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Extracting gene pathway relations using a hybrid grammar: the Arizona Relation Parser

D. M. McDonald, H. Chen, H. Su, B. B. Marshall
2004 Bioinformatics  
Results: We present the Arizona Relation Parser that differs from other parsers in its use of a broad coverage syntaxsemantic hybrid grammar.  ...  Expert evaluation showed that the parser extracted biologically relevant relations with 89% precision.  ...  Relations extracted are used by a gene network visualizer and are intended to help researchers construct gene pathways.  ... 
doi:10.1093/bioinformatics/bth409 pmid:15256411 fatcat:ll7xisyzufgg5eeohucdqonddq

A shallow parser based on closed-class words to capture relations in biomedical text

Gondy Leroy, Hsinchun Chen, Jesse D Martinez
2003 Journal of Biomedical Informatics  
It uses heuristics and a noun phraser to capture entities of interest in the text. Cascaded finite state automata structure the relations between individual entities.  ...  A shallow parser that captures the relations between noun phrases automatically from free text has been developed and evaluated.  ...  Acknowledgments This project was supported by the following grant: NIH/NLM, 1 R33 LM07299-01, 2002-2005, ''Genescene: a Toolkit for Gene Pathway Analysis''.  ... 
doi:10.1016/s1532-0464(03)00039-x pmid:14615225 fatcat:brfkh5e72rcitbrvrlgmjq5nf4

Global mapping of gene/protein interactions in PubMed abstracts: A framework and an experiment with P53 interactions

Xin Li, Hsinchun Chen, Zan Huang, Hua Su, Jesse D. Martinez
2007 Journal of Biomedical Informatics  
We demonstrate the application of the proposed framework using a testbed of P53-related PubMed abstracts, which shows that literature-based P53 networks exhibit small-world and scale-free properties.  ...  We also found that high degree genes in the literature-based networks have a high probability of appearing in the manually curated database and genes in the same pathway tend to form local clusters in  ...  Acknowledgment This work was supported by: NIH/NLM, 1 R33 LM07299-01, 2003-2005, ''Genescene: a Toolkit for Gene Pathway Analysis.''  ... 
doi:10.1016/j.jbi.2007.01.001 pmid:17317333 pmcid:PMC2047827 fatcat:wl3xjzdf4vcqfpwnk473q5lts4

Genescene: An ontology-enhanced integration of linguistic and co-occurrence based relations in biomedical texts

Gondy Leroy, Hsinchun Chen
2005 Journal of the American Society for Information Science and Technology  
The parser extracts precise and semantically rich relations from individual abstracts. Concept Space extracts relations that hold true for the collection of abstracts.  ...  We combined a linguistic parser with Concept Space, a cooccurrence based semantic net. Both techniques extract complementary biomedical relations between noun phrases from MEDLINE abstracts.  ...  Acknowledgments This project was supported by the following grant: NIH/NLM, 1 R33 LM07299-01, 2002-2005, "Genescene: a Toolkit for Gene Pathway Analysis."  ... 
doi:10.1002/asi.20135 fatcat:3uy3xkpborgk5eijwx6jrtm7u4

A framework of integrating gene relations from heterogeneous data sources: an experiment on Arabidopsis thaliana

J. Li, X. Li, H. Su, H. Chen, D. W. Galbraith
2006 Bioinformatics  
In this study we propose a framework for extraction and integration of gene functional relations from diverse biological data sources, including gene expression data, biological literature and genomic  ...  One of the most important goals of biological investigation is to uncover gene functional relations.  ...  This relation parser was reported to outperform other parsers in its use of a broad coverage syntax-semantic hybrid grammar (McDonald et al., 2004) .  ... 
doi:10.1093/bioinformatics/btl345 pmid:16820427 fatcat:frdzodghy5foxclute3qib42yi

BioSimplify: an open source sentence simplification engine to improve recall in automatic biomedical information extraction

Siddhartha Jonnalagadda, Graciela Gonzalez
2010 AMIA Annual Symposium Proceedings  
BioSimplify is an open source tool written in Java that introduces and facilitates the use of a novel model for sentence simplification tuned for automatic discourse analysis and information extraction  ...  We tested our tool on its impact to the task of PPI extraction and it improved the f-score of the PPI tool by around 7%, with an improvement in recall of around 20%.  ...  Special thanks to David McClosky, Filip Ginter and Sampo Pyysalo for their kind suggestions regarding the use of parsers.  ... 
pmid:21346999 pmcid:PMC3041388 fatcat:aft7k2whb5gljolwgoqosup6nq

BioSimplify: an open source sentence simplification engine to improve recall in automatic biomedical information extraction [article]

Siddhartha Jonnalagadda, Graciela Gonzalez
2011 arXiv   pre-print
BioSimplify is an open source tool written in Java that introduces and facilitates the use of a novel model for sentence simplification tuned for automatic discourse analysis and information extraction  ...  We tested our tool on its impact to the task of PPI extraction and it improved the f-score of the PPI tool by around 7%, with an improvement in recall of around 20%.  ...  Special thanks to David McClosky, Filip Ginter and Sampo Pyysalo for their kind suggestions regarding the use of parsers.  ... 
arXiv:1107.5744v1 fatcat:2wwwaou6qnfmxdm5jn6qyjcjou

OUP accepted manuscript

2018 Database: The Journal of Biological Databases and Curation  
We demonstrate that combining the extracted pathway fragments with existing biological data analysis algorithms that rely on curated models helps identify and explain a large number of previously unidentified  ...  . 1 www.pathwaycommons.org 2 Internal analysis of the Pathway Commons team.  ...  We also thank the anonymous reviewers for their insightful comments.  ... 
doi:10.1093/database/bay098 fatcat:xpnrphqq6jgsbeuafu5pogr2uq

Artificial intelligence and molecular biology

1994 ChoiceReviews  
Often experimenters both establish initial experimental conditions, and perturb the system at later times (often using a complex protocol) by adding reagents, applying heat or cold, etc.  ...  For a detailed description of the frame representation for imagery and the implementation of the depict function see [Papadias 1990 ]. 2.  ...  construction at the University of Arizona.  ... 
doi:10.5860/choice.31-3826 fatcat:5jmryy7mkbcrvifz6ahlbbdceu

Anthropogenic marine debris and its dynamics across peri-urban and urban mangroves on Penang Island, Malaysia [article]

Su Yin Chee, John Barry Gallagher, Jean Chai Yee, Danielle Carey, Yusri Yusup
2019 biorxiv/medrxiv   pre-print
Diversity of debris forms were consistent with the type of land use and population livelihood in each area.  ...  closer to the edge is increasingly sorted and lost to the water body in favour of smaller plastic items, for a constant wind field and irrespective of neap-spring phases.  ...  In my previous work, I studied the grammatical structure (syntax) of the language by creating a parser.  ... 
doi:10.1101/756106 fatcat:m6oy4besircffmdhmffppw6yra

Mining relations from the biomedical literature [article]

Jörg Hakenberg, Humboldt-Universität Zu Berlin, Humboldt-Universität Zu Berlin
2017
For relationship extraction, we develop a methodology to automatically annotate large amounts of unlabeled data for relations, and make use of such annotations in a pattern matching strategy.  ...  For the first, we describe two methods, one set up as a classification task, the other based on dictionary-matching.  ...  The ARIZONA RELATIONAL PARSER was reported to reach very good precision and recall values, but it required the creation of 1778 grammar rules and was evaluated on a very small corpus only, without cross  ... 
doi:10.18452/16073 fatcat:plwmke4zdffszi3pxcqlad47km

Announcements

2007 Journal of Language Contact  
The aim is to open theoretical reflection on the importance of 'contact' as a linguistic and anthropological phenomenon for the study of the evolution and dynamics of languages and of Language. II.  ...  A notion to be rethought?"  ...  The antipassive is used in other Mayan languages to extract agents for questioning, topicalization or relativization.  ... 
doi:10.1163/000000007792548279 fatcat:y4a6czjscfep3os56x3iulyjxy

Critical Assessment of Information Extraction in Molecular Biology Second BioCreative Challenge Evaluation Workshop Co-organizers Co-organizers

Main Organizer, Valencia, Lynette Hirschman, Martin Krallinger, Main Organizer, Valencia, Lynette Hirschman, Martin Krallinger
unpublished
is to analyse the logical forms of those sentences which contain the mentioning of relevant protein names, and to rank the sentences from which the relations where extracted using the class descriptors  ...  Prior to the Challenge, an information extraction pipeline was developed to extract entities and relations relevant to the biomedical domain, and to normalise the entities to appropriate ontologies.  ...  The relation extractor uses a maximum entropy model with a variety of shallow linguistic features, trained on annotated data, to extract mentions of protein-protein interactions from the text.  ... 
fatcat:mty5ef5zyrdaxmqdoh35dvbgpu

Open Knowledge: Promises and Challenges [chapter]

Rufus Pollock, Jo Walsh
2012 The Digital Public Domain: Foundations for an Open Culture  
tools can find the appropriate parser code for extracting the CC REL abstract model from the microformat, without having to know about all microformats in advance.  ...  , Arizona Law Review, 50 , and R. David Simpson and Roger ".  ...  CC recommends exposing a mechanism to extract the CC REL abstract model from the XML, so that CC tools need not know about every possible XML schema ahead of time.  ... 
doi:10.11647/obp.0019.07 fatcat:r3yre7bnmndbvbhggtzvdhdyaq

An Ethnographic Analysis of Names of Round Characters in Wole Soyinka's The Strong Breed

Idowu Olusola Odebode
2012 Theory and Practice in Language Studies  
This article highlights the progress of the images of Arabs in English literature. Europe owes a debt of gratitude to Arabia and the East.  ...  Modern English Orientalists work to explore the Arabian characters with reference to Islam. Islamist Arabs are represented as a threat to the West.  ...  Participants of the Study This study was conducted in a medical university in the second semester of the 2009-2010 academic year.  ... 
doi:10.4304/tpls.2.9.1776-1782 fatcat:ar4o6sw57bha7i3cfhxogoqk4q
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