PIs response to priority list: Difference between revisions
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[[Category:Advocacy and Outreach]] | |||
Here are our thoughts about the priorities for Outreach to groups | Here are our thoughts about the priorities for Outreach to groups | ||
seeking support in providing GO annotations for their genomes. | seeking support in providing GO annotations for their genomes. |
Latest revision as of 13:42, 2 July 2014
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.