WeedML is a proposed standard to formulate models of weed demography (or perhaps even complex models in general) that are both transparent and straightforward to reuse as building blocks for new models. The paper describes the design and thoughts behind WeedML which relies on XML and object-oriented systems development. Proof-of-concept software is provided as open-source C++ code and executables that can be downloaded freely.

The National Bureau of Plant genetic Resources (NBPGR), New Delhi carries out the registration of unique crop germplasm in order to protect the intrinsic intellectual property as well as to facilitate greater utilization of germplasm in crop improvement programmes. It is therefore imperative to enhance access to information on registered crop germplasm. Here, we present a concept of a search engine that can suffice dual functions of a Web-based and portable search application. The concept entails converting raw data through a series of transformations from a Microsoft-Excel to eXtensible Markup Language (XML) data format. XML data initialized on compatible Web browsers are then queried for the search term based on a looping regular expression matching. The results are then loaded onto the browser in a tabulated output. The concept is implemented in the form of ‘Inventory of Registered Crop Germplasm’ on the Web as well as on a portable memory (compact disk or flash drive). The portable search engine works with minimal hardware and software requirements to enable its widespread utility to ensure greater access to information on registered crop germplasm. The portable search engine can be obtained from the NBPGR, New Delhi and the Web-based search engine can be accessed at http://www.nbpgr.ernet.in/IRCG/index.htm.

Extensible Markup Language (XML) is a simple, very flexible text format derived from SGML. Originally designed to meet the challenges of large-scale electronic publishing, XML is also playing an increasingly important role in the exchange of a wide variety of data on the Web and elsewhere. XPath language is the result of an effort to provide address parts of an XML document. In support of this primary purpose, it becomes in a query language against an XML document. In this paper we present a proposal for the implementation of the XPath language in logic programming. With this aim we will describe the representation of XML documents by means of a logic program. Rules and facts can be used for representing the document schema and the XML document itself. In particular, we will present how to index XML documents in logic programs: rules are supposed to be stored in main memory, however facts are stored in secondary memory by using two kind of indexes: one for each XML tag, and other for each group of terminal items. In addition, we will study how to query by means of the XPath language against a logic program representing an XML document. It evolves the specialization of the logic program with regard to the XPath expression. Finally, we will also explain how to combine the indexing and the top-down evaluation of the logic program.

Prolog is an excellent tool for representing and manipulating data written in formal languages as well as natural language. Its safe semantics and automatic memory management make it a prime candidate for programming robust Web services. Although Prolog is commonly seen as a component in a Web application that is either embedded or communicates using a proprietary protocol, we propose an architecture where Prolog communicates to other components in a Web application using the standard HTTP protocol. By avoiding embedding in external Web servers, development and deployment become much easier. To support this architecture, in addition to the transfer protocol, we must also support parsing, representing and generating the key Web document types such as HTML, XML and RDF. This article motivates the design decisions in the libraries and extensions to Prolog for handling Web documents and protocols. The design has been guided by the requirement to handle large documents efficiently. The described libraries support a wide range of Web applications ranging from HTML and XML documents to Semantic Web RDF processing. The benefits of using Prolog for Web-related tasks are illustrated using three case studies.

We define XPathLog as a Datalog-style extension of XPath. XPathLog provides a clear, declarative language for querying and manipulating XML whose perspectives are especially in XML data integration. In our characterization, the formal semantics is defined wrt. an edge-labeled graph-based model, which covers the XML data model. We give a complete, logic-based characterization of XML data and the main language concept for XML, XPath. XPath-Logic extends the XPath language with variable bindings and embeds it into first-order logic. XPathLog is then the Horn fragment of XPath-Logic, providing a Datalog-style, rule-based language for querying and manipulating XML data. The model-theoretic semantics of XPath-Logic serves as the base of XPathLog as a logic-programming language, whereas also an equivalent answer-set semantics for evaluating XPathLog queries is given. In contrast to other approaches, the XPath syntax and semantics is also used for a declarative specification how the database should be updated: when used in rule heads, XPath filters are interpreted as specifications of elements and properties which should be added to the database.

Analyzing a single data set using multiple RNA informatics programs often requires a file format conversion between each pair of programs, significantly hampering productivity. To facilitate the interoperation of these programs, we propose a syntax to exchange basic RNA molecular information. This RNAML syntax allows for the storage and the exchange of information about RNA sequence and secondary and tertiary structures. The syntax permits the description of higher level information about the data including, but not restricted to, base pairs, base triples, and pseudoknots. A class-oriented approach allows us to represent data common to a given set of RNA molecules, such as a sequence alignment and a consensus secondary structure. Documentation about experiments and computations, as well as references to journals and external databases, are included in the syntax. The chief challenge in creating such a syntax was to determine the appropriate scope of usage and to ensure extensibility as new needs will arise. The syntax complies with the eXtensible Markup Language (XML) recommendations, a widely accepted standard for syntax specifications. In addition to the various generic packages that exist to read and interpret XML formats, an XML processor was developed and put in the open-source MC-Core library for nucleic acid and protein structure computer manipulation.

There is a crisis in the publication and archiving of archaeological field data in Europe. Computerized data are more fragile than paper archives but also more accessible via the Internet. This article explores the role of the Archaeology Data Service and examines some of the issues raised by the collection of digital data and their dissemination online and the implications for the future of archaeological publication. It discusses approaches to digital data preservation, the development of archival standards and ways of encouraging reuse. It explores the development of distributed online catalogues and archives and the need for metadata standards for cataloguing resources. Finally, it considers the role of XML as an emergent technology and introduces the European ARENA project which is developing a digital preservation and access infrastructure.

We discuss from a practical point of view a number of issues involved in writing distributed Internet and WWW applications using LP/CLP systems. We describe PiLLoW, a public-domain Internet and WWW programming library for LP/CLP systems that we have designed to simplify the process of writing such applications. PiLLoW provides facilities for accessing documents and code on the WWW; parsing, manipulating and generating HTML and XML structured documents and data; producing HTML forms; writing form handlers and CGI-scripts; and processing HTML/XML templates. An important contribution of PiLLoW is to model HTML/XML code (and, thus, the content of WWW pages) as terms. The PiLLoW library has been developed in the context of the Ciao Prolog system, but it has been adapted to a number of popular LP/CLP systems, supporting most of its functionality. We also describe the use of concurrency and a high-level model of client-server interaction, Ciao Prolog's active modules, in the context of WWW programming. We propose a solution for client-side downloading and execution of Prolog code, using generic browsers. Finally, we also provide an overview of related work on the topic.