oae-devel — Dev Maillist

[Oae-devel] Workshop Annoucement: Vaccine and Drug Ontology Studies (VDOS-2013)

[He, Y. <yon...@me...>]

In the conference of ICBO-2013 or ICBO/CSWS/DILS Semantic Trilogy (at Montreal Canada, 7 July 2013), there will be a workshop titled:

"Vaccine and Drug Ontology Studies (VDOS-2013)"
http://www.unbsj.ca/sase/csas/data/ws/semantic-trilogy-workshops/

The detailed information link is here:
http://informatics.mayo.edu/CNTRO/index.php/Events/VDOS_2013

Basically, it is an ontology workshop with a focus on vaccine and drug studies.

For the paper submission for this workshop, we will allow three submission formats:
    full research papers (10 pages) format
    work in progress / late breaking results (4 pages), and
    a statement of interest (one page) for podium presentation.
The paper format will be the same as the format used in ICBO.

Selected full research papers will be invited for extension and publication in the Journal of Biomedical Semantics (JBMS).

Individual Workshop Papers Due: April 15, 2013.

Workshop Organizers:
Cui Tao, PhD Department of Health Sciences Research Mayo Clinic College of Medicine
Yongqun "Oliver" He, DVM, PhD, University of Michigan Medical School
Luca Toldo, PhD Knowledge Management Merck KGaA 250, Frankfurterstrasse 64293 Darmstadt - Germany
Sivaram Arabandi, MD, MS Ontopro LLC Houston, TX

Please forward this announcement to anyone who might be interested. Thank you 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...<mailto:yon...@me...>
Tel: 734-615-8231 (O)
http://www.hegroup.org/

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[Oae-devel] Reminder: 2013 ICBO and DILS CfPs deadline approaching

[Sivaram A. M. <siv...@gm...>]

(with apologies for multiple copies)

++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
ICBO & DILS 2013 - Call for Participation

Concordia University, Montreal, Quebec
July 7th - 9th 2013

http://www.unbsj.ca/sase/csas/data/ws/icbo2013/cfp.html
http://www.unbsj.ca/sase/csas/data/ws/dils2013/cfp.html
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Conference (long & short) paper submission deadline is Feb 15, 2013 (midnight Hawaii time).

The conference aim is to foster discussion, exchange, and innovation in research and development in the areas of biomedical ontology, data integration and data management for the life sciences. Researchers and professionals from biology, medicine, computer science and engineering are invited to share their knowledge and experience. The events are part of the Semantic Trilogy 2013 featuring:

       * International Conference on Biomedical Ontologies (ICBO 2013)
       * Canadian Semantic Web Symposium (CSWS 2013)
       * Data Integration in the Life Sciences (DILS 2013) 

web site:    http://www.unbsj.ca/sase/csas/data/semantic-trilogy-2013/

More information can be found in the attached documents.


  


The next upcoming deadlines are:
	15 April 2013: 		System, early career and workshop paper submission deadline
	20 May 2013: 		Submission of late breaking reports and highlight track papers

Please let me know if you need more information or have any questions.

thanks
Sivaram
___________________________________

Sivaram Arabandi, MD, MS
ONTOPRO
www.ontopro.com
T  832.726.2322 
E  s.a...@on...

Think Semantics. Tame Silos.

[Oae-devel] ICBO 2013- Call for participation

[Melanie C. <mco...@gm...>]

Posted on behalf of Sivaram, siv...@gm....

> 
> 
> _____________________________________________________
> This message is posted to several lists. Apologies for cross-posting.
> Please forward it to everyone who might be interested.
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> ICBO 2013  Call for Participation
> 
> 4th International Conference on Biomedical Ontologies 2013 (ICBO2013) 
> Concordia University, Montreal, Quebec
> July 7th - 9th 2013
> http://www.unbsj.ca/sase/csas/data/ws/icbo2013/cfp.html
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> Workshop and tutorial proposal submission deadline extended to Jan 18, 2013.
> 
> The conference aim is to foster discussion, exchange, and innovation in research and development in the areas Biomedical Ontology. Researchers and professionals from biology, medicine, computer science and engineering are invited to share their knowledge and experience. The event is part of the Semantic Trilogy 2013 featuring:
> 
>        * International Conference on Biomedical Ontologies (ICBO 2013)
>        * Canadian Semantic Web Symposium (CSWS 2013)
>        * Data Integration in the Life Sciences (DILS 2013) 
> 
> web site:    http://www.unbsj.ca/sase/csas/data/semantic-trilogy-2013/
> 
> Topics
> 
> Ontologies for biomedical research and clinical applications
> Reports on ontologies for, and their application in high throughput omics data and systems biology, toxicology and environmental health, disorders, diseases, phenotypes and physiology, genetic variation and pharmacogenomics, translational research and personalized medicine, public health and electronic health care are invited..
> 
> Foundations and methodology
> Papers on foundational and methodological issues pertaining to biomedical ontology are invited. Eligible topics are, though not limited to, the following; knowledge representation and reasoning, philosophical foundations of ontology, upper-level ontologies, topics in ontology engineering including design and life cycle, methodologies for knowledge elicitation and capture, ontology-oriented text mining techniques, ontology modularity, mapping, merging, and alignment of ontologies, and ontology evaluation.
> 
> Biomedical ontologies and the Semantic Web
> Research on formal representation of biomedical knowledge using RDF and OWL, identifiers, mappings & normalization, biomedical research using linked data, integration strategies using the linked open data cloud, visualization and manipulation of ontology, federation of online resources, workflows and semantic web services for biomedical knowledge discovery.
> 
> Social aspects of biomedical ontologies
> Perspectives from biomedical ontologists on community standards, adoption, and proliferation of semantics, use of semantic wikis, bio-curation & crowdsourcing techniques, user engagement and feedback, semantic publishing and provenance, governance, evolution and sustainability.
> 
> 
> Submissions    http://www.easychair.org/conferences/?conf=icbo2013
> 
> All accepted submissions will be published as part of the Conference Proceedings. Papers are to be prepared using templates (available on website) and submitted via EasyChair. 
> 
> 1. Long Research Paper (up to 6 pages) should satisfy the following criteria: original research; novelty in methodology and/or in research results; significant development with large potential for impact; theoretical soundness and/or strong evaluation with demonstration of utility in applications.
> 
> 2. Short Research Paper (up to 4 pages) should satisfy the following criteria: original research; methodological soundness with either novel methodology & application, or demonstrated improvement over existing methods (with appropriate validation), or the use of existing methodology but in novel application. Short papers are appropriate for applied research or systems, or the development of new approaches.
> 
> 3. Systems Paper (up to 2 pages) must describe the functionality, availability, and an application of the system. The system itself must be demonstrated at the conference.
> 
> 4. Early Career Track (up to 4 pages) is to support the work of young investigators.
> There will be an Early Career Track session for the presentation of the papers. The ECT paper review and acceptance criteria are the same as the short research papers. The staggered submission dates allows submissions (from young investigators) that are not accepted as long or short research papers to be revised and re-submitted; as well as allow first time submissions from young investigators to the Early Career Track directly.
> 
> 5. Late Breaking Report (1 page) This track is for extended abstracts of posters. A limited set of the peer-reviewed reports will be selected to be presented as a flash talk. All reports must be presented as posters. Late breaking reports should address a clearly defined problem that is of interest to the ICBO community. A late breaking report is appropriate for interesting preliminary results; and systems updates.
> 
> 6. Highlights (up to 500 words) This track highlights original peer-reviewed research with significant impact on data integration research or life sciences research that is published between May 1, 2012 and May 1, 2013. The submission is a short abstract highlighting the importance of the work for the ICBO community. If the publication is not open access, then the authors must make the paper available to the review committee.
> 
> 
> 7. Workshops
> Workshops are half-day or full-day scientific events intended to provide a forum for the discussion of a specific topic through individual paper presentations. The workshop organizers will be responsible for advertising the workshop and reviewing and selecting the contributions. Workshops can be events focusing on a specific topic; they can also include interest group meetings, or meetings designed to disseminate the results of a research project on a specific topic.
> 
> 8. Tutorials
> Tutorials are educational events. They may be either for a full day or for a half day. They should focus on one specific topic presented by one or two experts and involve interaction with the audience. Tutorials can include hands-on training, in which case the proposal should specify the exact requirements (laptops, software to install, etc.).
> 
> Relevant dates    http://www.unbsj..ca/sase/csas/data/ws/icbo2013/dates.html
> 
> 18 January 2013:     	Workshop and tutorial proposal submission deadline
> 1 February 2013:   	Notification of acceptance of workshops and tutorial proposals
> 1 February 2013:	Conference (long & short) paper submission deadline
> 1 April 2013: 		Notification of conference paper acceptance 
> 15 April 2013: 		System, early career and workshop paper submission deadline
> 15 May 2013: 		Notification of system, early career and workshop paper acceptance
> 20 May 2013: 		Submission of late breaking reports and highlight track papers
> 1 June 2013: 		Notification of acceptance of late breaking reports and highlight-track papers
> 15 June 2013: 		Deadline for all camera-ready copies for the proceedings
> 
> 
> Contact
> For more information or to offer sponsorship, please send us a note at
>          contact: icb...@gm...
> 
> Organizing Committee
> Co-Scientific Chair: Michel Dumontier
> Co-Scientific Chair: Christopher Baker
> Local Organizer: Gregory Butler
> Programme Chair: Robert Hoehndorf
> Workshop and Tutorial Chair: Chris Mungall
> Poster and Demonstration Chair: Trish Whetzel
> Proceedings and Special Issue Chair: Janna Hastings
> Early Career Chair: Melissa Haendel
> Sponsorship and Publicity Chair: Sivaram Arabandi 
> 
> 

---
Mélanie Courtot
MSFHR/PCIRN Ph.D. Candidate,
BCCRC - Terry Fox Laboratory - 12th floor
675 West 10th Avenue
Vancouver, BC
V5Z 1L3, Canada

[Oae-devel] Sira's OAE-based vaccine AE study paper published now

[He, Y. <yon...@me...>]

Sira’s first-author paper is out now:

Sarntivijai S, Xiang Z, Shedden KA, Markel H, Omenn GS, Athey BD, and He Y. Ontology-based combinatorial comparative analysis of adverse events associated with killed and live influenza vaccines<http://dx.plos.org/10.1371/journal.pone.0049941>. PLoS ONE. 2012, 7(11): e49941. doi:10.1371/journal.pone.0049941.
URL: http://dx.plos.org/10.1371/journal.pone.0049941

This paper uses OAE to support the analysis of vaccine adverse events (VAEs) associated with killed or live influenza vaccines. The data used in this study came from the VAERS. Different VAE patterns, esp those associated with severe VAEs like GBS, were identified. OAE has been found to support this study significantly. From this study, OAE has been shown to be superior to MedDRA and SNOMED for AE term classification. In this paper, we have also introduced some recent updates on OAE.

After graduation from the University of Michigan Medical School Bioinformatics Program, Sira found a job in FDA as a research fellow. Some approaches introduced in this paper are being used in her current job research, which is focused on drug adverse events. For her PhD research, Sira was co-mentored by Drs. Brian Athey and me.

Sira: Congratulations for your nice paper publication, and Good luck with your continuous research in the exciting ontology-based AE research!

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...<mailto:yon...@me...>
Tel: 734-615-8231 (O)
http://www.hegroup.org/
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[Oae-devel] Informal session on the upcoming ICBO 2012: Knowledge Management in Public Health - Experiences Using an Ontology Based Approach (Saturday, 18:00-20:00)

[Laszlo B. <Las...@ec...>]

Dear all,



Warmly welcome to the planned informal session `Knowledge Management in Public Health - Experiences Using an Ontology Based Approach`<http://kr-med.org/icbofois2012/icboinformalmeetings/KMpublichealth.htm>. Here is what we plan to discuss with you, who will be interested.


-----------------------------------------------
Dr. Laszlo Balkanyi
Md PhD
knowledge manager
ECDC RMC ICKS KMLG
www.ecdc.europa.eu
tel: +46761010708



Knowledge Management in Public Health - Experiences Using an Ontology Based Approach

-          informal meeting on 21th July,  18:00 - 20:00, ICB0<http://kr-med.org/icbofois2012/icbo.htm>, Graz

Time(min)

What?

How?

Who?

0-10

Introduction of participants

roll call

participants

10 - 20

Warm up, focusing on one issue: why we think ontologies, terminology systems are needed in public health?

quick round table

Cecil, Laszlo and participants

20 - 35


First example in details: HL7 ORU in OWL -  in CDC

US Centers for Disease Control sponsored HL7 Meaningful Use Electronic Laboratory Reporting Nationally Notifiable Disease Ontology. The structure of the HL7 ORU lab reporting message in OWL and the binding of standards based terminologies (SNOMED and LOINC) will be demonstrated along with how these message based ontologies may be implemented to aid in automated laboratory disease reporting to public health authorities.

presentation

Cecil

35 - 45

Comments, questions to first example

quick round table

participants

45 - 60

Second example: ECDC<http://ecdc.europa.eu/en/Pages/home.aspx> terminology server

The development process of an (ontology based) terminology service at the European Centre of Disease Prevention and Control will be demonstrated. Lessons learned and current experiences with the system in production will be explained. Live access to (full) test version on line will show the system, both the human user interface to browse / edit the value sets and the machine user interface with a flexible, SOAP based interface answering queries of client applications.

Presentation
+ live access to ECDC TS

Laszlo

60-70

Comments, questions to second example

quick round table

participants

70 - 85

Third example will be the use of ontology for message validation and decision support in the US CDC National Tuberculosis surveillance system.

presentation

Cecil

85-95

Comments, questions to third example

quick round table

participants

95- 105

Other examples mentioned by the audience on using terminology systems in public health with / based on an ontology thinking

round table

participants

105-110

Demonstration of an open source OWL terminology construction tool

Live demonstration

Cecil

110-120

Wrap up - suggestion for a position paper

round table

participants








Confidentiality Notice
If you are not the intended recipient of this message, you are hereby kindly requested, to, consecutively, refrain from disclosing its content to any third party, delete it, and inform its sender of the erroneous transmittal.

[Oae-devel] OAE locked

[Xiang, A. <zx...@me...>]

Locked for BFO 1.1 to 2.0 transition.

-Allen

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[Oae-devel] ICBO 2012 workshop - Vaccine and Drug Ontology in the Study of Mechanism and Effect (VDOSME-2012)

[He, Y. <yon...@me...>]

DEADLINE EXTENDED to April 30th (Firm):
ICBO 2012 workshop - Vaccine and Drug Ontology in the Study of Mechanism and Effect (VDOSME-2012)
July 21st 2012, Graz, Austria

SUBMISSION DEADLINE: April 30th 2012 *FIRM*

Vaccines and drugs have contributed to dramatic improvements in public health worldwide. Over the last decade, there have been efforts in biomedical ontology that represent various areas associated with vaccines and drugs and which join existing health and clinical terminology systems (e.g., SNOMED, RxNorm, NDF-RT, and MedDRA) in their application to research and clinical data.
 
The "Vaccine and Drug Ontology in the Study of Mechanism and Effect" (VDOSME 2012) workshop will provide a platform for discussing problems and solutions in the development and application of biomedical ontologies to representing and analyzing vaccines/drugs, vaccine/drug administrations, vaccine/drug-induced immune responses, and similar topics. The workshop will cover:
 
Ontology Coverage: Ontologies of vaccines, of drugs, and of studies thereof.
Scope of Interest: Representations and analyses of vaccine and drug formation and preparation, administration, mechanisms, and effects based on such ontologies.
 
Examples of biomedical subject matter in the scope of this workshop: vaccine/drug components (e.g., vaccine antigens, drug active ingredients, and adjuvants), administration details (e.g., dosage, administration route, and frequency), gene immune responses and pathways, drug-drug or drug-food interactions. We will also focus on computational methods used to study these, for example, literature mining of vaccine/drug-gene interaction networks, meta-analysis of host immune responses, and time event analysis of vaccine/drug effects.
 
All workshop attendees will be expected, at the workshop, to present either descriptions of their work or to articulate a position. In addition a number of participants will be selected to lead interactive sessions on focused topics.

*** Submission Guidelines ***
Full papers must describe novel ontology-related research, not previously been published and not submitted to other conferences. Short papers describe research results which are more preliminary or communicate brief position statements. We also invite full length application-oriented papers, to showcase the development of novel and successful applications utilizing ontologies and knowledge-based technologies. 

The maximum allowed page lengths of contributions are as follows.

Full paper submission: 5 pages, due Apr 30 (Firm), 2012
Short paper submission: 3 pages, due Apr 30 (Firm), 2012
Statement of interest: 1-2 pages, due Apr 30 (Firm), 2012

*** Journal Publication ***
All full-length papers accepted in this workshop will be invited to extend the workshop papers and be included in a special issue in the Joural of Biomedical Semantics. We believe that the eventual inclusion of accepted full-length publication in the special issue will stimulate more submissions of high quality manuscripts.
 
*** Contact ***
If you have any question or which to enquire about the workshop, please contact us at org...@go....
 
*** Chairs ***
Yongqun “Oliver” He, University of Michigan
Luca Toldo, Merck KGaA
Gully Burns, Information Sciences Institute
Cui Tao, Mayo Clinic
Darrell R. Abernethy, U.S. Food and Drug Administration (FDA)

*** Program committee (PC) Members ***
Richard Boyce, University of Pittsburgh
Lindsay Cowell, University of Texas Southwestern Medical Center
Dingcheng Li, Mayo Clinic
Asiyah Yu Lin, University of Michigan
Bjoen Peters, La Jolla Institute for Allergy and Immunology
Sira Sarntivijai, University of Michigan/US FDA
Nigam Shah, Stanford University
Sunghwan Sohn, Mayo Clinic
Larisa Soldatova, Aberystwyth University
Stephen Wu, Mayo Clinic
Qian Zhu, Mayo Clinic

More information is available at:
http://kr-med.org/icbofois2012/vdosme/submission.htm 

A related workshop in ICBO 2012:
Workshop Name: Methods for adverse events representation Ontology and Information Model
URL: http://kr-med.org/icbofois2012/adverse_events/  

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/



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[Oae-devel] CFP Workshop on Methods for Adverse Events representation: Ontology and Information Model (AE@ICBO2012) - Less than a month to deadline!

[Melanie C. <mco...@gm...>]

2nd CALL FOR PAPERS - ICBO 2012 Workshop on Methods for Adverse Events representation: Ontology and Information Model (AE@ICBO2012)
July 22nd 2012, Graz, Austria

SUBMISSION DEADLINE: April 30th 2012 *FIRM*

A variety of information systems are used to record and process adverse event reports. Recently there have been efforts to build ontology to assist in the representation, retrieval, and assessment of adverse event reports. Still, a question remains about how the ontology might be used in conjunction with new and existing information models. For example, are ontology terms to be added to records as keywords for retrieval? Or should information models be revised in the light of a more careful ontological analysis, earlier explored knowledge representation systems, or emerging standards for web semantics?
 
*** Topics of Interest ***
AE@ICBO2012 solicits participants who have experience that can shed light on these questions, or who actively develop adverse event reporting systems and can serve to evaluate feasibility and utility of workshop proposals. Specific areas of interest include, but are not limited to:
•    Existing information models, their strengths, weaknesses, and competency criteria.
•    Ongoing efforts to build new information models for adverse event reporting or analysis.
•    Case studies demonstrating information systems that integrate ontology in clinical systems.
•    Reports of new developments in adverse event ontology.
 
All workshop attendees will be expected, at the workshop, to present either descriptions of their work or to articulate a position. In addition a number of participants will be selected to lead interactive sessions on focused topics.

*** Submission Guidelines ***
Full papers must describe novel ontology-related research, not previously been published and not submitted to other conferences. Short papers describe research results that are more preliminary or communicate brief position statements. We also invite full-length application-oriented papers, to showcase the development of novel and successful applications utilizing ontologies and knowledge-based technologies. The maximum allowed page lengths of contributions are as follows:
•    Full paper submission: 5 pages, due Apr 30, 2012
•    Short paper submission: 3 pages, due Apr 30, 2012
•    Statement of interest: 1-2 pages, due Apr 30, 2012

*** Best Papers ***
Selected papers will be invited to submit an extended version to the Journal of Biomedical Semantics, for publication as best papers. Note that those papers will undergo an additional round of revision pre-publication, and authors will be responsible for open-access processing costs.
 
*** Contact ***
If you have any question or which to enquire about the workshop, please contact us at inf...@gm....
 
*** Organizers ***
	• Sivaram Arabandi, Elsevier Health Sciences
	• Mélanie Courtot, British Columbia Cancer Research Centre
	• Albert Goldfain, Blue Highway, Inc
	• Chimezie Ogbuji, Case Western Reserve University
	• Alan Ruttenberg, University at Buffalo

*** Program committee ***
	• Naveen Ashish, University of California, Irvine
	• Eugene Blackstone, Thoracic and Cardiovascular Surgery, Cleveland Clinic
	• Olivier Bodenreider, US National Library of Medicine
	• Taxiarchis Botsis, Office of Biostatistics and Epidemiology, Food and Drug Administration
	• Michel Dumontier, Carleton University
	• David Eichmann, The University of Iowa
	• Kerstin Forsberg, AstraZeneca
	• Natalia Grabar, STL CNRS Université Lille 3
	• Christian Lovis, University Hospitals of Geneva
	• Thomas Rindflesch, US National Library of Medicine
	• Jean-Marie Rodrigues, UFR médecine, Université Jean Monnet, Saint-Etienne
	• Nigam Shah, Stanford University
	• Kent Spackman, International Health Terminology Standards Development Organisation (IHTSDO)
	• Romesh Stanislaus, Sanofi Pasteur
	• Sandy Weininger, US Food and Drug Administration


More information is available at http://purl.org/icbofois2012/adverse_events/submission.htm
Please forward this announcement to everyone who might be interested - a pdf version of the CFP is available at http://purl.org/icbofois2012/adverse_events/CFP.pdf


*** Related workshop in ICBO 2012 ***
Vaccine and Drug Ontology in the Study of Mechanism and Effect (VDOSME 2012) http://purl.org/icbofois2012/vdosme/ - July 21st 2012.



---
Mélanie Courtot
MSFHR/PCIRN trainee, TFL- BCCRC
675 West 10th Avenue
Vancouver, BC
V5Z 1L3, Canada

[Oae-devel] Plan for submitting a paper to the ICBO AE workshop

[He, Y. <yon...@me...>]

Dear Melanie, Alan, Ryan, and all OAE-developers,

As you probably know, there will be two adverse event-related workshops in the ICBO conference:

*             "Vaccine and Drug Ontology in the Study of Mechanism and Effect" (VDOSME 2012): http://kr-med.org/icbofois2012/vdosme/index.htm
*             "Methods for adverse events representation Ontology and Information Model": http://kr-med.org/icbofois2012/adverse_events/

In terms of AE study, VDOSME focuses on basic mechanism analysis, and the AE workshop focuses on clinical AE representation. More details are explained here:
http://kr-med.org/icbofois2012/vdosme/callforpapers.htm

Since last year's AE workshop in the ICBO 2011, we have made a lot of changes on OAE. Of course, the most obvious change is the naming change, from AEO to OAE. Another change is the basic definition of AE in current OAE. The AE definition in the last year's paper is now equivalent to the 'causal adverse event' in OAE. With this and other changes, now OAE and AERO agree on the basic definition of AE now.

With all these updates, I propose that we submit a general OAE paper to the AE workshop. This paper will summarize our updates since last year and make some good description of our new OAE development. I am now preparing an outline. Please let me know if you are interested in participating in this paper preparation.

The deadline of submission is April 30.  So we have about one month.

Best regards,
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...<mailto: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 

[Oae-devel] CALL FOR PAPERS - ICBO 2012 Workshop on Methods for Adverse Events representation: Ontology and Information Model (AE@ICBO2012)

[Melanie C. <mco...@gm...>]

CALL FOR PAPERS - ICBO 2012 Workshop on Methods for Adverse Events representation: Ontology and Information Model (AE@ICBO2012)
July 22nd 2012, Graz, Austria

SUBMISSION DEADLINE: April 30th 2012 *FIRM*

A variety of information systems are used to record and process adverse event reports. Recently there have been efforts to build ontology to assist in the representation, retrieval, and assessment of adverse event reports. Still, a question remains about how the ontology might be used in conjunction with new and existing information models. For example, are ontology terms to be added to records as keywords for retrieval? Or should information models be revised in the light of a more careful ontological analysis, earlier explored knowledge representation systems, or emerging standards for web semantics?
 
Topics of Interest
AE@ICBO2012 solicits participants who have experience that can shed light on these questions, or who actively develop adverse event reporting systems and can serve to evaluate feasibility and utility of workshop proposals. Specific areas of interest include, but are not limited to:
•    Existing information models, their strengths, weaknesses, and competency criteria.
•    Ongoing efforts to build new information models for adverse event reporting or analysis.
•    Case studies demonstrating information systems that integrate ontology in clinical systems.
•    Reports of new developments in adverse event ontology.
 
All workshop attendees will be expected, at the workshop, to present either descriptions of their work or to articulate a position. In addition a number of participants will be selected to lead interactive sessions on focused topics.

Submission Guidelines
Full papers must describe novel ontology-related research, not previously been published and not submitted to other conferences. Short papers describe research results that are more preliminary or communicate brief position statements. We also invite full-length application-oriented papers, to showcase the development of novel and successful applications utilizing ontologies and knowledge-based technologies. The maximum allowed page lengths of contributions are as follows:
•    Full paper submission: 5 pages, due Apr 30, 2012
•    Short paper submission: 3 pages, due Apr 30, 2012
•    Statement of interest: 1-2 pages, due Apr 30, 2012

Best Papers
Selected papers will be invited to submit an extended version to the Journal of Biomedical Semantics, for publication as best papers. Note that those papers will undergo an additional round of revision pre-publication, and authors will be responsible for open-access processing costs.
 
Contact
If you have any question or which to enquire about the workshop, please contact us at inf...@gm....
 
Organizers
•    Sivaram Arabandi, Elsevier Health Sciences
•    Mélanie Courtot, British Columbia Cancer Research Centre
•    Albert Goldfain, Blue Highway, Inc
•    Chimezie Ogbuji, Case Western Reserve University
•    Alan Ruttenberg, University at Buffalo
 
Related workshop in ICBO 2012
Vaccine and Drug Ontology in the Study of Mechanism and Effect (VDOSME 2012) http://purl.org/icbofois2012/vdosme/ - July 21st 2012.

More information is available at http://purl.org/icbofois2012/adverse_events/submission.htm
Please forward this announcement to everyone who might be interested - a pdf version of the CFP is available at http://purl.org/icbofois2012/adverse_events/CFP.pdf
---
Mélanie Courtot
MSFHR/PCIRN trainee, TFL- BCCRC
675 West 10th Avenue
Vancouver, BC
V5Z 1L3, Canada

[Oae-devel] Workshop Announcement: Vaccine & Drug Ontology in the Study of Mechanism and Effect (VDOSME 2012)

[He, Y. <yon...@me...>]

Dear all,

Here it is to announce the Vaccine and Drug Ontology in the Study of Mechanism and Effect (VDOSME 2012) workshop. The VDOSME 2012 workshop will be held in July, 2012, at Medical University of Graz, Austria. It is part of the 2012 International Conference on Biomedical Ontology (ICBO 2012).

Related information can be found at:
http://kr-med.org/icbofois2012/vdosme/
http://kr-med.org/icbofois2012/vdosme/callforpapers.htm
(Paper submission deadline: April 15)
LinkedIn site:
http://www.linkedin.com/groups?about=&gid=4313827&trk=anet_ug_grppro
(Note: You are welcome to join our VDOSME 2012 LinkedIn Group. It's free to join :) )

A related workshop in ICBO 2012:
Workshop Name: Methods for adverse events representation Ontology and Information Model
http://kr-med.org/icbofois2012/adverse_events/

---------------
Summary:

Vaccines and drugs have contributed to dramatic improvements in public health worldwide. Over the last decade, there have been efforts in biomedical ontology that represent various areas associated with vaccines and drugs and which join existing health and clinical terminology systems (e.g., SNOMED, RxNorm, NDF-RT, and MedDRA) in their application to research and clinical data.

The VDOSME 2012 workshop will provide a platform for discussing problems and solutions in the development and application of biomedical ontologies to representing and analyzing vaccines/drugs, vaccine/drug administrations, vaccine/drug-induced immune responses, and similar topics. The workshop will cover:
            Ontology Coverage: Ontologies of vaccines, of drugs, and of studies thereof.
            Scope of Interest: Representations and analyses of vaccine and drug formation and preparation, administration, mechanisms, and effects based on such ontologies.
 Examples of biomedical subject matter in the scope of this workshop: vaccine/drug components (e.g., vaccine antigens, drug active ingredients, and adjuvants), administration details (e.g., dosage, administration route, and frequency), gene immune responses and pathways, drug-drug or drug-food interactions.

We will also focus on computational methods used to study these, for example, literature mining of vaccine/drug-gene interaction networks, meta-analysis of host immune responses, and time event analysis of vaccine/drug effects.
---------------

It would be appreciated if you could distribute this announcement to any people or groups who might be interested. 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...<mailto: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 

Re: [Oae-devel] Name space change to OAE.

[He, Y. <yon...@me...>]

Hi Melanie,

Good discussion. I have added an editor's note about the time associated as you described. Sorry that I forget to add this part before. Basically, I think it is associated with 'adverse event incubation time', an OAE term I coined based on the 'incubation time' from an infectious disease. Practically, when we assign some AEs to a medical intervention for which AE information is not available, we (a clinician or a patient or a researcher) tend to think that potentially (even with low chance) this AE is caused by the medical intervention. Therefore, there is a possibility involved in the assignment process. This is what I tried to convert with my previous version of AE definition. We  can rethink about this if possible.

For the 'side effect' definition, I'm still not convinced that side effect is not an alternative term for adverse event. I think the wiki definition is right in a sense. However, we can discuss more about this later. For now, I have removed the term as an alternative term in OAE. Instead, I added an editor's note about this issue:

" There has been discussion regarding whether the term 'side effect' is an alternative term for 'adverse event'. In AERO, the term 'AERO:adverse event' represents a subset of those adverse events for which causality has been established. In OAE, an adverse event for which causality has been established is called 'causal adverse event'."

I hope that these make sense.

Also, as suggested by Luca Toldo from Merck KGaA, Germany, I have added to OAE four causal adverse event terms due to the following factors:

A) drug-drug interactions and

B) food-drug interactions

C) genetic predisposition (eg SNP)
Note: SNP is a subtype of the 'genetic predisposition'.
Note: Since Luca is from a company, sometimes he emails me directly instead of to the email list due to some company policy.

Thanks!
Oliver


From: Melanie Courtot [mailto:mco...@gm...]
Sent: Friday, November 18, 2011 3:20 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,

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


**********************************************************
Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues 

Re: [Oae-devel] Name space change to OAE. RE: [obo-admin] Request the addition of Adverse Event Ontology (AEO) into OBO foundry library

[Melanie C. <mco...@gm...>]

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

Re: [Oae-devel] Name space change to OAE. RE: [obo-admin] Request the addition of Adverse Event Ontology (AEO) into OBO foundry library

[He, Y. <yon...@me...>]

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.   

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.

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. 

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".

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 

Re: [Oae-devel] Name space change to OAE. RE: [obo-admin] Request the addition of Adverse Event Ontology (AEO) into OBO foundry library

[Melanie C. <mco...@gm...>]

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_______________________________________________
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> Oae...@li...
> https://lists.sourceforge.net/lists/listinfo/oae-devel

---
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MSFHR/PCIRN trainee, TFL- BCCRC
675 West 10th Avenue
Vancouver, BC
V5Z 1L3, Canada

[Oae-devel] Name space change to OAE. RE: [obo-admin] Request the addition of Adverse Event Ontology (AEO) into OBO foundry library

[He, Y. <yon...@me...>]

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...<mailto: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...<mailto: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...]<mailto:[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...<mailto: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...<mailto: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...]<mailto:[mailto:cjm...@lb...]>
Sent: Saturday, November 05, 2011 2:16 PM
To: He, Yongqun
Cc: obo...@li...<mailto: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<http://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<http://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...<mailto: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...<mailto: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...<mailto: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<http://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<http://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...<mailto: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 

Re: [Oae-devel] [obo-admin] Request the addition of Adverse Event Ontology (AEO) into OBO foundry library

[Xiang, A. <zx...@me...>]

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...<mailto: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...]<mailto:[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...<mailto: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...<mailto: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...]<mailto:[mailto:cjm...@lb...]>
Sent: Saturday, November 05, 2011 2:16 PM
To: He, Yongqun
Cc: obo...@li...<mailto: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<http://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<http://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...<mailto: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...<mailto: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...<mailto: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<http://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<http://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...<mailto:yon...@me...>
Tel: 734-615-8231 (O)
http://www.hegroup.org/

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<AEO_camera_ready_submit.pdf>


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