<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=utf-8">
<html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40"><head><meta name=Generator content="Microsoft Word 14 (filtered medium)"><!--[if !mso]><style>v\:* {behavior:url(#default#VML);}
o\:* {behavior:url(#default#VML);}
w\:* {behavior:url(#default#VML);}
.shape {behavior:url(#default#VML);}
</style><![endif]--><style><!--
/* Font Definitions */
@font-face
        {font-family:Calibri;
        panose-1:2 15 5 2 2 2 4 3 2 4;}
@font-face
        {font-family:Tahoma;
        panose-1:2 11 6 4 3 5 4 4 2 4;}
@font-face
        {font-family:Consolas;
        panose-1:2 11 6 9 2 2 4 3 2 4;}
@font-face
        {font-family:"Trebuchet MS";
        panose-1:2 11 6 3 2 2 2 2 2 4;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
        {margin:0in;
        margin-bottom:.0001pt;
        font-size:12.0pt;
        font-family:"Times New Roman","serif";}
a:link, span.MsoHyperlink
        {mso-style-priority:99;
        color:blue;
        text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
        {mso-style-priority:99;
        color:purple;
        text-decoration:underline;}
p
        {mso-style-priority:99;
        margin:0in;
        margin-bottom:.0001pt;
        font-size:12.0pt;
        font-family:"Times New Roman","serif";}
pre
        {mso-style-priority:99;
        mso-style-link:"HTML Preformatted Char";
        margin:0in;
        margin-bottom:.0001pt;
        font-size:10.0pt;
        font-family:"Courier New";}
p.MsoAcetate, li.MsoAcetate, div.MsoAcetate
        {mso-style-priority:99;
        mso-style-link:"Balloon Text Char";
        margin:0in;
        margin-bottom:.0001pt;
        font-size:8.0pt;
        font-family:"Tahoma","sans-serif";}
span.HTMLPreformattedChar
        {mso-style-name:"HTML Preformatted Char";
        mso-style-priority:99;
        mso-style-link:"HTML Preformatted";
        font-family:Consolas;}
span.BalloonTextChar
        {mso-style-name:"Balloon Text Char";
        mso-style-priority:99;
        mso-style-link:"Balloon Text";
        font-family:"Tahoma","sans-serif";}
p.msochpdefault, li.msochpdefault, div.msochpdefault
        {mso-style-name:msochpdefault;
        mso-style-priority:99;
        margin:0in;
        margin-bottom:.0001pt;
        font-size:10.0pt;
        font-family:"Times New Roman","serif";}
span.emailstyle19
        {mso-style-name:emailstyle19;
        font-family:"Calibri","sans-serif";
        color:#1F497D;}
span.ontologysubmissionstatus
        {mso-style-name:ontologysubmissionstatus;}
span.EmailStyle25
        {mso-style-type:personal;
        font-family:"Calibri","sans-serif";
        color:#1F497D;}
span.EmailStyle26
        {mso-style-type:personal-reply;
        font-family:"Calibri","sans-serif";
        color:#1F497D;}
.MsoChpDefault
        {mso-style-type:export-only;
        font-size:10.0pt;}
@page WordSection1
        {size:8.5in 11.0in;
        margin:1.0in 1.0in 1.0in 1.0in;}
div.WordSection1
        {page:WordSection1;}
--></style><!--[if gte mso 9]><xml>
<o:shapedefaults v:ext="edit" spidmax="1026" />
</xml><![endif]--><!--[if gte mso 9]><xml>
<o:shapelayout v:ext="edit">
<o:idmap v:ext="edit" data="1" />
</o:shapelayout></xml><![endif]--></head><body lang=EN-US link=blue vlink=purple><div class=WordSection1><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>We were just talking about this today in our daily developer meeting. <o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>If you submit an ontology manually then a submission is created immediately and this is visible on the summary page for the ontology. You should also see a status for the submission. It will be in the “uploaded” status until it gets parsed.<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>For “load from URL” ontologies the submission entry won’t get created until we detect a new ontology (roughly midnight, Pacific time).<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>We are considering having something a bit more “in your face” but we don’t have any immediate plans to implement something like this.<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Ray <o:p></o:p></span></p><p class=MsoNormal><a name="_MailEndCompose"><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></a></p><div><div style='border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0in 0in 0in'><p class=MsoNormal><b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span></b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'> Chung, Caty Elizabeth [mailto:c.chung@med.miami.edu] <br><b>Sent:</b> Thursday, November 20, 2014 4:09 PM<br><b>To:</b> Ray Fergerson<br><b>Cc:</b> support@bioontology.org; Stephan Schurer PhD<br><b>Subject:</b> Re: [bioontology-support] BioAssay Ontology<o:p></o:p></span></p></div></div><p class=MsoNormal><o:p> </o:p></p><div><p class=MsoNormal>Ray,<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>Please, do apologize the impatience, BioPortal is a phenomenal resource.  In the case of a new revision, could the system email a notification the Ontology has been parsed or not?<br><br>Caty<o:p></o:p></p></div><div><p class=MsoNormal style='margin-bottom:12.0pt'><br>On Nov 20, 2014, at 4:59 PM, "Ray Fergerson" <<a href="mailto:ray.fergerson@stanford.edu">ray.fergerson@stanford.edu</a>> wrote:<o:p></o:p></p></div><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Caty,</span><o:p></o:p></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'> </span><o:p></o:p></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>We pick up the “load from URL” ontologies nightly. Thus a one day delay is to be expected.</span><o:p></o:p></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><br>Ray</span><o:p></o:p></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'> </span><o:p></o:p></p><div><div style='border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0in 0in 0in'><p class=MsoNormal><b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span></b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'> Chung, Caty Elizabeth [<a href="mailto:c.chung@med.miami.edu">mailto:c.chung@med.miami.edu</a>] <br><b>Sent:</b> Thursday, November 20, 2014 7:25 AM<br><b>To:</b> Ray Fergerson; <a href="mailto:support@bioontology.org">support@bioontology.org</a><br><b>Cc:</b> Stephan Schurer PhD<br><b>Subject:</b> Re: [bioontology-support] BioAssay Ontology</span><o:p></o:p></p></div></div><p class=MsoNormal> <o:p></o:p></p><div id=divtagdefaultwrapper><p style='background:white'><span style='font-family:"Calibri","sans-serif";color:black'>Hi Ray,</span><o:p></o:p></p><p style='background:white'><span style='font-family:"Calibri","sans-serif";color:black'>Looks great!  The downloads are working fine too.</span><o:p></o:p></p><p style='background:white'><span style='font-family:"Calibri","sans-serif";color:black'><a href="http://bioportal.bioontology.org/ontologies/BAO" id=lnk712337>http://bioportal.bioontology.org/ontologies/BAO</a>​</span><o:p></o:p></p><p style='background:white'><span style='font-family:"Calibri","sans-serif";color:black'>Thanks,</span><o:p></o:p></p><p style='background:white'><span style='font-family:"Calibri","sans-serif";color:black'>Caty</span><o:p></o:p></p><div><div class=MsoNormal align=center style='text-align:center;background:white'><span style='font-family:"Calibri","sans-serif";color:#212121'><hr size=2 width="98%" align=center></span></div><div id=divRplyFwdMsg><p class=MsoNormal style='background:white'><b><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'>From:</span></b><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'> Chung, Caty Elizabeth<br><b>Sent:</b> Wednesday, November 19, 2014 12:36 PM<br><b>To:</b> Ray Fergerson; <a href="mailto:support@bioontology.org">support@bioontology.org</a><br><b>Cc:</b> Stephan Schurer PhD<br><b>Subject:</b> Re: [bioontology-support] BioAssay Ontology</span><span style='font-family:"Calibri","sans-serif";color:#212121'> </span><o:p></o:p></p><div><p class=MsoNormal style='background:white'><span style='font-family:"Calibri","sans-serif";color:#212121'> </span><o:p></o:p></p></div></div><div><div id=divtagdefaultwrapper><p style='background:white'><span style='font-family:"Calibri","sans-serif";color:black'>​Hi Ray,</span><o:p></o:p></p><p style='background:white'><span style='font-family:"Calibri","sans-serif";color:black'>In BioPortal the setting selection is "</span><span style='font-family:"Trebuchet MS","sans-serif";color:black'>Load from URL  </span><span style='font-size:8.5pt;font-family:"Trebuchet MS","sans-serif";color:black'>(new versions loaded daily)"</span><o:p></o:p></p><p style='background:white'><span style='font-family:"Calibri","sans-serif";color:black;background:white'>Yesterday before noon, we released BAO revision 2986.  BioPortal does not seem to pick up BAO.  ​</span><o:p></o:p></p><p style='background:white'><span style='font-family:"Calibri","sans-serif";color:black'>Should I submit manually?</span><o:p></o:p></p><p style='background:white'><span style='font-family:"Calibri","sans-serif";color:black'>Caty</span><o:p></o:p></p><pre style='background:white;word-wrap:break-word;white-space:pre-wrap'><span style='color:black'>        <rdfs:comment>Release date: November 18, 2014</rdfs:comment></span><o:p></o:p></pre><pre style='background:white'><span style='color:black'>        <rdfs:comment>svn:  2986</rdfs:comment></span><o:p></o:p></pre><p style='background:white'><span style='font-family:"Calibri","sans-serif";color:black'> </span><o:p></o:p></p><div><div class=MsoNormal align=center style='text-align:center;background:white'><span style='font-family:"Calibri","sans-serif";color:#212121'><hr size=2 width="98%" align=center></span></div><div id=divRplyFwdMsg><p class=MsoNormal style='background:white'><b><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'>From:</span></b><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'> Ray Fergerson <<a href="mailto:ray.fergerson@stanford.edu">ray.fergerson@stanford.edu</a>><br><b>Sent:</b> Tuesday, November 11, 2014 7:17 PM<br><b>To:</b> Chung, Caty Elizabeth; <a href="mailto:support@bioontology.org">support@bioontology.org</a><br><b>Cc:</b> Stephan Schurer PhD<br><b>Subject:</b> RE: [bioontology-support] BioAssay Ontology</span><span style='font-family:"Calibri","sans-serif";color:#212121'> </span><o:p></o:p></p><div><p class=MsoNormal style='background:white'><span style='font-family:"Calibri","sans-serif";color:#212121'> </span><o:p></o:p></p></div></div><div><div><p class=MsoNormal style='background:white'><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Please have a look at BAO now and let us know if you think that it needs to be changed. It appears that the most recent load has worked correctly.</span><o:p></o:p></p><p class=MsoNormal style='background:white'><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'> </span><o:p></o:p></p><p class=MsoNormal style='background:white'><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Ray</span><o:p></o:p></p><p class=MsoNormal style='background:white'><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'> </span><o:p></o:p></p><div><div style='border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0in 0in 0in'><p class=MsoNormal style='background:white'><b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";color:#212121'>From:</span></b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";color:#212121'> bioontology-support [<a href="mailto:bioontology-support-bounces@lists.stanford.edu">mailto:bioontology-support-bounces@lists.stanford.edu</a>] <b>On Behalf Of </b>Chung, Caty Elizabeth<br><b>Sent:</b> Saturday, November 1, 2014 5:35 AM<br><b>To:</b> <a href="mailto:support@bioontology.org">support@bioontology.org</a><br><b>Cc:</b> 'Stephan Schurer PhD'<br><b>Subject:</b> [bioontology-support] BioAssay Ontology</span><o:p></o:p></p></div></div><p class=MsoNormal style='background:white'><span style='color:#212121'> </span><o:p></o:p></p><p style='background:white'><span style='font-family:"Calibri","sans-serif";color:black'>Hello,</span><o:p></o:p></p><p style='background:white'><span style='font-family:"Calibri","sans-serif";color:black'> </span><o:p></o:p></p><p style='background:white'><span style='font-family:"Calibri","sans-serif";color:black'>Yesterday roughly 2 pm EST, we published on our site a new version of BAO.  Roughly 8 am EST I checked, did not see it updated on BioPortal.  I uploaded the file and I pointed to our site.  It seems that pointing to our site is not working.  <a href="http://www.bioassayontology.org/bao/bao_complete.owl" id=lnk171171>http://www.bioassayontology.org/bao/bao_complete.owl</a></span><o:p></o:p></p><p style='background:white'><span style='font-family:"Calibri","sans-serif";color:black'> </span><o:p></o:p></p><p style='background:white'><span style='font-family:"Calibri","sans-serif";color:black'>Now I see two lines, one breaks the other one works.  Sorry!  Can you clean up the for my mistake?</span><o:p></o:p></p><p style='background:white'><span style='font-family:"Calibri","sans-serif";color:black'> </span><o:p></o:p></p><p style='background:white'><span style='font-family:"Calibri","sans-serif";color:black'><a href="http://bioportal.bioontology.org/ontologies/BAO" id=lnk80178>http://bioportal.bioontology.org/ontologies/BAO</a></span><o:p></o:p></p><p style='background:white'><span style='font-family:"Calibri","sans-serif";color:black'> </span><o:p></o:p></p><table class=MsoNormalTable border=0 cellspacing=0 cellpadding=0 width="60%" style='width:60.0%;background:white;border-collapse:collapse;border-spacing:0px' id="ontology_versions"><tr><td style='border-top:none;border-left:none;border-bottom:solid #C1DAD7 1.0pt;border-right:solid #C1DAD7 1.0pt;padding:4.5pt 4.5pt 4.5pt 9.0pt'><p class=MsoNormal><span style='font-family:"Trebuchet MS","sans-serif"'>2.0 </span><span class=ontologysubmissionstatus><span style='font-size:10.0pt;font-family:"Trebuchet MS","sans-serif";color:gray'>(Uploaded)</span></span><o:p></o:p></p></td><td style='border-top:none;border-left:none;border-bottom:solid #C1DAD7 1.0pt;border-right:solid #C1DAD7 1.0pt;padding:4.5pt 4.5pt 4.5pt 9.0pt'><p class=MsoNormal><span style='font-family:"Trebuchet MS","sans-serif"'>04/25/2014</span><o:p></o:p></p></td><td style='border-top:none;border-left:none;border-bottom:solid #C1DAD7 1.0pt;border-right:solid #C1DAD7 1.0pt;padding:4.5pt 4.5pt 4.5pt 9.0pt'><p class=MsoNormal><span style='font-family:"Trebuchet MS","sans-serif"'>11/01/2014</span><o:p></o:p></p></td><td style='border-top:none;border-left:none;border-bottom:solid #C1DAD7 1.0pt;border-right:solid #C1DAD7 1.0pt;padding:4.5pt 4.5pt 4.5pt 9.0pt'><p class=MsoNormal><span style='font-family:"Trebuchet MS","sans-serif"'><a href="http://data.bioontology.org/ontologies/BAO/submissions/22/download?apikey=4ea81d74-8960-4525-810b-fa1baab576ff"><span style='color:#234979'>OWL</span></a></span><o:p></o:p></p></td></tr></table><p style='background:white'><span style='font-family:"Calibri","sans-serif";color:black'>Caty</span><o:p></o:p></p></div></div></div></div></div></div></div></div></blockquote></div></body></html>