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<p class="MsoNormal">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.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><b><span style="font-size:12.0pt;font-family:"Times New Roman",serif">____________________<o:p></o:p></span></b></p>
<p class="MsoNormal"><b><span style="font-size:12.0pt;font-family:"Times New Roman",serif">Carol J. Bult, Ph.D.</span></b><span style="font-size:12.0pt;font-family:"Times New Roman",serif"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Times New Roman",serif">Professor and Knowlton Family Chair<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Times New Roman",serif">Deputy Director, JAX Cancer Center<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Times New Roman",serif">Scientific Director, JAX PDX and Cancer Avatar Program<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Times New Roman",serif">The Jackson Laboratory (JAX)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Times New Roman",serif">600 Main Street<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Times New Roman",serif">Bar Harbor, ME 04609<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Times New Roman",serif">207-288-6324<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Times New Roman",serif">carol.bult@jax.org<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Times New Roman",serif">www.jax.org<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Times New Roman",serif"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Times New Roman",serif">The Jackson Laboratory:
<i>Leading the search for tomorrow's cures</i><o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><b><span style="font-size:12.0pt;color:black">From: </span></b><span style="font-size:12.0pt;color:black">go-friends <go-friends-bounces@lists.stanford.edu> on behalf of Valerie Wood <vw253@cam.ac.uk><br>
<b>Date: </b>Tuesday, March 6, 2018 at 3:40 PM<br>
<b>To: </b>"go-friends@lists.stanford.edu" <go-friends@lists.stanford.edu><br>
<b>Subject: </b>Re: [go-friends] NIH RFI on Strategic Plan for Data Science: Database vs Knowledge base<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><a name="_MailOriginalBody"><br>
I agree Chris, but this seems so obvious an error that its possibly just a mistake that requires correction?<br>
<br>
v.<br>
<br>
On 06/03/2018 19:56, Chris Mungall wrote:<o:p></o:p></a></p>
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<p><span style="mso-bookmark:_MailOriginalBody"><span style="font-family:"Arial",sans-serif">The NIH has put at an RFI together with a draft strategic plan:<br>
</span></span><a href="https://grants.nih.gov/grants/guide/notice-files/NOT-OD-18-134.html"><span style="mso-bookmark:_MailOriginalBody"><span style="font-family:"Arial",sans-serif;color:#3983C4">https://grants.nih.gov/grants/guide/notice-files/NOT-OD-18-134.html</span></span><span style="mso-bookmark:_MailOriginalBody"></span></a><span style="mso-bookmark:_MailOriginalBody"><span style="font-family:"Arial",sans-serif"><o:p></o:p></span></span></p>
<p><span style="mso-bookmark:_MailOriginalBody"><span style="font-family:"Arial",sans-serif">I want to draw people's attention to p10 of the report<o:p></o:p></span></span></p>
<p><span style="mso-bookmark:_MailOriginalBody"><em><span style="font-family:"Arial",sans-serif">"NIH will distinguish between
</span></em></span><span style="mso-bookmark:_MailOriginalBody"><strong><i><span style="font-family:"Arial",sans-serif">databases</span></i></strong></span><span style="mso-bookmark:_MailOriginalBody"><em><span style="font-family:"Arial",sans-serif"> and
</span></em></span><span style="mso-bookmark:_MailOriginalBody"><strong><i><span style="font-family:"Arial",sans-serif">knowledgebases</span></i></strong></span><span style="mso-bookmark:_MailOriginalBody"><em><span style="font-family:"Arial",sans-serif"> (see
 text box “Databases and Knowledgebases: What’s the Difference?”) and will </span>
</em></span><span style="mso-bookmark:_MailOriginalBody"><strong><i><span style="font-family:"Arial",sans-serif">support each separately from one another</span></i></strong></span><span style="mso-bookmark:_MailOriginalBody"><em><span style="font-family:"Arial",sans-serif">"</span></em></span><span style="mso-bookmark:_MailOriginalBody"><span style="font-family:"Arial",sans-serif"><o:p></o:p></span></span></p>
<p><span style="mso-bookmark:_MailOriginalBody"><span style="font-family:"Arial",sans-serif">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.<o:p></o:p></span></span></p>
<p><span style="mso-bookmark:_MailOriginalBody"><span style="font-family:"Arial",sans-serif">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:<o:p></o:p></span></span></p>
<ul type="disc">
<li class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;mso-list:l0 level1 lfo1">
<span style="mso-bookmark:_MailOriginalBody"><span style="font-family:"Arial",sans-serif">an example of what might be in a database is
<em><span style="font-family:"Arial",sans-serif">"functional annotations of gene products"</span></em>
<o:p></o:p></span></span></li><li class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;mso-list:l0 level1 lfo1">
<span style="mso-bookmark:_MailOriginalBody"><span style="font-family:"Arial",sans-serif">an example of what might be in a knowledgebase is
<em><span style="font-family:"Arial",sans-serif">"protein-protein interaction networks"</span></em>
<o:p></o:p></span></span></li></ul>
<p><span style="mso-bookmark:_MailOriginalBody"><span style="font-family:"Arial",sans-serif">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.<o:p></o:p></span></span></p>
<p><span style="mso-bookmark:_MailOriginalBody"><span style="font-family:"Arial",sans-serif">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.<o:p></o:p></span></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><br>
<br>
<br>
<o:p></o:p></span></p>
<pre><span style="mso-bookmark:_MailOriginalBody">_______________________________________________<o:p></o:p></span></pre>
<pre><span style="mso-bookmark:_MailOriginalBody">go-friends mailing list<o:p></o:p></span></pre>
<pre><span style="mso-bookmark:_MailOriginalBody"></span><a href="mailto:go-friends@lists.stanford.edu"><span style="mso-bookmark:_MailOriginalBody">go-friends@lists.stanford.edu</span><span style="mso-bookmark:_MailOriginalBody"></span></a><span style="mso-bookmark:_MailOriginalBody"><o:p></o:p></span></pre>
<pre><span style="mso-bookmark:_MailOriginalBody"></span><a href="https://mailman.stanford.edu/mailman/listinfo/go-friends"><span style="mso-bookmark:_MailOriginalBody">https://mailman.stanford.edu/mailman/listinfo/go-friends</span><span style="mso-bookmark:_MailOriginalBody"></span></a><span style="mso-bookmark:_MailOriginalBody"><o:p></o:p></span></pre>
</blockquote>
<p><span style="mso-bookmark:_MailOriginalBody"><o:p> </o:p></span></p>
<pre><span style="mso-bookmark:_MailOriginalBody">-- <o:p></o:p></span></pre>
<pre><span style="mso-bookmark:_MailOriginalBody">University of Cambridge <o:p></o:p></span></pre>
<pre><span style="mso-bookmark:_MailOriginalBody">PomBase </span><a href="http://www.pombase.org/"><span style="mso-bookmark:_MailOriginalBody">http://www.pombase.org/</span><span style="mso-bookmark:_MailOriginalBody"></span></a><span style="mso-bookmark:_MailOriginalBody"><o:p></o:p></span></pre>
<pre><span style="mso-bookmark:_MailOriginalBody">Cambridge Systems Biology Centre </span><a href="http://www.sysbiol.cam.ac.uk/Investigators/val-wood"><span style="mso-bookmark:_MailOriginalBody">http://www.sysbiol.cam.ac.uk/Investigators/val-wood</span><span style="mso-bookmark:_MailOriginalBody"></span></a><span style="mso-bookmark:_MailOriginalBody"><o:p></o:p></span></pre>
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