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Harmonization of gene/protein annotations: towards a gold standard MEDLINE
2012
Computer applications in the biosciences : CABIOS
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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
2014
F1000Research
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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
2014
F1000Research
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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
2012
BMC Bioinformatics
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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
2020
Scientific Data
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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
2017
Journal of Alzheimer's Disease
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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)
2010
BMC Bioinformatics
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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]
2018
bioRxiv
pre-print
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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
2014
F1000Research
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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
2014
F1000Research
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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
2015
Theoretical Biology and Medical Modelling
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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
2012
Briefings in Bioinformatics
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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
2007
Journal of Bioinformatics and Computational Biology
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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]
2012
Theory and Applications for Advanced Text Mining
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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
2014
Briefings in Functional Genomics
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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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