SGD December 2017
Funded via the GOC award during 2U41HG002273-17
J. Michael Cherry, PI
Gail Binkley, SGD Project Manager and DBA
Emily Heald, Biocuration Assistant
Kalpana Karra, Sr. Software Developer
Patrick Ng, Biocuration Assistant
Staff funded via other sources that provided curation or support for the GOC tasks.
Stuart Miyasato, Systems Administrator
Rob Nash, Sr. Biocuration Scientist
Edith Wong, Sr. Biocuration Scientist
Stacia Engel, Sr. Biocuration Scientist
Terry Jackson, Sr. Biocuration Scientist
Kevin MacPherson, Biocuration Assistant
Sage Hellerstedt, Biocuration Assistant
2. Annotation Progress
|Total by end of 2016||2017 activity|
|Genes with manual annotations||7121||319 genes annotated|
|Papers with manual annotations||10658||249 papers curated|
|Manual annotations||45330||768 new annotations|
|Genes with HTP annotations||3936||No new HTP annotations|
|Papers with HTP annotations||54||No new HTP annotations|
|HTP annotations||8308||No new HTP annotations|
3. Methods and strategies for annotation
(please note % effort on literature curation vs. computational annotation methods)
- Literature curation: 95%
Literature curation continues to be the major focus of SGD’s GO annotation efforts. GO annotation is a core task provided by all curators, as well as some of the curation assistants. SGD continues to enhance our curation process as defined by the GOC. We have also begun to train the team on the use of the LEGO editor Noctua.
- Computational annotation strategies: 5%
1. Yeast genes manually curated by other groups (including UniProt and GO Central) 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.
- Priorities for annotation: Annotation priorities are currently set via our ‘Literature Triage’ system in which we first evaluate papers for potential GO information. Genes to annotate are then selected based on ‘staleness’ (oldest ‘date last reviewed). Annotations to review are prioritized based on Annotation Consistency activity in the GO GitHub tracker.
4. Presentations and Publications
a. Papers with substantial GO content:
b. Presentations including Talks and Tutorials and Teaching
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
5. Other Highlights:
A. Ontology Development Contributions:
SGD curators request 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:
We had planned to do more outreach but due an unanticipated staffing change we not able to meet our goals.
C. Other Highlights:
Edith Wong and Emily Heald attended the Noctua workshop in Corvallis, Oregon on June 4, 2017.
The SGD Curation Team dedicated June and July 2017 to internal training on the Noctua anntoation tool. For eight consecutive weeks, curators worked independently to generate Noctua models from a designated paper, then came together as a group to discuss using the tool, including annotation philosophy regarding selection of GO terms, relations, and annotation extensions.
SGD curators regularly participate in biweekly GO Annotation and GO Noctua conference calls.
We continue to work with the programming staff at LBNL to transfer the geneontology.org resources to AWS. At that time the LBNL staff would take over management of those services. Progress is being made on this front, but the necessary changes have been delayed because of other staffing demands on the LBNL staff. Thus SGD continues to provide systems and programming support for geneontology.org services.