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Harmonization of gene/protein annotations: towards a gold standard MEDLINE

David Campos, Sérgio Matos, Ian Lewin, José Luís Oliveira, Dietrich Rebholz-Schuhmann
2012 Computer applications in the biosciences : CABIOS  
However, little effort has been spent on a systematic analysis of methods harmonizing the annotation results and measuring against a combination of Gold Standard Corpora (GSCs).  ...  Results: We present Totum, a machine learning solution that harmonizes gene/protein annotations provided by heterogeneous NER solutions.  ...  ACKNOWLEDGEMENT We have to thank to the members of the CALBC project: David Milward, Peter Corbett, Udo Hahn, Ekatarina Buyko, Katrin Tomanek, Jan Kors, Erik van Mulligen and Ning Kang.  ... 
doi:10.1093/bioinformatics/bts125 pmid:22419783 fatcat:ihh7bn22bvfppkxm7nlyqrfiai

An analysis on the entity annotations in biological corpora

Mariana Neves
2014 F1000Research  
Results show that while some semantic entities, such as genes, proteins and chemicals are consistently annotated in many collections, corpora available for diseases, variations and mutations are still  ...  Here I present an overview of 36 corpora and show an analysis on the semantic annotations they contain.  ...  I focus on gold-standard corpora which contain annotations for entity types, such as genes/proteins, chemicals and species.  ... 
doi:10.12688/f1000research.3456 fatcat:6ojbd65bnjd2hijdqx7a74spye

An analysis on the entity annotations in biological corpora

Mariana Neves
2014 F1000Research  
Results show that while some semantic entities, such as genes, proteins and chemicals are consistently annotated in many collections, corpora available for diseases, variations and mutations are still  ...  Here I present an overview of 36 corpora and show an analysis on the semantic annotations they contain.  ...  I focus on gold-standard corpora which contain annotations for entity types, such as genes/proteins, chemicals and species.  ... 
doi:10.12688/f1000research.3216.1 pmid:25254099 pmcid:PMC4168744 fatcat:eypyq7g3wjhwdjuao6zu4iq5nq

Concept annotation in the CRAFT corpus

Michael Bada, Miriam Eckert, Donald Evans, Kristin Garcia, Krista Shipley, Dmitry Sitnikov, William A Baumgartner, K Cohen, Karin Verspoor, Judith A Blake, Lawrence E Hunter
2012 BMC Bioinformatics  
Results: This paper presents the concept annotations of the Colorado Richly Annotated Full-Text (CRAFT) Corpus, a collection of 97 full-length, open-access biomedical journal articles that have been annotated  ...  Concept annotations were created based on a single set of guidelines, which has enabled us to achieve consistently high interannotator agreement.  ...  In BioInfer, the focus is the annotation of relationships among genes, proteins, and RNAs, and entities are only annotated if they are relevant to this focus and if they are named entities-a term itself  ... 
doi:10.1186/1471-2105-13-161 pmid:22776079 pmcid:PMC3476437 fatcat:kuulhujx4ratnkoywafxggkhmi

PGxCorpus, a manually annotated corpus for pharmacogenomics

Joël Legrand, Romain Gogdemir, Cédric Bousquet, Kevin Dalleau, Marie-Dominique Devignes, William Digan, Chia-Ju Lee, Ndeye-Coumba Ndiaye, Nadine Petitpain, Patrice Ringot, Malika Smaïl-Tabbone, Yannick Toussaint (+1 others)
2020 Scientific Data  
But existing works are limited by the absence of a high quality annotated corpus focusing on PGx domain. In particular, this absence restricts the use of supervised machine learning.  ...  This article introduces PGxCorpus, a manually annotated corpus, designed to fill this gap and to enable the automatic extraction of PGx relationships from text.  ...  In this case, the final annotation is considered as the gold standard, and the F1-score measures how automatic pre-annotation performs in regards to the final annotation ground truth.  ... 
doi:10.1038/s41597-019-0342-9 pmid:31896797 pmcid:PMC6940385 fatcat:ra3mar3jbbfubirg62t5gca6l4

Neuroimaging Feature Terminology: A Controlled Terminology for the Annotation of Brain Imaging Features

Anandhi Iyappan, Erfan Younesi, Alberto Redolfi, Henri Vrooman, Shashank Khanna, Giovanni B. Frisoni, Martin Hofmann-Apitius
2017 Journal of Alzheimer's Disease  
Ontologies and terminologies are used for interoperability of knowledge and data in a standard manner among interdisciplinary research groups.  ...  Existing imaging ontologies capture general aspects of the imaging domain as a whole such as methodological concepts or calibrations of imaging instruments.  ...  Data collection and sharing for this project was funded by the Alzheimer's Disease Neuroimaging Initiative (ADNI) (National Institutes of Health Grant U01 AG024904) and DOD ADNI (Department of Defense  ... 
doi:10.3233/jad-161148 pmid:28731430 pmcid:PMC5611802 fatcat:jb7h3ikqfrhddasmq6b2kymd4q

Discovering gene functional relationships using FAUN (Feature Annotation Using Nonnegative matrix factorization)

Elina Tjioe, Michael W Berry, Ramin Homayouni
2010 BMC Bioinformatics  
Its utility and performance as a knowledge discovery tool is demonstrated using a set of genes associated with Autism.  ...  Results: In this study, we develop a Web-based bioinformatics software environment called FAUN or Feature Annotation Using Nonnegative matrix factorization (NMF) to facilitate both the discovery and classification  ...  Acknowledgements This work is supported by NIH-subcontract (HD052472) involving the University of Tennessee, University of Memphis, Oak Ridge National Laboratory, and the University of British Columbia  ... 
doi:10.1186/1471-2105-11-s6-s14 pmid:20946597 pmcid:PMC3026361 fatcat:bfkhgpyt2bdkzac6mccrmxcke4

Transfer learning for biomedical named entity recognition with neural networks [article]

John M Giorgi, Gary Bader
2018 bioRxiv   pre-print
A fundamental task is the recognition of biomedical named entities in text (BNER) such as genes/proteins, diseases, and species.  ...  An alternative to GSCs are silver-standard corpora (SSCs), which are generated by harmonizing the annotations made by several automatic annotation systems.  ...  Acknowledgements We gratefully acknowledge the support of NVIDIA Corporation with the donation of the Titan Xp GPU used for this research.  ... 
doi:10.1101/262790 fatcat:birvfsyz5fcbnd4imxlgduhfwa

Detecting miRNA Mentions and Relations in Biomedical Literature

Shweta Bagewadi, Tamara Bobić, Martin Hofmann-Apitius, Juliane Fluck, Roman Klinger
2014 F1000Research  
Ogren PV: Knowtator: A Protégé plug-in for annotated corpus construction.  ...  Apart from the role of miRNAs in normal physiology, their dysregulation is implicated in a vast array of diseases.  ...  Acknowledgements We would like to thank Heinz-Theo Mevissen for all the support during implementation of the dictionaries and regular expressions in ProMiner.  ... 
doi:10.12688/f1000research.4591.2 pmid:26535109 pmcid:PMC4602280 fatcat:h4sc5dk5afbgbc46tc6vvlo3xq

Detecting miRNA Mentions and Relations in Biomedical Literature

Shweta Bagewadi, Tamara Bobić, Martin Hofmann-Apitius, Juliane Fluck, Roman Klinger
2014 F1000Research  
Ogren PV: Knowtator: A Protégé plug-in for annotated corpus construction.  ...  Apart from the role of miRNAs in normal physiology, their dysregulation is implicated in a vast array of diseases.  ...  Acknowledgements We would like to thank Heinz-Theo Mevissen for all the support during implementation of the dictionaries and regular expressions in ProMiner.  ... 
doi:10.12688/f1000research.4591.1 pmid:26535109 pmcid:PMC4602280 fatcat:xrm7n3y6gnhmxa6p5rxepqvjwy

PDON: Parkinson's disease ontology for representation and modeling of the Parkinson's disease knowledge domain

Erfan Younesi, Ashutosh Malhotra, Michaela Gündel, Phil Scordis, Alpha Tom Kodamullil, Matt Page, Bernd Müller, Stephan Springstubbe, Ullrich Wüllner, Dieter Scheller, Martin Hofmann-Apitius
2015 Theoretical Biology and Medical Modelling  
Disease ontologies provide a novel means for organizing, integrating, and standardizing the knowledge domains specific to disease in a compact, formalized and computer-readable form and serve as a reference  ...  Finally, a cause-and-effect model was built around PINK1 and two gene expression studies from the Gene Expression Omnibus database were re-annotated to demonstrate the usability of the ontology.  ...  Theo Mevissen, Jürgen Klein and Christian Ebeling from Fraunhofer Institute SCAI are acknowledged for their support in automatic annotation of GEO entries and full-text publications.  ... 
doi:10.1186/s12976-015-0017-y pmid:26395080 pmcid:PMC4580356 fatcat:ueseobwo4rga7bdggm3uicgg7e

Mining the pharmacogenomics literature--a survey of the state of the art

U. Hahn, K. B. Cohen, Y. Garten, N. H. Shah
2012 Briefings in Bioinformatics  
advanced text analytics, e.g. document corpora annotated with corresponding semantic metadata (gold standards and training data), biomedical terminologies and ontologies providing domain-specific background  ...  Therefore, publications span the intersection of research in genotypes, phenotypes and pharmacology, a topic that has increasingly become a focus of active research in recent years.This survey covers efforts  ...  F-measure using one annotator as the gold standard for the other(s) can be a more adequate alternative [137] .  ... 
doi:10.1093/bib/bbs018 pmid:22833496 pmcid:PMC3404399 fatcat:por4dnthkrcxjdsir6uc64kdaq

RAPID PATTERN DEVELOPMENT FOR CONCEPT RECOGNITION SYSTEMS: APPLICATION TO POINT MUTATIONS

J. GREGORY CAPORASO, WILLIAM A. BAUMGARTNER, DAVID A. RANDOLPH, K. BRETONNEL COHEN, LAWRENCE HUNTER
2007 Journal of Bioinformatics and Computational Biology  
We also discuss the development and evaluation of our recently published high-quality, human-annotated gold standard corpus, which contains 1,515 complete point mutation mentions annotated in 813 abstracts  ...  We applied our approach to develop MutationFinder, a system for automatically extracting mentions of point mutations from the text.  ...  Acknowledgments The authors would like to thank Jim Martin for helpful discussion and guidance in the initial stages of this project.  ... 
doi:10.1142/s0219720007003144 pmid:18172927 fatcat:vbmeigd5l5az7cxaw2fg53k3wa

Biomedical Named Entity Recognition: A Survey of Machine-Learning Tools [chapter]

David Campos, Sergio Matos, Jose Luis
2012 Theory and Applications for Advanced Text Mining  
Acknowledgements This work received funding from FEDER through the COMPETE programme and from Fundação para a Ciência e a Tecnologia FCT under grant agreement FCOMP---FED-ER-. S.  ...  Harmonisation of gene/protein annotations towards a gold standard MEDLINE. Bioinformatics, , -. [ ] Hsu, C. N., Chang, Y. M., Kuo, C. J., Lin, Y. S., Huang, H. S., & Chung, I. F. .  ...  However, the same semantic group contains annotations of DN", RN" and gene/protein.  ... 
doi:10.5772/51066 fatcat:yjvzpbiod5b4dejpqufsuvplsy

Event-based text mining for biology and functional genomics

S. Ananiadou, P. Thompson, R. Nawaz, J. McNaught, D. B. Kell
2014 Briefings in Functional Genomics  
The biological literature in particular is largely focused on describing relationships between entities (e.g. genes, proteins and complexes), including how such entities interact and affect each other.  ...  The assessment of genome function requires a mapping between genome-derived entities and biochemical reactions, and the biomedical literature represents a rich source of information about reactions between  ...  a test sample and results compared with a gold standard annotation of that sample.  ... 
doi:10.1093/bfgp/elu015 pmid:24907365 pmcid:PMC4499874 fatcat:qjl6uvt3wbbuplu6hrdsloyjlu
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