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Prototype semantic infrastructure for automated small molecule classification and annotation in lipidomics

Leonid L Chepelev, Alexandre Riazanov, Alexandre Kouznetsov, Hong Low, Michel Dumontier, Christopher JO Baker
2011 BMC Bioinformatics  
Firstly, a structural annotation service detects and enumerates relevant functional groups for a specified chemical structure.  ...  Since chemical function is often closely linked to structure, accurate structure-based classification and annotation of chemical entities is imperative to understanding their functionality.  ...  Acknowledgements This research was funded in part by the New Brunswick Innovation Foundation, New Brunswick, Canada; NSERC, Discovery Grant Program, Canada; NSERC CGS for LLC; and the CANARIE NEP-2 Program  ... 
doi:10.1186/1471-2105-12-303 pmid:21791100 pmcid:PMC3163564 fatcat:gwbmlbtxyja63fsa26hpfesuqi

A METHODOLOGY TO MIGRATE THE GENE ONTOLOGY TO A DESCRIPTION LOGIC ENVIRONMENT USING DAML+OIL

C. J. WROE, R. STEVENS, C. A. GOBLE, M. ASHBURNER
2002 Biocomputing 2003  
Each stage provides a step level increase in formal explicit semantic content with a view to supporting validation, extension and multiple classification of the Gene Ontology.  ...  The Gene Ontology Next Generation Project (GONG) is developing a staged methodology to evolve the current representation of the Gene Ontology into DAML+OIL in order to take advantage of the richer formal  ...  We would like to thank Midori Harris and Jane Lomax of the GO Consortium Editorial Team for their advice and guidance.  ... 
doi:10.1142/9789812776303_0058 fatcat:gjsw2sveebaebbt3fabwy7kz44

The Plant Ontology™Consortium and Plant Ontologies

The Plant Ontology Consortium
2002 Comparative and Functional Genomics  
Various trait ontologies (agronomic traits, mutant phenotypes, phenotypes, traits, and QTL) and plant ontologies (plant development, anatomy [incl. morphology]) for several taxa (Arabidopsis, maize/corn  ...  The goal of the Plant Ontology™Consortium is to produce structured controlled vocabularies, arranged in ontologies, that can be applied to plant-based database information even as knowledge of the biology  ...  The Q comes from the Phenotype and Trait Ontology (PATO) whereas the E comes from Plant Ontology (PO) when it is related to plant structures, Gene Ontology (GO) for subcellular components, Chemical Entities  ... 
doi:10.1002/cfg.154 pmid:18628842 pmcid:PMC2447263 fatcat:kpwbd7nmxjfyldwpgmvhz5pfcu

OOPS: The Ontology of Plant Stress, A Semi-Automated Standardization Methodology

Austin Meier, Marie-Angélique Laporte, Justin Elser, Laurel Cooper, Justin Preece, Pankaj Jaiswal, Jorrit H. Poelen
2018 International Conference on Biomedical Ontology  
This paper presents a semi-automated method to define and label plant stresses using a combination of web scraping and ontology design patterns.  ...  Standardizing the definitions and linking plant stress with established hierarchies leverages previous work of developed knowledge bases such as taxonomic classifications and other ontologies.  ...  That is part of the benefits of using these automated tools for developing an ontology; when issues arise, or additional parental classes are needed to further group stress, they can simply be added to  ... 
dblp:conf/icbo/MeierLECPJP18 fatcat:7mfulpxtkrc7fhznlwwu3hevoe

Structure-based classification and ontology in chemistry

Janna Hastings, Despoina Magka, Colin Batchelor, Lian Duan, Robert Stevens, Marcus Ennis, Christoph Steinbeck
2012 Journal of Cheminformatics  
Ontologies encode expert domain knowledge in a hierarchically organised machine-processable format. One such ontology for the chemical domain is ChEBI.  ...  An example of a structure-based class is 'pentacyclic compound' (compounds containing five-ring structures), while an example of a role-based class is 'analgesic', since many different chemicals can act  ...  We would also like to thank Evan Bolton for helpful input and stimulating discussions.  ... 
doi:10.1186/1758-2946-4-8 pmid:22480202 pmcid:PMC3361486 fatcat:54c73jnc6jgmjlbdob2vzyupi4

Semantic Web integration of Cheminformatics resources with the SADI framework

Leonid L Chepelev, Michel Dumontier
2011 Journal of Cheminformatics  
We conclude that envelopment of chemical computational resources as SADI SWS facilitates interdisciplinary research by enabling the definition of computational problems in terms of ontologies and formal  ...  Since each of these services has formal ontology-defined input and output classes, and each service consumes and produces RDF graphs, clients can automatically reason about the services and available reference  ...  Acknowledgements This research was funded in part by NSERC CGS for LLC and the CANARIE NEP-2 Program for the C-BRASS project. We would like to thank Dr.  ... 
doi:10.1186/1758-2946-3-16 pmid:21575200 pmcid:PMC3114010 fatcat:3oskwsqegje6fgrfongrxirk64

MicrO: an ontology of phenotypic and metabolic characters, assays, and culture media found in prokaryotic taxonomic descriptions

Carrine E. Blank, Hong Cui, Lisa R. Moore, Ramona L. Walls
2016 Journal of Biomedical Semantics  
the Gene Ontology (GO), the Phenotypic Quality Ontology (PATO), and the Chemical Entities of Biological Interest (ChEBI).  ...  MicrO has been integrated into the OBO Foundry Library (http://www.obofoundry.org/ontology/micro.html), so that other ontologies can borrow and re-use classes.  ...  at ChEBI for assistance in the incorporation of microbialspecific chemical terms and synonyms into ChEBI.  ... 
doi:10.1186/s13326-016-0060-6 pmid:27076900 pmcid:PMC4830071 fatcat:hb4pncif7rhmlcciev6plkibtq

The Chemical Information Ontology: Provenance and Disambiguation for Chemical Data on the Biological Semantic Web

Janna Hastings, Leonid Chepelev, Egon Willighagen, Nico Adams, Christoph Steinbeck, Michel Dumontier, Franca Fraternali
2011 PLoS ONE  
Ontologies enable the definition, classification, and support for querying objects in a particular domain, enabling intelligent computer applications to be built which support the work of scientists both  ...  Here, we describe our work in developing an ontology of chemical information entities, with a primary focus on data-driven research and the integration of calculated properties (descriptors) of chemical  ...  Acknowledgments The authors would like to thank Colin Batchelor, Andrew Dalke, Ola Spjuth, Peter Murray-Rust, Alan Ruttenberg and Robert Hoehndorf for comments on the ideas contained in this manuscript  ... 
doi:10.1371/journal.pone.0025513 pmid:21991315 pmcid:PMC3184996 fatcat:sm3qaz2fcja2pkwrdiby3u2kb4

Desiderata for domain reference ontologies in biomedicine

Anita Burgun
2006 Journal of Biomedical Informatics  
The purpose of this paper is to explore how two domain reference ontologies-the FMA and the Chemical Entities of Biological Interest (ChEBI) ontology, can be used (i) to align existing terminologies, (  ...  While a number of groups and communities have investigated general requirements for ontology design and desiderata for controlled medical vocabularies, we are focusing on application purposes.  ...  Acknowledgment The author thanks Olivier Bodenreider and Olivier Dameron for providing valuable insight.  ... 
doi:10.1016/j.jbi.2005.09.002 pmid:16266830 fatcat:rs266b2rh5bo5dvyccqzrgkcrq

Semantic input/output matching for waste processing in industrial symbiosis

Nikolaos Trokanas, Franjo Cecelja, Tara Raafat
2014 Computers and Chemical Engineering  
Chemicals Any material with a definite chemical composition. ChemicalElements Classification of all chemical elements.  ...  Figure 2 Domain Ontology Structure The IS matching process ontology ( Figure 1 ) incorporates all concepts relevant to the process of synergy identification, in particular algorithms and mathematical  ...  for the integration of tacit knowledge about the use of resources in different industries. canUse Inverse relation of hasApplicationIn, used for intelligent recommendations. hasQuantityType Links resources  ... 
doi:10.1016/j.compchemeng.2014.02.010 fatcat:736u7gcadfebhp3ylceeo533ee

A review of auditing methods applied to the content of controlled biomedical terminologies

Xinxin Zhu, Jung-Wei Fan, David M. Baorto, Chunhua Weng, James J. Cimino
2009 Journal of Biomedical Informatics  
We have performed an extensive literature review to identify published descriptions of these methods and have created a framework for characterizing them.  ...  Although controlled biomedical terminologies have been with us for centuries, it is only in the last couple of decades that close attention has been paid to the quality of these terminologies.  ...  Cimino was supported in part by funds from the intramural research program at the National Institutes of Health (NIH) Clinical Center and the National Library of Medicine (NLM).  ... 
doi:10.1016/j.jbi.2009.03.003 pmid:19285571 pmcid:PMC3505841 fatcat:afrfbtbxqnal5o5bxzbvquw6gm

Ontologies in Medicinal Chemistry: Current Status and Future Challenges

Asuncion Gomez-Perez, Marcos Martinez-Romero, Alejandro Rodriguez-Gonzalez, Guillermo Vazquez, Jose M. Vazquez-Naya
2013 Current Topics in Medicinal Chemistry  
In medicinal chemistry, multiple ontologies have been developed during the last years which contain knowledge about chemical compounds and processes of synthesis of pharmaceutical products.  ...  This article reviews the principal standards and ontologies in medicinal chemistry, analyzes their main applications and suggests future directions.  ...  Fig. 4 shows the subclasses provided by CHEMINF ontology for the class "chemical descriptor".  ... 
doi:10.2174/1568026611313050003 pmid:23548021 fatcat:6hyje3smivfldn2svxvnhtsw6i

Geospatial Resource Description Framework (GRDF) and security constructs

Ashraful Alam, Laitfur Khan, Bhavani Thuraisingham
2011 Computer Standards & Interfaces  
The Semantic Web enables an automated, ontology based information aggregation mechanism.  ...  broad, semantics-aware and expressive language for geospatial domain.  ...  INTRODUCTION Semantic Web enables an automated, ontology based information aggregation mechanism.  ... 
doi:10.1016/j.csi.2010.01.002 fatcat:66j6cgp425eidissqpmai5ey5y

Geospatial Resource Description Framework (GRDF) and security constructs

Ashraful Alam, Latifur Khan, Bhavani Thuraisingham
2008 2008 IEEE 24th International Conference on Data Engineering Workshop  
The Semantic Web enables an automated, ontology based information aggregation mechanism.  ...  broad, semantics-aware and expressive language for geospatial domain.  ...  INTRODUCTION Semantic Web enables an automated, ontology based information aggregation mechanism.  ... 
doi:10.1109/icdew.2008.4498363 dblp:conf/icde/AlamKT08 fatcat:fwjhnhv3zjeudlkzkmdotjzqoy

The Porifera Ontology (PORO): enhancing sponge systematics with an anatomy ontology

Robert W Thacker, Maria Díaz, Adeline Kerner, Régine Vignes-Lebbe, Erik Segerdell, Melissa A Haendel, Christopher J Mungall
2014 Journal of Biomedical Semantics  
Results: The Porifera Ontology is intended as a standardized coding system for sponge anatomical features currently used in systematics.  ...  to perform character mapping across the major clades of sponges to better understand the evolution of morphological features.  ...  Acknowledgements We acknowledge the support of the Phenotype Ontology Research Coordination Network (NSF-DEB-0956049) for supporting ES and organizing the meetings that brought the developers together.  ... 
doi:10.1186/2041-1480-5-39 pmid:25276334 pmcid:PMC4177528 fatcat:yxjfwfuk5beghginlusiyiaj7y
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