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From: Alexander D. <add...@gm...> - 2023-06-29 20:53:19
|
The *7th International Cells in Experimental Life Science Workshop**, CELLS 2023 <https://sites.google.com/view/cells2023/home>,* will be held in hybrid format in conjunction with the *14th International Conference on Biomedical Ontology, ICBO 2023 <https://www.icbo2023.ncor-brasil.org>,* on August 29, 2023. In person participation will occur at ICBO 2023, held at the University of Brasilia, Brazil, with online participation via Zoom. CELLS 2023 Workshop Themes (i) knowledge representation for newly-discovered and known cell types, particularly in light of single cell RNA sequencing data and other high-throughput data types (ii) understanding the relationships of cell types to their anatomical contexts (iii) the use of machine learning approaches for automatically assigning cell type data to ontology classes (iv) knowledge representation of cell types in disease states (v) evolutionary and differentiation relationships among cell types Submission Formats for CELLS 2023 (i) abstracts or extended abstracts (1-3 pages) for presentations (ii) papers (5-10 pages) Important Dates July 23, 2023 – Deadline for abstracts, extended abstracts, or paper submissions July 30, 2023 – Notification of acceptances August 29, 2023 – CELLS 2023 Workshop held as hybrid event (13:30 – 17:45 BRT, 12:30 pm - 4:45 pm EDT, 9:30 am - 1:45 pm PDT, 5:30 pm - 9:45 pm BST, 6:30 pm -10:45 pm CEST) We are soliciting abstracts, extended abstracts, and papers for presentations at CELLS 2023. Acceptance will be based on scientific content, not length, and authors may present in person or via Zoom. See website <https://sites.google.com/view/cells2023/home> for detailed instructions. Organizers: Alexander D. Diehl, University at Buffalo Yongqun "Oliver" He, University of Michigan David Osumi-Sutherland, EMBL-EBI Tiago Lubiana, University of São Paulo Feel free to email me with comments or questions. Thanks, Alex -- Alexander D. Diehl, Ph.D., Associate Professor Department of Biomedical Informatics Jacobs School of Medicine and Biomedical Sciences University at Buffalo, The State University of New York Buffalo, NY 14203 email: ad...@bu... |
From: Selja S. <sel...@gm...> - 2022-11-22 16:19:50
|
_______________________________________________ bioportal-announce mailing list bio...@li... https://mailman.stanford.edu/mailman/listinfo/bioportal-announce |
From: Alexander D. <add...@gm...> - 2021-07-21 06:49:00
|
*Call for Abstracts, 5th International Cells in Experimental Life Science Workshop, CELLS 2021 <https://sites.google.com/view/cells-2021-workshop/home>* A virtual workshop associated with *ICBO 2021 <https://icbo2021.inf.unibz.it/>* and *JOWO 2021 <https://www.iaoa.org/jowo/2021/index.html>* Date: September 15th, 2021, 10 am - 1 pm EDT (USA), 3 - 6 pm BST, 4 - 7 pm CEST We are seeking abstracts and extended abstracts for presentation at CELLS 2021. This is a great opportunity to highlight recent work on using ontologies for representation of cell-level knowledge. *_CELLS 2021 Workshop Themes_* (i) knowledge representation for newly-discovered and known cell types, particularly in light of single cell RNA sequencing data (ii) knowledge representation of cell types in disease states (iii) representation of homologous cell types across species (iv) identification and representation of cell types of importance as targets of SARS-CoV2 infection and in the immune response during COVID-19 *_Background_* Current high throughput methods such as single cell RNA sequencing and flow and mass cytometry are producing a large amount of data related to existing and novel cell types in health and disease. At the same time, experimental approaches such as microscopy, genomics, and metabolomics are expanding understanding of cellular functioning in relation to neighboring cells and the whole organism. Ontologies are being increasingly used as a tool for integrating and analyzing these diverse data types. The Cell Ontology (CL) and Cell Line Ontology (CLO) have long been established as reference ontologies in the OBO framework for representing cell type information, and additional ontologies such as the Gene Ontology, Protein Ontology, and the Ontology for Biomedical Investigation are also important for representing not only experimental data about cell types but also the methods used to produce that data. There is a continuing need for improve automated analysis techniques to link data about cells with appropriate ontologies. The 5th International Cells in Experimental Life Science Workshop, CELLS 2021, will provide a venue for discussions of the application of biomedical ontologies to represent and analyze in vivo and in vitro cell- and cell line-related knowledge and data, including single cell RNA sequencing data and stem cell technologies. The workshop will also cover the extension of CL and CLO for ontological representation of cell types and cell lines based on new methodologies and experiments. In addition it will cover real-world use cases which may require other ontological adaptations beyond CL and CLO. *_Submission Formats for CELLS 2021_* (i) full research papers (10 pages) (ii) short papers (5 pages) (iii) abstracts or extended abstracts (1-3 pages) for presentations Abstracts are one page, references optional. Extended abstracts are formatted as mini-papers, and should include references. The paper template for CELLS 2021 is the same used in ICBO 2021, and will be submitted via *EasyChair <https://easychair.org/my/conference?conf=cells2021>* using the *CEURART one column template <https://drive.google.com/file/d/1o15a2g0bNvQZewKjhLm0aV5cUR0OlzkA/view>*. All submissions will go through peer reviews by at least two reviewers. Papers and extended abstracts from CELLS 2021 will be published as part of the ICBO 2021 CEUR proceedings. The workshop is planned as a three hour event and will be organized into different sections based on the topics of presentations. Presentation time allocation will be determined after the number of each submission type is finalized. A panel discussion will be arranged at the end of the workshop. *_Important Dates_* July 30, 2021 – Extended abstract, abstract, and paper deadline for CELLS 2021 August 20, 2021 – Notification of paper and abstract acceptance September 15, 2021– CELLS 2021 Virtual Workshop will be held in conjunction with ICBO 2021 *Submissions to EasyChair <https://easychair.org/my/conference?conf=cells2021> * ** *_Organizers_* Alexander D. Diehl, PhD, University at Buffalo, ad...@bu... <mailto:ad...@bu...> Sirarat Sarntivijai, PhD, ELIXIR Hub, sir...@el... <mailto:sir...@el...> Yongqun “Oliver” He, DVM, PhD, University of Michigan Medical School, yon...@me... <mailto:yon...@me...> |
From: John G. <jgr...@st...> - 2020-08-31 23:39:17
|
_______________________________________________ bioportal-announce mailing list bio...@li... https://mailman.stanford.edu/mailman/listinfo/bioportal-announce |
From: Alexander D. <add...@gm...> - 2020-07-10 14:13:01
|
*Call for Papers and Abstracts * *4th International Cells in Experimental Life Science Workshop, CELLS 2020 <https://sites.google.com/view/cells-2020-workshop/home>* /A virtual workshop associated with ICBO 2020 <https://icbo2020.inf.unibz.it/> and JOWO 2020 <https://www.iaoa.org/jowo/2020/>, mid-September 2020/ The 4th International Cells in Experimental Life Science Workshop, CELLS 2020, will provide a venue for discussions of the development and application of biomedical ontologies to represent and analyze /in vivo/ and /in vitro/ cell- and cell line-related knowledge and data, including single cell RNA sequencing data and stem cell technologies. The workshop will also cover the extension of Cell Ontology and Cell Line Ontology for ontological representation of cell types and cell lines based on new methodologies and experiments. In addition it will cover real-world use cases which may require other ontological approaches beyond CL and CLO. *CELLS 2020 Workshop Themes*** (i) addressing the challenges of knowledge representation for newly-discovered and known cell types, particularly in light of single cell RNA sequencing data (ii) addressing the challenges of knowledge representation of cell types in disease states (iii) addressing the challenges of the representation of homologous cell types across species (iv) addressing the challenges of identification and representation of cell types of importance as targets of SARS-CoV2 infection and in the immune response during COVID-19 The paper template for CELLS 2020 will be the same used in ICBO 2020, from IOS Press <https://www.iospress.nl/service/authors/latex-and-word-tools-for-book-authors/>, and will be submitted via EasyChair <https://easychair.org/my/conference?conf=cells2020>. All full-length and short-length submissions will go through external peer review and abstracts will be reviewed by the organizers. We provide a late abstract deadline for short reports of late-breaking results as well. Selected submissions will be featured in a BMC Bioinformatics thematic CELLS 2020 issue. The workshop is planned as a half-day event including presentations and a virtual poster session with the opportunity to speak with poster authors. *Submission Formats for CELLS 2020* (i) full research papers (6-10 pages) (ii) work in progress reports (4 pages) (iii) extended abstracts (one page) for short presentations (iv) abstracts for virtual poster session *Important Dates* *July 24, 2020* – Paper and abstract deadline for CELLS 2020 (extended by 1 week) August 14, 2020 – Notification of paper and abstract acceptance August 25, 2020 – Late abstract deadline for short reports of late-breaking results September 4, 2020 – Notification of late abstract acceptance September 16-19, 2020 (to be determined) – Virtual Workshop in conjunction with ICBO 2020 *Organizers* Alexander D. Diehl, PhD Jacobs School of Medicine and Biomedical Sciences, University at Buffalo ad...@bu... <mailto:ad...@bu...> Sirarat Sarntivijai, PhD ELIXIR Interoperability Platform Coordinator sir...@el... <mailto:sir...@el...> Yongqun “Oliver” He, DVM, PhD University of Michigan Medical School yon...@me... <mailto:yon...@me...> |
From: Jennifer W. <Jen...@ne...> - 2020-06-13 00:54:02
|
(apologies for cross-posting ... please distribute) -------------------------------------------------------------- >> ICBO | ODLS 2020 << Call for Contributions Tools and Applications, Early Career and Poster Tracks https://icbo2020.inf.unibz.it/ Submissions due: July 7th, 2020 -------------------------------------------------------------- 11th International Conference on Biomedical Ontologies (ICBO) 10th Workshop on Ontologies and Data in Life Sciences (ODLS) held jointly as part of the Bolzano Summer of Knowledge (BOSK 2020) September 16-19, 2020 Bolzano, Italy -------------------------------------------------------------- == Coronavirus Update == ICBO 2020 will be held as a light-weight virtual event in September 2020, with a face-to-face meeting postponed to September 2021. Proceedings will be published as usual, and the Journal of Biomedical Semantics will invite authors of accepted papers to submit expanded versions to the journal. -------------------------------------------------------------- == Call for Contributions == The International Conference on Biomedical Ontologies (ICBO) [1] is a premier annual conference series that brings together researchers, students and professionals involved in the development and application of ontologies in all areas of biology, medicine, diseases, human health, genome biology, environment, biomes, nutrition, food, plants, agriculture and others. This year, ICBO will be held jointly with Ontologies and Data for the Life Sciences (ODLS), an annual workshop series that focuses on ontologies, data management and data processing in the life sciences and in health care. It covers the overall spectrum of biomedical information management, from experimental data acquisition and preprocessing across analysis, structuring and interpretation of data, up to developing structured representations of knowledge, in particular in the form of ontologies, with their various applications. == Important Dates == [all dates in 2020] Main research paper track dates: * Submission deadline (extended) --May 25 (Mon)-- [passed] * Notification June 22 (Mon) * Camera-ready versions July 15 (Wed) Other tracks comprise: ** Tools and Applications ** Early Career Contributions ** Poster Abstracts Other tracks dates: * Submission deadline July 07 (Tue) * Notification August 12 (Wed) * Camera-ready versions (TBA) Virtual event during September 16-19 (Wed-Sat) Face-to-face event postponed/merged with ICBO 2021, Sep 2021 All submission deadlines refer to 23:59:59 anywhere on earth (UTC-12). == Types of Papers == ICBO|ODLS 2020 is soliciting submissions of novel (not previously published nor concurrently submitted) research papers in the areas of the application of ontologies to biomedical problems, ontology-based methods, ontology design and ontology interoperability, at any stage in the process from data creation to use in applications or scientific analyses. Submissions will be welcome from a broad range of approaches to ontology building and use. In addition, we would like to invite contributions showcasing methods for ontology-based research, including statistical methods, and papers addressing the challenges associated with working with multiple ontologies at the same time, including ontology development, visualization, annotation of data, analysis, and applications. Accordingly, there are several categories of submissions, corresponding to distinct tracks of the conference: * --full-length research papers (8-10 pages)-- [deadline has passed] * full-length tools and applications papers (8-10 pages) * poster abstracts (2 pages) * early career researcher symposium abstracts (5 pages) Contributions must be delivered non-anonymously and as a single PDF file. They must be formatted using the IOS Press template [5] (one-column format, available for Microsoft Word and LaTeX) according to the guidelines for book authors. The same template is required for submissions to FOIS [4] as well as to ICBO and other workshops held in the context of BOSK [2]. == Submission and Proceedings == Contributions will need to be submitted via EasyChair at https://easychair.org/conferences/?conf=icbo2020 [6]. All accepted papers and abstracts will be published open access in an issue of the IAOA series of CEUR-WS [7]. Moreover, accepted papers will be invited to submit an expanded version to a special issue collection in the Journal of Biomedical Semantics (JBMS) [8]. == Contact == For more information please email us at icb...@un... [9]. == Organizing Committee == Conference Chairs: * Janna Hastings (University College London, UK) * Frank Loebe (Univ. of Leipzig, Germany) Tools and Applications Chairs: * Phillip Lord (Newcastle Univ., UK) * James Overton (Knocean, inc. & OBO Foundry) Workshop and Tutorial Chairs: * Robert Hoehndorf (KAUST, Thuwal, Saudi-Arabia) * Randi Vita (LJI, La Jolla, USA & OBO Foundry) Early Career Chairs: * Adrien Barton (IRIT, Toulouse, France & Univ. of Sherbrooke, Canada) * Nicole Vasilevsky (Oregon Health & Science Univ., Portland, USA) Publicity Chair: * Jennifer Warrender (Newcastle Univ., UK) Local Organizing Committee at Free Univ. of Bolzano, Italy: * Oliver Kutz [Local Chair] * Pietro Galliani * Guendalina Righetti * Nicolas Troquard == Links == [1] ICBO|ODLS 2020 website https://icbo2020.inf.unibz.it/ [2] BOSK 2020 website https://summerofknowledge.inf.unibz.it/ [3] Knowledge Engineering and Knowledge Management (EKAW) 2020 website https://ekaw2020.inf.unibz.it/ [4] Formal Ontology in Information Systems (FOIS) 2020 website https://fois2020.inf.unibz.it/ [5] IOS Press templates for book authors https://www.iospress.nl/service/authors/latex-and-word-tools-for-book-authors/ [6] ICBO 2020 submission page in EasyChair https://easychair.org/conferences/?conf=icbo2020 [7] CEUR Workshop Proceedings: IAOA Series http://ceur-ws.org/iaoa.html [8] Journal of Biomedical Semantics (JBMS) website https://jbiomedsem.biomedcentral.com/ [9] ICBO|ODLS 2020 contact email icb...@un... _______________________________________________ bioportal-announce mailing list bio...@li... https://mailman.stanford.edu/mailman/listinfo/bioportal-announce |
From: Alexander D. <add...@gm...> - 2020-05-22 02:52:01
|
*Call for Papers* *4th International Cells in Experimental Life Science Workshop, CELLS 2020 <https://sites.google.com/view/cells-2020-workshop/home>* /A virtual workshop associated with ICBO 2020 <https://icbo2020.inf.unibz.it/> and JOWO 2020 <https://www.iaoa.org/jowo/2020/>, mid-September 2020/ The 4th International Cells in Experimental Life Science Workshop, CELLS 2020, will provide a venue for discussions of the development and application of biomedical ontologies to represent and analyze /in vivo/ and /in vitro/ cell- and cell line-related knowledge and data, including single cell RNA sequencing data and stem cell technologies. The workshop will also cover the extension of Cell Ontology and Cell Line Ontology for ontological representation of cell types and cell lines based on new methodologies and experiments. In addition it will cover real-world use cases which may require other ontological approaches beyond CL and CLO. *CELLS 2020 Workshop Themes*** (i) addressing the challenges of knowledge representation for newly-discovered and known cell types, particularly in light of single cell RNA sequencing data (ii) addressing the challenges of knowledge representation of cell types in disease states (iii) addressing the challenges of the representation of homologous cell types across species (iv) addressing the challenges of identification and representation of cell types of importance as targets of SARS-CoV2 infection and in the immune response during COVID-19 The paper template for CELLS 2020 will be the same used in ICBO 2020, from IOS Press <https://www.iospress.nl/service/authors/latex-and-word-tools-for-book-authors/>, and will be submitted via EasyChair <https://easychair.org/my/conference?conf=cells2020>. All full-length and short-length submissions will go through external peer review and abstracts will be reviewed by the organizers. We provide a late abstract deadline for short reports of late-breaking results as well. Selected submissions will be featured in a BMC Bioinformatics thematic CELLS 2020 issue. The workshop is planned as a half-day event including presentations and a virtual poster session with the opportunity to speak with poster authors. *Submission Formats for CELLS 2020* (i) full research papers (6-10 pages) (ii) work in progress reports (4 pages) (iii) extended abstracts (one page) for short presentations (iv) abstracts for virtual poster session *Important Dates* July 17, 2020 – Paper and abstract deadline for CELLS 2020 August 14, 2020 – Notification of paper and abstract acceptance August 25, 2020 – Late abstract deadline for short reports of late-breaking results September 4, 2020 – Notification of late abstract acceptance September 16-19, 2020 (to be determined) – Virtual Workshop in conjunction with ICBO 2020 *Organizers* Alexander D. Diehl, PhD Jacobs School of Medicine and Biomedical Sciences, University at Buffalo ad...@bu... <mailto:ad...@bu...> Sirarat Sarntivijai, PhD ELIXIR Interoperability Platform Coordinator sir...@el... <mailto:sir...@el...> Yongqun “Oliver” He, DVM, PhD University of Michigan Medical School yon...@me... <mailto:yon...@me...> |
From: John G. <jgr...@st...> - 2020-04-10 23:00:39
|
_______________________________________________ bioportal-announce mailing list bio...@li... https://mailman.stanford.edu/mailman/listinfo/bioportal-announce |
From: Jennifer W. <Jen...@ne...> - 2020-03-25 22:11:18
|
(apologies for cross-posting ... please distribute) -------------------------------------------------------------- >> ICBO | ODLS 2020 << 2nd Call for Papers https://icbo2020.inf.unibz.it/ KEY UPDATES * In light of the coronavirus crisis, the conference may need to be held virtually. The final format of the conference (i.e. physical or virtual) will be determined during June 2020. * Accepted papers will be published independently of the form in which the event will be held this year * Research paper submission deadline extended to May 25 * Expanded versions of accepted papers will be invited for a special issue of the Journal of Biomedical Semantics (JBMS) * Submission link to EasyChair added Main research track submissions due: May 25, 2020 (strict) -------------------------------------------------------------- 11th International Conference on Biomedical Ontologies (ICBO) 10th Workshop on Ontologies and Data in Life Sciences (ODLS) held jointly as part of the Bolzano Summer of Knowledge (BOSK 2020) September 16-19, 2020 Bolzano, Italy -------------------------------------------------------------- == Coronavirus Update == The organisers are monitoring the ongoing situation with regard to the global coronavirus crisis. At present, there is still a chance that by the scheduled dates in September the situation may allow us to go ahead with the conference basically as planned, possibly extended by virtual participation. However, if the conference cannot be held as a physical in-person meeting, we aim at holding it in a virtual format that remains to be determined. The proceedings will still be published in either case. Moreover, the Journal of Biomedical Semantics will invite authors of accepted papers to submit expanded versions to the journal. Given the challenges that the current crisis and uncertainty poses, we have extended the submission deadline substantially to the date of ***May 25th, 2020*** (which will apply strictly). -------------------------------------------------------------- == Call for Papers == The International Conference on Biomedical Ontologies (ICBO) [1] is a premier annual conference series that brings together researchers, students and professionals involved in the development and application of ontologies in all areas of biology, medicine, diseases, human health, genome biology, environment, biomes, nutrition, food, plants, agriculture and others. This year, ICBO will be held jointly with Ontologies and Data for the Life Sciences (ODLS), an annual workshop series that focuses on ontologies, data management and data processing in the life sciences and in health care. It covers the overall spectrum of biomedical information management, from experimental data acquisition and preprocessing across analysis, structuring and interpretation of data, up to developing structured representations of knowledge, in particular in the form of ontologies, with their various applications. == Important Dates == [all dates in 2020] Main research paper track: * Submission deadline (extended) May 25 (Mon) <-- STRICT! * Notification June 22 (Mon) * Camera-ready versions July 15 (Wed) All other tracks TBA (submission not before June) Conference dates September 16-19 (Wed-Sat) All submission deadlines refer to 23:59:59 anywhere on earth (UTC-12). == Types of Papers == ICBO|ODLS 2020 is soliciting submissions of novel (not previously published nor concurrently submitted) research papers in the areas of the application of ontologies to biomedical problems, ontology-based methods, ontology design and ontology interoperability, at any stage in the process from data creation to use in applications or scientific analyses. Submissions will be welcome from a broad range of approaches to ontology building and use. In addition, we would like to invite contributions showcasing methods for ontology-based research, including statistical methods, and papers addressing the challenges associated with working with multiple ontologies at the same time, including ontology development, visualization, annotation of data, analysis, and applications. Accordingly, there are several categories of submissions, corresponding to distinct tracks of the conference: * full-length research papers (8-10 pages) * full-length tools and applications papers (8-10 pages) * poster abstracts (2 pages) * early career researcher symposium abstracts (5 pages) A selection of successful poster abstracts will be invited to give flash presentations during the conference. Contributions must be delivered non-anonymously and as a single PDF file. They must be formatted using the IOS Press template [5] (one-column format, available for Microsoft Word and LaTeX) according to the guidelines for book authors. The same template is required for submissions to FOIS [4] as well as to ICBO and other workshops held in the context of BOSK [2]. == Submission and Proceedings == Contributions will need to be submitted via EasyChair at https://easychair.org/conferences/?conf=icbo2020 [6]. A Best Paper Award, Best Poster Award, Best Tool and Application Award, and Best Early Career Contribution Award will be awarded at the conference. All accepted papers and abstracts will be published open access in an issue of the IAOA series of CEUR-WS [7]. Moreover, accepted papers will be invited to submit an expanded version to a special issue collection in the Journal of Biomedical Semantics (JBMS) [8]. == Contact == For more information please email us at icb...@un... [9]. == Organizing Committee == Conference Chairs: * Janna Hastings (University College London, UK) * Frank Loebe (Univ. of Leipzig, Germany) Tools and Applications Chairs: * Phillip Lord (Newcastle Univ., UK) * James Overton (Knocean, inc. & OBO Foundry) Workshop and Tutorial Chairs: * Robert Hoehndorf (KAUST, Thuwal, Saudi-Arabia) * Randi Vita (LJI, La Jolla, USA & OBO Foundry) Early Career Chairs: * Adrien Barton (IRIT, Toulouse, France & Univ. of Sherbrooke, Canada) * Nicole Vasilevsky (Oregon Health & Science Univ., Portland, USA) Publicity Chair: * Jennifer Warrender (Newcastle Univ., UK) Local Organizing Committee at Free Univ. of Bolzano, Italy: * Oliver Kutz [Local Chair] * Pietro Galliani * Guendalina Righetti * Nicolas Troquard == Links == [1] ICBO|ODLS 2020 website https://icbo2020.inf.unibz.it/ [2] BOSK 2020 website https://summerofknowledge.inf.unibz.it/ [3] Knowledge Engineering and Knowledge Management (EKAW) 2020 website https://ekaw2020.inf.unibz.it/ [4] Formal Ontology in Information Systems (FOIS) 2020 website https://fois2020.inf.unibz.it/ [5] IOS Press templates for book authors https://www.iospress.nl/service/authors/latex-and-word-tools-for-book-authors/ [6] ICBO 2020 submission page in EasyChair https://easychair.org/conferences/?conf=icbo2020 [7] CEUR Workshop Proceedings: IAOA Series http://ceur-ws.org/iaoa.html [8] Journal of Biomedical Semantics (JBMS) website https://jbiomedsem.biomedcentral.com/ [9] ICBO|ODLS 2020 contact email icb...@un... _______________________________________________ bioportal-announce mailing list bio...@li... https://mailman.stanford.edu/mailman/listinfo/bioportal-announce |
From: Franck M. <fra...@cn...> - 2020-03-25 22:08:36
|
Dear colleagues, The 3rd International Workshop on Semantics for Biodiversity (S4BioDiv) will take place on September 16th 2020, co-located with the 11th International Conference on Biomedical Ontologies (ICBO 2020). These events are part of the Bolzano Summer of Knowledge 2020 (https://summerofknowledge.inf.unibz.it). Call for Papers and submission guidelines: https://fusion.cs.uni-jena.de/s4biodiv2020/ Important dates: Abstracts due: June 26th, 2020 Workshop papers due: July 3rd, 2020, 2020 Notification of acceptance: July 31st, 2020 Camera ready version: August 17th, 2020 Best regards, Franck, for the S4BioDiv organizing committee. _______________________________________________ bioportal-announce mailing list bio...@li... https://mailman.stanford.edu/mailman/listinfo/bioportal-announce |
From: Diehl, A. <ad...@bu...> - 2020-03-11 15:29:17
|
See email below. -- Alexander D. Diehl, Ph.D., Associate Professor Department of Biomedical Informatics Jacobs School of Medicine and Biomedical Sciences University at Buffalo, The State University of New York Buffalo, New York 14203 work phone: +1 716-881-8975/+1 716-881-7466 email: ad...@bu...<mailto:ad...@bu...> From: Bjoern Peters <bp...@lj...> Date: Wednesday, March 11, 2020 at 10:44 AM To: vasilevs <vas...@oh...>, "Diehl, Alexander" <ad...@bu...>, "Maria Masci, Anna" <ann...@du...>, "Overton, James" <ja...@ov...>, "Vita, Randi" <rv...@lj...>, David Osumi-Sutherland <do...@gm...>, Chris Mungall <cmu...@gm...> Subject: Re: Organism specific cell types - writeup for the call Can someone forward to the mailing list? i dont have the right permission On Wed, Mar 11, 2020, 7:15 AM Bjoern Peters <bp...@lj...<mailto:bp...@lj...>> wrote: Here is a draft document capturing some of the issues we have come across with organism specific terms in CL, and proposals on how to address them. https://docs.google.com/document/d/1bSpiZc5p9VNCZ83I4VUEwOVGoFTZ3cpXZKOSRAaGBZc/edit?usp=sharing This will be discussed on the call in ~45 minutes. -- Bjoern Peters Professor La Jolla Institute for Allergy and Immunology 9420 Athena Circle La Jolla, CA 92037, USA Tel: 858/752-6914<tel:858%2F752-6914> Fax: 858/752-6987<tel:858%2F752-6987> http://www.liai.org/pages/faculty-peters |
From: Chris M. <cjm...@lb...> - 2019-10-17 19:16:53
|
Can CL editors comment on the following ticket, thanks: https://github.com/obophenotype/cell-ontology/issues/587 |
From: Jennifer L. V. <ven...@st...> - 2019-03-18 22:17:03
|
Greetings BioPortal community, The BioPortal team is in the process of building a new website to better explain our product offerings, and make it easier for our user community to find relevant documentation and support. We plan to include a section in our website with user testimonials. If you have used any of our products, we would greatly appreciate the opportunity to display a brief explanation of how your project benefitted from BioPortal. Testimonial submissions need not be longer than 3 to 4 sentences. Please submit via email to Jennifer Vendetti (vendetti at stanford.edu), and include your name and the name of your organization. Responding to this request is completely voluntary. We appreciate that many of you may not want to go public with your love for BioPortal. If that is the case, we will still love you back and your service from us will not be affected. Thank you very much in advance for your statements of support. Kindest regards, The BioPortal Team (Mark, John, Michael, Jennifer, & Alex) _______________________________________________ bioportal-announce mailing list bio...@li... https://mailman.stanford.edu/mailman/listinfo/bioportal-announce |
From: Clement J. <jo...@li...> - 2018-09-27 20:40:16
|
_______________________________________________ bioportal-announce mailing list bio...@li... https://mailman.stanford.edu/mailman/listinfo/bioportal-announce |
From: Jaiswal, P. <pan...@gm...> - 2018-06-01 22:46:14
|
ICBO2018 Submission deadline extension Final Deadline Extension for ICBO2018 submissions Dear, Based on number of requests we would like to inform you that the final deadline has been extended for ICBO2018 full/short scientific paper submission and extended abstract submission for posters, software and database demonstrations. New extended deadlines are: * *6/08/2018 Scientific paper (Full or Short Length) * * *6/15/2018 Workshop papers *as requested by workshop organizers o List of Workshops <https://oregonstate.us8.list-manage.com/track/click?u=937031f977b275688428917ce&id=3dd320dbe4&e=95159496e6> * *7/15/2018 Abstracts for Poster, Software/Tools and Database demo* *Submit Now </node/15>* If you are still planning to submit your work for review and publication in the ICBO proceedings, you have time to do so. This is also a good opportunity to showcase the new ontologies, results from data analytics, software tools and databases that you may be developing. It's always good to seek feedback from the community which may help in improvements. *Submit Now </node/15>* We want to see your work getting accolades and thumbs up from the community. For those that have submitted their papers, a Big Thank you from the ICBO2018 Program Committee. Sincerely Pankaj Jaiswal ICBO2018 Conference Chair http://icbo2018.cgrb.oregonstate.edu/ <http://> /Copyright © 2018 International Conference on Biomedical Ontologies, All rights reserved./ You are receiving this email because you opted in at our website or had a relationship with ICBO. *Our mailing address is:* International Conference on Biomedical Ontologies 2082 Cordley Hall Department of Botany and Plant Pathology, Oregon State University Corvallis, OR 97331 Add us to your address book <//oregonstate.us8.list-manage.com/vcard?u=937031f977b275688428917ce&id=dff8be5b7e> Want to change how you receive these emails? You can update your preferences <https://oregonstate.us8.list-manage.com/profile?u=937031f977b275688428917ce&id=dff8be5b7e&e=95159496e6> or unsubscribe from this list <https://oregonstate.us8.list-manage.com/unsubscribe?u=937031f977b275688428917ce&id=dff8be5b7e&e=95159496e6&c=14db89b625>. Email Marketing Powered by MailChimp <http://www.mailchimp.com/monkey-rewards/?utm_source=freemium_newsletter&utm_medium=email&utm_campaign=monkey_rewards&aid=937031f977b275688428917ce&afl=1> <https://oregonstate.us8.list-manage.com/track/click?u=937031f977b275688428917ce&id=7facf21c12&e=95159496e6> Share <https://oregonstate.us8.list-manage.com/track/click?u=937031f977b275688428917ce&id=98da02cdf2&e=95159496e6> <https://oregonstate.us8.list-manage.com/track/click?u=937031f977b275688428917ce&id=01ff4372f0&e=95159496e6> Tweet <https://oregonstate.us8.list-manage.com/track/click?u=937031f977b275688428917ce&id=0a2dabcdde&e=95159496e6> <http://us8.forward-to-friend.com/forward?u=937031f977b275688428917ce&id=14db89b625&e=95159496e6> Forward <http://us8.forward-to-friend.com/forward?u=937031f977b275688428917ce&id=14db89b625&e=95159496e6> |
From: Alexander D. D. <add...@gm...> - 2018-05-07 20:10:54
|
*_Call for Papers for the 2nd International Workshop on Oncology and Ontology, ONCONTO 2018 <http://icbo2018.cgrb.oregonstate.edu/node/20>_* ** *In conjunction with the International Conference on Biomedical Ontology (ICBO)* <http://icbo2018.cgrb.oregonstate.edu/> *August 7, 2018* ** *** Submission Deadline: June 8, 2018 *** *http://icbo2018.cgrb.oregonstate.edu/node/20* *https://easychair.org/conferences/?conf=icbo2018* *Workshop Theme and Topics* To effectively treat and prevent cancer, we need to bring together data from multiple domains, such as electronic medical records, genomic data, tissue data, epidemiological data, and clinical trial data. Personalized medicine requires the integration of clinical and research findings from multiple disciplines, and cancer strikes each affected individual in a unique and specific way from the molecular, cellular, anatomical, genetic, and emotional perspectives. We aim to convene an interdisciplinary group of ontologists and cancer researchers through the*ONCONTO*(oncology and ontology) workshop in order to advance the ontological representation of cancer and related entities to support both broader research in the domain and personalized treatment approaches. Topics include: * Revision and expansion of existing ontological resources for representing cancer and related biomedical entities and the creation of new ontologies for the oncology domain that address gaps in representation. * Ontology-based data analysis of cancer patient or basic research data related to epidemiology, etiology, genomics, diagnosis, and treatment of cancer. * Use of ontologies for translational research related to cancer and exploratory research or position papers related to ontologies and cancer. We will organize our workshop into different sections based on the topics of presentations. Presentation time allocation will be determined after the number of each submission type is finalized. Panel discussions at the end of each section will be arranged based on time availability. ------------------------------------------------------------------------ *Submission* For the paper submission, we will allow three submission formats: §full research papers (6-10 pages) format §work in progress / late breaking results (2-4 pages) §a statement of interest (one page) for podium presentation The paper format will be the same as the format used in ICBO. All the papers will be submitted and handled through Easy Chair: *https://easychair.org/conferences/?conf=icbo2018* Once you have logged into Easy Chair, choose*ONCONTO 2018: 2nd International Workshop on Oncology and Ontology*as the submission topic. ------------------------------------------------------------------------ *Workshop Schedule/Important Dates* §Individual Workshop Papers Due:*June 8, 2018* §Notification of Acceptance: June 22, 2018 §Early Bird Registration: July 1, 2018 §Meeting: August 7, 2018 ------------------------------------------------------------------------ *Workshop Organizers* Alexander D. Diehl, PhD Associate Professor of Biomedical Informatics Jacobs School of Medicine and Biomedical Sciences University at Buffalo, SUNY Buffalo, NY William D. Duncan, PhD Assistant Professor of Oncology Associate Director, Biomedical Data Science Shared Resource Roswell Park Comprehensive Cancer Center Buffalo, NY Carmelo Gaudioso, MD, PhD Assistant Member, Clinical Research Roswell Park Comprehensive Cancer Center Buffalo, NY — Alexander D. Diehl, Ph.D., Associate Professor Department of Biomedical Informatics Jacobs School of Medicine and Biomedical Sciences University at Buffalo, The State University of New York Buffalo, NY 14203 work phone: +1 716-881-8975/+1 716-881-7466 email: ad...@bu... <mailto:ad...@bu...> -- You received this message because you are subscribed to the Google Groups "Clinical and Translational Science Ontology Group" group. To unsubscribe from this group and stop receiving emails from it, send an email toc...@go... <mailto:cts...@go...>. For more options, visithttps://groups.google.com/d/optout. -- Alexander D. Diehl, Ph.D. Associate Professor of Biomedical Informatics Jacobs School of Medicine and Biomedical Sciences University at Buffalo, The State University of New York Buffalo, New York 14203 work phone: +1 716-881-8975 email: ad...@bu..., add...@gm... |
From: John G. <jgr...@st...> - 2018-03-22 09:03:37
|
_______________________________________________ bioportal-announce mailing list bio...@li... https://mailman.stanford.edu/mailman/listinfo/bioportal-announce |
From: Alexander D. D. <add...@gm...> - 2018-03-16 19:55:53
|
Dear all, We would like to call for participation for a new workshop - "Workshop on Ontologies for Stem Cells and Stem Cell Line Cells" (StemCellOW), to be held at the University of Michigan, Ann Arbor, MI, USA, on this April 26-27 (Thursday-Friday): https://sites.google.com/site/stemcellow/ Stem cells and stem cell lines are widely used in biomedical research. Stem cells are undifferentiated cells that can differentiate into specialized cells and can divide to produce more stem cells. To better study stem cells in vitro, thousands of stem cell lines, including embryonic and adult stem cell lines, and induced pluripotent stem cells (iPS/IPSCs), have been generated and used for different applications. With a large number of studies undergoing on stem cells and stem cell lines, many challenges have emerged, including the lack of community-based standards for representing stem cells and stem cell line cell development, formation, and characteristics. The Cell Ontology (CL) and Cell Line Ontology (CLO) are two community-based OBO Foundry ontologies in the domains of in vivo cells and in vitro cell line cells, respectively. CL can be used to represent stem cells, and CLO can be used to stem cell lines and stem cell line cells. However, the development of CLO and CLO for representing stem cells and stem cell line cells has just started, and many challenges still exist. To support community-wide data and knowledge sharing and integration, we will organize a workshop, titled "Workshop on Ontologies for Stem Cells and Stem Cell Line Cells" (StemCellOW), to discuss the development and application of CL, CLO, and other ontologies in relation to in vivo stem cells and in vitro stem cell line cell studies. The workshop aims to translate stem cell biology into the ontology framework supported by CL and CLO, and related OBO Foundry ontologies. This includes defining key ontology terms, ontology hierarchy design, ontology design patterns for crucial cell processes (e.g., stem cell differentiation, division, gene expression, and reprogramming), modelling of experimental use cases, ontology applications, and discussion of continuous collaborations. This workshop is expected to become a platform for active interdisciplinary discussions among experts with different backgrounds. The StemCellOW workshop website (https://sites.google.com/site/stemcellow/) includes registration information. Please register sooner than later. We will have a small fund from a LINCS eDSR grant to support some who need financial support to attend the workshop. Please contact us to apply for the fund. This workshop is co-organized by Drs. Yongqun Oliver He and Alexander D. Diehl. We also appreciate Dr. Sirarat (Sira) Sarntivijai’s participation in our workshop preparation. Thank you for your attention, Yongqun "Oliver" He, DVM, PhD Associate Professor Unit for Laboratory Animal Medicine Department of Microbiology and Immunology Center for Computational Medicine and Bioinformatics and Comprehensive Cancer Center University of Michigan Medical School Office: 2511F ARF, 1150 W. Medical Center Dr. Ann Arbor, MI 48109 Email: yon...@me... Tel: 734-615-8231 (O) http://www.hegroup.org/ and Alexander D. Diehl, Ph.D., Associate Professor Department of Biomedical Informatics Jacobs School of Medicine and Biomedical Sciences University at Buffalo, The State University of New York Buffalo, NY 14203 work phone: +1 716-881-8975/+1 716-881-7466 email: ad...@bu... |
From: Clement J. <jo...@li...> - 2017-09-13 18:40:01
|
_______________________________________________ bioportal-announce mailing list bio...@li... https://mailman.stanford.edu/mailman/listinfo/bioportal-announce |
From: Alexander D. D. <add...@gm...> - 2017-06-30 16:30:17
|
Dear Colleagues, Call for Papers for the Workshop on Cells in ExperimentaL Life Science (CELLS-2017) In conjunction with the 2017 International Conference on Biomedical Ontology (ICBO-2017) September 13, 2017 in Newcastle upon Tyne, UK *** Selected submissions will be published with BMC Bioinformatics - Submission Deadline Extended to July 9th, 2017 ***** Workshop Website: https://sites.google.com/site/cellsworkshop/ Paper submission deadline: *July 9, 2017* Workshop Theme and Topics CELLS is the latest addition to the workshop series at the International Conference on Biomedical Ontology (ICBO) that aims to cover topics of data and metadata representation, standardization, management, and analysis of experimental cells in the biological and biomedical context. The rise of single-cell RNA sequencing technologies has brought the challenge of metadata handling to the field of experimental biology and biomedical ontology. More urgent than ever now, biologists and ontologists have to reach the consensus on the agreement on various topics such as naming convention and standard for novel cell type nomenclature, and modeling the biological reality into an ontology and semantic framework. The rise of cell technologies has provided science with a fast lane to advance discovery in biomedical research. Experimental cell cultures and cell lines are widely used and often generated in a de Novo fashion at the laboratory. Normalization of experimental cell data produced in different laboratory settings is sometimes difficult, even when the cell types studied are nominally the same. It has also become unclear where the separation between data and metadata is due to the level of granularity of the details. Furthermore, there are no real unified modeling solutions that are universal to all experimental questions and situations. Therefore, data representation and modeling is very much driven by individual experiment. Consolidation of heterogeneous metadata in a large central data repository is a real challenge. New knowledge obtained by high-resolution technologies such as CyTOF and single-cell RNA sequencing introduces even more data that require robust representation, especially regarding novel cell populations that have never been seen before and do not belong to any existing classes of well-established OBO ontologies. CELLS-2017 workshop aims to provide a venue for discussion in various hot topics in the single-cell and multi-cell technology domains. This will include the input from both biology and ontology metadata sides of life sciences. The organizers will lay the background on the development, maintenance, and application of the Cell Ontology (CL) and the Cell Line Ontology (CLO) before expanding the presentations and discussions from the submissions which will: 1. Bring together the participants from all tiers in experimental cell research and data analysis to facilitate communications and collaboration towards a consensus data representation in experimental cell research. 2. Identify research problems and challenges in the ontological representation and applications of experimental cells, and related topics via the real use cases. 3. Identify and discuss possible solutions for the problems and challenged presented in the workshop. 4. Initiate a sustainable venue for future collaborations and discussions among the participants. Submission For the paper submission, we will allow three submission formats: full research papers (6-8 pages) format work in progress / late breaking results (2-4 pages), and a statement of interest (one page) for podium presentation. The paper format will be the same as the format used in ICBO. Templates can be found on the website: https://sites.google.com/site/cellsworkshop/. All the papers will be submitted and handled through Easy Chair. https://easychair.org/conferences/?conf=cells2017 After the full papers are accepted, we will work with BMC Bioinformatics editors and reviewers to decide which papers will be formally invited for extension to be included in a thematic series in the journal. All full-length (10 pages maximum) and short-length (4 pages maximum) submissions will go through peer reviews by at least two reviewers. The one-page statement-of-interest submissions will be reviewed by the workshop organizers. We invite the submission of research papers, work in progress/late-breaking results and statement of interest for presentation at CELLS-2017. Papers are invited in areas, such as availability and interoperability of existing resources for cell and cell line terminologies and catalogues, applications and challenges of cell modeling, and improvement and best practices of the current experimental cell ontology landscape. Example topics include (but not limited to): • Collaborative ontology development for experimental cell modeling. • Ontologies in cell type and cell culture metadata and standards. • Knowledge representation and knowledge discovery for novel discovery. • Biocuration of experimental cell data • The usage of standard cell and cell line nomenclatures in literature. • Updates on work in progress and statement of interest of cell modeling questions. Selected submissions will also be published in the CELLS thematic issue of BMC Bioinformatics. Should the authors accept the offer to publish BMC Bioinformatics, they will agree to a secondary review-for-publication process and the publishing fee. Workshop Schedule/Important Dates Individual Workshop Papers Due: *July 9, 2017* Notification of Acceptance: July 22, 2017 Camera Ready: July 30, 2017 Workshop: Sept. 13, 2017 First Revision due to BMC Bioinformatics: Sept 30, 2017 Workshop Organizers Sirarat Sarntivijai, PhD Samples, Phenotypes, and Ontologies Team, European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Hinxton, Cambridgeshire, UK. Yongqun “Oliver” He, DVM, PhD Department of Microbiology and Immunology Unit for Laboratory Animal Medicine Center for Computational Medicine and Bioinformatics University of Michigan Medical School, Ann Arbor, MI, USA. Alexander Diehl, PhD University at Buffalo, The State University of New York, Buffalo, NY, USA. Contact: icb...@gm... <mailto:icb...@gm...> |
From: Alexander D. <add...@gm...> - 2017-05-23 19:36:32
|
The deadline is July 1st, not June 9^th . Sorry for the confusion. *From:*He, Oliver *Sent:*Monday, May 22, 2017 7:35 AM *To:*Developers, OBI;ogm...@go... <mailto:ogm...@go...>;bfo...@go... <mailto:bfo...@go...>;obo...@li... <mailto:obo...@li...> *Cc:*Sirarat Sarntivijai (si...@eb... <mailto:si...@eb...>); Alexander Diehl (ad...@bu... <mailto:ad...@bu...>); He, Oliver *Subject:*Call for Papers: ICBO-2017 workshop on Cells in ExperimentaL Life Science (CELLS-2017) Dear Colleagues, Call for Papers for the Workshop on Cells in ExperimentaL Life Science (CELLS-2017) In conjunction with the 2017 International Conference on Biomedical Ontology (ICBO-2017) September 13, 2017 in Newcastle upon Tyne, UK ** Selected submissions will be published with BMC Bioinformatics - Submission Deadline: June 9th, 2017 ** Workshop Website: https://sites.google.com/site/cellsworkshop/ Paper submission deadline: July 1, 2017 Workshop Theme and Topics CELLS is the latest addition to the workshop series at the International Conference on Biomedical Ontology (ICBO) that aims to cover topics of data and metadata representation, standardization, management, and analysis of experimental cells in the biological and biomedical context. The rise of single-cell RNA sequencing technologies has brought the challenge of metadata handling to the field of experimental biology and biomedical ontology. More urgent than ever now, biologists and ontologists have to reach the consensus on the agreement on various topics such as naming convention and standard for novel cell type nomenclature, and modeling the biological reality into an ontology and semantic framework. The rise of cell technologies has provided science with a fast lane to advance discovery in biomedical research. Experimental cell cultures and cell lines are widely used and often generated in a de Novo fashion at the laboratory. Normalization of experimental cell data produced in different laboratory settings is sometimes difficult, even when the cell types studied are nominally the same. It has also become unclear where the separation between data and metadata is due to the level of granularity of the details. Furthermore, there are no real unified modeling solutions that are universal to all experimental questions and situations. Therefore, data representation and modeling is very much driven by individual experiment. Consolidation of heterogeneous metadata in a large central data repository is a real challenge. New knowledge obtained by high-resolution technologies such as CyTOF and single-cell RNA sequencing introduces even more data that require robust representation, especially regarding novel cell populations that have never been seen before and do not belong to any existing classes of well-established OBO ontologies. CELLS-2017 workshop aims to provide a venue for discussion in various hot topics in the single-cell and multi-cell technology domains. This will include the input from both biology and ontology metadata sides of life sciences. The organizers will lay the background on the development, maintenance, and application of the Cell Ontology (CL) and the Cell Line Ontology (CLO) before expanding the presentations and discussions from the submissions which will: 1. Bring together the participants from all tiers in experimental cell research and data analysis to facilitate communications and collaboration towards a consensus data representation in experimental cell research. 2. Identify research problems and challenges in the ontological representation and applications of experimental cells, and related topics via the real use cases. 3. Identify and discuss possible solutions for the problems and challenged presented in the workshop. 4. Initiate a sustainable venue for future collaborations and discussions among the participants. Submission For the paper submission, we will allow three submission formats: full research papers (6-8 pages) format work in progress / late breaking results (2-4 pages), and a statement of interest (one page) for podium presentation. The paper format will be the same as the format used in ICBO. Templates can be found on the website:https://sites.google.com/site/cellsworkshop/. All the papers will be submitted and handled through Easy Chair. https://easychair.org/conferences/?conf=cells2017 After the full papers are accepted, we will work with BMC Bioinformatics editors and reviewers to decide which papers will be formally invited for extension to be included in a thematic series in the journal. All full-length (10 pages maximum) and short-length (4 pages maximum) submissions will go through peer reviews by at least two reviewers. The one-page statement-of-interest submissions will be reviewed by the workshop organizers. We invite the submission of research papers, work in progress/late-breaking results and statement of interest for presentation at CELLS-2017. Papers are invited in areas, such as availability and interoperability of existing resources for cell and cell line terminologies and catalogues, applications and challenges of cell modeling, and improvement and best practices of the current experimental cell ontology landscape. Example topics include (but not limited to): • Collaborative ontology development for experimental cell modeling. • Ontologies in cell type and cell culture metadata and standards. • Knowledge representation and knowledge discovery for novel discovery. • Biocuration of experimental cell data • The usage of standard cell and cell line nomenclatures in literature. • Updates on work in progress and statement of interest of cell modeling questions. Selected submissions will also be published in the CELLS thematic issue of BMC Bioinformatics. Should the authors accept the offer to publish BMC Bioinformatics, they will agree to a secondary review-for-publication process and the publishing fee. Workshop Schedule/Important Dates Individual Workshop Papers Due: July 1, 2017 Notification of Acceptance: July 22, 2017 Camera Ready: July 30, 2017 Workshop: Sept. 13, 2017 First Revision due to BMC Bioinformatics: Sept 30, 2017 Workshop Organizers Sirarat Sarntivijai, PhD Samples, Phenotypes, and Ontologies Team, European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Hinxton, Cambridgeshire, UK. Yongqun “Oliver” He, DVM, PhD Department of Microbiology and Immunology Unit for Laboratory Animal Medicine Center for Computational Medicine and Bioinformatics University of Michigan Medical School, Ann Arbor, MI, USA. Alexander Diehl, PhD University at Buffalo, The State University of New York, Buffalo, NY, USA. Contact:icb...@gm... <mailto:icb...@gm...> ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues -- --- You received this message because you are subscribed to the Google Groups "ogms-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email too...@go... <mailto:ogm...@go...>. For more options, visithttps://groups.google.com/d/optout. |
From: Alexander D. <add...@gm...> - 2017-05-23 19:33:11
|
Dear Colleagues, Call for Papers for the Workshop on Cells in ExperimentaL Life Science (CELLS-2017) In conjunction with the 2017 International Conference on Biomedical Ontology (ICBO-2017) September 13, 2017 in Newcastle upon Tyne, UK ** Selected submissions will be published with BMC Bioinformatics - Submission Deadline: June 9th, 2017 ** Workshop Website: https://sites.google.com/site/cellsworkshop/ Paper submission deadline: July 1, 2017 Workshop Theme and Topics CELLS is the latest addition to the workshop series at the International Conference on Biomedical Ontology (ICBO) that aims to cover topics of data and metadata representation, standardization, management, and analysis of experimental cells in the biological and biomedical context. The rise of single-cell RNA sequencing technologies has brought the challenge of metadata handling to the field of experimental biology and biomedical ontology. More urgent than ever now, biologists and ontologists have to reach the consensus on the agreement on various topics such as naming convention and standard for novel cell type nomenclature, and modeling the biological reality into an ontology and semantic framework. The rise of cell technologies has provided science with a fast lane to advance discovery in biomedical research. Experimental cell cultures and cell lines are widely used and often generated in a de Novo fashion at the laboratory. Normalization of experimental cell data produced in different laboratory settings is sometimes difficult, even when the cell types studied are nominally the same. It has also become unclear where the separation between data and metadata is due to the level of granularity of the details. Furthermore, there are no real unified modeling solutions that are universal to all experimental questions and situations. Therefore, data representation and modeling is very much driven by individual experiment. Consolidation of heterogeneous metadata in a large central data repository is a real challenge. New knowledge obtained by high-resolution technologies such as CyTOF and single-cell RNA sequencing introduces even more data that require robust representation, especially regarding novel cell populations that have never been seen before and do not belong to any existing classes of well-established OBO ontologies. CELLS-2017 workshop aims to provide a venue for discussion in various hot topics in the single-cell and multi-cell technology domains. This will include the input from both biology and ontology metadata sides of life sciences. The organizers will lay the background on the development, maintenance, and application of the Cell Ontology (CL) and the Cell Line Ontology (CLO) before expanding the presentations and discussions from the submissions which will: 1. Bring together the participants from all tiers in experimental cell research and data analysis to facilitate communications and collaboration towards a consensus data representation in experimental cell research. 2. Identify research problems and challenges in the ontological representation and applications of experimental cells, and related topics via the real use cases. 3. Identify and discuss possible solutions for the problems and challenged presented in the workshop. 4. Initiate a sustainable venue for future collaborations and discussions among the participants. Submission For the paper submission, we will allow three submission formats: full research papers (6-8 pages) format work in progress / late breaking results (2-4 pages), and a statement of interest (one page) for podium presentation. The paper format will be the same as the format used in ICBO. Templates can be found on the website:https://sites.google.com/site/cellsworkshop/. All the papers will be submitted and handled through Easy Chair. https://easychair.org/conferences/?conf=cells2017 After the full papers are accepted, we will work with BMC Bioinformatics editors and reviewers to decide which papers will be formally invited for extension to be included in a thematic series in the journal. All full-length (10 pages maximum) and short-length (4 pages maximum) submissions will go through peer reviews by at least two reviewers. The one-page statement-of-interest submissions will be reviewed by the workshop organizers. We invite the submission of research papers, work in progress/late-breaking results and statement of interest for presentation at CELLS-2017. Papers are invited in areas, such as availability and interoperability of existing resources for cell and cell line terminologies and catalogues, applications and challenges of cell modeling, and improvement and best practices of the current experimental cell ontology landscape. Example topics include (but not limited to): • Collaborative ontology development for experimental cell modeling. • Ontologies in cell type and cell culture metadata and standards. • Knowledge representation and knowledge discovery for novel discovery. • Biocuration of experimental cell data • The usage of standard cell and cell line nomenclatures in literature. • Updates on work in progress and statement of interest of cell modeling questions. Selected submissions will also be published in the CELLS thematic issue of BMC Bioinformatics. Should the authors accept the offer to publish BMC Bioinformatics, they will agree to a secondary review-for-publication process and the publishing fee. Workshop Schedule/Important Dates Individual Workshop Papers Due: July 1, 2017 Notification of Acceptance: July 22, 2017 Camera Ready: July 30, 2017 Workshop: Sept. 13, 2017 First Revision due to BMC Bioinformatics: Sept 30, 2017 Workshop Organizers Sirarat Sarntivijai, PhD Samples, Phenotypes, and Ontologies Team, European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Hinxton, Cambridgeshire, UK. Yongqun “Oliver” He, DVM, PhD Department of Microbiology and Immunology Unit for Laboratory Animal Medicine Center for Computational Medicine and Bioinformatics University of Michigan Medical School, Ann Arbor, MI, USA. Alexander Diehl, PhD University at Buffalo, The State University of New York, Buffalo, NY, USA. Contact:icb...@gm... <mailto:icb...@gm...> |
From: John G. <jgr...@st...> - 2017-03-07 19:54:08
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From: John G. <jgr...@st...> - 2017-02-07 03:02:22
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All, We are pleased to announce the latest release of BioPortal, version 5.0.0! This release rewrites the BioPortal user interface to make it more responsive, extensible, easy to use and navigate, and compatible with mobile platforms. This release represents an overhaul of our user interface, using bootstrap as the front-end framework to enable immediate and longer-term improvements. You will see many of those enhancements in coming months. Since the October 2016 release, we have also made a number of minor changes, mostly under the hood, and recently added a few significant features to the Recommender. Release Notes will be added shortly for those changes. Please Note: Although we are aware of some bugs that have surfaced since the transition, so far they have been relatively minor and can be worked around by re-sizing the page or changing tabs. We thought the new interface was a large enough improvement that you would want to start using it right away. Rest assured, we will be working to squash those bugs in the next few days, so please bear with us for this brief period. Please see https://www.bioontology.org/wiki/index.php/BioPortal_Release_Notes for more detailed information about these changes. John ======================== John Graybeal Technical Program Manager Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal Stanford Center for Biomedical Informatics Research 650-736-1632 skype: graybealski _______________________________________________ bioportal-announce mailing list bio...@li... https://mailman.stanford.edu/mailman/listinfo/bioportal-announce |
From: John G. <jgr...@st...> - 2016-06-29 04:51:19
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