A key approach in genomic research is to divide the cellular contents into distinct sub-population, each given an -omic term. Broadly, these 'omes can be divided into those that represent a population of molecules, and those that define their actions. For example, the proteome is the full complement of proteins encoded by the genome, and the secretome is the part of it secreted from the cell.
各种不同的组学列表（OMES TABLE）：
【定义4】下面是网站bioplanet在2001年给出的定义：
Bioinformatics is the application of computer technology to the management of biological information. Computers are used to gather, store, analyze and integrate biological and genetic information which can then be applied to gene-based drug discovery and development.
该定义中的生物信息（biological information）可以理解为生物数据，强调数据的采集、存储、分析和整合。最后还给出了生物信息学的应用：基于基因的药物开发。该定义直到2017年，还有其他网站引用。
2005年
【定义5】以下是网站TechTarget给出的定义：
Bioinformatics is the science of developing computer databases and algorithms for the purpose of speeding up and enhancing biological research.
New academic programs are training students in bioinformatics by providing them with backgrounds in molecular biology, engineering, ethics and computer science, including database design and analytical approaches to data mining.
该定义强调数据库和算法，且提到了伦理学。
【定义6】下面是英属哥伦比亚大学THE SCIENCE CREATIVE QUARTERLY上面的一篇文章给出的定义：
Bioinformatics involves the integration of computers, software tools, and databases in an effort to address biological questions.
Many scientists today refer to the next wave in bioinformatics as systems biology, an approach to tackle new and complex biological questions. Systems biology involves the integration of genomics, proteomics, and bioinformatics information to create a whole system view of a biological entity.
The genes involved in the pathway, how they interact, and how modifications change the outcomes downstream, can all be modeled using systems biology. Any system where the information can be represented digitally offers a potential application for bioinformatics. Thus bioinformatics can be applied from single cells to whole ecosystems.
Genome sequence by itself has limited information. To interpret genomic information（基因组信息的解释）, comparative analysis of sequences needs to be done and an important reagent for these analyses are the publicly accessible sequence databases. Without the databases of sequences (such as GenBank), in which biologists have captured information about their sequence of interest, much of the rich information obtained from genome sequencing projects would not be available（公共数据库的重要性）.
The same way developments in microscopy foreshadowed discoveries in cell biology, new discoveries in information technology and molecular biology are foreshadowing discoveries in bioinformatics.
In many ways, bioinformatics provides the tools for applying scientific method to large-scale data and should be seen as a scientific approach for asking many new and different types of biological questions.
Although technology enables bioinformatics, bioinformatics is still very much about biology. Biological questions drive all bioinformatics experiments. Important biological questions can be addressed by bioinformatics and include understanding the genotype-phenotype connection for human disease, understanding structure to function relationships for proteins, and understanding biological networks.
这篇文章的定义也强调了数据库的重要性并给出了原因：一段基因组序列本身的信息是有限的，需要与其他已注释序列进行比较来研究其功能（例如利用Blast软件在公共数据库GenBank中注释一段新的DNA序列）。在当时（05年）已经有许多科学家提出"系统生物学"是下一个阶段的生物信息学。此外，文中提到："对于任何系统（从单个细胞到整个生态系统），只要其信息可以数字化，生物信息学在该系统就可能有用武之地"。生物信息学之于分子生物学，就像显微镜之于细胞生物学。
这篇文章还给出了很多有价值的观点：
生物信息学不仅仅可以作为工具来解决问题，也应该被当成一种科学方法来提出新的和不同类型的生物学问题；
尽管生物信息学依赖于技术，但是所有的生物信息学实验还是被生物学问题所驱动；
一些可以用生物信息学来处理的重要生物学问题：理解基因型-表型在人类疾病中的关联，理解蛋白质结构与功能之间的关系，理解生物网络；
生物信息学的进步也依赖于生产数据的工具和技术（例如新的更便宜的测序技术，高通量生物芯片技术，更精确的质谱技术等）的进步。
2010年
【定义7】下面两个定义收录于圣地亚哥州立大学（San Diego State University）计算机科学与生物学教授Dr. Robert Edwards的一篇博客中：