"The goal of the MAO project is to develop a controlled, structured vocabulary, that will provide a common language not only for the construction of multiple alignments, but also for the numerous applications that exploit the information available in an integrated, global multiple alignment of a protein family. An important issue in the development of MAO is the interoperability with existing information sources, in order to maximise its’ applicability and utility. Therefore, links should be provided to other kinds of information, including databases such as UniProt, PDB or InterPro, as well as existing ontologies such as GO or the HUPO Proteomics Standards Initiative (PSI).
A vocabulary of terms is provided in the form of a hierarchical network of concepts, together with precise, explanatory definitions of each term and the inter-relations between the different concepts. The aim is to include the great majority of the concepts relevant to multiple sequence alignments, ranging from fundamental concepts such as ‘sequence’ or ‘residue’ to more complex concepts such as structural environment, functional activity or evolutionary context.
The MAO is represented as a Directed Acyclic Graph (DAG), in which each node stands for a concept and the links connecting the nodes represent the relationship between them. Two hierarchical relations are defined: ‘is_a’ and ‘part_of’. The nodes can also have other information attached to them in the form of names (defined by the relation ‘is_name’), annotations (defined by ‘is_annotation’) or other attributes. An attribute is generally a simple string or number variable that contains additional information about the concept."