEA evidence code from GOA. Annotations from GOA for all categories are updated weekly.


  1. Priorities for annotation: Annotation priorities are currently set via our ‘Fast Track/Author Response’ system in which we first triage papers for potential GO information, then contact authors of those papers to ask them specific questions about relevant genes and results.

4. Presentations and Publications


a. Papers with substantial GO content:


N/A


b. Presentations including Talks and Tutorials and Teaching


1. SGD Webinar: SGD: A Catalyst for Biological Research https://www.youtube.com/watch?v=57VPZYdttzY


2. SGD Webinar: Predicting Chemotherapy Targets in YeastMine

https://www.youtube.com/watch?v=-Qefg1gm7ho


3. SGD Webinar: Exploring Expression Datasets & Coexpressed Genes w/SPELL

https://www.youtube.com/watch?v=NAUOx1BxmJ8


4. SGD Webinar: Homology and Disease Data at SGD https://www.youtube.com/watch?v=PI-nuN8uLdI


5. SGD Help video: YeastMine Scenario - Finding Uncharacterized Subunits of the Mitochondrial Ribosome

https://www.youtube.com/watch?v=AoVfmaZmTK4


6. SGD Help video: Uploading Gene Lists to JBrowse

https://www.youtube.com/watch?v=HUI-of9IYXo


7. SGD Help video: Exploring Expression Datasets with SPELL

https://www.youtube.com/watch?v=PnYD1D2ZjWU


8. SGD Help video: Introduction to SGD's Faceted Search

https://www.youtube.com/watch?v=hw4LZJJSHMw


9. SGD Help video: Finding Human Homology & Disease Information

https://www.youtube.com/watch?v=hzBHJZILkIE


10. Senior Biocuration Scientist Rob Nash presented a tutorial at the Yeast Genetics and Genomics course at CSHL in late July. He demonstrated the use of YeastMine and how to navigate through SGD's website, including the use of GO annotations provided by SGD.


c. Poster presentations


N/A


5. Other Highlights:


A. Ontology Development Contributions:


SGD curators requested new terms and participated in ontology-related discussions periodically throughout the past year on an as-needed basis.


B. Annotation Outreach and User Advocacy Efforts:

Both Edith Wong and Rob Nash continue to serve on the GO-help rota.


C. Other Highlights:

Stacia Engel served as a beta tester for the Noctua annotation tool, and participated in weekly development calls.


Edith Wong and Stacia Engel attended the Noctua workshop at USC on November 7, 2016.