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Combining Text Mining and Computational Chemistry Visually and Semantically Enriches Analytical Chemistry Literature Searches

Magnus Palmblad
2019 Analytical Chemistry  
The method is realized in shareable scientific workflows using only freely available data, services, and software that scale to millions of publications and named chemical entities in the literature.  ...  The method is demonstrated on comparisons of analytical-chemistry techniques and semantically enriched searches for proteins and their activities, but it may also be of general utility in experimental  ...  These annotations can be accessed programmatically from Europe PMC via the recently introduced Annotations API, which is similar to the web services used to access bibliographic information. 1 These  ... 
doi:10.1021/acs.analchem.8b05818 pmid:30835438 pmcid:PMC6448173 fatcat:bkantbxvlbaivf2oigbshzk634

Use of semantic technologies for the development of a dynamic trajectories generator in a Semantic Chemistry eLearning platform [article]

Richard Huber, Kirsten Hantelmann, Alexandru Todor, Sebastian Krebs, Ralf Heese, Adrian Paschke
2010 arXiv   pre-print
to the semantic profiles of the users.  ...  With up to 350.000 users per month the platform is the most frequently used scientific educational service in the German spoken Internet.  ...  The core part is StructWSF, a web service framework that provides access to a triplestore containing the eLearning data as well as allows for efficient faceted and fulltext search.  ... 
arXiv:1012.1646v1 fatcat:hvrykexzcvgr3pzzlfzvrytcvu

ChEBI in 2016: Improved services and an expanding collection of metabolites

Janna Hastings, Gareth Owen, Adriano Dekker, Marcus Ennis, Namrata Kale, Venkatesh Muthukrishnan, Steve Turner, Neil Swainston, Pedro Mendes, Christoph Steinbeck
2015 Nucleic Acids Research  
All content is freely available and can be accessed online at http://www. ebi.ac.uk/chebi. In this update paper, we describe recent improvements and additions to the ChEBI offering.  ...  ChEBI is a database and ontology containing information about chemical entities of biological interest.  ...  It is also used as a knowledge base for text and data mining purposes (7, 8) , and as the chemistry component of several ontologies including the popular Gene Ontology (9) .  ... 
doi:10.1093/nar/gkv1031 pmid:26467479 pmcid:PMC4702775 fatcat:wgoibg3ytza3zanpj5eww4sheq

Applying the Semantic Web to Computational Chemistry

Neil S. Ostlund, Mirek Sopek
2013 Workshop on Semantic Web Applications and Tools for Life Sciences  
Chemical Semantics is a new start-up devoted to bringing the Semantic Web to computational chemistry, with a future goal to cover chemical results of other kinds, including experimental.  ...  The semantics of computational chemistry oriented RDF data is defined by an ontology identified as "GC" (Gainesville Core).  ...  In the prototype version we have used: ChemSpider, Chebi and NIST web resources to illustrate data federation. The discoveries are made with the help of Inchi identifiers.  ... 
dblp:conf/swat4ls/OstlundS13 fatcat:6t6gc2fiojgwrnerrcr25t77mm

Interdisciplinary IoT and Emotion Knowledge Graph-Based Recommendation System to Boost Mental Health

Amelie Gyrard, Karima Boudaoud
2022 Applied Sciences  
To organize the knowledge, we employ technologies such as Artificial Intelligence with Knowledge Graphs and Semantic Reasoning.  ...  The set of ontology codes shared online can be semi-automatically processed; if not available, the scientific publications describing the emotion ontologies are semi-automatically processed with Natural  ...  Sample Availability: See Table 6 for the set of URLs, such as the emotion ontology, online demonstrators (ontology catalog, rule discovery, and full scenarios).  ... 
doi:10.3390/app12199712 fatcat:krxizgrjmbcrlgtboqzd3sa36a

The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013

Janna Hastings, Paula de Matos, Adriano Dekker, Marcus Ennis, Bhavana Harsha, Namrata Kale, Venkatesh Muthukrishnan, Gareth Owen, Steve Turner, Mark Williams, Christoph Steinbeck
2012 Nucleic Acids Research  
Finally, our website and web services have had several enhancements, most notably the provision of a dynamic new interactive graph-based ontology visualization.  ...  Over the past few years, ChEBI has continued to grow steadily in content, and has added several new features.  ...  ACKNOWLEDGEMENTS The authors are extremely grateful for the continuing contributions from many members of the scientific community to the success of ChEBI.  ... 
doi:10.1093/nar/gks1146 pmid:23180789 pmcid:PMC3531142 fatcat:7btmvq3i3zgtrcukjm7pkb35ii

Automated tagging of environmental data using a novel SKOS formatted environmental thesaurus

Daniel G. Wright, Kathryn A. Harrison, John Watkins
2014 Earth Science Informatics  
for better management and access to environmental data.  ...  By employing a Linked Open Data approach, we 35 anticipate that Web-based tools will be able to use concepts from the thesaurus to discover 36 and link data to other information sources, including use  ...  447 Thanks also to Chris Johnson and Sabera Patel for developing the user interface. 448  ... 
doi:10.1007/s12145-014-0183-1 fatcat:6vewf32vwve73jte7olfsr6aje

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  
Ontologies have emerged in AI as a key tool to formally represent and semantically organize aspects of the real world.  ...  However, with this data explosion, the storage, management and analysis of available data to extract relevant information has become even a more complex task that offers challenging research issues to  ...  To facilitate and enrich the use of RxNorm, the NLM provides several services which can be helpful to understand the RxNorm content, to facilitate the access to the RxNorm data and to make it easier to  ... 
doi:10.2174/1568026611313050003 pmid:23548021 fatcat:6hyje3smivfldn2svxvnhtsw6i

Navigating in vitro bioactivity data: investigating available resources using model compounds [article]

Sten Ilmjarv, Fiona Augsburger, Jerven Tjalling Bolleman, Robin Liechti, Alan Bridge, Jenny Sandstrom, Vincent Jaquet, Ioannis Xenarios, Karl-Heinz Krause
2018 bioRxiv   pre-print
In addition, we estimated accessibility of selected public resources using computational queries. Only a few public resources provided access to compound-related data using semantic web technology.  ...  The aim of this study is to investigate how available public online resources (tools and databases) support accessing and distribution of in vitro compound data.  ...  The problems can be solved with integrated approaches using ontologies, semantic-web technologies and better annotation of the data.  ... 
doi:10.1101/248898 fatcat:qaatz4vkubdz3kea47ezmzsg5q

Chemical Entity Semantic Specification: Knowledge representation for efficient semantic cheminformatics and facile data integration

Leonid L Chepelev, Michel Dumontier
2011 Journal of Cheminformatics  
Conclusions: By harnessing the power of Semantic Web technologies with CHESS, it is possible to provide a means of facile cross-domain chemical knowledge integration with full preservation of data correspondence  ...  Finally, we provide access to the tools necessary to carry out chemical entity encoding in CHESS, along with a sample knowledgebase.  ...  Acknowledgements This research was funded in part by National Science and Engineering Research Council of Canada CGS award for LLC and Discovery Grant funding to MD.  ... 
doi:10.1186/1758-2946-3-20 pmid:21595881 pmcid:PMC3121712 fatcat:lvl5p6ehp5fv3aipyz7jmsfbee

Interconnection of Biological Knowledge Using NikkajiRDF and Interlinking Ontology for Biological Concepts

Tatsuya Kushida, Kouji Kozaki, Takahiro Kawamura, Yuka Tateisi, Yasunori Yamamoto, Toshihisa Takagi
2019 New generation computing  
Furthermore, we developed KGs from IOBC and added protein, biological phenomena, and disease identifiers used in major biological databases: UniProt, Gene Ontology, and MeSH to the KGs.  ...  Using the extended KGs and federated search to the DisGeNET, we discovered more than 60 chemicals and 700 gene products, involved in 32 diseases.  ...  distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were  ... 
doi:10.1007/s00354-019-00074-y fatcat:hx4xpy5o7vfzhcjxzeljzsudcm

Cheminformatics and the Semantic Web: adding value with linked data and enhanced provenance

Jeremy G. Frey, Colin L. Bird
2013 Wiley Interdisciplinary Reviews. Computational Molecular Science  
The relationship with the related subject of bioinformatics is becoming stronger and better defined, owing to the influence of Semantic Web technologies, which enable researchers to integrate heterogeneous  ...  Cheminformatics is evolving from being a field of study associated primarily with drug discovery into a discipline that embraces the distribution, management, access, and sharing of chemical data.  ...  ACKNOWLEDGMENTS The authors acknowledge the direct and indirect support for this review flowing from the grants from EPSRC (GR/R67729/, EP/C6008863/, EP/G026238/, EP/K003569/) and JISC (Data Management  ... 
doi:10.1002/wcms.1127 pmid:24432050 pmcid:PMC3884755 fatcat:vpqawnligbbyrgjepzznugq3vi

Updates in Rhea: SPARQLing biochemical reaction data

Thierry Lombardot, Anne Morgat, Kristian B Axelsen, Lucila Aimo, Nevila Hyka-Nouspikel, Anne Niknejad, Alex Ignatchenko, Ioannis Xenarios, Elisabeth Coudert, Nicole Redaschi, Alan Bridge
2018 Nucleic Acids Research  
access to it.  ...  Rhea (http://www.rhea-db.org) is a comprehensive and non-redundant resource of over 11 000 expert-curated biochemical reactions that uses chemical entities from the ChEBI ontology to represent reaction  ...  We would also like to thank the Cheminformatics and Metabolism Team of EMBL-EBI for their work in maintaining and developing ChEBI and Andrea Cristofori of the Web Production team of EMBL-EBI for invaluable  ... 
doi:10.1093/nar/gky876 pmid:30272209 pmcid:PMC6324061 fatcat:sgbcc47ct5bkloc74x6kfm7vsm

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  
Recent years have seen an explosion in the availability of data in the chemistry domain.  ...  Ontologies encode expert domain knowledge in a hierarchically organised machine-processable format. One such ontology for the chemical domain is ChEBI.  ...  Acknowledgements The authors wish to thank Peter Ertl from Novartis for generating the scaffolds illustrated, and ChemAxon for providing the software used to generate the hierarchy by MCS, in Figure 2  ... 
doi:10.1186/1758-2946-4-8 pmid:22480202 pmcid:PMC3361486 fatcat:54c73jnc6jgmjlbdob2vzyupi4

Resource description framework technologies in chemistry

Egon L Willighagen, Martin P Brändle
2011 Journal of Cheminformatics  
Outlook The future of the use of RDF technologies as open standards in chemistry looks bright, and fills the needs in chemistry for semantically linking chemical data to other data sources.  ...  Ontologies With RDF we have a data structure to link resources and provide details about those resources, and SPARQL provides us with the tools to query and aggregate that data.  ... 
doi:10.1186/1758-2946-3-15 pmid:21569523 pmcid:PMC3118380 fatcat:psv6nlqssvh6bmi5bvkcovhewa
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