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

Jaiswal, Pankaj - OSU jaiswalp at
Tue Mar 6 13:11:26 PST 2018

a structured set of data held in a computer, especially one that is 
accessible in various ways.
It's more like a datastore/data archive in some format that may/may_not 
be tied to a DB schema etc. e.g. a catalog of sequences/SNPs (with no 
additional inference drawing capability)


    a store of information or data that is available to draw on. [tied
    to the Database/Data_store)
    **the underlying set of facts, assumptions, and rules that a
    computer system has available to solve a problem.

I agree with Chris.  In this reference I consider GO, Planteome and all 
MOD project databases/data_stores as Knowledgebase, because it satisfies 
the 'inference' making capability, provides analytical tools and informs 
about various topic areas and their contextual relationships. rather 
than a simple catalog of objects. May be there is a bigger message on 
how these resources will be funded.


On 3/6/2018 11:56 AM, Chris Mungall wrote:
> The NIH has put at an RFI together with a draft strategic plan:
> 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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> go-friends at

Pankaj Jaiswal, PhD
Associate Professor
Dept. of Botany and Plant Pathology
2082 Cordley Hall
Oregon State University
Corvallis, OR, 97331

Ph.: +1-541-737-8471
Fax: +1-541-737-3573
email: jaiswalp at

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