Fwd: Your article has been published in final version in Journal of Biomedical Semantics.

[Toshiaki Katayama]

Dear all,

I'm happy to inform you that the final version of our manuscript is now published.
Thank you very much for your contributions.

One more news:

Our proposal to launch a new thematic series in the Journal of BioMedical Semantics
is approved by the BMC this week. We'll soon announce an official call for papers
but please start finalizing your manuscripts on BioHackathon 2011 and 2012 sub-groups.

We need to decide deadlines for the initial submissions. How about two months from now?

Best regards,
Toshiaki Katayama

Begin forwarded message:

> 差出人: BioMed Central <post-pub...@biomedcentral.com>
> 件名: Your article has been published in final version in Journal of Biomedical Semantics.
> 日時: 2013年3月6日 22:20:10 JST
> 宛先: "${manuscript.contactUser.title} Toshiaki Katayama" <kt...@dbcls.jp>
>
>
> MS: 1262533519805310
>
> Title: The 3rd DBCLS BioHackathon: improving life science data integration with Semantic Web technologies
>
> Authors: Katayama Toshiaki, Wilkinson D Mark, Micklem Gos, Kawashima Shuichi, Yamaguchi Atsuko, Nakao Mitsuteru, Yamamoto Yasunori, Okamoto Shinobu, Oouchida Kenta, Chun Hong-Woo, Aerts Jan, Afzal Hammad, Antezana Erick, Arakawa Kazuharu, Aranda Bruno, Belleau Francois, Bolleman Jerven, Bonnal Raoul JP, Chapman Brad, Cock Peter JA, Eriksson Tore, Gordon Paul MK, Goto Naohisa, Hayashi Kazuhiro, Horn Heiko, Ishiwata Ryosuke, Kaminuma Eli, Kasprzyk Arek, Kawaji Hideya, Kido Nobuhiro, Kim Young Joo, Kinjo R Akira, Konishi Fumikazu, Kwon Kyung-Hoon, Labarga Alberto, Lamprecht Anna-Lena, Lin Yu, Lindenbaum Pierre, McCarthy Luke, Morita Hideyuki, Murakami Katsuhiko, Nagao Koji, Nishida Kozo, Nishimura Kunihiro, Nishizawa Tatsuya, Ogishima Soichi, Ono Keiichiro, Oshita Kazuki, Park Keun-Joon, Prins Pjotr, Saito L Taro, Samwald Matthias, Satagopam P Venkata, Shigemoto Yasumasa, Smith Richard, Splendiani Andrea, Sugawara Hideaki, Taylor James, Vos Rutger, Withers David, Yamasaki Chisato, Zmasek M Christian, Kawamoto Shoko, Okubo Kosaku, Asai Kiyoshi, Takagi Toshihisa,
>
> Journal: Journal of Biomedical Semantics
>
>
> Dear Toshiaki Katayama,
>
>
> We are delighted to confirm that the final versions of your manuscript have been published on the Journal of Biomedical Semantics website, with the following citation:
>
>
> Journal of Biomedical Semantics.2013, 4:6.
>
> DOI: 10.1186/2041-1480-4-6
>
> URL: http://www.jbiomedsem.com/content/4/1/6
>
> It has also been sent to the US National Library of Medicine for indexing in PubMed and archiving in PubMed Central.
>
>
> If you have any queries, please contact us using the details below.
>
> Best wishes,
> The BioMed Central Production Team
>
> email: post-pub...@biomedcentral.com
>

[Toshiaki Katayama]

Dear all,

On 2013/03/07, at 10:21, Toshiaki Katayama wrote:
> One more news:
>
> Our proposal to launch a new thematic series in the Journal of BioMedical Semantics
> is approved by the BMC this week. We'll soon announce an official call for papers
> but please start finalizing your manuscripts on BioHackathon 2011 and 2012 sub-groups.
>
> We need to decide deadlines for the initial submissions. How about two months from now?

Sorry for the delay, but here's an official Call for Papers to the new thematic series
for BioHackathons in the Journal of BioMedical Semantics.

We are asked to accumulate 5 or more papers for the initial submission, so we encourage
you to prepare your manuscript by May 7th (just two months since my previous mail).

Thanks to Mark and Kiyoko, we have almost finished writing the BH11/12 overview paper
based on your contributions at

* https://github.com/dbcls/bh12/wiki/BH11-submissions
* https://github.com/dbcls/bh12/wiki/BH12-submissions

and we also expect many of you are already working on candidate papers listed at
the above Wiki pages!


== CALL FOR PAPERS: the BioHackathon thematic series in JBMS ==

This is an formal Call for Papers invitation by the thematic series editors
of the Journal of BioMedical Semantics (http://www.jbiomedsem.com/).
All participants of the past BioHackathons are invited to submit your research
activities derived from the BioHackathons.

The series will be entitled as "Semantic interoperability and standardization
of bioinformatics data and Web services".

The thematic series is something like a mini-journal in a journal and handled
by the series editors. Therefore, we expect that your work will be more properly
evaluated in the context of the BioHackathon.

Please use this opportunity to take an advantage of publishing your work quickly!


= Important dates

* Our initial submission due is May 7th 2013 (via email to edi...@biohackathon.org)

As the system to submit to the series is not yet ready because the series will
be launched after we got enough amount of submissions. Therefore, please send
your manuscript to the edi...@biohackathon.org by the above submission due.

Please feel free to ask edi...@biohackathon.org if you have any questions.


= Background

The DBCLS/NBDC BioHackathon is an annual conference gathering open source
bioinformatics developers and life science database providers to address
issues in data integration and standardization by intensive discussions and
coding for a week on site. We have already run five annual BioHackathons that
gathered more than 60 participants for each event, including representatives
from major resources such as UniProt, DDBJ, PDBj and Open Bio* projects.
BioHackhathon is now established as the major community event that provides
not only specific solutions but also produces road maps and agendas for
the future developments in this area. Recent meetings, in particular,
have been focused on the use of Semantic Web technologies for exposing
heterogeneous data as Linked Open Data and consuming that data in various
biomedical applications.

The outcomes of the BioHackathon meetings have been reported as review papers
in Journal of Biomedical Semantics. These have consistently had the top numbers
of access hits (the 2008 report has the highest number of hits of all manuscripts
in JBMS). These manuscripts were summary-reports of the progress at each hackathon.
However, one paper per one conference is not sufficient to describe the specific
outcomes, developments, and ongoing projects arising from each of the BioHackathon
sub-groups. We have therefore concluded that a thematic series would be a better
venue for those groups to publish their group-specific details, and bring more
appropriate and targeted recognition to their achievements and outcomes.
Among the journals, we decided that Journal of Biomedical Semantics would provide
the best and most natural home for such a thematic series. This has been already
widely discussed (and accepted) within the community and with the editors of JBMS.


= Aims

This series would be primarily focusing on open source software developments related
to the topics covered at the BioHackathon events and in particular on standardization
and interoperability of various types of bioinformatics data and services.
The series will however be open to all contributions that are within the scope.


= Topics

The series will target standardization and interoperability issues focused on these topics:

* Large-scale semantic data repositories for life sciences

- Identifier schemes and systems in life sciences
- Biomedical ontologies, vocabularies, design patterns and datasets
- Data curation
- Data consistency checking and validation
- Provenance for biomedical data and scientific discourse
- Visualization of biomedical datasets

* Linked Data

- Linked Data for life sciences
- Linked Open Data publications
- Linked Data and metadata integration/fusion/consolidation
- Scientific analyses over Linked Data

* Reasoning and knowledge discovery

- Knowledge patterns, Ontology development
- Ontology learning
- Reasoning with biomedical ontologies
- Query interfaces for scientists
- Large scale and real time reasoning
- RDF- and OWL-based reasoning; Applications of reasoning

* Natural language processing for the Semantic Web for Life Sciences

- Semantic analysis of textual data
- Entity resolution and interlinking
- Managing the storage and publication of data, interlinks, and embedded LOD

* Data and service quality and evaluation metrics

- Performance evaluation of semantic services


= Series Editors

* Toshiaki Katayama, Database Center for Life Science, Japan, handling editor <kt...@dbcls.jp>
* Atsuko Yamaguchi, Database Center for Life Science, Japan <ats...@dbcls.jp>
* Shuichi Kawashima, Database Center for Life Science, Japan <kw...@dbcls.rois.ac.jp>
* Kiyoko F. Aoki-Kinoshita, Soka University, Japan <kki...@soka.ac.jp>
* Mark Wilkinson, University of British Columbia, Canada <ma...@illuminae.com>
* Michel Dumontier, Carleton University, Canada <michel.d...@gmail.com>
* Erick Antezana, Norwegian University of Science and Technology and Bayer CropScience <erick.a...@gmail.com>


Best regards,
Toshiaki Katayama on behalf of the thematic series editors

[Toshiaki Katayama]

Dear BioHackathon 2011 and/or 2012 participants,

We prepared a draft version of the BH11/12 overview paper at

https://docs.google.com/document/d/1_65PSmS1LEnoz6rTfstD-WFj3d6NJ_4ToUsIrUGQC4Y/edit?usp=sharing

based on the contributed summaries from

> * https://github.com/dbcls/bh12/wiki/BH11-submissions
> * https://github.com/dbcls/bh12/wiki/BH12-submissions

and hope to finalize the manuscript for submission by May 7th as we had announced before.


*** PLEASE ADD YOUR AFFILIATION ASAP !!! ***


The document is granted your "comment privilege" so please put your

* affiliation
* corrections/comments
* appropriate references

from the "Insert > Comment" menu of the Google docs.


Note that, I took names of co-authors from the above Wiki pages so your name could be missed by chance
(e.g., not listed in the sub-group summaries or I failed to copy&paste or ... whatever reasons).
In that case, please don't hesitate to add yourself!


We also encourage you to prepare/submit your manuscript to the thematic series!!

Best regards,
Toshiaki Katayama

[Toshiaki Katayama]

Hello,

Time flies. Only one week left before the targeted dead line!

I have applied suggested comments and corrections so far.
Thank you very much for your kind collaborations.

The problem is, we still don't have affiliations for about
a half of the co-authors. (T_T)

I know you are busy with watching the Stanley Cup playoffs but

> *** PLEASE ADD YOUR AFFILIATION ASAP !!! ***

otherwise, we may need to exclude your name...?!


Also, I should have taken your name from

* http://2011.biohackathon.org/participants
* http://2012.biohackathon.org/participants

however, as I have described before, we used the names listed
on the following Wiki pages for this time.

>> * https://github.com/dbcls/bh12/wiki/BH11-submissions
>> * https://github.com/dbcls/bh12/wiki/BH12-submissions

This DOES NOT mean that we had eliminated you from co-authors
of this paper. We are happy to share the authorship with all
participants and contributors! Please write to me and help us
to improve the manuscript in last-minute.

ALSO, you are encouraged to prepare sub-group papers to the
thematic series by May 7th (should we extend the limit?).
As I need to count the number of upcoming papers, please
let me know if your group is working on (or finished) writing.

Cheers,
Toshiaki

[Toshiaki Katayama]

Hello,

We are getting quick responses now. Thank you!

FYI: the draft only accepts "Insert > Comment" to track your changes
and to prevent anonymous user will edit the text.

>> https://docs.google.com/document/d/1_65PSmS1LEnoz6rTfstD-WFj3d6NJ_4ToUsIrUGQC4Y/edit?usp=sharing

If you found any difficulty, please write to me directly via e-mail.

> We are happy to share the authorship with all
> participants and contributors! Please write to me and help us
> to improve the manuscript in last-minute.

Actually, your proofreading and suggestion of references are
also very important contributions to the manuscript because
all sections in this paper is written based on your intensive
discussions/developments during the past two hackathons.
Please take this opportunity and don't hesitate to join us!

Regards,
Toshiaki

[Rutger Vos]

Hi Toshiaki,

would it be OK if I added myself, I did participate in Kyoto (though not, unfortunately, in Toyama)?

By the way: my time Kyoto was very (re-)productive, the girl I met there will be my wife, our daughter will be born in a few weeks :)

Rutger

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--

Dr. Rutger A. Vos
Bioinformaticist
Naturalis Biodiversity Center
Visiting address: Office A109, Einsteinweg 2, 2333 CC, Leiden, the Netherlands
Mailing address: Postbus 9517, 2300 RA, Leiden, the Netherlands
http://rutgervos.blogspot.com

[Toshiaki Katayama]

Hi Rutger,

On 2013/05/03, at 0:13, Rutger Vos wrote:
> Hi Toshiaki,
>
> would it be OK if I added myself, I did participate in Kyoto (though not, unfortunately, in Toyama)?

Sure.
I took your affiliation from the signature so please confirm your e-mail and affiliation addresses are correctly put on the manuscript.

> By the way: my time Kyoto was very (re-)productive, the girl I met there will be my wife, our daughter will be born in a few weeks :)

Wow, I didn't know that how you met your wife!
Congratulations a lot! Any photos? :)
I'm sure you'll be a very nice father.

Cheers,
Toshiaki

[Pjotr Prins]

Thank you Toshiaki, Kiyoko and Mark for the hard work. And all the
section authors!

I really like this paper and personally think it a valuable
contribution to the scientific effort.

Kudos!

Pj.

[Toshiaki Katayama]

Dear BH11 and/or BH12 participants,

Today is the due date for initial submissions to the new thematic series.

As for the BH11,12 overview paper, I still see some of the co-authors
have not yet filled their affiliations. Due to requests from some of the
co-authors, I'll extend the limit for three days - May 10th.

So please add your affiliations and comments/corrections if you have any.

At the time of submission, I may need to exclude you from authors if you still
have not yet filled your email/affiliation or not responded to me by May 10th.

As for the other submissions, deadline can be bit loose than the above.

* Joachim are finishing the BioInterchange paper
* Kiyoko almost finished writing "Implementation of Linked Data in the Life Sciences"
and I guess she is also preparing "Development of an RDF standard for glycobioinformatics databases".
* Chisato and Scott is working on DB metadata paper

How about FALDO (Jerven?), YummyData (Andrea?) and triple store survey (Wu?) papers? Any others?

If you decided to submit those papers to the thematic series in JBMS,
please indicate that your submission is targeted to the BioHackathon thematic series
in the cover letter. Your submissions are always welcome and sooner is better. :)

Cheers,
Toshiaki

[Andrea Splendiani]

Hi,
YummyData is in refactoring (in fact, at the moment it's even offline). The idea is to finalize it at the next hackathon (coming there with the structure ready). So it won't be a submission for the past edition.

As for the visualization review, as I was writing you, one of the co-authors took the lead, but asked for a 5 weeks extension. I should meet him (Artem) tomorrow.

Best,
Andrea

Apologies for typos, Sent from an iPhone

[Toshiaki Katayama]

Hi Andrea,

On 2013/05/07, at 1:11, Andrea Splendiani wrote:

> Hi,
> YummyData is in refactoring (in fact, at the moment it's even offline). The idea is to finalize it at the next hackathon (coming there with the structure ready). So it won't be a submission for the past edition.

I see. Once the series is launched, you can submit outcomes of the BioHackathon at any time.

> As for the visualization review, as I was writing you, one of the co-authors took the lead, but asked for a 5 weeks extension. I should meet him (Artem) tomorrow.

Sorry, I forget to mention about this one!
Please encourage Artem as the series editors are looking forward to having the article in the thematic series. :)

Cheers,
Toshiaki

[Rutger Vos]

If there's any way I can help out with the viz review please let me know - I'm going to be rather busy pretty soon (as I let slip out on the list by accident) but I'm hoping to be able to squeeze some time in before that.

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[Andrea Splendiani]

Ok,

let me check tomorrow the state of things.

Busy ? It rings a bell... ;)

ciao,

Andrea

[Mark Wilkinson]

I had the same feeling - I really liked the final manuscript! Let's hope
the reviewers do too :-)

M



On Mon, 06 May 2013 08:50:02 +0200, Pjotr Prins <pjot...@thebird.nl>
wrote:

[Peter Cock]

Hello all,

Maybe I missed an email thread, but have we heard anything back from
the journal yet?

I have see a few mentions online of the paper as "in press", e.g.
Mark's mendeley lists it as:

BioHackathon BioHackathon series in 2011 and 2012: penetration of
ontology and Linked Data in life science domains, (in press). In
Journal of Biomedical Semantics.

(I'm going over the references for the FALDO paper
https://github.com/JervenBolleman/FALDO-paper/ and hoped to fill in
the full reference details for this paper.)

Many thanks,

Peter

On Mon, May 6, 2013 at 4:52 PM, Toshiaki Katayama <kt...@dbcls.jp> wrote:
> Dear BH11 and/or BH12 participants,
>
> Today is the due date for initial submissions to the new thematic series.
>
> As for the BH11,12 overview paper, I still see some of the co-authors
> have not yet filled their affiliations. Due to requests from some of the
> co-authors, I'll extend the limit for three days - May 10th.
>
> So please add your affiliations and comments/corrections if you have any.
>
> At the time of submission, I may need to exclude you from authors if you still
> have not yet filled your email/affiliation or not responded to me by May 10th.
>
> As for the other submissions, deadline can be bit loose than the above.
>
> * Joachim are finishing the BioInterchange paper
> * Kiyoko almost finished writing "Implementation of Linked Data in the Life Sciences"
> and I guess she is also preparing "Development of an RDF standard for glycobioinformatics databases".
> * Chisato and Scott is working on DB metadata paper
>
> How about FALDO (Jerven?), YummyData (Andrea?) and triple store survey (Wu?) papers? Any others?
>
> If you decided to submit those papers to the thematic series in JBMS,
> please indicate that your submission is targeted to the BioHackathon thematic series
> in the cover letter. Your submissions are always welcome and sooner is better. :)
>
> Cheers,
> Toshiaki
>
>
> On 2013/05/02, at 19:01, Toshiaki Katayama wrote:
>
>> Hello,
>>
>> We are getting quick responses now. Thank you!
>>

>> ...

[Mark Wilkinson]

I believe it has been accepted, and Toshiaki-san is now making final
editorial changes... I believe!??

My Mendeley feed isn't authoritative :-) I just put papers in there to
make sure I don't forget them LOL!

M



On Mon, 18 Nov 2013 18:08:21 +0100, Peter Cock <p.j.a...@googlemail.com>
wrote:

[Toshiaki Katayama]

Hi,

Yes, our BH11-12 review is accepted and I already submitted editorial fixes.
We may still have a proofreading but I expect it will be soon published.

Peter, sorry for my delay but I just finished reading the current draft of
the FALDO paper (many thanks for pushing this project forward :).
I noticed several points to improve the manuscript and will work on the repository.

Cheers,
Toshiaki

H25/11/19 22:35、Mark Wilkinson <ma...@illuminae.com> のメール：

[Peter Cock]

On Tue, Nov 19, 2013 at 4:19 PM, Toshiaki Katayama <kt...@dbcls.jp> wrote:
> Hi,
>
> Yes, our BH11-12 review is accepted and I already submitted editorial fixes.
> We may still have a proofreading but I expect it will be soon published.

That is excellent news :)

Thank you for handling the editorial fixes.

> Peter, sorry for my delay but I just finished reading the current draft of
> the FALDO paper (many thanks for pushing this project forward :).
> I noticed several points to improve the manuscript and will work on
> the repository.
>
> Cheers,
> Toshiaki

Great. Yesterday and today I've been fixing some little problems
directly in the repository, and opening issues for things needing
discussion. I have just updated the citation for the BH11-12 review
to list this as "in press":
https://github.com/JervenBolleman/FALDO-paper

Regards,

Peter