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Title: Letter to the editor in "Wrestling with SUMO and bio-ontologies"

Abstract

In this article, we analyze the current state of application of ontologies in biology, try to reveal the reasons for the existing difficulties, recommend a possible solution to the current problems and describe prospects and future challenges for the application of ontologival engineering in biological domains. We focus on the example of the ontology developed by the Microarray Gene Expression Society (MGED) for describing microarray experiments. We have chosen this example not because it is particularly bad, but because it exhibits the typical problems of biologival ontologies, and beause MGED has been promoted as an international standard. We wholeheartedly agree that such standards are extremely valuable, but we also believe that their promoters are particularly obliged to get them right, otherwise their whole advantage is negated.

Authors:
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Publication Date:
Research Org.:
Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
909684
Report Number(s):
PNNL-SA-49465
Journal ID: ISSN 1087-0156; NABIF9; TRN: US200723%%134
DOE Contract Number:
AC05-76RL01830
Resource Type:
Journal Article
Resource Relation:
Journal Name: Nature Biotechnology, 24(1):21-22; Journal Volume: 24; Journal Issue: 1
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; BIOLOGY; GENES; PROMOTERS

Citation Formats

Stoeckert, Christian Jr. J., Ball, Cathy, Brazma, Alvis, Brinkman, Ryan, Causton, Helen C., Fan, Liju, Fostel, Jennifer, Fragoso, Gilberto, Heiskanen, Mervi, Holstege, Frank, Morrison, Norman, Parkinson, Helen E., Quackenbush, John, Rocca-Serra, Philippe, Sansone, Susanna A., Sarkans, Ugis, Sherlock, Gavin, Stevens, Robert, Taylor, Chris, Taylor, Ronald C., Whetzel, Patricia, and White, Joseph C. Letter to the editor in "Wrestling with SUMO and bio-ontologies". United States: N. p., 2006. Web. doi:10.1038/nbt0106-21b.
Stoeckert, Christian Jr. J., Ball, Cathy, Brazma, Alvis, Brinkman, Ryan, Causton, Helen C., Fan, Liju, Fostel, Jennifer, Fragoso, Gilberto, Heiskanen, Mervi, Holstege, Frank, Morrison, Norman, Parkinson, Helen E., Quackenbush, John, Rocca-Serra, Philippe, Sansone, Susanna A., Sarkans, Ugis, Sherlock, Gavin, Stevens, Robert, Taylor, Chris, Taylor, Ronald C., Whetzel, Patricia, & White, Joseph C. Letter to the editor in "Wrestling with SUMO and bio-ontologies". United States. doi:10.1038/nbt0106-21b.
Stoeckert, Christian Jr. J., Ball, Cathy, Brazma, Alvis, Brinkman, Ryan, Causton, Helen C., Fan, Liju, Fostel, Jennifer, Fragoso, Gilberto, Heiskanen, Mervi, Holstege, Frank, Morrison, Norman, Parkinson, Helen E., Quackenbush, John, Rocca-Serra, Philippe, Sansone, Susanna A., Sarkans, Ugis, Sherlock, Gavin, Stevens, Robert, Taylor, Chris, Taylor, Ronald C., Whetzel, Patricia, and White, Joseph C. Sun . "Letter to the editor in "Wrestling with SUMO and bio-ontologies"". United States. doi:10.1038/nbt0106-21b.
@article{osti_909684,
title = {Letter to the editor in "Wrestling with SUMO and bio-ontologies"},
author = {Stoeckert, Christian Jr. J. and Ball, Cathy and Brazma, Alvis and Brinkman, Ryan and Causton, Helen C. and Fan, Liju and Fostel, Jennifer and Fragoso, Gilberto and Heiskanen, Mervi and Holstege, Frank and Morrison, Norman and Parkinson, Helen E. and Quackenbush, John and Rocca-Serra, Philippe and Sansone, Susanna A. and Sarkans, Ugis and Sherlock, Gavin and Stevens, Robert and Taylor, Chris and Taylor, Ronald C. and Whetzel, Patricia and White, Joseph C.},
abstractNote = {In this article, we analyze the current state of application of ontologies in biology, try to reveal the reasons for the existing difficulties, recommend a possible solution to the current problems and describe prospects and future challenges for the application of ontologival engineering in biological domains. We focus on the example of the ontology developed by the Microarray Gene Expression Society (MGED) for describing microarray experiments. We have chosen this example not because it is particularly bad, but because it exhibits the typical problems of biologival ontologies, and beause MGED has been promoted as an international standard. We wholeheartedly agree that such standards are extremely valuable, but we also believe that their promoters are particularly obliged to get them right, otherwise their whole advantage is negated.},
doi = {10.1038/nbt0106-21b},
journal = {Nature Biotechnology, 24(1):21-22},
number = 1,
volume = 24,
place = {United States},
year = {Sun Jan 01 00:00:00 EST 2006},
month = {Sun Jan 01 00:00:00 EST 2006}
}