A Guide to Patenting Bioinformatics Inventions at the EPO

Many inventions in the field of bioinformatics (a term that we will use herein to encompass computational biology and medical informatics) are computer implemented methods or systems configured to implement such methods. As discussed in a previous post, the EPO uses a very specific approach to the assessment of patentability of such inventions, which is sometimes referred to as the “2 hurdles approach”. In this post, we will explore the second (and often most problematic) hurdle: inventive step (Article 56 EPC).

When assessing the inventiveness of a claim, the practice of the EPO is to consider only those features that contribute to the technical character of the invention. These features include: (a) features that are technical when taken in isolation, and (b) features that are non-technical when taken in isolation, but that in the context of the invention contribute to producing a technical effect serving a technical purpose.

What is a technical feature?

The European Patent Convention (EPC) does not define what constitutes a technical feature. Features that are technical when considered in isolation would include those that involve a physical step or technical entity. For example, a computing device (or any other hardware) is a technical feature, and so is a physical measurement step. Further, Article 52 EPC provides a list of things that are not considered inventions in a field of technology, i.e. features that would not be considered technical in isolation. This list includes, most notably in the present context, mathematical methods (such as clustering methods, and any other mathematical/statistical data analysis/processing methods that are frequently at the core of bioinformatics inventions, and data in isolation – even where the data represents a physical measurement), and the presentation of information (such as features associated with graphical user interfaces that can be essential to the practical benefits of a bioinformatics platform).

So in answer to that question: a computing device or a physical measurement step (e.g. “sequencing a DNA sample”) are technical features, but e.g. a mathematical method step (e.g. “identifying peaks in a series of curves by finding local maxima”) or the presentation of information (e.g. “displaying a series of curves together with indications of their local maxima”) are not technical features.

Therefore, features of a mathematical method and features of presentation of information will be completely ignored in the assessment of inventive step, unless it can be shown that serve a technical purpose in the context of the invention.

Here we look at how to do this for mathematical methods and for the presentation of information.

Part A - Patenting Bioinformatics Inventions at the EPO: mathematical methods

What is a technical purpose?

The European Patent Convention (EPC) does not define what constitutes a technical purpose. However, a body of case law and many years of practice are summarised in the EPO Guidelines for Examination, which provide specific examples of technical purposes. These include: controlling an X-ray apparatus, determining the energy expenditure of a subject by processing data obtained from physiological sensors, providing a genotype estimate based on an analysis of DNA samples, as well as providing a confidence interval for this estimate so as to quantify its reliability, and providing a medical diagnosis by an automated system processing physiological measurements.

From these examples, it is possible to draw some general guidance for identifying what is likely to be considered a technical purpose. This would seem to include at least:

• the control of a physical system or device (e.g. a dialysis machine, a sensor, a lab robot, a micromanipulation device, etc.); and
• the determination of a property of a system/individual which property is objective (independent of subjective interpretation by a user), (ideally) verifiable by physical / physiological measurements, and has a concrete technical meaning (e.g. in the context of steps/measures to be taken). In other words, a technical purpose is more likely to be acknowledged for a claimed method where the method produces a result that is objective and concrete in that it is directly usable (i.e. it is not an intermediate result that, with the right skill, can be used to derive information that is actionable).

The following examples, drawn from informal discussions with EPO examiners, may be helpful in illustrating these differences.

When does a non-technical feature serve a technical purpose?

For a non-technical feature (e.g. a mathematical step) to serve a technical purpose, it is necessary for a technical purpose to be present in the claim, either explicitly or through the claimed method resulting explicitly in the technical result that achieves said purpose. However, that is not sufficient. Indeed, the claim has to be worded such that the mathematical step is causally linked to the technical purpose. In other words, there must be a logical chain from the input of the method to the (technical) output of the method, where each step of the method may represent a chain link. If any of the steps of the method are missing or are described in terms that are so vague that they do not produce the result necessary to ensure that the method as a whole produces the technical output, then the causal link is broken and any mathematical step in the chain can no longer be considered to serve the technical purpose.

As explained above, if a mathematical step cannot be considered to serve the technical purpose of the claimed method, then it must be ignored in the assessment of inventive step. Of course the level of detail that is necessary for a step to be considered defined with enough detail in the claim to ensure the causal link will depend on the circumstances. For example, where multiple implementations of a step are known in the art and all are equally suitable to produce the intermediate result necessary to maintain the logical chain, then this step can be described at a relatively high level.

For example, a method of determining the genotype of an individual which requires normalisation of data for GC content need not necessarily include details of how this is done in the claim, if the normalisation procedure is standard. Conversely, if the normalisation is the distinguishing feature of the invention over the prior art and improvement over said prior art is dependent upon the use of a particular mathematical formula for GC content normalisation, then this mathematical formula (or possibly a concept underlying the formula or a generalised version of said formula) should be included in the claim.

Common pitfalls…

As discussed above, in order for the mathematical steps of a claim to a computer implemented method to be considered for the assessment of inventive step at the EPO, it is necessary (a) for the claim to have a technical purpose, and (b) for the mathematical steps to be causally linked to the technical purpose.

Both of these requirements have direct consequences in terms of drafting practices. Firstly, a claim can be acknowledged to have a technical purpose if this purpose is explicit (e.g. in the preamble of the claim) or implicit but inevitably achieved by the claim (for example through the explicit mention of the result that achieves said technical purpose). As such, the application as filed must disclose the technical purpose, or at least the result that the skilled person would immediately understand to achieve the technical purpose. For example, when the invention is a method for analysing DNA samples from a subject in order to determine whether the subject has cancer by identifying the presence of a particular chromosomal rearrangement signature, the specification must disclose (a) this purpose (determining whether the subject has a cancer) with a level of generality that one would be happy to include in a claim (e.g. not limited to a particular subtype of breast cancer if the invention is thought to apply to all breast cancers), or (b) that the particular chromosomal rearrangement signature is indicative of whether the subject has cancer (again specified with an appropriate level of generality). If the specification never explicitly draws the connection between the insight of whether or not a subject has cancer (or a particular type, subtype, etc. as appropriate), and the subject having the chromosomal rearrangement signature, then it will be difficult to craft a claim that includes the technical purpose of determining whether a subject has cancer based on determining whether the subject presents the chromosomal rearrangement signature.

In view of the relatively strict practice at the EPO in relation to amendments, this can be problematic where the specification consistently refers to “a method of identifying the presence of chromosomal rearrangement”, and only explicitly establishes a link between cancer and a specific chromosomal rearrangement in a very specific region (whereas the invention is believed to reside in the presence of a pattern that can be present in different / more broadly defined regions), or between a pattern of chromosomal rearrangement and a particular subtype of cancer (whereas the invention is believed to be applicable to a broader range of cancers).

Secondly, mathematical steps are unlikely to be considered to be causally linked to the technical purpose if steps that are essential to achieve that technical purpose are not defined in the claim, or if steps that are distinguishing features of the invention are not defined with enough detail. As such, features may need to be further defined in the claim, and basis for the definition of these features (at all or at an advantageous level of generalisation to ensure a useful scope of protection) must be present in the claim. Again, in view of the strict EPO practice in terms of amendments, this can be a non-resolvable issue if appropriate basis cannot be found, or it can result in the only allowable scope of claim being disappointingly narrow.

…and how to avoid them!

In order to avoid these common pitfalls, it is important to:

• mention the technical purpose or purposes of the invention in the specification – the technical purpose(s) should be described at a level such that it is credibly delivered by the invention, but sufficiently broad to provide commercially useful scope of protection; multiple fall back positions should ideally be available to provide ways to balance breadth and credibility successfully in prosecution;
• ensure that the specification describes all mathematical / algorithmic steps that are necessary to causally link the steps to the achievement of the technical purpose;
• define the distinguishing features with sufficient level of detail, and ideally with various levels of detail providing multiple fall-back positions – for example, if the invention involves the use of a mathematical formula, this formula must be provided and if appropriate the formula can also be provided in a manner that is generalised enough to provide a useful scope of protection while being specific enough that it can be used throughout its scope to arrive at the solution that underlies the technical purpose.

Further, it is worth noting that as eligibility requirements differ amongst jurisdictions, it is advantageous to draft the application with enough flexibility to incorporate the features that will be essential in one jurisdiction, and to remove limitations that are unnecessary or even problematic in other jurisdictions. This is particularly important to bear in mind in relation to jurisdictions that have a strict practice in relation to amendments, such as the EPO. For example, a claim to a computer-implemented diagnostic method that starts with genomic data and finishes with a diagnostic insight may be allowable in Europe in the absence of any explicit sample collection or downstream treatment step. These steps may in fact create other problems as methods of treatment or diagnosis practiced on the human/animal body are excluded subject-matter in Europe. Conversely, in the USA, such steps may be helpful to overcome eligibility (abstract subject-matter) objections. Therefore, it is useful for the specification to provide basis to include such steps in some jurisdictions and exclude them in others.

Drafting an application that optimally sets one up to address these challenges requires a good understanding of the field and of the invention, including the mathematical steps (and the concepts that they embody) as well as the underlying biology and practical purpose. Failing to provide enough detail or useful levels of generalisation is a common consequence of an inappropriate level of understanding of either of those aspects, the combination of which is ingrained in the very nature of bioinformatics inventions. Therefore, it is particularly important in this field to ensure that the right person or combination of people drafts and prosecutes such applications.

Conclusion

Contrary to widespread belief, many bioinformatics inventions (even those that relate mostly or exclusively to a computer implemented method of analysing/processing data) can be patentable in Europe, provided that the application satisfies the above-mentioned criteria.

Further, when a bioinformatics application is poised for success at the EPO, the scope of protection that is obtainable can be very broad. Indeed, claims that only recite algorithmic/mathematical steps can be allowable (with no explicit mention of a sample collection step or of a downstream application such as e.g. treatment step) if appropriately worded.

PART B – A Guide to Patenting Bioinformatics Inventions at the EPO: presentation of information  

When does a feature related to the presentation of information serve a technical purpose?

Again, the EPC does not provide a formal definition of this. However, a body of case law and many years of practice are summarised in the EPO Guidelines for Examination, which provide guidance as to when a feature related to the presentation of information can be considered to contribute to a technical purpose. The Guidelines provide that the presentation of information is the conveying of information to a user (by any means such as e.g. visual, haptic, audio, etc), including both (i) features related to the cognitive content of the information presented and (ii) features related to the manner of its presentation. In other words, features related to the presentation of information fall in two buckets: (i) what is output to the user, and (ii) how this is output. The Guidelines further provide that such a feature produces a technical effect if it “credibly assists the user in performing a technical task by means of a continued and/or guided human-machine interaction process”. There are multiple concepts in this sentence that are worth a closer look.

         What does “credibly assist” mean? In order to determine whether a feature credibly assists the user in performing a task, it is necessary to assess whether the assistance to the performance of the task is objectively, reliably and causally linked to the feature. A technical effect (assistance in performing a technical task) is not achieved if the effect depends on the subjective interests or preferences of the user. For example, the feature of displaying gene expression values as a colour scale instead of numerical values is not technical because it would only help the user to interpret those values if the user prefers to look at colours than numbers. On the other hand, displaying notifications on a computer screen near the user’s current visual focus of attention so that the notification can be seen immediately is technical because the visual focus is a physical objective property that is independent of the subjective preferences of the user.

         What is “performing a technical task”? A technical task is one that solves a technical problem in a field of technology. Assisting a user in performing an administrative task (e.g. administering patient records) will not produce a technical effect. However, operating a machine, diagnosing a disease or condition, providing a therapy, determining the structure of a protein, or the genotype of a person are all considered technical tasks. More discussion of what is and is not a technical task/purpose can be found in the companion part [link to post A] to this post.

         What is a “continued and/or guided human-machine interaction process”? Both of the terms “continued” and “guided” imply a dynamic process whereby information is dynamically processed and displayed to a user. For example, the display of operating instructions to a user as static information has not been considered to support a technical effect because the static information provided was akin to providing a paper operating manual. However, the display of a parameter related to the internal functioning of a system, which is detected automatically and dynamically updated, and prompts the user to interact with the system (e.g. to operate it more appropriately or avoid technical malfunctions) has been considered to support a technical effect.

How do these criteria apply in practice? 

Applying the criteria explained above, a feature related to the cognitive content of the present information (what) will likely not be considered technical if the content relates to a non-technical task (e.g. an administrative task) and/or represents static information. Conversely, such a feature may be considered technical if the content relates to an internal state prevailing in a technical system and enables the user to properly operate this technical system (typically prompting user interaction). For example, in T690/11, a dialysis system which displays information related to a therapy set-up procedure and illustrating the progress of therapy, where the information displayed was depended on user input, was deemed to have a technical effect by credibly assisting the user in assessing progress of dialysis by a continued guided human-machine interaction process.

A feature related to “how” information is presented to a user will likely not be considered technical if the effect depends on psychological or other subjective factors (and even if the information is arguably conveyed in a more appealing, lucid or logical way, because such features relate to lowering the cognitive burden on the user, which is not considered a technical effect). In T1741/08 it was argued that the layout of the invention enabled the user to respond more quickly, reducing computational resources. This was not deemed to support a technical effect because the effect on computational resources use is not directly linked to the layout and instead depends on how the user responds. Conversely, a feature related to “how” information is presented to a user may be considered technical if it credibly assists the user in performing a technical task by reliance on physiological/physical (i.e. objective) parameters.

So what about Graphical User Interfaces (GUIs)?

GUIs typically include an output aspect and an input aspect. The output aspect will be captured by features related to the presentation of information, and the above criteria will apply to these features. The input aspect will be captured by features related to mechanisms (physical and algorithmic) enabling a user to interact with a machine (e.g. computing system), for example by entering text, making a selection or submitting a command. Features related to physical input means are typically of a technical nature, although novelty and inventiveness are often challenging to establish for such features in view of the prior art. Features related to algorithmic steps involved in user input can be considered technical, particularly when they relate to or enable compatibility with the predetermined protocol of a machine. However, user input features that achieve an effect that is dependent exclusively on the subjective user abilities or preferences (for example, enabling more convenient input based on user preferences) or that applies to the decision-making process of the user (for example, providing information that helps a user decide what to input) will not be considered to have a technical effect.

Conclusion

Contrary to widespread belief, inventions that relate to the presentation of information to a user may be patentable at the EPO, in specific circumstances. In particular, claim features that can be shown to credibly assist the user in performing a technical task by means of a continued and/or guided human-machine interaction process will be considered to contribute to the technical character of the invention, and as such will be considered for the assessment of inventive step. While these circumstances are arguably relatively narrow, they still leave open some important possibilities in the field of bioinformatics in particular in the context of interfaces for medical devices, analytical equipment, etc.

Careful assessment of the invention in light of the criteria mentioned above can enable applicants to assess the chances of inventions related to the presentation of information being favourably looked at by the EPO, and to prioritise their resources accordingly. Further, a good knowledge of the EPO approach may enable an application to be drafted so as to set out how some features may credibly assist the user in performing a technical task by means of a continued and/or guided human-machine interaction process. This increases the chances of starting out prosecution at the EPO on the right foot, and of concluding it successfully.

Finally, it is important to keep in mind that many inventions in the field of bioinformatics contain a mixture of features that relate to the presentation of information and features that relate to the processing / analysis of data, resulting in information that enables a user to achieve a purpose. When this purpose is technical (e.g. diagnosing a disease, determining a physiological/physical property of a subject or sample, etc.), those data processing steps may also contribute to the technical character of the invention, and ultimately support the finding of an inventive step (as explained in part A of this guide).