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Semi-automated named entity annotation

Kuzman Ganchev, Fernando Pereira, Mark Mandel, Steven Carroll, Peter White
2007 Proceedings of the Linguistic Annotation Workshop on - LAW '07   unpublished
We investigate a way to partially automate corpus annotation for named entity recognition, by requiring only binary decisions from an annotator.  ...  We ask an annotator to decide whether each mention produced by a high recall tagger is a true mention or a false positive.  ...  We use the standard B,I,O encoding for named entities (Ramshaw and Marcus, 1995) .  ... 
doi:10.3115/1642059.1642068 fatcat:42vquuqxw5br3pbmv6atagsvkm

Unsupervised Approaches for Textual Semantic Annotation, A Survey

Xiaofeng Liao, Zhiming Zhao
2019 ACM Computing Surveys  
Common sub-tasks of semantic annotation observed in the literature set include but are not limited to the following: -At the entity level: named entity extraction, named entity recognition, named entity  ...  Yes MnM 2002 Semi- automated, semi-supervised A user views documents and annotates segments of text using tags given in ontologies.  ... 
doi:10.1145/3324473 fatcat:fg5ucwtloze6ljdlh4hqjkqxfe

A text-mining perspective on the requirements for electronically annotated abstracts

Florian Leitner, Alfonso Valencia
2008 FEBS Letters  
The first experiments have concentrated on the annotation of gene/protein names and those of organisms, as these are the best resolved problems.  ...  The recent introduction of the first meta-server for the annotation of biological text, with the possibility of collecting annotations from available text-mining systems, adds credibility to the technical  ...  Despite these problems, the advantages of semi-automated annotations of journal articles are manifold: The annotators (authors) will not require extensive training in annotation.  ... 
doi:10.1016/j.febslet.2008.02.072 pmid:18328824 fatcat:umlsoplbdrds5ope6fzexaxmv4

Construction of biological networks from unstructured information based on a semi-automated curation workflow

Justyna Szostak, Sam Ansari, Sumit Madan, Juliane Fluck, Marja Talikka, Anita Iskandar, Hector De Leon, Martin Hofmann-Apitius, Manuel C. Peitsch, Julia Hoeng
2015 Database: The Journal of Biological Databases and Curation  
for semi-automated against 191 statements and 46 annotations for manual) ( Table 1) .  ...  the annotations also are considered (1.2 min per statement for semi-automated knowledge extraction with annotations and 2.6 min for the manual knowledge extraction with annotations).  ... 
doi:10.1093/database/bav057 pmid:26200752 pmcid:PMC5630939 fatcat:5sgpnfvinjgsxdfbgfvuadvjne

11.3 TIB AV-Portal: Semantic Content Mining with Semi-Automatic Metadata Editing

Saurbier, Felix; Waitelonis, Jörg
2017 Zenodo  
In addition, the analytical results are mapped against common authority files and knowledge bases via a process of automated named entity linking (NEL) to facilitate reuse as well as interlinking of information  ...  This is mainly due to different qualities in primary materials and ontologies as well as inherent ambiguities, which may impede correct detection and linking with named entities.  ...  Named Entity Linking -Annotation Data Model ▪ Open Annotation Data Model ▪ NLP Interchange Format ▪ Internationalization Tag Set (ITS) Ontology https://av.tib.eu/opendata tib:asr/31031_26463533_23007#char  ... 
doi:10.5281/zenodo.3611286 fatcat:x3f4rkhwibhqflf4jvf2lzulgm

Smart Qualitative Data: Methods and Community Tools for Data Mark-Up (SQUAD)

Louise Corti, Libby Bishop
2020 Zenodo  
The third strand aims to use natural language processing technology to develop and implement user-friendly tools for semi-automating processes to prepare qualitative data (format and mark-up using TEI)  ...  for 'data processing' n n data clean up tool data clean up tool n n named entity and annotation mark named entity and annotation mark up tool up tool n n anonymise tool anonymise tool  ...  entities) up features (e.g.. named entities) n n linking between sources (e.g.. text, annotations, analysis, linking between sources (e.g.. text, annotations, analysis, audio etc) audio etc) n n for 5  ... 
doi:10.5281/zenodo.3783075 fatcat:haen6cs6xzennmpzgxyyyrvggy

Semi-Automated Semantic Annotation of the Biomedical Literature

Fabio Rinaldi
2014 International Semantic Web Conference  
We briefly describe the results of the SASEBio project (Semi Automated Semantic Enrichment of the Biomedical Literature) which aims at adding semantic annotations to PubMed abstracts, in order to present  ...  The biomedical literature is a major source of knowledge, which however is underutilized due to the lack of rich annotations that would allow automated knowledge discovery.  ...  While it is possible to access the automatically generated annotations for further processing by a reasoner or integrator tool, we strongly believe that at present a process of semi-automated validation  ... 
dblp:conf/semweb/Rinaldi14 fatcat:hele5czq4naylebqpzpgwd7bii

ODIN: An Advanced Interface for the Curation of Biomedical Literature

Fabio Rinaldi, Fabio Rinaldi, Simon Clematide, Gerold Schneider, Martin Romacker, Therese Vachon
2010 Nature Precedings  
We present ODIN (Ontogene Document INspector): a system for interactive curation of biomedical literature, developed within the scope of the SASEBio project (Semi-Automated Semantic Enrichment of the Biomedical  ...  The curator/annotator can view the whole document with in-line annotations highlighted, or can browse the extracted entities and be pointed back to the mentions of the entities within the original document  ...  Introduction ODIN (Ontogene Document INspector) is a system for interactive curation of biomedical literature, developed within the scope of the SASEBio project (Semi-Automated Semantic Enrichment of the  ... 
doi:10.1038/npre.2010.5169 fatcat:odoo6tnngbem3iu4wn6x46g65m

Tagging Named Entities in Croatian Tweets

Krešimir Baksa, Dino Golović, Goran Glavaš, Jan Šnajder
2017 Slovenščina 2.0: Empirične, Aplikativne in Interdisciplinarne Raziskave  
Named entity extraction tools designed for recognizing named entities in texts written in standard language (e.g., news stories or legal texts) have been shown to be inadequate for user-generated textual  ...  In this work, we propose a supervised approach to named entity recognition and classification for Croatian tweets.  ...  To reduce the annotation effort, we performed semi-automated annotation.  ... 
doi:10.4312/slo2.0.2016.1.20-41 fatcat:24rggk6nlnd3lpmfkosgeycdeq

Generating structured Profiles of Linked Data Graphs

Besnik Fetahu, Stefan Dietze, Bernardo Pereira Nunes, Davide Taibi, Marco Antonio Casanova
2013 International Semantic Web Conference  
We adopt and integrate techniques for Named Entity Recognition and automated data validation, providing a consistent workflow for dataset profiling and annotation.  ...  In this paper, we introduce a processing pipeline to automatically assess, annotate and index available linked datasets.  ...  Moreover, to ensure high annotation accuracy a semi-automated evaluation approach is proposed.  ... 
dblp:conf/semweb/FetahuDNTC13 fatcat:4fkqy2fj2nhrvfxiocmav6zfge

Semantic Disambiguation and Linking of Quantitative Mentions in Textual Content

Mehrnaz Ghashghaei, Ebrahim Bagheri, John Cuzzola, Ali A. Ghorbani, Zeinab Noorian
2016 International Journal of Semantic Computing (IJSC)  
Results obtained from the developed gold standard dataset show that the proposed automated semantic annotation platform is quite effective in detecting and disambiguating numerical content, and connecting  ...  In spite of their many application areas, current semantic annotation systems have some limitations.  ...  Semi-automated Annotation Tools To overcome the shortcomings of manual annotation tools, semi-automated annotation was proposed.  ... 
doi:10.1142/s1793351x16500021 fatcat:dyua7isabvd77njaernr4udraa

Extraction of System States from Natural Language Requirements

Florian Pudlitz, Florian Brokhausen, Andreas Vogelsang
2019 2019 IEEE 27th International Requirements Engineering Conference (RE)  
Named-entity Recognition is a sub-task from the field of automated information retrieval and is used to classify parts of natural language texts into categories.  ...  We present an almost entirely automated approach and an iterative semi-automated approach to train our model.  ...  In this paper, we introduce and compare a semi-automated and an almost entirely automated approach for ML-based Named-entity Recognition to automatically extract system state candidates from natural language  ... 
doi:10.1109/re.2019.00031 dblp:conf/re/PudlitzBV19 fatcat:oedzlkkg7bc3riayjvr4riviaa

Automated Transformation of Semi-Structured Text Elements

Johannes Heurix, Antonio Rella, Stefan Fenz, Thomas Neubauer
2012 Americas Conference on Information Systems  
This paper presents a rule-based transformation system that converts semi-structured (annotated) text into standardized formats, such as HL7 CDA.  ...  , such as names or dates (named-entity recognition).  ...  Each text block in turn can have multiple named-entities, again annotated with XML tags (e.g., <a_firstname>).  ... 
dblp:conf/amcis/HeurixRFN12 fatcat:ywze2w7wdbcn5p7vwbw4wkvfx4

Named-Entity Dataset for Medieval Latin, Middle High German and Old Norse

Clément Besnier, William Mattingly
2021 Journal of Open Humanities Data  
Since the annotation is on low-resource pre-modern languages, they may be important to build named-entity recognition tools for languages with little data and high linguistic variation.  ...  We present a dataset of named entities in three languages: Medieval Latin, Middle High German and Old Norse.  ...  REUSE POTENTIAL The dataset combines named-entity annotations of texts written in several pre-modern languages.  ... 
doi:10.5334/johd.36 fatcat:jsext6ihfndk5cij63nhjdmmta

Identifying Chemical Entities based on ChEBI

Tiago Grego, Francisco R. Pinto, Francisco M. Couto
2012 International Conference on Biomedical Ontology  
This software demonstration paper presents Identifying Chemical Entities (ICE), a platform composed by algorithms for chemical entity recognition, entity resolution to a reference database, namely ChEBI  ...  entities in the entity recognition and resolution process.  ...  All four entities were in fact correct, but the indication of consistent and outlier entities still provide interesting and meaningful explanation that users can use in a semi-automated fashion.  ... 
dblp:conf/icbo/GregoPC12 fatcat:dyuf5c5r75eafm6alejposcpm4
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