FORCE2016 Micro-grant Report

ISB Micro-grant awarded to: Dr. Melissa Haendel  & Dr. Nicole Vasilevsky.
Affiliation: Oregon Health & Science University Library

The 2016 Future of Research Communication and e-Scholarship conference (FORCE2016, https://www.force11.org/meetings/force2016) was held from April 17-19 in Portland, Oregon. The conference aimed to host a trans-disciplinary summit and lively discussion around opportunities, challenges, and progress in advancing research scholarship through new technologies and practices. Force11 aims to bring about a positive change in scholarly communications through both the effective use of information technology and a deeper understanding of the nature of evolving scholarly practice.

The FORCE2106 conference included a variety of session formats including workshops, keynote talks, presentations and panel discussions, a hack-a-thon, demos, and poster sessions. The audience included a diverse group of participants including researchers across various disciplines, biocurators from Model Organism Databases and other databases, librarians, publishers, technologists, information scientists, funders, and administrators from academic and private institutions around the world. The keynote talks include speakers from Harvard, Indiana University at Bloomington, the Alan Alda Institute, and the US National Institutes of Health.

Highlights from FORCE2016:

The funds from this micro grant were used to sponsor the FORCE2016 conference by way of a best poster/demo award. The awards went to:

  • Centralizing content and distributing labor: a community model for curating the very long tail of microbial genomes. Authors: Timothy Putman, Sebastian Burgstaller-Muehlbacher, Andra Waagmeester, Chunlei Wu, Andrew I. Su, Benjamin M. Good.
  • Too big to share? Scaling up knowledge transfer workflows from little science to big science. Authors: Bernadette M. Randles, Ashley E. Sands, Christine L. Borgman.
  • Think global, act local: innovating nationally with the Italian ORCID hub. Authors: Michele Mennielli, Andrea Bollini, Josh Brown.

Slides from the conference are available in the FORCE2016 FigShare collection at https://force16.figshare.com/

The video archives will be soon available on the FORCE2016 website.

Learn more about ISB Micro-Grants and how to apply at http://biocuration.org/community/microgrants/

New ISB Mailing List

ISB is now ready to distribute your messages to the biocuration community through the new mailing list.

To subscribe to the list and receive instructions for use, please send a blank message to this address. ISB moderators will process your request as promptly as possible.

When messaging biocurators via the ISB Mailing List, please consider:

ISB Mailing List User Agreement: The ISB is a non profit organisation for biocurators, developers, and researchers with an interest in biocuration. The society promotes the field of biocuration and provides a forum for information exchange on the topics of interest to its members. The ISB will do its best to only distribute information deemed pertinent to the field of biocuration, and it reserves the right to prevent posting to this mailing list in the event of use of inflammatory and/or abusive language, unwelcome advertisement, and in other events when appropriate. The ISB Mailing List is moderated by members of the ISB Executive Committee.

Please contact ISB Executive Committee with comments and questions.

Recipient of the Inaugural Biocuration Career Award 2016

It is our great pleasure to announce the recipient of the Inaugural Biocuration Career Award – 2016

 

Dr. John Westbrook
Dr. John Westbrook

In April of 2016 the International Society for Biocuration awarded its inaugural Career Award to Dr. John Westbrook.

John works at the Research Collaboratory for Structural
Bioinformatics Protein Databank (RCSB PDB), where his work over the past 20+ years has helped launch the field of biocuration.

He designed the PDBx/mmCIF data representation for biological macromolecular data used by PDB for data submission (now having 117K structures), which is utilized by a variety of software applications to validate a PDB submissions and analyze PDB data. John keeps the model and related tools up to date with new definitions and modeling based in new technologies, which provisions for community buy-in and participation. Searching for “protein data bank” OR “protein databank” in Pubmed gives 2988 publications. PDB is used by Pharma and biotech companies.

John’s data modeling of protein structures and his development of a variety of software tools has been pivotal to make these data maximally useful to a very large and diverse community. Representation of molecular complexity of macromolecular structure, experimental methodologies, and biological context has enabled John to facilitate integration with a spectrum of biomedical resources.

Our most sincere congratulations to John!

Best regards,

Your colleagues at the ISB Executive Committee, and the 2016
Biocuration Awards Committee

The 2016 Biocuration Awards Committee are:
Melissa Haendel – Chair
Emma Ganley 
Takashi Gojobori
David Landsman
Michele Magrane
Kimberly Van Auken
Alfonso Valencia

ISB White Paper

Please join us in drafting a white paper on behalf of the International Society for Biocuration.

This document was first presented as a draft to the community during the  Workshop on Curation Innovation at the 9th International Biocuration Conference in Geneva, Switzerland.

Your suggestions and contributions can be added on the shared document available online as a Google Document at http://tinyurl.com/ISB2016-WS2-whitepaper

Announcing 2016 ISB Travel Fellowships Awardees

Congratulations are in order!

Please join us as we extend our best wishes to the winners of the 2016 ISB Travel Fellowships to attend the
9th International Biocuration Conference to be held in
Geneva, Switzerland on April 10-14.

This year’s ISB Travel Fellowships were awarded to:

Alba Gutierrez
Alex Vesztrocy
Francesco Russo
Hayda Almeida
Hayley Dingerdissen
Jean-Philippe Gourdine
Jinmeng Jia
Qingyu Chen
Timothy Putman

Congratulations again, and see you in Geneva!

Our sincere thanks to the 2016 ISB Travel Fellowships Committee:
Cecilia Airghi, Pascale Gaudet, and Sandra Orchard.

2016 Biocuration Career Award

The International Society for Biocuration
is proud to announce the first
Biocuration Career Award.

 

The Biocuration Career Award recognizes biocurators in non-leadership positions who have made sustained contributions to the field of biocuration.

The nominations will be reviewed by the newly formed ISB Award Committee, comprised of one member of the ISB’s Executive Committee (ISB-EC) and six (6) additional members from the wider research community; these members were nominated by the ISB-EC based on diversity in area of expertise, organization type, role, and geographic location.

Who can nominate and/or be nominated?

  • Any currently active ISB member may nominate anyone in the field of biocuration, whether the potential nominee is a member of ISB or not.
  • Members of the ISB can make no more than 1 nomination per year.
  • Those who hold Principal Investigator or Group Leader positions, or who are current members of the ISB Executive Committee or the ISB Award Committee, are not be eligible for this award.
  • Self-nominations will not be considered.

How to submit your nomination:

  • Nominations should be sent via email to the award committee at intsocbio [at] gmail.com with the subject line “Biocuration Career Award Nominations“.
  • The nomination email should contain the following fields:
    • Nominator details (name, e-mail and affiliation, member of ISB);
    • Nominee details (name, e-mail and affiliation);
    • Short list of scholarly contributions (a maximum of 50 words);
    • Brief description of why you are recommending this person (a maximum of 350 words).

The recipient of the award will be invited to give a presentation at the following International Biocuration Conference, with all expenses paid by the ISB.

Important Dates for 2016

Deadline to submit nominations: Sunday 20-March-2016
Award Announcement: April, 2016 at the 9th International Biocuration Conference

 

Sincerely,

The 2016 ISB Award Committee.

 

The 2016 “Biocuration Career” Award Committee are:
Melissa Haendel (Chair)
Emma Ganley
Takashi Gojobori
David Landsman
Michele Magrane
Kimberly Van Auken
Alfonso Valencia

CTD turned 10!

The Comparative Toxicogenomics Database (CTD) recently celebrated its 10-year anniversary on the web. Since its beginnings, CTD has been devoted to centralizing and harmonizing information about genes responding to environmental toxic agents across diverse species. The database has now evolved into a premier toxicology resource, allowing scientists to discover information and develop testable hypotheses about the biological consequences of chemical exposure (both environmental and drug). Today, CTD includes over 24 million toxicogenomic connections relating chemicals/drugs, genes/proteins, diseases, taxa, phenotypes, Gene Ontology annotations, and pathways.

This celebratory milestone was recently published in the journal Nucleic Acids Research, which summarized the history and evolution of CTD, including descriptions of curation processes, new content, and enhanced visualization and analysis tools. The article also detailed a new “Pathway View” tool that leverages gene interaction data from BioGRID to allow users to build unique toxicogenomic interaction modules connecting chemical exposure to disease events.

As it was ten years ago, CTD today is still managed by a small team of biologists and software engineers who work with both the toxicology and biocuration communities to advance understanding of chemical-gene-disease data and how best to extract and code this information from the published literature. All CTD data are freely available to the public. As well, CTD content has been disseminated further into the scientific community via more than 55 other databases that routinely incorporate CTD’s annotations. If interested in establishing links to CTD data, please notify us and follow these instructions.

CDT_10yearsCDT

2013/2014 ISB Executive Committee

The term of the 2013/2014 ISB Executive Committee (EC) starts on November 1st, 2013. We are delighted to welcome Melissa Haendel and Jennifer Harrow to the ISB EC, joining Teresa Attwood, Alex Bateman, J. Michael Cherry, Pascale Gaudet, Monica Munoz-Torres, Claire O’Donovan, and Marc Robinson-Rechavi. We are grateful to Renate Kania and Chisato Yamasaki for having served on the committee since 2011.

DORA

The ISB signs the San Francisco Declaration on Research Assessment (DORA), initiated by the American Society for Cell Biology (ASCB) together with a group of editors and publishers of scholarly journals, that aims to improve the ways in which the outputs of scientific research are evaluated.

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