Omics classification paper




The hierarchical classification of Omes and Omics.



Jong Bhak


Omes and Omics are a new classification paradigm of analyzing biological entities(biological information objects). The essence of omics  is that biological understanding of life forms requires philosophical principles on how we represent data, information, knowledge, and decision making. Philosophical principles need to be practical enough to be applied to computers so that computers can process the omic data. It is based on the concept that is biology is all about information processing. The atom of biological information processing is 'interaction' among biological entities. The physical outcome of any interaction is switching. All biological entities are the sum of such 'switches' derived from interaction. Therefore, the new classification and reorganization of biology may be based on networks and graphs of nodes and their edges. The aim of this report is to organize omes as the nodes and omics as the interaction network type of such omes classified to be practically applicable to computers. 


Introduction: switch, signal, data, information, knowledge, and wisdom(decision making to predict)

The universe can be depicted as information processing object. I assume the start of the universe the first state change invoking a switching. A switch is a physical object whether it is the whole universe or the smallest possible particle within the universe. Regardless of the physical size, any object is denoted as a switch. A switch defined to generate a signal. A signal is the smallest unit of information and the sum of signals in a certain period of time is called data. Data is a time concept where one single signal has been added or expaned in time by other signals. Therefore, any data in the universe can be represented as a sting with an order. A string with an order is sequence. Multiple data or the sequence objects form cam produce two or more dimentional arrangement in space. When this multi-dimentional data are represented as an object, it is called information. Information's major feature is multi-axis or multi-dimention. This means that informational objects can have multiple possible association links within themselves. In other words, information contains nodes and edges made of data where data are sequence objects. Information can be represented by five types:signal(single digit or letter), string, table, coordinates, and the networks of the previous four types. These types are understood or feedable to computing devices. These information types can be processed in many ways by computing devices such as human brains and generate synthetic and additional information types. These added information part that is derived from the original set is defined as knowledge. The key of knowledge is a sum of procedural or instant(almost, physically) processing product. For example, if there is a string of five zeros (00000), a knowlegde piece is 5 that is added after a process of counting. Therefore, representing it as [00000, 5] an added piece of information that has a relevance to the original information piece. Knowledge generation after generation is the most useful part of computation. Once knowledge expansion circuit is on, wisdom can be made. Wisdom is a simple term of decision making to make a prediction. Decision making is a final information piece added to the knowledge building and expansion. When decisions are produced they form a structure of decisions as a protocol. A protocol is a set of decisions in time to be made in a sequence. Any protocol's purpose is to produce predictions. The final goal of any information object in the universe is making one or more predictions in time. Although no objects know 


The classification of omes and omics to produce prediction



Types of Omes and omics: The following division is not always clear-cut. However, it can be a good way to understand the characteristics of omes.

(1) Object oriented omes/omics: this is after biological information objects. For example, Genomics is the omics for gene objects. 

(2) Action oriented omes/omics: this is after biological action and information types. For example, Expressome is the ome of cellular activity of expression and expression information. Reactionome and reactome are also action oriented omes.