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Capturing the Relationship between Evolving Biomedical Concepts via Background Knowledge

Cédric Pruski, Júlio Cesar dos Reis, Marcos Da Silveira
2016 Workshop on Semantic Web Applications and Tools for Life Sciences  
The approach uses ontological properties and mappings between ontologies from online repositories to deduce the nature of the relationship between a concept and its successive version.  ...  This article proposes exploiting domain-specific external source of knowledge to characterize the evolution of concepts in dynamic ontologies.  ...  Acknowledgements This work is supported by the National Research Fund (FNR) of Luxembourg and São Paulo Research Foundation (FAPESP) (Grant #2014/14890-0).  ... 
dblp:conf/swat4ls/PruskiRS16 fatcat:pcam6nnh6vgepbnx6f7xb2kwra

Semantic Similarity-Driven Decision Support in the Skeletal Dysplasia Domain [chapter]

Razan Paul, Tudor Groza, Andreas Zankl, Jane Hunter
2012 Lecture Notes in Computer Science  
Grounding clinical and radiographic findings in concepts defined by a biomedical ontology, e.g., the Human Phenotype Ontology, enables us to compute semantic similarity between them.  ...  Biomedical ontologies have become a mainstream topic in medical research. They represent important sources of evolved knowledge that may be automatically integrated in decision support methods.  ...  Acknowledgments The work presented in this paper is supported by the Australian Research Council (ARC) under the Discovery Early Career Researcher Award (DECRA) -DE120100508 and the Linkage grant SKELETOME  ... 
doi:10.1007/978-3-642-35173-0_11 fatcat:ge427radlrezzf6q2khpdak7c4

Improving Literature-Based Discovery with Advanced Text Mining [chapter]

Anna Korhonen, Yufan Guo, Simon Baker, Meliha Yetisgen-Yildiz, Ulla Stenius, Masashi Narita, Pietro Liò
2015 Lecture Notes in Computer Science  
Based on fairly shallow methods, current LBD captures only some of the information available in literature.  ...  with science, in particular when combined with sophisticated, state-of-the-art knowledge discovery techniques.  ...  Acknowledgments We would like to thank the Royal Society (UK) and the Swedish Research Council (Sweden) for financial support.  ... 
doi:10.1007/978-3-319-24462-4_8 fatcat:o2xgldznlndstbdei6kbiytiqu

The Bone Dysplasia Ontology: integrating genotype and phenotype information in the skeletal dysplasia domain

Tudor Groza, Jane Hunter, Andreas Zankl
2012 BMC Bioinformatics  
It enables links between individual cases and publicly available genotype and phenotype resources based on a community-driven curation process that ensures a shared conceptualisation of the domain knowledge  ...  Conclusions: The Bone Dysplasia Ontology represents the most comprehensive structured knowledge source for the skeletal dysplasias domain.  ...  Especial thanks also to Tania Tudorache, Timothy Redmond and Matthew Horridge for the extremely useful feed-back on the logical correctness of the class axioms and of the grounding in BFO.  ... 
doi:10.1186/1471-2105-13-50 pmid:22449239 pmcid:PMC3338382 fatcat:flu5hsohtvahhmd5kwfec4es6u

Strategic Health Information Management and Forecast: The Birdwatching Approach [chapter]

Arash Shaban-Nejad, Volker Haarslev
2010 Lecture Notes in Computer Science  
To facilitate communication and the exchange of information between patients, nurses, lab technicians, health insurers, physicians, policy makers, and existing knowledge-based systems, a set of shared  ...  When the datasets and their conveyed knowledge are changed, the ontological structure is altered accordingly.  ...  e-health systems [21] and analyzing the evolutionary relationships between fungal species [22] .  ... 
doi:10.1007/978-3-642-16696-9_49 fatcat:cpfimy5pebdzpe4xp3rbcqba5e

Semantic and Time-Dependent Expertise Profiling Models in Community-Driven Knowledge Curation Platforms

Hasti Ziaimatin, Tudor Groza, Jane Hunter
2013 Future Internet  
Hence, Expertise Profiling is presented with major challenges in the context of dynamic and evolving knowledge.  ...  In our previous study, we proposed a comprehensive, domain-independent model for expertise profiling in the context of evolving knowledge.  ...  Acknowledgments This research is funded by the Australian Research Council (ARC) under the Linkage grant SKELETOME-LP100100156 and the Discovery Early Career Researcher Award (DECRA)-DE120100508.  ... 
doi:10.3390/fi5040490 fatcat:tutrangcofhvff2me4j3txzfqi

State of the art and open challenges in community-driven knowledge curation

Tudor Groza, Tania Tudorache, Michel Dumontier
2013 Journal of Biomedical Informatics  
With the adoption of ontologies, especially by the broad biomedical community, the further development of ontologies and knowledge bases has evolved into a community-driven process [3] .  ...  In addition to acting as an ontology repository, BioPortal allows users in the community to create mappings between concepts defined in different ontologies and to attach notes to them.  ... 
doi:10.1016/j.jbi.2012.11.007 pmid:23219718 fatcat:odppdhmlkrgqfk67zhphysoa5m

Capturing domain knowledge from multiple sources: the rare bone disorders use case

Tudor Groza, Tania Tudorache, Peter N Robinson, Andreas Zankl
2015 Journal of Biomedical Semantics  
In order to support lightweight query and integration, the knowledge captured by RBDO has also been made available as a SPARQL Endpoint at http://bio-lark. org/se_skeldys.html.  ...  perspectives on the same knowledge.  ...  Acknowledgements This research is funded by the Australian Research Council (ARC) under the Discovery Early Career Researcher Award (DECRA) -DE120100508. Author details  ... 
doi:10.1186/s13326-015-0008-2 pmid:25926964 pmcid:PMC4414390 fatcat:pkfol7iopjbqfiydyb7kikrdqa

An integrative knowledge graph for rare diseases, derived from the Genetic and Rare Diseases Information Center (GARD)

Qian Zhu, Dac-Trung Nguyen, Ivan Grishagin, Noel Southall, Eric Sid, Anne Pariser
2020 Journal of Biomedical Semantics  
providers of consumer health information, such as GARD, that may struggle with the needs of maintaining knowledge reliant on an evolving and growing evidence-base.  ...  Background The Genetic and Rare Diseases (GARD) Information Center was established by the National Institutes of Health (NIH) to provide freely accessible consumer health information on over 6500 genetic  ...  Availability of data and materials All data can be accessed via https://disease.ncats.io Ethics approval and consent to participate Not applicable. Consent for publication Not applicable.  ... 
doi:10.1186/s13326-020-00232-y pmid:33183351 fatcat:rkdvfkksd5g7td3m6me3hh6g6y

Ontologies in Biological Data Visualization

Sheelagh Carpendale, Min Chen, Daniel Evanko, Nils Gehlenborg, Carsten Gorg, Larry Hunter, Francis Rowland, Margaret-Anne Storey, Hendrik Strobelt
2014 IEEE Computer Graphics and Applications  
a relation between two concepts.  ...  Ontologies in Biological Data Visualization I n computer science, an ontology is essentially a graph-based knowledge representation in which each node corresponds to a concept and each edge specifi es  ...  For more information, see the "Exploring On tologies in Biological Visualization" sidebar.  ... 
doi:10.1109/mcg.2014.33 pmid:24808195 fatcat:mkgfjlp4k5hodfbffq36hwjnsi

Contexts and contradictions: a roadmap for computational drug repurposing with knowledge inference

Daniel N Sosa, Russ B Altman
2022 Briefings in Bioinformatics  
KGs derived from biomedical literature are semantically rich and up-to-date representations of scientific knowledge.  ...  The task of drug repurposing hypothesis generation is well-posed as a link prediction problem in a knowledge graph (KG) of interacting of drugs, proteins, genes and disease phenotypes.  ...  The most commonly used network model for knowledge is the knowledge graph (KG). KGs are flexible frameworks for storing information about relationships between entities.  ... 
doi:10.1093/bib/bbac268 pmid:35817308 pmcid:PMC9294417 fatcat:c6z5tlj2kbeafjy4ltzzksq6va

GOMMA: a component-based infrastructure for managing and analyzing life science ontologies and their evolution

Toralf Kirsten, Anika Gross, Michael Hartung, Erhard Rahm
2011 Journal of Biomedical Semantics  
GOMMA complements OnEX by providing functionalities to manage various versions of mappings between two ontologies and allows combining different match approaches.  ...  These components are used by analysis tools, such as the Ontology Evolution Explorer (OnEX) and the detection of unstable ontology regions.  ...  Acknowledgements We thank the anonymous reviewers for their valuable and constructive comments.  ... 
doi:10.1186/2041-1480-2-6 pmid:21914205 pmcid:PMC3198872 fatcat:7ol5dkzicbah3gefucpvifob6m

User-centered semantic harmonization: A case study

Chunhua Weng, John H. Gennari, Douglas B. Fridsma
2007 Journal of Biomedical Informatics  
In the context of the Cancer Biomedical Informatics Grid program, the Biomedical Research Integrated Domain Group (BRIDG) has been making an ambitious effort to harmonize existing information models for  ...  Semantic interoperability is one of the great challenges in biomedical informatics.  ...  The authors express their great appreciation to the two reviewers for their constructive and insightful review comments. The manuscript has benefited tremendously from the reviews.  ... 
doi:10.1016/j.jbi.2007.03.004 pmid:17452021 fatcat:toyojd6ggvgbbpl4zc3wgj2pwe

What is biomedical informatics?

Elmer V. Bernstam, Jack W. Smith, Todd R. Johnson
2010 Journal of Biomedical Informatics  
The emphasis on data plus meaning also suggests that biomedical informatics problems tend to be difficult when they deal with concepts that are hard to capture using formal, computational definitions.  ...  Biomedical informatics is the science of information as applied to or studied in the context of biomedicine.  ...  Acknowledgments The authors thank Drs. M. Sriram Iyengar and Dean F. Sittig for valuable discussions regarding the ideas expressed in this manuscript.  ... 
doi:10.1016/j.jbi.2009.08.006 pmid:19683067 pmcid:PMC2814957 fatcat:mbua4m25b5h4pozjaopaqsdppy

Structured reviews for data and knowledge-driven research

2020 Database: The Journal of Biological Databases and Curation  
Acknowledgements The authors thank Dr Mitali Tambe  ...  Knowledge graphs are computer-readable semantic representations of relational information, where concepts are encoded as nodes, and the relationships between those concepts are represented as edges.  ...  Finally, we again used the Monarch database to retrieve pairwise relationships between network nodes.  ... 
doi:10.1093/database/baaa015 pmid:32283553 pmcid:PMC7153956 fatcat:sk3sogsf2zdktau7d4d5hmjs6u
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