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[go-friends] NIH RFI on Strategic Plan for Data Science: Database vs Knowledge base
cjmungall at lbl.gov
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
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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