Category: The ISB

RESULTS OF 2019 ELECTIONS OF ISB EXECUTIVE COMMITTEE

The results of the 2019 Elections of the ISB Executive Committee (EC) are in:

Congratulations to Ruth Lovering and Randi Vita!

Thank you to the ISB members who participated in this year’s election.

Welcome Ruth and Randi as new EC members, who are filling two open positions when the terms of Pete McQuilton and Andrew Su come to completion on 31 October 2019.

We would like to also express our sincere gratitude to Paola Roncaglia and Tamsin Jones, who who considered volunteering their time as part of the ISB EC this year.

Please join us in thanking Pete and Andrew for all their work over the past years.

We are also very grateful with the following ISB members who volunteered their time for a successful execution of the 2019 EC election:

2019 Nominating Committee:

  • Lorna Richardson (Elections officer)
  • Marc Robinson-Rechavi
  • Susan Clew
  • Rachael Huntley
  • Zhang Zhang
  • Raja Mazumder

Thank you again for participating in the 2019 ISB electoral process.

Sincerely,
Your Colleagues at the ISB Executive Committee

Registration open for Biocuration 2020

Registration for the Biocuration 2020 conference is now open. The conference will be held from May 17-20, 2020 in Bar Harbor, Maine, USA.

Please be aware of key dates below:

October 31, 2019 – Paper Submission Deadline
January 24, 2020 – Abstract  and Workshop Submission Deadline
March 6, 2020 – Notification of Acceptance
April 6, 2020 – Early Bird Registration Ends
May 8, 2020 – Registration Deadline


More information is available on the Biocuration 2020 website.

Call for Papers: 13th International Society for Biocuration meeting, DATABASE Journal Virtual Issue

The International Biocuration Conference is a unique event for biocurators and developers of biological databases to discuss their work, promote collaborations, and foster a sense of community in this very active and growing area of research.  For the 13th International Biocuration Conference in Bar Harbor, Maine, USA, you are invited to submit your work for publication. This call for papers is done in collaboration between DATABASE: The Journal of Biological Databases and Curation and the International Society for Biocuration. The DATABASE journal will publish an online Virtual Issue of the accepted papers. See below for a link to last year’s issue. This is the perfect opportunity to enhance the recognition of your work and of our profession by the greater biological research communities.  Additionally, the Biocuration 2020 scientific committee will consider inclusion of accepted papers for full oral presentations at the conference. Note that you must also register and submit your abstract separately for the meeting. 

The manuscript review process will be expedited by the journal’s associated editors and they will thus need to be firm on the submission deadlines:

Submission deadline: October 31, 2019
First decisions: December 6, 2019
Deadline for revisions: January 10, 2020
Final decisions: February 28, 2020
Conference: May 17-20, 2020

Authors wishing to submit to DATABASE for the 2020 Biocuration Virtual issue should go to the DATABASE home page and click on the “Submission Site”  Submit menu option after having read the “Instructions to Authors”. Authors should CLEARLY state that they are submitting the manuscript for consideration for the Biocuration 2020 conference so that the DATABASE staff will ensure appropriate fast-track for inclusion in this meeting’s proceedings.  In addition, within the database submission form, you should also select “Biocuration Conference Paper” as a manuscript type.  We look forward to your participation at Biocuration 2020, the 13th International Biocuration Conference.

IMPORTANT NOTE: Submitting a paper to DATABASE does not in itself automatically register you to give a talk or poster at the Biocuration 2020 conference.  You must register for the meeting and submit your abstract separately to be considered for a presentation.  Information about abstract submission for the meeting will be announced soon.

The proceedings of the past International Biocuration Conference, the Biocuration Virtual Issue are online.

ISB membership payment issues resolved

If you have delayed joining the Society, or renewing an existing membership due to the problems we have been experiencing with our payment system, we are happy to announce that these have now been resolved and invite you to start/renew your membership now (www.biocuration.org/membership/membership-levels/).


Please remember you must be a member of the Society to vote in the upcoming elections, which will be held from October 14-20, 2019. More information about the election is here. 


We apologize for any inconvenience we may have caused you.

Deadline extended for ISB Executive Committee (EC) Election 2019

The deadline for nominations for the ISB EC Election has been extended to 15 September, 2019

The election of the new International Society for Biocuration Executive Committee (ISB EC) will be held from 14 -20 October, 2019. The Executive Committee is composed of nine (9) members, each with a 3-year term. Being a member of the Executive Committee is a great way to become directly involved with the work of our society, and contribute to the decisions that are taken on behalf of the biocuration community. We would like to encourage all members interested in running for election to get involved in the process.

Serving on the ISB EC minimally involves attending monthly (1 hour)  teleconference meetings, following up on any action items from meetings, and  promoting the ISB’s activity to members and non-members. Examples of activities performed by EC members include reviewing micro-grant submissions, preparing call for participation for hosting Biocuration meetings, preparing materials for the ISB election, monitoring ISB mail and maintaining the website. There are specific positions such as Chair, Secretary and Treasurer that will require a larger time commitment, as they will be in charge of leading the steps of the EC and by extension the membership.

This year, there are two (2) open positions, as the terms of Andrew Su and Pete McQuilton will come to completion. (The current ISB EC members are here.)

2019 Electoral Process

A) The Nominating Committee:

A Nominating Committee (NC) has been formed to oversee the electoral process, to review applications, and establish the final list of candidates. We are very grateful for their assistance with the execution of this election. The members of the 2019 Nominating Committee are:

  • Marc Robinson-Rechavi 
  • Susan Clew
  • Rachael Huntley
  • Zhang Zhang
  • Raja Mazumder

B) Instructions to Candidates: 

  1. If you would like to run for a position on the Executive Committee, you must first register your intent with the NC by emailing isb-election-2019@googlegroups.com
  2. Please fill out this form by 15 September 2019, which includes a ‘statement of intent‘, a brief biographical sketch, and a ‘conflict of interests‘ statement describing any activities, memberships of other associations, editorial positions on journals, etc. (Please email us at isb-election-2019@googlegroups.com if you are unable to access this form.)

C) Timeline:

  • Nominations will be received until 15 September 2019.
  • The NC will review all candidacies and share their selections with the ISB Executive Committee by 29 September 2019.
  • Candidates must be announced to the membership and on website (with letters of intent) by 11 October 2019.
  • Voting will take place online over the course of one week from 14 October – 20 October 2019. (Further details about the voting process will be shared closer to the date). Lorna Richardson will act as election officer.
  • Only paying members* with registration fees cleared on or before 11 October 2019 will be allowed to vote. If you pay your registration via bank transfer, please allow at least 2-3 working days for the payment to be processed.

*Note – please contact us at intsocbio@gmail.com if you have issues with registering or renewing your membership. Known issues exist with our membership payment system.

The Nominating Committee is looking forward to receiving your applications!

Qaaifah Gillani Syed and Zannatun Nayema awarded travel fellowships to BC2 conference

Congratulations to Qaaifah Gillani Syed and Zannatun Nayema, who have been selected for the [BC]2 Travel Fellowships.

Qaaifah Gillani Syed (University of Kashmir, IN)
Qaaifah Gillani Syed is a PhD student in the group of Shaida Andrabi in the Department of Biochemistry at the University of Kashmir in India. Her research is focusing on Cancer Biology and by using different bioinformatics tools, she is studying the mitotic and oncogenic role of different kinases.
Zannatun Nayema (Kanazawa University, JP)
Zannatun Nayema is a first-year PhD student in the group of Atsushi Tajima in the Department of Bioinformatics and Genomics at the Kanazawa University in Japan. Her main research focus is on the analysis of Genome Wide Association Studies connected to the Metabolic syndrome (a cluster of conditions that increases the risk of heart disease, stroke and diabetes) and polygenic risk score analyses.

Read more about their fellowships here. Read the announcement about the travel fellowship opportunity here.

Biocuration 2019 – Workshop Reports

GREEKC

The COST Action GREEKC held a workshop inviting community feedback on its work to align efforts to curate, standardize, archive and share information about the regulation of gene expression. A status report was presented by the Work Group leaders, and feedback on the organisation of the next events was received. Some of the feedback that GREEKC needs can still be given through these surveys: “The Work of Curators” and “The Experience of Curators”. One of the main discussion points concerned a re-design of the Sequence Ontology, and a comprehensive set of term requests necessary to annotate the regulatory genome are now being worked on with the SO team (Eilbeck group, Utah). The status of the SO was further discussed with a much wider group of users within the Biocuration community, at an impromptu lunch discussion later during the Biocuration 2019 main event.  We hope to be able to present a significantly updated SO at our upcoming workshops, the first week of November 2019.

The IMEx Consortium of Molecular Interaction databases

The IMEx Consortium is a collaboration between interaction databases willing to share data and curation effort. This workshop focused on the coordination and further definition of curation practices. Topics covered were curation coordination tools such as IMExcentral and targeted curation practices, glycan-related physical interactions, nucleic acid-protein interactions and the influence of variation upon interaction outcome. In a joint session with the GREEKC community, transcription factor-target gene interactions and causal relationships were also discussed, developing already active areas of collaboration between the two communities on the representation of this type of data. If you are interested in contributing to the work of IMEx, contact us on intact-help@ebi.ac.uk

Practical ontology applications, tooling and interoperability best practices for FAIRification

This workshop provided an interactive introduction to FAIRification and interoperability best practices in the context of ontology services and semantic web technologies such as the OBO Foundry, ontology service suite at the EMBL-EBI and ELIXIR’s Recommended Interoperability Resources (RIRs). The day started with a general introduction to interoperable data management and FAIR principles before a series of talks and practical demonstrations on resources including the OBO Foundry in general, and specifically OBO core, the single cell expression Atlas (scAtlas), the EMBL-EBI Ontology Tooling Suite and a number of ELIXIR Recommended Interoperability Resources (RIRs) such as FAIRsharing (slides), InterMine and BridgeDb. The workshop concluded with an open-floor discussion on the needs of the biocuration community with respect to FAIR resources and ontologies, and ontology and FAIRification best practice.

Curating Evidence for Gene:Disease Validity for Clinical Omics

Three Gene Curation Coalition (GenCC)  member groups (Genomics England PanelApp, ClinGen and Orphanet) presented an overview of their gene curation strategies and focus, leading to dialogue about the merits and challenges of each approach. The conversations reinforced some of the challenges we face in performing manual curation of gene:disease associations, and the rules we have in place to ensure consistent annotation. We reviewed where we could most benefit from incorporating additional ontologies and mappings into our resources, and areas that required further clarity; it quickly became apparent that even the term ‘panel’ can be ambiguous given its different use between resources- are we talking about a panel of genes, or a panel of people? Curators are already familiar with the need for consistent curation terminology, and the workshop provided the perfect opportunity to poll attendees for their views on clinical evidence descriptions. We were then able to demonstrate how the recent efforts of the GenCC to establish consensus terms for validating gene:disease associations will allow us to work together and allow efficient data sharing. Overall we hope that the workshop provided an insight in to the roles and diversity of data curation in the clinical setting.

Equality, Diversity, and Inclusion (EDI)

The introductory slides explained what these terms mean and how they are being embraced by scientific institutes in different countries. This was followed by a more in-depth presentation by the invited speaker Dr Saher Ahmed, head of EDI at the Wellcome Sanger Institute, Cambridge, UK, who discussed gender discrepancies in the workplace, and highlighted some efforts at Sanger to address these issues, such as pay transparency, changes to their leave policies, and creating a family-friendly workplace. The remaining time exchanging views on the gender pay gap, maternity, paternity & carers leave, cultural differences in working practices and accessibility. As an outcome of this workshop, attendees agreed there is a need for the ISB to create an EDI subcommittee and that this workshop should be held at subsequent Biocuration meetings. The EDI subcommittee is currently being formed, and the exact roles are to be defined, but they will address issues including a code of conduct amongst the Society as a whole and at conferences, and accessibility at conferences and for ISB activities.

“Not Everything That Counts Can Be Counted” – how biological resources should be evaluated

As scientific data output continues to grow, biological resources are increasingly critical for data discoverability and re-use. However, many highly-used biological resources find it increasingly difficult to secure and maintain funding. This discordance implies that the value of curated resources to the research infrastructure is still not fully appreciated in the wider scientific community, or that the money saved by curated resources is not fully factored into funding models. In this workshop, we hoped to address questions surrounding this disparity.  A short introduction to the issues was provided by Marc Gillespie. A funder’s perspective was provided by David Carr (Wellcome Open Research). Jo McEntyre (EBI, Literature Services, UK)  provided an overview of the Elixir indicators designed to evaluate resource quality in a standardized way.  Two major priorities emerged from the discussion. Firstly, knowledge bases not only capture data but also synthesize new knowledge. The differences in requirements for evaluating archive and knowledge-base database should be made clearer. Secondly, the need to educate the scientific communit and funding bodies about the hidden work and benefits of data curation is urgently required. Suggestions ideas and recommendations gathered during the conference and post-meeting are documented here, and we encourage curators to add further ideas, with an aim to develop into an ISB position paper during 2019-2020.

Biocuration in Industry

The Biocuration in Industry workshop was organised by Jane Lomax (SciBite) and Yasmin Alam-Faruque (Eagle Genomics) with an aim to discuss the experiences of, and challenges faced by, non-academic biocurators. The workshop attracted ~100 participants, with most coming from academia. The workshop began with short talks from commercial companies, including Nebion, Hoffman-La Roche, Healx and Eagle Genomics, who described their curation pipelines, standards and scientific interests, which included cancer immunotherapy, microbiomes and Parkinson’s disease. A common theme was the use of public standards and ontologies, emphasising the importance of key resources such as MONDO, GO, HPO and MeSH to aid drug discovery and knowledge management. This also came through in the subsequent panel discussion where the panel agreed that, in order to maintain the high-quality of these resources, there is an onus on the commercial sector to contribute back improvements to these open-source efforts. The main challenge for the panel, as in the academic sector, is data cleansing to create high-quality and reproducible datasets for downstream processes. However, this was seen as a valuable, and transferable, skill for biocurators as the biomedical industry increasingly recognises the need for clean data.

The Phenotypes Traversing All the Organisms (POTATO)

The POTATO workshop is part of an ongoing effort to reconcile phenotype ontologies across species. This, the second workshop in the series, brought together 24 curators and ontology developers from a variety of backgrounds including representatives of many important groups in the phenotype curation space: Monarch Initiative, the Alliance of Genome Resources, ZFIN, PomBase, dictyBase, PHIBase, GO, SGD, HPO, FlyBase, MGI, Phenoscape and more. The Phenotype Ontology Reconciliation Effort aims to align phenotype ontologies using a common set of design patterns. These design patterns depend on a variety of external ontologies including the Phenotype and Trait Ontology (PATO) and the multi-species anatomy ontology, Uberon. The workshop included training in editing these two ontologies. It also featured an extended session to develop a strategy to deal with shortcomings and current limitations of PATO and its usage, as identified by the Phenotype Ontology Reconciliation group. During this session, focus groups discussed a number of PATO related issues, including how to improve PATO definitions in general and how to improve PATO representation of increased and decreased amounts (including absence), frequencies and rates. A number of edits to PATO have already been implemented as a result of this work. The results of the discussion are currently being written up as a meeting report, which will guide future improvements to PATO.

Data Licensing Workshop

The data licensing workshop at Biocuration 2019 was focused on helping scientists to understand important factors in the selection of a data license, as well as the implications of that selection on downstream use and reuse.  We had a diverse line up of speakers who each shared their unique perspective — data owners, data miners, and a legal expert — followed by a robust discussion among all participants. The goal of the workshop was not to achieve consensus on the “best” license, but rather to share experiences, perspectives, and questions.

Mapping the Landscape of Biocuration

This well attended pre-conference workshop asked questions such as: What is the state of biocuration in 2019? Where are biocurators based? What are their skills and levels of expertise? What training do they need? What are the tools they use? As part of an ELIXIR Implementation Study, members of EMBL-EBI, FAIRsharing.org/Oxford and SIB ran a survey to capture information on biocurators and the resources they run, the life science/health domains they operate in, and their expertise and training requirements. In the workshop we described the current biocuration landscape, and ran an interactive session to compile feedback on career progression and training roadblocks. Slides from the workshop can be found here: Survey: 10.7490/f1000research.1116798.1; FAIRsharing: 10.7490/f1000research.1116785.1; TeSS: 10.7490/f1000research.1116784.1). More information on the Implementation Study and follow-up work can be found here: https://elixir-europe.org/about-us/implementation-studies/mapping-biocuration

Apply for travel fellowship to [BC]2 Basel Computational Biology Conference

ISB is happy to announce that it will provide two travel fellowships to current ISB members in the amount of 500 CHF (approx. USD $500) to attend the [BC]2Basel Computational Biology Conference, from September 10-11, 2019 at the Congress Centre in Basel, Switzerland.

To apply, and for more information, click here. Note, you must be a member* of the ISB to apply. The applicant must submit an accompanying letter explaining why s/he is requesting travel funds and how s/he envisions that attending the [BC]2 conference will benefit her/his career.

Application materials should be sent via email to bc2@sib.swiss with the subject line ‘ISB Travel Fellowships to [BC]2 2019′ by Sunday, 16 June 2019, 23:59 CET.

Notification of award will be sent via email on 24 June, 2019 and announced on the ISB and [BC]2 website after acceptance of the award.

Students, junior curators, curators from low-income countries, and curators from countries suffering from natural disasters are encouraged to apply.

The [BC]2 Basel Computational Biology Conference is the key computational biology event in Switzerland and one of the major bioinformatics events in Europe. It unites scientists working in a broad range of disciplines, including bioinformatics, computational biology, and systems biology. The conference will feature presentations of latest research results, workshops, tutorials, poster sessions, and keynote lectures by international experts providing a prime opportunity to learn about cutting-edge research in computational biology and bioinformatics, and to network with other members of our community.

This year’s thematic focus is on the use of “Big Data in Molecular Medicine” with plenary sessions on single-cell data, evolutionary medicine, clinical population genomics, systems biology of disease and multi-level data integration. Tutorials and workshops will focus on a variety of topics such as “Introduction and advanced usage of machine learning for biological problems”, “Handling and accessing genomic data”, “Analysis of single cell data” and “Analysis of viral and bacterial genomic data”.

In 2019, [BC]2 will take place in the context of Basel Life – Europe’s leading congress in the Life Sciences – and participants are free to attend all sessions of Basel Life including the EMBO meeting on “Next-generation molecular medicine”.

Click below for more details on:

*We have recently been experiencing some technical difficulties with our membership registration system. Please contact us at intsocbio@gmail.com if you have any issues. If you are having difficulties with renewing or registering for membership, are still encouraged and eligible to apply for the [BC]2 travel fellowship.

Equality, Diversity, and Inclusion (EDI) at Biocuration 2019

The workshop on ‘Equality, Diversity, and Inclusion (EDI)’ was chaired by Executive Committee member and GigaScience’s, Mary Ann Tuli. The introductory slides explained what these terms mean and how they are being embraced by scientific institutes in different countries. This was followed by a more in-depth and very informative presentation by the invited speaker Dr Saher Ahmed, head of EDI at the Wellcome Sanger Institute, Cambridge, UK. Dr. Ahmed discussed gender discrepancies in the workplace, and highlighted some efforts at Sanger to address these issues, such as pay transparency, changes to their leave policies, and creating a family-friendly workplace.

The remaining time was spent on some lively discussion by the 30 attendees, exchanging views on the gender pay gap, maternity, paternity & carers leave, cultural differences in working practices and accessibility. As an outcome of this workshop, attendees agreed there is a need for the ISB to create an EDI subcommittee and that this workshop should be held at subsequent Biocuration meetings. The EDI subcommittee is currently being formed, and the exact roles are to be defined, but they will address issues including a code of conduct amongst the Society as a whole and at conferences, and accessibility at conferences and for ISB activities.

Image credit: George Georghiou

Apply now for PgCert in Biocuration at Cambridge University

This one year, masters’ level course has been jointly designed by EMBL-EBI and Cambridge University, with input from members of this society.
It has been designed to be studies around full time employment – the course consist of 3 modules, each comprised of a 3 day face to face workshop followed by 8-10 weeks of study offsite, coordinated using the University online learning system.


For further details and links to apply please visit the website: https://www.ice.cam.ac.uk/course/postgraduate-certificate-biocuration


Applications for this year close on the 17th May, with the course starting in October 2019.


If you have any queries please do not hesitate to get in touch.

Search by Categories