Search Mailing List Archives


Limit search to: Subject & Body Subject Author
Sort by: Reverse Sort
Limit to: All This Week Last Week This Month Last Month
Select Date Range     through    

[go-friends] NIH RFI on Strategic Plan for Data Science: Database vs Knowledge base

Chris Mungall cjmungall at lbl.gov
Wed Mar 7 19:46:40 PST 2018


Good point.

Not to re-enact the 'function wars' again, but everyone here should read
the chapter on what GO believes to be the meaning of biological function
from the GO handbook:

https://link.springer.com/protocol/10.1007/978-1-4939-3743-1_2/fulltext.html

On Tue, Mar 6, 2018 at 1:12 PM, Valerie Wood <vw253 at cam.ac.uk> wrote:

>
> That's interesting, and clearly  does require a robust response.
>
> What constitutes  "functional data" was massively confused by
> https://www.ncbi.nlm.nih.gov/pubmed/17571346
> .....we are still dealing with the consequences...
>
> v
>
>
>
>
> On 06/03/2018 20:53, Carol Bult wrote:
>
> I don’t think the errors in concepts are obvious to the individuals who
> drafted the report. Chris’ comments mirror the same points I raised in a
> closed session of NHGRI’s Advisory Council a few weeks ago when this report
> was previewed. The positive thing is that NIH realizes that they need a
> different approach to funding data resources and that the criteria for
> evaluation need to be different than for a typical R01 grant….  But the
> individuals on the internal NIH committee that drafted the data science
> plan are not data scientists and this is reflected in the lack of clarity
> that Chris noted. It is really important to have robust community responses
> to this plan to help shape the directions for future funding models of data
> resources at NIH.
>
>
>
>
>
>
>
> *____________________*
>
> *Carol J. Bult, Ph.D.*
>
> Professor and Knowlton Family Chair
>
> Deputy Director, JAX Cancer Center
>
> Scientific Director, JAX PDX and Cancer Avatar Program
>
> The Jackson Laboratory (JAX)
>
> 600 Main Street
>
> Bar Harbor, ME 04609
>
> 207-288-6324 <(207)%20288-6324>
>
> carol.bult at jax.org
>
> www.jax.org
>
>
>
> The Jackson Laboratory: *Leading the search for tomorrow's cures*
>
>
>
> *From: *go-friends <go-friends-bounces at lists.stanford.edu>
> <go-friends-bounces at lists.stanford.edu> on behalf of Valerie Wood
> <vw253 at cam.ac.uk> <vw253 at cam.ac.uk>
> *Date: *Tuesday, March 6, 2018 at 3:40 PM
> *To: *"go-friends at lists.stanford.edu" <go-friends at lists.stanford.edu>
> <go-friends at lists.stanford.edu> <go-friends at lists.stanford.edu>
> *Subject: *Re: [go-friends] NIH RFI on Strategic Plan for Data Science:
> Database vs Knowledge base
>
>
>
>
> I agree Chris, but this seems so obvious an error that its possibly just a
> mistake that requires correction?
>
> v.
>
> On 06/03/2018 19:56, Chris Mungall wrote:
>
> The NIH has put at an RFI together with a draft strategic plan:
> https://grants.nih.gov/grants/guide/notice-files/NOT-OD-18-134.html
>
> I want to draw people's attention to p10 of the report
>
> *"NIH will distinguish between **databases** and **knowledgebases** (see
> text box “Databases and Knowledgebases: What’s the Difference?”) and will **support
> each separately from one another**"*
>
> OK, this is interesting. But caution advised, these are two pretty squishy
> terms that are used differently by different communities. For those of us
> with an AI background, "databases" are typically closer to the raw data,
> are curated at the level of metadata rather than data, whereas "knowledge
> bases" contain curated generalizations of the data. GO is a classic
> knowledge base (or Knowledge Graph, now that google has made that trendy).
> However it's historically been called a "database" since that is the term
> the community normally uses.
>
> Anyway, the distinction that the NIH makes in the report (box at bottom of
> p10 of the report) doesn't make any sense to me:
>
>    - an example of what might be in a database is *"functional
>    annotations of gene products"*
>    - an example of what might be in a knowledgebase is *"protein-protein
>    interaction networks"*
>
> To me this is precisely reversed. PPI networks are often raw data, e.g.
> coIP. A functional annotation is as absolutely paradigmatic case of
> knowledge as you could wish for.
>
> Normally I save terminological minutiae such as "what's the difference
> between an ontology and terminology" to the bar or to the filing cabinet
> marked Pointless Discussions We Used To Have In The Early Days of GO.
> However, if the NIH is going to make important funding decisions based on a
> difference between "Database" and "Knowledge Base", it's crucial that we
> educate them. This is important for GO (and for other knowledge
> databases/repositories/resources/whatever you want to call them). Given
> that functional annotation is explicitly called out in the draft report, I
> think this calls for a specific response from the entire GO community.
>
>
>
>
> _______________________________________________
>
> go-friends mailing list
>
> go-friends at lists.stanford.edu
>
> https://mailman.stanford.edu/mailman/listinfo/go-friends
>
>
>
> --
>
> University of Cambridge
>
> PomBase http://www.pombase.org/
>
> Cambridge Systems Biology Centre http://www.sysbiol.cam.ac.uk/Investigators/val-wood
>
> ---
>
> The information in this email, including attachments, may be confidential
> and is intended solely for the addressee(s). If you believe you received
> this email by mistake, please notify the sender by return email as soon as
> possible.
>
>
> --
> University of Cambridge
> PomBase http://www.pombase.org/
> Cambridge Systems Biology Centre http://www.sysbiol.cam.ac.uk/Investigators/val-wood
>
>
> _______________________________________________
> go-friends mailing list
> go-friends at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/go-friends
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.stanford.edu/pipermail/go-friends/attachments/20180307/5cc79337/attachment-0001.html>


More information about the go-friends mailing list