International
Tables for
Crystallography
Volume G
Definition and exchange of crystallographic data
Edited by S. R. Hall and B. McMahon

International Tables for Crystallography (2006). Vol. G, ch. 5.5, pp. 541-542

Section 5.5.3.1. ADIT: functional description

J. D. Westbrook,a* H. Yang,a Z. Fenga and H. M. Bermana

aProtein Data Bank, Research Collaboratory for Structural Bioinformatics, Rutgers, The State University of New Jersey, Department of Chemistry and Chemical Biology, 610 Taylor Road, Piscataway, NJ 08854-8087, USA
Correspondence e-mail:  jwest@rcsb.rutgers.edu

5.5.3.1. ADIT: functional description

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The basic functions of the ADIT deposition system are shown in Fig. 5.5.3.2[link]. Users interact with the ADIT system through a web server. The CGI components of the ADIT system (that is, functional software components interacting with web input data through the Common Gateway Interface protocol) dynamically build the HTML that provides the system user interface. These CGI components are currently implemented as compiled binaries from C++ source code.

[Figure 5.5.3.2]

Figure 5.5.3.2 | top | pdf |

Schematic diagram of ADIT editing, format translation and validation functions.

User data can be provided in the form of data files or as keyboard input. Input files can be accepted in a variety of formats. ADIT uses a collection of format filters to convert input data to the data specification defined in a persistent data dictionary. Data in the form of data files are typically loaded first. Any input data that are not included in uploaded files can be keyed in by the user. ADIT builds a set of HTML forms for each category of data to be input. At any point during an input session, a user may choose to view or deposit the input data. Users who are depositing data may also use the data-validation services through the ADIT interface.

Comprehensive data ontologies like the PDB exchange dictionary contain vast numbers of data definitions. A data-input application may only need to access a small fraction of these definitions at any point. To address the problem of selecting only the relevant set of input data items from a data dictionary ADIT uses a view database. In addition to defining the scope of the data items to be edited by the ADIT application, an ADIT data view also stores presentation details that are used in building the HTML input forms. An important use of the data view is to provide a simple and intuitive presentation of information for novice users which disguises the complex details of a data dictionary.

Fig. 5.5.3.3[link] shows an example ADIT editing screen for the crystallographic unit cell. The data dictionary category containing this information is named CELL, and the length of the first cell axis is defined in the dictionary as _cell.length_a (Fig. 5.5.2.2b[link]). In this case, the data view has substituted Unit Cell and Length a for the dictionary data names. Although this example is simple, some dictionary data names are as long as 75 characters, and in these instances the ability to display a simpler name is essential.

[Figure 5.5.3.3]

Figure 5.5.3.3 | top | pdf |

Example ADIT data-input screen.

Precise dictionary definitions and examples obtained from the data dictionary are accessible from the ADIT interface through buttons next to each data item. ADIT makes full use of the dictionary specification in data-input operations. Data items defined to assume only specific values have pulldown menus or selection boxes. Data type and range restrictions are checked when data are input and diagnostics are displayed to the user if errors are detected.

For performance reasons, the data dictionary is converted from its tabular text structure to an object representation using CIFOBJ. The class supporting the object representation provides efficient access functions to all of the data dictionary attributes. A dictionary loader is used to check the consistency of the data dictionary and to load the object representation from the text form of the data dictionary.

Any dictionary that complies with the dictionary description language (DDL2) can be loaded and used by ADIT. All ADIT software components gain their knowledge of the input data from the data dictionary and any associated data views. Consequently, ADIT can be tailored for use in virtually any data-input and data-processing application.








































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