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Re: [Oae-devel] Name space change to OAE. RE: [obo-admin] Request the addition of Adverse Event Ontology (AEO) into OBO foundry library
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From: Melanie C. <mco...@gm...> - 2011-11-18 20:20:40
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Hi Oliver, Please see my comments inline. On 2011-11-18, at 11:47 AM, He, Yongqun wrote: > Hi Melanie, > > Time is for sure important for adverse events. The importance of time is also indicated by the current definition of 'adverse event'. The vaccine injury table provides some good information. I have previously generated many AE terms specific to different vaccines (e.g., many killed or live flu vaccines). I envision that a large knowledgebase of vaccine- and drug-specific AEs would help a lot to the AE research community. > In my opinion, the current definition of adverse event doesn't reflect the importance of time, as it reads "a pathological bodily process that occurs after a medical intervention." When we discussed how to reconcile AERO and AEO, we agreed that we would had an editor note to that effect, and that it was important to work on adding time appropriately in that definition. The editor note reads "Some work is needed on how to restrict the scope of a term to be an 'adverse event', notably regarding temporal association. When is an appropirate time interval between a medical intervention and a adverse event observed? One week, one month, one year, or a lifetime? For some well studied medical interventions (e.g., many vaccines or drugs), we probably have a general idea. For some new intervention, we probably don't know much." I am wondering how we could work towards integrating this more formally in the above mentioned definition. > I am not sure if I agree with you on the difference between "side effect" for "adverse event". On website: http://en.wikipedia.org/wiki/Adverse_effect > "An adverse effect may be termed a "side effect", when judged to be secondary to a main or therapeutic effect." > On VAERS website: http://vaers.hhs.gov/index > "VAERS is a post-marketing safety surveillance program, collecting information about adverse events (possible side effects) that occur after the administration of vaccines licensed for use in the United States." > All these references indicate that "side effect" and "adverse event" are synonyms. I don't have the same reading of those 2 sources. On the page you cite, http://en.wikipedia.org/wiki/Adverse_effect, the full citation reads: "An adverse effect may be termed a "side effect", when judged to be secondary to a main or therapeutic effect. If it results from an unsuitable or incorrect dosage or procedure, this is called a medical error and not a complication. Adverse effects are sometimes referred to as "iatrogenic" because they are generated by a physician/treatment. Some adverse effects only occur only when starting, increasing or discontinuing a treatment." Note that they also deem adverse effects to be iatrogenic, which is certainly not desired for our adverse event case. I would like to add that while wikipedia is a useful source of information, I don't think it it the best one for very specific (and potentially controversial) topics - for example there are pages for adverse effect and adverse event, with suggestion of merging (or not). http://en.wikipedia.org/wiki/Adverse_event also refers specifically to clinical trials, whereas our scope is clearly larger. VAERS states indeed that adverse events are possible side effects, which matches the AERO definition: adverse events are those such as reported in the VAERS system, and side effect are a subset of those adverse events for which causality has been established. You may remember that in our past discussions I had mentioned that a bridge between AERO-AEO could be done by asserting equivalence between AERO:side effect and AEO:adverse event (note that I refer to AEO:adverse event, i.e. the old version in which causality was asserted) > > It's good that you will develop the causality assessment part within AERO as suitable. I believe that the causality assessment is important for both AERO and OAE. As I also mentioned in a couple of my previous emails, we will provide knowledge-oriented representation of AE causality assessment in OAE. Indeed, we have generated many such terms in OAE out of our collaborations with Dr. Richard Boyce and others. Our current focus is on causality assessment of adverse drug events. For example, we have represented the 'Naranjo ADR probability score' and 'DIPS score' for causal assessment of ADEs out of the reactions to drug and drug-drug interaction, respectively. Sira's PhD study focuses on making statistic association between AEs and different type of vaccines based on MedDRA annotation of VAERS data. We have developed a novel combinatorial biostatistical/bioinformatics pipeline to assess the significance of vaccine-AE association. Sira's paper is currently at the final stage of preparation. I guess that your research focus is on ontology representation of causality assessment of vaccine adverse events (VAE) and VAE data reporting based on Brighton's definitions. Whenever possible, let's communicate more on this topic. I have no problem of transferring some existing OAE terms (e.g., a current OAE term called 'adverse event reporting') to AERO if appropriate and needed. More people working on this important AE representation area will make this study progress further and faster. Sure, happy to discuss any of those further. I have been busy setting up our Brighton working group and am now able to dedicate more time to the AERO editing - feel free to submit reporting terms directly under the tracker at http://code.google.com/p/adverse-event-reporting-ontology/issues/list and I'll add them asap. > > I will soon add the annotation you suggested to the AE definition in OAE, "adverse reaction is more specifically used by the drug ( in the sense "drug and not vaccine") community". I would suggest to add it to the "adverse reaction" annotation rather than to the adverse event class itself to make it clearer. Thanks, Melanie > > Thanks! > Oliver > > > -----Original Message----- > From: Melanie Courtot [mailto:mco...@gm...] > Sent: Friday, November 18, 2011 1:13 PM > To: He, Yongqun > Cc: Xiang, Allen; oae...@li... > Subject: Re: [Oae-devel] Name space change to OAE. RE: [obo-admin] Request the addition of Adverse Event Ontology (AEO) into OBO foundry library > > Hi Oliver, > > Thanks for the update. I have been thinking about the adverse event definition. We need to formalize the temporal association, and maybe the vaccine injury table at http://www.hrsa.gov/vaccinecompensation/vaccinetable.html is a good start? > > There currently is an alternative term "side effect" for "adverse event" - in the AERO we consider "side effects" to be those adverse events for which causality has been established. Would it be possible to remove that alternative term from OAE? As agreed, we will develop the causality assessment part within AERO. > > Finally, I think the term "adverse reaction is more specifically used by the drug ( in the sense "drug and not vaccine") community, maybe adding a annotation to the alternative term showing this would be helpful? > > Thanks, > Melanie > > On 2011-11-17, at 2:45 PM, He, Yongqun wrote: > >> Hi all OAE members, >> >> I am sorry to say that we have changes our name space from AEO to OAE. I tried to reserve the AEO name space because I was the first to submit it to NCBO Bioportal and at that time this name space did not exist in OBO foundry yet. It was mistake that I did not reserve it in OBO Foundry. Then the AEO name space was reserved in the OBO Foundry by another group. Now, we have to change it. Fortunately, I (and many others) think the OAE (Ontology of Adverse Events) is still a good name for our ontology development. >> >> News for our OAE development: >> (1) First, our OAE new name space has been reserved now in OBO Foundry. >> (2) I have reserved a new domain name: http://www.oae-ontology.org/. Allen has transferred our previous website (aeo-ontology.org) contents to this new website. >> (3) Allen has generated a new sourceforge site for OAE as shown in the forwarded email. Allen has updated the oae.owl file by changing all AEO words to OAE, etc. Please follow his instruction for creating a new SVN local copy in your computer. >> (4) In a couple of months ago, I have talked to Melanie and Alan in the AERO development group. We have agreed to collaborate on the AE related ontology development. OAE will focus on general AE knowledge representation, and AERO will focus on AE reporting. The definition of 'adverse event' from OAE has been updated to cover those possible non-causal adverse events. After many discussions between OAE and AERO, the new definition of 'adverse event' in OAE is finalized to: "a pathological bodily process that occurs after a medical intervention". AERO will import this definition and ontology term from OAE. We envision to maintain our close communication between OAE and AERO. >> (5) Richard Boyce, an assistant professor in the Department of Biomedical Informatics, University of Pittsburgh, has joined our OAE development group. His interest is to do ADE causality analysis. >> (6) Abra Guo, an undergraduate student (major: neuroscience), University of Michigan, has been working now on an OAE research project under my supervision. Her research project aims to represent and analyze neuropathy adverse events induced by chemotherapy drugs. >> (7) Sira has been preparing a paper submission that uses OAE for her PhD thesis research. She is expected to grant early next year. >> >> Thanks! >> Oliver >> >> Yongqun "Oliver" He, DVM, PhD >> Associate Professor >> Unit for Laboratory Animal Medicine >> Department of Microbiology and Immunology and Center for Computational >> Medicine and Bioinformatics University of Michigan Medical School Ann >> Arbor, MI 48109 >> Email: yon...@me... >> Tel: 734-615-8231 (O) >> http://www.hegroup.org/ >> >> >> >> From: Xiang, Allen >> Sent: Thursday, November 17, 2011 4:23 PM >> To: He, Yongqun >> Cc: oae...@li... >> Subject: RE: [obo-admin] Request the addition of Adverse Event >> Ontology (AEO) into OBO foundry library >> >> Hi, >> >> Due name conflict, we are switch to new name space OAE now. The following are the new sites/settings. >> >> Sourceforge: http://sourceforge.net/projects/oae/ >> Maillist: oae...@li... >> SVN: svn+ssh:// vn.code.sf.net/p/oae/code/trunk. >> SVN(https): https://svn.code.sf.net/p/oae/code/trunk >> Website: http://www.oae-ontology.org/ >> >> Before submit any changes to the new SVN repository, please make sure check out a fresh copy from the repository. Please check out to a different local folder other than your original AEO folder. >> >> Thanks, >> Allen >> >> >> >> From: He, Yongqun >> Sent: Wednesday, November 16, 2011 12:56 PM >> To: 'Chris Mungall' >> Cc: 'obo...@li...'; 'obo-admin'; 'OBO Coordinators'; Xiang, >> Allen >> Subject: RE: [obo-admin] Request the addition of Adverse Event >> Ontology (AEO) into OBO foundry library >> >> Dear Chris and OBO foundry, >> >> No problem. Thanks for reserving the OAE for us. I will provide you the required metadata for OAE soon. >> >> Best, >> Oliver >> >> >> From: Chris Mungall [mailto:cjm...@lb...] >> Sent: Wednesday, November 16, 2011 1:14 PM >> To: He, Yongqun >> Cc: 'obo...@li...'; 'obo-admin'; 'OBO Coordinators'; Xiang, >> Allen >> Subject: Re: [obo-admin] Request the addition of Adverse Event >> Ontology (AEO) into OBO foundry library >> >> >> Thanks for being accommodating Oliver >> >> I had asked Jonathan, he has already submitted an AEO publication. >> >> OAE is yours. If you can provide the required metadata we'll add it to >> the page >> >> On Nov 14, 2011, at 2:47 PM, He, Yongqun wrote: >> >> >> Hi Chris and OBO foundry, >> >> I don't know if you have considered my options. After second thoughts, we think the easiest way for us to do is to take the name space of "OAE", representing "Ontology of Adverse Events". Please consider this as our final proposal of solving this conflicts. I hope that you can confirm this option for us soon. >> Once confirmed, we will make changes on our website domain name, sourceforge SVN, and NCBO Bioportal. >> >> I look forward to hearing from you soon. >> >> Thanks, >> Oliver >> >> Yongqun "Oliver" He, DVM, PhD >> Associate Professor >> Unit for Laboratory Animal Medicine >> Department of Microbiology and Immunology and Center for Computational >> Medicine and Bioinformatics University of Michigan Medical School Ann >> Arbor, MI 48109 >> Email: yon...@me... >> Tel: 734-615-8231 (O) >> http://www.hegroup.org/ >> >> >> From: He, Yongqun >> Sent: Saturday, November 05, 2011 3:18 PM >> To: 'Chris Mungall' >> Cc: obo...@li...; obo-admin; OBO Coordinators >> Subject: RE: [obo-admin] Request the addition of Adverse Event >> Ontology (AEO) into OBO foundry library >> >> Hi Chris, >> >> Thanks for your prompt reply. For this conflict, a few options to consider here: >> >> (1) Use another name space, for example, OAE for "Ontology of Adverse Event(s)". >> (2) Stick with the AEO name space, but use the prefix of >> http://purl.bioontology.org/ontology instead of http://purl.bioontology.org/ontology/AEO . >> (3) Share IDs with AERO as you suggested. >> (4) Try to stick with AEO and continue to negotiate with OBO and the Anatomical Entity Ontology development team. >> >> I think it is very difficult to use the third strategy for the time being. Although we envision we will be more integrated in the future, we are now developing AEO and AERO in two separate and independent groups, have different focuses, and often try different strategies. >> >> The second option is a feasible but probably tentative strategy. We would eventually like to be part of OBO foundry, so we would like to get us registered as soon as we can. The first option is a good option. However, we have got our first AEO paper published, our AEO sourceforge and SVN generated, and our AEO website established (http://www.aeo-ontology.org/). It is much harder for us to make the change. If the Anatomical Entity Ontology (AEO) is going to stay, is that possible for you/OBO to negotiate with them and ask them/Jonathan to use another namespace like OAE for "Ontology of Anatomic Entities"? >> >> I notice that in OBO library, there is an ontology OMRSE, for "Ontology of Medically Related Social Entities". Therefore, it may not be a bad idea to have OAE for "Ontology of Anatomic Entities". If you think it is appropriate, I am happy to contact Jonathan by myself and negotiate this with him. >> >> By the way, once I submitted our Brucellosis Ontology to OBO and propose to use "BO" as the name space. I was suggested to keep it for other ontologies. I thought it was reasonable and so have agreed. Now we have the name IDOBRU. The IDOBRU paper was just accepted and published. I am wondering if I need to request to reserve the name "IDOBRU" for Brucellosis Ontology in OBO library. >> >> Thank you for your consideration! >> >> Oliver >> >> >> From: Chris Mungall [mailto:cjm...@lb...] >> Sent: Saturday, November 05, 2011 2:16 PM >> To: He, Yongqun >> Cc: obo...@li...; obo-admin; OBO Coordinators >> Subject: Re: [obo-admin] Request the addition of Adverse Event >> Ontology (AEO) into OBO foundry library >> >> Hi Oliver >> >> >> One possible issue is about the AEO acronym. It appears that the "AEO" acronym is now taken by Anatomical Entity Ontology, which is an ontology of anatomical structures that expands CARO, the Common Anatomy Reference Ontology. I am sorry that I did not apply for the AEO acronym before. But when we generated this "AEO" acronym for Adverse Event Ontology, the CARO-derived AEO was not in the obofoundry.org list yet. What I did before was to take an easy way -- submitted our AEO to NCBO BioPortal. Our AEO acronym in NCBO Bioportal was the first: >> http://bioportal.bioontology.org/ontologies/1489 >> http://purl.bioontology.org/ontology/AEO >> >> I'm afraid AEO was first in the OBO registry - people can put what they like in BioPortal, it doesn't affect the purl.obolibrary.org/obo set of URLs. AEO has become more established since July, it's been linked to from other ontologies such as Uberon and EHDAA2. >> >> Is it not possible to share IDs in the AERO space? >> >> On Nov 5, 2011, at 1:53 PM, He, Yongqun wrote: >> >> >> Dear Chris and OBO admin/coordinators, >> >> I am wondering if you have asked Jonathan on it or not. We would like to solve the AEO name space conflict soon. This conflict makes many difficulties for our development. >> >> One note is that we have talked Melanie and Alan and solved a >> potential conflict between our Adverse Event Ontology (AEO) and the Adverse Event Reporting Ontology (AERO) generated by Melanie and Alan. We have all agreed to complement our work rather than compete with each other. As a result, AERO will use the AEO 'adverse event' definition and import (MIREOT) the AEO 'adverse event' term. As discussed and agreed by AEO and AERO and collaborators (including OGMS), the updated AEO 'adverse event' is defined as adverse event = def. "a pathological bodily process that occurs after a medical intervention" >> AEO and AERO will have different focuses. Briefly, AERO will focus on adverse event reporting, and AEO will focus on adverse event knowledge representation. >> >> More information about AEO can be found in our AEO website: >> http://www.aeo-ontology.org/ >> Here you can see the team of the AEO developers: >> http://www.aeo-ontology.org/dev_team.php >> >> Thanks for your consideration! >> Oliver >> >> Yongqun "Oliver" He, DVM, PhD >> Associate Professor >> Unit for Laboratory Animal Medicine >> Department of Microbiology and Immunology and Center for Computational >> Medicine and Bioinformatics University of Michigan Medical School Ann >> Arbor, MI 48109 >> Email: yon...@me... >> Tel: 734-615-8231 (O) >> http://www.hegroup.org/ >> >> >> From: He, Yongqun >> Sent: Thursday, July 28, 2011 4:45 PM >> To: Chris Mungall; obo...@li... >> Cc: obo-admin; OBO Coordinators >> Subject: RE: [obo-admin] Request the addition of Adverse Event >> Ontology (AEO) into OBO foundry library >> >> Hi Chris, >> Thanks for your prompt reply. >> Yes. It would be great if you could ask Jonathan. Thanks!! >> Oliver >> >> From: Chris Mungall [cjm...@lb...] >> Sent: Thursday, July 28, 2011 3:47 PM >> To: obo...@li... >> Cc: obo-admin; He, Yongqun; OBO Coordinators >> Subject: Re: [obo-admin] Request the addition of Adverse Event >> Ontology (AEO) into OBO foundry library >> >> >> Hi Oliver >> >> I'm afraid AEO is already taken (see obofoundry.org for a complete list). I will ask Jonathan if he intends to keep his ID space, as his may be merged into CARO. >> >> >> >> On Jul 28, 2011, at 2:54 PM, He, Yongqun wrote: >> >> >> Dear OBO foundry, >> >> I would like to request the addition of the Adverse Event Ontology (AEO) into OBO foundry library. The AEO aligns with BFO and RO and follows the OBO foundry principles. The updated AEO is always available on page: >> http://sourceforge.net/projects/aeo/ >> specifically here: >> http://aeo.svn.sourceforge.net/viewvc/aeo/trunk/src/ontology/ >> >> The AEO website is here: >> http://www.aeo-ontology.org/ >> >> We just had an Adverse Event Representation workshop in ICBO: >> http://icbo.buffalo.edu/2011/WorkshopA.pdf >> In the workshop I presented the AEO and have received a lot of positive feedback, suggestions and comments. Attached is the AEO paper for the ICBO workshop. The adverse event community is large and covers vaccine adverse events, drug adverse events, medical device adverse events, nutritional product adverse event, surgery adverse events, etc. >> >> I see that the Adverse Event Reporting Ontology (AERO) is now listed in OBO library: >> http://www.obofoundry.org/ >> The AERO is focused on adverse event reporting. AEO is different from AERO in different ways, for example, AEO is focused on development of adverse event knowledge base. Barry Smith was in the workshop and knows the difference between these two very well. We also have two full length papers in the ICBO proceedings that discuss these two ontologies. >> >> One possible issue is about the AEO acronym. It appears that the "AEO" acronym is now taken by Anatomical Entity Ontology, which is an ontology of anatomical structures that expands CARO, the Common Anatomy Reference Ontology. I am sorry that I did not apply for the AEO acronym before. But when we generated this "AEO" acronym for Adverse Event Ontology, the CARO-derived AEO was not in the obofoundry.org list yet. What I did before was to take an easy way -- submitted our AEO to NCBO BioPortal. Our AEO acronym in NCBO Bioportal was the first: >> http://bioportal.bioontology.org/ontologies/1489 >> http://purl.bioontology.org/ontology/AEO >> >> The CARO is NCBO BioPortal is still labeled as CARO (not AEO): >> http://bioportal.bioontology.org/ontologies/1063 >> http://purl.bioontology.org/ontology/CARO >> it appears that the CARO-derived Anatomical Entity Ontology does not exist in NCBO BioPortal now (I know it was listed in NCBO Bioportal before, but not now. I don't know why). >> >> So I hope that the OBO foundry can consider our request of using the AEO as the official acronym for the Adverse Event Ontology after discussing the current CARO/Anatomical Entity Ontology developers, and list our AEO in the OBO library. >> >> Your consideration is sincerely appreciated! Thanks! >> >> Oliver >> >> Yongqun "Oliver" He, DVM, PhD >> Assistant Professor >> Unit for Laboratory Animal Medicine >> Department of Microbiology and Immunology and Center for Computational >> Medicine and Bioinformatics University of Michigan Medical School Ann >> Arbor, MI 48109 >> Email: yon...@me... >> Tel: 734-615-8231 (O) >> http://www.hegroup.org/ >> ********************************************************** >> Electronic Mail is not secure, may not be read every day, and should >> not be used for urgent or sensitive issues >> <AEO_camera_ready_submit.pdf> >> >> ********************************************************** >> Electronic Mail is not secure, may not be read every day, and should >> not be used for urgent or sensitive issues >> >> ********************************************************** >> Electronic Mail is not secure, may not be read every day, and should >> not be used for urgent or sensitive issues >> >> ********************************************************** >> Electronic Mail is not secure, may not be read every day, and should >> not be used for urgent or sensitive issues >> ---------------------------------------------------------------------- >> -------- All the data continuously generated in your IT infrastructure >> contains a definitive record of customers, application performance, >> security threats, fraudulent activity, and more. Splunk takes this >> data and makes sense of it. IT sense. And common sense. >> http://p.sf.net/sfu/splunk-novd2d_____________________________________ >> __________ >> Oae-devel mailing list >> Oae...@li... >> https://lists.sourceforge.net/lists/listinfo/oae-devel > > --- > Mélanie Courtot > MSFHR/PCIRN trainee, TFL- BCCRC > 675 West 10th Avenue > Vancouver, BC > V5Z 1L3, Canada > > > > > > > > ********************************************************** > Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues > --- Mélanie Courtot MSFHR/PCIRN trainee, TFL- BCCRC 675 West 10th Avenue Vancouver, BC V5Z 1L3, Canada |
