Tag Archives: biocuration


Video Tip of the Week: Introduction to Biocuration and the career path


The ISB is a professional organization for biocurators

At OpenHelix, we’ve long sung the praises of curators. Some of us have been curators and worked with curation and database development teams. All of us have relied on quality information in the databases for research and teaching. But I think there are a lot of people who don’t understand the value of quality curation, how it’s done, and who curators are. They are widely taken for granted.

A recent talk by Claire O’Donovan of EBI-EMBL helps to explain the roles and the importance of biocurators. So although this talk isn’t a typical software talk, I think understanding this is crucial to everyone’s appreciation of how information you rely on gets into the databases you use. And if you find yourself in situations where you are guiding students, knowing about this career is also worthwhile.

Claire O’Donovan has had a front row seat to the development of this field, and has great enthusiasm for the future. And going forward, in your doctor’s office as precision medicine and treatments become a thing–how much do you want correct information in the databases? Mining data, standardizing language for descriptions of features, and sharing this information is crucial for all of us.

Here’s what’s covered in this video, from the agenda slide:

  • Introduction to the concept of biocuration.
  • The different kinds of biocurators, and the skill set needed.
  • Our community: Biocuration Society and conference.
  • The future of biocuration and career paths.

Specific examples of what curators do are illustrated (~6:30min). A sample UniProt entry illustrates what kind of information is captured and where it appears. She also touches on their work with Gene Ontology. And a bit about the ecosystem of curation, how teams at different resources help each other but don’t wish to duplicate work, using HGNC nomenclature as an example.

About 8min, the skill sets for biocuration are covered: data basics, curation skills, programming and database concepts, ontologies, and usability of the data collected. This also includes data access and management, as well as dissemination and outreach. This includes user training (yay!) and the concepts of data analysis for users.

There’s no formal degree path for curation practitioners at this point, and different groups will have different needs. But the community is begining to think about this, and about professional qualifications. She also mentioned a recent report from the National Academy of Sciences press on the topic of the future workforce skills and needs (linked below). This is an alternative career route for people with science training, and it’s important to understand not only the science but computational pieces. And it should be taken seriously as a discipline. There is now a journal that reflects this (also linked below).

Claire also takes a look at the future of biocuration, using the Center for Target Validation (CTTV) as an example. And she talks about the importance of quality information in medical records as we increasingly have genomic details in diagnosis and treatment situations. If we want precision medicine to work, we have to have the precise and correct information in the databases. So respect and value the curators. They are worth it. And if you know anyone that deserves special recognition–nominate!

Quick links:

International Society for Biocuration:  http://biocuration.org/

Preparing the Workforce for Digital Curation: http://www.nap.edu/catalog/18590/preparing-the-workforce-for-digital-curation 



Holliday, G., Bairoch, A., Bagos, P., Chatonnet, A., Craik, D., Finn, R., Henrissat, B., Landsman, D., Manning, G., Nagano, N., O’Donovan, C., Pruitt, K., Rawlings, N., Saier, M., Sowdhamini, R., Spedding, M., Srinivasan, N., Vriend, G., Babbitt, P., & Bateman, A. (2015). Key challenges for the creation and maintenance of specialist protein resources Proteins: Structure, Function, and Bioinformatics, 83 (6), 1005-1013 DOI: 10.1002/prot.24803

Gaudet, P., Munoz-Torres, M., Robinson-Rechavi, M., Attwood, T., Bateman, A., Cherry, J., Kania, R., O’Donovan, C., & Yamasaki, C. (2013). DATABASE, The Journal of Biological Databases and Curation, is now the official journal of the International Society for Biocuration Database, 2013 DOI: 10.1093/database/bat077

Calling all Biocurators: the ISB would like your input!

Are you, or have you ever been a biocurator?

If so the International Society for Biocuration requests that you take their career survey, which will take about 10-15 minutes (depending on how much metadata that you include :) ) and asks about career saticfaction, which tasks you enjoy/don’t enjoy, etc. The goal is to get input from as many biocurators as possible, analyze the data & then use it to guide the ISB’s efforts. I consider myself involved in biocuration, since we do outreach & software testing on these resources continuously, and so I filled out the survey myself. It wasn’t at all bad & asks some useful questions.

Biocuration has been a phenomenal career choice for me & my family. It has allowed me to stay in science, and yet follow my spouse when he has had to move and occasionally volunteer at my child’s school during the days. I think expanding biocuration career opportunities is a great way of motivating more people to get into science. The big thing is to 1) provide a variety of opportunities, 2) raise appreciation for what biocurators do (data overload would be SO much worse without the biocuration lot), and 3) get all these biocuration careers funded through steady, reliable and substantial funding – in my opinion.

So if you are a biocurator, please fill out the survey. If you know biocurators, please pass the survey onto them.

Get Your Abstract In for Biocuration2010

As I’ve posted before, the next Biocuration meeting will be in Tokyo, Oct 11-14th. I recently got notified that they are now accepting abstracts for the meeting:

We cordially invite you to join us for Biocuration2010, the Conference
of International Society for Biocuration (ISB) and the 4th International Biocuration
Conference, is held in Tokyo, Japan, from October 11-14, 2010.

Abstract submission and registration are now open!

* abstract submission
* registration

Currently abstracts are only being accepted June 1- July 14th and the organizers say authors will be notified by August 14th as to whether their abstracts have been accepted for presentation.

OpenHelix’s abstract was selected for presentation & I was really happy with all the comments, feedback and interest that we received – both from the poster presentation and the 15 minute talk we were able to give. If you’ve got a resource that you’d like to present, or get feedback on, from this group I highly suggest that you submit an abstract now!


Are you curious about what biocurators do?

It may not surprise you that we at OpenHelix are pretty heavy-duty users of curated information from databases. It might surprise you to know that some of us have been involved in actually curating them as well. In both public and commercial situations, we’ve been on the curation side. And lately we’ve been heavily on the end-user side.

So we’ve been huge supporters of curators for a long time. We know that they are the ones responsible for the most trustworthy data in the databases. We know the intelligence, the focus, the attention to detail, and the training it takes to do this well.

Biocurators rock. If you do biomedical research and use the data from the databases, you can thank a biocurator.

But maybe you don’t know that much about exactly what biocurators do if you are mostly an end user of the databases. I’d like you to meet some of them. The new International Society for Biocuration has been established to foster development and respect for biocuration as a career choice and career path.

They are also currently holding an election for their board.  Have a look at the slate of candidates, and read some of those statements.  Check out the varied backgrounds on these folks–you’ll be seriously impressed with their skills and dedication to good data.

And if you are a biocurator, and a member of the society, I would encourage you to have a special look at Jennifer Williams of OpenHelix.  Jennifer is an incredible member of our team, and we totally support her candidacy for the ISB board.  She would bring useful skills to the job from the project management perspective, I assure you.  She knows both sides of curation equally well: getting data in and getting data out.  She’s also very much a bridge-builder with a very gentle and effective way of bringing people together in the right place.

If you have a membership and intend to vote, please consider voting for Jennifer Williams for one of the 6 board members.  She is a real gem, and she’s certain to serve capably and effectively.

Heads Up: ISB to Hold First Election in September

ISB_election Just a heads-up that the fairly new International Society for Biocuration is accepting nominations during August for their executive board, with elections to be held in September. I’ve included a bit of their email below, but you can see the whole announcement here, and join the society as well, if you haven’t yet.

Dear Colleagues,

We are ready for the first election of the executive board. The complete executive board shall be composed of nine (9) members, each with a 2-year term. The interim executive board remains for another year to ensure proper transition and six (6) new members will be elected this year…

It's official – You Too Can Join the ISB!

That’s right, I got a couple of emails today and the International Society for Biocuration is open for membership! I unofficially joined right after I got home from the 3rd International Biocuration Conference where the society was introduced. I plan on paying my dues shortly after I get this post out, but  since I don’t want to hog all the fun I wanted to blog about this oportunity ASAP.Here’s the text of the original announcement:

Dear Colleagues,

The International Society for Biocuration has redesigned the biocurator.org website, and we are happy to announce that member registration is now active. The member registration page is here: http://colleagues.biocurator.org/join

We strongly encourage people from the biocuration community to become members of the ISB. There are many goals we wish to achieve and that can only accomplished with the help and support from all of you (http://www.biocurator.org/mission.shtml). The membership rates for 2009-2010 are as follows:

Principal investigator: 60 CHF
Curator: 40 CHF Student: 20 CHF

Principal investigator: 120 CHF Curator: 80 CHF

Conversion rates for June 18, 2009:
1 CHF = 0.921 USD – 0.664 EUR – 0.563 GBP

Lydie, Pascale and Lorna

Seriously, I do believe with wide community support this society could really be valuable for curators and others associated with building and supporting bioinformatic resources. So please, help me spread the word!

The 3rd International Biocuration Conference was Amazing!

I’m nowhere close to being able to describe all that I saw and learned at the conference – I have pages and pages of notes, all full of good stuff – but I did want to give you a brief update today. The conference occurred April 16th-20th in Berlin at the brand new Seminaris conference center just south of Berlin. I had never been to Berlin before & so I went a few days early to sight see. I really enjoyed Berlin & suggest that if you have the chance to visit there that you do. But this is a science blog, not a travel blog, so onto the science…

ism_biocuration_logo On the first day of the conference we celebrated the inauguration of the International Society for Biocuration, or ISB. If you are interested in learning about the society, or joining, you can check them out here.

Also, all poster and talks from the conference are requested to be published at Nature Proceedings, and several are already available. My submission just completed its way through Nature’s curation process and is available here. If you find presentations there that you support, or want to “applaud”, you can “vote” for them. I’d appreciate any support you’d care to give my talk (hint hint) :)

OK, I’ll probably blog more about the conference after I cull my notes & get further on my meeting report, but in the meantime enjoy the links I’ve provided, maybe join the ISB & HAPPY FRIDAY!

Biocuration Meeting: already heard a good talk

Today was the beginning of the 3rd annual Biocuration Conference & I’ve already heard an interesting talk by Janet Thornton of EBI. She gave a talk entitled “Data Curation in Biology – Past, Present and Future.” Then Pascale Gaudet spoke on the inauguration of the International Society for Biocuration. Janet talked about lots of interesting things including PDB & some future aims for bioinformatics in Europe. Pascale promised more details on the society as the meeting progresses & I’ll pass on any info that I hear.

Tomorrow morning is only about 9 hours away – I’m still on US Eastern time instead of Berlin time – but tomorrow’s plenary talk from Phil Bourne should be well worth a few extra cups of cappuccino!

More from Berlin later!

The Deadline is This Friday for the Biocuration Conference!

biocurator_berlin_logoI just got an email that the registration for the 3rd International Biocuration Conference closes this Friday, March 27th. The conference is April 16th-20th in Berlin and if there is ANY way you can get there, I suggest you do! It is a GREAT meeting – I’ve had the pleasure of attending both the 1st & 2nd meetings in the past, and will be representing OpenHelix at this one too. This meeting is a really cool, small meeting where resource creators and curators come together to exchange ideas and discuss solutions to current and future bioinformatics problems. I really hope that some of the bloggers I met at ScienceOnline in January make it to this meeting – I think the two groups have a lot in common. It is also a great place to hear about new resources. OpenHelix (ok, I) will be introducing a new resource in fact. Mary alluded to it in her comment reply to Theadore. If you are going to be in Berlin with me, you can stop by poster F12 on Friday night 4/17 19:00-22:00, or come to my talk during the Sunday morning session 4/20 8:30-10:00 to hear more!