Developing a web-based SKOS editor.

BACKGROUND: The Simple Knowledge Organization System (SKOS) was introduced to the wider research community by a 2005 World Wide Web Consortium (W3C) working draft, and further developed and refined in a 2009 W3C recommendation. Since then, SKOS has become the de facto standard for representing and sharing thesauri, lexicons, vocabularies, taxonomies, and classification schemes. In this paper, we describe the development of a web-based, free, open-source SKOS editor built for the development, curation, and management of small to medium-sized lexicons for health-related Natural Language Processing (NLP). RESULTS: The web-based SKOS editor allows users to create, curate, version, manage, and visualise SKOS resources. We tested the system against five widely-used, publicly-available SKOS vocabularies of various sizes and found that the editor is suitable for the development and management of small to medium-size lexicons. Qualitative testing has focussed on using the editor to develop lexical resources to drive NLP applications in two domains. First, developing a lexicon to support an Electronic Health Record-based NLP system for the automatic identification of pneumonia symptoms. Second, creating a taxonomy of lexical cues associated with Diagnostic and Statistical Manual of Mental Disorders (DSM-5) diagnoses with the goal of facilitating the automatic identification of symptoms associated with depression from short, informal texts. CONCLUSIONS: The SKOS editor we have developed is - to the best of our knowledge - the first free, open-source, web-based, SKOS editor capable of creating, curating, versioning, managing, and visualising SKOS lexicons.

MODULEWRITER: a program for automatic generation of database interfaces.

MODULEWRITER is a PERL object relational mapping (ORM) tool that automatically generates database specific application programming interfaces (APIs) for SQL databases. The APIs consist of a package of modules providing access to each table row and column. Methods for retrieving, updating and saving entries are provided, as well as other generally useful methods (such as retrieval of the highest numbered entry in a table). MODULEWRITER provides for the inclusion of user-written code, which can be preserved across multiple runs of the MODULEWRITER program.

The PlantsP and PlantsT Functional Genomics Databases.

PlantsP and PlantsT allow users to quickly gain a global understanding of plant phosphoproteins and plant membrane transporters, respectively, from evolutionary relationships to biochemical function as well as a deep understanding of the molecular biology of individual genes and their products. As one database with two functionally different web interfaces, PlantsP and PlantsT are curated plant-specific databases that combine sequence-derived information with experimental functional-genomics data. PlantsP focuses on proteins involved in the phosphorylation process (i.e., kinases and phosphatases), whereas PlantsT focuses on membrane transport proteins. Experimentally, PlantsP provides a resource for information on a collection of T-DNA insertion mutants (knockouts) in each kinase and phosphatase, primarily in Arabidopsis thaliana, and PlantsT uniquely combines experimental data regarding mineral composition (derived from inductively coupled plasma atomic emission spectroscopy) of mutant and wild-type strains. Both databases provide extensive information on motifs and domains, detailed information contributed by individual experts in their respective fields, and descriptive information drawn directly from the literature. The databases incorporate a unique user annotation and review feature aimed at acquiring expert annotation directly from the plant biology community. PlantsP is available at http://plantsp.sdsc.edu and PlantsT is available at http://plantst.sdsc.edu.