<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>Hi James, </div><div><br></div><div>Here are some suggestions for values:</div><div>-status - Discussion and review</div><div>-domain - Biomedical Resources</div><div>-format - OWL</div><div>-patho_type - can be left blank, but include tab for spacing</div><div>-subtypes_of - can be left blank, but include tab for spacing</div><div>-is_obsolete - can be left blank, but include tab for spacing</div><div>-granularity - can be left bank, but include tab for spacing</div><div><br></div><div>I think that should take care of things. A metadata file for EFO is also needed. It was not clear previously that 2 files are needed for the process, one with repository information that we keep on our side and another with the ontology metadata that needs to be within a subfolder where the ontology is located within SVN on your side. </div><div><br></div><div>Trish</div><div><br></div><br><div><div>On Dec 11, 2009, at 8:06 AM, James Malone wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Hi Trish,<br><br>I'm trying to complete the metadata for the software ontology. Some of it made no sense to me outside of the context of the example given and i didn't know what valid values for these fields were. Is there a definition for some of the fields and the values they can take (I've listed them below)? Thanks.<br><br>Access info is:<br><br>SVN directory:<br>/trunk/src/softwareontologyinowl/InferredSWOOWLview<br>OWL file is:<br>/trunk/src/softwareontologyinowl/InferredSWOOWLview/SWO_inferred.owl<br><br>Anonymous check out is enabled.<br>For metadata, I need help on these fields:<br><br>status<br>patho_type    granularity relevant_organism    - *no idea for software<br>domain<br>subtypes_of<br>is_obsolete   format <br>Cheers,<br><br>James<br><br><br><br>Trish Whetzel wrote:<br><blockquote type="cite">Hi James, <br></blockquote><blockquote type="cite">The code to do the automatic pull from SVN repositories is now ready for testing. Can you generate the ontology metadata file as described below and send the following:<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">    * Access information for the SVN repository for the Software ontology<br></blockquote><blockquote type="cite">    * Full path to the ontology metadata file. I believe that one file<br></blockquote><blockquote type="cite">      with information for both ontologies should be fine.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Thanks,<br></blockquote><blockquote type="cite">Trish<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">On Dec 3, 2009, at 12:46 PM, Michael Dorf wrote:<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><blockquote type="cite">Hi Trish/James,<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">First, I'd like to clarify that the current production version of<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">BioPortal only supports CVS based ontology auto-pull.  Our next release,<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">due in production in about ten days, does introduce support for SVN<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">repositories.<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Below are the artifacts we will need for including the repository into our<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">automatic pull:<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">1. SVN Access URL with the full path to the ontology file location<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">2. Username/password (if any)<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">3. Full path (in the repository) to a text file that stores ontology<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">metadata in the following format (also, see the attached sample):<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">id caro<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">title Common Anatomy Reference Ontology<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">namespace CARO<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">foundry Yes<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">status Discussion and review<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">download<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><a href="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/caro/ca">http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/caro/ca</a><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">ro.obo<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">source<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">home CARO Wiki|<a href="http://www.bioontology.org/wiki/index.php/CARO:Main_Page">http://www.bioontology.org/wiki/index.php/CARO:Main_Page</a><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">documentation<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">contact Melissa Haendel obo-anatomy lists.sourceforge.net<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">format obo<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">description The Common Anatomy Reference Ontology (CARO) is being<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">developed to facilitate interoperability between existing anatomy<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">ontologies for different species, and will provide a template for building<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">new anatomy ontologies. CARO will be described in Anatomy Ontologies for<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Bioinformatics: Principles and Practice Albert Burger, Duncan Davidson and<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Richard Baldock (Editors)<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">relevant_organism all<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">subtypes_of bfo:IndependentContinuant<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">domain anatomy<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">patho_type canonical<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">granularity organismal<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">I recommend pasting this snippet into an editor that lets you view the<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">tabs, spaces and line breaks so you can distinguish between the various<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">delimiters used in the file.  These are important for proper parsing of<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">the values on our end.<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Let me know if you have questions.<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Thanks,<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Misha<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">-----Original Message-----<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">From: Trish Whetzel [<a href="mailto:whetzel@stanford.edu">mailto:whetzel@stanford.edu</a>]<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Sent: Thursday, December 03, 2009 9:34 AM<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">To: James Malone; Michael Dorf<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Cc: <a href="mailto:support@bioontology.org">support@bioontology.org</a><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Subject: Re: [bioontology-support] Software Ontology<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Hi James,<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Very much interested to see the Software Ontology. Has the location of  this ontology been included in your SVN repository file for the  automatic pull?<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">***Misha, can you confirm if anything additional to the repository  file is needed to include this ontology in the automatic pull?<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">James, do you have mappings generated for the Software Ontology? Also,  would it make sense to load this as a 'view' of EFO - is this a subset  of EFO or does this extend from the software class in EFO? I can talk  to via Skype about views further if you like.<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Trish<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">On Dec 3, 2009, at 9:17 AM, James Malone wrote:<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Hi,<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">We have had a project working on creating a software ontology that  we needed for a branch of EFO. We've kept it separate though so it  can be reused as separate ontology. I'd like to get this Software  Ontology uploaded to BioPortal if possible please!  I've uploaded to  our public SVN, but can you let me know what details you require for  me to get it uploaded to BioPortal. I guess you might need some  extra bits like a description etc.<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Many thanks in advance!<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">James<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">-- <br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">European Bioinformatics Institute, Wellcome Trust Genome Campus,  Hinxton, Cambridge, CB10 1SD, United Kingdom<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Tel: + 44 (0) 1223 494 676<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Fax: + 44 (0) 1223 492 468<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">_______________________________________________<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">bioontology-support mailing list<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><a href="mailto:bioontology-support@lists.stanford.edu">bioontology-support@lists.stanford.edu</a><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><a href="https://mailman.stanford.edu/mailman/listinfo/bioontology-support">https://mailman.stanford.edu/mailman/listinfo/bioontology-support</a><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><ontologies.txt><br></blockquote></blockquote><blockquote type="cite"><br></blockquote><br><br>-- <br>European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom<br>Tel: + 44 (0) 1223 494 676<br>Fax: + 44 (0) 1223 492 468 <br></div></blockquote></div><br><div apple-content-edited="true"> <span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><div>Trish Whetzel, PhD</div><div>Outreach Coordinator</div><div>The National Center for Biomedical Ontology</div><div>Ph: 650-721-2378</div><div><a href="mailto:whetzel@stanford.edu">whetzel@stanford.edu</a></div><div><a href="http://www.bioontology.org">http://www.bioontology.org</a></div><div><br></div><div> </div></div></div></span> </div><br></body></html>