PIs response to priority list
Here are our thoughts about the priorities for Outreach to groups
seeking support in providing GO annotations for their genomes.
1. The highest priority at the moment is to provide the documentation and procedures for initial annotations of new genomes as 'guidelines recommended by the GO Consortium'. This task is essentially 'Aim 3' in the grant.
The initial step would be to create a document that outlines the annotation process. In addition, a case study, such as how the Chicken genome came to be annotated—what order events happened in, how the timing worked, what software was used, how they interacted with their GOA mentors, and so on—would be very useful.
As far as the documentation; you might start with this outline...
First, a brief statement about how the annotation process starts once the genes or gene products are defined (i.e. unique, stable IDs/ identifiers from UniProt or RefSeq are available for their sequences). Then, the document should include steps for doing GO annotations by various methods including automated methods such as InterProScan approach or by incorporating experimentally based annotations of orthologs; and curated methods such as assigning literature (experimentally) based GO annotations. The document should provide pointers to the existing documentation wherever possible. Thirdly, there should be information on the gene association file format and how to submit.
Once this documentation [essentially a 'standard operating procedure' not a detailed how-to] is defined, it can then be used to frame the inquiries of annotation groups and to support these groups in many contexts.
a. It can be turned into a tutorial (your flash tutorial mentioned below would be one implementation, but we do not see that as the highest priority, we are concerned that it could easily consume lots of time with little return).
b. It can help mentors as a guide as they work with new annotation groups.
c. It can provide the guide for GOC to evaluate annotation sets provided by these new groups although groups don't have to use these methods necessarily and may find other approaches more applicable for their own genome annotation effort.
2. As far as the tasks you listed, we include our responses below.
a. "Get the database so it is accessible to all in this group for reading and adding info.”—We think that currently the database is essential to track groups and information about them, but is primarily for your own use and therefore there is no need to make it accessible to anyone else. We hope that you will use the database to monitor the status and progress of each group as they proceed through the steps of generating and submitting annotations.
b. “Make a start on a flash tutorial on annotation.”—See above.
c. “Put species-specific contacts on the website so people interested in annotating can get in touch with the right person.”—At the moment, the contacts would be the persons noted in the table in the grant, or their replacements. It would be one of your tasks as 'primary contact person' to directly communicate with a person wanting to provide annotations, and point them towards the appropriate contact person. Is this too many people? The list should go on the current web site (see #g.)
d. “Get AmiGO changed so that if a person searches on a gene product name and it is not annotated then a page shows up saying that we can help people learn annotation and giving the contact details of this group.”—Please provide this idea to the AmiGO working group; they will have to prioritize this feature with the others on their list. Other than input to this group you need not be involved in AmiGO development.
e. “Work out how to deal with the fact that we are running out of mentors.”—We don't understand this. Can you give details? Where are we running out of mentors?
f. “Find out if there are meetings that we should be sending people to for outreach.”—Right now, it is most important that we get the documentation/SOP in place before we seek out more annotation groups.
g. “Get a place on the Wiki to list talks that have been given at outreach events.”—We are looking into making the GO_wiki pages public. When we do that, we can see about posting recent talks. You should also be considering developing pages for the web site itself specifically aimed at introductory material, such as this, for emerging genome groups.