Category: The ISB

Call: Host the 13th International Biocuration Conference

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Dear Colleagues,

The Executive Committee of the International Society for Biocuration would like to once again invite tenders to host the 13th International Biocuration Conference during the Northern Spring or Summer of 2020.

Individuals and organizations interested in applying may do so by sending a proposal to the ISB Executive Committee (intsocbio@gmail.com) on or before August 31,  2018.

The successful bidder will be notified by October 1,  2018. The ISB Executive Committee will publicly announce the selected organization or individuals during the 12th International Biocuration Conference, to be held in Cambridge, UK in April, 2019.

Format:  

Proposals should be short; length should not exceed one side of an A4 or US letter size sheet, using 11 point font.

The proposal should contain:

  • The name and institution of the local organizer
  • Details of the proposed venue for up to 350 participants
  • The range of dates available for the conference
  • A brief outline of a strategic plan to attract a broad range of participants from the Biocuration community
  • As fair gender representation is positively encouraged by the ISB; we would also like to know how the applicant intends to promote this.

In a continued effort to bring our meeting to curators in all geographic regions, we strongly encourage ISB members to put forward proposals to bring the ISB meeting to your region once again, or for the first time! Based on ISB meeting region rotation, for ISB 2020 we are encouraging a location in the Americas, but will also consider other locations.

REGIONS ROTATION:

Asia and Australasia

Europe

Americas

 

We look forward to hearing from you!

Your colleagues at the ISB Executive Committee.

ISB response to NIH RFI: NIH Strategic Plan for Data Science

On behalf of the International Society for Biocuration (ISB), we provide the following response to the Request for Information: NIH STRATEGIC PLAN FOR DATA SCIENCE, which describes NIH’s overarching goals, strategic objectives, and implementation tactics for modernizing the NIH-funded biomedical data-resource ecosystem.

We are a community highly involved in the development and maintenance of biological and biomedical databases, and the task of biocuration: the translation and integration of information relevant to biology into a database enabling the integration of the scientific literature as well as large data sets (distilling data into knowledge). The International Society for Biocuration (ISB) community includes, among others, biocurators, software developers, bioinformaticians, and standard developers. We are thus familiar with the pitfalls of current funding mechanisms for databases and recognize the importance of developing a different model which is what the strategic plan for data science intends to address. In this response, we focus exclusively on selected aspects of Goal 2: Promote Modernization of the Data-Resources Ecosystem, and Goal 4: Enhance Workforce Development for Biomedical Data Science.

Information requested:

* The appropriateness of the goals of the plan and of the strategies and implementation tactics proposed to achieve them:
Goal 2: Promote Modernization of the Data-Resources Ecosystem
Whilst overall the ISB is generally supportive of the statements made in this RFI, we feel that some terminology used needs to be improved. The RFI refers to databases and repositories indistictively. It should be noted that the term database is an overarching term, and we see the separation as being between primary data repositories, such as members of the INSDC (http://www.insdc.org/), with set submission criteria and minimal subsequent expert curation of the data (biocuration), and Knowledgebases [1]. Then both repositories and knowledgebases are types of databases. We suggest that the terms database, repositories and knowledgebase are clearly defined. Here are our proposed definitions and changes to the text:

A database is a computerized storehouse of data that provides a standardized way for locating, adding, removing, and changing data [2].

Data Repositories and Knowledgebases: What’s the Difference?
Data repositories and knowledgebases are both types of databases which store, organize, validate, and make accessible the core data related to a particular system or set of technologies. In the case of a data repository, the data is deposited by researchers following a set of guidelines and, other than ensuring the guidelines are adhered to, receives minimal subsequent input or modification.

Knowledgebases accumulate, organize, and link growing bodies of information related to the deposited data. A knowledgebase may contain information about gene models, transcript/protein expression patterns, splicing variants, localization, and protein-protein interaction and pathway networks related to an organism or set of organisms. Knowledgebases typically require significant semi-automated as well as manual biocuration by domain experts (e.g., literature-based gene ontology and phenotype annotations) beyond the quality assurance/quality control and annotation needed for data repositories.

We propose that the definition of biocuration is added to the glossary.

Biocuration is the extraction of knowledge from unstructured biological data (typically but not limited to publications) into a structured, computable form. Biocurators are typically Ph.D. level biologists, often with lab bench experience, coupled with
specialized expertise in computational knowledge representation. Their work entails the synthesis and integration of information from multiple sources, including, for example, peer-reviewed papers, large-scale projects, or conference abstracts. They contact authors directly for clarification, digest supplemental information, and resolve
identifiers, in order to accurately capture a researcher’s conclusion and their evidence for that conclusion. Biocurators strive to distill the current ‘best view’ from conflicting sources and ensure that their resources provide data that is not only
Findable, Accessible, Interoperable, and Reproducible (FAIR), but also Traceable, appropriately Licensed, and inter-Connected (collectively, the FAIR-TLC principles) [3].

Goal 4-Enhance Workforce Development for Biomedical Data Science
Again, the ISB is in favor of this proposed goal as training different stakeholders in data science is key for the NIH to achieve the stewardship goals outlined in the NIH-wide strategic plan. However, the enhancement of the workforce is only discussed in terms of data-scientists, and we believe biocurators are relevant stakeholders as well.
In section 4.1 “In addition, NIH will recruit a cohort of data scientists and others with expertise in areas such as project management, systems engineering, and computer science from the private sector and academia for short-term (1- to 3-year) national service sabbaticals. These “NIH Data Fellows” will be embedded within a range of high-profile, transformative NIH projects such as All of Us, the Cancer MoonshotSM and the BRAIN initiative and will serve to provide innovation and expertise not readily available within the federal government.”
We think that biocurators would offer a unique perspective to these NIH projects given their training in formulating and using standards, in data analysis and integration, working with a variety of research communities for adoption of FAIR principles [3]. We suggest that biocurators are explicitly listed and considered as potential “NIH Data Fellows”.
One of the ISB goals is to train the next generation of biocurators, and have developed/collected training materials that could be used by NIH for training grant reviewers (https://www.biocuration.org/dissemination/biocuration-training-materials/).

* Opportunities for NIH to partner in achieving these goals:
NIH should establish a closer interaction with the International Society for Biocuration (ISB) to learn about biocuration and data science. ISB could collect/prepare training materials that could contribute to NIH training goals. ISB members could serve as NIH Data Fellows.
NIH should consult FAIRsharing (a catalogue of data preservation, management and sharing policies from international funding agencies, regulators and journals) and the BioDBcore guidelines [4-5], a community-defined, uniform, generic description of the core attributes of biological databases; ensuring consistency and interoperability between resources.
Encourage and provide guidance to R01 and R21 proposal writers to budget correctly for data sharing. Dumping data into a repository is not trivial, it takes time to deposit data with adequate information. There needs to be clear instructions to grant recipients to submit structured data to journals and/or databases. The biocuration community could help identify a few examples of how such structured data can be submitted. In addition, minimal common standards for databases are already described in BioDBcore guidelines, mentioned in the previous point.
There should be more emphasis on how NIH intramural researchers could collaborate with external groups to link resources. The plan discusses linking all NIH data resources in detail. However, there is a need to also link to external resources and vice-versa.

* Additional concepts that should be included in the plan:
We propose that the definitions of database and biocuration be added to the glossary.

* Performance measures and milestones that could be used to gauge the success of elements of the plan and inform course corrections:
Nothing to comment at this point

* Any other topic the respondent feels is relevant for NIH to consider in developing this strategic plan:

Sustained long-term funding for key resources. Whilst we appreciate that resources need to be constantly re-evaluated and shown to be keeping pace with the demands of new technologies and new use cases, constantly moving from one short-term grant to another, with no guarantee of renewed funding is not beneficial to the resource growth and the user community that relies on it.

References:
1. Gabella C, Durinx C, Appel R. Funding knowledgebases: Towards a sustainable funding model for the UniProt use case. F1000Res. 2017 Nov 27;6. Pii: ELIXIR-2051. doi: 10.12688/f1000research.12989.1. eCollection 2017. PubMed PMID: 29333230; PubMed Central PMCID: PMC5747334.

2. Mount D. Bioinformatics: Sequence and Genome Analysis, Second Edition (2004). Chapter 2. Cold Spring Harbor Laboratory Press

3. International Society for Biocuration. Biocuration: Distilling data into knowledge. PLOS Biology (2018) in press.

4. Gaudet P, Bairoch A, Field D, Sansone SA, Taylor C, Attwood TK, Bateman A, Blake JA, Bult CJ, Cherry JM, Chisholm RL, Cochrane G, Cook CE, Eppig JT, Galperin MY, Gentleman R, Goble CA, Gojobori T, Hancock JM, Howe DG, Imanishi T, Kelso J, Landsman D, Lewis SE, Karsch Mizrachi I, Orchard S, Ouellette BF, Ranganathan S, Richardson L, Rocca-Serra P, Schofield PN, Smedley D, Southan C, Tan TW, Tatusova T, Whetzel PL, White O, Yamasaki C; BioDBCore Working Group.Towards BioDBcore: a community-defined information specification for biological databases. Database (Oxford). (2011) baq027. doi:10.1093/database/baq027. Print 2011. PubMed PMID: 21205783; PubMed Central PMCID: PMC3017395.

5. Gaudet P, Bairoch A, Field D, Sansone SA, Taylor C, Attwood TK, Bateman A, Blake JA, Bult CJ, Cherry JM, Chisholm RL, Cochrane G, Cook CE, Eppig JT, Galperin MY, Gentleman R, Goble CA, Gojobori T, Hancock JM, Howe DG, Imanishi T, Kelso J, Landsman D, Lewis SE, Mizrachi IK, Orchard S, Ouellette BF, Ranganathan S, Richardson L, Rocca-Serra P, Schofield PN, Smedley D, Southan C, Tan TW, Tatusova T, Whetzel PL, White O, Yamasaki C; BioDBCore Working Group. Towards BioDBcore: a community-defined information specification for biological databases. (2011) Nucleic Acids Res. 39(Database issue):D7-10. doi:10.1093/nar/gkq1173. Epub 2010 Nov 18. PubMed PMID: 21097465; PubMed CentralPMCID: PMC3013734.

Additional information requested:
Name: Cecilia Arighi, Nicole Vasilevsky and Sandra Orchard
Work Email: intsocbio@gmail.com
Name of Organization:International Society for Biocuration (ISB) (www.biocuration.org)

 

For members of advocacy groups or professional societies (optional): Please indicate your role and indicate whether you are responding on behalf of your organization.
Cecilia Arighi is the Chair of the Society, Nicole Vasilevsky is the Secretary and Sandra Orchard the Treasurer. This RFI is submitted on behalf of the ISB.

Sent April 01, 2018

Biocuration Exchange Fellowship

The International Society for Biocuration is pleased to announce Luana Licata, from the University of Rome Tor Vergata as the first recipient of the Biocuration Exchange Fellowship. During her fellowship, she will visit the Protein Function Team at EMBL-EBI and the Gene Annotation Team, UCL London, to learn Gene Ontology (GO) annotation.

The Biocuration Exchange Fellowship is a short-term fellowship to promote collaborations and exchanges between groups working in the field of biocuration. The fellowship funds the visit of a biocurator to another laboratory or organization with long experience in biocuration. This visit constitutes a unique opportunity to learn new methods, experience biocuration in different settings and/or in different fields, and to establish mutually beneficial collaborations across groups and disciplines.

More information on Biocuration Exchange Fellowship can be found here.

FSCI Summer Training

 The FORCE11 Scholarly Communications Institute at the University of California, San Diego is a week long summer training course, incorporating intensive coursework, seminar participation, group activities, lectures and hands-on training. Participants will attend courses taught by world-wide leading experts in scholarly communications. Participants will also have the opportunity  to discuss the latest trends and gain expertise in new technologies in research flow, new forms of publication, new standards and expectations, and new ways of measuring and demonstrating success that are transforming science and scholarship.

FORCE11 Scholarly Communication Institute (FSCI)

July 30 – August 3, 2018
University of California San Diego (UCSD)
UCSD School of Medicine – Medical Education and Telemedicine (MET). La Jolla, CA 92161 USA

https://www.force11.org/fsci/2018

Contact name: Stephanie Hagstrom
info@force11.org

Eleanor Williams on winning the Biocuration Award 2018

mouse dissociated embryonic kidney cells reforming into a kidney organoid
Mouse dissociated embryonic kidney cells reforming into a kidney organoid – from the Image Data Resource

In mid-January, I got an email saying I had won the 2018 Biocuration Career Award from the International Society for Biocuration!  I was excited to win the award, thrilled to be going to the Biocuration conference in China and wondered what I would say in a presentation about “my career” at the conference.

That week I had just started in a new biocuration position and after hearing about the award, my new colleagues suggested I give a lunchtime talk on my scientific background so that the others in the team could get to know me better.  As I worked on a timeline and slides about each of my past biocuration positions, I realized that there actually was a lot that I wanted to say.

I have worked on several different projects over the last 17 years that I would describe as “biocuration.”  These jobs have varied greatly.  I started curating data in a research position at the Fred Hutchinson Cancer Research Center, collating information about mouse and human olfactory receptors. Then back in the UK I worked in a more “service” role in the established resources of ArrayExpress and Expression Atlas at the European Bioinformatics Institute (EMBL-EBI), curating data submissions, talking with submitters and I started to delve into the world of ontologies.  More recently I have been the primary curator setting up the metadata processing pipeline for the Image Data Resource at the University of Dundee.  This resource was built from scratch, and went where few others have dared to go, creating a robust data repository for complex bioimaging data, with the added value of metadata integration. It has been immensely satisfying to see this project grow both in size and reputation.

Now, after spending a lifetime in academia, I am off on a new adventure working as a Scientific Curator for a company, Genomics England, set up to  to provide a genomic medicine service for the UK National Health Service using data from the 100,000 Genomes Project.

My biocuration career has been partly driven by the external forces i.e. what fits with family life and funding opportunities, and partly by my own interests and desire to develop skills.  In hindsight each job seems a logical progression from the last, with new experiences, new skills, new technologies (github and conference calling were not around in the early 2000s) and new challenges that have made for a fun and interesting career.

I am very proud to receive the International Society of Biocuration Career Award.  It has helped me reflect on my work and recognize that I have had a career and not just a series of jobs!  I hope that by sharing my story and the skills I have found to be most useful, I can help others think about their own journeys.  It is also wonderful to appreciate the international community of biocurators who meet together to share experiences and recognize the importance of data and biocuration in the sciences. I am looking forward to meeting many of you in Shanghai!

Dr Eleanor Williams will be presenting her work at the International Biocuration Conference in Shanghai in April 2018, her talk will be on:

Title: Curating bioimaging data – lessons from the first 40 terabytes

Synopsis: I have experienced three very different types of biocuration work in my career. My first taste of biocuration was in a research lab curating information about olfactory receptor genes. I then moved to work on the well-established functional genomics databases of ArrayExpress and the Expression Atlas at EMBL-EBI curating data submissions submissions. From there I moved to a project at the University of Dundee setting up the Image Data Resource for bioimaging data. This was my biggest curation  challenge, starting almost from scratch to develop a method to capture the biomolecular, experimental and analytic annotations associated with images, and to create a pipeline to populate the database. I will describe the most useful biocuration skills I have learnt and some of the challenges I’ve encountered. I will finish by describing my new position, working as a scientific curator in a company performing analyses of the genomes of patients with rare diseases.

 

ISB members’ survey

The ISB is continually looking to improve and optimise its services for members. To help improve the benefits of your membership we are inviting you to fill in a short survey. In this way, you can tell us what you have observed so far and what you would like to see.

We appreciate your participation to help us ensure that we meet (or surpass) all your expectations.

This survey should take approximately 5 minutes to fill in.

Complete survey on Google Forms

We would like to have all responses back by March 21st, 2018 so we can report back to the community at the Biocuration meeting in Shanghai in April.

If you have any problems accessing Google forms, please contact the ISB Exec using intsocbio [at] gmail.com

New ISB Executive Committee (2017-2018)

The election of the 2017 – 2018 ISB Executive Committee (EC) took place last October. Please join us again in giving a warm welcome to Nicole Vasilevsky and Rama Balakrishnan to the Executive Committee, and congratulating Sylvain Poux for his reelection.

Cecilia Arighi has been elected as the new Chair of ISB, Nicole Vasilevsky is the new Secretary, and Sandra Orchard continues serving as Treasurer for the 2017-2018 period. The Executive Committee is also composed by Suzanna Lewis, Peter McQuilton, Andrew Su, and Zhang Zhang. As always, please reach out to any of us on the ISB EC as your representatives. The official handover date for the new EC took place November 1st.

After many years of service to the Biocuration community as members of the ISB Executive Committee, we bid farewell to Melissa Haendel and Monica Munoz-Torres. We are thankful for their invaluable contributions to the improvement of the International Society for Biocuration.

We again would like to thank all the candidates for their time and effort in running for election, and of course, all the ISB members who voted. Your participation in the society’s activities is greatly appreciated. We would like to also thank this year’s volunteers which oversaw the electoral process:

  • 2017 Nominating Committee: Pascale Gaudet, Stanley Laulederkind,  Raja Mazumder, Elvira Mitraka, and Randi Vita.
  • Elections Officer: Mary Ann Tuli
  • Membership Officer: Lorna Richardson

Announcing the 2018 Biocuration Awards

The International Society for Biocuration (ISB) is happy to announce the 2018 Biocuration award. Next year, the ISB will give the Biocuration career award to a person who has made sustained contributions to the field of biocuration.

Biocuration Career Award

The Biocuration Career Award recognizes biocurators in non-leadership positions who have made sustained contributions to the field of biocuration. The recipient will be required to present a talk at the Biocuration 2018 Conference, with expenses paid by the ISB. The nominations will be reviewed by the ISB Award Committee, comprised of one member of the ISB’s Executive Committee (ISB-EC) and six (6) additional members from the wider biocuration 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 award.
  •  Those who hold Principal Investigator or Group Leader positions are not eligible for the Biocuration Career Award.
  • Current members of the Executive Committee or the ISB Award Committee are not eligible for the awards.
  • Self-nominations will not be considered.

 How to submit your nomination:

  • Nominations should be sent via email to the award committee at intsocbio@gmail.com with the subject line “Biocuration 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 upcoming International Biocuration Conference, in Shanghai, China, from 08-11 April 2018, with all expenses paid by the ISB.

Deadline for submitting nominations: 15 December 2017

Results of 2017 Elections of ISB Executive Committee

The results of the 2017 Elections of the
ISB Executive Committee are in!

Congratulations to 
Dr. Rama Balakrishnan, Dr. Nicole Vasilevsky,
and Dr. Sylvain Poux!

 

We express our sincere gratitude to all ISB members who participated in this year’s electoral process with your vote. One hundred and four out of 226 eligible ISB members voted in this year’s election; a breakdown of the votes we captured is attached.

Your votes have elected Rama and Nicole as new members, and re-elected Sylvain for a second term in the Executive Committee. Rama and Nicole will fill two open positions when the terms of Monica Munoz-Torres and Melissa Haendel come to completion on 31-October-2017.

Please join us in thanking Moni and Melissa for all their work over the past years! 

We would like to also express our sincere gratitude to the rest of the nominated candidates who considered volunteering their time as part of the ISB-EC this year:

Dr. Sirarat Sarntivijai, Dr. Taner Z Sen, and
Dr. Christopher Southan.

We are also very grateful with the following ISB members who volunteered their time for a successful execution of the 2017 EC election:

  • 2017 Nominating Committee: Pascale Gaudet, Stanley Laulederkind,  Raja Mazumder, Elvira Mitraka, and Randi Vita.
  • Elections Officer: Mary Ann Tuli
  • Membership Officer: Lorna Richardson

Thank you again for participating in the 2017 ISB Electoral Process!

Sincerely,
Your Colleagues at the ISB Executive Committee. 

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