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

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

Microgrant Report: Krysiak 2018

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. On the morning of the second day, groups presented the outcome of each session in short presentations covering multiple topics. Topics in the cancer variant sessions included the expansion of cancer variant databases to cover structural variants and copy number variants. The current capabilities of CIViC and other cancer variant knowledgebases to represent such variants was assessed, and strategies for future instances of such knowledgebases to implement these representations were covered. In addition, a system for quantifying somatic cancer variant oncogenicity/pathogenicity was proposed, and discussed extensively. This system was derived from the current standard for germline variant pathogenicity assessment based on ACMG codes. These discussions informed subsequent proposals for potential future guidelines. Other topics in the cancer variant sessions included machine learning in cancer variant annotation, and the standardization of generalized categories for cancer variant classification. SEPIO modeling of cancer variants was also covered. Parallel curation sessions covered a broad set of topics including methods to incentivize community curation of free and public knowledgebases such as CIViC, and hands-on curation of diagnostic evidence in pediatric cancer was performed. In multiple hackathon sessions, work was performed integrating CIViC and CRAVAT, integrating CIViC with igv.js, JBrowse and IGV genome browsers and CIViC-Wikidata integration. A session was held to work on a system for data transfer between the ClinGen VCI and CIViC named Linked Data Hub. NDEx made available CIViC drug-variant, gene-disease, gene-variant and variant-disease association networks.

Microgrant Report: ICBO2018

9th annual International Conference on Biological Ontologies (ICBO2018)
Ontologies for Health, Food, Nutrition and Environment: A partnership with BIG-Data and Analytics

Conference website: http://icbo2018.cgrb.oregonstate.edu

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  attended by over 130 participants from 10 countries, provided a venue for presenting and discussing research, development and usefulness of biomedical ontologies (including human health and diseases, vectors, drugs, bio-chemicals, biodiversity, plants, agriculture, food and environment) on building data standards, annotation workflows and data analytics. Attendees represented significant areas of biology, medicine, ecology, computer science, mathematics, text-mining, data analytics, and software and tool development. Dr. Pankaj Jaiswal from Oregon State University was the Conference Chair. The Conference Program co-Chairs Dr.Chris Mungall from the Lawrence Berkeley National Laboratory (LBNL) and Dr. Melissa Haendel from the Oregon State University organized the conference program.with help from the Program Committee members The scientific presentations were in the form of 30 plenary talks and 32 posters and software demonstrations.

The three thought-provoking ICBO2018 Keynote talks were given by Dr. Kwan Liu-Ma from the University of California Davis on “Visualization: A Powerful Tool for Data Exploration and Storytelling”, Josh Clark from Big Medium Inc. on “The Care and Feeding of Algorithms” for design, analytics and user engagement and Dr. Parag Chitnis from National Inst. of Food and National Institute of Food and Agriculture (NIFA) on “Changing Face of Agriculture: Data-driven opportunities for nutrition and health”.

The four invited talks were by Niklaus Grunwald from USDA ARS on “Taxa, metacoder, poppr and vcfR: Four packages for parsing, visualization, and manipulation of genetic, genomic and metagenomic data in R”, David LeBauer from TerraRef project on “Vocabularies, Ontologies, APIs, and Formats for Heterogeneous High Throughput Crop Phenotyping Data”, Carolyn Lawrence from Iowa State University on “GO-MAP Implements CAFA Tools: Improved Automated Gene Function Annotation for Plants” and Matthew Lange from UC Davis on “Designing and Building the IC-FOODS Foundry: Community, Technology, and Standards for a Semantic Web of Food”.

Thirteen pre and post-conference workshop held at ICBO2018 included the Phenotype Ontologies Traversing All The Organisms (POTATO) Aligning phenotype ontologies using design patterns, ONCONTO 2018: 2nd International Workshop on Oncology and Ontology, Ontology-driven text-mining analysis and normalization of free-text specimen descriptions, Data Standards and Knowledge Sharing in Biodiversity -Tools and Applications, Deep Learning in the Life Sciences and Biological pathway curation jamboree. Each of the workshop session included talks, demo, hands-on exercises and discussion forums relevant to their theme.

The Biological pathway curation jamboree was organized by Sushma Naithani of the NSF-funded Gramene database. In the jamboree participants learned about the biocuration process, literature and data mining, pathway analysis, and biocuration tools with particular emphasis on using the Reactome Curator Tool and plant pathways. The curation of plant pathways is an ongoing work of the Plant Reactome database. The workshop report is available from Gramene News.

The day-long pre-conference workshop on Phenotype Ontologies Traversing All The Organisms (POTATO) was a venue to discuss data standards on phenotype annotation tools for pattern-based development (Dead Simple Ontology Design Patterns (DOSDP) and the Ontology Development Kit (ODK). The workshop report is available at Medium

The two-day post-conference workshop “Deep Learning in the Life Sciences” was an introductory hands-on workshop on Machine Learning to train students and researchers working on various biological datasets. The workshop was co-organized with the Center for Genome Research and Biocomputing (CGRB). The instruction was provided by experts from IBM.

The plenary talks and posters were selected after peer-review of over 60 scientific articless. The ICBO2018 conference abstracts are available online. The articles will be published later in an online open access conference proceedings.

We thanks our Sponsors, the International Society for Biocuration, the College of Agricultural Sciences, Department of Botany and Plant Pathology, Department of Environment and Molecular Toxicology, College of Engineering (EECS) and the Sponsored Research Office at Oregon State University and industry partners, Illumina Inc., Sanmita Inc, and Sensiplicity LLC. The conference was partially supported by the grants to Pankaj Jaiswal for the Gramene database (IPGA: Gramene – Exploring Function through Comparative Genomics and Network Analysis; NSF-PGRP Award 1127112)  and the Planteome project (cROP: Common Reference Ontologies and Applications for Plant Biology; NSF-PGRP Award 1340112) and the NIH conference grant to Melissa Haendel and Peter Robinson (Forums for Integrative phenomics; NIH award 1U13CA221044).

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.

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 !

RESULTS OF 2018 ELECTIONS OF ISB EXECUTIVE COMMITTEE

The results of the 2018 Elections of the ISB Executive Committee are in!

Congratulations to
Frederic Bastian, Sandra Orchard, Jane Lomax and Mary-Ann Tuli

Thank you to the ISB members who participated in this year’s election. A total of 97 members voted, out of the 198 current ISB members (49%).

Welcome Frederic, Jane and Mary-Ann as new members, and congratulations to Sandra for your re-election to a second term. Frederic, Jane and Mary-Ann will fill three open positions when the terms of Ceci Arighi, Suzi Lewis and Zhang Zhang come to completion on 31-October-2018.

Please join us in thanking Ceci, Suzi and Zhang for all their work over the past years!

We would like to also express our sincere gratitude to Lei Lui, who who considered volunteering his time as part of the ISB-EC this year.

We are also very grateful with the following ISB members who volunteered their time for a successful execution of the 2018 EC election:

2018 Nominating Committee:

  • Mike Cherry (Chair)
  • Fiona McCarthy
  • Lilly Winfree
  • Sue Bello
  • Luana Licata

Thank you again for participating in the 2018 ISB electoral process!

Sincerely,
Your Colleagues at the ISB Executive Committee

ISB Newsletter – September 2018

Hello! This is the third quarter newsletter for the International Society for Biocuration, a series providing with the latest information on activities and ideas contributed by our community members

Luana Licata’s recap from ISB fellowship visit to EMBL-EBI

By Luana Licata

The short-term fellowship conferred by the International Society for Biocuration (ISB) has given me the opportunity to spend, as a visitor, two weeks, from the 2nd to the 13th of July 2018, at the EMBL-EBI, Hinxton, UK.

At the EMBL-EBI, I have been hosted by the IntAct team and I have worked with the Protein Function Team (EMBL-EBI) and the Gene Annotation Team of the Centre for Cardiovascular Genetics (UCL, London) and with the Molecular Interaction Team (IntAct, EMBL-EBI). Read more here.

Microgrant funding for GCCBOSC 2018


The first joint event of the Galaxy Community Conference and the Bioinformatics Open Source Conference (GCCBOSC 2018) was held from June 25-30 at Portland’s Reed College, and the conference received a microgrant from the ISB to help offer childcare at the conference.  To read more, go here

Hackathons for Education and Rapid Prototyping, Research, and Production

By Ben Busby

Solving a scientific problem or building a new bioinformatics tool in just three days – sound impossible? It’s not, when you bring together groups of participants with diverse backgrounds and skill sets in an NCBI-style hackathon! Unlike competitive hackathons, in which many teams vie to create the best solution to a single problem, NCBI-style hackathons are cooperative, with each team tackling its own project, and sharing ideas and expertise with other teams. Participants have ranged from undergraduates to biomedical librarians to front-end developers to senior bioinformaticians, and over the course of 30 hackathons, they’ve developed over a hundred products. They’ve also benefited from the opportunity to learn from and network with their teammates, and the gratification of (hopefully!) creating a cool new tool or resource that can be shared with the scientific community. Since hackathons bring together participants from varied subject matter and computational backgrounds, who typically wouldn’t collaborate otherwise, teams are able to come up with novel and unique solutions that wouldn’t likely come out of a more traditional scientific setting.

If you’re interested in participating in a hackathon, check out the list of upcoming hackathons happening all over the United States (and the world)! No hackathon happening near you? Run your own! A few tips for planning a successful hackathon:

  • Be realistic about selecting projects – be sure to pick a problem that can feasibly be solved in three days.
  • Make sure to keep your participants fed (and caffeinated) to keep energy and productivity up.
  • Document your work and make it open source so that others can benefit from your work.
  • Most importantly, have fun and meet some new people!

If you’re interested in learning more about hackathons or seeing examples of projects, visit the Biohackathons page or the Hackathons channel at F1000 Research.

ELIXIR Resources for Biocurators

by Peter McQuilton on behalf of ELIXIR

ELIXIR, an intergovernmental organisation that brings together life science resources from across Europe, has a lot to offer biocurators from across the globe. The goal of ELIXIR is to coordinate these resources so that they form a single infrastructure that makes it easier for scientists to find and share data, exchange expertise, and agree on best practices. ELIXIR activities are grouped into five platforms (Compute, Data, Tools, Training and Interoperability), which are developing a range of bioinformatics services and resources. The Interoperability Platform offers a number of useful resources:

  • FAIRsharing (https://www.fairsharing.org) – A manually curated registry of databases (both repositories and knowledgebases), the standards they use (reporting guidelines, ontologies, identifier schema, models and formats), and the funder and journal data policies that recommend their use.
  • Identifiers.org (https://www.identifiers.org) – a universal identifier resolution service for data identifier schemes in the life sciences.
  • Bioschemas.org (https://www.bioschemas.org) – an extension of schema.org that allows the detailed mark-up of biological datasets, data repositories, training and more. Marked-up webpages are used by ELIXIR services and by the new Google Dataset Search Tool.

In addition, those interested in bioinformatics training can use the ELIXIR Training portal, TeSS (https://tess.elixir-europe.org/). TeSS brings together training materials and events from Europe and beyond and links them to other resources within the ELIXIR infrastructure.

Visit the ELIXIR catalogue of services to find out about the full range of resources available through ELIXIR: www.elixir-europe.org/services. For more information about the ELIXIR Platforms visit: https://www.elixir-europe.org/platforms/

The new ISB-TeSS training widget

By Peter McQuilton

Working with the ELIXIR TeSS Training and Events Portal (https://tess.elixir-europe.org/)  and the GOBLET training organisation (https://www.mygoblet.org/), we have added a new widget to the ISB website.

This widget calls the TeSS API directly to provide the latest information on training materials and events around the world. If you have a training event or training materials you would like to add to the widget (which will also mean that material is listed on TeSS and GOBLET) you can add it to the TeSS website here: https://tess.elixir-europe.org/about/registering

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 organisations, and industry. Please check biocuration2019.org, or follow #biocuration2019 on Twitter, for the latest information and details on how to register.

Note that the paper submission deadline for inclusion in the Biocuration virtual issue of Database is October 31st 2018.

Executive Committee Elections

The Executive Committee Elections will be held this fall for 4 vacancies. The following EC member is up for re-election:

The following EC members will be stepping down from the EC:

  • Cecilia Arighi
  • Suzanna Lewis
  • Zhang Zhang

Candidates will be announced on the website by September 28th. The election will run from October 01-08, 2018. Only ISB members are able to vote. More info here: https://www.biocuration.org/isb-ec-elections-2018

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.

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

Microgrant report: GCCBOSC 2018


By Karsten Hokamp on behalf of the GCCBOSC 2018 organizing committee

The first joint event of the Galaxy Community Conference and the Bioinformatics Open Source Conference (GCCBOSC 2018) was held from June 25-30 at Reed College in Portland, OR. The Galaxy Community supports data-intensive biomedical research through the open-source Galaxy platform. BOSC is organized by the Open Bioinformatics Foundation, a nonprofit group dedicated to promoting the practice and philosophy of open source software development and open science within the biological research community. This was the 19th annual BOSC, but the first one to be held together with GCC.

The conference brought together over 300 bioinformatics researchers, biocurators, developers and users of open source software from academic and private institutions around the world in a relaxed and collegial atmosphere. A wide range of topics in bioinformatics open source projects, open science and open data were covered. This included workflows, developer tools and libraries, translational/medical bioinformatics, community building and standards for representing and sharing data.

Posters, software demos, birds-of-a-feather meetings, talks, invited keynotes, training, and collaborative work events were presented and held over six days. A panel session discussed the importance and underfunding of documentation and training in open source bioinformatics. Presentations of specific interest to biocurators included reports on miRTop, InterMine and the Mammalian Ortholog and Annotation Database, amongst many others. Several presentations covered resources that support biocurators in their work, such as BioThings Hub, Apollo and JBrowse.

GCCBOSC 2018 sought to be a family-friendly conference, and the ISB Micro-grant helped make this happen. These funds allowed the conference to offer subsidized child care and enabled parents with young children to attend (including one of the keynote speakers). This support for families received a lot of attention, both at the conference and online.

The International Society for Biocuration was listed as a sponsor in the conference materials, including the printed program, presentation slides and web pages.

Luana Licata’s fellowship report

By Luana Licata

The short-term fellowship conferred by the International Society for Biocuration (ISB) has given me the opportunity to spend, as a visitor, two weeks, from the 2nd to the 13th of July 2018, at the EMBL-EBI, Hinxton, UK.

At the EMBL-EBI, I have been hosted by the IntAct team and I have worked with the Protein Function Team (EMBL-EBI) and the Gene Annotation Team of the Centre for Cardiovascular Genetics (UCL, London) and with the Molecular Interaction Team (IntAct, EMBL-EBI).

During my stay, I have been worked on the following topics:

I worked with both Protein Function and Gene Annotation Teams to learn Gene Ontology annotation and how to use Protein2GO. In particular, Ruth Lovering and Rachael Huntley (Gene Annotation, UCL, London) introduced me to GO annotation practices, Extensions and rules and how to use the curation tool, Protein2GO. This has allowed me to start to annotate some proteins and protein relationships involved in the Acute Myeloid Leukemia (AML) pathway already annotated in SIGNOR database, one of the database that I curate at the Bioinformatics and Computational Biology Unit, at University of Rome Tor Vergata. Moreover, with the help of Penelope Garmiri (Protein Function, EMBL-EBI), I had the opportunity to learn the basis of NOCTUA annotation and how to use NOCTUA platform. Noctua annotation allows to combine simple GO annotations in order to generate a network of annotations. This acquired knowledge has allowed me to start to annotate, at a basic level, also in NOCTUA platform some relationships relevant to Acute Myeloid Leukemia (AML) pathway coming form SIGNOR database in order to be able to produce some GO-CAM models. GO-CAM models are the models produced with Noctua. The final goal of this collaboration has been not only to improve and enhance knowledge about current GO annotation practice but also to be able, in the next future, to represent and compare information relevant to the AML pathway that I have annotated in different ways, such as SIGNOR, GO and NOCTUA annotation.

I worked with the Molecular Interaction Team to further develop protein-nucleic acid interaction annotation in MINT database. In particular, I have learned how biocurators in the Molecular Interaction Team capture information about protein-nucleic acid interactions and I have annotated in the IntAct editor (IntAct curation tool) articles containing information on the interaction between transcription factor and transcribed gene. Moreover, during my visit, working in close contact with colleagues from the molecular interaction team has allowed to strengthen the work of the MINT database (the other database that I coordinate and curate) inside the IMEx Consortium through a better curation coordination.

Executive Committee Election

The election of the new International Society for Biocuration Executive Committee (ISB EC) will be held in October 2018. 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 teleconference meetings (1 hour in length) and following up on any action points from meetings, as well as 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 ISB election, monitoring ISB mail and 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 executive committee and by extension the membership.

This year, there are four (4) open positions, as the terms of Sandra Orchard, Cecilia Arighi, Suzanna Lewis and Zhang Zhang will come to completion. (The current ISB EC members are here.)

2018 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 2018 Nominating Committee are:

  • Mike Cherry (Chair)
  • Fiona McCarthy
  • Lilly Winfree
  • Sue Bello
  • Luana Licata

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 emailing isbelection@gmail.com
  2. Please fill out this form by 31 August 2018, 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.

C) Timeline:

  • Nominations will be received until 31 August 2018.
  • The NC will review all candidacies and share their selections with the ISB Executive Committee by 14 September 2018.
  • Candidates must be announced to the membership and on website (with letters of intent) by 28 September 2018
  • Voting will take place online over the course of one week from 01-08 October 2018. (Further details about the voting process will be shared soon). Eleanor Williams will act as election officer.
  • Only paying members with registration fees cleared on or before 28 September 2018 will be entitled and 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.

The Nominating Committee is looking forward to receiving your applications!

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