Priorities

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We have been discussing the priorities that we all set in our individual work. This is for a consortium meeting action item.

It was suggested in the conference call that each person in an annotation database group might report back for their whole database group as the information will be required for all GO people and so this will save time for others. The individual priority lists are shown below:


Jennifer Clark (GO Editorial Office)

1) Content meetings
2) Outreach visits to departments
3) answering mail help queries from users
4) editing content and doing content conference calls
5) working on sourceforge items
6) filling in outreach database and writing SOPs


Pascale Gaudet reporting for Dictybase

Hi Jen,

I am doing this now or else I'll forget.

Here are the 'official' dictybase priorities:

1a. meetings, grants, papers are always top priority (this can be 90% of the week sometimes)

1b. regular meetings: dictybase group (about 3-6 hr/month), curators (2h/week), then working groups:

-AmiGO, Annotation Outreach, obo-edit, GO newsletter (about 2-4 h per week) [5-10]

2. dictybase new software updates: suggest/test new features [variable; can take up to 40% of the time, on average I would say 10-15%]

3. user requests (either though the dictybase mailing or direct requests; so far we have not answered any GO-help or other GO questions) [this can involve some GO curation, for example when a user suggest genes to curate we usually curate them as completely as possible, including GO]. At dictybase we have "service week" which means that the same curator answers all requests for a entire week. I would say that requires 2-10 hours the week you do it, depending on the requests you get [5-25% of the time, GO= 2-10%].

4. Working group stuff: test amigo, outreach stuff [variable, average ~ 10% of the time]

5. curate current literature [usually 2-3 papers per curator per week]; usually involves some GO curation, also requesting new GO terms or editing existing GO terms/tree structure (~5 hours a week, lets say half on GO) [10% of the time]

6. do "similarity-based curation": we check the gene models and do GO annotations (ISS); our aim is to do 10 genes each per week. This involves a lot of InterPro2GO mappings and we suggest quite a lot of edits to the mappings (see SF!! it's 90% Val and myself!). [30% of the time; 15% GO]


7. annotate reference genome genes (sometimes overlapping with #6, similarity-based curation) essentially all GO curation [10-20%]

8. Maintain dictyBase pages, documentation, SOPs etc [5-10%]

9. Curation consistency: Once a month (we try to) All three dictybase curators curate 3 papers (1 suggested by each curator) and annotate it fully, and then we compare annotations and make sure we do things in a consistent manner (technically, 3-5 hours each month, but we had to skip this quite a bit) [2% of the time]

10. Miscellaneous Email, informal chats, discussions, lunch ;)

I am not sure the numbers quite add up; you can add whatever's missing to 'lunch' ;) Let me know if that's detailed enough.

Pascale

Rama Balakrishnan for SGD

For me #1 and #2 never shifts. Others shift depending on what is involved with each project.

1. User suppport (SGD and GO)

2. Fix any errors that are reported by SGD's checking scripts (this is on a rotation schedule at SGD).

3. Curation (Literature guide, GO annotations, phenotypes, writing gene summary paragraphs, metabolic pathways). GO annotations sometimes involves improving the ontology and/or requesting new terms

4. Attend meetings (SGD weekly meetings, AmiGO chat, Outreach chat). Follow up on issues that come out of these meetings

5. Reference genome project (curators at SGD take turns to curate reference genome genes. So, each curator gets a turn once in 2-3 months).

6. Commenting on other Source Forge items

7. Testing any SGD related interfaces, AmiGO, documentation etc.

Fiona McCarthy for AgBase

GO Related Tasks

95% of time is GO related activity. 0% is paid for by the GOC Grant.

(Typically the first 3 priorities do not change. The order of the others may change based on need.)


GO Related Priorities

1. Obtaining competitive funding for AgBase (in my case this is primarily but not exclusively GO related activity) and writing papers to serve as preliminary data for future grants.

2. Promoting the use of AgBase by agricultural researchers (this is primarily but not exclusively GO related activity). A large proportion of this work includes introducing people to GO and demonstrating how the GO can be useful for their work.

3. Answering AgBase user requests and queries.

4. Supervising (with Susan Bridges) the AgBase website, database updates and the development and testing of AgBase GO and Proteomics related computational tools.

5. Supervision of a PhD student. (50% GO related activity)

6. Collaboration projects with non-MSU researchers to provide annotation for their array datasets. Typically there have been 2-3 of these collaborative projects a year.

7. Collaboration with MSU research groups to provide functional analysis for chicken, cow, corn, poplar, pig, Pasteurella, loblolly pine, Salmonella datasets.

8. Providing chick annotations for the Reference genome Project.

9. Co-ordinating the AgBase GO annotation effort. In addition to the GO literature-based GO annotations I provide, I have 2 part time workers who provide ISS annotations for chicken and cow proteins not represented in UniProtKB (and which do not have IEA mappings). I am responsible for collation & QC all AgBase GO annotations and submission to EBI-GOA via the Protein2GO tool.

10. Literature based annotation for agricultural species other than chicken (eg. cow, sheep). In practice this is very rare due to time constraints. On rare occasions I have been asked to annotate a particular gene product for a researcher (eg. Marek’s Disease Virus and Channel Catfish).

11. Collaboration with the MSU library to improve access to journals for AgBase GO annotators.


Michelle Gwinn at TIGR

Continuous (or semi-continuous) demands on my time:

-PAMGO term development and advising PAMGO (I am funded to spend 15% of my time on this - it includes organizing and attending workshops, attending conferences, phone calls, email, etc.)

-attending meetings, giving posters/presentations/staffing booths (to promote TIGR tools and services like the Annotation Engine, to give annotation workshops)

-GO term requests for annotation needs of team

-TIGR GO data management

-GO association file generation and updating

-any outreach activities not associated with my regular annotation courses or the Annotation Engine or conferences


Sporadic demands on my time - but when it is time for these activities, they are my absolute top priority and all other things get put off

-teaching annotation classes, or preparing to teach classes (this occurs 4 times per year during spring/summer/fall and is the top priority right before and during each class)

-grant writing

-training of new team members at TIGR

I've ordered the items in the two sections according to priority.