gmod-devel — GMOD developer's mailing list

[GMOD-devel] Apollo Developers Hackathon, Jan 2016, La Jolla, CA - Save the Date!

[Monica Munoz-T. <mcm...@lb...>]

*Save the Date!*

*Berkeley Bioinformatics Open-Source Projects <http://www.berkeleybop.org/>
at Lawrence Berkeley National Laboratory*
and
*The Su Lab <http://sulab.org/> at The Scripps Research Institute*

invite you to join us this winter for the second *Apollo Developers
Hackathon *in La Jolla, California.

For three days developers will work on new features of interest to their
research communities, will be able to improve on existent Apollo
<http://genomearchitect.org/> & JBrowse <http://jbrowse.org/> features, and
will collaborate in the development of features of interest to other
colleagues.

*Participants should: *
- be able to set up your own Apollo server before arriving to Berkeley;
including Postgres, Tomcat, etc.
- code comfortably in JavaScript (client) and Java (server).

*What will we do at the hackathon?:*
The plan is still brewing, but we have a few ideas:
- New tracks for visualization of variant data. We want interactive tracks,
and tracks that aggregate many data at once. Including exploration of
synergies with with the myvariant.info tool.
- Integration of JBrowse / Apollo with Gene-Wiki.
- Usage of EBI's protein modification data format (some examples of their
implementation at http://www.ebi.ac.uk/pride/archive/).
- Creating a plugin to design CRISPR experiments.
- *your ideas go here!*

Please send your suggestions for feature development, your questions, and
any additional comments to the Apollo Developers email at: apollo [dash]
dev [at] lists [dot] lbl [dot] gov

*When: *Thursday January 14 - Saturday January 16, 2016 (immediately after
PAG <http://www.intlpag.org/>).
*Where:* The Scripps Research Institute, Molecular and Experimental
Medicine Building, 3545 Cray Court, La Jolla, CA 92121. USA.
*Registration:* A nominal registration fee of $75 will be collected, to
cover the cost of refreshments, and minor logistics charges.* Registration
page coming soon!*
*Getting there, accommodations: *Participants are responsible for arranging
travel and accommodations on their own. *Details about hotel blocks and
directions coming soon!*

See you in January!

Berkeley Bioinformatics Open-Source Projects & The Su Lab
www.GenomeArchitect.org

[image: Inline image 2]

It is very likely you will receive this message more than once. We offer
our sincere apologies for the redundancy.
p.s: The bee image is CopyRight of www.AlexanderWild.com | DNA image from
ShutterStock.com


-- 
Mentorship Matters!
--
Monica Munoz-Torres, PhD.
Berkeley Bioinformatics Open-source Projects (BBOP)
Environmental Genomics and Systems Biology Division
Lawrence Berkeley National Laboratory

Mailing Address:
Lawrence Berkeley National Laboratory
1 Cyclotron Road Mailstop 977
Berkeley, CA 94720

Re: [GMOD-devel] track metadata in CSV file

[Scott C. <sc...@sc...>]

Hi Kalpana,

I think you're asking a question about JBrowse, so I'm going to cc the
JBrowse mailing list here.  If I've got that wrong, please let me know.

Scott


On Mon, Oct 12, 2015 at 1:15 PM, Kalpana Karra <kk...@st...> wrote:

> Hello,
>
> I have track metadata in a CSV file with different column headers/names
> from modencode example and the facets would not work. If I use the same
> header as in the modencode file, it works.
>
> - Do the column names matter for the faceted search to work?
>
> - Where can I find the code that parses the CSV file? Looked in github,
> but am not able to find it.
>
> Thanks,
> -Kalpana
>
>
>
> ------------------------------------------------------------------------------
> _______________________________________________
> Gmod-devel mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-devel
>



-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot
net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

[GMOD-devel] track metadata in CSV file

[Kalpana K. <kk...@st...>]

Hello,

I have track metadata in a CSV file with different column headers/names from modencode example and the facets would not work. If I use the same header as in the modencode file, it works.  

- Do the column names matter for the faceted search to work? 

- Where can I find the code that parses the CSV file? Looked in github, but am not able to find it.

Thanks,
-Kalpana
 

[GMOD-devel] [CFP] Semantic Web Journal - Special Issue on Quality Management of Semantic Web Assets (Data, Services and Systems) - Only 1 month left

[Amrapali Z. <pr...@in...>]

*CFP: Semantic Web Journal - Special Issue on Quality Management of 
Semantic Web Assets (Data, Services and Systems):* 
http://www.semantic-web-journal.net/blog/call-papers-special-issue-quality-management-semantic-web-assets-data-services-and-systems 
<http://www.semantic-web-journal.net/blog/call-papers-special-issue-quality-management-semantic-web-assets-data-services-and-systems>


    Submission guidelines

*Deadline (_only 1 month left_):October 31, 2015
*

Submissions shall be made through the Semantic Web journal website at 
http://www.semantic-web-journal.net 
<http://www.semantic-web-journal.net/>. Prospective authors must take 
notice of the submission guidelines posted at 
http://www.semantic-web-journal.net/authors 
<http://www.semantic-web-journal.net/authors>. Note that you need to 
request an account on the website for submitting a paper. Please 
indicate in the cover letter that it is for the Special Issue on Quality 
Management of Semantic Web Assets (Data, Services and Systems).

Submissions are possible in the following categories: full research 
papers, application reports, reports on tools and systems, and case 
studies. While there is no upper limit, paper length must be justified 
by content.


    Guest editors

  * Amrapali Zaveri, University of Leipzig, AKSW Group, Germany
  * Dimitris Kontokostas, University of Leipzig, AKSW Group, Germany
  * Sebastian Hellmann, University of Leipzig, AKSW Group, Germany
  * Jürgen Umbrich, Vienna University of Economics and Business, Austria

*Overview and Topics*

The standardization and adoption of Semantic Web technologies has 
resulted in a variety of assets, including an unprecedented volume of 
data being semantically enriched and systems and services, which consume 
or publish this data. Although gathering, processing and publishing data 
is a step towards further adoption of Semantic Web, quality does not yet 
play a central role in these assets (e.g., data lifecycle, 
system/service development).

Quality management essentially refers to activities and tasks involved 
to guarantee a certain level of consistency and to meet the quality 
requirements for the assets. In general, quality management consists of 
the following four phases and components: (i) quality planning, (ii) 
quality control, (iii) quality assurance and (iv) quality improvement.

The quality planning phase in the Semantic Web typically involves the 
design of procedures, strategies and policies to support the management 
of the assets. The quality control and assurance components have their 
primary aim in preventing errors and to meet quality requirements 
pertaining to the Semantic Web standards. A core part for both 
components are quality assessment methods which provide the necessary 
input for the controlling and assurance tasks.

Quality assessment of Semantic Web Assets (data, services and systems), 
in particular, presents new challenges that were not handled before in 
other research areas. Thus, adopting existing approaches for data 
quality assessment is not a straightforward solution. These challenges 
are related to the openness of the Semantic Web, the diversity of the 
information and the unbounded, dynamic set of autonomous data sources, 
publishers and consumers (legal and software agents). Additionally, 
detecting the quality of available data sources and making the 
information explicit is yet another challenge. Moreover, noise in one 
data set, or missing links between different data sets, propagates 
throughout the Web of Data, and imposes great challenges on the data 
value chain.

In case of systems and services, different implementations follow the 
specifications for RDF and SPARQL to varying extents, or even propose 
and offer new, non-standardized extensions. This causes strong 
incompatibilities between systems, e.g., between the used SPARQL 
features in the query engines and support features in RDF stores. The 
potential heterogeneity and incompatibility poses several challenges for 
the quality assessments in and for such systems and services.

Eventually, quality improvement methods are used to further enhance the 
value of the Semantic Web Assets. One important step to improve the 
quality of data is identifying the root cause of the problem and then 
designing corresponding data improvement solutions. These solutions 
select the most effective and efficient strategies and related set of 
techniques and tools to improve quality. Quality improvement metrics for 
products and services entails understanding and improving operational 
processes and establishing valid and reliable service performance measures.

This Special Issue is addressed to those members of the community 
interested in providing novel methodologies or frameworks in managing, 
assessing, monitoring, maintaining and improving the quality of the 
Semantic Web data, services and systems and also introduce tools and 
user interfaces which can effectively assist in this management.


    Topics of Interest

We welcome original high quality submissions on (but are not restricted 
to) the following topics:

  * Methodologies and frameworks to plan, control, assure or improve the
    quality of Semantic Web Assets
  * Quality exploration and analysis interfaces
  * Quality monitoring
  * Developing, deploying and managing quality service ecosystems
  * Assessing the quality evolution of Semantic Web Assets
  * Large-scale quality assessment of structured datasets
  * Crowdsourcing data quality assessment
  * Quality assessment leveraging background knowledge
  * Use-case driven quality management
  * Evaluation of trustworthiness of data
  * Web Data and LOD quality benchmarks
  * Data Quality improvement methods and frameworks, e.g., linkage,
    alignment, cleaning, enrichment, correctness
  * Service/system quality improvement methods and frameworks
  * Managing sustainability issues in services
  * Guarantee of service (availability, performance)
  * Systems for transparent management of open data

[GMOD-devel] tripal_feature_load_gff3 v gmod_bulk_load_gff3 and load performance

[Cook, M. <ME...@st...>]

Hi,

I notice that some gmod_bulk_load_gff3 are not present in its apparent replacement, tripal_feature_load_gff3, and wonder why.
		
In particular the gmod_bulk_load_gff3 --drop_indexes and--skip_vacuum options seems no longer present in tripal_feature_load.

Also, can anyone confirm that:

	--notransact is replaced by use_transaction

I am asking these questions in pursuit of helping a colleague (hi Sofia) sleuth options for speeding up a large GFF3 load under tripal.

In addition to normal pg tuning, advice I have seen before with Drupal includes:
	Split up a large GFF into multiple files
	Don't use transactions
	Drop indices and add them back post-load

Anyone have additions of amendments to these suggestions in the context of Tripal?  I.E, which if any of these strategies still works, or would still work if modified appropriately.

Finally, I see a web interface in Tripal to invoking tripal_feature_load_gff3 but see no command line equivalent.  Can someone explain why, or am I missing something?  Must GFF be loaded via web interface now?

References 

	http://iubio.bio.indiana.edu/gmod/genbank2chado/bin/gmod_bulk_load_gff3.pl
	http://api.tripal.info/api/tripal/tripal_feature%21includes%21tripal_feature.gff_loader.inc/function/tripal_feature_load_gff3/2.x

Thanks

Malcolm Cook
Computational Biology
Stowers Institute for Medical Research
1000 E 50th Street
Kanas City, MO 64110
(816) 926-4449
me...@st...

[GMOD-devel] Call for Participation: SEMANTiCS 2015, 11th International Conference on Semantic Systems

[Tassilo P. <pr...@in...>]

== Apologies for Crossposting ==


Below you will find useful information and links about the program, our 
satellite events and registration opportunities for

SEMANTiCS 2015 -- 11th International Conference on Semantic Systems

15-17 September 2015, Vienna / Austria
http://www.semantics.cc/ // #semantics2015 // #semanticsconf

*— Conference Scope ---*
The annual SEMANTiCS conference is the meeting place for professionals 
who make semantic computing work, and understand its benefits and know 
its limitations. Every year, SEMANTiCS attracts information managers, 
IT-architects, software engineers, and researchers, from organisations 
ranging from NPOs, universities, public administrations to the largest 
companies in the world.



*— Conference Program ---*

The 2015 edition offers a rich program consisting of 5 keynotes, 24 
scientific presentations, 30 industry talks, 38 posters and various 
workshops and social events. For details please visit our program page:

http://www.semantics.cc/programme



*— Keynote Speakers --- *

·Jeanne Holms -- Chief Knowledge Architect at NASA

·Peter Mika -- Director Semantic Lab at Yahoo

·Oscar Orcho -- Associate Professor for Artifical Intelligence, 
Universidad de Madrid

·Klaus Tochtermann -- Leibniz Information Center for Economics

·Sam Rehman -- CTO at EPAM Systems

*— Workshops & Satellite Events ---*

*MeetUp: SMART DATA SOLUTIONS*

An outlook into the world of data centric business, technologies and 
innovations: Data is everywhere these days and efficient data management 
is THE key factor for success in nearly all industries in the meantime. 
McKinsey lists data as a key factor for production alongside with labor 
and capital in one of their recent reports. Furthermore, Data is 
produced in huge amounts by sensors, social networks or mobile devices 
and the amounts of data available worldwide grow exponentially…

Place: Haus der Ingenieure, Eschenbachgasse 9, 1010 Wien
Date: 15.09.2015, Entrance: 18:30pm CET ; Start event: 19:30 - 22:30pm CET

*2nd International Workshop on Geospatial Linked Data*

In recent years, Semantic Web technologies have strengthened their 
position in the areas of data and knowledge management. Standards for 
organizing and querying semantic information, such as RDF(S) and SPARQL 
are adopted by large academic communities, while corporate vendors adopt 
semantic technologies to organize, expose, exchange and retrieve their 
datasets as Linked Data.

Chairs: Alejandra Garcia-Rojas M. (Ontos AG), Robert Isele or Rene 
Pietzsch, Jens Lehmann (AKSW, University of Leipzig)
Date: 15th of September 2015, 09.00 to 13.00 CEST


*The SEMANTIC EXPERIENCE Coffee & Cocktail LOUNGE*

Sponsored Event: Enjoy semantic technology inspiration in a relaxed 
atmosphere. Refresh yourself with Viennese coffee or a cocktail and get 
in touch with semantic industry experts.

Date: 15th of September 2015, 15.45 to 18.00 CEST
Room: LC Club Room

*Linked Data in Industry 4.0*

The overall goal of the workshop is to identify challenges and 
limitations from the manufacturing engineering industry in the scope of 
the mentioned design principles, and bring them together with experts 
and solution approaches from the linked data community in the scope of 
Industry 4.0.

Chairs: Thomas Moser (FH St. Pölten), Stefan Hupe (IoT Austria)
Date: 15th of September 2015, 14.00 to 17.00 CEST

*European Data Economy Workshop - Focus Data Value Chain & Big and Open 
Data*

This workshop is to overview the state of the art in Europe regarding 
Big and Open Data initiatives and its impact in the Europan economy and 
benefits for theEuropean society. Representatives from the Big Data 
Value Association, the annual European Data Forum and data related 
projects will participate during the first session of the workshop. 
Furthermore it gives information about the Austrian Big Data Study 
carried out in 2014 by AIT and IDC

Chairs: Nelia Lasierra (STI Innsbruck), Martin Kaltenböck (Semantic Web 
Company)
Date: 15th of September 2015, 09.00 to 13.00 CEST

*1st Workshop on Data Science: Methods, Technology and Applications 
(DSci15)*

This workshop is meant as an opportunity to bring together researchers 
and practitioners interested in data science to present their ideas and 
discuss the most important scientific, technical and socio-economical 
challenges of this emerging field.

Chairs: Bernhard Haslhofer (AIT - Austrian Institute of Technology), 
Elena Simperl (Univ. Southampton), Rainer Stütz (AIT - Austrian 
Institute of Technology), Ingo Feinerer (FH Wiener Neustadt)
Date: 15th of September 2015, 09.00 to 17.00 CEST

*Workshop on Linked Data Strategies - Commercialisation of Interlinked Data*

In this workshop, we will give several demos and concrete examples of 
how Linked Data can be used by enterprises in various industries. The 
workshop aims to give users and providers of Linked Data valuable 
methods and best practices at hand, which help them to make profound 
decisions in their Linked Data projects.

Chairs: Christian Dirschl (Wolters Kluwer), Andreas Blumauer (Semantic 
Web Company), Tassilo Pellegrini (FH St. Pölten)
Date: 15th of September 2015, 14.00 to 15.30 CEST

*Hackathon on "The power of Linked Data in Agriculture and Food Safety"*

“Data+Need=Hack”, this is the idea of a hackathon that brings together 
like-minded people to develop, in a short time frame, novel solutions to 
problems around the theme “Agriculture and Food Safety”.

Chairs: Christian Blaschke (Semantic Web Company, Vienna), Stasinos 
Konstantopoulos (Institute of Informatics & Telecommunications of the 
NCSR Demokritos, Athens)
Date: 18th of September 2015, 10.00 to 16.00 CEST



*— Registration ---*

To register, please go to:
http://www.semantics.cc/registration

We are looking forward to meet you at SEMANTiCS 2015!

[GMOD-devel] New Apollo Release 2.0.0(JB1.11.6)

[Monica Munoz-T. <mcm...@lb...>]

 *We are please to announce the release of Apollo 2*

Dear colleagues,

This release is a major rewrite of the Apollo 1.0.x backend, focused on
making the framework more scalable and interoperable while maintaining the
core functionality that annotators have come to expect. Apollo 2.0.0 also
brings new functionality that continues to improve the user experience.

The following are some of the *new features *in Apollo 2:
- As mentioned above, a major *rewrite of the backend* using Grails
<https://grails.org/>, which is a scalable, high-concurrency framework
based on Spring <http://spring.io/> and Hibernate <http://hibernate.org/>.
- Ability to support *multiple organisms* in a single application instance.
- The new *Annotator Panel*, a side-bar for viewing annotations, reference
sequences, options for data export, and administrative functions.
- *Permissions* can now be given at the organism-level.
- *Reporting*, including customizable reports for annotations and .
- *Single database* integration (e.g. MySQL, PostgreSQL, Oracle, H2).
- Implementation of *Websockets*.
- *Simplified* configuration and installation.

We look forward to receiving your questions and suggestions.

Sincerely,
The Apollo Development Team <http://genomearchitect.org/about-us>



*If you currently have Apollo instances running, please be sure to read
carefully through the updated documentation. *

** The latest release *can be downloaded from GitHub at:
https://github.com/GMOD/Apollo/releases/

** Detailed, searchable documentation* on pre-requisites, configuration,
and installation guides for Apollo 2 can be found at:
http://webapollo.readthedocs.org

** A detailed account of all changes*, is available in the Apollo
ChangeLog:
https://github.com/GMOD/Apollo/blob/master/ChangeLog.md

** Quick-Start Guide for Apollo 2: *If you already have Apollo instances
running, you can use your current JBrowse data directories. The quick-start
guide is available at:
http://webapollo.readthedocs.org/en/latest/Apollo2Build.html

** Migrate your annotations: *A rewrite of the backend means you will need
to migrate existing annotations from Web Apollo 1.0.x. Please find detailed
information about migrating annotations at
http://webapollo.readthedocs.org/en/latest/Migration.html.

* *Troubleshooting guide, GitHub issue tracker, Mailing List: *
- should you come across any problems, browse the Troubleshooting guide (
http://webapollo.readthedocs.org/en/latest/Troubleshooting.html) for
answers,
- open a GitHub issue at https://github.com/GMOD/Apollo/issues/
- or post your questions on the mailing list at ap...@li...
Please join the conversation by providing your contact information on this
form
<https://docs.google.com/forms/d/1PkOm2SKiaAiAhCaMHEc0YFwFZ9nrZaZkbt29R8PW-W8/viewform>
.

** The Apollo User Guide* is available at
http://genomearchitect.org/web_apollo_user_guide

* *Public Demo:* If you are new to Apollo we encourage you to learn more
about our software and its functionality by taking a tour of our Apollo
Demo at http://genomearchitect.org/WebApolloDemo.

** These and more details are available from the README* file on the Apollo
repository:
https://github.com/GMOD/Apollo/blob/master/README.md



[image: Inline image 3]


--
Mentorship Matters!
--
Monica Munoz-Torres, PhD.
Berkeley Bioinformatics Open-source Projects (BBOP)
Environmental Genomics and Functional Biology Division
Lawrence Berkeley National Laboratory

Mailing Address:
Lawrence Berkeley National Laboratory
1 Cyclotron Road Mailstop 977
Berkeley, CA 9472

[GMOD-devel] [CFP] Semantic Web Journal - Special Issue on Quality Management of Semantic Web Assets (Data, Services and Systems)

[Jürgen U. <pr...@in...>]

*CFP: Semantic Web Journal - Special Issue on Quality Management of 
Semantic Web Assets (Data, Services and Systems):* 
http://www.semantic-web-journal.net/blog/call-papers-special-issue-quality-management-semantic-web-assets-data-services-and-systems 
<http://www.semantic-web-journal.net/blog/call-papers-special-issue-quality-management-semantic-web-assets-data-services-and-systems>


    Submission guidelines

*Deadline:October 31, 2015*

Submissions shall be made through the Semantic Web journal website at 
http://www.semantic-web-journal.net 
<http://www.semantic-web-journal.net/>. Prospective authors must take 
notice of the submission guidelines posted at 
http://www.semantic-web-journal.net/authors 
<http://www.semantic-web-journal.net/authors>. Note that you need to 
request an account on the website for submitting a paper. Please 
indicate in the cover letter that it is for the Special Issue on Quality 
Management of Semantic Web Assets (Data, Services and Systems).

Submissions are possible in the following categories: full research 
papers, application reports, reports on tools and systems, and case 
studies. While there is no upper limit, paper length must be justified 
by content.


    Guest editors

  * Amrapali Zaveri, University of Leipzig, AKSW Group, Germany
  * Dimitris Kontokostas, University of Leipzig, AKSW Group, Germany
  * Sebastian Hellmann, University of Leipzig, AKSW Group, Germany
  * Jürgen Umbrich, Vienna University of Economics and Business, Austria

*Overview and Topics*

The standardization and adoption of Semantic Web technologies has 
resulted in a variety of assets, including an unprecedented volume of 
data being semantically enriched and systems and services, which consume 
or publish this data. Although gathering, processing and publishing data 
is a step towards further adoption of Semantic Web, quality does not yet 
play a central role in these assets (e.g., data lifecycle, 
system/service development).

Quality management essentially refers to activities and tasks involved 
to guarantee a certain level of consistency and to meet the quality 
requirements for the assets. In general, quality management consists of 
the following four phases and components: (i) quality planning, (ii) 
quality control, (iii) quality assurance and (iv) quality improvement.

The quality planning phase in the Semantic Web typically involves the 
design of procedures, strategies and policies to support the management 
of the assets. The quality control and assurance components have their 
primary aim in preventing errors and to meet quality requirements 
pertaining to the Semantic Web standards. A core part for both 
components are quality assessment methods which provide the necessary 
input for the controlling and assurance tasks.

Quality assessment of Semantic Web Assets (data, services and systems), 
in particular, presents new challenges that were not handled before in 
other research areas. Thus, adopting existing approaches for data 
quality assessment is not a straightforward solution. These challenges 
are related to the openness of the Semantic Web, the diversity of the 
information and the unbounded, dynamic set of autonomous data sources, 
publishers and consumers (legal and software agents). Additionally, 
detecting the quality of available data sources and making the 
information explicit is yet another challenge. Moreover, noise in one 
data set, or missing links between different data sets, propagates 
throughout the Web of Data, and imposes great challenges on the data 
value chain.

In case of systems and services, different implementations follow the 
specifications for RDF and SPARQL to varying extents, or even propose 
and offer new, non-standardized extensions. This causes strong 
incompatibilities between systems, e.g., between the used SPARQL 
features in the query engines and support features in RDF stores. The 
potential heterogeneity and incompatibility poses several challenges for 
the quality assessments in and for such systems and services.

Eventually, quality improvement methods are used to further enhance the 
value of the Semantic Web Assets. One important step to improve the 
quality of data is identifying the root cause of the problem and then 
designing corresponding data improvement solutions. These solutions 
select the most effective and efficient strategies and related set of 
techniques and tools to improve quality. Quality improvement metrics for 
products and services entails understanding and improving operational 
processes and establishing valid and reliable service performance measures.

This Special Issue is addressed to those members of the community 
interested in providing novel methodologies or frameworks in managing, 
assessing, monitoring, maintaining and improving the quality of the 
Semantic Web data, services and systems and also introduce tools and 
user interfaces which can effectively assist in this management.


    Topics of Interest

We welcome original high quality submissions on (but are not restricted 
to) the following topics:

  * Methodologies and frameworks to plan, control, assure or improve the
    quality of Semantic Web Assets
  * Quality exploration and analysis interfaces
  * Quality monitoring
  * Developing, deploying and managing quality service ecosystems
  * Assessing the quality evolution of Semantic Web Assets
  * Large-scale quality assessment of structured datasets
  * Crowdsourcing data quality assessment
  * Quality assessment leveraging background knowledge
  * Use-case driven quality management
  * Evaluation of trustworthiness of data
  * Web Data and LOD quality benchmarks
  * Data Quality improvement methods and frameworks, e.g., linkage,
    alignment, cleaning, enrichment, correctness
  * Service/system quality improvement methods and frameworks
  * Managing sustainability issues in services
  * Guarantee of service (availability, performance)
  * Systems for transparent management of open data

Re: [GMOD-devel] [Gmod-tripal-devel] [Gmod-schema] Anyone using Mimosa?

[Chris C. <gen...@gm...>]

Hi Scott,

I've seen a few groups that use Sequence server, and it seemed pretty
straightforward to stand up and customize.

Another alternative is the BLAST application we are using, developed in
Django. This runs in parallel to our Tripal and annotation resources.
https://i5k.nal.usda.gov/webapp/blast/
The source is available up on github
<https://github.com/hotdogee/django-blast> if you are interested in
checking it out.

Chris


On Wed, Jul 15, 2015 at 11:32 AM, Scott Cain <sc...@sc...> wrote:

> Hi Peter,
>
> Actually, I want it for use in WormBase, so it's not exactly a GMOD
> website (that is, it doesn't use Tripal--I just sent it to the Tripal
> website to have a reasonably large audience, and since Tripal people are
> interested in web development, it seemed reasonable).  I'll take a look at
> SequenceServer.
>
> Thanks,
> Scott
>
>
> On Wed, Jul 15, 2015 at 11:21 AM, Peter Cock <p.j...@go...>
> wrote:
>
>> Hi Scott,
>>
>> >From your original email I was going to suggest something like
>> http://www.sequenceserver.com/ but you've clarified you want
>> a BLAST interface within a GMOD website?
>>
>> Peter
>>
>> P.S. I have a conflict of interest in promoting BLAST+ in Galaxy
>> http://dx.doi.org/10.1101/014043
>>
>>
>> On Wed, Jul 15, 2015 at 4:02 PM, Scott Cain <sc...@sc...> wrote:
>> > Hi Chris,
>> >
>> > Galaxy is an outstanding tool, but the point of Mimosa is to have a tool
>> > that easily integrates into a MOD website to allow users to blast/blat
>> their
>> > sequences easily and have those results tie back into the website.  I
>> don't
>> > think Galaxy fits that bill.
>> >
>> > Scott
>> >
>> >
>> > On Wed, Jul 15, 2015 at 10:18 AM, Fields, Christopher J
>> > <cjf...@il...> wrote:
>> >>
>> >> Sounds cool, but there are a ton of issues filed for it, mainly from a
>> few
>> >> users/devs (Duke Leto is one of them and he’s not really involved on
>> >> GMOD-related work anymore).
>> >>
>> >> My only concern is how much of this effort replicates what Galaxy does.
>> >> Or is the emphasis on the ease of installation and setup?
>> >>
>> >> chris
>> >>
>> >> On Jul 15, 2015, at 8:53 AM, Scott Cain <sc...@sc...> wrote:
>> >>
>> >> Hi All,
>> >>
>> >> I'm wondering if anybody is using Mimosa, a project started a few years
>> >> ago to provide a flexible web interface for sequence similarity
>> searching
>> >> tools like BLAST (https://github.com/GMOD/mimosa).  I'm looking for
>> >> something very much along these lines but I realize Mimosa has been
>> >> quiescent since the developers working on it have left.  I wouldn't
>> mind
>> >> seeing it resurrected but I also don't have a huge amount of time to
>> put
>> >> into it either.
>> >>
>> >> Thanks,
>> >> Scott
>> >>
>> >>
>>
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain
> dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
>
>
> ------------------------------------------------------------------------------
> Don't Limit Your Business. Reach for the Cloud.
> GigeNET's Cloud Solutions provide you with the tools and support that
> you need to offload your IT needs and focus on growing your business.
> Configured For All Businesses. Start Your Cloud Today.
> https://www.gigenetcloud.com/
> _______________________________________________
> Gmod-tripal-devel mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel
>
>

Re: [GMOD-devel] [Gmod-schema] Anyone using Mimosa?

[Scott C. <sc...@sc...>]

Hi Peter,

Actually, I want it for use in WormBase, so it's not exactly a GMOD website
(that is, it doesn't use Tripal--I just sent it to the Tripal website to
have a reasonably large audience, and since Tripal people are interested in
web development, it seemed reasonable).  I'll take a look at SequenceServer.

Thanks,
Scott


On Wed, Jul 15, 2015 at 11:21 AM, Peter Cock <p.j...@go...>
wrote:

> Hi Scott,
>
> From your original email I was going to suggest something like
> http://www.sequenceserver.com/ but you've clarified you want
> a BLAST interface within a GMOD website?
>
> Peter
>
> P.S. I have a conflict of interest in promoting BLAST+ in Galaxy
> http://dx.doi.org/10.1101/014043
>
> On Wed, Jul 15, 2015 at 4:02 PM, Scott Cain <sc...@sc...> wrote:
> > Hi Chris,
> >
> > Galaxy is an outstanding tool, but the point of Mimosa is to have a tool
> > that easily integrates into a MOD website to allow users to blast/blat
> their
> > sequences easily and have those results tie back into the website.  I
> don't
> > think Galaxy fits that bill.
> >
> > Scott
> >
> >
> > On Wed, Jul 15, 2015 at 10:18 AM, Fields, Christopher J
> > <cjf...@il...> wrote:
> >>
> >> Sounds cool, but there are a ton of issues filed for it, mainly from a
> few
> >> users/devs (Duke Leto is one of them and he’s not really involved on
> >> GMOD-related work anymore).
> >>
> >> My only concern is how much of this effort replicates what Galaxy does.
> >> Or is the emphasis on the ease of installation and setup?
> >>
> >> chris
> >>
> >> On Jul 15, 2015, at 8:53 AM, Scott Cain <sc...@sc...> wrote:
> >>
> >> Hi All,
> >>
> >> I'm wondering if anybody is using Mimosa, a project started a few years
> >> ago to provide a flexible web interface for sequence similarity
> searching
> >> tools like BLAST (https://github.com/GMOD/mimosa).  I'm looking for
> >> something very much along these lines but I realize Mimosa has been
> >> quiescent since the developers working on it have left.  I wouldn't mind
> >> seeing it resurrected but I also don't have a huge amount of time to put
> >> into it either.
> >>
> >> Thanks,
> >> Scott
> >>
> >>
>



-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot
net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

Re: [GMOD-devel] [Gmod-schema] Anyone using Mimosa?

[Peter C. <p.j...@go...>]

Hi Scott,

>From your original email I was going to suggest something like
http://www.sequenceserver.com/ but you've clarified you want
a BLAST interface within a GMOD website?

Peter

P.S. I have a conflict of interest in promoting BLAST+ in Galaxy
http://dx.doi.org/10.1101/014043

On Wed, Jul 15, 2015 at 4:02 PM, Scott Cain <sc...@sc...> wrote:
> Hi Chris,
>
> Galaxy is an outstanding tool, but the point of Mimosa is to have a tool
> that easily integrates into a MOD website to allow users to blast/blat their
> sequences easily and have those results tie back into the website.  I don't
> think Galaxy fits that bill.
>
> Scott
>
>
> On Wed, Jul 15, 2015 at 10:18 AM, Fields, Christopher J
> <cjf...@il...> wrote:
>>
>> Sounds cool, but there are a ton of issues filed for it, mainly from a few
>> users/devs (Duke Leto is one of them and he’s not really involved on
>> GMOD-related work anymore).
>>
>> My only concern is how much of this effort replicates what Galaxy does.
>> Or is the emphasis on the ease of installation and setup?
>>
>> chris
>>
>> On Jul 15, 2015, at 8:53 AM, Scott Cain <sc...@sc...> wrote:
>>
>> Hi All,
>>
>> I'm wondering if anybody is using Mimosa, a project started a few years
>> ago to provide a flexible web interface for sequence similarity searching
>> tools like BLAST (https://github.com/GMOD/mimosa).  I'm looking for
>> something very much along these lines but I realize Mimosa has been
>> quiescent since the developers working on it have left.  I wouldn't mind
>> seeing it resurrected but I also don't have a huge amount of time to put
>> into it either.
>>
>> Thanks,
>> Scott
>>
>>

Re: [GMOD-devel] [Gmod-schema] Anyone using Mimosa?

[Fields, C. J <cjf...@il...>]

Ok, so a focus on ease of use and installation makes sense (as well as possibly packaging it up with other GMOD tools ala GMOD in the Cloud, maybe).  We just had someone ask for a very similar thing locally.

Then, as you already mentioned, it really depends who can take it on.

chris

On Jul 15, 2015, at 10:02 AM, Scott Cain <sc...@sc...<mailto:sc...@sc...>> wrote:

Hi Chris,

Galaxy is an outstanding tool, but the point of Mimosa is to have a tool that easily integrates into a MOD website to allow users to blast/blat their sequences easily and have those results tie back into the website.  I don't think Galaxy fits that bill.

Scott


On Wed, Jul 15, 2015 at 10:18 AM, Fields, Christopher J <cjf...@il...<mailto:cjf...@il...>> wrote:
Sounds cool, but there are a ton of issues filed for it, mainly from a few users/devs (Duke Leto is one of them and he’s not really involved on GMOD-related work anymore).

My only concern is how much of this effort replicates what Galaxy does.  Or is the emphasis on the ease of installation and setup?

chris

On Jul 15, 2015, at 8:53 AM, Scott Cain <sc...@sc...<mailto:sc...@sc...>> wrote:

Hi All,

I'm wondering if anybody is using Mimosa, a project started a few years ago to provide a flexible web interface for sequence similarity searching tools like BLAST (https://github.com/GMOD/mimosa<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_GMOD_mimosa&d=AwMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=fbHa8Njtvh9VmSnzJxiEUTW9NWDwMMwQAzhgZDO41GQ&m=52gmQu5j-AgwO1L_jB8DWj3o-I8l5GtqCnFL7yV-wwc&s=YpnGguDpiA9JiNnRIcKBuYIzrqphIdsdKWdH57NS_RQ&e=>).  I'm looking for something very much along these lines but I realize Mimosa has been quiescent since the developers working on it have left.  I wouldn't mind seeing it resurrected but I also don't have a huge amount of time to put into it either.

Thanks,
Scott


--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/<https://urldefense.proofpoint.com/v2/url?u=http-3A__gmod.org_&d=AwMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=fbHa8Njtvh9VmSnzJxiEUTW9NWDwMMwQAzhgZDO41GQ&m=52gmQu5j-AgwO1L_jB8DWj3o-I8l5GtqCnFL7yV-wwc&s=E6sWfacChIKH3BmpUl4iJeoTztibWaTZo5-1hMoLzRI&e=>)                     216-392-3087<tel:216-392-3087>
Ontario Institute for Cancer Research
------------------------------------------------------------------------------
Don't Limit Your Business. Reach for the Cloud.
GigeNET's Cloud Solutions provide you with the tools and support that
you need to offload your IT needs and focus on growing your business.
Configured For All Businesses. Start Your Cloud Today.
https://www.gigenetcloud.com/_______________________________________________<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.gigenetcloud.com_-5F-5F-5F-5F-5F-5F-5F-5F-5F-5F-5F-5F-5F-5F-5F-5F-5F-5F-5F-5F-5F-5F-5F-5F-5F-5F-5F-5F-5F-5F-5F-5F-5F-5F-5F-5F-5F-5F-5F-5F-5F-5F-5F-5F-5F-5F-5F&d=AwMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=fbHa8Njtvh9VmSnzJxiEUTW9NWDwMMwQAzhgZDO41GQ&m=_Z1237tGrsSqu4-HR6uVFPuI0EPWaoq0HyJOUNbBXbs&s=fVWW0nBdIkOIloFLNc8doPGRnf59L8aJuPf4UCUqY0U&e=>
Gmod-schema mailing list
Gmo...@li...<mailto:Gmo...@li...>
https://lists.sourceforge.net/lists/listinfo/gmod-schema<https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.sourceforge.net_lists_listinfo_gmod-2Dschema&d=AwMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=fbHa8Njtvh9VmSnzJxiEUTW9NWDwMMwQAzhgZDO41GQ&m=_Z1237tGrsSqu4-HR6uVFPuI0EPWaoq0HyJOUNbBXbs&s=H2Ui0rGrjoknEaPNzmb3IV4i2sdPkuyABeKjXRDk7mE&e=>




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/<https://urldefense.proofpoint.com/v2/url?u=http-3A__gmod.org_&d=AwMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=fbHa8Njtvh9VmSnzJxiEUTW9NWDwMMwQAzhgZDO41GQ&m=_Z1237tGrsSqu4-HR6uVFPuI0EPWaoq0HyJOUNbBXbs&s=Wh1FXewFwWBWx6xAQIyzGJt1qHO14IqqAa5iLN6bkMU&e=>)                     216-392-3087
Ontario Institute for Cancer Research

Re: [GMOD-devel] [Gmod-schema] Anyone using Mimosa?

[Scott C. <sc...@sc...>]

Hi Chris,

Galaxy is an outstanding tool, but the point of Mimosa is to have a tool
that easily integrates into a MOD website to allow users to blast/blat
their sequences easily and have those results tie back into the website.  I
don't think Galaxy fits that bill.

Scott


On Wed, Jul 15, 2015 at 10:18 AM, Fields, Christopher J <
cjf...@il...> wrote:

>  Sounds cool, but there are a ton of issues filed for it, mainly from a
> few users/devs (Duke Leto is one of them and he’s not really involved on
> GMOD-related work anymore).
>
>  My only concern is how much of this effort replicates what Galaxy does.
> Or is the emphasis on the ease of installation and setup?
>
>  chris
>
>  On Jul 15, 2015, at 8:53 AM, Scott Cain <sc...@sc...> wrote:
>
>  Hi All,
>
>  I'm wondering if anybody is using Mimosa, a project started a few years
> ago to provide a flexible web interface for sequence similarity searching
> tools like BLAST (https://github.com/GMOD/mimosa
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_GMOD_mimosa&d=AwMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=fbHa8Njtvh9VmSnzJxiEUTW9NWDwMMwQAzhgZDO41GQ&m=52gmQu5j-AgwO1L_jB8DWj3o-I8l5GtqCnFL7yV-wwc&s=YpnGguDpiA9JiNnRIcKBuYIzrqphIdsdKWdH57NS_RQ&e=>).
> I'm looking for something very much along these lines but I realize Mimosa
> has been quiescent since the developers working on it have left.  I
> wouldn't mind seeing it resurrected but I also don't have a huge amount of
> time to put into it either.
>
>  Thanks,
> Scott
>
>
>  --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain
> dot net
> GMOD Coordinator (http://gmod.org/
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__gmod.org_&d=AwMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=fbHa8Njtvh9VmSnzJxiEUTW9NWDwMMwQAzhgZDO41GQ&m=52gmQu5j-AgwO1L_jB8DWj3o-I8l5GtqCnFL7yV-wwc&s=E6sWfacChIKH3BmpUl4iJeoTztibWaTZo5-1hMoLzRI&e=>)
>                    216-392-3087
> Ontario Institute for Cancer Research
>
> ------------------------------------------------------------------------------
> Don't Limit Your Business. Reach for the Cloud.
> GigeNET's Cloud Solutions provide you with the tools and support that
> you need to offload your IT needs and focus on growing your business.
> Configured For All Businesses. Start Your Cloud Today.
>
> https://www.gigenetcloud.com/_______________________________________________
> Gmod-schema mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>
>
>


-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot
net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

Re: [GMOD-devel] [Gmod-schema] Anyone using Mimosa?

[Fields, C. J <cjf...@il...>]

Sounds cool, but there are a ton of issues filed for it, mainly from a few users/devs (Duke Leto is one of them and he’s not really involved on GMOD-related work anymore).

My only concern is how much of this effort replicates what Galaxy does.  Or is the emphasis on the ease of installation and setup?

chris

On Jul 15, 2015, at 8:53 AM, Scott Cain <sc...@sc...<mailto:sc...@sc...>> wrote:

Hi All,

I'm wondering if anybody is using Mimosa, a project started a few years ago to provide a flexible web interface for sequence similarity searching tools like BLAST (https://github.com/GMOD/mimosa<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_GMOD_mimosa&d=AwMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=fbHa8Njtvh9VmSnzJxiEUTW9NWDwMMwQAzhgZDO41GQ&m=52gmQu5j-AgwO1L_jB8DWj3o-I8l5GtqCnFL7yV-wwc&s=YpnGguDpiA9JiNnRIcKBuYIzrqphIdsdKWdH57NS_RQ&e=>).  I'm looking for something very much along these lines but I realize Mimosa has been quiescent since the developers working on it have left.  I wouldn't mind seeing it resurrected but I also don't have a huge amount of time to put into it either.

Thanks,
Scott


--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/<https://urldefense.proofpoint.com/v2/url?u=http-3A__gmod.org_&d=AwMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=fbHa8Njtvh9VmSnzJxiEUTW9NWDwMMwQAzhgZDO41GQ&m=52gmQu5j-AgwO1L_jB8DWj3o-I8l5GtqCnFL7yV-wwc&s=E6sWfacChIKH3BmpUl4iJeoTztibWaTZo5-1hMoLzRI&e=>)                     216-392-3087
Ontario Institute for Cancer Research
------------------------------------------------------------------------------
Don't Limit Your Business. Reach for the Cloud.
GigeNET's Cloud Solutions provide you with the tools and support that
you need to offload your IT needs and focus on growing your business.
Configured For All Businesses. Start Your Cloud Today.
https://www.gigenetcloud.com/_______________________________________________
Gmod-schema mailing list
Gmo...@li...
https://lists.sourceforge.net/lists/listinfo/gmod-schema

[GMOD-devel] Anyone using Mimosa?

[Scott C. <sc...@sc...>]

Hi All,

I'm wondering if anybody is using Mimosa, a project started a few years ago
to provide a flexible web interface for sequence similarity searching tools
like BLAST (https://github.com/GMOD/mimosa).  I'm looking for something
very much along these lines but I realize Mimosa has been quiescent since
the developers working on it have left.  I wouldn't mind seeing it
resurrected but I also don't have a huge amount of time to put into it
either.

Thanks,
Scott


-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot
net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

[GMOD-devel] [CFP] Semantic Web Journal Special Issue on Quality Management of Semantic Web Assets (Data, Services and Systems)

[Amrapali Z. <pr...@in...>]

The standardization and adoption of Semantic Web technologies has 
resulted in  a variety of assets, including an unprecedented volume of 
data being semantically enriched and systems and services, which consume 
or publish this data. Although gathering, processing and publishing data 
is a step towards further adoption of Semantic Web, quality does not yet 
play a central role in these assets (e.g., data lifecycle, 
system/service development).

Quality management essentially refers to activities and tasks involved 
to guarantee a certain level of consistency and to meet the quality 
requirements for the assets. In general, quality management consists of 
the following four phases and components: (i) quality planning, (ii) 
quality control, (iii) quality assurance and (iv) quality improvement.

The quality planning phase in the Semantic Web typically involves the 
design of procedures, strategies and policies to support the management 
of the assets. The quality control and assurance components have their 
primary aim in preventing errors and to meet quality requirements 
pertaining to the Semantic Web standards. A core part for both 
components are quality assessment methods which provide the necessary 
input for the controlling and assurance tasks.

Quality assessment of Semantic Web Assets (data, services and systems), 
in particular, presents new challenges that were not handled before in 
other research areas. Thus, adopting existing approaches for data 
quality assessment is not a straightforward solution. These challenges 
are related to the openness of the Semantic Web, the diversity of the 
information and the unbounded, dynamic set of autonomous data sources, 
publishers and consumers (legal and software agents). Additionally, 
detecting the quality of available data sources and making the 
information explicit is yet another challenge. Moreover, noise in one 
data set, or missing links between different data sets, propagates 
throughout the Web of Data, and imposes great challenges on the data 
value chain.

In case of systems and services, different implementations follow the 
specifications for RDF and SPARQL to varying extents, or even propose 
and offer new, non-standardized extensions. This causes strong 
incompatibilities between systems, e.g., between the used SPARQL 
features in the query engines and support features in RDF stores. The 
potential heterogeneity and incompatibility poses several challenges for 
the quality assessments in and for such systems and services.

Eventually, quality improvement methods are used to further enhance the 
value of the Semantic Web Assets. One important step to improve the 
quality of data is identifying the root cause of the problem and then 
designing corresponding data improvement solutions. These solutions 
select the most effective and efficient strategies and related set of 
techniques and tools to improve quality. Quality improvement metrics for 
products and services entails understanding and improving operational 
processes and establishing valid and reliable service performance measures.

This Special Issue is addressed to those members of the community 
interested in providing novel methodologies or frameworks in managing, 
assessing, monitoring, maintaining and improving the quality of the 
Semantic Web data, services and systems and also introduce tools and 
user interfaces which can effectively assist in this management.

Topics of Interest
We welcome original high quality submissions on (but are not restricted 
to) the following topics:
- Methodologies and frameworks to plan, control, assure or improve the 
quality of - - Semantic Web Assets
- Quality exploration and analysis interfaces
- Quality monitoring
- Developing, deploying and managing quality service ecosystems
- Assessing the quality evolution of Semantic Web Assets
- Large-scale quality assessment of structured datasets
- Crowdsourcing data quality assessment
- Quality assessment leveraging background knowledge
- Use-case driven quality management
- Evaluation of trustworthiness of data
- Web Data and LOD quality benchmarks
- Data Quality improvement methods and frameworks e.g., linkage, 
alignment, cleaning, enrichment, correctness
- Service/system quality improvement methods and frameworks
-- Managing sustainability issues in services
-- Guarantee of service (availability, performance)
- Systems for transparent management of open data

Submissions
October 31, 2015 - Paper submission deadline

Submissions shall be made through the Semantic Web journal website at   
http://www.semantic-web-journal.net. Prospective authors must take 
notice of the submission guidelines posted at 
http://www.semantic-web-journal.net/authors. Note that you need to 
request an account on the website for submitting a paper. Please 
indicate in the cover letter that it is for the Special Issue on 
“Quality Management of Semantic Web Assets (Data, Services and Systems)”.

Submissions are possible in the following categories: full research 
papers, application reports, reports on tools and systems and case studies.

Guest editors
Amrapali Zaveri, University of Leipzig, AKSW Group, Germany
Dimitris Kontokostas, University of Leipzig, AKSW Group, Germany
Sebastian Hellmann, University of Leipzig, AKSW Group, Germany
Jürgen Umbrich, Vienna University of Economics and Business, Austria

The editors can be reached using the following email: 
swj...@go....

[GMOD-devel] 4th DBpedia Community Meeting in Poznan 2015 - Call for contribution/participarion

[Dimitris K. <pr...@in...>]

**Registration & talk submissions are still open**

he 4th DBpedia community meeting will be held in Poznan, Poland, 
co-located with the 18th International Conference on Business 
Information Systems (BIS 2015) <http://bis.kie.ue.poznan.pl/bis2015/>.

  * *Twitter:*#DBpediaPoznan
    <https://twitter.com/search?q=#DBpediaPoznan&f=realtime>
  * *Optional DBpedia support ticket*: We additionally offer an optional
    DBpedia Support ticket:https://event.gg/1205-4th-dbpedia-meeting-poznan


    Quick Facts

  * *Web URL:*http://wiki.dbpedia.org/meetings/Poznan2015
  * *When:*June 25th, 2015 (Thursday)
  * *Where:*Poznan University of Economics
    <http://ue.poznan.pl/en/> (Al. Niepodleglosci 10, 61-875 Poznan,
    Google Maps
    <https://www.google.pl/maps/place/Uniwersytet+Ekonomiczny/@52.406158,16.918355,17z/data=%213m1%214b1%214m2%213m1%211s0x47045b36c0620a03:0x32be4cbef2a2ae12>)

  * *Host:*Poznan University of Economics (http://kie.ue.poznan.pl/en)
    and the DBpedia Polish Chapter
  * *Call for Contribution:*Please submit your contribution (talk,
    presentation, poster, ...) inthis form
    <https://docs.google.com/forms/d/1Wg_jZ_1hEUwWKsEytnu9yZ-K6CXG52QyRBzy1nvQPpQ/viewform>
  * *Publications: for details please see below.*
  * *Registration:* Free to participate butneeds registration
    <https://goo.gl/PN073B>.
  * *Optional DBpedia support ticket*: We additionally offer an optional
    DBpedia Support ticket: https://event.gg/1205-4th-dbpedia-meeting-poznan

Acknowledgements

If you would like to become a sponsor for the 4th DBpedia Community 
Meeting, please contact theDBpedia Association <mailto:db...@in...>.

<http://aligned-project.eu/> 	H2020 ALIGNED Project
<http://infai.org/> 	Institute for Applied Informatics
<http://www.openlinksw.com/> 	OpenLink Software for continuous hosting 
of the main DBpedia Endpoint


    Organisation

  * Agata Filipowska, Poznan University of Economics
  * Adrian Paschke, DBpedia Germany, University of Berlin
  * Marta Bartkowiak, Adam Mickiewicz University, Poznan
  * Dimitris Kontokostas <http://aksw.org/DimitrisKontokostas>, DBpedia
    Association and AKSW, Uni Leipzig
  * Sebastian Hellmann
    <http://bis.informatik.uni-leipzig.de/SebastianHellmann,>, DBpedia
    Association and AKSW, Uni Leipzig


    Registration

You can register by adding yourselfhere <https://goo.gl/PN073B> or send 
an email to one of the organizers.Please indicate if you have an 
"eduroam" account for arranging internet access. Registration is free 
but we offer an optional Support Ticket if you would like to support the 
DBpedia Association (https://event.gg/1205-4th-dbpedia-meeting-poznan).
*Note that registration closes on 18/06/15.*


    Call for Contributions

Please submit your proposal through ourWeb form 
<https://docs.google.com/forms/d/1Wg_jZ_1hEUwWKsEytnu9yZ-K6CXG52QyRBzy1nvQPpQ/viewform>.
Contribution proposals include (but not limited to) presentation, 
posters, demos, lightning talks and session suggestions. Please note the 
publication opportunities.


    Important information (Opportunity for publication)

As DBpedia Workshop is a regular conference workshop there is a 
possibility of having the publication included in the 
post-conference LNBIP Proceedings 
http://bis.kie.ue.poznan.pl/bis2015/proceedings/.  A short or regular 
paper corresponding to the presentation at the DBpedia Workshop may be 
submitted after the conference. It will then be subject to the review by 
the DBpedia Programme Committee.  If accepted, the author will have to 
register with a fee of 100 EUR to have the paper included in the volume 
(the rest of cost is covered by our sponsors). Moreover, if someone 
would like to stay for the whole BIS conference (three days), he is to 
pay (in case of publication) 250 EUR (or 320 EUR in case of very late 
registration). If someone would like to stay for the whole conference 
without the publication, he would have to cover the cost of catering 
(please contact Agata). The registration form for the conference may be 
found at:http://bis.kie.ue.poznan.pl/bis2015/registration/(please do not 
use this form in case of attending only the DBpedia Workshop).


    Location / Venue

The meeting will take place in the main building of Poznan University of 
Economics (Google Maps 
<https://www.google.pl/maps/place/Uniwersytet+Ekonomiczny/@52.406158,16.918355,17z/data=%213m1%214b1%214m2%213m1%211s0x47045b36c0620a03:0x32be4cbef2a2ae12>). 
Details on the room numbers will be provided soon.

[GMOD-devel] 4th DBpedia Community Meeting in Poznan 2015 - Call for contribution/participarion

[Agata F. <pr...@in...>]

The 4th DBpedia community meeting will be held in Poznan Polald, 
co-located with the 18th International Conference on Business 
Information Systems (BIS 2015) <http://bis.kie.ue.poznan.pl/bis2015/>.

  *

    Twitter: #DBpediaPoznan
    <https://twitter.com/search?q=#DBpediaPoznan&f=realtime>

  *

    Optional DBpedia support ticket: We additionally offer an optional
    DBpedia Support ticket:https://event.gg/1205-4th-dbpedia-meeting-poznan

  *

    Keynote: The Journey is the Reward – Towards New Paradigms in Web
    Search by Dr. Harald Sack


    Quick Facts

  *

    Web URL: http://wiki.dbpedia.org/meetings/Poznan2015

  *

    When: June 25th, 2015 (Thursday)

  *

    Where: Poznan University of Economics <http://ue.poznan.pl/en/> (Al.
    Niepodleglosci 10, 61-875 Poznan, Google Maps
    <https://www.google.pl/maps/place/Uniwersytet+Ekonomiczny/@52.406158,16.918355,17z/data=%213m1%214b1%214m2%213m1%211s0x47045b36c0620a03:0x32be4cbef2a2ae12>)


  *

    Host: Poznan University of Economics (http://kie.ue.poznan.pl/en)
    and the DBpedia Polish Chapter

  *

    Call for Contribution: Please submit your contribution (talk,
    presentation, poster, ...) in this form
    <https://docs.google.com/forms/d/1Wg_jZ_1hEUwWKsEytnu9yZ-K6CXG52QyRBzy1nvQPpQ/viewform>

  *

    Publications: for details please see below.

  *

    Registration: Free to participate but needs registration
    <https://goo.gl/PN073B>.

  *

    Optional DBpedia support ticket: We additionally offer an optional
    DBpedia Support ticket: https://event.gg/1205-4th-dbpedia-meeting-poznan


    Acknowledgements

If you would like to become a sponsor for the 4rd DBpedia Meeting, 
please contact the DBpedia Association <mailto:db...@in...>

H2020 ALIGNED Project

Institute for Applied Informatics

OpenLink Software for continuous hosting of the main DBpedia Endpoint


    Organisation

  *

    Agata Filipowska, Poznan University of Economics

  *

    Adrian Paschke, DBpedia Germany, University of Berlin

  *

    Marta Bartkowiak, Adam Mickiewicz University, Poznan

  *

    Dimitris Kontokostas <http://aksw.org/DimitrisKontokostas>, DBpedia
    Association and AKSW, Uni Leipzig

  *

    Sebastian Hellmann
    <http://bis.informatik.uni-leipzig.de/SebastianHellmann,>, DBpedia
    Association and AKSW, Uni Leipzig


    Registration

You can register by adding yourself here <https://goo.gl/PN073B> or send 
an email to one of the organizers. Please indicate if you have an 
"eduroam" account for arranging internet access. Registration is free 
but we offer an optional Support Ticket if you would like to support the 
DBpedia Association (https://event.gg/1205-4th-dbpedia-meeting-poznan).
Note that registration closes on 18/06/15.


    Call for Contributions

Please submit your proposal through our Web form 
<https://docs.google.com/forms/d/1Wg_jZ_1hEUwWKsEytnu9yZ-K6CXG52QyRBzy1nvQPpQ/viewform>.
Contribution proposals include (but not limited to) presentation, 
posters, demos, lightning talks and session suggestions. Please note the 
publication opportunities.


    Important information (Opportunity for publication)

As DBpedia Workshop is a regular conference workshop there is a 
possibility of having the publication included in the post-conference 
LNBIP Proceedings http://bis.kie.ue.poznan.pl/bis2015/proceedings/.  A 
short or regular paper corresponding to the presentation at the DBpedia 
Workshop may be submitted after the conference. It will then be subject 
to the review by the DBpedia Programme Committee.  If accepted, the 
author will have to register with a fee of 100 EUR to have the 
paper included in the volume (the rest of cost is covered by our 
sponsors). Moreover, if someone would like to stay for the whole BIS 
conference (three days), he is to pay (in case of publication) 250 EUR 
(or 320 EUR in case of very late registration). If someone would like to 
stay for the whole conference without the publication, he would have to 
cover the cost of catering (please contact Agata). The registration form 
for the conference may be found at: 
http://bis.kie.ue.poznan.pl/bis2015/registration/ (please do not use 
this form in case of attending only the DBpedia Workshop).


    Location / Venue

The meeting will take place in the main building of Poznan University of 
Economics (Google Maps 
<https://www.google.pl/maps/place/Uniwersytet+Ekonomiczny/@52.406158,16.918355,17z/data=%213m1%214b1%214m2%213m1%211s0x47045b36c0620a03:0x32be4cbef2a2ae12>). 
Details on the room numbers will be provided soon.


    Schedule (to be announced)

[GMOD-devel] SEMANTiCS 2015 *Deadline extension*, Vienna, Call for Research & Innovation Papers

[Josiane X. P. <pr...@in...>]

**** DEADLINE EXTENSION****
NOTE: Due to a number of requests, we have extended the paper submission 
deadline until June 12th. The new deadline is final and no more 
extensions will be possible.
****************************


Call for Research & Innovation Papers
SEMANTiCS 2015
Transfer // Engineering // Community

11th International Conference on Semantic Systems
Vienna, Austria September 15-17, 2015
http://www.semantics.cc


Important Dates (Research & Innovation)  (Deadline Extension)
------------------------------------------------------
* Abstract Submission Deadline: June 5, 2015 (Hawaiian Time)
* Paper Submission Deadline: June 12, 2015  (Hawaiian Time)
* Notification of Acceptance: July 20, 2015
* Camera-Ready Paper: July 31, 2015

SEMANTiCS proceedings will be published by ACM ICP.
Submissions via Easychair: 
https://easychair.org/conferences/?conf=semantics2015research

The calls for Industry & Use Case Presentations and "Posters and Demos" 
at SEMANTiCS 2015 can be found here: http://www.semantics.cc/
The annual SEMANTiCS conference is the meeting place for professionals 
who make semantic computing work, who understand its benefits and 
encounter its limitations. Every year, SEMANTiCS attracts information 
managers, IT-architects, software engineers and researchers from 
organisations ranging from NPOs, through public administrations to the 
largest companies in the world. Attendees learn from industry experts 
and top researchers about emerging trends and topics in the fields of 
semantic software, enterprise data, linked data & open data strategies, 
methodologies in knowledge modelling and text & data analytics. The 
SEMANTiCS community is highly diverse; attendees have responsibilities 
in interlinking areas like knowledge management, technical 
documentation, e-commerce, big data analytics, enterprise search, 
document management, business intelligence and enterprise vocabulary 
management.
The success of last years conference in Leipzig with more than 230 
attendees from 22 countries proves that SEMANTiCS 2015 will continue a 
long tradition of bringing together colleagues from around the world. 
There will be presentations on industry implementations, use case 
prototypes, best practices, panels, papers and posters to discuss 
semantic systems in birds-of-a-feather sessions as well as informal 
settings. SEMANTICS addresses problems common among information 
managers, software engineers, IT-architects and various specialist 
departments working to develop, implement and/or evaluate semantic 
software systems.
The SEMANTiCS program is a rich mix of technical talks, panel 
discussions of important topics and presentations by people who make 
things work - just like you. In addition, attendees can network with 
experts in a variety of fields. These relationships provide great value 
to organisations as they encounter subtle technical issues in any stage 
of implementation. The expertise gained by SEMANTiCS attendees has a 
long-term impact on their careers and organisations. These factors make 
SEMANTiCS for our community the major industry related event across Europe.


The following 'horizontals' (research) and verticals' (industries) 
topics are of interest:

* Business Models, Governance & Data Strategies
* Knowledge Discovery & Intelligent Search
* Data Integration & Enterprise Linked Data
* Big Data & Text Analytics
* Data Portals & Knowledge Visualization
* Semantic Information Management
* Document Management & Content Management
* Terminology, Thesaurus & Ontology Management

* Industry & Engineering
* Life Sciences & Health Care
* Public Administration
* Galleries, Libraries, Archives & Museums (GLAM)
* Media, Publishing & Advertising
* Financial & Insurance Industry
* Telecommunications
* Energy, Transport & Environment


Research / Innovation Papers
--------------------------------------
The Research & Innovation track at SEMANTiCS welcomes the submission of 
papers on novel scientific research and/or innovations relevant to the 
topics of the conference. Submissions must be original and must not have 
been submitted for publication elsewhere. Papers should follow the ACM 
ICPS guidelines for formatting 
(http://www.acm.org/sigs/publications/proceedings-templates) and must 
not exceed 8 pages in length for full papers and 4 pages for short 
papers, including references and optional appendices.


All accepted full papers and short papers will be published in the 
digital library of the ACM ICP Series under the ISBN-No.: 
978-1-4503-1972-0. Research & Innovation papers should be submitted 
through EasyChair at: 
https://easychair.org/conferences/?conf=semantics2015research. Papers 
must be submitted in PDF (Adobe's Portable Document Format) format. 
Other formats will not be accepted. For the camera-ready version, the 
source files (Latex, Word Perfect, Word) will also be needed.



Important Dates (Research & Innovation)  (Deadline Extension)
------------------------------------------------------
* Abstract Submission Deadline: June 5, 2015 (Hawaiian Time)
* Paper Submission Deadline: June 12, 2015  (Hawaiian Time)
* Notification of Acceptance: July 20, 2015
* Camera-Ready Paper: July 31, 2015

Research and Innovation Chairs:
Sebastian Hellmann, AKSW, Universität Leipzig
Josiane Xavier Parreira, Siemens AG Österreich


Programme Committee:
* Alessandro Adamou, Knowledge Media Institute, The Open University
* Guadalupe Aguado-De-Cea, Universidad Politécnica de Madrid
* Rajendra Akerkar, Western Norway Research Institute
* Nathalie Aussenac-Gilles, IRIT CNRS
* Ciro Baron, University of Leipzig
* Charalampos Bratsast, Aristotle University of Thessaloniki
* Martin Brümmer, Universität Leipzig
* Volha Bryl, University of Mannheim
* Paul Buitelaar, Insight centre for Data Analytics, National University 
of Ireland Galway
* Irene Celino, CEFRIEL
* Pierre-Antoine Champin, LIRIS
* Christian Chiarcos, Goethe-Universität
* Key-Sun Choi, KAIST
* Ioana-Georgiana Ciuciu, Université Joseph Fourier
* Roland Cornelissen, Metamatter
* Gianluca Correndo, University of Southampton
* Roberta Cuel, University of Trento
* Aba-Sah Dadzie, University of Birmingham
* Enrico Daga, The Open University
* Mauro Dragoni, Fondazione Bruno Kessler
* Claudia D'Amato University of Bari
* Mathieu D'Aquin, Knowledge Media Institute, The Open University
* Tommaso Di Noia, Politecnico di Bari
* Stefan Dietze, L3S Research Center
* Marin Dimitrov, Ontotext
* Samhaa El-Beltagy, Cairo University
* Henrik Eriksson, Linkping University
* Anna Fensel, Semantic Technology Institute (STI) Innsbruck, University 
of Innsbruck
* Miriam Fernandez, Knowledge Media Institute, The Open University
* Agata Filipowska, Department of Information Systems, Poznan University 
of Economics
* Marco Fossati, Fondazione Bruno Kessler
* Fabien Gandon, INRIA
* Roberto Garcia, Universitat de Lleida
* José María García, Semantic Technology Institute (STI) Innsbruck, 
University of Innsbruck
* Wolfgang Gassler, Insitute of Computer Science, University of Innsbruck
* Alain Giboin, INRIA Sophia Antipolis – Méditerranée
* Jose Manuel Gomez-Perez, Intelligent Software Components (iSOCO) S.A.
* Jorge Gracia, Ontology Engineering Group, Universidad Politécnica de 
Madrid
* Michael  Granitzer, University of Passau
* Andreas Harth, AIFB, Karlsruhe Institute of Technology
* Bernhard Haslhofer, Austrian Institute of Technology
* Benjamin Heitmann, Insight centre for Data Analytics, National 
University of Ireland Galway
* Eelco Herder, L3S Research Center
* Andreas Hotho, University of Wuerzburg
* Sirko Hunnius, IfG.CC - The Potsdam eGovernment Competence Center
* Anja Jentzsch, Hasso Plattner Institut
* Efstratios Kontopoulos, CERTH-ITI
* Christoph Lange, University of Bonn
* Ivo Lašek, Faculty of Mathematics and Physics, Charles University
* Nelia Lasierra Beamonte, STI Technology Institute (STI) Innsbruck, 
University of Innsbruck
* Steffen Lohmann, University of Stuttgart
* Vanessa Lopez, IBM Research
* Sandra Lovrenčić, University of Zagreb
* Markus Luczak-Roesch, University of Southampton
* Elisa Marengo, Free University of Bozen-Bolzano
* John P.    Mccrae, Cognitive Interaction Technology, Center of Excellence
* Pablo Mendes, IBM Research Almaden
* Uroš Milošević, Institute Mihailo Pupin
* Elena Montiel-Ponsoda, Ontology Engineering Group, Universidad 
Politécnica de Madrid
* Andrea Moro, Universita di Roma, Sapienza
* Lyndon Nixon, MODUL University Vienna
* Andrea Giovanni Nuzzolese, STLab, ISTC-CNR
* Leo, Obrst, MITRE
* Vito Claudio Ostuni, Politecnico di Bari
* Viviana Patti, Università di Torino
* Heiko Paulheim, University of Mannheim
* Silvio Peroni, University of Bologna and ISTC-CNR
* Mateusz Radzimski, Universidad Carlos III Madrid
* Achim Rettinger, Karlsruhe Institute of Technology
* Giuseppe Rizzo, EURECOM
* Marco Rospocher, Fondazione Bruno Kessler
* Matthew Rowe, Lancaster University
* Eugen Ruppert, FG Language Technology , TU Darmstadt
* Marta Sabou, MODUL University Vienna
* Muhammad Saleem, AKSW
* Felix Sasaki, W3C
* Bernhard Schandl, mySugr GmbH
* Pavel Shvaiko, Informatica Trentina
* Elena Simperl, University of Southampton
* Ronald Stamper, Measur Ltd
* Nadine Steinmetz, Hasso Plattner Institute for Software Systems 
Engineering
* Holger Stenzhorn, Saarland University Hospital
* Mari Carmen Suárez-Figueroa, Universidad Politécnica de Madrid
* Vojtěch Svátek, University of Economics, Prague
* Alexandru Todor, AG Corporate Semantic Web
* Robert Tolksdorf, Networked Information Systems , Freie Universität Berlin
* Ioan Toma, STI Technology Institute (STI) Innsbruck, University of 
Innsbruck
* Jürgen Umbrich, Vienna University of Economy and Business
* Ricardo Usbeck, University of Leipzig
* Pierre-Yves Vandenbussche, Fujitsu Laboratories
* Ruben Verborgh, Ghent University – iMinds
* Maria Esther Vidal, Universidad Simon Bolivar
* Boris Villazón-Terrazas, iSOCO, Intelligent Software Components
* Krzysztof Wecel, Poznan University of Economics
* Katrin Weller, GESIS Leibniz Institute for the Social Sciences
* Rupert Westenthaler, Salzburg Research
* Patrick Westphal Universität Leipzig
* Wolfram Wöß, Institute for Application Oriented Knowledge Processing, 
Johannes Kepler University Linz
* Eva Zangerle, University of Innsbruck


SEMANTiCS 2015 Organisation Committee:
* Axel Polleres, Conference Chair
* Tassilo Pellegrini, Conference Chair
* Christian Dirschl, Industry Chair
* Sebastian Hellmann, Research & Innovation Chair
* Josiane Xavier Parreira, Research & Innovation Chair
* Agata Filipowska, Poster and Demo Chair
* Ruben Verborgh, Poster and Demo Chair
* Anna Fensel, Workshop Chair

[GMOD-devel] 2015 Galaxy Community Conference, 4-8 July, Norwich UK

[Dave C. <cle...@ga...>]

Hello all,

The 2015 Galaxy Community Conference (GCC2015, http://gcc2015.tsl.ac.uk/)
is being held at the Sainsbury Lab in Norwich, United Kingdom, 4-8 July.
GCC2015 is an opportunity to meet with 200+ others working at the forefront
data-intensive biomedical research.  The 2015 edition of GCC includes more
than ever before (http://gcc2015.tsl.ac.uk/programme/):

   - Coding and Data Wrangling Hackathons (and a colocated BioJS Hackathon
   too)
   - Two days of training offering 18 sessions on 15 topics in up to 5
   parallel tracks, covering topics ranging from analysis to administration to
   tool development.
   - A two day meeting featuring accepted talks, poster presentations,
   keynote talks, vendor exhibits, lightning talks, birds-of-a-feather
   meetups, and plenty of networking.

Early registration is now open (but closes Friday, 22 May, *which is this
Friday)*.  Registering early saves you 40%.  Registering now ensures you'll
get a spot in the hackathon and training sessions of your choice.

Finally, there are also many other events going on before and after
GCC2015, and GCC itself ends right before ISMB / ECCB starts in Dublin.
See https://wiki.galaxyproject.org/News/NearGCC2015 for a complete list.

Hope to see you in Norwich!

Dave Clements, on behalf of the GCC2015 Organising Committee

-- 
http://galaxyproject.org/
http://getgalaxy.org/
http://usegalaxy.org/
https://wiki.galaxyproject.org/

[GMOD-devel] SEMANTiCS 2015, Vienna, Call for Research & Innovation Papers

[Sebastian H. <pr...@in...>]

Call for Research & Innovation Papers
SEMANTiCS 2015
Transfer // Engineering // Community

11th International Conference on Semantic Systems
Vienna, Austria September 15-17, 2015
http://www.semantics.cc


Important Dates (Research & Innovation)
------------------------------------------------------
* Abstract Submission Deadline: May 22, 2015
* Paper Submission Deadline: May 29, 2015
* Notification of Acceptance: July 10, 2015
* Camera-Ready Paper: July 24, 2015
SEMANTiCS proceedings will be published by ACM ICP.
Submissions via Easychair: 
https://easychair.org/conferences/?conf=semantics2015research

The calls for “Industry & Use Case Presentations” and “Posters and 
Demos” at SEMANTiCS 2015 can be found here:http://www.semantics.cc/ 
<http://www.semantics.cc/>


The annual SEMANTiCS conference is the meeting place for professionals 
who make semantic computing work, who understand its benefits and 
encounter its limitations. Every year, SEMANTiCS attracts information 
managers, IT-architects, software engineers and researchers from 
organisations ranging from NPOs, through public administrations to the 
largest companies in the world. Attendees learn from industry experts 
and top researchers about emerging trends and topics in the fields of 
semantic software, enterprise data, linked data & open data strategies, 
methodologies in knowledge modelling and text & data analytics. The 
SEMANTiCS community is highly diverse; attendees have responsibilities 
in interlinking areas like knowledge management, technical 
documentation, e-commerce, big data analytics, enterprise search, 
document management, business intelligence and enterprise vocabulary 
management.
The success of last year’s conference in Leipzig with more than 230 
attendees from 22 countries proves that SEMANTiCS 2015 will continue a 
long tradition of bringing together colleagues from around the world. 
There will be presentations on industry implementations, use case 
prototypes, best practices, panels, papers and posters to discuss 
semantic systems in birds-of-a-feather sessions as well as informal 
settings. SEMANTICS addresses problems common among information 
managers, software engineers, IT-architects and various specialist 
departments working to develop, implement and/or evaluate semantic 
software systems.
The SEMANTiCS program is a rich mix of technical talks, panel 
discussions of important topics and presentations by people who make 
things work - just like you. In addition, attendees can network with 
experts in a variety of fields. These relationships provide great value 
to organisations as they encounter subtle technical issues in any stage 
of implementation. The expertise gained by SEMANTiCS attendees has a 
long-term impact on their careers and organisations. These factors make 
SEMANTiCS for our community the major industry related event across Europe.


The following ‘horizontals’ (research) and ‘verticals’ (industries) 
topics are of interest:

* Business Models, Governance & Data Strategies
* Knowledge Discovery & Intelligent Search
* Data Integration & Enterprise Linked Data
* Big Data & Text Analytics
* Data Portals & Knowledge Visualization
* Semantic Information Management
* Document Management & Content Management
* Terminology, Thesaurus & Ontology Management

* Industry & Engineering
* Life Sciences & Health Care
* Public Administration
* Galleries, Libraries, Archives & Museums (GLAM)
* Media, Publishing & Advertising
* Financial & Insurance Industry
* Telecommunications
* Energy, Transport & Environment


Research / Innovation Papers
--------------------------------------
The Research & Innovation track at SEMANTiCS welcomes the submission of 
papers on novel scientific research and/or innovations relevant to the 
topics of the conference. Submissions must be original and must not have 
been submitted for publication elsewhere. Papers should follow the ACM 
ICPS guidelines for formatting 
(http://www.acm.org/sigs/publications/proceedings-templates) and must 
not exceed 8 pages in length for full papers and 4 pages for short 
papers, including references and optional appendices.


All accepted full papers and short papers will be published in the 
digital library of the ACM ICP Series under the ISBN-No.: 
978-1-4503-1972-0. Research & Innovation papers should be submitted 
through EasyChair at: 
https://easychair.org/conferences/?conf=semantics2015research. Papers 
must be submitted in PDF (Adobe's Portable Document Format) format. 
Other formats will not be accepted. For the camera-ready version, the 
source files (Latex, Word Perfect, Word) will also be needed.


Important Dates (Research & Innovation)
* Abstract Submission Deadline: May 22, 2015
* Paper Submission Deadline: May 29, 2015
* Notification of Acceptance: June 26, 2015
* Camera-Ready Paper: July 15 , 2015


Research and Innovation Chairs:
Sebastian Hellmann, AKSW, Universität Leipzig
Josiane Xavier Parreira, Siemens AG Österreich


Programme Committee:
* Alessandro Adamou, Knowledge Media Institute, The Open University
* Guadalupe Aguado-De-Cea, Universidad Politécnica de Madrid
* Rajendra Akerkar, Senior Researcher/Professor, Western Norway Research 
Institute
* Nathalie Aussenac-Gilles, IRIT CNRS
* Ciro Baron, University of Leipzig
* Charalampos Bratsas, Web Science Program, Mathematics Department, 
Aristotle University of Thessaloniki, Greece
* Martin Brümmer, Universität Leipzig
* Volha Bryl, University of Mannheim
* Paul Buitelaar, Insight centre for Data Analytics, National University 
of Ireland Galway
* Irene Celino, CEFRIEL
* Pierre-Antoine Champin, LIRIS
* Christian Chiarcos,
* Key-Sun Choi, KAIST
* Ioana-Georgiana Ciuciu, Université Joseph Fourier, Grenoble
* Roland Cornelissen, Metamatter
* Gianluca Correndo, University of Southampton
* Roberta Cuel, University of Trento
* Claudia D'Amato, University of Bari
* Mathieu D'Aquin, Knowledge Media Institute, the Open University
* Aba-Sah Dadzie, University of Birmingham
* Enrico Daga, The Open University
* Tommaso Di Noia, Politecnico di Bari
* Stefan Dietze, L3S Research Center
* Marin Dimitrov, Ontotext
* Mauro Dragoni, Fondazione Bruno Kessler
* Samhaa El-Beltagy, Cairo University
* Henrik Eriksson, Linkping University
* Anna Fensel, Semantic Technology Institute (STI) Innsbruck, University 
of Innsbruck
* Miriam Fernandez, Knowledge Media Institute
* Agata Filipowska, Department of Information Systems, Poznan University 
of Economics
* Marco Fossati, Fondazione Bruno Kessler
* Fabien Gandon, Inria
* Roberto Garcia, Universitat de Lleida
* José María García, STI Innsbruck, University of Innsbruck
* Wolfgang Gassler, University of Innsbruck, Insitute of Computer 
Science, Research Group Databases and Information Systems
* Alain Giboin, INRIA Sophia Antipolis - Méditerranée
* Jose Manuel Gomez-Perez, Intelligent Software Components (iSOCO) S.A.
* Jorge Gracia, Ontology Engineering Group. Universidad Politécnica de 
Madrid
* Michael Granitzer, University of Passau
* Andreas Harth, AIFB, Karlsruhe Institute of Technology
* Bernhard Haslhofer,
* Benjamin Heitmann, Digital Enterprise Research Institute, National 
University of Ireland, Galway
* Eelco Herder, L3S Research Center
* Andreas Hotho, University of Wuerzburg
* Sirko Hunnius, IfG.CC - The Potsdam eGovernment Competence Center
* Anja Jentzsch, Hasso Plattner Institut
* Efstratios Kontopoulos, CERTH-ITI
* Christoph Lange, University of Bonn
* Ivo Lašek, Faculty of Mathematics and Physics, Charles University
* Nelia Lasierra Beamonte, STI, University of Innsbruck
* Steffen Lohmann, University of Stuttgart
* Vanessa Lopez, IBM Research
* Sandra Lovrenčić, University of Zagreb, Faculty of organization and 
informatics Varazdin, Pavlinska 2, HR-42000 Varazdin, Croatia
* Markus Luczak-Roesch, University of Southampton
* Elisa Marengo, Faculty of Computer Science, Free University of 
Bozen-Bolzano
* John P. Mccrae, Cognitive Interaction Technology, Center of Excellence
* Pablo Mendes, IBM Research Almaden
* Uroš Milošević, Institute Mihailo Pupin
* Elena Montiel-Ponsoda, Ontology Engineering Group. Laboratorio de 
Inteligencia Artificial. Facultad de Informática. Universidad 
Politécnica de Madrid
* Andrea Moro, Sapienza, Universita di Roma
* Lyndon Nixon, MODUL University
* Andrea Giovanni Nuzzolese, STLab, ISTC-CNR
* Leo Obrst, MITRE
* Vito Claudio Ostuni, Politecnico di Bari
* Viviana Patti, Dipartimento di Informatica, Università di Torino
* Heiko Paulheim, University of Mannheim
* Silvio Peroni, University of Bologna and ISTC-CNR
* Axel Polleres, Vienna University of Economics and Business - WU Wien
* Mateusz Radzimski, Universidad Carlos III Madrid
* Achim Rettinger, Karlsruhe Institute of Technology
* Giuseppe Rizzo, EURECOM
* Marco Rospocher, Fondazione Bruno Kessler
* Matthew Rowe, Lancaster University
* Eugen Ruppert, TU Darmstadt - FG Language Technology
* Marta Sabou, MODUL University Vienna
* Muhammad Saleem, AKSW
* Felix Sasaki, W3C
* Bernhard Schandl, mySugr GmbH
* Pavel Shvaiko, Informatica Trentina
* Elena Simperl, University of Southampton
* Ronald Stamper, Measur Ltd
* Nadine Steinmetz, Hasso Plattner Institute for Software Systems 
Engineering
* Holger Stenzhorn, Saarland University Hospital
* Mari Carmen Suárez-Figueroa, Universidad Politécnica de Madrid
* Vojtěch Svátek, University of Economics, Prague
* Alexandru Todor, AG Corporate Semantic Web
* Robert Tolksdorf, Freie Universität Berlin, Networked Information Systems
* Ioan Toma, STI Innsbruck
* Jürgen Umbrich, Vienna University of Economy and Business (WU)
* Ricardo Usbeck, University of Leipzig
* Pierre-Yves Vandenbussche, INSERM UMRS 872, éq.20, 15, rue de l’école 
de médecine, 75006 Paris, France
* Ruben Verborgh, Ghent University - iMinds
* Maria Esther Vidal, Universidad Simon Bolivar, Dept. Computer Science
* Boris Villazón-Terrazas, iSOCO, Intelligent Software Components
* Krzysztof Wecel, Poznan University of Economics
* Katrin Weller, GESIS Leibniz Institute for the Social Sciences
* Rupert Westenthaler, Salzburg Research
* Patrick Westphal, Universität Leipzig
* Wolfram Wöß, Institute for Application Oriented Knowledge Processing, 
Johannes Kepler University Linz, Austria
* Eva Zangerle, Databases and Information Systems, Department of 
Computer Science, University of Innsbruck


SEMANTiCS 2015 Organisation Committee:
* Axel Polleres, Conference Chair
* Tassilo Pellegrini, Conference Chair
* Christian Dirschl, Industry Chair
* Sebastian Hellmann, Research & Innovation Chair
* Josiane Xavier Parreira, Research & Innovation Chair
* Agata Filipowska, Poster and Demo Chair
* Ruben Verborgh, Poster and Demo Chair
* Anna Fensel, Workshop Chair



-- 
Sebastian Hellmann
AKSW/NLP2RDF research group
Insitute for Applied Informatics (InfAI) and DBpedia Association
Events:
* *Sept. 1-5, 2014* Conference Week in Leipzig, including
** *Sept 2nd*, MLODE 2014 <http://mlode2014.nlp2rdf.org/>
** *Sept 3rd*, 2nd DBpedia Community Meeting 
<http://wiki.dbpedia.org/meetings/Leipzig2014>
** *Sept 4th-5th*, SEMANTiCS (formerly i-SEMANTICS) <http://semantics.cc/>
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[GMOD-devel] The latest BioMart community paper

[Arek K. <are...@gm...>]

Dear All,

I would like to draw your attention to the latest BioMart community
publication:

http://nar.oxfordjournals.org/content/early/2015/04/20/nar.gkv350.full?keytype=ref&ijkey=fc0AUhLB3EyWJNt

and in particular to the two examples on how the BioMart open source
philosophy promotes collaboration and code reuse:

http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0096821

http://www.oasis-genomics.org/



Kind regards,
Arek




-- 

"You have enemies? Good. That means you've stood up for something, sometime
in your life."

-- Winston Churchill

Re: [GMOD-devel] [Gmod-schema] PRIMARY KEYs should be of type `bigint` [CASCADE]

[Karl O. P. <ko...@me...>]

On Thu, 23 Apr 2015 14:07:14 -0500
Siddhartha Basu <bi...@gm...> wrote:

> Secondly, it really does not matter if i start from scratch with
> bigint, but what about existing installation. 
> Is it just executing bunch of alter datatype queries 
> and everything will be bigint, no issues whatsoever. Is
> there is any precaution have to be taken.

Without having done it, I'd say the main precaution
is ensuring that when a key is changed to bigint
that all the related foreign keys are also changed.

I suppose that if you miss one and try to insert a
bigint value into a int column you'll just get a
integer out of range error and the transaction will
roll back.  So, as long as you've got sensible
transactions things would be ok and you'd just
have to alter the foreign key to bigint and
retry the transaction.

So, the main concern would be having sensible
transactions in your applications in case you goof.

Given performance concerns, perhaps the best approach
is to let people convert specific foreign keys to bigint on
an as-needed basis.


Karl <ko...@me...>
Free Software:  "You don't pay back, you pay forward."
                 -- Robert A. Heinlein

Re: [GMOD-devel] [Gmod-schema] PRIMARY KEYs should be of type `bigint` [CASCADE]

[Siddhartha B. <bi...@gm...>]

On Tue, 21 Apr 2015, Mara Kim wrote:

>    On 4:42PM, Mon, Apr 20, 2015A Karl O. Pinc <ko...@me...> wrote:
> 
>      The good news is that this change does not need to be
>      made to _every_ primary key.A  The only ones that come
>      to mind are FEATURE.Feature_Id and FEATURELOC.Featureloc_Id.
> 
>    That is true. We could get away with starting there. However, I first
>    encountered this problem on featureprop, which makes sense as this table
>    has a 1-to-many relationship with feature. We would need to change every
>    table with either a 1-to-1 or 1-to-many relationship, which would pull in
>    all the feature_* linker tables as well as analysisfeature.
> 
>      Wow.A  There really are features that are more than 2 billion long?
> 
>    Not sure about the present, but it's only a matter of time.A  The largest
>    sequenced genome is currentlyA Pinus taedaA at 23.18 Gbp over 12
>    chromosomes.A  In the best case scenario where these are distributed
>    equally over all chromosomes, that gives a chromosome size of 1.93 Gbp,
>    which is uncomfortably close. A Paris japonica is known to have a genome
>    size of ~150 Gbp.
That's very interesting information indeed. However, i think we have
to consider performance with that gigantic number of rows. The indexes
going to be bloated and all the queries should also be affected. I think
it will require some degree of table partitioning/sharding and maybe
even host partitioning depending on the cases. Whatever it is that will
add some administrative overhead/maintenance. Though its a change in
datatype, additional database setup/architecture is a prerequisite for
performance reason. Now since this all in theory(in my head), have
somebody actually dealt with performance related to large number of
rows. Would be interesting to know.

Secondly, it really does not matter if i start from scratch with bigint,
but what about existing installation. 
Is it just executing bunch of alter datatype queries 
and everything will be bigint, no issues whatsoever. Is
there is any precaution have to be taken. 

thanks,
-siddhartha


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Re: [GMOD-devel] [Gmod-schema] PRIMARY KEYs should be of type `bigint` [CASCADE]

[Karl O. P. <ko...@me...>]

On Tue, 21 Apr 2015 12:50:32 -0500
Mara Kim <mar...@va...> wrote:

> Wow.  There really are features that are more than 2 billion long?
> 
> Not sure about the present, but it's only a matter of time.  The
> largest sequenced genome is currently *Pinus taeda* at 23.18 Gbp over
> 12 chromosomes.  In the best case scenario where these are
> distributed equally over all chromosomes, that gives a chromosome
> size of 1.93 Gbp, which is uncomfortably close.  *Paris japonica *is
> known to have a genome size of ~150 Gbp.

The bad news is that having featureloc be bigint could really
affect performance, as, potentially, does moving some of the
keys to bigint.

Step 1 would then be to measure just what the performance impact
is.  No point in making a fuss if it does not matter.
My back-of-the-pants feeling is that it will matter, especially
as you start to get into billions of rows.

If it does matter then perhaps whether to use bigints could
be an install-time choice.  At least in some cases.
I can't see at lot of current chado users ever wanting 
bigints for feature offsets, as critical as it might be
for some.  (We are "feature oriented" here and
wouldn't want to see our storage needs balloon, or
increase the amount of time it takes to process
the storage.)

Karl <ko...@me...>
Free Software:  "You don't pay back, you pay forward."
                 -- Robert A. Heinlein