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Ontologies and Knowledge Graphs in Oncology Research

Marta Contreiras Silva, Patrícia Eugénio, Daniel Faria, Catia Pesquita
2022 Cancers  
A holistic view of cancer—which is critical for precision medicine approaches—hinges on integrating a variety of heterogeneous data sources under a cohesive knowledge model, a role which biomedical ontologies  ...  This study reviews the application of ontologies and knowledge graphs in cancer research.  ...  The immense potential of ontologies and the knowledge graph paradigm to support cancer research data management and analysis is increasingly recognized by the oncology research community as an essential  ... 
doi:10.3390/cancers14081906 pmid:35454813 pmcid:PMC9029532 fatcat:t6erzohmvnextkix4infnk7kza

OpenPVSignal: Advancing Information Search, Sharing and Reuse on Pharmacovigilance Signals via FAIR Principles and Semantic Web Technologies

Pantelis Natsiavas, Richard D. Boyce, Marie-Christine Jaulent, Vassilis Koutkias
2018 Frontiers in Pharmacology  
However, this type of communication does not allow for systematic access, discovery and explicit data interlinking and, therefore, does not facilitate automated data sharing and reuse.  ...  OpenPVSignal is built upon widely-accepted semantic models, namely, the provenance ontology (PROV-O), the Micropublications semantic model, the Web Annotation Data Model (WADM), the Ontology of Adverse  ...  Therefore, a dedicated ontology had to be defined, in order to leverage all these information types into one cohesive knowledge representation structure.  ... 
doi:10.3389/fphar.2018.00609 pmid:29997499 pmcid:PMC6028717 fatcat:doms7q6kfzbezojswppiiytfla

Automatic negation detection in narrative pathology reports

Ying Ou, Jon Patrick
2015 Artificial Intelligence in Medicine  
Furthermore, they also facilitate efficient extraction of information for cancer registries, data collection and research purposes.  ...  The goal of this thesis is to extract pertinent information from free-text pathology reports and automatically populate structured reports for three cancer diseases, namely melanoma, colorectal cancer,  ...  Accurate identification of section headings is critical for the detection of section contexts, which is a key step towards further automated or semi-automated clinical language processing.  ... 
doi:10.1016/j.artmed.2015.03.001 pmid:25990897 fatcat:yrijkncnsvht7lonmaqt7uyya4

IMIA LaMB WG related event: Proceedings of 3rd International Conference on Biomedical Ontology, 2012, Graz

Ronald Cornet, Robert Stevens, Melanie Courtot, Trish Whetzel, Janna Hastings, Stefan Schulz, Ludger Jansen
2019 Zenodo  
This conference carried on the tradition of discussing medical ontologies, increasingly used in biology and medicine, and their use in annotation of both clinical and experimental data is now a common  ...  It brings together representatives of all major communities involved in the development and application of ontologies in biomedical research ...  ...  information to a Gene Ontology annotation.  ... 
doi:10.5281/zenodo.3381830 fatcat:pnndilxgzzbujnoqz7pytggtdi

EMBnet.journal 18 Suppl. B

EMBnet Journal
2012 EMBnet journal  
This paper revises and extends the paper "ONCO-i2b2: improve patients selection through case-based information retrieval techniques", by D.  ...  Italy (CNR) and the Polish Academy of Sciences (PAN Acknowledgements This work is partial fulfillment of the research objective of "DM19410 -Laboratorio di Bioinformatica per la Biodiversità Molecolare  ...  In our own work we have used such databases as knowledge sources for the process of semi-automated information extraction.  ... 
doi:10.14806/ej.18.b.592 fatcat:wlwsmbdlfzbjtk7vyhiabdov6q

On the Role of Artificial Intelligence in Medical Imaging of COVID-19

Jannis Born, David Beymer, Deepta Rajan, Adam Coy, Vandana V Mukherjee, Matteo Manica, Prasanth Prasanna, Deddeh Ballah, Michal Guindy, Dorith Shaham, Pallav L Shah, Emmanouil Karteris (+3 others)
2021 Patterns  
We conducted the largest systematic review of the literature addressing the utility of AI in imaging for COVID-19 patient care.  ...  Although a plethora of research articles on AI methods on COVID-19 medical imaging are published, their clinical value remains unclear.  ...  While this can be attributed to an overall gap in knowledge of the long-term effects of COVID-19 and a lack of historical data to enable training on large-scale prognosis data, it is constructive toward  ... 
doi:10.1016/j.patter.2021.100269 pmid:33969323 pmcid:PMC8086827 fatcat:p4xslz325ja55pmznupkcg7h5u

The environment ontology in 2016: bridging domains with increased scope, semantic density, and interoperation

Pier Luigi Buttigieg, Evangelos Pafilis, Suzanna E. Lewis, Mark P. Schildhauer, Ramona L. Walls, Christopher J. Mungall
2016 Journal of Biomedical Semantics  
Further, we applied text-mining approaches to extract habitat information from the Encyclopedia of Life and automatically create experimental habitat classes within ENVO.  ...  The current release version of the ontology, in OWL format, is available at http://purl.obolibrary.org/obo/envo.owl.  ...  Acknowledgements Foremost, we would like to acknowledge the community of contributors who have driven forward ENVO's development.  ... 
doi:10.1186/s13326-016-0097-6 pmid:27664130 pmcid:PMC5035502 fatcat:4gznhpc35nashnqdtvpovs4xza

Vision based hand gesture recognition for human computer interaction: a survey

Siddharth S. Rautaray, Anupam Agrawal
2012 Artificial Intelligence Review  
The main goal of this survey is to provide researchers in the field of gesture based HCI with a summary of progress achieved to date and to help identify areas where further research is needed.  ...  This paper provides an analysis of comparative surveys done in this area.  ...  Such features are skin color, shape, motion and anatomical models of hands.  ... 
doi:10.1007/s10462-012-9356-9 fatcat:qtmmnc5bdfatnjyryw724nvy2i

MIRages: an account of music audio extractors, semantic description and context-awareness, in the three ages of MIR

Perfecto Herrera Boyer, Xavier Serra, Emilia Gómez
2018 Zenodo  
This tesis reports on research carried out and published during the last twenty years on different problems of Music Information Retrieval (MIR).  ...  In the age of semantic descriptors work on describing music with high-level concepts, such as mood, instruments, similarities, cover versions or genres, usually inferred with machine learning from annotated  ...  Bogdanov et al. / Information Processing and Management 49 (2013) 13-33 31  ... 
doi:10.5281/zenodo.2278110 fatcat:uturvyw2gnfzdgtelvtxot3etq

MIRages: an account of music audio extractors, semantic description and context-awareness, in the three ages of MIR

Perfecto Herrera Boyer, Xavier Serra, Emilia Gómez
2018 Zenodo  
This tesis reports on research carried out and published during the last twenty years on different problems of Music Information Retrieval (MIR).  ...  In the age of semantic descriptors work on describing music with high-level concepts, such as mood, instruments, similarities, cover versions or genres, usually inferred with machine learning from annotated  ...  Bogdanov et al. / Information Processing and Management 49 (2013) 13-33 31  ... 
doi:10.5281/zenodo.1882316 fatcat:6yhrlcyexrgyhhwayeau2gu7f4

Scientific Papers

2000 Technology and Health Care  
system of systems interacting among the VHOSs themselves and between the VHOSs and their territory toward a continuous improvement and a continuous improvement of the improvement.  ...  The collected plans can be added as precedent to the knowledge base by a knowledge engineer. This will lead to a dose atlas always showing the state of the art of radiotherapy planning.  ...  From the pool of annotated information objects created by the authors a variety of information offers can be configured.  ... 
doi:10.3233/thc-2000-83-406 fatcat:i2fpmzfem5gtxmxvwzb5hz3p44

Defense Advanced Research Projects Agency (Darpa) Fiscal Year 2015 Budget Estimates

Department Of Defense Comptroller's Office
2014 Zenodo  
The budget request details the proposed investments $80 million to develop new sets of tools for imaging and analytics of neural and synaptic brain activities that will improve diagnosis and care of wounded  ...  DARPA seeks to improve the analysis of large neural data sets by creating interfaces that will allow researchers to generate new models across multiple scales.  ...  FY 2015 -Implemented preliminary algorithms that use domain knowledge to infer implicit information from multiple facts and statements, answer questions, and generate hypotheses in domains of military  ... 
doi:10.5281/zenodo.1215345 fatcat:fjzhmynqjbaafk67q2ckcblj2m

Clinical Practice Guideline Formalization: Translating Clinical Practice Guidelines to Computer Interpretable Guidelines

Wessam Gad El-Rab
2016
The main benefit of a CPG is to improve the quality of care, and the consistency of care.  ...  Nevertheless, integrating CPG knowledge into clinical systems, such as decision support systems, has shown to be more effective.  ...  The motivation of our work is to build a semi-automated information extraction based system that provides the human modellers a mechanism to control the granularity of the clinical knowledge to be extracted  ... 
doi:10.7939/r3pr7n26z fatcat:g6xqreezxfcj7i4fqhntvhlyve

Canadian Conference on Medical Education 2022 abstracts

Heather Hickey
2022 Canadian Medical Education Journal  
Editing has been restricted to some corrections of spelling and style where appropriate.  ...  Key anatomical concepts were highlighted during each exercise and students were cued to recall this information at various points during the session.  ...  Students delivered an oral case presentation, based on information extracted. Self-reflection and feedback from peers and preceptor followed.  ... 
doi:10.36834/cmej.75002 pmid:35572020 pmcid:PMC9099163 fatcat:4rqywmdt6fbjbhwvd4ybihcvm4

Enriching the University ELT Curriculum with Insights from ELF

Franca Poppi
2016 LCM - La Collana / The Series  
The BEI-IBI Project gual Education in Primary School: Aspects of Immersion, CLIL and Bilingual Modules, edited by Daniela Elsner and Jörg-Ulrich Kessler, 1-6. Tübingen: Gunter Narr Verlag.  ...  Stage 1: Knowledge Retrieval / Organisation This stage involves recalling information, observing reality in the field of knowledge and finding/extracting information in/from texts.  ...  ' mental linguistic processes: e.g. logical links of cohesion, speed of translation, chronology of information heard, or memory lapses (terminology or chunks of information).  ... 
doi:10.7359/791-2016-popp fatcat:trj3vywsmvc65djpe5dr5tzhga
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