Category Archives: Conference

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

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.

Call: Host the 13th International Biocuration Conference

ISB_logo

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 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

Deadline extension for Biocuration 2018

If you haven’t yet submitted your abstract for talks, posters or workshops for the 11th International Biocuration Conference, fear not! The deadline has been extended to 15th January 2018. 

Abstracts for talks and posters

Full details on abstract submissions can be found in the original call. They have a maximum length of 300 words and can cover a wide variety of topics from data ontologies to precision medicine.

Submit your abstracts at https://easychair.org/cfp/biocuration2018

Any questions should be sent to biocuration2018@126.com

Workshop proposals

Workshops are a great way to build connections, crowdsource ideas and to promote topics and standards in the global community.  If you’ve got an idea for a workshop, you can submit a proposal be emailing biocuration2018@126.com.

This should be a short paragraph (or two) describing the following:

  • Proposed scope and main objective, and their relation to biocuration
  • Brief discussion of why the topic is of particular interest at this time
  • Suggested format (talks, panel discussion, etc.)
  • Potential speakers, panels, or other activities

Visas

Biocuration 2018 is set to be a great conference and Shanghai is a wonderful location. Many people will require a visa so please remember to apply well in advance.

If you need an invitation letter for the visa, please send an email to biocuration2018@126.com , including your registration form. Local organizers will send the invitation letter within two days.

We look forward to seeing you in April!

Biocuration 2018 Call for Abstracts

DEADLINE EXTENDED: 15th January 2018

The 11th International Biocuration Conference will be held from April 08-11, 2018 in Shanghai, China. The 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.

You are invited to submit an abstract for a talk or poster presentation at the upcoming conference. This is a great occasion to enhance the recognition of your work and of our profession by the greater biological research communities.

This year abstracts are invited for the following topic areas:

  • Precision Medicine
  • Phenotypes, genotypes, and variants
  • Data Standards and Ontologies
  • Text Mining
  • Functional Annotation
  • Community Annotation
  • Data Integration and Visualization
  • Deep Learning in curation process
  • Softwares, Applications and Systems in biocuration
  • Curation Standards and Best Practice; inference from evidence; data and annotation quality

Abstracts on topics outside the above will also be considered for presentation.

Please be mindful of the following deadlines:

Submission deadline: EXTENDED to: January 15, 2018

Notifications: January 15, 2018

Conference: April 8-11, 2018

Please submit your abstract here: https://easychair.org/cfp/biocuration2018

All questions about submissions should be emailed to biocuration2018@126.com

Before submitting your abstracts please take into consideration:
  • All abstracts must be written in English.
  • The title and the abstract should be entered in plain text and should not contain HTML elements.
  • The abstract should be written in an unstructured format. Separate sections for Background, Materials and Methods, etc., are not needed.
  • Copy-paste text may include hidden formatting that exceeds the character limit. We recommend either: saving as ‘text only’ in your editor or e-mail program, OR copy-pasting it into Notepad and then onto the website.
  • Abstracts should not exceed 300 words, with the limit of 2000 characters (with spaces).
  • Some web browsers do not accept abstracts close to the 2000-character count.
  • If you have special symbols in your text, please ensure you are using Unicode characters; otherwise these will not be recognized.

Biocuration 2018 Travel Fellowships

Call for Applications: ISB Travel Fellowships for Biocuration 2018

The International Society for Biocuration and the 11th International Biocuration Conference invite current ISB members to apply for Travel Fellowships to attend the 2018 conference in Shanghai, China.

Details

We are pleased to provide current ISB members with a travel fellowship opportunity. We intend to support up to ten (10) applicants. Students, junior curators, curators from low-income countries, and curators from countries suffering from natural disasters are encouraged to apply. Selections will be prioritized by financial need.

Please note that applying for a fellowship does not guarantee that you will receive funding.

Awards
Each award will be issued as reimbursement for up to CHF $ 1,000 per fellowship depending on the costs of your registration and travel (e.g. hotel, flight, and ground transportation)

  • ISB Travel Fellows must be able to cover their own conference registration fees and travel cost before attending the conference. ISB Travel Fellows will then submit receipts to request a reimbursement from ISB. Save your receipts! 
  • A bank transfer for up to CHF $1,000 – depending on your registration and travel costs – will be arranged for ISB Travel Fellows.
  • The Biocuration Travel Fellowships Committee will advise you on how to receive these funds as reimbursement at the end of the conference.

Requirements and Procedures
Each applicant for a travel fellowship must satisfy the following conditions:

  • The applicant must be an active ISB member. To become a member go here: https://www.biocuration.org/membership/membership-levels/
  • The applicant should have submitted a poster or oral presentation at the Eleventh International Biocuration Conference.
  • Only the presenting author from a multi-author abstract may apply for a fellowship.
  • The applicant must submit an accompanying letter explaining why s/he is requesting travel funds and how s/he envisions that attending the Biocuration Conference will benefit her/his career.
  • Application Deadline: application materials should be sent to ISB via email to intsocbio@gmail.com with the subject line ‘Travel Fellowships to Biocuration 2018’ on or before January 31, 2018.

Notification of award will be sent via email by 16 February, 2018 and announced on the ISB website after acceptance of the award.

Applicants should review visa requirements and make all necessary arrangements on their own. The conference can provide an invitation letter for registered participants. Please contact biocuration2018@126.com to request a letter of invitation.

Sincerely,

Your colleagues at the ISB Executive Committee.

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

Call: Host The 12th International Biocuration Conference

ISB_logo

Dear Colleagues,

The Executive Committee of the International Society for Biocuration would like to once again invite tenders to host the 12th International Biocuration Conference during the Northern Spring or Summer of 2019.

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,  2017.

The successful bidder will be notified by October 1,  2017. The ISB Executive Committee will publicly announce the selected organization or individuals during the 11th International Biocuration Conference, to be held in Shanghai, China in April, 2018.

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 2019 we are encouraging a European location, but will also consider other locations.

REGIONS ROTATION:

Asia and Australasia

Europe

North America

This Call for Applications is also available on the ISB website at http://www.biocuration.org

For more information about the ISB and our previous conferences, please visit: http://www.biocuration.org

We look forward to hearing from you!

Your colleagues at the ISB Executive Committee.