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

Chris Mungall cjmungall at
Tue Mar 6 11:56:54 PST 2018

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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