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Re: [Obo-phenotype] [Obo-discuss] Joining OBO foundry; and getting help to develop/improve/maintain the ontology further
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From: Robinson, P. <pet...@ch...> - 2013-06-04 20:39:30
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Hi Sira, it depends exactly on how you are trying to model things, but a side effect can be modeled as a simple set of phenoypic features (for many of which, but not all of which, there are currently HPO terms). It may be interesting to model other things such as the temporal relationship to ingestion of a medication etc. It may also be the case that persons with a particular disease are more suceptible to certain side effects. It is difficult to give a very general answer to you question other than "it depends". Could you give us a few use cases and perhaps mention some specific problems you are trying to solve? -Peter Dr. med. Peter N. Robinson, MSc. Professor of Medical Genomics Institut für Medizinische Genetik und Humangenetik Charité - Universitätsmedizin Berlin Augustenburger Platz 1 13353 Berlin Germany +4930 450566006 Mobile: 0160 93769872 pet...@ch... http://compbio.charite.de http://www.human-phenotype-ontology.org Introduction to Bio-Ontologies: http://www.crcpress.com/product/isbn/9781439836651 To give your data to the bioinformatician after the experiment is done may be no more than asking him to perform a post-mortem examination: he may be able to say what the experiment died of. ~ after Sir Ronald Aylmer Fisher ________________________________________ Von: Sirarat Sarntivijai [si...@um...] Gesendet: Dienstag, 4. Juni 2013 21:07 An: obo...@li... Cc: obo...@li... list; Barry Smith Betreff: Re: [Obo-discuss] Joining OBO foundry; and getting help to develop/improve/maintain the ontology further Dear Pradeep, Peter, Suzanna, and Chris, I'd very much be interested in this phenotype alignment work and learning from you. I am also looking at cardiovascular section of HPO in my work on drug-induced cardiotoxicity AE as adverse events can be described as a clinical phenotype. How do you see the definition in terms of, phenotype,disease, and induced phenotype (like adverse event for example) lining up with each other? I am very much interested to see how this work can be applied to how you would describe phenotypes in different settings as I am working on refining Ontology of Adverse Event to fit the clinical application. Thank you very much, Sira On Mon, Jun 3, 2013 at 3:04 PM, Chris Mungall <cjm...@lb...<mailto:cjm...@lb...>> wrote: Hi Pradeed, Can you provide a link to the ontology? The main way to imrpove the ontology would be to work closely with others developing related ontologies, like Peter. There is a mailing list dedicated specifically to phenotype ontologies, I recommend you join this: https://lists.sourceforge.net/lists/listinfo/obo-phenotype On Jun 2, 2013, at 7:37 PM, Pradeep Kumar Sreenivasaiah wrote: Hello OBO foundry, I have been developing a mammalian cardiovascular phenotype ontology for some time now. Following are characteristics of developed ontology: * Currently it has roughly >2000 phenotype/disease terms. Many of the general terms are from other existing ontologies such as from MPO, DO, ULMS, SNOMED, ICD-9,10 etc. Added to them are more domain specific hand curated cardiovascular terms from literature (mostly absent in other ontologies). * The ontology is hierarchically (Subsumption IS_A is the only relationship used) structured and developed using OBO edit. * These terms belong to developmental, morphological, physiological phenotype categories including >850 inherited, developmental and acquired human cardiovascular diseases. * The terms are organized (at least a serious try has been made) by biological layers as cellular, tissue, organ and organismal phenotypes in a species neutral way * Most of the terms are cross-referenced to existing vocabulary. Also contains definition and references ( Xrefs, url, PMID etc) I would like to know about the following and also need your help for: 1. How can I submit this ontology to OBO foundry and make it available besides other otologies? 2. Would OBO foundry help me to quality check my ontology? and also help me with advise to improve it? Please do the needful and oblige. Thank you, Sincerely, --Pradeep Kumar S Postdoc, Systems Bio Ressearch Center, GIST, South Korea ------------------------------------------------------------------------------ Get 100% visibility into Java/.NET code with AppDynamics Lite It's a free troubleshooting tool designed for production Get down to code-level detail for bottlenecks, with <2% overhead. Download for free and get started troubleshooting in minutes. http://p.sf.net/sfu/appdyn_d2d_ap2_______________________________________________ Obo-discuss mailing list Obo...@li...<mailto:Obo...@li...> https://lists.sourceforge.net/lists/listinfo/obo-discuss ------------------------------------------------------------------------------ How ServiceNow helps IT people transform IT departments: 1. A cloud service to automate IT design, transition and operations 2. Dashboards that offer high-level views of enterprise services 3. A single system of record for all IT processes http://p.sf.net/sfu/servicenow-d2d-j _______________________________________________ Obo-discuss mailing list Obo...@li...<mailto:Obo...@li...> https://lists.sourceforge.net/lists/listinfo/obo-discuss |