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Formalizing biomedical concepts from textual definitions

Alina Petrova, Yue Ma, George Tsatsaronis, Maria Kissa, Felix Distel, Franz Baader, Michael Schroeder
2015 Journal of Biomedical Semantics  
We develop a method that uses machine learning in combination with several types of lexical and semantic features and outputs formal definitions that follow the structure of SNOMED CT concept definitions  ...  (2) How do different feature representations, e.g., the restrictions of relations' domain and range, impact on the generated definition quality?  ...  The most common way is to use the lexical representation of the text in order to generate typical patterns for the target relations.  ... 
doi:10.1186/s13326-015-0015-3 pmid:25949785 pmcid:PMC4422531 fatcat:ic2fn6etybcztk336nhoj6rbmq

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

Yuan Luo, Peter Szolovits
2018 2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)  
We also developed a utility to convert an inline annotation format to stand-off annotations to enable the reuse of clinical text datasets with in-line annotations.  ...  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.  ...  In the relational implementation, we maintain a corpora table that holds the name and unique id of the corpus, metadata, and the above-mentioned structural description.  ... 
doi:10.1109/bibm.2018.8621521 pmid:33376623 pmcid:PMC7769694 dblp:conf/bibm/LuoS18 fatcat:7zzfa4niinfr5prh47xwwumkzm

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

Yuan Luo, Peter Szolovits
2018 arXiv   pre-print
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.  ...  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.  ...  In the relational implementation, we maintain a corpora table that holds the name and unique id of the corpus, metadata, and the above-mentioned structural description.  ... 
arXiv:1811.06179v1 fatcat:2sp34rl5fvhixmyegylbalj6qy

Overview of STEM Science as Process, Method, Material, and Data Named Entities [article]

Jennifer D'Souza
2022 arXiv   pre-print
In this work, we develop and analyze a large-scale structured dataset of STEM articles across 10 different disciplines, viz.  ...  Our analysis is defined over a large-scale corpus comprising 60K abstracts structured as four scientific entities process, method, material, and data.  ...  ., 2020) , for the semantic concepts, these corpora build on years of careful knowledge representation work and are semantically consistent with a wide variety of other efforts that exploit these community  ... 
arXiv:2205.11863v1 fatcat:rvu7p4i6dnhz3euuevfqxdi6sm

Application of Corpus Technologies in Conceptual Studies (based on the Concept Ukraine Actualization in English and Ukrainian Political Media Discourse)

Nataliia Romanyshyn
2020 International Conference on Computational Linguistics and Intelligent Systems  
allowed to develop the frame model of the concept in both discourses and define common cognitive features of the concept Ukraine in the discussed linguistic cultures.  ...  The analysis of the discussed concept was performed on the basis of created textual corpus that includes 412 texts.  ...  The Notion of Text Corpora Corpus linguistics is a relatively recent method in linguistics. Scholars argue on the definition and typology of corpora.  ... 
dblp:conf/colins/Romanyshyn20 fatcat:roz5ktibgjg6zigf7j2bf6uitu

Knowledge management for more sustainable water systems

Stephen R. Mounce, Christopher Brewster, Richard M. Ashley, Louise Hurley
2010 Journal of Information Technology in Construction  
The management and sharing of complex data, information and knowledge is a fundamental and growing concern in the Water and other Industries for a variety of reasons.  ...  Hence current computer science research is investigating generating ontologies automatically from documents using text mining and natural language techniques.  ...  More recent development for Lexical Knowledge extraction in NLP led to systems being developed for Extraction of Semantic Lexicons from corpora (a corpora is a large and structured set of texts) e.g.  ... 
dblp:journals/itcon/MounceBAH10 fatcat:j2ug7h7uhrckrlehxtjdwrq5ii

Interoperability of Corpora and Annotations [chapter]

Christian Chiarcos
2012 Linked Data in Linguistics  
Additionally, representing corpora in OWL and RDF allows to interlink resources freely, e.g., different annotation layers of a multi-layer corpus, translated texts in parallel corpora, or linguistic corpora  ...  Modeled in this way, corpora can be fully integrated in a Linked Open Data (sub-)cloud of linguistic resources, along with lexical-semantic resources and knowledge bases of information about languages  ...  of Tübingen, 2006-2008, OLiA ontologies) and through the Collaborative Research Center (SFB) 632 "Information Structure" (University of Potsdam, 2008-2011, OLiA ontologies, POWLA)  ... 
doi:10.1007/978-3-642-28249-2_16 fatcat:xer3z2to3be5nnjjrigyxipq2i

Building a semantic recommendation engine for news feeds based on emerging topics from tweets

Mihai Tabara, Mihai Dascalu, Stefan Trausan-Matu
2016 2016 15th RoEduNet Conference: Networking in Education and Research  
We propose a strategy to extract the concepts by means of Natural Language Processing and use of the semantic cohesion measurements to leverage the matching process.  ...  The rise of social networks powered by the emergence of Web 2.0 unleashed a massive amount of generated user content.  ...  Acknowledgment The work presented in this paper was partially funded by the EC H2020 project RAGE (Realising and Applied Gaming Eco-System) http://www.rageproject.eu/ Grant agreement No 644187.  ... 
doi:10.1109/roedunet.2016.7753209 fatcat:fywcfbdd3bdkznzhsvdiyxih3y

POWLA: Modeling Linguistic Corpora in OWL/DL [chapter]

Christian Chiarcos
2012 Lecture Notes in Computer Science  
This paper describes POWLA, a generic formalism to represent linguistic annotations in an interoperable way by means of OWL/DL.  ...  Unlike other approaches in this direction, POWLA is not tied to a specific selection of annotation layers, but it is designed to support any kind of text-oriented annotation.  ...  RDF also formalizes directed (multi-)graphs, so, an RDF linearization of the PAULA data model yields a generic RDF representation of text-based linguistic annotations and corpora in general.  ... 
doi:10.1007/978-3-642-30284-8_22 fatcat:enjhja5nzfexpbqdepwezgbpcy

Toward a Deep Neural Approach for Knowledge-Based IR [article]

Gia-Hung Nguyen, Lynda Tamine, Laure Soulier, Nathalie Bricon-Souf
2016 arXiv   pre-print
However, they do not necessarily represent implicit relations that could be hidden in a corpora. This latter issue is tackled by recent works dealing with deep representation learn ing of texts.  ...  In this paper, we review the main approaches of neural-based document ranking as well as those approaches for latent representation of entities and relations via KBs.  ...  In this paper, we argue that combining (1) distributional semantics learned through deep architectures from the text corpora, and (2) symbolic semantics held by extracted concepts or entities from texts  ... 
arXiv:1606.07211v1 fatcat:jdypcyno3zcwphnoclk44dsfxi

Towards Generating Text from Discourse Representation Structures

Valerio Basile, Johan Bos
2011 European Workshop on Natural Language Generation  
DRSs can be viewed as the output of macro planning, and form the rough plan and structure for generating a text.  ...  We present the first ideas of building a large DRS corpus that enables the development of broad-coverage, robust text generators.  ...  Acknowledgments We are grateful to Michael White, who provided us with useful feedback to the idea of using a DRS corpus for developing and training text generation systems.  ... 
dblp:conf/enlg/BasileB11 fatcat:juvfbbcjajenji255sl2i7aw3q

Using Pathfinder networks to discover alignment between expert and consumer conceptual knowledge from online vaccine content

Muhammad Amith, Rachel Cunningham, Lara S. Savas, Julie Boom, Roger Schvaneveldt, Cui Tao, Trevor Cohen
2017 Journal of Biomedical Informatics  
Applying automated text analysis to this content may elucidate differences between the knowledge structures of laypeople (heath consumers) and professionals (health experts).  ...  In doing so, we extend the original application of PFNETS to infer knowledge structures from individual participants, to infer the prevailing knowledge structures within communities of content authors.  ...  distribution across a large corpus of text [62] .  ... 
doi:10.1016/j.jbi.2017.08.007 pmid:28823922 pmcid:PMC5641252 fatcat:5sgvt27okbgafcqvrtdkobb35e

Bridging semantics and syntax with graph algorithms—state-of-the-art of extracting biomedical relations

Yuan Luo, Özlem Uzuner, Peter Szolovits
2016 Briefings in Bioinformatics  
The ability to accurately capture both semantic and syntactic structures in text expressing these relations becomes increasingly critical to enable deep understanding of scientific papers and clinical  ...  In this article, we place biomedical relation extraction against the backdrop of its versatile applications, present a gentle introduction to its general pipeline and shared resources, review the current  ...  Acknowledgement The work was supported in part by Grant Number U54LM008748 from the National Library of Medicine, NIH 154HG007963 from the National Human Genome Research Institute and by the Scullen Center  ... 
doi:10.1093/bib/bbw001 pmid:26851224 pmcid:PMC5221425 fatcat:z6sptxngubempdx6kthsyab7be

Towards Unrestricted, Large-Scale Acquisition of Feature-Based Conceptual Representations from Corpus Data

Barry Devereux, Nicholas Pilkington, Thierry Poibeau, Anna Korhonen
2009 Research on Language and Computation  
In recent years a number of methods have been proposed for the automatic acquisition of feature-based conceptual representations from text corpora.  ...  In this article we investigate the challenges that need to be met in both methodology and evaluation when moving towards the acquisition of more comprehensive conceptual representations from corpora.  ...  We are grateful to Ken McRae and colleagues for making their norms publically available, and to Aurelie Herbelot for help with the Wikipedia parsing.  ... 
doi:10.1007/s11168-010-9068-8 fatcat:zdzhgcly4bhwxnnebmqr3wesvy

Categorization in the Wild: Generalizing Cognitive Models to Naturalistic Data across Languages [article]

Lea Frermann, Mirella Lapata
2019 arXiv   pre-print
We present a Bayesian cognitive model designed to jointly learn categories and their structured representation from natural language text which allows us to (a) evaluate performance on a large scale, and  ...  We show that meaningful categories comprising hundreds of concepts and richly structured featural representations emerge across languages.  ...  It was also not involved in the writing of the report and the decision to submit the article for publication.  ... 
arXiv:1902.08830v1 fatcat:w5y7aavbbnfnjmj6xlmbbmc5fq
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