Guide: AskNature AI Data Training

AskNature is making it easier for people to share and organize biological literature so that it can be used to inspire innovators around the world. You can help by training a new algorithm to identify functions and organisms in short blocks of text.

Read this guide, then start training!

Invite your friends and colleagues to participate:

For the past several years our team has been investigating ways to improve the quality and breadth of ​the biology content available on asknature.org. One of the challenges we currently face is that the process of manually assigning functions and living systems to biological strategy records is time consuming and requires specialized knowledge. So earlier this year we started working with a small group of data scientists and programmers to automate these components of AskNature’s content generation process via several machine learning algorithms. If we’re successful, future content contributors will be able to quickly select from ranked lists of suggestions rather than having to manually cull through options from long lists.

The suggestions this tool makes will only be as good as the associations we manually teach it, and with your help, we hope to generate enough associated data (upwards of 10,000 submissions) to get started.

Participating is easy; our colleagues have created a short online survey in which you’ll read the title and abstract of a biology article and then identify key concepts described therein. Each time you take this survey you’ll be training this algorithm to make associations accurately and consistently.

Each time you take the survey you’ll be shown the title and abstract from a peer reviewed article that may be appropriate to include on AskNature. If it is relevant, you’ll be asked to identify relevant functions and living systems, and copy/paste the phrases that led you to make those associations. If it’s not relevant you should still submit, since we’re also teaching the algorithm to distinguish between text that may be useful vs text that isn’t.

In the event you’re presented with an article that you’ve already reviewed, just click the “Skip” button at the bottom of the form until you’re presented with an article you haven’t seen yet

We suggest you review the brief tutorial below before you begin so you can start making effective contributions right off the bat. If you have any questions, please reach out to us via our contact formThank you!!!

Key Concepts

AskNature is an online resource that inspires designers, architects, business strategists, and other innovators with biological information that offers a new lens to solving their product, service, and system design challenges.

Biomimicry is an approach to innovation that seeks sustainable solutions to human challenges by emulating nature’s time-tested patterns and strategies.

A living system is an identifiable biological entity. It can be a protein, cell, tissue, organ, organism, population, community, or anything in between. In most cases, living systems are referenced by the common and/or scientific names of the organism being studied (e.g. the seeds of the Lesser Burdock / Arctium lappa).

A mechanism is a form or process that helps a living system achieve a function. For example, Burdock seeds use a mechanism of tiny hooked projections to achieve a function of temporarily attaching to the wooly coats of passing-by animals.

A function is what a living system achieves in response to a problem or opportunity it faces in its environment. In the example above, temporarily attaching is the function achieved by the tiny hooked projections of Burdock seeds.

Curious? Confused?

Check out the Biomimicry Toolbox to learn more about how to bring biology into your innovation process.

Example 1: Annotating a potentially relevant abstract

Papers that are relevant to AskNature typically describe how a living system responds to its environment to achieve one or more functions via one or more mechanisms. If the abstract you’re shown refers to a living thing and things that it does, it’s probably relevant. The example below shows how AskNature’s Content Manager, Jeanette Lim, responded to the survey questions about a relevant paper:

Paper Title

Adaptation to life in aeolian sand: how the sandfish lizard, Scincus scincus, prevents sand particles from entering its lungs.

Authors

Anna T. Stadler, Boštjan Vihar, Mathias Günther, Michaela Huemer, Martin Riedl, Stephanie Shamiyeh, Bernhard Mayrhofer, Wolfgang Böhme, Werner Baumgartner

Abstract

The sandfish lizard, Scincus scincus (Squamata: Scincidae), spends nearly its whole life in aeolian sand and only comes to the surface for foraging, defecating and mating. It is not yet understood how the animal can respire without sand particles entering its respiratory organs when buried under thick layers of sand. In this work, we integrated biological studies, computational calculations and physical experiments to understand this phenomenon. We present a 3D model of the upper respiratory system based on a detailed histological analysis. A 3D-printed version of this model was used in combination with characteristic ventilation patterns for computational calculations and fluid mechanics experiments. By calculating the velocity field, we identified a sharp decrease in velocity in the anterior part of the nasal cavity where mucus and cilia are present. The experiments with the 3D-printed model validate the calculations: particles, if present, were found only in the same area as suggested by the calculations. We postulate that the sandfish has an aerodynamic filtering system; more specifically, that the characteristic morphology of the respiratory channel coupled with specific ventilation patterns prevent particles from entering the lungs.

Do you think the paper may be relevant to AskNature?

Yes
No

Does the paper refer to a living system?

Yes
No

Paste the word or phrase from the abstract that identifies the living system

lizard

Select the best label that characterizes a function of the living system discussed in the paper

Get, store, or distribute resources (e.g. Camel noses prevent water loss during exhalation)

Paste the phrase from the abstract that identifies the function

how the animal can respire without sand particles entering its respiratory organs when buried under thick layers of sand.

Paste the phrase from the abstract that describes a mechanism that performs the function above (if present in the text)

We postulate that the sandfish has an aerodynamic filtering system; more specifically, that the characteristic morphology of the respiratory channel coupled with specific ventilation patterns prevent particles from entering the lungs.

Optional: In your own words, summarize how the living system achieves the referenced function/s via the referenced mechanism/s

The sandfish lizard spends much of its life buried in sand. It is able to breathe and take air into its airways and lungs while filtering out sand. The filter is aerodynamic, meaning that the airways’ shape and the lizard’s breathing patterns manipulate airflow to keep particles out of the lungs.

How confident are you in evaluating this paper?

Very confident
Somewhat confident
Not confident

Describe the reasoning behind your level of confidence

The abstract refers to an organism and a potential problem it faces in its environment (breathing and not inhaling sand particles while buried in sand). This biological problem could feasibly be a problem in a human-designed system, e.g., how to filter air, how to keep sensors free of dust. The abstract also refers to a proposed solution that the organism uses (an aerodynamic filtering system), and how the components of the solution work.

Example 2: Annotating a potentially irrelevant abstract

Papers that are relevant to AskNature typically describe how a living system responds to its environment to achieve one or more functions via one or more mechanisms. If the abstract you’re shown doesn’t refer to a living thing and things that it does, it’s probably not relevant. The example below shows how AskNature’s Content Manager, Jeanette Lim, responded to the survey questions about an irrelevant paper:

Paper Title

Testing hypotheses about individual variation in plasma corticosterone in free-living salamanders.

Authors

Jessica R. Thomas, Andrew J. Magyan, Peter E. Freeman, Sarah K. Woodley

Abstract

In vertebrates, many responses to stress as well as homeostatic maintenance of basal metabolism are regulated by plasma glucocorticoid hormones (GCs). Despite having crucial functions, levels of GCs are typically variable among individuals. We examined the contribution of several physiological factors to individual variation in plasma corticosterone (CORT) and the number of corticotropin-releasing hormone (CRH) neurons in the magnocellular preoptic area of the brain in free-living Allegheny Mountain dusky salamanders.We addressed three hypotheses: the current-condition hypothesis, the facilitation hypothesis and the trade-off hypothesis. Differential white blood cell count was identified as a strong contributor to individual variation in baseline CORT, stress-induced CORT and the number of CRH neurons. In contrast, we found no relationship between CORT (or CRH) and body condition, energy stores or reproductive investment, providing no support for the current-condition hypothesis or the trade-off hypothesis involving reproduction. Because of the difficulties of interpreting the functional consequences of variation in differential white blood cell counts, we were unable to distinguish between the facilitation hypothesis or the trade-off hypothesis related to immune function. However, the strong association between differential white blood cell count and hypothalamic-pituitary–adrenal/interrenal (HPA/I) activation suggests that a more thorough examination of immune profiles is critical to understanding variation in HPA/I activation.

Do you think the paper may be relevant to AskNature?

Yes
No

How confident are you in evaluating this paper?

Very confident
Somewhat confident
Not confident

Describe the reasoning behind your level of confidence

There is not an obvious function or related mechanism mentioned in the abstract. The hormones studied in this paper likely have functions in an organism that could be relevant to biomimicry, but the abstract indicates that this paper focuses on how and why those hormones vary.