obo-phenotype — A discussion list for the phenotype ontology group

[Obo-phenotype] SEMANTiCS 2017, Amsterdam, Sep 11-14, Extended Submission Deadline July 25, 2017

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

***DEADLINE EXTENSION***

2nd Call for Posters & Demos
SEMANTiCS 2017 - The Linked Data Conference
13th International Conference on Semantic Systems

Amsterdam, Netherlands
September 11 -14, 2017
http://2017.semantics.cc

For details please go to: https://2017.semantics.cc/calls

Important Dates (Posters & Demos Track):
*Submission Deadline:            extended: July 25, 2017 (11:59 pm, 
Hawaii time)
*Notification of Acceptance:    August 10, 2017 (11:59 pm, Hawaii time)
*Camera-Ready Paper:        August 18, 2017 (11:59 pm, Hawaii time)

As in the previous years, SEMANTiCS’17 proceedings will be published by 
ACM ICPS (pending) and CEUR WS proceedings.

This year, SEMANTiCS features a special Data Science track, which is an 
opportunity to bring together researchers and practitioners interested 
in data science and its intersection with Linked Data to present their 
ideas and discuss the most important scientific, technical and 
socio-economical challenges of this emerging field.

SEMANTiCS 2017 will especially welcome submissions for the following hot 
topics:
*Metadata, Versioning and Data Quality Management
*Semantics for Safety, Security & Privacy
*Web Semantics, Linked (Open) Data & schema.org
*Corporate Knowledge Graphs
*Knowledge Integration and Language Technologies
*Economics of Data, Data Services and Data Ecosystems

Special Track (please check appropriate topic in submission system)
*Data Science

Following the success of previous years, we welcome any submissions 
related but not limited to the following ‘horizontal’ (research) and 
‘vertical’ (industries) topics:

Horizontals:
*Enterprise Linked Data & Data Integration
*Knowledge Discovery & Intelligent Search
*Business Models, Governance & Data Strategies
*Semantics in Big Data
*Text Analytics
*Data Portals & Knowledge Visualization
*Semantic Information Management
*Document Management & Content Management
*Terminology, Thesaurus & Ontology Management
*Smart Connectivity, Networking & Interlinking
*Smart Data & Semantics in IoT
*Semantics for IT Safety & Security
*Semantic Rules, Policies & Licensing
*Community, Social & Societal Aspects

Data Science Special Track Horizontals:
*Large-Scale Data Processing (stream processing, handling large-scale 
graphs)
*Data Analytics (Machine Learning, Predictive Analytics, Network Analytics)
*Communicating Data (Data Visualization, UX & Interaction Design, 
Crowdsourcing)
*Cross-cutting Issues (Ethics, Privacy, Security, Provenance)

Verticals:
*Industry & Engineering
*Life Sciences & Health Care
*Public Administration
*e-Science
*Digital Humanities
*Galleries, Libraries, Archives & Museums (GLAM)
*Education & eLearning
*Media & Data Journalism
*Publishing, Marketing & Advertising
*Tourism & Recreation
*Financial & Insurance Industry
*Telecommunication & Mobile Services
*Sustainable Development: Climate, Water, Air, Ecology
*Energy, Smart Homes & Smart Grids
*Food, Agriculture & Farming
*Safety, Security & Privacy
*Transport, Environment & Geospatial

Posters & Demos Track

The Posters & Demonstrations Track invites innovative work in progress, 
late-breaking research and innovation results, and smaller contributions 
in all fields related to the broadly understood Semantic Web. These 
include submissions on innovative applications with impact on end users 
such as demos of solutions that users may test or that are yet in the 
conceptual phase, but are worth discussing, and also applications, use 
cases or pieces of code that may attract developers and potential 
research or business partners. This also concerns new data sets made 
publicly available.

The informal setting of the Posters & Demonstrations Track encourages 
participants to present innovations to the research community, business 
users and find new partners or clients and engage in discussions about 
the presented work. Such discussions can be invaluable inputs for the 
future work of the presenters, while offering conference participants an 
effective way to broaden their knowledge of the emerging research trends 
and to network with other researchers.

Poster and demo submissions should consist of a paper that describe the 
work, its contribution to the field or novelty aspects. Submissions must 
be original and must not have been submitted for publication elsewhere.

Accepted papers will be published in HTML (RASH) in CEUR and, as such, 
the camera-ready version of the papers will be required in HTML, 
following the poster and demo guidelines (https://goo.gl/3BEpV7). Papers 
should be submitted through EasyChair 
(https://easychair.org/conferences/?conf=semantics2017 and should be 
less than 2200 words in length (equivalent to 4 pages), including the 
whole content of the paper.

For the initial reviewing phase, authors may submit a PDF version of the 
paper following any layout. After acceptance, authors are required to 
submit the camera-ready in HTML (RASH).

Submissions will be reviewed by experienced and knowledgeable 
researchers and practitioners; each submission will receive detailed 
feedback. For demos, we encourage authors to include links enabling the 
reviewers to test the application or review the component.

For details please go to: https://2017.semantics.cc/calls

[Obo-phenotype] SEMANTICS2017 - Early registration discount reminder

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

Dear all,

There are only two weeks left to benefit from the reduced registration 
fee for the SEMANTICS2017 <https://2017.semantics.cc/> conference in 
Amsterdam.

*To get the discount, please register 
<https://2017.semantics.cc/prices>* *before July 1th, 2017*

Looking forward to meeting you at the conference!

Semantics Organizing Team

[Obo-phenotype] SEMANTiCS 2017, Amsterdam, Sep 11-14, Call for Posters & Demos

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

Apologies for cross-posting

Call for Posters & Demos
SEMANTiCS 2017 - The Linked Data Conference
13th International Conference on Semantic Systems

Amsterdam, Netherlands
September 11 -14, 2017
http://2017.semantics.cc

For details please go to: https://2017.semantics.cc/calls

Important Dates (Posters & Demos Track):
*Submission Deadline:        July 10, 2017 (11:59 pm, Hawaii time)
*Notification of Acceptance:         August 10, 2017 (11:59 pm, Hawaii time)
*Camera-Ready Paper:         August 18, 2017 (11:59 pm, Hawaii time)

As in the previous years, SEMANTiCS’17 proceedings will be published by 
ACM ICPS (pending) and CEUR WS proceedings.

This year, SEMANTiCS features a special Data Science track, which is an 
opportunity to bring together researchers and practitioners interested 
in data science and its intersection with Linked Data to present their 
ideas and discuss the most important scientific, technical and 
socio-economical challenges of this emerging field.

SEMANTiCS 2017 will especially welcome submissions for the following hot 
topics:
*Metadata, Versioning and Data Quality Management
*Semantics for Safety, Security & Privacy
*Web Semantics, Linked (Open) Data & schema.org
*Corporate Knowledge Graphs
*Knowledge Integration and Language Technologies
*Economics of Data, Data Services and Data Ecosystems

Special Track (please check appropriate topic in submission system)
*Data Science

Following the success of previous years, we welcome any submissions 
related but not limited to the following ‘horizontal’ (research) and 
‘vertical’ (industries) topics:

Horizontals:
*Enterprise Linked Data & Data Integration
*Knowledge Discovery & Intelligent Search
*Business Models, Governance & Data Strategies
*Semantics in Big Data
*Text Analytics
*Data Portals & Knowledge Visualization
*Semantic Information Management
*Document Management & Content Management
*Terminology, Thesaurus & Ontology Management
*Smart Connectivity, Networking & Interlinking
*Smart Data & Semantics in IoT
*Semantics for IT Safety & Security
*Semantic Rules, Policies & Licensing
*Community, Social & Societal Aspects

Data Science Special Track Horizontals:
*Large-Scale Data Processing (stream processing, handling large-scale 
graphs)
*Data Analytics (Machine Learning, Predictive Analytics, Network Analytics)
*Communicating Data (Data Visualization, UX & Interaction Design, 
Crowdsourcing)
*Cross-cutting Issues (Ethics, Privacy, Security, Provenance)

Verticals:
*Industry & Engineering
*Life Sciences & Health Care
*Public Administration
*e-Science
*Digital Humanities
*Galleries, Libraries, Archives & Museums (GLAM)
*Education & eLearning
*Media & Data Journalism
*Publishing, Marketing & Advertising
*Tourism & Recreation
*Financial & Insurance Industry
*Telecommunication & Mobile Services
*Sustainable Development: Climate, Water, Air, Ecology
*Energy, Smart Homes & Smart Grids
*Food, Agriculture & Farming
*Safety, Security & Privacy
*Transport, Environment & Geospatial

Posters & Demos Track

The Posters & Demonstrations Track invites innovative work in progress, 
late-breaking research and innovation results, and smaller contributions 
in all fields related to the broadly understood Semantic Web. These 
include submissions on innovative applications with impact on end users 
such as demos of solutions that users may test or that are yet in the 
conceptual phase, but are worth discussing, and also applications, use 
cases or pieces of code that may attract developers and potential 
research or business partners. This also concerns new data sets made 
publicly available.

The informal setting of the Posters & Demonstrations Track encourages 
participants to present innovations to the research community, business 
users and find new partners or clients and engage in discussions about 
the presented work. Such discussions can be invaluable inputs for the 
future work of the presenters, while offering conference participants an 
effective way to broaden their knowledge of the emerging research trends 
and to network with other researchers.

Poster and demo submissions should consist of a paper that describe the 
work, its contribution to the field or novelty aspects. Submissions must 
be original and must not have been submitted for publication elsewhere.

Accepted papers will be published in HTML (RASH) in CEUR and, as such, 
the camera-ready version of the papers will be required in HTML, 
following the poster and demo guidelines (https://goo.gl/3BEpV7). Papers 
should be submitted through EasyChair 
(https://easychair.org/conferences/?conf=semantics2017 and should be 
less than 2200 words in length (equivalent to 4 pages), including the 
whole content of the paper.

For the initial reviewing phase, authors may submit a PDF version of the 
paper following any layout. After acceptance, authors are required to 
submit the camera-ready in HTML (RASH).

Submissions will be reviewed by experienced and knowledgeable 
researchers and practitioners; each submission will receive detailed 
feedback. For demos, we encourage authors to include links enabling the 
reviewers to test the application or review the component.

For details please go to: https://2017.semantics.cc/calls

Re: [Obo-phenotype] Migration of obo-phenotype from sourceforge to google groups

[Melissa H. <ha...@oh...>]

Thanks for organizing us Chris!

On Jun 19, 2017, at 3:14 PM, Chris Mungall <cjm...@lb...<mailto:cjm...@lb...>> wrote:


Hi phenotype ontologists,

I have created a new google group for us:
https://groups.google.com/forum/#!forum/obo-phenotype
Email: obo...@go...<mailto:obo...@go...>

We are abandoning this list on sourceforge. To see the reasons why, consult this ticket: https://github.com/OBOFoundry/OBOFoundry.github.io/issues/435

Note I am unable to see the list of subscribers to this list, as sourceforge turned this feature off, so I am unable to auto-subscribe you. If you are the maintainer of a phenotype ontology I may add you automatically based on your contact info in the OBO registry.

For everyone else, if you want to stay informed, you will have to subscribe yourself - this is easy to do if you go to https://groups.google.com/forum/#!forum/obo-phenotype and click "Apply to join group".

I realize this list has been silent for a while, but there has been a lot of off-list activity, including:

  *   shared OWL design patterns across OBO phenotype ontologies: https://github.com/obophenotype/upheno/tree/master/src/patterns
  *   general good practice guidelines and SOPs for managing your phenotype ontology release process, QC etc
  *   standard exchange formats for phenotype data: http://phenopackets.org<http://phenopackets.org/>
  *   use of phenotype ontologies for annotating a variety of data in humans and MODs
  *   portals for phenotype data, e.g. http://monarchinitiative.org<http://monarchinitiative.org/>, http://planteome.org<http://planteome.org/>

Now is a good time to bring things back to a community forum.

------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org<http://slashdot.org>! http://sdm.link/slashdot_______________________________________________
Obo-phenotype mailing list
Obo...@li...<mailto:Obo...@li...>
https://lists.sourceforge.net/lists/listinfo/obo-phenotype

Melissa Haendel, PhD
Associate Professor
Library & Dept. of Medical Informatics and Clinical Epidemiology
ha...@oh...<mailto:ha...@oh...>
503-407-5970
www.monarchinitiative.org<http://www.monarchinitiative.org>

Appointments: Shanez De Silva
de...@oh...<mailto:de...@oh...>

[Obo-phenotype] Migration of obo-phenotype from sourceforge to google groups

[Chris M. <cjm...@lb...>]

Hi phenotype ontologists,

I have created a new google group for us:
https://groups.google.com/forum/#!forum/obo-phenotype
Email: obo...@go...

We are abandoning this list on sourceforge. To see the reasons why, 
consult this ticket: 
https://github.com/OBOFoundry/OBOFoundry.github.io/issues/435

Note I am unable to see the list of subscribers to this list, as 
sourceforge turned this feature off, so I am unable to auto-subscribe 
you. If you are the maintainer of a phenotype ontology I may add you 
automatically based on your contact info in the OBO registry.

For everyone else, **if you want to stay informed, you will have to 
subscribe yourself** - this is easy to do if you go to 
https://groups.google.com/forum/#!forum/obo-phenotype and click "Apply 
to join group".

I realize this list has been silent for a while, but there has been a 
lot of off-list activity, including:

  - shared OWL design patterns across OBO phenotype ontologies: 
https://github.com/obophenotype/upheno/tree/master/src/patterns
  - general good practice guidelines and SOPs for managing your 
phenotype ontology release process, QC etc
  - standard exchange formats for phenotype data: 
http://phenopackets.org
  - use of phenotype ontologies for annotating a variety of data in 
humans and MODs
  - portals for phenotype data, e.g. http://monarchinitiative.org, 
http://planteome.org

Now is a good time to bring things back to a community forum.

[Obo-phenotype] SEMANTiCS 2017, Amsterdam, Sep 11-14, Extended Submission Deadline May 31, 2017

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

**** DEADLINE EXTENSION****

Due to several requests the SEMANTiCS 2017 conference extends its 
submission deadlines.

3rd Call for Research & Innovation Papers
SEMANTiCS 2017 - The Linked Data Conference
13th International Conference on Semantic Systems

Amsterdam, Netherlands
September 11 -14, 2017
http://2017.semantics.cc

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 lenght for full papers and 4 pages for short 
papers, including references and optional appendices.

Research & Innovation Papers are published within ACM ICP Series.

Important Dates (Research & Innovation)
* Abstract Submission Deadline:           extended: May 31, 2017 (11:59 
pm, Hawaii time)
* Paper Submission Deadline:                extended: June 7, 2017 
(11:59 pm, Hawaii time)
* Notification of Acceptance:                 July 3, 2017 (11:59 pm, 
Hawaii time)
* Camera-Ready Paper:                         August 14, 2017 (11:59 pm, 
Hawaii time)

For details please go to: https://2017.semantics.cc/calls
or contact the Research and Innovation Chairs:
Catherine Faron Zucker, faron [@] i3s.unice.fr, Université Nice Sophia 
Antipolis
Rinke Hoekstra, rinke.hoekstra [@] vu.nl, Vrije Universiteit 
Amsterdam/University of Amsterdam

As in the previous years, SEMANTiCS’17 proceedings will be published by 
ACM ICP (pending).

SEMANTiCS 2017 will especially welcome submissions for the following hot 
topics:
* Data Science (special track, see below)
* Web Semantics, Linked (Open) Data & schema.org
* Corporate Knowledge Graphs
* Knowledge Integration and Language Technologies
* Data Quality Management
* Economics of Data, Data Services and Data Ecosystems

Following the success of previous years, the ‘horizontals’ (research) 
and ‘verticals’ (industries) below are of interest for the conference:

Horizontals
* Enterprise Linked Data & Data Integration
* Knowledge Discovery & Intelligent Search
* Business Models, Governance & Data Strategies
* Semantics in Big Data
* Text Analytics
* Data Portals & Knowledge Visualization
* Semantic Information Management
* Document Management & Content Management
* Terminology, Thesaurus & Ontology Management
* Smart Connectivity, Networking & Interlinking
* Smart Data & Semantics in IoT
* Semantics for IT Safety & Security
* Semantic Rules, Policies & Licensing
* Community, Social & Societal Aspects

Data Science Special Track Horizontals
* Large-Scale Data Processing (stream processing, handling large-scale 
graphs)
* Data Analytics (Machine Learning, Predictive Analytics, Network Analytics)
* Communicating Data (Data Visualization, UX & Interaction Design, 
Crowdsourcing)
* Cross-cutting Issues (Ethics, Privacy, Security, Provenance)

Verticals
* Industry & Engineering
* Life Sciences & Health Care
* Public Administration
* e-Science
* Digital Humanities
* Galleries, Libraries, Archives & Museums (GLAM)
* Education & eLearning
* Media & Data Journalism
* Publishing, Marketing & Advertising
* Tourism & Recreation
* Financial & Insurance Industry
* Telecommunication & Mobile Services
* Sustainable Development: Climate, Water, Air, Ecology
* Energy, Smart Homes & Smart Grids
* Food, Agriculture & Farming
* Safety, Security & Privacy
* Transport, Environment & Geospatial

For details please go to: https://2017.semantics.cc/calls

[Obo-phenotype] SEMANTiCS 2017, Amsterdam, Sep 11-14, open Calls

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

Apologies for cross-posting

Call for Papers, Posters & Workshops and Tutorials
SEMANTiCS 2017 - The Linked Data Conference
13th International Conference on Semantic Systems

Amsterdam, Netherlands
September 11 -14, 2017
http://2017.semantics.cc

For details please go to: https://2017.semantics.cc/calls

Important Dates (Research & Innovation Track):
*Abstract Submission Deadline:May 17, 2017 (11:59 pm, Hawaii time)
*Paper Submission Deadline:      May 24, 2017 (11:59 pm, Hawaii time)
*Notification of Acceptance:     July 3, 2017 (11:59 pm, Hawaii time)
*Camera-Ready Paper:             August 14, 2017 (11:59 pm, Hawaii time)

Important Dates (Posters & Demos Track):
*Submission Deadline:            July 10, 2017 (11:59 pm, Hawaii time)
*Notification of Acceptance:     August 10, 2017 (11:59 pm, Hawaii time)
*Camera-Ready Paper:             August 18, 2017 (11:59 pm, Hawaii time)

Important Dates (Workshops & Tutorials):
*Proposals for Tutorials and Workshops without Call for Papers: June 30, 
2017 (23:59 Hawaii Time)
*Notification of Acceptance:                 April 13, 2017 (23:59 
Hawaii Time)
*Workshop Website/Call for Papers Online:    April 30, 2017 (23:59 
Hawaii Time)
*Camera-Ready Proceedings:                   September 4, 2017 (23:59 
Hawaii Time)
*SEMANTiCS 2017 Workshop & Tutorial Days:    September 11 and 14, 2017

Important Dates (Industry & Use Case Presentations):
*Submission Deadline June 23, 2017
*Notification of Acceptance July 4, 2017
*Presentation Ready August 15, 2017

As in the previous years, SEMANTiCS’17 proceedings will be published by 
ACM ICPS (pending) and CEUR WS proceedings.

SEMANTiCS 2017 will especially welcome submissions for the following hot 
topics:
*Data Science (special track, see below)
*Web Semantics, Linked (Open) Data & schema.org
*Corporate Knowledge Graphs
*Knowledge Integration and Language Technologies
*Data Quality Management
*Economics of Data, Data Services and Data Ecosystems


Following the success of previous years, the ‘horizontals’ (research) 
and ‘verticals’ (industries) below are of interest for the conference:

Horizontals:
*Enterprise Linked Data & Data Integration
*Knowledge Discovery & Intelligent Search
*Business Models, Governance & Data Strategies
*Semantics in Big Data
*Text Analytics
*Data Portals & Knowledge Visualization
*Semantic Information Management
*Document Management & Content Management
*Terminology, Thesaurus & Ontology Management
*Smart Connectivity, Networking & Interlinking
*Smart Data & Semantics in IoT
*Semantics for IT Safety & Security
*Semantic Rules, Policies & Licensing
*Community, Social & Societal Aspects

Data Science Special Track Horizontals:
*Large-Scale Data Processing (stream processing, handling large-scale 
graphs)
*Data Analytics (Machine Learning, Predictive Analytics, Network Analytics)
*Communicating Data (Data Visualization, UX & Interaction Design, 
Crowdsourcing)
*Cross-cutting Issues (Ethics, Privacy, Security, Provenance)

Verticals:
*Industry & Engineering
*Life Sciences & Health Care
*Public Administration
*e-Science
*Digital Humanities
*Galleries, Libraries, Archives & Museums (GLAM)
*Education & eLearning
*Media & Data Journalism
*Publishing, Marketing & Advertising
*Tourism & Recreation
*Financial & Insurance Industry
*Telecommunication & Mobile Services
*Sustainable Development: Climate, Water, Air, Ecology
*Energy, Smart Homes & Smart Grids
*Food, Agriculture & Farming
*Safety, Security & Privacy
*Transport, Environment & Geospatial

[Obo-phenotype] SEMANTiCS 2017, Amsterdam, Sep 11-14, Open Calls

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

Apologies for cross-posting

Call for Papers, Posters & Workshops and Tutorials
SEMANTiCS 2017 - The Linked Data Conference
13th International Conference on Semantic Systems

Amsterdam, Netherlands
September 11 -14, 2017
http://2017.semantics.cc

For details please go to: https://2017.semantics.cc/calls

Important Dates (Research & Innovation Track):
*Abstract Submission Deadline:          May 17, 2017 (11:59 pm, Hawaii time)
*Paper Submission Deadline:            May 24, 2017 (11:59 pm, Hawaii time)
*Notification of Acceptance:           July 3, 2017 (11:59 pm, Hawaii time)
*Camera-Ready Paper:                    August 14, 2017 (11:59 pm, 
Hawaii time)

Important Dates (Posters & Demos Track):
*Submission Deadline:                July 10, 2017 (11:59 pm, Hawaii time)
*Notification of Acceptance:             August 10, 2017 (11:59 pm, 
Hawaii time)
*Camera-Ready Paper:                 August 18, 2017 (11:59 pm, Hawaii time)

Important Dates (Workshops & Tutorials):
*Proposals for Workshops with Call for Papers: March 31, 2017 (23:59 
Hawaii Time)
*Proposals for Tutorials and Workshops without Call for Papers: June 
30,  2017 (23:59 Hawaii Time)
*Notification of Acceptance: April 13,  2017 (23:59 Hawaii Time)
*Workshop Website/Call for Papers Online: April 30, 2017 (23:59 Hawaii Time)
*Camera-Ready Proceedings:  September 4, 2017 (23:59 Hawaii Time)
*SEMANTiCS 2017 Workshop & Tutorial Days: September 11 and 14, 2017

Important Dates (Industry & Use Case Presentations):
*Submission Deadline:                 June 23, 2017
*Notification of Acceptance:        July 4, 2017
*Presentation Ready:            August 15, 2017

As in the previous years, SEMANTiCS’17 proceedings will be published by 
ACM ICPS (pending) and CEUR WS proceedings.

SEMANTiCS 2017 will especially welcome submissions for the following hot 
topics:
*Data Science (special track, see below)
*Web Semantics, Linked (Open) Data & schema.org
*Corporate Knowledge Graphs
*Knowledge Integration and Language Technologies
*Data Quality Management
*Economics of Data, Data Services and Data Ecosystems

Following the success of previous years, the ‘horizontals’ (research) 
and ‘verticals’ (industries) below are of interest for the conference:

Horizontals:
*Enterprise Linked Data & Data Integration
*Knowledge Discovery & Intelligent Search
*Business Models, Governance & Data Strategies
*Semantics in Big Data
*Text Analytics
*Data Portals & Knowledge Visualization
*Semantic Information Management
*Document Management & Content Management
*Terminology, Thesaurus & Ontology Management
*Smart Connectivity, Networking & Interlinking
*Smart Data & Semantics in IoT
*Semantics for IT Safety & Security
*Semantic Rules, Policies & Licensing
*Community, Social & Societal Aspects

Data Science Special Track Horizontals:
*Large-Scale Data Processing (stream processing, handling large-scale 
graphs)
*Data Analytics (Machine Learning, Predictive Analytics, Network Analytics)
*Communicating Data (Data Visualization, UX & Interaction Design, 
Crowdsourcing)
*Cross-cutting Issues (Ethics, Privacy, Security, Provenance)

Verticals:
*Industry & Engineering
*Life Sciences & Health Care
*Public Administration
*e-Science
*Digital Humanities
*Galleries, Libraries, Archives & Museums (GLAM)
*Education & eLearning
*Media & Data Journalism
*Publishing, Marketing & Advertising
*Tourism & Recreation
*Financial & Insurance Industry
*Telecommunication & Mobile Services
*Sustainable Development: Climate, Water, Air, Ecology
*Energy, Smart Homes & Smart Grids
*Food, Agriculture & Farming
*Safety, Security & Privacy
*Transport, Environment & Geospatial

Re: [Obo-phenotype] Making abolished (process) analogous to absent

[Melissa H. <ha...@oh...>]

yep, this is related to the need for not just opposites but things on a continuum being related.
Same for aplastic vs. hypoplastic. The relationship is probably not one of subclassing, as it is a matter of degree.




On Mar 8, 2017, at 6:47 AM, Dr Midori A. Harris <ma...@ca...<mailto:ma...@ca...>> wrote:



On Wed, 8 Mar 2017, Köhler, Sebastian wrote:

Hi,

My fellow PomBase curators have returned to this outstanding question, so I thought it might be fodder for the re-awakening obo-phenotype list.

As far as I know, this ticket still has the latest thinking, although it hasn't seen any activity for two years:

https://github.com/pato-ontology/pato/issues/46

We would still like a resolution, especially since I'm not sure FYPO is even up to date with its design patterns in this area.

We'll be happiest if we end up with a design pattern that lets "abolished process" fall under "decreased occurrence of a process" (or the grounds that not happening at all is indeed happening less than in a reference organism for the phenotypes we're modeling), but any clarification will be better than our present situation.

I think for HPO we ÿÿcurrently" decided to use ÿÿlacks processual partsÿÿ, but now I saw the ticket and I am not sure anymore. Here is a summary of our current thoughts on design patterns (HP/MP-centric): https://docs.google.com/document/d/10NCd9jXGXA4BETSBxdbVGfDFM2w4gAIbY6vpm4ERTBo/edit#

We're using "lacking processual parts" for our absent-in-mutant processes, but my colleagues are a bit unsatisfied because that doesn't get classified under "decreased occurrence" (unless I were to attempt it manually - run away!), which they find counter-intuitive. That's the issue I hope to address.

And here is the current process pattern: https://github.com/obophenotype/upheno/blob/master/src/patterns/missingProcess.yaml

Thanks for the links. I'll have a look soon.

Midori

Best,
Seb


Apologies to those who receive multiple coipes of this via two lists.

Thanks,
Midori


Midori A. Harris, PhD
Database Curator, PomBase
Department of Biochemistry
University of Cambridge
Cambridge, UK
ma...@ca...<mailto:ma...@ca...>


On Tue, 3 Mar 2015, Chris Mungall wrote:

I don't have strong opinions on what the best lexical label is. but see latest comments on the tracker, there's already some terminological confusion in pato here.

On 3 Mar 2015, at 15:29, Robinson, Peter wrote:

That only makes sense if we mean "abolished enyzme activity"; but I do not think that the naked worked "abolished" necessarily has this connotation?
-Peter
Dr. med. Peter N. Robinson, MSc.
Professor of Medical Genomics
Professor in the Bioinformatics Division of the Department of Mathematics and Computer Science of the Freie Universität Berlin
Institut für Medizinische Genetik und Humangenetik
Charité - Universitätsmedizin Berlin
Augustenburger Platz 1
13353 Berlin
Germany
+4930 450566006
Mobile: 0160 93769872
pet...@ch...
http://compbio.charite.de
http://www.human-phenotype-ontology.org
Introduction to Bio-Ontologies: http://www.crcpress.com/product/isbn/9781439836651
I have learned from my mistakes, and I am sure I can repeat them exactly
ORCID ID:http://orcid.org/0000-0002-0736-9199
Scopus Author ID 7403719646
Appointment request: http://doodle.com/pnrobinson
________________________________________
Von: phe...@go... [phe...@go...] im Auftrag von Dr Midori A. Harris [ma...@ca...]
Gesendet: Dienstag, 3. März 2015 18:20
An: Cynthia Smith
Cc: phe...@go...
Betreff: Re: Making abolished analogous to absent
would be great for me (FYPO)
m
On Tue, 3 Mar 2015, Cynthia Smith wrote:
makes sense to me
On 3/3/15 10:29 AM, "Chris Mungall" <cjm...@lb...> wrote:
Shall we put abolished under 'decreased efficacy'?
https://github.com/gkoutos/pato/issues/46#issuecomment-76961544
I think so
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--
Dr. rer. nat. Sebastian Köhler
NeuroCure Cluster of Excellence
Charité - Universitätsmedizin Berlin
Charitéplatz 1
D-10117 Berlin
Germany
email: dr....@gm...<mailto:dr....@gm...>
web: http://drseb.github.io


Melissa Haendel, PhD
Associate Professor
Library & Dept. of Medical Informatics and Clinical Epidemiology
ha...@oh...<mailto:ha...@oh...>
503-407-5970
www.monarchinitiative.org<http://www.monarchinitiative.org>

Appointments: Shanez De Silva
de...@oh...<mailto:de...@oh...>

Re: [Obo-phenotype] Making abolished (process) analogous to absent

[Dr M. A. H. <ma...@ca...>]

On Wed, 8 Mar 2017, Köhler, Sebastian wrote:

> Hi,
>
>> My fellow PomBase curators have returned to this outstanding question, so I thought it might be fodder for the re-awakening obo-phenotype list.
>>
>> As far as I know, this ticket still has the latest thinking, although it hasn't seen any activity for two years:
>>
>> https://github.com/pato-ontology/pato/issues/46
>>
>> We would still like a resolution, especially since I'm not sure FYPO is even up to date with its design patterns in this area.
>>
>> We'll be happiest if we end up with a design pattern that lets "abolished process" fall under "decreased occurrence of a process" (or the grounds that not happening at all is indeed happening less than in a reference organism for the phenotypes we're modeling), but any clarification will be better than our present situation.
>
> I think for HPO we ÿÿcurrently" decided to use ÿÿlacks processual partsÿÿ, but now I saw the ticket and I am not sure anymore. Here is a summary of our current thoughts on design patterns (HP/MP-centric): https://docs.google.com/document/d/10NCd9jXGXA4BETSBxdbVGfDFM2w4gAIbY6vpm4ERTBo/edit#

We're using "lacking processual parts" for our absent-in-mutant processes, 
but my colleagues are a bit unsatisfied because that doesn't get 
classified under "decreased occurrence" (unless I were to attempt it 
manually - run away!), which they find counter-intuitive. That's the issue 
I hope to address.

> And here is the current process pattern: https://github.com/obophenotype/upheno/blob/master/src/patterns/missingProcess.yaml

Thanks for the links. I'll have a look soon.

Midori

> Best,
> Seb
>
>>
>> Apologies to those who receive multiple coipes of this via two lists.
>>
>> Thanks,
>> Midori
>>
>>
>> Midori A. Harris, PhD
>> Database Curator, PomBase
>> Department of Biochemistry
>> University of Cambridge
>> Cambridge, UK
>> ma...@ca...
>>
>>
>> On Tue, 3 Mar 2015, Chris Mungall wrote:
>>
>>> I don't have strong opinions on what the best lexical label is. but see latest comments on the tracker, there's already some terminological confusion in pato here.
>>>
>>> On 3 Mar 2015, at 15:29, Robinson, Peter wrote:
>>>
>>>> That only makes sense if we mean "abolished enyzme activity"; but I do not think that the naked worked "abolished" necessarily has this connotation?
>>>> -Peter
>>>> Dr. med. Peter N. Robinson, MSc.
>>>> Professor of Medical Genomics
>>>> Professor in the Bioinformatics Division of the Department of Mathematics and Computer Science of the Freie Universität Berlin
>>>> Institut für Medizinische Genetik und Humangenetik
>>>> Charité - Universitätsmedizin Berlin
>>>> Augustenburger Platz 1
>>>> 13353 Berlin
>>>> Germany
>>>> +4930 450566006
>>>> Mobile: 0160 93769872
>>>> pet...@ch...
>>>> http://compbio.charite.de
>>>> http://www.human-phenotype-ontology.org
>>>> Introduction to Bio-Ontologies: http://www.crcpress.com/product/isbn/9781439836651
>>>> I have learned from my mistakes, and I am sure I can repeat them exactly
>>>> ORCID ID:http://orcid.org/0000-0002-0736-9199
>>>> Scopus Author ID 7403719646
>>>> Appointment request: http://doodle.com/pnrobinson
>>>> ________________________________________
>>>> Von: phe...@go... [phe...@go...] im Auftrag von Dr Midori A. Harris [ma...@ca...]
>>>> Gesendet: Dienstag, 3. März 2015 18:20
>>>> An: Cynthia Smith
>>>> Cc: phe...@go...
>>>> Betreff: Re: Making abolished analogous to absent
>>>> would be great for me (FYPO)
>>>> m
>>>> On Tue, 3 Mar 2015, Cynthia Smith wrote:
>>>>> makes sense to me
>>>>> On 3/3/15 10:29 AM, "Chris Mungall" <cjm...@lb...> wrote:
>>>>>> Shall we put abolished under 'decreased efficacy'?
>>>>>> https://github.com/gkoutos/pato/issues/46#issuecomment-76961544
>>>>>> I think so
>>>>>> --
>>>>>> You received this message because you are subscribed to the Google Groups
>>>>>> "phenotype-ontologies-editors" group.
>>>>>> To unsubscribe from this group and stop receiving emails from it, send an
>>>>>> email to phe...@go....
>>>>>> For more options, visit https://groups.google.com/d/optout.
>>>>> The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.
>>>>> --
>>>>> You received this message because you are subscribed to the Google Groups "phenotype-ontologies-editors" group.
>>>>> To unsubscribe from this group and stop receiving emails from it, send an email to phe...@go....
>>>>> For more options, visit https://groups.google.com/d/optout.
>>>> --
>>>> You received this message because you are subscribed to the Google Groups "phenotype-ontologies-editors" group.
>>>> To unsubscribe from this group and stop receiving emails from it, send an email to phe...@go....
>>>> For more options, visit https://groups.google.com/d/optout.
>>>
>>> --
>>> You received this message because you are subscribed to the Google Groups "phenotype-ontologies-editors" group.
>>> To unsubscribe from this group and stop receiving emails from it, send an email to phe...@go....
>>> For more options, visit https://groups.google.com/d/optout.
>
>
> --
> Dr. rer. nat. Sebastian Köhler
> NeuroCure Cluster of Excellence
> Charité - Universitätsmedizin Berlin
> Charitéplatz 1
> D-10117 Berlin
> Germany
> email: dr....@gm...
> web: http://drseb.github.io
>
>

Re: [Obo-phenotype] Making abolished (process) analogous to absent

[Dr M. A. H. <ma...@ca...>]

Hi,

My fellow PomBase curators have returned to this outstanding question, so 
I thought it might be fodder for the re-awakening obo-phenotype list.

As far as I know, this ticket still has the latest thinking, although it 
hasn't seen any activity for two years:

https://github.com/pato-ontology/pato/issues/46

We would still like a resolution, especially since I'm not sure FYPO 
is even up to date with its design patterns in this area.

We'll be happiest if we end up with a design pattern that lets "abolished 
process" fall under "decreased occurrence of a process" (or the grounds 
that not happening at all is indeed happening less than in a reference 
organism for the phenotypes we're modeling), but any clarification will be 
better than our present situation.

Apologies to those who receive multiple coipes of this via two lists.

Thanks,
Midori


Midori A. Harris, PhD
Database Curator, PomBase
Department of Biochemistry
University of Cambridge
Cambridge, UK
ma...@ca...


On Tue, 3 Mar 2015, Chris Mungall wrote:

> I don't have strong opinions on what the best lexical label is. but see 
> latest comments on the tracker, there's already some terminological confusion 
> in pato here.
>
> On 3 Mar 2015, at 15:29, Robinson, Peter wrote:
>
>> That only makes sense if we mean "abolished enyzme activity"; but I do not 
>> think that the naked worked "abolished" necessarily has this connotation?
>> -Peter
>> 
>> Dr. med. Peter N. Robinson, MSc.
>> Professor of Medical Genomics
>> Professor in the Bioinformatics Division of the Department of Mathematics 
>> and Computer Science of the Freie Universität Berlin
>> Institut für Medizinische Genetik und Humangenetik
>> Charité - Universitätsmedizin Berlin
>> Augustenburger Platz 1
>> 13353 Berlin
>> Germany
>> +4930 450566006
>> Mobile: 0160 93769872
>> pet...@ch...
>> http://compbio.charite.de
>> http://www.human-phenotype-ontology.org
>> Introduction to Bio-Ontologies: 
>> http://www.crcpress.com/product/isbn/9781439836651
>> I have learned from my mistakes, and I am sure I can repeat them exactly
>> ORCID ID:http://orcid.org/0000-0002-0736-9199
>> Scopus Author ID 7403719646
>> Appointment request: http://doodle.com/pnrobinson
>> ________________________________________
>> Von: phe...@go... 
>> [phe...@go...] im Auftrag von Dr Midori A. 
>> Harris [ma...@ca...]
>> Gesendet: Dienstag, 3. März 2015 18:20
>> An: Cynthia Smith
>> Cc: phe...@go...
>> Betreff: Re: Making abolished analogous to absent
>> 
>> would be great for me (FYPO)
>> 
>> m
>> 
>> On Tue, 3 Mar 2015, Cynthia Smith wrote:
>> 
>>> makes sense to me
>>> 
>>> On 3/3/15 10:29 AM, "Chris Mungall" <cjm...@lb...> wrote:
>>> 
>>>> Shall we put abolished under 'decreased efficacy'?
>>>> https://github.com/gkoutos/pato/issues/46#issuecomment-76961544
>>>> 
>>>> I think so
>>>> 
>>>> --
>>>> You received this message because you are subscribed to the Google Groups
>>>> "phenotype-ontologies-editors" group.
>>>> To unsubscribe from this group and stop receiving emails from it, send an
>>>> email to phe...@go....
>>>> For more options, visit https://groups.google.com/d/optout.
>>> 
>>> 
>>> The information in this email, including attachments, may be confidential 
>>> and is intended solely for the addressee(s). If you believe you received 
>>> this email by mistake, please notify the sender by return email as soon as 
>>> possible.
>>> 
>>> --
>>> You received this message because you are subscribed to the Google Groups 
>>> "phenotype-ontologies-editors" group.
>>> To unsubscribe from this group and stop receiving emails from it, send an 
>>> email to phe...@go....
>>> For more options, visit https://groups.google.com/d/optout.
>>> 
>> 
>> -- 
>> You received this message because you are subscribed to the Google Groups 
>> "phenotype-ontologies-editors" group.
>> To unsubscribe from this group and stop receiving emails from it, send an 
>> email to phe...@go....
>> For more options, visit https://groups.google.com/d/optout.
>
> -- 
> You received this message because you are subscribed to the Google Groups 
> "phenotype-ontologies-editors" group.
> To unsubscribe from this group and stop receiving emails from it, send an 
> email to phe...@go....
> For more options, visit https://groups.google.com/d/optout.
>

Re: [Obo-phenotype] Making abolished (process) analogous to absent

[Köhler, S. <seb...@ch...>]

Hi,

> My fellow PomBase curators have returned to this outstanding question, so I thought it might be fodder for the re-awakening obo-phenotype list.
> 
> As far as I know, this ticket still has the latest thinking, although it hasn't seen any activity for two years:
> 
> https://github.com/pato-ontology/pato/issues/46
> 
> We would still like a resolution, especially since I'm not sure FYPO is even up to date with its design patterns in this area.
> 
> We'll be happiest if we end up with a design pattern that lets "abolished process" fall under "decreased occurrence of a process" (or the grounds that not happening at all is indeed happening less than in a reference organism for the phenotypes we're modeling), but any clarification will be better than our present situation.

I think for HPO we “currently" decided to use “lacks processual parts”, but now I saw the ticket and I am not sure anymore. Here is a summary of our current thoughts on design patterns (HP/MP-centric): https://docs.google.com/document/d/10NCd9jXGXA4BETSBxdbVGfDFM2w4gAIbY6vpm4ERTBo/edit#

And here is the current process pattern: https://github.com/obophenotype/upheno/blob/master/src/patterns/missingProcess.yaml

Best,
Seb

> 
> Apologies to those who receive multiple coipes of this via two lists.
> 
> Thanks,
> Midori
> 
> 
> Midori A. Harris, PhD
> Database Curator, PomBase
> Department of Biochemistry
> University of Cambridge
> Cambridge, UK
> ma...@ca...
> 
> 
> On Tue, 3 Mar 2015, Chris Mungall wrote:
> 
>> I don't have strong opinions on what the best lexical label is. but see latest comments on the tracker, there's already some terminological confusion in pato here.
>> 
>> On 3 Mar 2015, at 15:29, Robinson, Peter wrote:
>> 
>>> That only makes sense if we mean "abolished enyzme activity"; but I do not think that the naked worked "abolished" necessarily has this connotation?
>>> -Peter
>>> Dr. med. Peter N. Robinson, MSc.
>>> Professor of Medical Genomics
>>> Professor in the Bioinformatics Division of the Department of Mathematics and Computer Science of the Freie Universität Berlin
>>> Institut für Medizinische Genetik und Humangenetik
>>> Charité - Universitätsmedizin Berlin
>>> Augustenburger Platz 1
>>> 13353 Berlin
>>> Germany
>>> +4930 450566006
>>> Mobile: 0160 93769872
>>> pet...@ch...
>>> http://compbio.charite.de
>>> http://www.human-phenotype-ontology.org
>>> Introduction to Bio-Ontologies: http://www.crcpress.com/product/isbn/9781439836651
>>> I have learned from my mistakes, and I am sure I can repeat them exactly
>>> ORCID ID:http://orcid.org/0000-0002-0736-9199
>>> Scopus Author ID 7403719646
>>> Appointment request: http://doodle.com/pnrobinson
>>> ________________________________________
>>> Von: phe...@go... [phe...@go...] im Auftrag von Dr Midori A. Harris [ma...@ca...]
>>> Gesendet: Dienstag, 3. März 2015 18:20
>>> An: Cynthia Smith
>>> Cc: phe...@go...
>>> Betreff: Re: Making abolished analogous to absent
>>> would be great for me (FYPO)
>>> m
>>> On Tue, 3 Mar 2015, Cynthia Smith wrote:
>>>> makes sense to me
>>>> On 3/3/15 10:29 AM, "Chris Mungall" <cjm...@lb...> wrote:
>>>>> Shall we put abolished under 'decreased efficacy'?
>>>>> https://github.com/gkoutos/pato/issues/46#issuecomment-76961544
>>>>> I think so
>>>>> --
>>>>> You received this message because you are subscribed to the Google Groups
>>>>> "phenotype-ontologies-editors" group.
>>>>> To unsubscribe from this group and stop receiving emails from it, send an
>>>>> email to phe...@go....
>>>>> For more options, visit https://groups.google.com/d/optout.
>>>> The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.
>>>> --
>>>> You received this message because you are subscribed to the Google Groups "phenotype-ontologies-editors" group.
>>>> To unsubscribe from this group and stop receiving emails from it, send an email to phe...@go....
>>>> For more options, visit https://groups.google.com/d/optout.
>>> --
>>> You received this message because you are subscribed to the Google Groups "phenotype-ontologies-editors" group.
>>> To unsubscribe from this group and stop receiving emails from it, send an email to phe...@go....
>>> For more options, visit https://groups.google.com/d/optout.
>> 
>> --
>> You received this message because you are subscribed to the Google Groups "phenotype-ontologies-editors" group.
>> To unsubscribe from this group and stop receiving emails from it, send an email to phe...@go....
>> For more options, visit https://groups.google.com/d/optout.


--
Dr. rer. nat. Sebastian Köhler
NeuroCure Cluster of Excellence
Charité - Universitätsmedizin Berlin
Charitéplatz 1
D-10117 Berlin
Germany
email: dr....@gm...
web: http://drseb.github.io

[Obo-phenotype] the return of the obo-phenotype mail list

[Chris M. <cjm...@lb...>]

The obo-phenotype list has been a bit dormant for a while. There has 
been a lot of work in the last few years on topics like unifying 
ontology design patterns for phenotype ontologies, but it has tended to 
take place amongst smaller groups and other communication channels. I 
think it's time to bring together some of the groups doing this in 
different species, share best practice, ontology tool tips, etc.

If you aren't already signed up, the info is here:
https://lists.sourceforge.net/lists/listinfo/obo-phenotype

We'll likely start having more announcements and discussions there over 
the next few weeks.

If there is interest, we could also try a gitter or slack channel as 
well. With gitter it's easy to set up a channel for repos on github, and 
most ontologies are on github now. Here is a gitter for phenotypes:

https://gitter.im/obophenotype

But if you're not into this new fangled chat business just sign up for 
the list and we'll make sure things are posted there.

[Obo-phenotype] DBpedia Open Text Extraction Challenge - TextExt

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

*DBpedia Open Text Extraction Challenge - TextExt*

Website: http://wiki.dbpedia.org/textext

*_Disclaimer: The call is under constant development, please refer to 
the news section. We also acknowledge the initial engineering effort and 
will be lenient on technical requirements for the first submissions and 
will focus evaluation on the extracted triples and allow late 
submissions, if they are coordinated with us_*.


      Background

DBpedia and Wikidata currently focus primarily on representing factual 
knowledge as contained in Wikipedia infoboxes. A vast amount of 
information, however, is contained in the unstructured Wikipedia article 
texts. With the DBpedia Open Text Extraction Challenge, we aim to spur 
knowledge extraction from Wikipedia article texts in order to 
dramatically broaden and deepen the amount of structured 
DBpedia/Wikipedia data and provide a platform for benchmarking various 
extraction tools.


      Mission

Wikipedia has become the ubiquitous source of knowledge for the world 
enabling humans to lookup definitions, quickly become familiar with new 
topics, read up background infos for news event and many more - even 
settling coffee house arguments via a quick mobile research. The mission 
of DBpedia in general is to harvest Wikipedia’s knowledge, refine and 
structure it and then disseminate it on the web - in a free and open 
manner - for IT users and businesses.


      News and next events

Twitter: Follow @dbpedia <https://twitter.com/dbpedia>, Hashtag: 
#dbpedianlp <https://twitter.com/search?f=tweets&q=%23dbpedianlp&src=typd>

  *

    LDK <http://ldk2017.org/> conference joined the challenge (Deadline
    March 19th and April 24th)

  *

    SEMANTiCS <http://2017.semantics.cc/> joined the challenge (Deadline
    June 11th and July 17th)

  *

    Feb 20th, 2017: Full example added to this website

  *

    March 1st, 2017: Docker image (beta)
    https://github.com/NLP2RDF/DBpediaOpenDBpediaTextExtractionChallenge

Coming soon:

  *

    beginning of March: full example within the docker image

  *

    beginning of March: DBpedia full article text and tables (currently
    only abstracts) http://downloads.dbpedia.org/2016-10/core-i18n/


      Methodology

The DBpedia Open Text Extraction Challenge differs significantly from 
other challenges in the language technology and other areas in that it 
is not a one time call, but a continuous growing and expanding challenge 
with the focus to *sustainably* advance the state of the art and 
transcend boundaries in a *systematic* way. The DBpedia Association and 
the people behind this challenge are committed to provide the necessary 
infrastructure and drive the challenge for an indefinite time as well as 
potentially extend the challenge beyond Wikipedia.

We provide the extracted and cleaned full text for all Wikipedia 
articles from 9 different languages in regular intervals for download 
and as Docker in the machine readable NIF-RDF 
<http://persistence.uni-leipzig.org/nlp2rdf/> format (Example for 
Barrack Obama in English 
<https://github.com/NLP2RDF/DBpediaOpenDBpediaTextExtractionChallenge/blob/master/BO.ttl>). 
Challenge participants are asked to wrap their NLP and extraction 
engines in Docker images and submit them to us. We will run 
participants’ tools in regular intervals in order to extract:

 1.

    Facts, relations, events, terminology, ontologies as RDF triples
    (Triple track)

 2.

    Useful NLP annotations such as pos-tags, dependencies, co-reference
    (Annotation track)

We allow submissions 2 months prior to selected conferences (currently 
_http://ldk2017.org/_ and _http://2017.semantics.cc/_ ). Participants 
that fulfil the technical requirements and provide a sufficient 
description will be able to present at the conference and be included in 
the yearly proceedings. *Each conference, the challenge committee will 
select a winner among challenge participants, which will receive 1000€. *


      Results

Every December, we will publish a summary article and proceedings of 
participants’ submissions at _http://ceur-ws.org/_ . The first 
proceedings are planned to be published in Dec 2017. We will try to 
briefly summarize any intermediate progress online in this section.


      Acknowledgements

We would like to thank the Computer Center of Leipzig University to give 
us access to their 6TB RAM server Sirius to run all extraction tools.

The project was created with the support of the H2020 EU project HOBBIT 
<https://project-hobbit.eu/> (GA-688227) and ALIGNED 
<http://aligned-project.eu/> (GA-644055) as well as the BMWi project 
Smart Data Web <http://smartdataweb.de/> (GA-01MD15010B).


      Challenge Committee

  *

    Sebastian Hellmann, AKSW, DBpedia Association, KILT Competence
    Center, InfAI, Leipzig

  *

    Sören Auer, Fraunhofer IAIS, University of Bonn

  *

    Ricardo Usbeck, AKSW, Simba Competence Center, Leipzig University

  *

    Dimitris Kontokostas, AKSW, DBpedia Association, KILT Competence
    Center, InfAI, Leipzig

  *

    Sandro Coelho, AKSW, DBpedia Association, KILT Competence Center,
    InfAI, Leipzig

Contact Email: _db...@in..._ 
<mailto:dbp...@in...>

[Obo-phenotype] DBpedia Newsletter

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

Dear all,

please find below the first edition of the DBpedia Newsletter, which 
will be sent to all subscribers in a three month interval. Of course, we 
would welcome any people who are interested to sign up 
(_http://eepurl.com/crrrkz_). We decided to use the newsletter as the 
major outlet for updates on DBpedia, so no further Newsletter edition 
will be sent to this list. Smaller and concise announcements will be 
posted on our _blog_ <http://blog.dbpedia.org/>.

Also we would welcome anyone to contribute to the Newsletter with 
DBpedia (and Linked Open Data) related announcements by sending an email 
to _db...@in..._ <mailto:db...@in...>. Announcement/News can 
include links and should be less than 100 words and are subject to 
moderation and editorial editing (mostly shortening).

Newsletter sign up form:<http://eepurl.com/crrrkz>_http://eepurl.com/crrrkz_

Thank you very much,

Sebastian


    *(Belated) Happy New Year to all DBpedians!*

We are a proud to look retrospectively at a successful year 2016 and 
would like to welcome 2017 with our new newsletter (~4 times per year), 
which will allow you to stay up to date and provide feedback, e.g. via 
the included survey and the planned events in 2017.

*New members *- We kickstarted 
the<http://wiki.dbpedia.org/dbpedia-association>_DBpedia Association_ 
<http://wiki.dbpedia.org/dbpedia-association> with a first wave of new 
members: OpenLink Software, Semantic Web Company, Ontotext, FIZ 
Karlsruhe, Mannheim University, Poznań University of Economics and 
Business, the Business Information Systems Institute Ltd and the Open 
Knowledge Foundation Greece joined the DBpedia Association in 2016. We 
created two web pages that summarize reasons 
to<http://wiki.dbpedia.org/why-is-dbpedia-so-important>_support DBpedia 
via donations_ <http://wiki.dbpedia.org/why-is-dbpedia-so-important> 
and<http://wiki.dbpedia.org/membership>_become a member_ 
<http://wiki.dbpedia.org/membership>.

*DBpedia in Dutch* (_http://nl.dbpedia.org_ <http://nl.dbpedia.org/>) is 
the first chapter which formalized an official DBpedia Chapter 
consortium. The cooperation was initiated by Koninklijke Bibliotheek 
(National Library of the Netherlands) and Huygens ING (research 
institute of History and Culture). Other partners like imec/Ghent 
University, the Netherlands Institute of Sound and Vision and the 
Network Institute (Vrije Universiteit) joined as well. This cooperation 
will strengthen the DBpedia Dutch chapter and community of contributors 
as well improve the cooperation with the Dutch research infrastructure 
and the Dutch Digital Heritage.

We are in intensive contact with the Japanese, the German and the 
Italian chapters to form official chapters and gain institutional 
support for DBpedia. You would like to know how to start a DBpedia 
chapter? Please check 
here:<http://wiki.dbpedia.org/about/language-chapters>_http://wiki.dbpedia.org/about/language-chapters_

*DBpedia Releases *- Since 2015 we provide bi-annual DBpedia releases. 
The latest 
one,<http://wiki.dbpedia.org/dbpedia-version-2016-04>_2016-04_ 
<http://wiki.dbpedia.org/dbpedia-version-2016-04>, featured a new 
Wikipedia references & citation dataset for the English Wikipedia. In 
addition, we separated the data which we received from heuristic-based 
infobox extractors from the already mapped and quality-controlled data 
to remove low quality data and avoid duplicates & low quality 
information. We improved on 
our<http://www.semantic-web-journal.net/content/wikidata-through-eyes-dbpedia-1>_Wikidata 
extraction_ 
<http://www.semantic-web-journal.net/content/wikidata-through-eyes-dbpedia-1> 
and mapped all our data to Wikidata-based DBpedia IRIs. Wikidata will 
become more and more the core of future extractions.

*Consortium partners for EU and national projects - *Since its 
conception DBpedia has never been funded directly, but was supported 
only by individual tasks in different projects and by the spirit of 
volunteers. With the establishment of the DBpedia Association, we are 
now in a position to receive direct funding and are eligible as a full 
consortium partner for EU and International projects. Furthermore, we 
are able to mediate trusted partners - who have worked with us in the 
past and contributed greatly to DBpedia - for national proposals in over 
30 countries worldwide (contact via reply to this email.)

*Events - *In addition to our participation in the 12th edition of the 
SEMANTiCS, in the 19th International Conference on Business Information 
Systems and in the Google Summer of Code project, we arranged three 
DBpedia community meetings, in The Hague, Leipzig and Sunnyvale, 
California. In order to get updates on our events and projects, stay 
tuned and check the<http://blog.dbpedia.org/>_DBpedia blog_ 
<http://blog.dbpedia.org/>. Please check out the dates to the two new 
DBpedia meetings below.

*Links - *We have revived the portal, that allows the LOD community to 
contribute their links, so we can include them in DBpedia Releases. If 
your database links to DBpedia, you can submit your links 
here:<https://github.com/dbpedia/links>_https://github.com/dbpedia/links_ 
. We provide additional support for this and also provide a service, 
that - once you have contributed your links - will tell you which data 
is linking to your knowledge base via 
DBpedia<http://downloads.dbpedia.org/links/backlinks/>_http://downloads.dbpedia.org/links/backlinks/_, 
available only for Association members.

/We would like to thank again all people who were involved to enable this!/


    *2017 - New Year - New Opportunities*

To make 2017 as great as 2016 we have already reviewed community 
feedback and worked out some plans to bring the DBpedia community closer 
together whereas we attain our goals and follow our visions. Below are 
the most important points for 2017.

*User Survey - *Sören Auer and the DBpedia Board prepared a survey to 
assess the direction of DBpedia and the DBpedia Association. We would 
like to know what you think should be our priorities. Please take a 
minute and vote 
here:<https://goo.gl/forms/NQxrMWskcKlZJAU63>_https://goo.gl/forms/NQxrMWskcKlZJAU63_

*User support *- We set up a new portal to streamline support requests 
for DBpedia. We would encourage you to submit all questions 
to<http://wiki.dbpedia.org/support>_http://wiki.dbpedia.org/support_.

And … if you are already an experienced DBpedia user, you can sign up 
and answer questions and get kudos. Upon request, we can issue a 
certificate for your CV. During the course of 2017 we will also provide 
a priority support channel for members and Chapters.

*Save the Date* *- Galway 21 Jun and Amsterdam 14 Sep*. DBpedia will be 
part of the_Language, Data and Knowledge (LDK) conference_ 
<http://ldk2017.org/> in Galway, Ireland (*Submission open until Feb 
16th*). This new biennial conference series aims at bringing together 
researchers from across disciplines. The DBpedia community will have a 
full day event on 21th of June 2017. Also during 
the<http://2017.semantics.cc/>_SEMANTiCS 2017 in Amsterdam_ 
<http://2017.semantics.cc/>, Sep 11-14 (*Submission open until May 17th 
or June 23rd*), the DBpedia community will get together on the 14th of 
September for a DBpedia community meeting. Updates will be posted in the 
respective<http://wiki.dbpedia.org/events>_events section_ 
<http://wiki.dbpedia.org/events> and the<http://blog.dbpedia.org/>_blog_ 
<http://blog.dbpedia.org/>.

*TextExt: DBpedia’s Open Text Extraction Challenge -* 
(_http://wiki.dbpedia.org/textext_) As DBpedia and Wikidata currently 
focus primarily on representing factual knowledge as contained in 
Wikipedia infoboxes, we created the DBpedia Open Text Extraction 
Challenge. Participants are asked to submit their engines that extract 
facts and knowledge from Wikipedia article texts to dramatically broaden 
and deepen the amount of structured DBpedia/Wikipedia data.

*Community coordination* - *You'd like to get involved in DBpedia? *We 
set up a new Get Involved section. If you are interested in details or 
would like to get in touch with the DBpedia community, please read 
here:<http://wiki.dbpedia.org/get-involved>_http://wiki.dbpedia.org/get-involved_

*Community chairs *- The active community of developers and engineers 
comes together in the DBpedia community committee. We will build up this 
committee with the help of Pablo Mendes and Magnus Knuth who will serve 
as provisional chairs. The committee can be joined by recommendation 
only based on merit. If you would like to get in contact with the 
community committee please check 
here:<http://wiki.dbpedia.org/about/contact>_http://wiki.dbpedia.org/about/contact_

Two delegates from the community committee are elected chairs and will 
take seats at the Board of Trustees. This board is the main 
decision-making body of the DBpedia Association and oversees the 
association and its work, as its ultimate corporate authority. There are 
four board meetings per year, please have a look at the public minutes 
here:<http://wiki.dbpedia.org/board-minutes>_http://wiki.dbpedia.org/board-minutes_

*Technical development I: Wikidata - *Many DBpedians are excited about 
the progress<https://www.wikidata.org/>_Wikidata_ 
<https://www.wikidata.org/> is making and we are planning to use 
Wikidata’s data as the new core for our extraction and fusion. This 
means that in future releases we will fuse data from Wikidata with the 
usual data we extract from over 100 Wikipedia language editions with 
additional data from other high quality LOD sources and do the usual 
refinement, typing and quality-control. We hope that this will provide 
an unprecedented knowledge graph with superior coverage, completeness 
and correctness.

*Technical development II: UnifiedViews - *our plan to achieve the above 
mentioned fusion will be realized by an active collaboration with 
the<https://www.semantic-web.at/>_Semantic Web Company (SWC)_ 
<https://www.semantic-web.at/>, where DBpedia developers work side by 
side with the<http://www.poolparty.biz/>_PoolParty Semantic Suite_ 
<http://www.poolparty.biz/> technical team to add scalability, 
provenance tracking and linking/fusion capabilities into the Data 
Processing Units of 
the<https://www.poolparty.biz/unifiedviews/>_UnifiedViews_ 
<https://www.poolparty.biz/unifiedviews/> workflows.

*Technical development III - *For 2017, we hope to establish further 
hands-on collaboration with companies and organisations to push all 
aspects of DBpedia, in particular: search and visualisation, ontology 
maintenance, querying and indexing crawling data from web and social 
media. We also work together with our members to prioritize on 
integrating data that they think useful.

*Membership* - If you would like to become a member of the DBpedia 
Association, please check all benefits 
here:<http://wiki.dbpedia.org/membership>_http://wiki.dbpedia.org/membership_.

If you require any further information, feel free to contact us by 
replying to this email. We are already very excited to spend time with 
you on further community meetings and to publish new DBpedia releases.

All the best,

Julia, Dimitris & Sebastian

DBpedia Association

[Obo-phenotype] SEMANTiCS 2017, Amsterdam, Sep 11-14, Open Calls

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

Apologies for cross-posting

Call for Papers, Posters & Workshops
SEMANTiCS 2017 - The Linked Data Conference
13th International Conference on Semantic Systems

Amsterdam, Netherlands
September 11 -14, 2017
http://2017.semantics.cc

For details please go to: https://2017.semantics.cc/calls

Important Dates (Research & Innovation):
*Abstract Submission Deadline:       May 17, 2017 (11:59 pm, Hawaii time)
*Paper Submission Deadline:          May 24, 2017 (11:59 pm, Hawaii time)
*Notification of Acceptance:         July 3, 2017 (11:59 pm, Hawaii time)
*Camera-Ready Paper:                 August 14, 2017 (11:59 pm, Hawaii time)

Important Dates (Workshops & Tutorials):
*Submission of Proposals for Workshops with Call for Papers: March 31, 
2017 (23:59 Hawaii Time)
*Submission of Proposals for Tutorials and Workshops without Call for 
Papers: June 30, 2017 (23:59 Hawaii Time)
*Workshop Proposals Notification of Acceptance: April 13, 2017 (23:59 
Hawaii Time)
*Workshop Website/Call for Papers Online: April 30, 2017 (23:59 Hawaii Time)
*Workshop Camera-Ready Proceedings:  September 4, 2017 (23:59 Hawaii Time)
*SEMANTiCS 2017 Workshop & Tutorial Days: September 11 and 14, 2017

As in the previous years, SEMANTiCS’17 proceedings will be published by 
ACM ICPS (pending) and CEUR WS proceedings.

SEMANTiCS 2017 will especially welcome submissions for the following hot 
topics:
*Data Science (special track, see below)
*Web Semantics, Linked (Open) Data & schema.org
*Corporate Knowledge Graphs
*Knowledge Integration and Language Technologies
*Data Quality Management
*Economics of Data, Data Services and Data Ecosystems

Following the success of previous years, the ‘horizontals’ (research) 
and ‘verticals’ (industries) below are of interest for the conference:

Horizontals:
*Enterprise Linked Data & Data Integration
*Knowledge Discovery & Intelligent Search
*Business Models, Governance & Data Strategies
*Semantics in Big Data
*Text Analytics
*Data Portals & Knowledge Visualization
*Semantic Information Management
*Document Management & Content Management
*Terminology, Thesaurus & Ontology Management
*Smart Connectivity, Networking & Interlinking
*Smart Data & Semantics in IoT
*Semantics for IT Safety & Security
*Semantic Rules, Policies & Licensing
*Community, Social & Societal Aspects

Data Science Special Track Horizontals:
*Large-Scale Data Processing (stream processing, handling large-scale 
graphs)
*Data Analytics (Machine Learning, Predictive Analytics, Network Analytics)
*Communicating Data (Data Visualization, UX & Interaction Design, 
Crowdsourcing)
*Cross-cutting Issues (Ethics, Privacy, Security, Provenance)

Verticals:
*Industry & Engineering
*Life Sciences & Health Care
*Public Administration
*e-Science
*Digital Humanities
*Galleries, Libraries, Archives & Museums (GLAM)
*Education & eLearning
*Media & Data Journalism
*Publishing, Marketing & Advertising
*Tourism & Recreation
*Financial & Insurance Industry
*Telecommunication & Mobile Services
*Sustainable Development: Climate, Water, Air, Ecology
*Energy, Smart Homes & Smart Grids
*Food, Agriculture & Farming
*Safety, Security & Privacy
*Transport, Environment & Geospatial

For call details please go to: https://2017.semantics.cc/calls

[Obo-phenotype] SEMANTiCS 2017, Amsterdam, Sep 11-14, 2nd Call for Research & Innovation Papers

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

Apologies for cross-posting

2nd Call for Research & Innovation Papers
SEMANTiCS 2017 - The Linked Data Conference
13th International Conference on Semantic Systems

Amsterdam, Netherlands
September 11 -14, 2017
http://2017.semantics.cc

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 lenght for full papers and 4 pages for short 
papers, including references and optional appendices.
Research & Innovation Papers are published within ACM ICP Series.

Important Dates (Research & Innovation)
     Abstract Submission Deadline:           May 17, 2017 (11:59 pm, 
Hawaii time)
     Paper Submission Deadline:            May 24, 2017 (11:59 pm, 
Hawaii time)
     Notification of Acceptance:             July 3, 2017 (11:59 pm, 
Hawaii time)
     Camera-Ready Paper:                     August 14, 2017 (11:59 pm, 
Hawaii time)

For details please go to: https://2017.semantics.cc/calls
or contact the Research and Innovation Chairs:
     Catherine Faron Zucker, faron [@] i3s.unice.fr, Université Nice 
Sophia Antipolis
     Rinke Hoekstra, rinke.hoekstra [@] vu.nl, Vrije Universiteit 
Amsterdam/University of Amsterdam

As in the previous years, SEMANTiCS’17 proceedings will be published by 
ACM ICP (pending).

SEMANTiCS 2017 will especially welcome submissions for the following hot 
topics:
*Data Science (special track, see below)
*Web Semantics, Linked (Open) Data & schema.org
*Corporate Knowledge Graphs
*Knowledge Integration and Language Technologies
*Data Quality Management
*Economics of Data, Data Services and Data Ecosystems

Following the success of previous years, the ‘horizontals’ (research) 
and ‘verticals’ (industries) below are of interest for the conference:

Horizontals
*Enterprise Linked Data & Data Integration
*Knowledge Discovery & Intelligent Search
*Business Models, Governance & Data Strategies
*Semantics in Big Data
*Text Analytics
*Data Portals & Knowledge Visualization
*Semantic Information Management
*Document Management & Content Management
*Terminology, Thesaurus & Ontology Management
*Smart Connectivity, Networking & Interlinking
*Smart Data & Semantics in IoT
*Semantics for IT Safety & Security
*Semantic Rules, Policies & Licensing
*Community, Social & Societal Aspects

Data Science Special Track Horizontals
*arge-Scale Data Processing (stream processing, handling large-scale graphs)
*Data Analytics (Machine Learning, Predictive Analytics, Network Analytics)
*Communicating Data (Data Visualization, UX & Interaction Design, 
Crowdsourcing)
*Cross-cutting Issues (Ethics, Privacy, Security, Provenance)

Verticals
*Industry & Engineering
*Life Sciences & Health Care
*Public Administration
*e-Science
*Digital Humanities
*Galleries, Libraries, Archives & Museums (GLAM)
*Education & eLearning
*Media & Data Journalism
*Publishing, Marketing & Advertising
*Tourism & Recreation
*Financial & Insurance Industry
*Telecommunication & Mobile Services
*Sustainable Development: Climate, Water, Air, Ecology
*Energy, Smart Homes & Smart Grids
*Food, Agriculture & Farming
*Safety, Security & Privacy
*Transport, Environment & Geospatial

For details please go to: https://2017.semantics.cc/calls

[Obo-phenotype] SEMANTiCS 2017, Amsterdam, Sep 11-14, Call for Research & Innovation Papers

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

Call for Research & Innovation Papers
SEMANTiCS 2017 - The Linked Data Conference
13th International Conference on Semantic Systems

Amsterdam, Netherlands
September 11 -14, 2017
http://2017.semantics.cc

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 lenght for full papers and 4 pages for short 
papers, including references and optional appendices.
Research & Innovation Papers are published within ACM ICP Series.

Important Dates (Research & Innovation)
     Abstract Submission Deadline:           May 17, 2017 (11:59 pm, 
Hawaii time)
     Paper Submission Deadline:                May 24, 2017 (11:59 pm, 
Hawaii time)
     Notification of Acceptance:             July 3, 2017 (11:59 pm, 
Hawaii time)
     Camera-Ready Paper:                     August 14, 2017 (11:59 pm, 
Hawaii time)

For details please go to: https://2017.semantics.cc/calls
or contact the Research and Innovation Chairs:
     Catherine Faron Zucker, faron [@] i3s.unice.fr, Université Nice 
Sophia Antipolis
     Rinke Hoekstra, rinke.hoekstra [@] vu.nl, Vrije Universiteit 
Amsterdam/University of Amsterdam

As in the previous years, SEMANTiCS’17 proceedings will be published by 
ACM ICP (pending).

SEMANTiCS 2017 will especially welcome submissions for the following hot 
topics:
*Data Science (special track, see below)
*Web Semantics, Linked (Open) Data & schema.org
*Corporate Knowledge Graphs
*Knowledge Integration and Language Technologies
*Data Quality Management
*Economics of Data, Data Services and Data Ecosystems

Following the success of previous years, the ‘horizontals’ (research) 
and ‘verticals’ (industries) below are of interest for the conference:

Horizontals
*Enterprise Linked Data & Data Integration
*Knowledge Discovery & Intelligent Search
*Business Models, Governance & Data Strategies
*Semantics in Big Data
*Text Analytics
*Data Portals & Knowledge Visualization
*Semantic Information Management
*Document Management & Content Management
*Terminology, Thesaurus & Ontology Management
*Smart Connectivity, Networking & Interlinking
*Smart Data & Semantics in IoT
*Semantics for IT Safety & Security
*Semantic Rules, Policies & Licensing
*Community, Social & Societal Aspects

Data Science Special Track Horizontals
*arge-Scale Data Processing (stream processing, handling large-scale graphs)
*Data Analytics (Machine Learning, Predictive Analytics, Network Analytics)
*Communicating Data (Data Visualization, UX & Interaction Design, 
Crowdsourcing)
*Cross-cutting Issues (Ethics, Privacy, Security, Provenance)

Verticals
*Industry & Engineering
*Life Sciences & Health Care
*Public Administration
*e-Science
*Digital Humanities
*Galleries, Libraries, Archives & Museums (GLAM)
*Education & eLearning
*Media & Data Journalism
*Publishing, Marketing & Advertising
*Tourism & Recreation
*Financial & Insurance Industry
*Telecommunication & Mobile Services
*Sustainable Development: Climate, Water, Air, Ecology
*Energy, Smart Homes & Smart Grids
*Food, Agriculture & Farming
*Safety, Security & Privacy
*Transport, Environment & Geospatial

For details please go to: https://2017.semantics.cc/calls

Re: [Obo-phenotype] [Obo-discuss] Phenomics Conference Grant Endorsement

[Melissa H. <ha...@oh...>]

Thank you Philippe,
This is all very relevant; also related is evidence of (G+E)2P associations - we are already trying to work to align clinGen and OBO efforts in this area, but there are many others. I too would like to see OBO-discuss be more of a community forum as well. I don’t know the answer wrt how to reign in all the listserves and communities but hopefully we can find a way to do that under the umbrella focus of phenomics :-).

Cheers,
Melissa

On Nov 18, 2016, at 11:37 AM, Philippe <pro...@gm...<mailto:pro...@gm...>> wrote:

Absolutely. In fact, this is very timely and bearing in mind that efforts such as GA4GH have endorsed the phenopackets.org<http://phenopackets.org> approach validates the works.
>From the obofoundry standpoint, it is high time that coordination occurs when it comes when it comes to reporting 'treatment', 'intervention' and the likes.
I have already expressed my concerns about having species specific ontologies being developed for reporting stressors (plant experimental conditions ontology, zebrafish experimental conditions)... While I appreciate there are specifics, we need to develop a generic framework to express those.
Furthermore, as efforts such as OBI or BAO or Clinical Measurement ontology also provide a range of classes of direct relevance to these issues, a broad cross talk is needed
I have gathered from Chris that work in progress on this front.
It would be great to see and have more discussions about this topic on list to engage with our community, identify, contribute use cases + acceptance tests.

By all means, a great initiative. Let's make obo-discuss active again

Best wishes

Philippe

On 18/11/2016 17:00, Jaiswal, Pankaj - OSU wrote:

On 11/18/2016 8:23 AM, Melissa Haendel wrote:
However, as this is an NIH proposal, we necessarily need to focus on
things that can be conceived of as biomedical in nature.
This is an excellent area and I would suggest that many of the
biomedical states/conditions in terms of phenotypes are associated with
the food, nutrition and environment. Therefore, it is essential that NIH
starts recognizing plants and derived food,  nutrition and active bio
entities/drugs, medications as part of learning about processes and
diseases essential to biomedical research. This does not leave
environment where we as humans can't survive without plants. Therefore,
when we talk of biomedical research we often are looking at the
downstream events, but we need to look upstream in the process to solve
problems including many of the genetic and phenotype dispositions
associated with quality and quantity of food. Thus  plants are core to
this supply chain to sustain and maintain a healthy diet, calories and
nutrition, for everything in the food chain.

We will be happy to help.

Pankaj




Melissa Haendel, PhD
Associate Professor
Library & Dept. of Medical Informatics and Clinical Epidemiology
ha...@oh...<mailto:ha...@oh...>
503-407-5970
www.monarchinitiative.org<http://www.monarchinitiative.org>

Appointments: Shanez De Silva
de...@oh...<mailto:de...@oh...>

Re: [Obo-phenotype] [Obo-discuss] Phenomics Conference Grant Endorsement

[Melissa H. <ha...@oh...>]

Yes to all of this!

On Nov 18, 2016, at 11:28 AM, Ramona Walls <rlw...@gm...<mailto:rlw...@gm...>> wrote:

Here, here, Pankaj!

------------------------------------------------------
Ramona L. Walls, Ph.D.
Senior Scientific Analyst, CyVerse, University of Arizona
Research Associate, Bio5 Institute, University of Arizona

On Fri, Nov 18, 2016 at 11:00 AM, Jaiswal, Pankaj - OSU <jai...@sc...<mailto:jai...@sc...>> wrote:


On 11/18/2016 8:23 AM, Melissa Haendel wrote:
However, as this is an NIH proposal, we necessarily need to focus on things that can be conceived of as biomedical in nature.

This is an excellent area and I would suggest that many of the biomedical states/conditions in terms of phenotypes are associated with the food, nutrition and environment. Therefore, it is essential that NIH starts recognizing plants and derived food,  nutrition and active bio entities/drugs, medications as part of learning about processes and diseases essential to biomedical research. This does not leave environment where we as humans can't survive without plants. Therefore, when we talk of biomedical research we often are looking at the downstream events, but we need to look upstream in the process to solve problems including many of the genetic and phenotype dispositions associated with quality and quantity of food. Thus  plants are core to this supply chain to sustain and maintain a healthy diet, calories and nutrition, for everything in the food chain.

We will be happy to help.

Pankaj


--
Pankaj Jaiswal, PhD
President, OSU Chapter Phi Kappa Phi
Associate Professor
Dept. of Botany and Plant Pathology
2082 Cordley Hall
Oregon State University
Corvallis, OR, 97331
USA

Ph.: +1-541-737-8471<tel:%2B1-541-737-8471>
Fax: +1-541-737-3573<tel:%2B1-541-737-3573>
email: jai...@or...<mailto:jai...@or...>
Web: http://jaiswallab.cgrb.oregonstate.edu<http://jaiswallab.cgrb.oregonstate.edu/>
     http://icbo-conference.org<http://icbo-conference.org/>
     http://phikappaphi.oregonstate.edu<http://phikappaphi.oregonstate.edu/>



Melissa Haendel, PhD
Associate Professor
Library & Dept. of Medical Informatics and Clinical Epidemiology
ha...@oh...<mailto:ha...@oh...>
503-407-5970
www.monarchinitiative.org<http://www.monarchinitiative.org>

Appointments: Shanez De Silva
de...@oh...<mailto:de...@oh...>

Re: [Obo-phenotype] [Obo-discuss] Phenomics Conference Grant Endorsement

[Ramona W. <rlw...@gm...>]

Here, here, Pankaj!

------------------------------------------------------
Ramona L. Walls, Ph.D.
Senior Scientific Analyst, CyVerse, University of Arizona
Research Associate, Bio5 Institute, University of Arizona

On Fri, Nov 18, 2016 at 11:00 AM, Jaiswal, Pankaj - OSU <
jai...@sc...> wrote:

>
>
> On 11/18/2016 8:23 AM, Melissa Haendel wrote:
>
>> However, as this is an NIH proposal, we necessarily need to focus on
>> things that can be conceived of as biomedical in nature.
>>
>
> This is an excellent area and I would suggest that many of the biomedical
> states/conditions in terms of phenotypes are associated with the food,
> nutrition and environment. Therefore, it is essential that NIH starts
> recognizing plants and derived food,  nutrition and active bio
> entities/drugs, medications as part of learning about processes and
> diseases essential to biomedical research. This does not leave environment
> where we as humans can't survive without plants. Therefore, when we talk of
> biomedical research we often are looking at the downstream events, but we
> need to look upstream in the process to solve problems including many of
> the genetic and phenotype dispositions associated with quality and quantity
> of food. Thus  plants are core to this supply chain to sustain and maintain
> a healthy diet, calories and nutrition, for everything in the food chain.
>
> We will be happy to help.
>
> Pankaj
>
>
> --
> Pankaj Jaiswal, PhD
> President, OSU Chapter Phi Kappa Phi
> Associate Professor
> Dept. of Botany and Plant Pathology
> 2082 Cordley Hall
> Oregon State University
> Corvallis, OR, 97331
> USA
>
> Ph.: +1-541-737-8471
> Fax: +1-541-737-3573
> email: jai...@or...
> Web: http://jaiswallab.cgrb.oregonstate.edu
>      http://icbo-conference.org
>      http://phikappaphi.oregonstate.edu
>
>

Re: [Obo-phenotype] [Obo-discuss] Phenomics Conference Grant Endorsement

[Jaiswal, P. - O. <jai...@sc...>]

On 11/18/2016 8:23 AM, Melissa Haendel wrote:
> However, as this is an NIH proposal, we necessarily need to focus on 
> things that can be conceived of as biomedical in nature. 

This is an excellent area and I would suggest that many of the 
biomedical states/conditions in terms of phenotypes are associated with 
the food, nutrition and environment. Therefore, it is essential that NIH 
starts recognizing plants and derived food,  nutrition and active bio 
entities/drugs, medications as part of learning about processes and 
diseases essential to biomedical research. This does not leave 
environment where we as humans can't survive without plants. Therefore, 
when we talk of biomedical research we often are looking at the 
downstream events, but we need to look upstream in the process to solve 
problems including many of the genetic and phenotype dispositions 
associated with quality and quantity of food. Thus  plants are core to 
this supply chain to sustain and maintain a healthy diet, calories and 
nutrition, for everything in the food chain.

We will be happy to help.

Pankaj


-- 
Pankaj Jaiswal, PhD
President, OSU Chapter Phi Kappa Phi
Associate Professor
Dept. of Botany and Plant Pathology
2082 Cordley Hall
Oregon State University
Corvallis, OR, 97331
USA

Ph.: +1-541-737-8471
Fax: +1-541-737-3573
email: jai...@or...
Web: http://jaiswallab.cgrb.oregonstate.edu
      http://icbo-conference.org
      http://phikappaphi.oregonstate.edu

Re: [Obo-phenotype] [Obo-discuss] Phenomics Conference Grant Endorsement

[Melissa H. <ha...@oh...>]

Sorry reading backwards,

Yes Ramona it will - the idea is to coalesce all phenomics informatics. However, as this is an NIH proposal, we necessarily need to focus on things that can be conceived of as biomedical in nature. That said we definitely want to continue to unite phenomics informatics from the biodiversity, evolution, plant, and veterinary and livestock communities. Also, we plan to engage other agencies with support letters to support this notion as well.

Do you think we should get a separate letter from Cyverse? Anyone else who wants to write a separate letter we’d be grateful, we will be targeting some of you but really will be delighted to include any and all letters, there is no limit.

Thanks again!
Melissa


On Nov 18, 2016, at 10:01 AM, Ramona Walls <rlw...@gm...<mailto:rlw...@gm...>> wrote:

I also agree this is a good idea. Will it extend beyond the biomedical arena (i.e. human and model species phenotypes)? There is a huge amount of plant phenotype data being collected from sensors now, and I would hate to see a completely different framework evolve for plants and animals. Also, CyVerse is actively pursuing infrastructure for phenotype data, and we would be happy to be a part of this discussion for both plants and animals.

Ramona

------------------------------------------------------
Ramona L. Walls, Ph.D.
Senior Scientific Analyst, CyVerse, University of Arizona
Research Associate, Bio5 Institute, University of Arizona

On Thu, Nov 17, 2016 at 7:53 PM, Peter Robinson <Pet...@ja...<mailto:Pet...@ja...>> wrote:
thanks for the support Lynn!
-Peter

Peter Robinson
Professor of Computational Biology
The Jackson Laboratory for Genomic Medicine
10 Discovery Drive
Farmington, CT 06032
860.837.2095<tel:860.837.2095> t | 860.990.3130<tel:860.990.3130> m
pet...@ja...<mailto:pet...@ja...>
www.jax.org<http://www.jax.org/>

The Jackson Laboratory: Leading the search for tomorrow's cures


________________________________________
From: Lynn Schriml <lyn...@gm...<mailto:lyn...@gm...>>
Sent: Thursday, November 17, 2016 7:42 PM
To: Chris Mungall
Cc: obo...@li...<mailto:obo...@li...> list; obo...@li...<mailto:obo...@li...>
Subject: Re: [Obo-discuss] [Obo-phenotype] Phenomics Conference Grant   Endorsement

Hello Chris,
  Great idea.
Is there a google doc to sign ?
How will the workshop link in disease ?
  Connecting across genotype, phenotype, environment and disease would be great !!
And DO could contribute to these efforts, and extend our HPO and DO connections.  And this would tie in well with our molecular subtyping  projects.

Cheers,
Lynn

Sent from my iPhone

> On Nov 17, 2016, at 5:39 PM, Chris Mungall <cjm...@lb...<mailto:cjm...@lb...>> wrote:
>
> Hi all,
>
> I'm writing to request a signature for a letter of support from members
> of the OBO community.
>
> Melissa Haendel and Peter Robinson are preparing to submit a proposal in
> response to RFA-CA-16-020 “BD2K Support for Meetings of Data Science
> Related Organizations (U13)”
> (https://grants.nih.gov/grants/guide/rfa-files/RFA-CA-16-020.html) in
> which they outline a series of conferences and community gatherings to
> coalesce phenomics informatics data structures, ontologies, algorithms,
> and tools.
>
> Despite the advances in search engine and text mining technologies for
> other types of data, phenomics data is surprisingly hard to harness due
> to the scope and heterogeneity of phenotype standards and terminologies.
> Such barriers have made it a significant challenge to link and integrate
> with the necessary precision and richness for mechanistic discovery for
> precision medicine. Further, there are also crucial gaps for which new
> standards and tooling have yet to be developed. The phenomics community
> has been working towards addressing these issues within a diversity of
> areas, but to date in an insufficiently coordinated way. This is where
> we need to learn from each other and advance the field with unity. A
> series of conferences and hands-on workshops to bring people together to
> share ideas, techniques and evolve technologies is very timely in the
> eras of big data and genomic medicine, where sophisticated informatics
> is needed to address the relationship between phenotype and genotype,
> environment, medical care, and treatments. Finally, how we represent
> evidence and provenance of this information will be needed to support
> clinically actionable mechanistic outcomes that will come with the
> ‘omics revolution.
>
> Please consider signing the letter of support here:
> https://www.surveymonkey.com/r/K9TYYCV
>
> Thanks,
> Chris
>
> ------------------------------------------------------------------------------
> _______________________________________________
> Obo-phenotype mailing list
> Obo...@li...<mailto:Obo...@li...>
> https://lists.sourceforge.net/lists/listinfo/obo-phenotype

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---

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Obo...@li...<mailto:Obo...@li...>
https://lists.sourceforge.net/lists/listinfo/obo-discuss

------------------------------------------------------------------------------
_______________________________________________
Obo-phenotype mailing list
Obo...@li...<mailto:Obo...@li...>
https://lists.sourceforge.net/lists/listinfo/obo-phenotype

Melissa Haendel, PhD
Associate Professor
Library & Dept. of Medical Informatics and Clinical Epidemiology
ha...@oh...<mailto:ha...@oh...>
503-407-5970
www.monarchinitiative.org<http://www.monarchinitiative.org>

Appointments: Shanez De Silva
de...@oh...<mailto:de...@oh...>

Re: [Obo-phenotype] [Obo-discuss] Phenomics Conference Grant Endorsement

[Melissa H. <ha...@oh...>]

Yes thanks to all of you! It will really help the Foundry community to have funds to get together more often around these topics. Please help us get it funded, its is for all of us :-).


On Nov 17, 2016, at 7:53 PM, Peter Robinson <Pet...@ja...<mailto:Pet...@ja...>> wrote:

thanks for the support Lynn!
-Peter

Peter Robinson
Professor of Computational Biology
The Jackson Laboratory for Genomic Medicine
10 Discovery Drive
Farmington, CT 06032
860.837.2095 t | 860.990.3130 m
pet...@ja...<mailto:pet...@ja...>
www.jax.org

The Jackson Laboratory: Leading the search for tomorrow's cures


________________________________________
From: Lynn Schriml <lyn...@gm...>
Sent: Thursday, November 17, 2016 7:42 PM
To: Chris Mungall
Cc: obo...@li... list; obo...@li...
Subject: Re: [Obo-discuss] [Obo-phenotype] Phenomics Conference Grant   Endorsement

Hello Chris,
 Great idea.
Is there a google doc to sign ?
How will the workshop link in disease ?
 Connecting across genotype, phenotype, environment and disease would be great !!
And DO could contribute to these efforts, and extend our HPO and DO connections.  And this would tie in well with our molecular subtyping  projects.

Cheers,
Lynn

Sent from my iPhone

On Nov 17, 2016, at 5:39 PM, Chris Mungall <cjm...@lb...> wrote:

Hi all,

I'm writing to request a signature for a letter of support from members
of the OBO community.

Melissa Haendel and Peter Robinson are preparing to submit a proposal in
response to RFA-CA-16-020 “BD2K Support for Meetings of Data Science
Related Organizations (U13)”
(https://grants.nih.gov/grants/guide/rfa-files/RFA-CA-16-020.html) in
which they outline a series of conferences and community gatherings to
coalesce phenomics informatics data structures, ontologies, algorithms,
and tools.

Despite the advances in search engine and text mining technologies for
other types of data, phenomics data is surprisingly hard to harness due
to the scope and heterogeneity of phenotype standards and terminologies.
Such barriers have made it a significant challenge to link and integrate
with the necessary precision and richness for mechanistic discovery for
precision medicine. Further, there are also crucial gaps for which new
standards and tooling have yet to be developed. The phenomics community
has been working towards addressing these issues within a diversity of
areas, but to date in an insufficiently coordinated way. This is where
we need to learn from each other and advance the field with unity. A
series of conferences and hands-on workshops to bring people together to
share ideas, techniques and evolve technologies is very timely in the
eras of big data and genomic medicine, where sophisticated informatics
is needed to address the relationship between phenotype and genotype,
environment, medical care, and treatments. Finally, how we represent
evidence and provenance of this information will be needed to support
clinically actionable mechanistic outcomes that will come with the
‘omics revolution.

Please consider signing the letter of support here:
https://www.surveymonkey.com/r/K9TYYCV

Thanks,
Chris

------------------------------------------------------------------------------
_______________________________________________
Obo-phenotype mailing list
Obo...@li...
https://lists.sourceforge.net/lists/listinfo/obo-phenotype

------------------------------------------------------------------------------
_______________________________________________
Obo-discuss mailing list
Obo...@li...
https://lists.sourceforge.net/lists/listinfo/obo-discuss
---

The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.


------------------------------------------------------------------------------
_______________________________________________
Obo-discuss mailing list
Obo...@li...
https://lists.sourceforge.net/lists/listinfo/obo-discuss

Melissa Haendel, PhD
Associate Professor
Library & Dept. of Medical Informatics and Clinical Epidemiology
ha...@oh...<mailto:ha...@oh...>
503-407-5970
www.monarchinitiative.org<http://www.monarchinitiative.org>

Appointments: Shanez De Silva
de...@oh...<mailto:de...@oh...>

Re: [Obo-phenotype] [Obo-discuss] Phenomics Conference Grant Endorsement

[Ramona W. <rlw...@gm...>]

I also agree this is a good idea. Will it extend beyond the biomedical
arena (i.e. human and model species phenotypes)? There is a huge amount of
plant phenotype data being collected from sensors now, and I would hate to
see a completely different framework evolve for plants and animals. Also,
CyVerse is actively pursuing infrastructure for phenotype data, and we
would be happy to be a part of this discussion for both plants and animals.

Ramona

------------------------------------------------------
Ramona L. Walls, Ph.D.
Senior Scientific Analyst, CyVerse, University of Arizona
Research Associate, Bio5 Institute, University of Arizona

On Thu, Nov 17, 2016 at 7:53 PM, Peter Robinson <Pet...@ja...>
wrote:

> thanks for the support Lynn!
> -Peter
>
> Peter Robinson
> Professor of Computational Biology
> The Jackson Laboratory for Genomic Medicine
> 10 Discovery Drive
> Farmington, CT 06032
> 860.837.2095 t | 860.990.3130 m
> pet...@ja...
> www.jax.org
>
> The Jackson Laboratory: Leading the search for tomorrow's cures
>
>
> ________________________________________
> From: Lynn Schriml <lyn...@gm...>
> Sent: Thursday, November 17, 2016 7:42 PM
> To: Chris Mungall
> Cc: obo...@li... list;
> obo...@li...
> Subject: Re: [Obo-discuss] [Obo-phenotype] Phenomics Conference Grant
>  Endorsement
>
> Hello Chris,
>   Great idea.
> Is there a google doc to sign ?
> How will the workshop link in disease ?
>   Connecting across genotype, phenotype, environment and disease would be
> great !!
> And DO could contribute to these efforts, and extend our HPO and DO
> connections.  And this would tie in well with our molecular subtyping
> projects.
>
> Cheers,
> Lynn
>
> Sent from my iPhone
>
> > On Nov 17, 2016, at 5:39 PM, Chris Mungall <cjm...@lb...> wrote:
> >
> > Hi all,
> >
> > I'm writing to request a signature for a letter of support from members
> > of the OBO community.
> >
> > Melissa Haendel and Peter Robinson are preparing to submit a proposal in
> > response to RFA-CA-16-020 “BD2K Support for Meetings of Data Science
> > Related Organizations (U13)”
> > (https://grants.nih.gov/grants/guide/rfa-files/RFA-CA-16-020.html) in
> > which they outline a series of conferences and community gatherings to
> > coalesce phenomics informatics data structures, ontologies, algorithms,
> > and tools.
> >
> > Despite the advances in search engine and text mining technologies for
> > other types of data, phenomics data is surprisingly hard to harness due
> > to the scope and heterogeneity of phenotype standards and terminologies.
> > Such barriers have made it a significant challenge to link and integrate
> > with the necessary precision and richness for mechanistic discovery for
> > precision medicine. Further, there are also crucial gaps for which new
> > standards and tooling have yet to be developed. The phenomics community
> > has been working towards addressing these issues within a diversity of
> > areas, but to date in an insufficiently coordinated way. This is where
> > we need to learn from each other and advance the field with unity. A
> > series of conferences and hands-on workshops to bring people together to
> > share ideas, techniques and evolve technologies is very timely in the
> > eras of big data and genomic medicine, where sophisticated informatics
> > is needed to address the relationship between phenotype and genotype,
> > environment, medical care, and treatments. Finally, how we represent
> > evidence and provenance of this information will be needed to support
> > clinically actionable mechanistic outcomes that will come with the
> > ‘omics revolution.
> >
> > Please consider signing the letter of support here:
> > https://www.surveymonkey.com/r/K9TYYCV
> >
> > Thanks,
> > Chris
> >
> > ------------------------------------------------------------
> ------------------
> > _______________________________________________
> > Obo-phenotype mailing list
> > Obo...@li...
> > https://lists.sourceforge.net/lists/listinfo/obo-phenotype
>
> ------------------------------------------------------------
> ------------------
> _______________________________________________
> Obo-discuss mailing list
> Obo...@li...
> https://lists.sourceforge.net/lists/listinfo/obo-discuss
> ---
>
> The information in this email, including attachments, may be confidential
> and is intended solely for the addressee(s). If you believe you received
> this email by mistake, please notify the sender by return email as soon as
> possible.
>
>
> ------------------------------------------------------------
> ------------------
> _______________________________________________
> Obo-discuss mailing list
> Obo...@li...
> https://lists.sourceforge.net/lists/listinfo/obo-discuss
>