How to increase profile [meetings, workshops, software, training, etc]

[J Clark]

Hi Shane,

Thanks for this update on AgBase below. It's really hard for us to know 
how much buffering of questions you're doing so it's good to hear about 
that. I didn't realise that you were getting funding related to corn. 
Are you annotating that then? I've had real trouble getting groups with 
money to annotate corn (you mean Zea mays right?).

In response to your point about GO and PAG, we have had talks there 
every year for several years but this is our first full day session. The 
plant ontology consortium also do a lot there. I think that as long as 
there is demand we will be welcome to have a long session like this. 
There were no problems at all when I wrote and asked for the space.
Would you perhaps like to explore the idea of having an Agriculture/Farm 
animal GO session? I think it may not be too late to set one up if the 
group feel the need more airtime. It took all of about 20 minutes to get 
my GO session organised and it would be great publicity.

Thanks,

Jen


> 
> - Plant & Animal Genome (San Diego) - we should make a concerted effort to
> spread the idea 
> 
> I am speaking in the Chicken genome section of this meeting specifically
> on ChickGO at AgBase and Fiona is speaking in the Ruminant Section on
> CowGO and SheepGO. I am also invited to the speak at the general
> proteomics  section and GO will be mentioned there as the fundamental
> basis for our Modeling. Of course Jen has her very own GO session. Jen and
> I are discussing how we can best integrate this whole thing. Do you all
> think that we  could/should push to have a specific GO/Ontology/Annotation
> session session at PAG every year? Certainly, given the fundamental nature
> of GO (and other ontologies) for modeling functional genomics data (and
> even structurally annotating genomes to some degrees), there is a strong
> argument here. Especially as proteomics, with a much smaller interest
> group, has its own session. Also I plan to speak with the USDA genome
> administrators at PAG. 
> 
> - so what would be useful would be to share powerpoint slides, make a
> common poster - other ideas?
> Yes. Susan Fi and I do this routinely send each other our ppts and,
> speaking for Fi and I at least, I am very happy to send these to be
> archived somewhere "on the www" if it helps all involved.
> 
> A common poster would be great. If we hurry I can put it up at PAG.
>  
> - as part of our grant proposals we will have - travel, training, sharing
> of software 
> Yes we really need to generate a lot of support , and letters of support,
> from the animal and plant communities (in addition of letters of support
> from each other). I mention plants here because Dawn Luthe (corn) has been
> greatly involved in the money for AgBase and, in the USA at least, plants
> have MUCH more access to  money. This one of the reasons why it's "agBase"
> and not "LivestockBase". Though having said at AgBase, money earmarked for
> a species is spent on that species. This is why chicken is the most
> advanced animal, followed by cow.
>  
> - In addition we should be proactive and enlist those we think will be
> interested in this project (either as annotators, users?).
> Yes I agree. 
> 
> The paradigm that we have here at AgBase is that we provide a service and
> port of call for people who are interested in using GO in Ag species.
> Also, at AgBase, we think that the communities are too small and poorly
> funded to replicate what is happening at , for example, MGI in mouse. So
> we are encouraging those PIs who need GO annotations for their genes of
> interest, and in situations were we haven't already done the manual
> annotations, to manually annotate their genes of interest as experts in
> their area of interest. We also hold a database of all papers PMID numbers
> that we manually annotate (you just can’t see it on AgBase yet) so that 1.
> people don’t have to re-annotate the same papers over and over again
> (believe me, no wants to annotate more papers than they need to) and 2. we
> can identify papers that can be used in annotation QC. Christine at TAMU
> will hold a database for her bovine manual GO annotations and Christine
> and AgBase will swap these with each other.Of course we have come full
> circle here because people will need to know how to GO annotate. 
> 
> So here at AgBase we have a 12 hour long course (we developed this after
> Fiona spent two weeks at MGI with Judy Blake’s group). This course is kind
> of an expanded version of what Jen is doing at PAG. 
> 
> We have run this course on campus here twice and we have it pretty well
> ironed out. We have trained about 12 annotators across various species. We
> have not had any issues with annotations sent by these people to GOA via
> AgBase. I have recently been asked if we can do the same course for others
> outside of MSU. I said, that yes we could (in theory). Fiona is speaking
> about this at the 1st annual  Biocurator meeting.
> 
> At AgBase we are acting at the moment as a kind of buffer for GOA so that
> we can answer a lot (all?) of the Agriculture beginners questions in GO
> and save the GOA folks for answering our hard questions.
>