[Obi-devel] contribution to manuscript

[Bjoern Peters]

All, 

I was asked by Ramona Walls if I could write a short paragraph on OBI / IAO for a paper on a "Ontology for Biodiversity" that will be submitted to a conference. Philippe had been at two workshops with this consortium and informed them about the possibilities to work with OBI. Right now, BCO has a lot of terms that are overlapping with OBI. The paper acknowledges this, and describes the plans to in the future coordinate better with OBI and other foundry ontologies. I am pasting below what I have written (based on the draft from Ramona; the content I have is essentially the same though). 

OBI is an ontology that aims to enable describing all biological and clinical investigations with a shared vocabulary.  The notion of material sample, subsamples, observations and measurements are all covered in OBI, but were developed independent of the BCO effort, so that coordination is just now starting. At first blush, the shared terms align well between the BCO and OBI, and several OBI terms are included directly in the BCO. However, given OBIs much broader scope, many of OBI’s term names are not familiar to biodiversity scientists, even if the definitions are familiar. We are considering ways to align the BCO with OBI, such as importing OBI terms into BCO but providing them with alternative labels readily understandable to biodiversity scientists. The future use of OBI terms in BCO will ensure that it is interoperable with other descriptions of investigations in the OBO foundry.

I had asked to add the OBI consortium as an author rather than myself, and I think it would be good to take this as an opportunity. Ramona agreed, and now I am asking if anyone has any issues with it. If anyone has any problems, please let me know immediately. In that case, we would (at least temporarily) remove the OBI consortium authorship. Deadline for submission is very soon, so please let me know right now. I realize I should have asked this earlier; sorry. 

Ramona, can I share the link to the document (viewing only) with the OBI list? 

Best, 

Bjoern

[jiez...@pcbi.upenn.edu]

Looks good to me.

Thanks, Bjoern.

Jie

Quoting Bjoern Peters <bpe...@liai.org>:

>
> All,
>
>
> I was asked by Ramona Walls if I could write a short paragraph on
> OBI / IAO for a paper on a "Ontology for Biodiversity" that will be
> submitted to a conference. Philippe had been at two workshops with
> this consortium and informed them about the possibilities to work
> with OBI. Right now, BCO has a lot of terms that are overlapping
> with OBI. The paper acknowledges this, and describes the plans to in
> the future coordinate better with OBI and other foundry ontologies.
> I am pasting below what I have written (based on the draft from
> Ramona; the content I have is essentially the same though).
>
>
>
> OBI is an ontology that aims to enable describing all biological and
> clinical investigations with a shared vocabulary. The notion of
> material sample, subsamples, observations and measurements are all
> covered in OBI, but were developed independent of the BCO effort, so
> that coordination is just now starting. At first blush, the shared
> terms align well between the BCO and OBI, and several OBI terms are
> included directly in the BCO. However, given OBIs much broader

> scope, many of OBI?s term names are not familiar to biodiversity

> scientists, even if the definitions are familiar. We are considering
> ways to align the BCO with OBI, such as importing OBI terms into
> BCO but providing them with alternative labels readily
> understandable to biodiversity scientists. The future use of OBI
> terms in BCO will ensure that it is interoperable with other
> descriptions of investigations in the OBO foundry.
>
>
>
> I had asked to add the OBI consortium as an author rather than
> myself, and I think it would be good to take this as an opportunity.
> Ramona agreed, and now I am asking if anyone has any issues with
> it. If anyone has any problems, please let me know immediately. In
> that case, we would (at least temporarily) remove the OBI
> consortium authorship. Deadline for submission is very soon, so
> please let me know right now. I realize I should have asked this
> earlier; sorry.
>
>
>
> Ramona, can I share the link to the document (viewing only) with the
> OBI list?
>
>
> Best,
>
>
> Bjoern
>
>

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[Larisa Soldatova]

Hi Bjoern and All,

Your and BCO decision to include OBI Consortium as a co-author of a
paper could not be objected in principle because it follows the
policies we all have agreed on.
I remember we discussed a policy for authorship of papers which are
using OBI. It was recommended to include OBI Consortium to the authors
list if the reported work was substantially based on OBI, but
ultimately it was up to the authors.

I would like to thank Ramona and BCO for using OBI and looking for
constructive ways to align these projects.

Regards,
Larisa

[Philippe]

Hi Ramona, Bjoern,

This is a very nice development.
It will also bode well for forthcoming OBI review, indicating a
plurality of users.
The only alteration to the text could be a few words towards organizing
term request and triage to maintain OBI aware of additions that may
occur under BCO (for instance, biodiversity specific assays).

Thanks both for this.

Philippe

On 14/03/2013 05:00, Bjoern Peters wrote:
> All,
>
> I was asked by Ramona Walls if I could write a short paragraph on OBI /
> IAO for a paper on a "Ontology for Biodiversity" that will be submitted
> to a conference. Philippe had been at two workshops with this consortium
> and informed them about the possibilities to work with OBI. Right now,
> BCO has a lot of terms that are overlapping with OBI. The paper
> acknowledges this, and describes the plans to in the future coordinate
> better with OBI and other foundry ontologies. I am pasting below what I
> have written (based on the draft from Ramona; the content I have is
> essentially the same though).
>

> *OBI is an ontology that aims to enable describing all biological and

> clinical investigations with a shared vocabulary. The notion of
> material sample, subsamples, observations and measurements are all
> covered in OBI, but were developed independent of the BCO effort, so
> that coordination is just now starting. At first blush, the shared terms
> align well between the BCO and OBI, and several OBI terms are included
> directly in the BCO. However, given OBIs much broader scope, many of
> OBI’s term names are not familiar to biodiversity scientists, even if
> the definitions are familiar. We are considering ways to align the BCO
> with OBI, such as importing OBI terms into BCO but providing them with
> alternative labels readily understandable to biodiversity scientists.
> The future use of OBI terms in BCO will ensure that it is interoperable

> with other descriptions of investigations in the OBO foundry.*

>
> I had asked to add the OBI consortium as an author rather than myself,
> and I think it would be good to take this as an opportunity. Ramona
> agreed, and now I am asking if anyone has any issues with it. If anyone
> has any problems, please let me know immediately. In that case, we would
> (at least temporarily) remove the OBI consortium authorship. Deadline
> for submission is very soon, so please let me know right now. I realize
> I should have asked this earlier; sorry.
>
> Ramona, can I share the link to the document (viewing only) with the OBI
> list?
>
> Best,
>
> Bjoern
>
>
>

[Chris Stoeckert]

OBI Consortium authorship and the paragraph both look good to me. And I look forward to seeing this alignment happen.

Cheers, 

Chris

[Scheuermann, Richard]

Who is the OBI consortium?

Richard

--------------------------------------------

Richard H. Scheuermann, Ph.D.

Director of Informatics

J. Craig Venter Institute

10355 Science Center Dr.

San Diego, CA 92121

rscheu...@jcvi.org

858-200-1876

[Melissa Haendel]

Hi Bjoern, Ramona,

This is great! I think another thing that you could discuss would be design patterns for evidence and phenotypic assays - we've discussed this on a number of occasions in OBI and at RCN meetings and it would seem a natural intersection of the two projects. I also think that modularization of OBI for such purposes might be a good topic for an upcoming workshop. Ramona, where is BCO?

I think it would be great to have OBI be an author too.

Melissa

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Dr. Melissa Haendel

Assistant Professor
Ontology Development Group, OHSU Library

http://www.ohsu.edu/library/

Department of Medical Informatics and Epidemiology
Oregon Health & Science University
hae...@ohsu.edu
skype: melissa.haendel

503-407-5970

[He, Yongqun]

Looks good to me. Thanks!
Oliver

-----Original Message-----
From: jiez...@pcbi.upenn.edu [mailto:jiez...@pcbi.upenn.edu]
Sent: Thursday, March 14, 2013 2:06 AM
To: Bjoern Peters
Cc: obi-...@lists.sourceforge.net Developers; Ramona Walls
Subject: Re: [Obi-devel] contribution to manuscript

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

[Chris Stoeckert]

Hi Richard,

Good question. Checking with Jie, we aren't sure. Is the current OBI Consortium essentially everyone on this mailing list?

I don't think what is posted on the web site is correct: http://obi-ontology.org/page/Consortium - there is no longer a coordinating committee.

We might want to update that page/ link.

Chris

[Ramona Walls]

Sent this from the wrong email address, so I don't think it got through to obi-discuss.

Ramona

On Thu, Mar 14, 2013 at 9:42 AM, Ramona Walls <rwa...@nybg.org> wrote:

Thanks everyone for the positive feedback. Bjoern, thank you for drafting the paragraph. It is okay if you share read acces to the document with OBI consortium members, but bear in mind that it is still in progress.

Ramona

[Melanie Courtot]

We updated the list in December 2008 and moved everybody in the obi.owl file as dc:creators (which list we then used for example for the MIREOT paper) See http://sourceforge.net/mailarchive/message.php?msg_id=21049763

Maybe when new people join the project they could be added to the obi.owl file which would then be the reference as to who is the OBI consortium?

Melanie

[Bjoern Peters]

Hi Ramona, 

Both Philippe's and Melissa's suggestions are thinks we should actually do, but I think for your present manuscript with the purpose of introducing BCO to users, it is not necessary to spell out more details of how BCO and OBI would interact. (That could get very long quickly; I tried to focus on the most obvious at hand). 

Best, 

Bjoern

---

Thanks, Melissa. I am interesting in thinking more about what you suggest (design patterns for evidence and phenotypic assays). Are there any OBI discussion threads you can point me to on this topic? We are trying to get this manuscript out fairly quickly, and given the preliminary state of the BCO, such a discussion might be premature for this paper. However, I hope there will be more ontology development and a more in depth paper in the not too distant future, so we should keep this in mind as we go forward.

Ramona

On Thu, Mar 14, 2013 at 7:13 AM, Melissa Haendel <hae...@ohsu.edu> wrote:

Hi Bjoern, Ramona,

This is great! I think another thing that you could discuss would be design patterns for evidence and phenotypic assays - we've discussed this on a number of occasions in OBI and at RCN meetings and it would seem a natural intersection of the two projects. I also think that modularization of OBI for such purposes might be a good topic for an upcoming workshop. Ramona, where is BCO?

I think it would be great to have OBI be an author too.

Melissa

On Mar 13, 2013, at 10:00 PM, Bjoern Peters wrote:

All, 

I was asked by Ramona Walls if I could write a short paragraph on OBI / IAO for a paper on a "Ontology for Biodiversity" that will be submitted to a conference. Philippe had been at two workshops with this consortium and informed them about the possibilities to work with OBI. Right now, BCO has a lot of terms that are overlapping with OBI. The paper acknowledges this, and describes the plans to in the future coordinate better with OBI and other foundry ontologies. I am pasting below what I have written (based on the draft from Ramona; the content I have is essentially the same though). 

OBI is an ontology that aims to enable describing all biological and clinical investigations with a shared vocabulary.  The notion of material sample, subsamples, observations and measurements are all covered in OBI, but were developed independent of the BCO effort, so that coordination is just now starting. At first blush, the shared terms align well between the BCO and OBI, and several OBI terms are included directly in the BCO. However, given OBIs much broader scope, many of OBI’s term names are not familiar to biodiversity scientists, even if the definitions are familiar. We are considering ways to align the BCO with OBI, such as importing OBI terms into BCO but providing them with alternative labels readily understandable to biodiversity scientists. The future use of OBI terms in BCO will ensure that it is interoperable with other descriptions of investigations in the OBO foundry.

I had asked to add the OBI consortium as an author rather than myself, and I think it would be good to take this as an opportunity. Ramona agreed, and now I am asking if anyone has any issues with it. If anyone has any problems, please let me know immediately. In that case, we would (at least temporarily) remove the OBI consortium authorship. Deadline for submission is very soon, so please let me know right now. I realize I should have asked this earlier; sorry. 

Ramona, can I share the link to the document (viewing only) with the OBI list? 

Best, 

Bjoern

------------------------------------------------------------------------------
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Dr. Melissa Haendel

Assistant Professor
Ontology Development Group, OHSU Library

http://www.ohsu.edu/library/

Department of Medical Informatics and Epidemiology
Oregon Health & Science University
hae...@ohsu.edu
skype: melissa.haendel

503-407-5970

------------------------------------------------------------------------------
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Make your web apps faster with AppDynamics
Download AppDynamics Lite for free today:
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--

Bjoern Peters
Assistant Professor
La Jolla Institute for Allergy and Immunology
9420 Athena Circle
La Jolla, CA 92037, USA
Tel: 858/752-6914
Fax: 858/752-6987
http://www.liai.org/pages/faculty-peters

[Scheuermann, Richard]

Thanks Chris.  I'm a little sensitive to the issue because after spending many years trying to contribute to OBI development from its inception, I am not a co-author on the one paper currently available to cite for OBI (Brinkman et al.).  I know I haven't been an active developer recently, but remain an advocate and active adopter.

[Chris Stoeckert]

Hi Richard,

I think your point underscores the need for us to get the official OBI paper out. We should make that a top priority again once the OBI core review is finished. 

I've been absent from weekly calls while on sabbatical but plan to start attending again and ready to help in the review where I can.

Chris

[Chris Stoeckert]

Hi Melanie,

> Maybe when new people join the project they could be added to the obi.owl file which would then be the reference as to who is the OBI consortium?

I like this approach. Something to work on for the next obi.owl release.
Chris

[Scheuermann, Richard]

Since you all will be getting together next week and the issue of the official OBI manuscript will likely come up, I would like to put on the table how authorship will be determined.  Specifically, should individuals actively involved in the past be included, even though they might not be able to actively contribute in the present.

Thanks,

Richard

--------------------------------------------

Richard H. Scheuermann, Ph.D.

Director of Informatics

J. Craig Venter Institute

10355 Science Center Dr.

San Diego, CA 92121

rscheu...@jcvi.org

858-200-1876

[Chris Taylor]

I'd say yes :)

C.

"Scheuermann, Richard" <RScheu...@jcvi.org> wrote:

Cheers, 

Chris

All, 

I was asked by Ramona Walls if I could write a short paragraph on OBI / IAO f or a paper on a "Ontology for Biodiversity" that will be submitted to a conference. Philippe had been at two workshops with this consortium and informed them about the possibilities to work with OBI. Right now, BCO has a lot of terms that are overlapping with OBI. The paper acknowledges this, and describes the plans to in the future coordinate better with OBI and other foundry ontologies. I am pasting below what I have written (based on the draft from Ramona; the content I have is essentially the same though). 

OBI is an ontology that aims to enable describing all biological and clinical investigations with a shared vocabulary.  The notion of material sample, subsamples, observations and measurements are all covered in OBI, but were developed independent of the BCO effort, so that coordination is just now starting. At first blush, the shared terms align well between the BCO and OBI, and several OBI terms are included directly in the BCO. However, given OBIs much broader scope, many of OBI’s term names are not familiar to biodiversity scientists, even if the definitions are familiar. We are considering ways to align the BCO with OBI, such as importing OBI terms into BCO but providing them with alternative labels readily understandable to biodiversity scientists. The future use of OBI terms in BCO will ensure that it is interoperable with other descriptions of investigations in the OBO foundry.

I had asked to add the OBI consortium as an author rather than myself, and I think it would be good to take this as an opportunity. Ramona agreed, and now I am asking if anyone has any issues with it. If anyone has any problems, please let me know immediately. In that case, we would (at least temporarily) remove the OBI consortium authorship. Deadline for submission is very soon, so please let me know right now. I realize I should have asked this earlier; sorry. 

Ramona, can I share the link to the document (viewing only) with the OBI list? 

Best, 

Bjoern

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[jiez...@pcbi.upenn.edu]

Hi Richard,

We have discussed this issue in the OBI developer call. All persons
involved in OBI development both in the past and in the present will
be listed as authors in the first official OBI manuscript. The authors
will be listed in alphabet order and Bjoern is the corresponding
author because active developers all agree that he is the one who
contribute a lot to manuscript preparation. There is an Excel file
listing the authors' contribution on last submission in 2010. I think
the file will be sent out again before next submission.

Best,

Jie

> rscheu...@jcvi.org<mailto:rscheu...@jcvi.org>

> 858-200-1876
>
>
> From: Chris Stoeckert
> <stoe...@pcbi.upenn.edu<mailto:stoe...@pcbi.upenn.edu>>
> Date: Thursday, March 14, 2013 10:20 AM
> To: "Richard H. Scheuermann"
> <rscheu...@jcvi.org<mailto:rscheu...@jcvi.org>>
> Cc: Bjoern Peters <bpe...@liai.org<mailto:bpe...@liai.org>>,
> "obi-...@lists.sourceforge.net<mailto:obi-...@lists.sourceforge.net>
> Developers"
> <obi-...@lists.sourceforge.net<mailto:obi-...@lists.sourceforge.net>>
> Subject: Re: [Obi-devel] contribution to manuscript
>
> Hi Richard,
> Good question. Checking with Jie, we aren't sure. Is the current OBI
> Consortium essentially everyone on this mailing list?
> I don't think what is posted on the web site is correct:
> http://obi-ontology.org/page/Consortium - there is no longer a
> coordinating committee.
> We might want to update that page/ link.
> Chris
>
> On Mar 14, 2013, at 9:57 AM, "Scheuermann, Richard"

> <RScheu...@jcvi.org<mailto:RScheu...@jcvi.org>> wrote:
>
> Who is the OBI consortium?
>
> Richard
> --------------------------------------------
> Richard H. Scheuermann, Ph.D.
> Director of Informatics
> J. Craig Venter Institute
> 10355 Science Center Dr.
> San Diego, CA 92121
>

> rscheu...@jcvi.org<mailto:rscheu...@jcvi.org>

> 858-200-1876
>
>
> From: Chris Stoeckert
> <stoe...@pcbi.upenn.edu<mailto:stoe...@pcbi.upenn.edu>>
> Date: Thursday, March 14, 2013 5:41 AM
> To: Bjoern Peters <bpe...@liai.org<mailto:bpe...@liai.org>>
> Cc:
> "obi-...@lists.sourceforge.net<mailto:obi-...@lists.sourceforge.net>
> Developers"
> <obi-...@lists.sourceforge.net<mailto:obi-...@lists.sourceforge.net>>,
> Ramona Walls <rwa...@nybg.org<mailto:rwa...@nybg.org>>
> Subject: Re: [Obi-devel] contribution to manuscript
>
> OBI Consortium authorship and the paragraph both look good to me.
> And I look forward to seeing this alignment happen.
> Cheers,
> Chris
>
> On Mar 14, 2013, at 1:00 AM, Bjoern Peters

> Obi-...@lists.sourceforge.net<mailto:Obi-...@lists.sourceforge.net>
> https://lists.sourceforge.net/lists/listinfo/obi-devel
>
>
>




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_______________________________________________

[Susanna Sansone]

Thanks Jie,
I would like to suggest that - if the journal allows it or accordingly - the author is "The OBI Consortium" followed by all names, as Wellcome Trust Case Control Consortium and others have done.
Thanks,
Susanna

-- 
Susanna-Assunta Sansone, PhD
uk.linkedin.com/in/sasansone

University of Oxford e-Research Centre
 Associate Director, PI and Team Leader
 isacommons.org | biosharing.org

Nature Publishing Group
 Consultant, Scientific Data
 www.nature.com/scientificdata
-- 

[Susanna Sansone]

To clarify: ....and of course for Bjoern being the corresponding author.
Susanna

[Scheuermann, Richard]

Terrific

Sent from my iPhone

[Bjoern Peters]

Susanna's suggestion is actually what was already agreed upon in the initial vote ( http://obi-ontology.org/page/Votes_results ):

"Authorship will be the OBI Consortium followed by an alphabetical listing of the members. Contributions of the authors will be placed in the appendix"

Jie's comment was more regarding who is included in the author list, and that was discussed several times in the past. Exactly as Jie said, the 'initial/main' paper will include everyone that has contributed to OBI development until now, not just the currently active people. This will then change for future papers.

- Bjeorn

--

--
Bjoern Peters
Assistant Professor
La Jolla Institute for Allergy and Immunology
9420 Athena Circle
La Jolla, CA 92037, USA
Tel: 858/752-6914
Fax: 858/752-6987
http://www.liai.org/pages/faculty-peters

[Alan Ruttenberg]

I don't recall whether we've discussed it, but I'm fond of, and many journals request, that we include an authors contributions list. Contributions in our group range from being representative for discipline communities, driving OBI development by using it in specific projects through term development, review and different kinds of operational and technical support. With such a large list of authors, I think use having such a list gives an opportunity to both say something specific (though brief) about each author, as well as give another picture of the spectrum of efforts that contribute to a project of this size. 

A simple way of constructing this is to start a wiki page where each of us can put our name and a list of contributions, attempting to order those contributions by our own assessment of impact. Then the paper editors can take these verbatim, or edit to reorganize and reduce space.

-Alan