Towards a query language for annotation graphs

The multidimensional, heterogeneous, and temporal nature of speech databases raises interesting challenges for representation and query. Recently, annotation graphs have been proposed as a general-purpose representational framework for speech databases. Typical queries on annotation graphs require path expressions similar to those used in semistructured query languages. However, the underlying model is rather different from the customary graph models for semistructured data: the graph is acyclic and unrooted, and both temporal and inclusion relationships are important. We develop a query language and describe optimization techniques for an underlying relational representation.Comment: 8 pages, 10 figure

A General Framework for Representing, Reasoning and Querying with Annotated Semantic Web Data

We describe a generic framework for representing and reasoning with annotated Semantic Web data, a task becoming more important with the recent increased amount of inconsistent and non-reliable meta-data on the web. We formalise the annotated language, the corresponding deductive system and address the query answering problem. Previous contributions on specific RDF annotation domains are encompassed by our unified reasoning formalism as we show by instantiating it on (i) temporal, (ii) fuzzy, and (iii) provenance annotations. Moreover, we provide a generic method for combining multiple annotation domains allowing to represent, e.g. temporally-annotated fuzzy RDF. Furthermore, we address the development of a query language -- AnQL -- that is inspired by SPARQL, including several features of SPARQL 1.1 (subqueries, aggregates, assignment, solution modifiers) along with the formal definitions of their semantics

Annotation Graphs and Servers and Multi-Modal Resources: Infrastructure for Interdisciplinary Education, Research and Development

Annotation graphs and annotation servers offer infrastructure to support the analysis of human language resources in the form of time-series data such as text, audio and video. This paper outlines areas of common need among empirical linguists and computational linguists. After reviewing examples of data and tools used or under development for each of several areas, it proposes a common framework for future tool development, data annotation and resource sharing based upon annotation graphs and servers.Comment: 8 pages, 6 figure

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

ATLAS: A flexible and extensible architecture for linguistic annotation

We describe a formal model for annotating linguistic artifacts, from which we derive an application programming interface (API) to a suite of tools for manipulating these annotations. The abstract logical model provides for a range of storage formats and promotes the reuse of tools that interact through this API. We focus first on ``Annotation Graphs,'' a graph model for annotations on linear signals (such as text and speech) indexed by intervals, for which efficient database storage and querying techniques are applicable. We note how a wide range of existing annotated corpora can be mapped to this annotation graph model. This model is then generalized to encompass a wider variety of linguistic ``signals,'' including both naturally occuring phenomena (as recorded in images, video, multi-modal interactions, etc.), as well as the derived resources that are increasingly important to the engineering of natural language processing systems (such as word lists, dictionaries, aligned bilingual corpora, etc.). We conclude with a review of the current efforts towards implementing key pieces of this architecture.Comment: 8 pages, 9 figure

An Integrated Framework for Treebanks and Multilayer Annotations

Treebank formats and associated software tools are proliferating rapidly, with little consideration for interoperability. We survey a wide variety of treebank structures and operations, and show how they can be mapped onto the annotation graph model, and leading to an integrated framework encompassing tree and non-tree annotations alike. This development opens up new possibilities for managing and exploiting multilayer annotations.Comment: 8 page