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

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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.

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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
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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.

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Call: Host the 14th International Biocuration Conference

Dear Colleagues,

The Executive Committee of the International Society for Biocuration would like to once again invite tenders to host the 14th International Biocuration Conference during the Northern Spring or Summer of 2021.

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, 2019.

The successful bidder will be notified by October 1, 2019. The ISB Executive Committee will publicly announce the selected organization or individuals during the 13th International Biocuration Conference, the venue for which will be announced at the Cambridge conference.

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 2021 we are encouraging an Australasian location, but will also consider other locations.

REGIONS ROTATION:

Asia and Australasia

Europe

Americas

For more information about the ISB and our previous conferences, please visit: https://www.biocuration.org/community/conferences/international-biocuration-meetings/

We look forward to hearing from you!

Your colleagues at the ISB Executive Committee.

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Anne Morgat and Val Wood – recipients of the 2019 biocuration awards

It is our great pleasure to announce the recipients of the 2019 biocuration awards

Dr. Anne Morgat from the SIB Swiss Institute of Bioinformatics for the Biocuration Career Award. Anne has worked for over 15 years on the development of resources and vocabularies for the description of enzymatic reactions and metabolic pathways, such as UniPathway and Rhea, and their integration in UniProtKB.

Dr. Val Wood from the University of Cambridge for the Exceptional Contributions to Biocuration Award. Val leads the Model Organism Database for the fission yeast PomBase. Her team has made essential contributions to the Gene Ontology (GO) consortium, from the ontology development, through annotations and quality control, as well as informatics methods. She has been a huge innovator in the biocuration field, pioneering community curation with the CANTO tool, and developing Fission Yeast Phenotype Ontology (FYPO), a cellular phenotype ontology, to annotate phenotypes of mutant alleles.

Congratulations to Anne and Val!

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Nominations for 2019 Biocuration Awards – now open

The International Society for Biocuration is happy to announce the 2019 Biocuration Awards.

In 2019 ISB will give two different awards to people who have made a significant impact in the field of biocuration. We welcome your nominations!

Description of the awards:

1) Award for Exceptional Contributions to Biocuration
ISB’s Exceptional Contributions Award recognizes a person who is a leader or a pioneer in the field of biocuration, and whose work has been fundamental to the advancement of biocuration.

2) Biocuration Career Award
The Biocuration Career Award recognizes biocurators in non-leadership positions who have made sustained contributions to the field of biocuration. Those who hold Principal Investigator or Group Leader positions are not eligible for the Biocuration Career Award.

Each award recipient will be invited to present a talk at the 2019 International Biocuration Conference that will take place in Cambridge (UK) in April (https://www.biocuration2019.org/), with all expenses paid by ISB.

Nomination process:
Nominations will be reviewed by the 2019 ISB Awards 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 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 a nomination:

Nominations should be sent via email to the awards committee at intsocbio@gmail.com with the subject line “Biocuration Awards Nominations”.

The nomination email should contain all the following fields:

  • Nominator details (name, e-mail and affiliation, member of ISB);
  • Nominee details (name, e-mail and affiliation);
  • Type of award nomination (either Exceptional Contributions to Biocuration or Biocuration Career Award);
  • Short list of scholarly contributions (a maximum of 50 words);
  • Brief description of why you are recommending this person (a maximum of 350 words).

Deadline for submitting nominations:  Friday 4-January-2019

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ISB Newsletter – December 2018

Hello!

This is the fourth quarter newsletter for the International Society for Biocuration, and the first newsletter from your new 2018/2019 ISB Executive Committee.


Welcome to the New Executive Committee!

I would like, on behalf of all the membership, to welcome our new committee members, Jane Lomax, Fredric Bastian and Mary-Ann Tuli, to their roles and to thank the outgoing members, Cecilia Arighi, Suzanna Lewis and Zhang Zhang for all their hard work. We look forward to a busy 12 months with both the  Biocuration Career Award and the Exceptional Contribution to Biocuration Award to be made, and conference travel fellowships, microgrants and exchange fellowships to be decided upon. We hope you will contact us with ideas on how we enhance the profile of Biocuration in the scientific community and take the opportunity to talk to members of the EC if you are attending the 2019 Biocuration conference in Cambridge UK.

We look forward to working with you, and for you, in 2018/19

Sandra Orchard, Chair

The Executive Committee


Submit your nominations for 2019 Biocuration Awards

In 2019 ISB will give two different awards to people who have made a significant impact in the field of biocuration. We welcome your nominations! The deadline is January 04, 2019.

More info here.


Postgraduate Certificate in Biocuration

This October, the University of Cambridge, UK was pleased to welcome its first cohort of students on the Postgraduate Certificate in Biocuration.

This Master’s level award is offered by the Institute of Continuing Education (ICE) and is completed in one year.

The course has been been designed to provide a route for new biocurators to develop a knowledge of the field and the skills required to work within it; provide those already working in the field with the opportunity to expand their knowledge and current skill set, and to provide a formally recognized qualification for Biocuration.

Most of the three module course is delivered via the VLE (Virtual Learning Environment), with a 3 or 4 day face-to-face workshop providing more hands on learning.

More information can be found here.

The first 3 day workshop took place at the magnificent Madingley Hall in Cambridge, UK in October, and introduced the students to the Principles of Biocuration. The workshop gave the students a chance to get to know each other and many of the course tutors. 


Microgrant Report: CIViC-hosted hackathon and curation workshop

By Kilannin Krysiak

The second CIViC-hosted hackathon and curation workshop was held as an open-format one and a half day pre-conference to the 2018 ASHG meeting in San Diego. Over 50 Attendees were present representing over 20 organizations and institutions from multiple countries. Session topics were suggested by attendees and CIViC team members and covered coding (hackathon) and issues in cancer variant representation and curation.

Read more here.


 Microgrant Report: 9th annual International Conference on Biological Ontologies (ICBO2018)

Ontologies for Health, Food, Nutrition and Environment: A partnership with BIG-Data and Analytics

By Pankaj Jaiswal

Oregon State University hosted the 9th annual International Conference on Biological Ontologies (http://icbo2018.cgrb.oregonstate.edu). The theme of the ICBO2018 was Ontologies for Health, Food, Nutrition and Environment A partnership with BIG-Data and Analytics. ICBO2018 was a marquee event celebrating the 150th anniversary of the founding of Oregon State University (OSU150).

ICBO2018 concluded with a vote of thanks and the announcement for 10th ICBO (ICBO2019) to be held at the University at Buffalo, New York, USA. More info will be shared when it is available.

Read the full microgrant report on ICBO2018 here.


Announcement: 21st Genomic Standards Consortium Meeting

Dates: May 20-23, 2019

GSC 21st 3-day meeting will highlight the nexus of genomic standards and innovative methods in genomics. The meeting in charming Vienna will bring together people from many fields, including microbiology, microbial ecology, bioinformatics, medicine and system biology.

Registration will open January 14th, 2019


Recommendations for sustainable genomics and genetics databases for agriculture

The AGBioData Consortium is made up of scientists from 32 genetic, genomic and breeding databases in the agricultural sector.  A list of member databases can be seen here:  https://www.agbiodata.org/databases.

This group is developing standards and best practices that can be adopted uniformly across agricultural databases to increase both interoperability and user experience.  Focus areas include biocuration, metadata and persistence, ontologies, database platforms, programmatic access to data, and communication. A recent publication outlining AgBioData consortium recommendations is here: https://academic.oup.com/database/article/2018/2018/bay088/5096675

​The challenge with standards and best practices is not defining them, but implementing them. They will be focused on implementation of standards and best practices in the next few years.


Congratulations to Ruth Lovering!

Ruth Lovering was recently promoted to a Professorial Research Fellow at UCL!

Ruth serves as the Lead of the UCL Functional Gene Annotation, a group which provides literature curation to support Gene Ontology (GO) and protein interaction data annotation. The Functional Gene Annotation team also teaches a bioinformatics module for the UCL Genetics Institute’s MSc in Genetics of Human Disease and an annual workshop on GO and other bioinformatics resources.


Save the date!
12th International Biocuration Conference

West Road concert hall in Cambridge UK will provide the location of the 12th International Biocuration Conference in April 7-10, 2019. This is an ideal forum for biocurators, developers and researchers to collaborate and promote their work within this active and growing community. Participants and submissions are welcome from academia, government and healthcare organizations, and industry. Please check biocuration2019.org, or follow #biocuration2019 on Twitter, for the latest information and details on how to register.

Register here

Abstract submissions and workshop proposals are due December 21st 2018. More info here.


Funding Opportunities from the ISB

The ISB offers microgrants to sponsor local and regional short meetings of ISB members to foster synergy of their work efforts. We’d like to promote requests for funding that address issues surrounding diversity or accessibility.

To promote collaboration and exchange between biocuration groups ISB offers fellowships. The fellowship will fund the visit of a biocurator to another laboratory or organization with extensive experience in biocuration.


Share your news and ideas with the ISB

Have an upcoming paper that you’d like to highlight for the ISB community? Let us know.

We welcome your feedback and ideas. Please contact us at intsocbio@gmail.com

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Registration for Biocuration 2019 now open!

We are pleased to announce that the registration for Biocuration 2019 is now open ! Visit the conference site here: https://www.biocuration2019.org/
or directly access  the registration page at: https://www.biocuration2019.org/registration

The conference will be held on April 7-10th, 2019 at The West Road Concert Hall, Cambridge, UK.

You may now submit talk/poster abstracts (https://www.biocuration2019.org/submit-an-abstract) – please read details of the session topics listed on that page before doing so.

May we also remind you of the opportunity to organise workshops, both before and during the conference (https://www.biocuration2019.org/submit-a-workshop)

We are looking forward to seeing you in Cambridge in 2019 !

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