Data Standards and Controlled Vocabularies for Proteomics

Martens, Lennart; Palazzi, Luisa Montecchi; Hermjakob, Henning

doi:10.1007/978-1-59745-398-1_18

Cited by 8 publications

(2 citation statements)

References 14 publications

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“…Algunos ejemplos son: Minimum Information About a Microarray Experiment (MIAME) (Brazma et al, 2001); Minimun Information About a Proteomic Experiment (MIAPE) (Martens et al, 2008) y Minimun Information for Biological and Biomedical Investigation (MIBBI) (Taylor, 2008). …”

Section: Manejo De Datos (Data Management Standards)mentioning

confidence: 99%

Bioinformática: herramienta en el análisis de sistemas biológicos

Almazar¹,

González²

2015

Ontare

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ResumenBioinformática es la ciencia que permite adquirir, almacenar, organizar, archivar, analizar o visualizar datos complejos relacionados en su mayoría con sistemas biológicos. La bioinformática requiere de herramientas de Software, que permitan el manejo de datos, la creación de modelos, la evaluación de hipótesis y la interpretación de los resultados con sentido biológico. Este artículo describe algunas de las herramientas y Software empleados en bioinformática. PalabRas clave

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Section: Manejo De Datos (Data Management Standards)mentioning

confidence: 99%

Bioinformática: herramienta en el análisis de sistemas biológicos

Almazar¹,

González²

2015

Ontare

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“…With this requirement in mind, controlled vocabularies (CV) and ontologies have been created. A CV is defined as a limited list of clearly defined terms, with optional relationships between the terms, while an ontology moves beyond a mere CV by attempting to extensively model a part of the real world [2]. …”

Section: Introductionmentioning

confidence: 99%

OLS Dialog: An open-source front end to the Ontology Lookup Service

et al. 2010

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BackgroundWith the growing amount of biomedical data available in public databases it has become increasingly important to annotate data in a consistent way in order to allow easy access to this rich source of information. Annotating the data using controlled vocabulary terms and ontologies makes it much easier to compare and analyze data from different sources. However, finding the correct controlled vocabulary terms can sometimes be a difficult task for the end user annotating these data.ResultsIn order to facilitate the location of the correct term in the correct controlled vocabulary or ontology, the Ontology Lookup Service was created. However, using the Ontology Lookup Service as a web service is not always feasible, especially for researchers without bioinformatics support. We have therefore created a Java front end to the Ontology Lookup Service, called the OLS Dialog, which can be plugged into any application requiring the annotation of data using controlled vocabulary terms, making it possible to find and use controlled vocabulary terms without requiring any additional knowledge about web services or ontology formats.ConclusionsAs a user-friendly open source front end to the Ontology Lookup Service, the OLS Dialog makes it straightforward to include controlled vocabulary support in third-party tools, which ultimately makes the data even more valuable to the biomedical community.

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Bioinformatics for Proteomics: Opportunities at the Interface Between the Scientists, Their Experiments, and the Community

et al. 2014

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Within the last decade, bioinformatics has moved from command line scripts dedicated to single experiments towards production grade software integrated in experimental workflows providing a rich environment for biological investigation. Located at the interface between the scientists, their experiments, and the community, bioinformatics acts as a gateway to a wide source of information. This chapter does not list tools and methods, but rather hints at how bioinformatics can help in improving biological projects, all the way from their initial design to the dissemination of the results.

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Data Standards and Controlled Vocabularies for Proteomics

Cited by 8 publications

References 14 publications

Bioinformática: herramienta en el análisis de sistemas biológicos

Bioinformática: herramienta en el análisis de sistemas biológicos

OLS Dialog: An open-source front end to the Ontology Lookup Service

Bioinformatics for Proteomics: Opportunities at the Interface Between the Scientists, Their Experiments, and the Community

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