Begin forwarded message:
> From: Chris Mungall <[email protected]> > Subject: Re: RDF, Linked Data, Semantic Web, SPARQL, OWL, etc. > Date: May 12, 2013 1:31:25 PM EDT > To: Todd DeLuca <[email protected]> > Cc: Suzanna Lewis <[email protected]> > > Hi Todd, > > See my email below for some answers to your questions. > > Suzi, can you forward the message to the list? I will try and re-sub with my > other address (sigh...) > > > Begin forwarded message: > >> From: Mail Delivery Subsystem <[email protected]> >> Subject: Delivery Status Notification (Failure) >> Date: May 9, 2013 11:02:25 PM PDT >> To: [email protected] >> >> Hello [email protected], >> >> We're writing to let you know that the group you tried to contact >> (orthologs) may not exist, or you may not have permission to post messages >> to the group. A few more details on why you weren't able to post: >> >> * You might have spelled or formatted the group name incorrectly. >> * The owner of the group may have removed this group. >> * You may need to join the group before receiving permission to post. >> * This group may not be open to posting. >> >> If you have questions related to this or any other Google group, visit the >> Help Centre at http://groups.google.com/support/?hl=en-GB_GB. >> >> Thanks, >> >> Google Groups >> >> >> >> ----- Original message ----- >> >> X-Received: by 10.66.8.69 with SMTP id p5mr3416293paa.46.1368165745247; >> Thu, 09 May 2013 23:02:25 -0700 (PDT) >> Return-Path: <[email protected]> >> Received: from fe1.lbl.gov (fe1.lbl.gov. [128.3.41.133]) >> by gmr-mx.google.com with ESMTP id xb6si182327pab.0.2013.05.09.23.02.25 >> for <[email protected]>; >> Thu, 09 May 2013 23:02:25 -0700 (PDT) >> Received-SPF: pass (google.com: best guess record for domain of >> [email protected] designates 128.3.41.133 as permitted sender) >> client-ip=128.3.41.133; >> Authentication-Results: gmr-mx.google.com; >> spf=pass (google.com: best guess record for domain of [email protected] >> designates 128.3.41.133 as permitted sender) [email protected] >> X-Ironport-SBRS: 4.8 >> X-IronPort-Anti-Spam-Filtered: true >> X-IronPort-Anti-Spam-Result: >> AocGAB6MjFHRVd+zlGdsb2JhbABSgz6DM4EnI4EgqAmJM4ZegVV/Fg4BAQEBBwsLCRIqgh8BAQQBThoKBwULC0YxAwEFAQsRDgcEARwEh2UGDKBXnSCCU4sTEIEuBAeCdGEDiRqKQ4R1jio/glqBe06BBA >> X-IronPort-AV: E=Sophos;i="4.87,646,1363158000"; >> d="scan'208,217";a="17240453" >> Received: from mail-ie0-f179.google.com ([209.85.223.179]) >> by fe1.lbl.gov with ESMTP; 09 May 2013 23:02:24 -0700 >> Received: by mail-ie0-f179.google.com with SMTP id c13so7226694ieb.38 >> for <[email protected]>; Thu, 09 May 2013 23:02:23 -0700 (PDT) >> X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; >> d=google.com; s=20120113; >> h=x-received:x-received:subject:mime-version:content-type:from >> :in-reply-to:date:cc:message-id:references:to:x-mailer >> :x-gm-message-state; >> bh=xD6N7OO/tnCDv7esqnNdhP9pZFe0C9gcBY8YYN4LOYE=; >> b=RGoCcRo9wzu6ZOSjG2UVZy5/Aq4YP2+MzWyH+fY+dMnuTzLm1dSvziGWv7669cvERM >> r/AOjeWQ35V1hzRDd3IXih/Z7ohckj/SCniEWoKiDT8P2zbIbcN27o0fyepjIMIyCnpJ >> TuRi6CRLByo+bDU8pEKlxXIhub4sYZ5rqoH6RNCS/Qe/zv9LHoqgploorjlF8hdnyje6 >> 1pAFCvJGSSw2eoLY5cpFY4fV2X49S44Bq+N9D6Gz57oywWqpHAfMY3aHD8FAbg0wCshW >> qIqd9qec2DQVUh+fxiG2mmQ0rguMg4VXO1R4GWA8mD9hzLHJNB9n4tT+gCGb/0oD4A1i >> eR4Q== >> X-Received: by 10.42.48.7 with SMTP id q7mr6498878icf.35.1368165743926; >> Thu, 09 May 2013 23:02:23 -0700 (PDT) >> X-Received: by 10.42.48.7 with SMTP id q7mr6498869icf.35.1368165743636; >> Thu, 09 May 2013 23:02:23 -0700 (PDT) >> Return-Path: <[email protected]> >> Received: from wireless-207-192.uchicago.edu (wireless-207-192.uchicago.edu. >> [128.135.207.192]) >> by mx.google.com with ESMTPSA id c2sm2331225igv.1.2013.05.09.23.02.19 >> for <multiple recipients> >> (version=TLSv1 cipher=ECDHE-RSA-RC4-SHA bits=128/128); >> Thu, 09 May 2013 23:02:20 -0700 (PDT) >> Subject: Re: RDF, Linked Data, Semantic Web, SPARQL, OWL, etc. >> Mime-Version: 1.0 (Apple Message framework v1278) >> Content-Type: multipart/alternative; >> boundary="Apple-Mail=_BD3D3132-4F08-47D7-8FF1-1E07F141248A" >> From: Chris Mungall <[email protected]> >> In-Reply-To: <[email protected]> >> Date: Thu, 9 May 2013 23:02:18 -0700 >> Cc: Frederic Bastian <[email protected]>, >> Jerven Bolleman <[email protected]> >> Message-Id: <[email protected]> >> References: <[email protected]> >> To: [email protected] >> X-Mailer: Apple Mail (2.1278) >> X-Gm-Message-State: >> ALoCoQnHxLotfGZOED1uVRtzO90IbJ+0y4vSYyyrZMqqJXTcerOx97vg+zQiKcsVpgOhYbT4RpO/Jt78iU65w24LjJVlxnf9gEoQlpDxoO++KnGryGgXrx1zTZZl6Tq7uzE9WmylJILE4W35NgtUHi57Ka0M7lz/IQ== >> >> >> Hi Todd, >> >> I'll answer your questions out of order. >> >> * Which ontologies already exist? >> >> See the publication "An Ontology to clarify homology-related concepts" by >> Roux and Robinson-Rechavi, and its associated ontology: >> http://dx.doi.org/10.1016/j.tig.2009.12.012 >> >> This is a broad treatment covering both gross anatomical structures and >> molecules. >> >> So has a "homology" attribute >> http://ols.wordvis.com/q=SO:0000857 >> >> CDAO may be of interest >> https://www.nescent.org/wg_evoinfo/CDAO >> it has "homologous to" ( http://purl.obolibrary.org/obo/CDAO_0000181 ) but >> no sub-relations. >> >> It wasn't clear to me how to download OGO, it looks like it has a fairly >> basic notion of orthology. >> >> As far as I can tell, there isn't really an ontology or vocabulary that >> enumerates the various subtypes of homology, including for example in and >> out paralogs (together with precise formal definitions). But I'm sure this >> could be added to an ontology like HOM. >> >> In my view, a truly satisfying representatin would be based on phylogeny, >> with the ability to infer orthology/paralogy using reasoners (somewhat >> outside the scope of OWL, but possible with some extensions). >> >> You may have more luck with this question on the obo-discuss list. >> >> * is there an OrthoOWL equivalent to OrthoXML >> >> OrthoXML covers more than just homology relations. E.g. genes, blast scores, >> taxa. One of the advantages of RDF is that it's easier to mix and match >> different vocabularies, and that is what I would do here. Use parts of CDAO, >> HOM, SO, the ontologization of the NCBITaxon ontology, etc. >> >> * Value of representing orthologs as RDF >> >> Compared to what? There are certain benefits, such as easier integration >> with (some) other data resources, resuing parts of other vocabularies (see >> above). You may get more religious answers from others. >> >> There are certain unique modeling questions. E.g. do you represent homology >> relations as predicates (and use reification to record provenance), or turn >> the predicate into a node in its own right? Fairly geeky stuff I'd be >
