annotation
Previously, in Section 5.2, the strategy for the argumentation process was chosen. The discussion continues by considering the data available for arguing and how it may be applied in the generation of arguments and counterarguments. The following terminology, although not widely used in biology, shall be used in this work to aid clarity:
Experiment The actual research undertaken including the experimental result (an image for in situ data);
Result The published outcome, i.e. the researcher’s interpretation of the experimen- tal result;
Annotation The (EMAGE or GXD) editors’ analysis of the experiment, including their own interpretation of the result - may be textual or spatial;
Verdict The statement that a gene is (not) expressed in a tissue, which is either stated directly in an annotation or may be derived from an annotation. The term may be used to refer to the final conclusion drawn by the user.
The relationship between the concepts is documented in Figure 5.2. In an abstract sense, an experiment is performed and analysed to produce a result. The combination of the experiment and the result provides the source material for the annotation. That annotation contains limited provenance information and an analysis of the result. This analysis will contain one or more conclusions, e.g. gene bmp4 is expressed in the future brain, and bmp4 is not expressed in the neural fold. This information will lead to a user inferring a particular verdict, e.g. bmp4 is expressed in the future brain.
Information on the raw experiment is stored in the journal article (assuming it was not part of a large screening program), and as such is not available unless the journal article can be textmined. Consequently, this work will access the experimental information contained within the annotation, as illustrated in Figure 5.2 through the use of a double line defining the extent of the system.
Figure 5.2: Illustrating the relationships between the original experiment, the original (published) result and the notions of annotation and verdict used in this work; green lines indicate a support or inference relationship with red lines depicting attack.
When viewed informally from an argumentation stance, the experiment and the result combine to allow the annotation to be generated. Thus if the experiment and result are trustworthy it increases the likelihood that the annotation is correct. In a similar vein, the annotation directly supports the inference of the verdict. These relationships are demonstrated in Figure 5.2 by the use of green lines. Considering the annotation in more depth: the analysis of the result is supported by the provenance information. The notion of experimental provenance contains all the data the resource holds on the experiment including the researcher, the probe, the sample, and the genuine result (image) produced by the experiment.
Normally the annotation is a subset of the information in the experiment and result, possibly with a small extension provided by the resource. However, it is possible that one experiment, when published, refers to a second experiment, in which case the annotation may be generated from two experiments and results. Occasionally, when examining the experimental result, the database’s editors decide they disagree
with the published result. As the experimental result is part of the experiment, the resulting annotation can still be considered a subset of the information in the experiment-result pair.
There is a difference between the two relationships: experiment/result to anno- tation; and, annotation to verdict. The annotation is, in some form, a view (in the database sense) over the experiment and result. Therefore the experiment is not a rea- son to believe the annotation as they are, at some level, equivalent; however, reasons to trust the experiment are automatically reasons to trust the annotation. In contrast, the annotation does provide a reason to believe the verdict. This occurs because the verdict is based either on the raw provenance information3 (i.e. the image taken as the result of the experiment) or on the resources’ analysis of the result. Either way, the verdict is inferred from the provenance information rather than simply being a re-publication of raw information.
There is another way of examining this difference in the relationships. Without an experiment there is no annotation. Yet, a verdict - bmp4 is expressed in the future brain of stage 12 - can exist, albeit irrational, without an annotation to support it. However, if the annotation does exist it is possible to use it as a justification of why the verdict is correct. As such, the latter is the traditional argumentation notion of sup- port where one entity allows the other to be inferred with some degree of confidence. A more detailed consideration of the relationship between the experiment/result and annotation is tangential, as the raw experimental information is not available, and shall not be pursued.
Figure 5.2 uses red lines to indicate potential lines of attack within the area of the system4, with a double headed line pointing at the potential for rebuttal and a single
headed arrow indicating an undercut. Immediately, a red line seems to be missing: the line attacking the support between the annotation and the verdict. This is not included because such an attack is not viable within the current work.
To attack the support between an annotation and a verdict would imply that there was something wrong with the notion that “an annotation provides a reason to believe a verdict”. Here the discussion is not about a particular annotation but the
3Experts often prefer to perform their own results analysis. 4Lines of attack outside the system are ignored.
principle in general. In biology the basic principle stands and is not deemed open to negotiation, thus such an attack is not considered here.
Considering the attack relationships in Figure 5.2, the most obvious is the rebuttal between the annotations. As annotations directly lead to verdicts, it is possible for the verdicts to contradict one another.
The final line of attack is between the experimental provenance and the result analysis. Without access to the underlying article (assuming there is one), the ex- perimental provenance contains all the information that can be used to evaluate the experiment and the resource’s analysis of that experiment. Clearly this information has the potential to influence the reader’s confidence in the result analysis. Accord- ingly, there is both a green line of support and an undercut of that support depicted in Figure 5.2 between the notions of experimental provenance and result analysis. It is worth noting that if an annotation is defeated in this manner, and the verdict is no longer supported, that does not provide a reason to support the opposite verdict.
For instance, if a verdict suggesting that bmp4 is expressed in the future brain, is defeated by removing the supporting annotation then at most it is possible to say that it is unknown if bmp4 is expressed in the future brain. In contrast, if the verdict’s only supporting argument is defeated by a stronger rebutting argument, then with the currently available knowledge, it is possible to claim that bmp4 is not expressed. Ultimately, an annotation is deemed to be a reason to support a verdict. The information contained within the annotation provides the reason to trust that anno- tation, and thus the verdict it supports. However, it may contain the information necessary to reject the annotation and its associated verdict too.