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

Valerie Wood vw253 at cam.ac.uk
Tue Mar 6 13:12:29 PST 2018


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
>
> 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> on behalf 
> of Valerie Wood <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>
> *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.
>
>
>
>
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University of Cambridge
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Cambridge Systems Biology Centre http://www.sysbiol.cam.ac.uk/Investigators/val-wood

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