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A controlled vocabulary for pathway entities and events

S. Jupe, B. Jassal, M. Williams, G. Wu
2014 Database: The Journal of Biological Databases and Curation  
We have devised a controlled vocabulary (CV) that creates concise, unambiguous and unique names for reactions (pathway events) and all the molecular entities they involve.  ...  The CV could be reapplied in any situation where names are used for pathway entities and events.  ...  Acknowledgements The authors thank Peter D'Eustachio, Henning Hermjakob, Phani Garapati, Mike Caudy and Marija Milacic for discussions, feedback and suggestions that contributed to the development of the  ... 
doi:10.1093/database/bau060 pmid:24951798 pmcid:PMC4064568 fatcat:wxun6ejep5adjpou2b6lvx4lfa

RULE-BASED REASONING FOR SYSTEM DYNAMICS IN CELL SYSTEMS

EUNA JEONG, MASAO NAGASAKI, SATORU MIYANO
2008 Genome Informatics Series  
A system-dynamics-centered ontology, called the Cell System Ontology (CSO), has been developed for representation of diverse biological pathways.  ...  Simultaneously, we have investigated how logic-based rules can be used for the ontology to extend its expressiveness and to complement the ontology by reasoning, which aims at qualifying pathway knowledge  ...  In the figure, the property values for a biological event, a cellular compartment, and a fea- ture type refer to the controlled vocabulary terms defined in CSO, prefixed with ME_, CC_, and FT_, respectively  ... 
doi:10.11234/gi1990.20.25 fatcat:wenwbbixtvfhtkh5fpjhdcbkia

CONVERSION FROM BIOPAX TO CSO FOR SYSTEM DYNAMICS AND VISUALIZATION OF BIOLOGICAL PATHWAY

EUNA JEONG, MASAO NAGASAKI, SATORU MIYANO
2007 Genome Informatics Series  
Major new standards for representation of pathway data and the ability to check inconsistency in pathways are inevitable for the development of a reliable pathway data repository.  ...  We demonstrate how CSO can be used to build a complete and consistent pathway repository and enhance the interoperability among applications.  ...  The bp: control interaction must have one controller as a physical entity and one controlled interaction as a conversion.  ... 
doi:10.11234/gi1990.18.225 fatcat:fozw4oi7ezf65nwwi6qkll7ebq

Conversion from BioPAX to CSO for system dynamics and visualization of biological pathway

Euna Jeong, Masao Nagasaki, Satoru Miyano
2007 Genome Informatics Series  
Major new standards for representation of pathway data and the ability to check inconsistency in pathways are inevitable for the development of a reliable pathway data repository.  ...  We demonstrate how CSO can be used to build a complete and consistent pathway repository and enhance the interoperability among applications.  ...  Core vocabulary BioPAX refers to external controlled vocabulary to annotate biological pathway data such as cell types, cellular locations, evidence, and experimental forms.  ... 
pmid:18546490 fatcat:64jxucdtcnflrnenjboscva3zu

Rule-based reasoning for system dynamics in cell systems

Euna Jeong, Masao Nagasaki, Satoru Miyano
2008 Genome Informatics Series  
A system-dynamics-centered ontology, called the Cell System Ontology (CSO), has been developed for representation of diverse biological pathways.  ...  Simultaneously, we have investigated how logic-based rules can be used for the ontology to extend its expressiveness and to complement the ontology by reasoning, which aims at qualifying pathway knowledge  ...  In the figure, the property values for a biological event, a cellular compartment, and a fea- ture type refer to the controlled vocabulary terms defined in CSO, prefixed with ME , CC , and FT , respectively  ... 
pmid:19425120 fatcat:ak57cwqh2rfh3d5h4a2fudal3q

Extracting Biological Pathway Models From NLP Event Representations [article]

Michael Spranger and Sucheendra K. Palaniappan and Samik Ghosh
2016 arXiv   pre-print
It is part of a larger effort to make results of the NLP community available for system biology pathway modelers.  ...  This paper describes an an open-source software system for the automatic conversion of NLP event representations to system biology structured data interchange formats such as SBML and BioPAX.  ...  We use controlled vocabulary from the Systems Biology Ontology (SBO) and the Gene Ontology (GO).  ... 
arXiv:1608.03764v1 fatcat:jyjp4tubsndhng4lp3ady6xafq

Extracting Biological Pathway Models From NLP Event Representations

Michael Spranger, Sucheendra Palaniappan, Samik Ghosh
2015 Proceedings of BioNLP 15  
It is part of a larger effort to make results of the NLP community available for system biology pathway modelers.  ...  This paper describes an an open-source software system for the automatic conversion of NLP event representations to system biology structured data interchange formats such as SBML and BioPAX.  ...  We use controlled vocabulary from the Systems Biology Ontology (SBO) and the Gene Ontology (GO).  ... 
doi:10.18653/v1/w15-3805 dblp:conf/bionlp/SprangerPG15 fatcat:2qccccwkr5fvlpkxfdj2lomeky

ONTOLOGIES MOST USED IN AGRICULTURE: Make your data interpretable and interoperable with ontologies [article]

Céline Aubert, Elizabeth Arnaud, Marie Angélique Laporte, Erick Antezana
2021 Zenodo  
The webpage also offers a list of generic ontologies and thesauri and ontologies repositories.  ...  This webpage, published in the site of the CGIAR Platform for big data in agriculture (https://bigdata.cgiar.org/ontologies-for-agriculture/), provides a visual thematic access to the most used ontologies  ...  National Agricultural Library's Agricultural Thesaurus and Glossary (NAL) Online vocabulary tools English and Spanish to select controlled vocabulary terms for subject indexing of AGRICOLA, PubAg and other  ... 
doi:10.5281/zenodo.6609665 fatcat:zmvzelw63faalbsxn3cjcoob6y

Empowering industrial research with shared biomedical vocabularies

Lee Harland, Christopher Larminie, Susanna-Assunta Sansone, Sorana Popa, M. Scott Marshall, Michael Braxenthaler, Michael Cantor, Wendy Filsell, Mark J. Forster, Enoch Huang, Andreas Matern, Mark Musen (+6 others)
2011 Drug Discovery Today  
In this article we highlight the risks to future productivity that are associated with incomplete biological and chemical vocabularies and suggest a new model to address this long-standing issue.  ...  The life science industries (including pharmaceuticals, agrochemicals and consumer goods) are exploring new business models for research and development that focus on external partnerships.  ...  Acknowledgments This topic was first discussed at a Pistoia Alliance-sponsored meeting on industry vocabulary strategies.  ... 
doi:10.1016/j.drudis.2011.09.013 pmid:21963522 pmcid:PMC7098809 fatcat:rs35p6w34bgifaz7gcdta36mka

Creating a Structured Adverse Outcome Pathway Knowledgebase via Ontology-Based Annotations

Cataia Ives, Ivana Campia, Rong-Lin Wang, Clemens Wittwehr, Stephen Edwards
2017 Applied In Vitro Toxicology  
and other controlled vocabularies.  ...  Annotation of KEs with ontology classes from fourteen ontologies and controlled vocabularies resulted in a total of 685 KEs being annotated with a total of 809 Event Components.  ...  Acknowledgments The authors would like to thank the AOP developers in the OECD AOP Development Programme for their patience in translating the information they have entered into the AOP-Wiki into a formal  ... 
doi:10.1089/aivt.2017.0017 pmid:30057931 pmcid:PMC6060416 fatcat:qvd4vsl6wfbolnqj7s2plhlnqa

The Comparative Toxicogenomics Database: update 2019

2018 Nucleic Acids Research  
In this biennial update, we present our new chemical-phenotype module that codes chemical-induced effects on phenotypes, curated using controlled vocabularies for chemicals, phenotypes, taxa, and anatomical  ...  chemical-gene molecular initiating events with phenotypic key events, diseases, and population-level health outcomes).  ...  Interactions are curated in a structured format using controlled vocabularies for chemicals (C), phenotype entities (E), action qualifiers (Q, 'increased', 'decreased', or 'affects'), organisms (T) and  ... 
doi:10.1093/nar/gky868 pmid:30247620 pmcid:PMC6323936 fatcat:4qvewpc42jhsvic7phptfwy6im

The protein-protein interaction ontology: for better representing and capturing the biological context of protein interaction

Mansheng Li, Qiang He, Chunyuan Yang, Jie Ma, Fuchu He, Tao Chen, Yunping Zhu
2021 BMC Genomics  
Results Inspired by the event model and the distinct characteristics of PPI events, PPIO consists of six core aspects of the information required for reporting a PPI event, including the interactor (who  ...  Background With the rapid increase in the amount of Protein-Protein Interaction (PPI) data, the establishment of an event-centered PPI ontology that contains temporal and spatial vocabularies is urgently  ...  Weimin Zhu at the National Center for Protein Sciences (Beijing) for inspiring discussions and helpful comments.  ... 
doi:10.1186/s12864-021-07827-4 pmid:34789143 pmcid:PMC8596923 fatcat:jc475guwvndhtmqmzg7u5vzaey

Using the Semantic Web for Rapid Integration of WikiPathways with Other Biological Online Data Resources

Andra Waagmeester, Martina Kutmon, Anders Riutta, Ryan Miller, Egon L. Willighagen, Chris T. Evelo, Alexander R. Pico, Christos A. Ouzounis
2016 PLoS Computational Biology  
In order to convert WikiPathways content into meaningful triples we developed two new vocabularies that capture the graphical representation and the pathway logic, respectively.  ...  The diversity of online resources storing biological data in different formats provides a challenge for bioinformaticians to integrate and analyse their biological data.  ...  Acknowledgments We acknowledge the help from the teams behind UniProt, DisGeNET and EBI's Array atlas for the help on the various SPARQL queries.  ... 
doi:10.1371/journal.pcbi.1004989 pmid:27336457 pmcid:PMC4918977 fatcat:tkjaukwptfe4tct6kflm4ssyry

CausalTAB: the PSI-MITAB 2.8 updated format for signalling data representation and dissemination

2019 Bioinformatics  
A key task is the formalization of such information in models describing how biological entities interact to mediate the response to external and internal signals.  ...  Here, we present a common standard for the representation and dissemination of signalling information: the PSI Causal Interaction tabular format (CausalTAB) which is an extension of the existing PSI-MI  ...  Acknowledgements We thank Birgit Meldal for critically reading and reviewing the manuscript. Funding  ... 
doi:10.1093/bioinformatics/btz132 pmid:30793173 pmcid:PMC6896241 fatcat:jgsbahpzwvcatdk2cn4usdyjyi

Erratum: Corrigendum: The BioPAX community standard for pathway data sharing

Emek Demir, Michael P Cary, Suzanne Paley, Ken Fukuda, Christian Lemer, Imre Vastrik, Guanming Wu, Peter D'Eustachio, Carl Schaefer, Joanne Luciano, Frank Schacherer, Irma Martinez-Flores (+78 others)
2010 Nature Biotechnology  
.; Pandey, A.; Thomas, P.; Wingender, E.; Karp, P. D.; Sander, C.; and Bader, G. D., "The BioPAX Community Standard for Pathway Data Sharing" (2010). Biology Faculty Works. 22.  ...  .; Lopez-Fuentes, A.  ...  See Supplementary Table 5 for a full list of author contributions.  ... 
doi:10.1038/nbt1210-1308c fatcat:2jwkkkz2gvdctmvgnej3gagrdu
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