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A controlled vocabulary for pathway entities and events
2014
Database: The Journal of Biological Databases and Curation
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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
2008
Genome Informatics Series
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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
2007
Genome Informatics Series
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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
2007
Genome Informatics Series
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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
2008
Genome Informatics Series
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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]
2016
arXiv
pre-print
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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
2015
Proceedings of BioNLP 15
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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]
2021
Zenodo
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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
2011
Drug Discovery Today
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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
2017
Applied In Vitro Toxicology
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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
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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
2021
BMC Genomics
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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
2016
PLoS Computational Biology
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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
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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
2010
Nature Biotechnology
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.; 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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