Antonio Jimeno Yepes  Antonio Jimeno Yepes photo       

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2015

Identification and Analysis of Medical Entity Co-occurrences in Twitter
Andrew MacKinlay, Antonio Jimeno Yepes, Bo Han
Proceedings of the ACM Ninth International Workshop on Data and Text Mining in Biomedical Informatics, pp. 22--22, 2015

Investigating Public Health Surveillance using Twitter
Antonio Jimeno Yepes, Andrew MacKinlay, Bo Han
ACL / BioNLP, 2015

Identifying Diseases, Drugs and Symptoms in Twitter
Antonio Jimeno Yepes, Andrew MacKinlay, Bo Han, Qiang Chen
MedInfo, 2015

Feature engineering for MEDLINE citation categorization with MeSH
Antonio Jimeno Yepes, Laura Plaza, Jorge Carrillo-de-Albornoz, James G Mork, Alan R Aronson
BMC Bioinformatics16, 113, 2015


2014


Literature mining of genetic variants for curation: quantifying the importance of supplementary material
A Jimeno Yepes, K Verspoor
Database: The Journal of Biological Databases and Curation, 2014

BioC interoperability track overview
DC Comeau, RT Batista-Navarro, HJ Dai, RI Doan, A Jimeno Yepes, R Khare, et al.
Databasebau053, 2014

Improving consistency of emergency department triage categorisation: Machine learning applied to clinical notes
MT Vassiliou, A Jimeno Yepes, MF Gerdtz, J Knott, R Wynne, K Verspoor
HIC, 2014

Identifying Twitter location mentions
B Han, A Jimeno Yepes, A MacKinlay, Q Chen
ALTA, 2014

Deep Belief Networks and Biomedical Text Categorisation
Antonio Jimeno Yepes, Andrew Mackinlay, Justin Bedo, Rahil Garnavi, Qiang Chen
ALTA, 2014
Abstract

Mutation extraction tools can be combined for robust recognition of genetic variants in the literature
A Jimeno Yepes, K Verspoor
F1000Research, 2014

Associating disease-related genetic variants in intergenic regions to the genes they impact
G Macintyre, A Jimeno Yepes, CS Ong, K Verspoor
PeerJ 2(e639), 2014


2013

Annotating the biomedical literature for the human variome
K Verspoor, A Jimeno Yepes, L Cavedon, T McIntosh, A Herten-Crabb et al.
Database, 2013

Towards automatic large-scale curation of genomic variation: improving coverage based on supplementary material
A Jimeno Yepes, K Verspoor
ISMB BioLink SIG, 2013

Identifying Publication Types Using Machine Learning
A Jimeno Yepes, JG Mork, AR Aronson
BioASQ, 2013

The NLM Medical Text Indexer System for Indexing Biomedical Literature
JG Mork, AJ Jimeno Yepes, AR Aronson
BioASQ, 2013

Impact of Corpus Diversity and Complexity on NER Performance
T Shmanina, I Zukerman, A Jimeno Yepes, L Cavedon, K Verspoor
ALTA, 2013

Brat2BioC: conversion tool between brat and BioC
A Jimeno Yepes, M Neves, K Verspoor
BioCreative Challenge Evaluation Workshop, 2013

Performance analysis of different protein/gene tagging solutions against public gold standard corpora
D Rebholz-Schuhmann, S Kafkas, JH Kim, A Jimeno Yepes, R Hoehndorf, et al.
Journal of Biomed Semantics, 2013

Using the argumentative structure of scientific literature to improve information access
A Jimeno Yepes, JG Mork, AR Aronson
ACL BioNLP, 2013

Extracting Biomedical Events and Modifications Using Subgraph Matching with Noisy Training Data
A MacKinlay, D Martinez, A Jimeno Yepes, H Liu, WJ Wilbur, K Verspoor
ACL BioNLP Shared Task, 2013

Monitoring named entity recognition: the League Table
D Rebholz-Schuhmann, S Kafkas, JH Kim, A Jimeno Yepes, I Lewin
Journal of biomedical semantics 4 (1)(19), 2013

NEROC: Named Entity Recognizer of Chemicals
M Choi, A Jimeno Yepes, J Zobel, K Verspoor
BioCreative Challenge Evaluation Workshop, 2013

Entity Recognition in Parallel Multi-lingual Biomedical Corpora: The CLEF-ER Laboratory Overview
Dietrich Rebholz-Schuhmann, Simon Clematide, Fabio Rinaldi, Senay Kafkas, Erik M van Mulligen, Chinh Bui, Johannes Hellrich, Ian Lewin, David Milward, Michael Poprat, others
Information Access Evaluation. Multilinguality, Multimodality, and Visualization, pp. 353--367, Springer, 2013

Context-Dependent Semantic Annotation in Cross-Lingual Biomedical Resources
Rafael Berlanga, Antonio Jimeno-Yepes, Mar\'\ia P\'erez-Catal\'an, Dietrich Rebholz-Schuhmann
Information Access Evaluation. Multilinguality, Multimodality, and Visualization, pp. 120--123, Springer, 2013

Effect of additional in-domain parallel corpora in biomedical statistical machine translation
Antonio Jimeno-Yepes, Aurlie Nvol
The 4th International Workshop on Health Document Text Mining and Information Analysis with the Focus of Cross-Language Evaluation, 2013

An evaluation of the concept retrieval annotation for Spanish-English CLEFER parallel corpora
Rafael Berlanga, Antonio Jimeno-Yepes, Mara Prez-Cataln, Dietrich Rebholz-Shuchmann
CLEF, 2013

MeSH indexing based on automatically generated summaries
Antonio J Jimeno-Yepes, Laura Plaza, James G Mork, Alan R Aronson, Alberto D\'\iaz
BMC bioinformatics 14(1), 208, BioMed Central Ltd, 2013

Comparison and combination of several MeSH indexing approaches
Antonio Jimeno-Yepes, JG Mork, D Demner-Fushman, AR Aronson
AMIA Annual Symposium Proceedings, 2013

PCorral—interactive mining of protein interactions from MEDLINE
Chen Li, Antonio Jimeno-Yepes, Miguel Arregui, Harald Kirsch, Dietrich Rebholz-Schuhmann
Database2013, bat030, Oxford University Press

Multilingual semantic resources and parallel corpora in the biomedical domain: the CLEF-ER challenge
Dietrich Rebholz-Schuhmann, Simon Clematide, Fabio Rinaldi, Senay Kafkas, Erik M van Mulligen, Chinh Bui, Johannes Hellrich, Ian Lewin, David Milward, Michael Poprat, others
Proceedings CLEF Conference, 2013

Evaluating gold standard corpora against gene/protein tagging solutions and lexical resources.
Dietrich Rebholz-Schuhmann, Senay Kafkas, Jee-Hyub Kim, Chen Li, Antonio Jimeno-Yepes, Robert Hoehndorf, Rolf Backofen, Ian Lewin
J. Biomedical Semantics4, 28, 2013

GeneRIF indexing: sentence selection based on machine learning
Antonio J Jimeno-Yepes, J Caitlin Sticco, James G Mork, Alan R Aronson
BMC bioinformatics 14(1), 171, BioMed Central Ltd, 2013


2012

Integration of UMLS and MEDLINE in Unsupervised Word Sense Disambiguation.
Antonio Jimeno-Yepes, Alan R Aronson
AAAI Fall Symposium: Information Retrieval and Knowledge Discovery in Biomedical Text, 2012

Disambiguating automatically-generated semantic annotations for Life Science open registries.
Antonio Jimeno-Yepes, Rafael Berlanga Llavori, Mar\'\ia P\'erez Catal\'an
E-LKR, 2012


The NLM Indexing Initiative: Current Status and Role in Improving Access to Biomedical Information
Alan R Aronson, James G Mork, Fran\c{c}ois-Michel Lang, Willie J Rogers, Antonio J Jimeno-Yepes, J Caitlin Sticco
2012 - ii.nlm.nih.gov

Knowledge-based and knowledge-lean methods combined in unsupervised word sense disambiguation
Antonio Jimeno Yepes, Alan R Aronson
Proceedings of the 2nd ACM SIGHIT International Health Informatics Symposium, pp. 733--736, 2012

MeSH indexing: machine learning and lessons learned
A Jimeno-Yepes, B Wilkowski, JG Mork, D Demner-Fushman, AR Aronson
ACM SIGHIT International Health Informatics Symposium, Miami, FL, USA, 2012

NLM at TREC 2012 Medical Records track
Dina Demner-Fushman, Swapna Abhyankar, Antonio Jimeno-Yepes, Russell Loane, Francois Lang, James G Mork, Nicholas Ide, Alan R Aronson
Technical Report, DTIC Document, 2012

MEDLINE MeSH indexing: lessons learned from machine learning and future directions
Antonio Jimeno Yepes, James G Mork, BartBomiej Wilkowski, Dina Demner Fushman, Alan R Aronson
Proceedings of the 2nd ACM SIGHIT International Health Informatics Symposium, pp. 737--742, 2012

A One-Size-Fits-All Indexing Method Does Not Exist: Automatic Selection Based on Meta-Learning.
Antonio Jimeno-Yepes, James G Mork, Dina Demner-Fushman, Alan R Aronson
JCSE 6(2), 151--160, 2012


2011

Assessment of NER solutions against the first and second CALBC Silver Standard Corpus
D Rebholz-Schuhmann, A Jimeno-Yepes, C Li, S Kafkas, I Lewin, N Kang et al.
Journal of Biomedical Semantics 2 (Suppl 5)(S11), 2011

Workshop E-LKR
Rafael Berlanga, Antonio Jimeno-Yepes, Maria Jose Aramburu, Ernesto Jimenez-Ruiz, Ismael Sanz, Torben Bach Pedersen, Sven Casteleyn, Roxana Danger, Giovanna Guerrini, Johannes Hoart, others
Database and Expert Systems Applications , 2011

MetaMap in the CALBC Workshop II
James Mork, Lee Peters, Antonio Jimeno-Yepes, Alan R Aronson, Olivier Bodenreider
1st CALBC Workshop, 2011

Preliminary results for Biomedical Word Sense Disambiguation based on Semantic Clustering
Tamara Martin-Wanton, Rafael Berlanga-Llavori, Antonio Jimeno-Yepes
Database and Expert Systems Applications (DEXA), 2011 22nd International Workshop on, pp. 460--464

Self-training and co-training in biomedical word sense disambiguation
Antonio Jimeno-Yepes, Alan R Aronson
Proceedings of BioNLP 2011 Workshop, pp. 182--183

A bottom-up approach to MEDLINE indexing recommendations
Antonio Jimeno-Yepes, Bart\lomiej Wilkowski, James G Mork, Elizabeth Van Lenten, Dina Demner Fushman, Alan R Aronson
AMIA Annual Symposium Proceedings, pp. 1583, 2011

Automatic algorithm selection for MeSH Heading indexing based on meta-learning
Antonio Jimeno-Yepes, J Mork, D Fushman, A Aronson
Proceedings of the Fourth International Symposium on Languages in Biology and Medicine, 2011

Collocation analysis for UMLS knowledge-based word sense disambiguation
Antonio Jimeno-Yepes, Bridget T Mclnnes, Alan R Aronson
BMC bioinformatics 12(Suppl 3), S4, BioMed Central Ltd, 2011

Studying the correlation between different word sense disambiguation methods and summarization effectiveness in biomedical texts
Laura Plaza, Antonio J Jimeno-Yepes, Alberto D\'\iaz, Alan R Aronson
BMC bioinformatics 12(1), 355, BioMed Central Ltd, 2011

A Knowledge-Based Approach to Medical Records Retrieval.
Dina Demner-Fushman, Swapna Abhyankar, Antonio Jimeno-Yepes, Russell F Loane, Bastien Rance, Fran\c{c}ois-Michel Lang, Nicholas C Ide, Emilia Apostolova, Alan R Aronson
TREC, 2011

Exploiting MeSH indexing in MEDLINE to generate a data set for word sense disambiguation
Antonio J Jimeno-Yepes, Bridget T McInnes, Alan R Aronson
BMC bioinformatics 12(1), 223, BioMed Central Ltd, 2011


2010

CALBC silver standard corpus
D Rebholz-Schuhmann, A Jimeno Yepes, EM Van Mulligen, N Kang, et al.
J Bioinform Comput Biol 8 (1)(163-79), 2010

Applications of Ontologies and Text Mining in the Biomedical Domain
A Jimeno-Yepes, R Berlanga-Llavori, D Rebholz-Schuchmann
Ontology Theory, Management, and Design: Advanced Tools and Models, 261, IGI Global Snippet, 2010

Improving an automatically extracted corpus for UMLS Metathesaurus word sense disambiguation
Antonio Jimeno Yepes, Alan R Aronson
Procesamiento de Lenguaje Natural, 2010

Query expansion for UMLS Metathesaurus disambiguation based on automatic corpus extraction
Antonio Jimeno-Yepes, Alan R Aronson
Machine Learning and Applications (ICMLA), 2010 Ninth International Conference on, pp. 965--968

The CALBC Silver Standard Corpus for Biomedical Named Entities-A Study in Harmonizing the Contributions from Four Independent Named Entity Taggers.
Dietrich Rebholz-Schuhmann, Antonio Jos\'e Jimeno-Yepes, Erik M van Mulligen, Ning Kang, Jan A Kors, David Milward, Peter T Corbett, Ekaterina Buyko, Katrin Tomanek, Elena Beisswanger, others
LREC, 2010

Measuring prediction capacity of individual verbs for the identification of protein interactions
Dietrich Rebholz-Schuhmann, Antonio Jimeno-Yepes, Miguel Arregui, Harald Kirsch
Journal of biomedical informatics 43(2), 200--207, Elsevier, 2010

Knowledge-based biomedical word sense disambiguation: comparison of approaches
Antonio J Jimeno-Yepes, Alan R Aronson
BMC bioinformatics 11(1), 569, BioMed Central Ltd, 2010

Ontology refinement for improved information retrieval
Antonio Jimeno-Yepes, Rafael Berlanga-Llavori, Dietrich Rebholz-Schuhmann
Information Processing \& Management 46(4), 426--435, Elsevier, 2010


2009

Using Biomedical Terminological Resources for Information Retrieval
P Pezik, A Jimeno Yepes, D Rebholz-Schuhmann
Information retrieval in biomedicine: natural language processing for knowledge integration, Medical Info Science Reference, 2009


Reuse of terminological resources for efficient ontological engineering in Life Sciences
Antonio Jimeno Yepes, Ernesto Jimenez Ruiz, Rafael Berlanga Llavori, Dietrich Rebholz-Schuhmann
BMC Bioinformatics 10 (Suppl 10)(S4), 2009

A Thesaurus and an Application Ontology for the Juvenile Arthritis Domain
Ernesto Jimnez-Ruiz, Rafael Berlanga-Llavori, Victoria Nebot, Antonio Jimeno-Yepes, Dietrich Rebholz-Schuhmann
The 3rd International Symposium on Languages in Biology and Medicine, 2009

Comparison of methods for topic template queries in the biomedical domain
Antonio Jimeno-Yepes, Rafael Berlanga-Llavori, Dietrich Rebholz-Schuhmann
Languages in Biology and Medicine, 2009

Lexical, terminological and ontological resources for biological text mining
P Pezik, A Jimeno-Yepes, D Rebholz-Schuhmann
Information Retrieval in Biomedicine: Natural Language Processing for Knowledge Integration. IGI Global Publishing, 2009

Topic template queries to enhance document retrieval
A Jimeno-Yepes, R Berlanga-Llavori, D Rebholz-Schuhmann
ECIR workshop on Contextual Information Access, Seeking and Retrieval Evaluation, 2009

Terminological cleansing for improved information retrieval based on ontological terms
Antonio Jimeno-Yepes, Rafael Berlanga-Llavori, Dietrich Rebholz-Schuhmann
Proceedings of the WSDM'09 Workshop on Exploiting Semantic Annotations in Information Retrieval, pp. 6--14, 2009

Exploitation of ontological resources for scientific literature analysis: searching genes and related diseases
Antonio Jimeno-Yepes, Rafael Berlanga-Llavori, Dietrich Rebholz-Schuhmann
Engineering in Medicine and Biology Society, 2009. EMBC 2009. Annual International Conference of the IEEE, pp. 7073--7078

Annotation of protein residues based on a literature analysis: cross-validation against UniProtKb
Kevin Nagel, Antonio Jimeno-Yepes, Dietrich Rebholz-Schuhmann
BMC bioinformatics 10(Suppl 8), S4, BioMed Central Ltd, 2009

Reuse of terminological resources for efficient ontological engineering in Life Sciences
Antonio Jimeno-Yepes, Ernesto Jim\'enez-Ruiz, Rafael Berlanga-Llavori, Dietrich Rebholz-Schuhmann
BMC bioinformatics 10(Suppl 10), S4, BioMed Central Ltd, 2009


2008

Assessment of modifying versus non-modifying protein interactions
Dietrich Rebholz-Schuhmann, A Jimeno Yepes, Miguel Arregui, Harald Kirsch
The Third International Symposium on Semantic Mining in Biomedicine, 2008

Text processing through Web services: calling Whatizit
D Rebholz-Schuhmann, M Arregui, S Gaudan, H Kirsch, A Jimeno-Yepes
Bioinformatics24 (2), 296-298, 2008

Assessment of diseases named entity recognition on a corpus of annotated sentences
A Jimeno-Yepes, E Jimenez-Ruiz, V. Lee, S. Gaudan, R. Berlanga-Llavori and D. Rebholz-Schuhmann
BMC Bioinformatics9, S3, 2008

Study of named entity recognition in biomedicine: towards the refinement of ontologies
A Jimeno-Yepes, R Berlanga-Llavori
Technical Report, Technical report, Master Thesis, Universitat Jaume I, 2008

Use of shared lexical resources for efficient ontological engineering
Antonio Jimeno-Yepes, Ernesto Jim\'enez-Ruiz, Rafael Berlanga, Dietrich Rebholz-Schuhmann
Semantic Web Applications and Tools for Life Sciences Workshop (SWAT4LS). CEUR WS Proceedings, 2008

Static dictionary features for term polysemy identification
P Pezik, A Jimeno-Yepes, V Lee, D Rebholz-Schuhmann
Building and evaluating resources for biomedical text mining, LREC Workshop, 2008

Combining evidence, specificity, and proximity towards the normalization of gene ontology terms in text
Sylvain Gaudan, A Jimeno Yepes, Vivian Lee, Dietrich Rebholz-Schuhmann, others
EURASIP journal on bioinformatics and systems biology2008, Hindawi Publishing Corporation


2007

Information retrieval and information extraction in trec genomics 2007
A Jimeno Yepes, P Pezik, D Rebholz-Schuhmann
In Proceeding of Ninth Text REtrieval Conference (TREC-15). National Institute of Standards and Technology, Special Publication, 2007

Automatic Text Analysis Based on Web Services
D Rebholz-Schuhmann, M Arregui, AJJ Yepes, H Kirsch, G Nenadic
Handout for the ISMB, 2007

Towards the enrichment of a biomedical ontology based on text mining
Antonio Jimeno-Yepes, Ernesto Jim\'enez-Ruiz, R Berlanga-Llavori, D Rebholz-Schuhmann
Technical Report, Citeseer, 2007


2006

Data-poor categorization and passage retrieval for gene ontology annotation in Swiss-Prot
F Ehrler, A Geissbhler, A Jimeno-Yepes, P Ruch
BMC bioinformatics 6 (Suppl 1)(S23), 2006

Report on the TREC 2006 Experiment: Genomics Track
P Ruch, A Jimeno Yepes, F Ehrler, J Gobeill, I Tbahriti
TREC, 2006


2004


LHC Reference Database
P Le Roux, A Vergara Fernandez, B Maire, S Chemli, M Zerlauth, H Prin, A Jimeno Yepes
Technical Report, 2004

LHC Reference Database: Towards a mechanical, optical and electrical Layout Database
Pascal Le Roux, S Chemli, A Jimeno Yepes, B Maire, Herve Prin, A Vergara-Fern\'andez, M Zerlauth
EPAC2004, Lucerne, 1882


2003

The electrical circuits in the LHC reference database
M Zerlauth, A Jimeno Yepes, G Morpurgo
Technical Report, CERN, 2003


2002

Manufacturing and test folder: MTF
C Delamare, A Jimeno-Yepes, SM Amrigo, E Manola-Poggioli, P Martel et al.
Proceedings of EPAC, 2002

The electrical circuit description for the LHC
M Zerlauth, A Jimeno Yepes, G Morpurgo, R Schmidt
Proceedings of the EPAC, 2002


2000

Design of a telerobotic interface system by using object recognition techniques
R Marn, P Sanz, A Jimeno Yepes, J Iesta
Advances in Pattern Recognition, 832-841, 2000