Author: Rob Davidson

Eleanor Williams on winning the Biocuration Award 2018

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

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

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

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

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

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

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

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

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

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

 

ISB members’ survey

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

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

This survey should take approximately 5 minutes to fill in.

Complete survey on Google Forms

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

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

Microgrant report: Arighi Oct.2017

ISB-Microgrant report of the BioCreative VI workshop
By Cecilia Arighi

The BioCreative VI workshop took place on October 18-20, 2017 in Bethesda, Maryland, USA.

BioCreative is a community-wide effort for evaluating text mining systems applied to the biological and biomedical domain. The meeting attracted participants from the biomedical natural language processing, biocuration, literature/publishing, research and funding
domains (over 60 workshop participants, one third being students), and 36 teams participated in the track activities (with representation from America, Asia, Europe and Australia).

The scientific program covered:

  1. the talks related to the individual tracks (ran previous to the workshop) with biocuration relevant topics (assignment of bioentity IDs to facilitate downstream curation; text mining services for triage for human kinases; extraction of causal network information using the Biological Expression Language; mining protein-protein interactions affected by mutations; and annotation of chemical-protein interactions)
  2. a panel about Innovation in biomedical digital curation with views presented by users, publishers, literature service providers
  3. a panel on funding stakeholders where funding opportunities and needs for text mining and collaborations were presented by representatives from various funding agencies;
  4. a general session for text mining topics that showcased other interesting bioNLP work;
  5. 2 keynote speakers (Dr. Patricia Flatley Brennan, Director, National Library of Medicine, talked about future of data-powered health, and Dr. Hongfang Liu, Mayo Clinic, discussed opportunities and challenges of text mining in precision medicine.
  6. a poster session with Additional points discussed included the challenges of using real data over a gold standard; the strategic direction of BioCreative; and the relationship with other NLP challenge evaluations.

Corpora and datasets from the different tracks are publicly available (with prior registration). The workshop Proceedings is publicly available on the BioCreative website.

Funds were used towards the rental of room for the poster session, and the ISB was listed as sponsor.

The OHSU Library Data Science Institute Promotes Biocuration and the ISB to Librarians and Researchers

By Nicole Vasilevsky

The Oregon Health Science University Library in Portland, Oregon hosted the “OHSU Library Data Science Institute” (GitHub repo) from November 6-8, 2017 in downtown, Portland.

The event was targeted towards researchers, librarians and information specialists with an interest in gaining beginner level skills in data science. The goal was to provide face-to-face, interactive instruction over a  three-day workshop. The learning objectives for the training were:

  • Increase awareness of key skills in data science and how these can be applied to the participants own daily practices, such as research or serving patrons
  • Increase confidence with using data science techniques
  • Increase the ability of participants to use or apply data science techniques in problems outlined in the course

Over 75 participants attended this event, which was held over the 3 days. Participants came from within and outside Portland,  Washington, Idaho, California, British Columbia and Kansas. The topics for the workshop included topics relevant to the biocuration community such as biomedical data standards; data description, sharing and reuse; and data cleaning and preparation. All of the  materials are openly available on our website. I gave a brief talk on the “Trials and Tribulations of a Biocurator” and described the lessons learned as a biocurator and how she wished she knew the things she knows now when she was a bench researcher (and how her biocuration skills can be applied in her current role as well). We hope that we instilled the value of biocuration and proper data management on researchers and librarians alike, and hope that they will apply the skills they learned to better manage and curate their data. We informed participants about efforts that are currently underway at the International Society for Biocuration, and distributed ISB stickers as well. Funds from the micro-grant were used to provide coffee each morning for attendees, which was greatly appreciated, and the ISB is listed as a sponsor on our website.

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!