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

Karen Eilbeck keilbeck at
Tue Mar 6 12:18:41 PST 2018

I agree with Chris here, this is also the opposite of my understanding of the difference between a database and a knowledgebase

From: go-friends <go-friends-bounces at> on behalf of Chris Mungall <cjmungall at>
Date: Tuesday, March 6, 2018 at 12:59 PM
To: "go-friends at" <go-friends at>
Subject: [go-friends] NIH RFI on Strategic Plan for Data Science: Database vs Knowledge base

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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