HUP-ML: Human Proteome Markup Language for Proteomics Database

Kamijo, Keita; Mizuguchi, Hiroyuki; Kenmochi, Akihisa; Satô, Masao; Takaki, Yoko; Tsugita, Akira

doi:10.5702/massspec.51.542

Cited by 3 publications

(1 citation statement)

References 4 publications

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“…The Systems Biology Markup Language (SBML), 7 Genome Annotation Markup Elements (GAME), 14 and Human Proteome Markup Language for Proteomics Database (HUP-ML) 13 are some significant examples. We believe GLYDE similarly fulfills an important requirement for rapid evolution of glycomics by providing a common standard for glycomics data representation.…”

Section: Discussionmentioning

confidence: 99%

GLYDE—an expressive XML standard for the representation of glycan structure

Sahoo

Thomas

Sheth

et al. 2005

Carbohydrate Research

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Section: Discussionmentioning

confidence: 99%

GLYDE—an expressive XML standard for the representation of glycan structure

Sahoo

Thomas

Sheth

et al. 2005

Carbohydrate Research

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Current literature in mass spectrometry

2005

J. Mass Spectrom.

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In order to keep subscribers up‐to‐date with the latest developments in their field, John Wiley & Sons are providing a current awareness service in each issue of the journal. The bibliography contains newly published material in the field of mass spectrometry. Each bibliography is divided into 11 sections: 1 Books, Reviews & Symposia; 2 Instrumental Techniques & Methods; 3 Gas Phase Ion Chemistry; 4 Biology/Biochemistry: Amino Acids, Peptides & Proteins; Carbohydrates; Lipids; Nucleic Acids; 5 Pharmacology/Toxicology; 6 Natural Products; 7 Analysis of Organic Compounds; 8 Analysis of Inorganics/Organometallics; 9 Surface Analysis; 10 Environmental Analysis; 11 Elemental Analysis. Within each section, articles are listed in alphabetical order with respect to author (6 Weeks journals ‐ Search completed at 15th. Dec. 2004)

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A review of standards for data exchange within systems biology

Strömbäck¹,

Hall²,

Lambrix³

2007

Proteomics

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The rapid increase in experimental data within systems biology has increased the need for exchange of data to allow analysis and comparison of larger datasets. This has resulted in a need for standardized formats for representation of such results and currently many formats for representation of data have been developed or are under development. In this paper, we give an overview of the current state of available standards and ontologies within systems biology. We focus on XML-based standards for exchange of data and give a thorough description of similarities and differences of currently available formats. For each of these, we discuss how the important concepts such as substances, interactions, and experimental data can be represented. In particular, we note that the purpose of a standard is often visible in the structures it provides for the representation of data. A clear purpose is also crucial for the success of a standard. Moreover, we note that the development of representation formats is parallel to the development of ontologies and the recent trend is that representation formats make more and more use of available ontologies.

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HUP-ML: Human Proteome Markup Language for Proteomics Database

Cited by 3 publications

References 4 publications

GLYDE—an expressive XML standard for the representation of glycan structure

GLYDE—an expressive XML standard for the representation of glycan structure

Current literature in mass spectrometry

A review of standards for data exchange within systems biology

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