Visual Interactive Pedigree ExploreR (VIPER)

本项目旨在开发一种工具，以消除由于管理和数据处理错误而导致的动物谱系信息错误。在动物育种研究的过程中，记录和存储了大量的动物谱系和特征数据。然而，为了对进一步的程序或分析有任何用处，数据需要尽可能没有错误。数据存储中的错误，例如记录错误的动物父亲或相关基因数据中未被注意到的变化，很容易在处理数百或数千只动物时引入。不幸的是，虽然处理这些数据以发现错误的存在相对容易，但发现和纠正错误的原因却更加困难。例如，要知道错误是在谱系中，即孩子-父母关系中还是在与动物相关的特征中，并不简单。一个动物可能被记录为具有某种特征，在检查时可能不可能从它的两个记录的父母遗传。那么，到底是对父母一方或双方的记录有误，还是对子代动物特征的记录有误，还是父母一方的特征有误呢？为了回答这个问题，有必要进一步研究动物在系谱中的关系。然而，在基于文本或电子表格的文档中，即使检测和显示数据中的错误的操作可用，这也很快变得乏味和令人困惑。然而，如果我们切换到一个更图形化的，用户友好的显示数据的风格，那么它将更容易遵循系谱中的关系。如果我们在上面添加交互式显示错误发生的位置以及可能导致错误的位置的功能，我们将有一种检查谱系数据并提出问题的方法，可以清除或缩小错误。这种显示和与数据交互的方式被称为信息可视化（IV）。与人类家谱不同，大多数记录在案的动物谱系都有很大程度的近亲繁殖，因为科学家和育种家试图通过选择性育种来鼓励某些特征。这使得动物谱系的绘制更加复杂，因为两个个体可能最终通过两条或更多路线相关联。通过扩展目前的IV技术，这类数据，该项目将使界面不那么复杂，交互式显示只有选定的个人和他们的关系。最重要的是，科学家们还希望看到一些与动物相关的特征的显示，并且再次通过一次只观察少数特征来降低复杂性。即便如此，一只雄性动物可以很容易地生下几十个孩子，这些孩子又与几十个雌性父母有关，然后又可能有自己的孩子-科学家可能有兴趣探索这些动物的几个特征。将开发从显示谱系的一部分无缝转移到另一部分的方法，以帮助科学家探索大规模谱系。一旦一个初始的接口是建立然后探索错误的手段，问“如果”的问题将被开发。可能性包括“屏蔽”问题个体或问题特征的能力，以查看其对谱系和错误的影响，或者实际编辑信息并重新计算对谱系的影响。需要重做和撤销过去的操作的能力，最终科学家将产生一组操作，从而产生一个干净的数据集，或者尽可能接近。在整个项目过程中，这项工作将由使用谱系数据的科学家进行测试。最后，我们将开发一个工具，让从事家谱研究的科学家能够轻松清理数据，并与其他科学家分享有用的数据。

This project aims to produce a tool to remove errors in animal pedigree information caused by administrative and data handling faults. Large amounts of animal pedigree and characteristic data are logged and stored during the course of animal breeding studies. However, to be of any use for further programmes or analysis the data needs to be as free of error as possible. Errors in data storage such as recording the wrong father for an animal or unnoticed change in associated gene data are easy to introduce when hundreds or thousands of individual animals are being dealt with. Unfortunately while it is relatively easy to process this data to find the existence of errors, finding and correcting the cause of the errors is more difficult. For example, it isn't straightforward to know if an error is in the pedigree i.e. the child-parent relationships or in the characteristics associated with the animals. An animal may be recorded as having a certain characteristic that on examination may not be possibly inherited from its two recorded parents. So is the recording of one or both of the parents wrong, the recording of the characteristic in the child animal incorrect, or the characteristic in one of the parent animals wrong? To answer this question further examination of the problem animals' relations in the pedigree is necessary. However, in a text or spreadsheet-based document this quickly becomes tedious and confusing even when the operations to detect and show errors in the data are available. However, if we were to switch to a more graphical, user-friendly style of displaying the data then it would be easier to follow relationships in the pedigree. If we added on top the capabilities to interactively show up where errors occurred and where they could possibly be caused from we would have a way of examining the pedigree data and asking questions that would clear up or narrow down errors. Such a way of displaying and interacting with data is called Information Visualisation (IV). Unlike human family trees, most recorded animal pedigrees have a large degree of in-breeding as scientists and breeders try to encourage certain characteristics through selective breeding. This makes the drawing of animal pedigrees more complex as two individuals may end up being related through two or more routes. By extending current IV techniques for this type of data this project will make the interface less complex by interactively showing only selected individuals and their relationships. On top of this the scientists will also wish to view some display of the characteristics associated with the animals and again the complexity can be reduced by viewing only a handful of characteristics at a time. Even so, one male animal can easily sire dozens of children who are in turn related to dozens of female parents and then in turn again may have children of their own - and there may be a several characteristics at a time a scientist is interested in exploring for these animals. Methods for seamlessly moving from showing one part of a pedigree to another will be developed to help scientists explore massive pedigrees. Once an initial interface is built then a means for exploring errors by asking 'what-if' questions will be developed. Possibilities include the ability to 'mask out' problem individuals or problem characteristics to see what effect that has on the pedigree and errors, or to actually edit information and recalculate the effect on the pedigree again. The ability to redo and undo past actions will be needed and in the end the scientist will produce a set of actions that lead to a clean data set, or as close as can be achieved. Throughout the course of the project the work will be tested with scientists who use pedigree data. In the end we will produce a tool that will benefit scientists who work with pedigrees by allowing them to readily clean their data, allowing them to share it usefully with other scientists.