MOTIVATION: There have been several endeavours to address the problem of annotating sequence data computationally, but the task is non-trivial and few tools have emerged that gather useful information on a given sequence, or set of sequences, in a simple and convenient manner. As more genome projects bear fruit, the mass of uncharacterized sequence data accumulating in public repositories grows ever larger. There is thus a pressing need for tools to support the process of automatic analysis and annotation of newly determined sequences. With this in mind, we have developed PRECIS, which automatically creates protein reports from sets of SWISS-PROT entries, collating results into structured reports, detailing known biological and medical information, literature and database cross-references, and relevant keywords.

There have been several attempts at addressing the problem of annotating sequence data computationally. Annotation generation can be considered a pipeline of processes: first harvesting data from a variety of data sources, then distilling and transforming it into a form more appropriate for the end database. This task is usually performed by human annotators, a solution that is clearly not scaleable. There have been several attempts to mimic some of these pipelines in software. However, these have generally focused on low level annotation, such as database cross-references, or by harvesting data from computational techniques such as gene finding or similarity searches. Higher level annotation such as that seen in the PRINTS database is usually formed from data that is free text, or only partly structured. This presents a much greater computational challenge. Therefore we studied the pipeline that is used to generate annotation for the PRINTS database, and have developed prototype software that reflects and automates this pipeline. As this software operates primarily on data culled from the SWISS-PROT database, we have called it PRECIS (Protein Reports Engineered from Concise Information in SWISS-PROT). This software is currently being used to generate annotation for the prePRINTS database. As the output is a structured report detailing the function, structure and disease associations of a protein, and providing literature references and keywords we believe it will be of more generic use. The software is available on request from [email protected].

While I was investigating methods to construct 'controlled vocabularies' and 'ontologies', I created a set of 'ontological design patterns'. These engineering design patterns and terminologies specific to some protein families were represented within the object-oriented programming language CLOS (Common Lisp Object System). Within bioinformatics, 'ontologies' are represented on the World Wide Web (WWW) in terminology files that are tagged and marked up by the syntax and keywords of HTML or XML. Therefore, I specified, designed and partially implemented a compiler to translate specified 'controlled vocabularies' and 'ontologies' represented in CLOS and structured by 'ontological design patterns' into the language called 'Simple Hypertext Ontology Extension' (SHOE). First results show that a 'one-step-look-ahead' parser can automatically print the original CLOS version of the 'ontologies' into a file reorganised according to the SHOE syntax.

Taxonomy Manager (TM) is a computer-based, full-text method dedicated to represent biological knowledge allowing scientists to continuously revise and reorganize the conceptual framework of data and their interpretation. The system architecture distinguishes clients and a task oriented server. TM provides a distinct, precise, yet user-friendly, formalism for knowledge specification by biologic experts and for factual knowledge input by general scientists on interactive interfaces. An incremental compiler translates and transforms new information specified within full-text editors into an internal format and back again. A retrieval dialog allows access to the results of text analyses including information units and associated rules, and a browser offers free navigation through the network of data. External users can access the information contained within TM by a communication protocol. Copyright © 1999 John Wiley & Sons, Ltd.