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Overview of the BioCreative VI Precision Medicine Track: mining protein interactions and mutations for precision medicine

Rezarta Islamaj Doğan, Sun Kim, Andrew Chatr-aryamontri, Chih-Hsuan Wei, Donald C Comeau, Rui Antunes, Sérgio Matos, Qingyu Chen, Aparna Elangovan, Nagesh C Panyam, Karin Verspoor, Hongfang Liu (+15 others)
2019 Database: The Journal of Biological Databases and Curation  
The goal of BioCreative VI Precision Medicine Track was to extract this particular type of information and was organized in two tasks: (i) document triage task, focused on identifying scientific literature  ...  Given the level of participation and the individual team results we find the precision medicine track to be successful in engaging the text-mining research community.  ...  Acknowledgements We thank the BioGRID database curators Rose Oughtred, Jennifer Rust, Christie S. Chang and Lorrie Boucher for annotating the evaluation data set. Conflict of interest. None declared.  ... 
doi:10.1093/database/bay147 pmid:30689846 pmcid:PMC6348314 fatcat:jvsf4xwr7jbbnb75d3oqczrjrq

Biomedical document triage using a hierarchical attention-based capsule network

Jian Wang, Mengying Li, Qishuai Diao, Hongfei Lin, Zhihao Yang, YiJia Zhang
2020 BMC Bioinformatics  
Biomedical document triage is the foundation of biomedical information extraction, which is important to precision medicine.  ...  The proposed model effectively employs hierarchical attention mechanism and capsule networks to capture valuable features across sentences and construct a final latent feature representation for a document  ...  Ethics approval and consent to participate No ethics approval was required for the study. Consent for publication Not applicable. Published: 17 September 2020  ... 
doi:10.1186/s12859-020-03673-5 pmid:32938366 pmcid:PMC7495737 fatcat:hc3stf5gvvg6pob4vu6mxha3xy

Hierarchical bi-directional attention-based RNNs for supporting document classification on protein–protein interactions affected by genetic mutations

Aris Fergadis, Christos Baziotis, Dimitris Pappas, Haris Papageorgiou, Alexandros Potamianos
2018 Database: The Journal of Biological Databases and Curation  
With this system we participated in the Document Triage Task of the BioCreative VI Precision Medicine Track and we achieved 0.6289 Precision, 0.7656 V C The Author(s)  ...  Hierarchical bi-directional attention-based RNNs for supporting document classification on protein-protein interactions affected by genetic mutations.  ...  Acknowledgements We acknowledge support of this work by the project "Computational Science and Technologies: Data, Content and Interaction" (MIS 5002437) which is implemented under the Action "Reinforcement  ... 
doi:10.1093/database/bay076 pmid:30137284 pmcid:PMC6105093 fatcat:lmoi72c25ncljomrro64dkkhii

An end-to-end deep learning architecture for extracting protein–protein interactions affected by genetic mutations

Tung Tran, Ramakanth Kavuluru
2018 Database: The Journal of Biological Databases and Curation  
The BioCreative VI Track IV (mining protein interactions and mutations for precision medicine) challenge was organized in 2017 with the goal of applying biomedical text mining methods to support advancements  ...  As part of the challenge, a new dataset was introduced for the purpose of building a supervised relation extraction model capable of taking a test article and returning a list of interacting protein pairs  ...  Funding National Library of Medicine (grant R21LM012274) and NVIDIA Corporation with the donation of the Titan X Pascal GPU.  ... 
doi:10.1093/database/bay092 pmid:30239680 pmcid:PMC6146129 fatcat:rbqd5xhkivfkbgnzprnxf3vhbm

EMBnet.journal 19 Suppl. B

EMBnet Journal
2013 EMBnet journal  
Acknowledgements This work was supported by the Innovative Medicines Initiative Joint Undertaking under grant agreement n° 115191 for Open PHACTS, resources of which are composed of financial contribution  ...  Acknowledgements The Project Grant [TIN2011-25840) (Spanish Ministry of Education and Science) and P11-TIC-7529 (Innovation, Science and Enterprise Ministry of the regional government of the Junta de Andalucía  ...  Ontology-based annotation and querying of protein interaction data Protein-protein interaction (PPI) databases store interactions among proteins and offer to the user the possibility to retrieve data of  ... 
doi:10.14806/ej.19.b.749 fatcat:h6kgq2g4ljbn7jrq6xpkbh2eie

Overview of the Interactive Task in BioCreative V

Qinghua Wang, Fabio Rinaldi, Et Al
2015
The BioCreative Interactive task (IAT) is a track designed for exploring user-system interactions, promoting development of useful text mining tools, and providing a communication channel between the biocuration  ...  The BioCreative Interactive task (IAT) is a track designed for exploring user-system interactions, promoting development of useful text mining tools, and providing a communication channel between the biocuration  ...  BioCreative is partially funded by NIH/NIGMS R13-GM109648-01A1; DOE: DE-SC0010838; NIH Intramural Research Program, National Library of Medicine.  ... 
doi:10.5167/uzh-116471 fatcat:elfvz7vs3zcx3obt33nak26rii

BIAS: Transparent reporting of biomedical image analysis challenges [article]

Lena Maier-Hein, Annika Reinke, Michal Kozubek, Anne L. Martel, Tal Arbel, Matthias Eisenmann, Allan Hanbuary, Pierre Jannin, Henning Müller, Sinan Onogur, Julio Saez-Rodriguez, Bram van Ginneken (+2 others)
2020 arXiv   pre-print
To address the discrepancy between the impact of challenges and the quality (control), the Biomedical I mage Analysis ChallengeS (BIAS) initiative developed a set of recommendations for the reporting of  ...  The purpose of the checklist is to standardize and facilitate the review process and raise interpretability and reproducibility of challenge results by making relevant information explicit.  ...  Overview of the Bio Creative VI precision medicine track: mining protein interactions and mutations for precision medicine. Database (Oxford), 2019, 2019. doi: 10.1038/10.1093/database/bay147.  ... 
arXiv:1910.04071v5 fatcat:v3ar4ijs6vfz7ep2wgabzpobli

An overview of the BIOASQ large-scale biomedical semantic indexing and question answering competition

George Tsatsaronis, Georgios Balikas, Prodromos Malakasiotis, Ioannis Partalas, Matthias Zschunke, Michael R Alvers, Dirk Weissenborn, Anastasia Krithara, Sergios Petridis, Dimitris Polychronopoulos, Yannis Almirantis, John Pavlopoulos (+10 others)
2015 BMC Bioinformatics  
Acknowledgements The research leading to these results has received funding from the European  ...  Similar biomedical information extraction and data mining challenges have been (and continue to be) organised in the context of BioCreative, with a recent additional emphasis on helping curators of biomedical  ...  The research on targets play a crucial role in turn for the study of sensitivity, selectivity, mutations of genes and biological functions that are connected to the disease.  ... 
doi:10.1186/s12859-015-0564-6 pmid:25925131 pmcid:PMC4450488 fatcat:u5enfjjos5gv5k3wkjxxa5ebry

Extracting information for biology [article]

Jasmin Saric, Universität Stuttgart, Universität Stuttgart
2006
The present work is thematically divided into three parts. The first part is about text mining in the life sciences and is subdivided in two subsections.  ...  As a consequence these results accelerate the pace of research and development in the field of biomedicine.  ...  The genome, the gene and its parts Genome: The genome consists of the complete genetic information of an organism. This means the total set of all genes of an organism (see Lackie and Dow (2000) ).  ... 
doi:10.18419/opus-2585 fatcat:6z25jb7vpjhcjihxayyo6p7y7i

DEVELOPMENT OF A HEPATITIS C VIRUS KNOWLEDGEBASE WITH COMPUTATIONAL PREDICTION OF FUNCTIONAL HYPOTHESIS OF THERAPEUTIC RELEVANCE KOJO KWOFIE SAMUEL

Vladimir Bajic, Alan Christoffels
2011 unpublished
IDs of journal articles reporting the interactions, annotated protein interaction IDs from external databases, and via "string searches".  ...  The multitudes of metadata originating from HCV clinical trials as well as low and high-throughput experiments embedded in text corpora can be mined as data sources for the implementation of HCV-specific  ...  interaction, for example the names of the interacting protein partners and the detection methods used to infer the interactions.  ... 
fatcat:dxh5kptlxfdojbqc7dngtunu4a

DEVELOPMENT OF A HEPATITIS C VIRUS KNOWLEDGEBASE WITH COMPUTATIONAL PREDICTION OF FUNCTIONAL HYPOTHESIS OF THERAPEUTIC RELEVANCE KOJO KWOFIE SAMUEL

Vladimir Bajic, Alan Christoffels
2011 unpublished
IDs of journal articles reporting the interactions, annotated protein interaction IDs from external databases, and via "string searches".  ...  The multitudes of metadata originating from HCV clinical trials as well as low and high-throughput experiments embedded in text corpora can be mined as data sources for the implementation of HCV-specific  ...  interaction, for example the names of the interacting protein partners and the detection methods used to infer the interactions.  ... 
fatcat:khbuvbkjujbk3dvhoinrnwxqq4

Personalized Medicine through Automatic Extraction of Information from Medical Texts

Oana Magdalena Frunza, Université D'Ottawa / University Of Ottawa, Université D'Ottawa / University Of Ottawa
2012
The challenge that comes with accessing and using such vast and diverse sources of data stands in the ability to distil and extract reliable and relevant information.  ...  From the numerous research problems that need to be answered when implementing personalized medicine, the scope of this thesis is restricted to four, as follows: 1.  ...  Acknowledgements To my entire family and to all the wonderful people that offered their support and encouraged me throughout this dream come true journey.  ... 
doi:10.20381/ruor-5599 fatcat:djpbv4eadjaqznfraykuw62zjq

Knowledge-driven entity recognition and disambiguation in biomedical text [article]

Amy Siu, Universität Des Saarlandes, Universität Des Saarlandes
2017
The first contribution is a fast dictionary lookup method for entity recognition that maximizes throughput while balancing the loss of precision and recall.  ...  Entity recognition and disambiguation (ERD) for the biomedical domain are notoriously difficult problems due to the variety of entities and their often long names in many variations.  ...  and gene mutations, and their interactions such as protein pathways.  ... 
doi:10.22028/d291-26790 fatcat:twz6ditmfzgldghwk6cia3gle4

Towards a natural language processing pipeline and search engine for biomedical associations derived from scientific literature

Dieter Galea, Kirill Veselkov, Zoltan Takats, Imperial College London
2020
Beyond ML methods, this work presents a number of dictionarybased approaches and graph-based dictionaries for more than 13 sources covering metabolites, genes/proteins, species, chemicals, toxins, drugs  ...  Starting by optimizing how biomedical language is represented in machine learning (ML) models, state-of-the-art representations are obtained and subsequently used in downstream tasks, including bioentity  ...  protein-1% for chemical-disease interactions from the CID corpus (compared to the original BioCreative V shared task highest performer reporting 57.03%).  ... 
doi:10.25560/83109 fatcat:f4ntlogk6retxctpj3hx357gvm