XML to Annotations Mapping Patterns

Configuration languages based on XML and source code annotations are very popular in the industry. There are situations in which there are reasons to move configuration languages from one format to the other, or to support multiple configuration languages. In such cases mappings between languages based on these formats have to be defined. Mapping can be used to support multiple configuration languages or to seamlessly move configurations from annotations to XML or vice versa. In this paper, we present XML to annotations mapping patterns that can be used to map languages from one format to the other

Implementing a Portable Clinical NLP System with a Common Data Model - a Lisp Perspective

This paper presents a Lisp architecture for a portable NLP system, termed LAPNLP, for processing clinical notes. LAPNLP integrates multiple standard, customized and in-house developed NLP tools. Our system facilitates portability across different institutions and data systems by incorporating an enriched Common Data Model (CDM) to standardize necessary data elements. It utilizes UMLS to perform domain adaptation when integrating generic domain NLP tools. It also features stand-off annotations that are specified by positional reference to the original document. We built an interval tree based search engine to efficiently query and retrieve the stand-off annotations by specifying positional requirements. We also developed a utility to convert an inline annotation format to stand-off annotations to enable the reuse of clinical text datasets with inline annotations. We experimented with our system on several NLP facilitated tasks including computational phenotyping for lymphoma patients and semantic relation extraction for clinical notes. These experiments showcased the broader applicability and utility of LAPNLP.Comment: 6 pages, accepted by IEEE BIBM 2018 as regular pape

The Semantic Automated Discovery and Integration (SADI) Web service Design-Pattern, API and Reference Implementation

Background. 
The complexity and inter-related nature of biological data poses a difficult challenge for data and tool integration. There has been a proliferation of interoperability standards and projects over the past decade, none of which has been widely adopted by the bioinformatics community. Recent attempts have focused on the use of semantics to assist integration, and Semantic Web technologies are being welcomed by this community.

Description. 
SADI – Semantic Automated Discovery and Integration – is a lightweight set of fully standards-compliant Semantic Web service design patterns that simplify the publication of services of the type commonly found in bioinformatics and other scientific domains. Using Semantic Web technologies at every level of the Web services “stack”, SADI services consume and produce instances of OWL Classes following a small number of very straightforward best-practices. In addition, we provide codebases that support these best-practices, and plug-in tools to popular developer and client software that dramatically simplify deployment of services by providers, and the discovery and utilization of those services by their consumers.

Conclusions.
SADI Services are fully compliant with, and utilize only foundational Web standards; are simple to create and maintain for service providers; and can be discovered and utilized in a very intuitive way by biologist end-users. In addition, the SADI design patterns significantly improve the ability of software to automatically discover appropriate services based on user-needs, and automatically chain these into complex analytical workflows. We show that, when resources are exposed through SADI, data compliant with a given ontological model can be automatically gathered, or generated, from these distributed, non-coordinating resources - a behavior we have not observed in any other Semantic system. Finally, we show that, using SADI, data dynamically generated from Web services can be explored in a manner very similar to data housed in static triple-stores, thus facilitating the intersection of Web services and Semantic Web technologies

A tool for enhancing MetaMap performance when annotating clinical guideline documents with UMLS concepts

We developed a tool that integrates the National Library of Medicine's MetaMap software with GATE, an open-source text an- alytics framework. The tool allows non-ASCII encoded documents of numerous formats to be annotated with UMLS concepts. We created a GATE pipeline to chunk cardiovascular disease guideline text into default segments (blank-line delimited), XML element content, sentences and phrases, which were sequentially submitted to MetaMap for annotation. XML element, sentence and phrase chunking allowed term extraction and mapping to be completed in around 1/3 of the time taken with de- fault chunking, although with slight loss of accuracy (F1.0s=0.94-0.99). However, phrase chunking allows more complex input to be processed in real time, which is not possible with the other approaches. We discuss the results in relation to use of MetaMap's --term processing option for generating pre- and post-coordinated mappings from composite phrases

Semantic web service automation with lightweight annotations

Web services, both RESTful and WSDL-based, are an increasingly important part of the Web. With the application of semantic technologies, we can achieve automation of the use of those services. In this paper, we present WSMO-Lite and MicroWSMO, two related lightweight approaches to semantic Web service description, evolved from the WSMO framework. WSMO-Lite uses SAWSDL to annotate WSDL-based services, whereas MicroWSMO uses the hRESTS microformat to annotate RESTful APIs and services. Both frameworks share an ontology for service semantics together with most of automation algorithms

Identification of Design Principles

This report identifies those design principles for a (possibly new) query and transformation language for the Web supporting inference that are considered essential. Based upon these design principles an initial strawman is selected. Scenarios for querying the Semantic Web illustrate the design principles and their reflection in the initial strawman, i.e., a first draft of the query language to be designed and implemented by the REWERSE working group I4

A Programming Language for Web Service Development

There is now widespread acceptance of Web services and service-oriented architectures. But despite the agreement on key Web services standards there remain many challenges. Programming environments based on WSDL support go some way to facilitating Web service development. However Web services fundamentally rely on XML and Schema, not on contemporary programming language type systems such as those of Java or .NET. Moreover, Web services are based on a messaging paradigm and hence bring forward the traditional problems of messaging systems including concurrency control and message correlation. It is easy to write simple synchronous Web services using traditional programming languages; however more realistic scenarios are surprisingly difficult to implement. To alleviate these issues we propose a programming language which directly supports Web service development. The language leverages XQuery for native XML processing, supports implicit message correlation and has high level join calculus-style concurrency control. We illustrate the features of the language through a motivating example