Section 5.2.6.4.  starlib

BioMagResBank (BMRB) is a repository for NMR spectroscopy data on proteins, peptides and nucleic acids at the University of Wisconsin – Madison (Ulrich et al., 1989). For some time, NMR data sets have been exchanged within this environment using STAR Files; an NMRStar data dictionary to define the data names used for tagging NMR data is under development (BioMagResBank, 2004). The starlib class library was developed at BMRB for handling NMRStar files, but its initial application to such files independently of the prototype data dictionary means that it is applicable to any STAR File. It does not provide a relational database paradigm (although this is a long-term goal). However, it does provide objects and methods suitable for searching and manipulating STAR data.

Table 5.2.6.1 lists the top-level classes used in starlib. ASTnode is a formal base class, providing the types and methods that can be used in other derived classes. StarFileNode is the root parent of all other objects contained in an in-memory representation of a STAR File; in practice it contains a single StarListNode, which is the list of all items contained in the file. BlockNode is a class which contains a partition of the STAR File: the class handles both data blocks and global blocks. Data-block names are stored in instances of the HeadingNode object, which also holds save-frame identification codes and is therefore useful for accessing named portions of the file.

DataNode is a virtual class representing the types of data objects handled by the library (accessed directly as DataItemNode, Data­LoopNode and SaveFrameNode).

Looped data items are handled by a number of objects. Data­LoopNameListNode is a list of lists of names in a loop. The first list of names is the list of names for the outermost loop, the second list of names is the list of names for the next nesting level and so on. LoopNameListNode is a list of tag names representing one single nesting level of a loop's definition. LoopTableNode is a table of rows in a DataLoopNode (not itemized in Table 5.2.6.1; it is an object representing a list of tag names and their associated values, a particular case of DataNode). starlib views a loop in a STAR file as a table of values, with each iteration of the loop being a row of the table. Each row of the table can have another table under it (another nesting level), but such tables are the same structure as the outermost one. Thus LoopTableNode stores a table at some arbitrary nesting level in the loop. A simple singly nested loop will have only one loop table node, but a multiply nested loop will have a whole tree of loop tables. LoopRowNode is a single row of values in a loop.

DataNameNode holds the name of a tag/value pair or a loop tag name. DataValueNode is the type that holds a single string value from the STAR file and the delimiter type that is used to quote it.

DataListNode and SaveFrameListNode store lists of data within higher-order data objects or save frames, and are internal classes rarely invoked directly by a programmer.

A number of observations may be made regarding this approach. Firstly, the objects can be mapped with reasonable fidelity to the high-level Backus–Naur form representation of STAR (Chapter 2.1 ). Secondly, it is computationally convenient to abstract common features into parent classes, so that, for example, individual data items, looped data and save frames are represented as child objects of the Data­Node object, and not themselves as first-generation children of the base class. Thirdly, the handling of nested loops may be achieved in different ways; starlib has chosen a particular view that is perhaps well suited to relational data models.

As expected within a programming toolkit, starlib offers a large number of methods for retrieving STAR data values, adding new data items, extending or re-ordering list structures, and performing structural transformations of the in-memory data representation. Unlike the stand-alone Star_Base application, it does not guarantee that output data will be in a STAR-conformant format; and the programmer is left with the responsibility of validating transformed data at a low level.

Nevertheless, this is a substantial and important library which, as with CIFOBJ, has played an important role in the functioning of a major public data repository. Development of the class libraries continues, with a Java version now available.