From: He, Y. <yon...@me...> - 2014-06-10 19:38:45
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That sounds great. Mathias, let's find a way to coordinate. I will talk to my group later and come back to you with more details. Thanks, Oliver ________________________________ From: Mathias Brochhausen [mbr...@gm...] Sent: Tuesday, June 10, 2014 3:31 PM To: Alan Ruttenberg Cc: Harris, Marcelline; Eisenhauer, Elizabeth; Karnovsky, Alla; obo...@li...; Frank J. Manion (fm...@um...); Lin, Yu Subject: Re: [Obo-discuss] Request namespace for ICO: Informed Consent Ontology Yes, I am absolutely willing to work with Oliver and his group on coordinating development of d-acts and ICO. Best, Mathias On Tue, Jun 10, 2014 at 2:16 PM, Alan Ruttenberg <ala...@gm...<mailto:ala...@gm...>> wrote: It might make most sense to collaborate with Mathias Brochhausen on the Document Acts ontology which deals with other kinds of legal documents. I'm copying Mathias. Current work is at http://purl.obolibrary.org/obo/iao/d-acts.owl Google site: https://code.google.com/p/d-acts/ Perhaps have a look through that and see what you think. D-acts itself is an example of delegating a portion of an existing ontology namespace to a project that comes within the scope of another, but which is maintained for the most part by a different group of people. -Alan On Tue, Jun 10, 2014 at 1:43 PM, He, Yongqun <yon...@me...<mailto:yon...@me...>> wrote: This is a good suggestion. I am not sure if we should ask for IRIs under which ontology, though. It can be OBI, or OGMS, IDO, or IAO. Informed consent is mostly related to clinical studies, however, some basic or translational studies also need informed consent… Oliver From: Mathias Brochhausen [mailto:mbr...@gm...<mailto:mbr...@gm...>] Sent: Tuesday, June 10, 2014 12:33 PM To: obo-discuss Cc: Lin, Yu; Harris, Marcelline; Karnovsky, Alla; Frank J. Manion (fm...@um...<mailto:fm...@um...>); Eisenhauer, Elizabeth Subject: Re: [Obo-discuss] Request namespace for ICO: Informed Consent Ontology Just a suggestion: When I applied for a namespace for the document act ontology Alan assigned a specific number of IRIs under the IAO to us. So far, that has worked pretty well. Maybe something similar would work for ICO with OBI? Best, Mathias On Tue, Jun 10, 2014 at 11:24 AM, Chris Mungall <cjm...@lb...<mailto:cjm...@lb...>> wrote: I'm still not following why a new ID space is required here. I would expect every class with the proposed ICO ID space to be something specific to the domain of informed consent. Why then are there ICO classes like 'study title'? This should go in an ontology with broader scope. Can you not just get an ID range in a broader ontology? I would much rather we didn't proliferate ID spaces for narrow domains. On Tue, Jun 10, 2014 at 9:11 AM, He, Yongqun <yon...@me...<mailto:yon...@me...>> wrote: >From previous discussions, it appears that the initiation of the ICO development has got positive feedback in general. We appreciate Colin’s insightful comments. The ICO group has met and updated the ICO to address Colin’s comments. Below is our reply to Colin’s comments: -- * many of the definitions in here are just the name of the process prefixed with “a process which”, which doesn’t make any sense. Reply: We have fixed the definitions that we could find. In case you find something we have missed, please let us know. Thanks. * quite a few of the children of OBI’s planned process (OBI_0000011) are really parts of (OBI_0000810) Reply: We have added ‘is part of’ relation between ‘signing informed consent form’ and ‘informed consent process’ (OBI_0000810). We also added one term ‘explaining human subject with study information’ as part of ‘informed consent process’ (OBI_0000810). There are many other terms that are associated with ‘informed consent’; however, we do not think they are part of ‘informed consent process’, for example, information consent form design, information consent form approval, information consent form validation. * in general there ought to be tighter links to OBI, and possibly ERO. Reply: We have tried to use OBI terms as many as we can. * What size do you intend it to grow to? It certainly looks like the wrong place for “blood test” or “urine test”. Might it actually be better to work as part of a larger ontology? Reply: We have deleted the term ‘blood test’ and ‘urine test’, and will propose them to OBI. These two terms are in the scope of OBI. ICO extends OBI, OGMS, IAO, which are all aligned with BFO. We don’t think that ICO is a part of any particular larger ontology per se because ICO covers an interdisciplinary area, and the granularity and complexity of ICO may not be an interest to any particular ontology. * It’s not at all clear to me that “risk” and “benefit” are dispositional. This will have to be more carefully argued. Also “Biomedical Ethnic Ontology” should read “Biomedical Ethics Ontology” (this is just one of many examples of insufficiently careful writing throughout). Perhaps “risk” ought to be “risk of harm”, which would have a processual manifestation. As DuBois points out in a not-uncontroversial paper where he turns his nose up at open-source ways of working (PMC 2838195), “vulnerability” sounds more like something that inheres in a human being. Reply: We have updated the definition of ‘risk’ and ‘benefit’ in ICO. The definitions are adopted from NCIt’s definition of ‘risk’(C17102) and ‘benefit’(C25387) with modifications. Of course, these can be further argued and discussed later. * It’s very odd to have ‘study’ title in one part of the tree and ‘title of study for informed consent’ and ‘title of a clinical trial study’ elsewhere. Unfortunately the definitions aren’t detailed enough for me to work out what is going on. Reply: We updated the definition of a ‘study title’ by adapting its definition from NCIt: http://purl.obolibrary.org/obo/ICO_0000121 We have also removed the term ‘title of study for informed consent’ and asserted the ‘title of a clinical trial study’ under ‘study title’. * “UMHS medical record” looks as if it’s opening the door to all manner of medical records around the world. Reply: We have deleted this term from the ontology. Thanks. What other ontologies do you know of in this space and to what extent have you sounded people out about them? Reply: We have discussed a lot in Obo-discuss in other emails about related works and potential applications of ICO. -- Any other comments and suggestions are welcome. Thanks! Oliver and Asiyah From: Colin Batchelor [mailto:Bat...@rs...<mailto:Bat...@rs...>] Sent: Tuesday, May 20, 2014 12:11 PM To: obo...@li...<mailto:obo...@li...> Cc: Lin, Yu Subject: Re: [Obo-discuss] Request namespace for ICO: Informed Consent Ontology Hello, Some very quick observations: * many of the definitions in here are just the name of the process prefixed with “a process which”, which doesn’t make any sense. * quite a few of the children of OBI’s planned process (OBI_0000011) are really parts of (OBI_0000810) * in general there ought to be tighter links to OBI, and possibly ERO. * What size do you intend it to grow to? It certainly looks like the wrong place for “blood test” or “urine test”. Might it actually be better to work as part of a larger ontology? * It’s not at all clear to me that “risk” and “benefit” are dispositional. This will have to be more carefully argued. Also “Biomedical Ethnic Ontology” should read “Biomedical Ethics Ontology” (this is just one of many examples of insufficiently careful writing throughout). Perhaps “risk” ought to be “risk of harm”, which would have a processual manifestation. As DuBois points out in a not-uncontroversial paper where he turns his nose up at open-source ways of working (PMC 2838195), “vulnerability” sounds more like something that inheres in a human being. * It’s very odd to have ‘study’ title in one part of the tree and ‘title of study for informed consent’ and ‘title of a clinical trial study’ elsewhere. Unfortunately the definitions aren’t detailed enough for me to work out what is going on. * “UMHS medical record” looks as if it’s opening the door to all manner of medical records around the world. What other ontologies do you know of in this space and to what extent have you sounded people out about them? Best wishes, Colin. From: He, Yongqun [mailto:yon...@me...] Sent: 20 May 2014 16:24 To: obo...@li...<mailto:obo...@li...> Cc: Lin, Yu Subject: [Obo-discuss] Request namespace for ICO: Informed Consent Ontology Dear OBO-discuss: Here we would like to request the addition to an Informed Consent Ontology (ICO) as an OBO Foundry ontology. ICO is an ontology of clinical informed consents. It is aligned with OBO Foundry library ontologies including BFO, OBI, IAO, and OGMS. As part of the consenting process in human subjects research, potential participants receive information about the purpose of the study, potential risks and benefits of participation, their rights, and the procedures to be undergone as part of the study. If the individual decides to participate, an informed consent document is signed and preserved as a record of voluntary participation in the research study. Following the OBO Foundry principles, the Informed Consent Ontology (ICO) logically represents the terms and their relations related to the informed consent process and content. The basic information about ICO is here: - requested prefix: ICO - ontology title: Informed Consent Ontology - ontology of development version download link: http://ico-ontology.googlecode.com/svn/trunk/src/ontology/ - ontology home page: https://code.google.com/p/ico-ontology/ - point person contact email: Asiyah Yu Lin lin...@gm...<mailto:lin...@gm...>, PURL user ID: linyumichigan or yon...@me...<mailto:yon...@me...> (yongqun “Oliver” he), PURL user ID: yongqunhe - ontology discussion mailing-list: https://groups.google.com/forum/#!forum/ico-discuss - ontology issue tracker link: https://code.google.com/p/ico-ontology/issues/list Thanks for your consideration, Asiyah Yu Lin & Oliver He Yongqun "Oliver" He, DVM, PhD Associate Professor Unit for Laboratory Animal Medicine Department of Microbiology and Immunology Center for Computational Medicine and Bioinformatics and Comprehensive Cancer Center University of Michigan Medical School Mail: 018 ARF, 1150 W. 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