|
|
本帖最后由 biostar 于 2010-6-19 10:21 编辑
功能：分三个方面描述一个基因产物的数据库，比如对某个基因的产物，GO从三方面描述：它有什么功能，它参加了什么生物学过程，它的在细胞的什么位置。
访问网址：http://www.geneontology.org
简介：
GO数据库提供在三个非重叠的分子生物学领域描述基因产物属性的本体。
MF（Molecular Function)描述了在分子水平的活动性（activities）,例如接触反应的或捆绑的活动性的。GO分子功能术语要求活动性而不是执行这个活动的实体 (分子或复合物),并且并不规定在何处，何时或在什么上下文这个活动发生。例如接受了个体分子功能术语广泛的“kinase activity（激酶活动性）”和更为专门的“6-phosphofructokinase 活动性”概念，它们表示激酶活动性“kinase activity”的一个子类。
BP（Biological Process ) 描述一个或多个有序的分子功能集结的生物目标。高层过程例如“细胞死亡（cell death）”可能有两个子类型,例如“粉蚀apoptosis”, 和子过程,例如“粉蚀染色体浓缩apoptotic chromosome condensation”。
CC（Cellular Component)以子细胞结构和维分子联合体水平描述位置。例如细胞成分包括“核的内膜nuclear inner membrane”,具有同义词“内包膜inner envelope”；和“普遍连接酶联合体ubiquitin ligase complex”，具有表示这些联合体的几个子类。在每一个本体中,术语都有自由文本的定义，和稳定独特的标识。在有“is-a”和“part-of”关系支持的分类中的词汇是结构化的。在参考(5±7)中更详细地描述GO词汇的范围和结构。在当前研究环境中不断地有许多新的基因序列迅速生成，并且有相当多的基因组分析要求综合来自多源的数据, 因此生物学界特别要求提供可能被生物学界共享的严格本体。
当前还有正在发展的序列本体SO。SO（Sequence Ontology)允许序列特性的分类和标准化表示。规范的序列特性包括例如“外显子exon”术语, 它的意义正在被广泛接受，但更有疑问的术语“pseudogene”，和还有几个不同的使用至今没有解决。虽然SO是一个相当新的词汇表，并且它依然正在经受推敲并且它已经被应用于果蝇（Drosophila）和Caenorhabditis elegans的基因组注释项目中。
帮助：
General GO QuestionsWhat is GO?
The Gene Ontology (GO) project is a collaborative effort to address the need for consistent descriptions of gene products in different databases. The GO collaborators are developing three structured, controlled vocabularies (ontologies) that describe gene products in terms of their associated biological processes, cellular components and molecular functions in a species-independent manner. There are three separate aspects to this effort: first, we write and maintain the ontologies themselves; second, we make cross-links between the ontologies and the genes and gene products in the collaborating databases; and third, we develop tools that facilitate the creation, maintainence and use of ontologies.
The use of GO terms by several collaborating databases facilitates uniform queries across them. The controlled vocabularies are structured so that you can query them at different levels: for example, you can use GO to find all the gene products in the mouse genome that are involved in signal transduction, or you can zoom in on all the receptor tyrosine kinases. This structure also allows annotators to assign properties to gene products at different levels, depending on how much is known about a gene product.
Why do we need GO?
To ask meaningful questions, biologists often need to retrieve and analyse data from disparate sources. For example, if you were searching for new targets for antibiotics, you might want to find all the gene products that are involved in bacterial protein synthesis, but that have significantly different sequences or structures from those in humans. But if one database describes these molecules as being involved in 'translation', whereas another uses the phrase 'protein synthesis', it will be difficult for you - and even harder for a computer - to find functionally equivalent terms.
The Gene Ontology (GO) project is a collaborative effort to address the need for consistent descriptions of gene products in different databases. The GO collaborators are developing three ontologies - a word used by computer scientists to mean 'specifications of a relational vocabulary' - that describe biological processes, cellular components and molecular functions in a species-independent manner.
Ontologies provide a vocabulary for representing and communicating knowledge about a topic, and a set of relationships that hold among the terms of the vocabulary. They can be structurally very complex, or relatively simple. Most importantly, ontologies capture domain knowledge in a way that can easily be dealt with by a computer . Because the terms in an ontology and the relationships between the terms are carefully defined, the use of ontologies facilitates making standard annotations, improves computational queries, and can support the construction of inference statements from the information at hand.
Genomic sequencing projects and microarray experiments alike produce electronically-generated data flows that require computer accessible systems to work with the information. As systems that make domain knowledge available to both humans and computers, bio-ontologies such as GO and the many other bio-ontologies being created (see the OBO web page for some examples) for are essential to the process of extracting biological insight from enormous sets of data.
Which biological domains are supported by GO?
The current ontologies of the GO project are molecular function, biological process, and cellular component. These three areas are considered independent of each other. The ontologies are developed to include all terms falling into these domains without consideration of whether the biological attribute is restricted to certain taxonomic groups. Therefore, biological processes that occur only in plants (e.g. photosynthesis) or mammals (e.g. lactation) are included.
Other biological ontologies are discussed in the OBO web site.
Can I reason over GO?
It is possible to do some reasoning over GO now, and we expect to do much more in the future. We provide logical definitions or 'cross-products' for some terms as part of the extended GO file, which can be reasoned over. Our ontology editor OBO-Edit has a reasoner integrated.
For more information see the cross-product documentation and this recent paper.
What is beyond the scope of the GO project?Almost as important as understanding the scope of the GO project is understanding what the GO project is not. The most common misapprehensions are (1) that the GO is a system for naming genes and proteins and (2) that the GO attempts to describe all of biology. The GO neither names genes or gene products, nor attempts to provide structured vocabularies beyond its three domains: molecular function, biological process and cellular component.
GO is not a nomenclature for genes or gene products. The vocabularies describe molecular phenomena (e.g. programmed cell death), not biological objects (e.g. proteins or genes). Sharing gene product names would entail tracking evolutionary histories and reflecting both orthologous and paralogous relationships between gene products. Different research communities have different naming conventions. Different organisms have different numbers of members in gene families. The GO project focuses on the development of vocabularies to describe attributes of biological objects, not on the naming of the objects themselves. This point is particularly important to understand because many genes and gene products are named for their function.
How do I find GO annotations for 'my' genes?
The GO Consortium has developed AmiGO for searching and browsing the Gene Ontology and the gene products that member databases have annotated using GO terms. Using AmiGO, you can search for one or more gene products and view its GO annotations. More AmiGO questions...
Where can I view or download the complete sets of GO annotations?
As with the vocabularies, the gene product sets (gene association files) from contributing groups are freely available; you can download them from the annotation downloads section of the GO website. The files are in tab-delimited text; the file format is described in the GO annotation guide. Gene association files contain all evidence pertinent to the annotation, including database IDs and gene product names, as well as citation and evidence data.
How do I browse the GO?
The GO Consortium has developed AmiGO for searching and browsing the Gene Ontology and the gene products that member databases have annotated using GO terms. Browsing the GO tree or searching for a term allows you to see term information and the hierarchy for the term, crossreferences to external databases, and the complete set of gene product associations for the term and any of its children. More AmiGO questions...
Other tools with GO browsing capabilities can be found on the GO tools page of the GO website.
How do I cite GO?
The GO database and vocabularies are in the public domain. The annotations provided by member organizations in the Current Annotations table are also in the public domain. There are no restrictions on their use, although third parties are asked to give appropriate acknowledgement to the GO Consortium and to the appropriate member organization(s). To reference the Gene Ontology Consortium, please cite this paper:
Gene Ontology: tool for the unification of biology. The Gene Ontology Consortium (2000) Nature Genet. 25: 25-29 PDF
We also recommend that you include the date you scanned the GO information within your paper. The GO ontology, gene_associations, and documentation files have version numbers and dates, which may be used for this purpose. The GO is evolving and changes will occur with time.
Retrieved from "http://wiki.geneontology.org/index.php/GO_FAQ"
|
|
发表于 2010-6-19 10:18:01