Todd Harris, PhD

Facilitating scientific discovery at the intersection of genetics, genomics, bioinformatics, big data, cloud computing, and open science.

The Worm Reader’s Gazette: audio transcripts of the scientific literature

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Digital media has had a profound effect on scientific publishing. But by and large, consuming that literature is still a tedious process of reading that does not lend itself well to today’s active lifestyles. Do you have a long commute or need your hands and eyes free for other tasks like pipetting or microinjecting? Then we think you’ll love the Worm Reader’s Gazette.

The Worm Breeder’s Gazette is pleased to announce the Worm Reader’s Gazette: audio recordings of scientific literature read aloud by lead authors, now in private invite only alpha testing.

At the Worm Reader’s Gazette, lead authors can create and submit audio recordings of their publications. We’re starting with seminal papers in the C. elegans field and adding new papers as they are published.

Making audio recordings a standard part of the manuscript submission process.

To improve the coverage of available articles, we are working with publishers to make audio recordings a required part of the manuscript submission materials.

Following acceptance and approval of the final galleys, web-based authoring tools will make it simple for authors to create and edit their audio recordings from their mobile phone.

Borrowing from the popular photo sharing service Instagram, special audio filters will add humor, drama, or august ambience as required by the tone and conclusions of your manuscript. These include the mysterious “Irreproducible Result”, the lo-fi “Graduate Seminar”, the visceral “Thesis Defense”, and the noble “Nobel Address” and many, many others.

We’ve included high quality audio samples that authors can drag and drop into their recording, too. Add dog barks after particularly important points, bomb explosions during and after paradigm shifting pronouncements, and audience applause whenever warranted.

Our natural language processing filters will automatically markup your recording with special auditory hyperlinks to primary databases. Users can “click” on these hyperlinks during playback using voice activation via Siri, Cortana, or Alexa: “Hey Siri, order the antibody mentioned in the fifth paragraph and have it sent priority overnight mail to my bench”. Yes, it’s that easy.

We hope you enjoy this new service. And we look forward to seeing — and hearing! — your next publication.

Announcing: The Bioresource Project Manager Directory

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Are you a Project Manager or Team Leader of a biological resource, database, or repository?

Add yourself to the Bioresource Project Manager Directory.

Let’s get to know each other. There’s much to discuss. Start by adding yourself to the directory. Don’t worry, your information will be kept private.

Initially, I plan to create a mailing list (Google Groups, perhaps?).

And stay tuned for an upcoming announcement, one you’ll hopefully find exciting!

How do we assess the value of biological data repositories?

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In an era of constrained funding and shifting focus, how do we effectively measure the value of online biological data repositories? Which should receive sustained funding? Which should be folded into other resources? What efficiencies can be gained over how these repositories are currently operated?

Everyday it seems a new biological data repository is launched. Flip through the annual NAR Database issue if you do not believe this.

Quick aside: I want to differentiate repositories from resources. Repositories are typically of two varieties. The first collects primary data in support of a single or small consortium of labs. The second culls data from the scientific literature or collects it by author submissions before, during, or after the publication process. Resources may have some characteristics of repositories but are usually more tool oriented and aim to process data that users bring to it.

Encouraging the creation of a large number of repositories has been an important development in the rapid advancement of bioinformatics. These repositories, in turn, have played a critical role in the genomic- and post-genomic research world.

The current community of biological repositories allow for experimentation and innovation of data modeling and user interface. They provide opportunities for education. And they let small labs participate in the grand process of Scientific Curation: the documentation of scientific progress outside of the traditional prose-based publication narrative. We should continue to carefully create new repositories when warranted for the innovation and educational opportunities that they present.

On the flip side, these repositories are often brittle: graduate students and postdocs move on and create knowledge vacuums. Elements of the repository break due to software upgrades and security patches. Data becomes unreliable (eg as genomic coordinates are refined). Interest declines yet the cost of maintaining the resource remain. And daving many repositories carrying slightly different versions of data also introduces confusion for downstream analyses and hinders reproducibility.

Clearly, we need an effective way of measuring the reach and value of biological data repositories. When a repository crosses a certain threshold, it’s funding should be decreased or removed. Remaining funds should used (or allocated if necessary) to port the repository to a parent resource for long-term maintenance.

How can we determine the value of a biological repository?

1. Page views.

Simple metrics like page views, taken in isolation, are wholly insufficient for assessing the value of a repository. Each repository, for example, may have different tolerances for robots, different definitions of what constitutes a robot, or different architectures that mitigate the importance of page views. Page views is only one element that should be taken into account. I personally believe that it’s one of the least effective ways of defining the value of a repository and worry that too much emphasis might be placed on it.

2. Size of the user community.

How big is the user community? This should include registered users (if the repository has such an implementation), users determined via analytics, and the rate of citation.

3. Collective funding of the core user community.

How much money has the core user community of the repository been entrusted with? How much of that money would be lost or wasted if the repository were to be placed in a maintenance mode or defunded altogether? There is no sense in throwing good money after bad and sometimes tough choices must be made, but if the core research community — and all of the money vested in that as well — is affected, funding choices of the repository should be weighed very, very carefully.

Don’t get me wrong: repositories that serve relatively small communities (with a relatively small amount of funding have value. But the net value of such repositories cannot compare to one that serves a user community 10x the size with 100x the funding.

4. Frequency of use.

How frequently to members of the core user community access the repository? Is it essential for day-to-day lie at the bench? Or maybe it is used in a more referential manner on a periodic basis.

5. Difficulty of assimilation.

How difficult and time consuming would it be to fold an existing repository into another? Repositories containing very specialized data, data models, or analysis tools that still support moderately sized communities with substantive funding could actually be MORE expensive to fold into another repository than to continue its maintenance independently.

In sum, page views are insufficient. We need to define the size of the user community, the extent of its funding, and how critical the repository is to continued progress of that community. Finally, we need to carefully weigh sustained funding vs. maintenance funding vs. assimilation costs.

Without knowing these five parameters, making consistent decisions about the value of biological repositories will be challenging at best.

And even with these metrics in hand, the real question — and the one that is much more difficult to address — is:

What are the thresholds for continued support of a repository?
I will address my thoughts on this in an upcoming post.

What are your thoughts? What other metrics should we be using to determine the value of biological data repositories? Leave a comment or ping me on Twitter.

Community annotation — by any name — still isn’t a part of the research process. It should be.

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In order for community annotation efforts to succeed, they need to become part of the established research process: mine annotations, generate hypotheses, do experiments, write manuscripts, submit annotations. Rinse and repeat.

A few weeks ago, I posted the following tweet:

Bioinformatics people like to orate about "community annotation". I've never heard a biologist use the phrase. Therein lies the problem.

A few retweeters responded that in their particular realm of bioinformatics, community annotation was called “community curation” or a “jamboree” and they’ve had various degrees of success. Points taken and effort applauded.

The real essence of my tweet was that community annotation — regardless of what it is called — largely fails or is undertaken on a very small scale because it simply isn’t a priority for biologists.

Working at the bench, community annotation doesn’t even make the long list of things to do: conducting experiments, writing manuscripts and grants, mentoring, sitting on committees, teaching. Contributing to community annotation efforts simply does not make the cut.

How might we fix this?

1. Top-down emphasis on the importance of community annotation.

Community annotation isn’t required of publishers or funding agencies except in the most minimal degree (eg submission of sequences). This needs to be changed. By making community annotation part of the process of doing research, the research itself will become more reproducible, more accessible to a broader audience, and more stable over time. It should be complementary to writing a manuscript.

Publishers benefit because extracted entities become markup targets to enhance their online product. Funding agencies benefit since having primary authors and domain experts submit annotation suits the mission of transparency and reproducibility and has a presumed efficiency over third party curation.

2. Better tools.

The tools for community annotation are embryonic and do not match the user experience people have come to expect in the Facebook / Pinterest / Instagram / Google Docs era. Bioinformatics teams need to begin employing user interface, user experience, and graphic design professionals to build friendlier, more efficient, and more beautiful tools to encourage participation.

3. Recognition.

Again, in an effort to encourage participation, we need to recognize the efforts of people who do contribute. This system must have professional currency to it, akin to writing a review paper, and should be citable for two reasons. First, it adds legitimacy to the contribution. It’s now part of the scientific record that can be extended by other researchers. Second, the primary contributor can now make note of their effort expended on CVs and in the tenure or job performance review process.

Nanopublications and microattribution represent the most promising avenues for providing suitable recognition with scientific legitimacy that maps to the current academic and professional status quo.