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Showing 1 to 12 of 291 entries
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Why functions are not special dispositions: an improved classification of realizables for top-level ontologies.

Journal of biomedical semantics

Röhl J, Jansen L.
PMID: 25009736
J Biomed Semantics. 2014 Jun 02;5:27. doi: 10.1186/2041-1480-5-27. eCollection 2014.

BACKGROUND: The concept of function is central to both biology and technology, but neither in philosophy nor in formal ontology is there a generally accepted theory of functions. In particular, there is no consensus how to include functions into...

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Röhl J, Jansen L. Why functions are not special dispositions: an improved classification of realizables for top-level ontologies. J Biomed Semantics. 2014;5:27doi: 10.1186/2041-1480-5-27.
Röhl, J., & Jansen, L. (2014). Why functions are not special dispositions: an improved classification of realizables for top-level ontologies. Journal of biomedical semantics, 527. https://doi.org/10.1186/2041-1480-5-27
Röhl, Johannes, and Jansen, Ludger. "Why functions are not special dispositions: an improved classification of realizables for top-level ontologies." Journal of biomedical semantics vol. 5 (2014): 27. doi: https://doi.org/10.1186/2041-1480-5-27
Röhl J, Jansen L. Why functions are not special dispositions: an improved classification of realizables for top-level ontologies. J Biomed Semantics. 2014 Jun 02;5:27. doi: 10.1186/2041-1480-5-27. eCollection 2014. PMID: 25009736; PMCID: PMC4089563.
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Development of an Ontology for Periodontitis.

Journal of biomedical semantics

Suzuki A, Takai-Igarashi T, Nakaya J, Tanaka H, Barrera M.
PMID: 26140188
J Biomed Semantics. 2015 Jul 01;6:30. doi: 10.1186/s13326-015-0028-y. eCollection 2015.

BACKGROUND: In the clinical dentists and periodontal researchers' community, there is an obvious demand for a systems model capable of linking the clinical presentation of periodontitis to underlying molecular knowledge. A computer-readable representation of processes on disease development will...

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Suzuki A, Takai-Igarashi T, Nakaya J, et al. Development of an Ontology for Periodontitis. J Biomed Semantics. 2015;6:30doi: 10.1186/s13326-015-0028-y.
Suzuki, A., Takai-Igarashi, T., Nakaya, J., Tanaka, H., & Barrera, M. (2015). Development of an Ontology for Periodontitis. Journal of biomedical semantics, 630. https://doi.org/10.1186/s13326-015-0028-y
Suzuki, Asami, et al. "Development of an Ontology for Periodontitis." Journal of biomedical semantics vol. 6 (2015): 30. doi: https://doi.org/10.1186/s13326-015-0028-y
Suzuki A, Takai-Igarashi T, Nakaya J, Tanaka H, Barrera M. Development of an Ontology for Periodontitis. J Biomed Semantics. 2015 Jul 01;6:30. doi: 10.1186/s13326-015-0028-y. eCollection 2015. PMID: 26140188; PMCID: PMC4488034.
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Comparative analysis of knowledge representation and reasoning requirements across a range of life sciences textbooks.

Journal of biomedical semantics

Chaudhri VK, Elenius D, Goldenkranz A, Gong A, Martone ME, Webb W, Yorke-Smith N.
PMID: 25785183
J Biomed Semantics. 2014 Dec 18;5:51. doi: 10.1186/2041-1480-5-51. eCollection 2014.

BACKGROUND: Using knowledge representation for biomedical projects is now commonplace. In previous work, we represented the knowledge found in a college-level biology textbook in a fashion useful for answering questions. We showed that embedding the knowledge representation and question-answering...

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Chaudhri VK, Elenius D, Goldenkranz A, et al. Comparative analysis of knowledge representation and reasoning requirements across a range of life sciences textbooks. J Biomed Semantics. 2014;5:51doi: 10.1186/2041-1480-5-51.
Chaudhri, V. K., Elenius, D., Goldenkranz, A., Gong, A., Martone, M. E., Webb, W., & Yorke-Smith, N. (2014). Comparative analysis of knowledge representation and reasoning requirements across a range of life sciences textbooks. Journal of biomedical semantics, 551. https://doi.org/10.1186/2041-1480-5-51
Chaudhri, Vinay K, et al. "Comparative analysis of knowledge representation and reasoning requirements across a range of life sciences textbooks." Journal of biomedical semantics vol. 5 (2014): 51. doi: https://doi.org/10.1186/2041-1480-5-51
Chaudhri VK, Elenius D, Goldenkranz A, Gong A, Martone ME, Webb W, Yorke-Smith N. Comparative analysis of knowledge representation and reasoning requirements across a range of life sciences textbooks. J Biomed Semantics. 2014 Dec 18;5:51. doi: 10.1186/2041-1480-5-51. eCollection 2014. PMID: 25785183; PMCID: PMC4362633.
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Development and application of an interaction network ontology for literature mining of vaccine-associated gene-gene interactions.

Journal of biomedical semantics

Hur J, Özgür A, Xiang Z, He Y.
PMID: 25785184
J Biomed Semantics. 2015 Jan 06;6:2. doi: 10.1186/2041-1480-6-2. eCollection 2015.

BACKGROUND: Literature mining of gene-gene interactions has been enhanced by ontology-based name classifications. However, in biomedical literature mining, interaction keywords have not been carefully studied and used beyond a collection of keywords.METHODS: In this study, we report the development...

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Hur J, Özgür A, Xiang Z, et al. Development and application of an interaction network ontology for literature mining of vaccine-associated gene-gene interactions. J Biomed Semantics. 2015;6:2doi: 10.1186/2041-1480-6-2.
Hur, J., Özgür, A., Xiang, Z., & He, Y. (2015). Development and application of an interaction network ontology for literature mining of vaccine-associated gene-gene interactions. Journal of biomedical semantics, 62. https://doi.org/10.1186/2041-1480-6-2
Hur, Junguk, et al. "Development and application of an interaction network ontology for literature mining of vaccine-associated gene-gene interactions." Journal of biomedical semantics vol. 6 (2015): 2. doi: https://doi.org/10.1186/2041-1480-6-2
Hur J, Özgür A, Xiang Z, He Y. Development and application of an interaction network ontology for literature mining of vaccine-associated gene-gene interactions. J Biomed Semantics. 2015 Jan 06;6:2. doi: 10.1186/2041-1480-6-2. eCollection 2015. PMID: 25785184; PMCID: PMC4362819.
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Ontorat: automatic generation of new ontology terms, annotations, and axioms based on ontology design patterns.

Journal of biomedical semantics

Xiang Z, Zheng J, Lin Y, He Y.
PMID: 25785185
J Biomed Semantics. 2015 Jan 09;6:4. doi: 10.1186/2041-1480-6-4. eCollection 2015.

BACKGROUND: It is time-consuming to build an ontology with many terms and axioms. Thus it is desired to automate the process of ontology development. Ontology Design Patterns (ODPs) provide a reusable solution to solve a recurrent modeling problem in...

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Xiang Z, Zheng J, Lin Y, et al. Ontorat: automatic generation of new ontology terms, annotations, and axioms based on ontology design patterns. J Biomed Semantics. 2015;6:4doi: 10.1186/2041-1480-6-4.
Xiang, Z., Zheng, J., Lin, Y., & He, Y. (2015). Ontorat: automatic generation of new ontology terms, annotations, and axioms based on ontology design patterns. Journal of biomedical semantics, 64. https://doi.org/10.1186/2041-1480-6-4
Xiang, Zuoshuang, et al. "Ontorat: automatic generation of new ontology terms, annotations, and axioms based on ontology design patterns." Journal of biomedical semantics vol. 6 (2015): 4. doi: https://doi.org/10.1186/2041-1480-6-4
Xiang Z, Zheng J, Lin Y, He Y. Ontorat: automatic generation of new ontology terms, annotations, and axioms based on ontology design patterns. J Biomed Semantics. 2015 Jan 09;6:4. doi: 10.1186/2041-1480-6-4. eCollection 2015. PMID: 25785185; PMCID: PMC4362828.
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Can SNOMED CT be squeezed without losing its shape?.

Journal of biomedical semantics

López-García P, Schulz S.
PMID: 27655655
J Biomed Semantics. 2016 Sep 21;7(1):56. doi: 10.1186/s13326-016-0101-1.

BACKGROUND: In biomedical applications where the size and complexity of SNOMED CT become problematic, using a smaller subset that can act as a reasonable substitute is usually preferred. In a special class of use cases-like ontology-based quality assurance, or...

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López-García P, Schulz S. Can SNOMED CT be squeezed without losing its shape?. J Biomed Semantics. 2016;7(1):56doi: 10.1186/s13326-016-0101-1.
López-García, P., & Schulz, S. (2016). Can SNOMED CT be squeezed without losing its shape?. Journal of biomedical semantics, 7(1), 56. https://doi.org/10.1186/s13326-016-0101-1
López-García, Pablo, and Schulz, Stefan. "Can SNOMED CT be squeezed without losing its shape?." Journal of biomedical semantics vol. 7,1 (2016): 56. doi: https://doi.org/10.1186/s13326-016-0101-1
López-García P, Schulz S. Can SNOMED CT be squeezed without losing its shape?. J Biomed Semantics. 2016 Sep 21;7(1):56. doi: 10.1186/s13326-016-0101-1. PMID: 27655655; PMCID: PMC5031277.
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My Corporis Fabrica: an ontology-based tool for reasoning and querying on complex anatomical models.

Journal of biomedical semantics

Palombi O, Ulliana F, Favier V, Léon JC, Rousset MC.
PMID: 24936286
J Biomed Semantics. 2014 May 06;5:20. doi: 10.1186/2041-1480-5-20. eCollection 2014.

BACKGROUND: Multiple models of anatomy have been developed independently and for different purposes. In particular, 3D graphical models are specially useful for visualizing the different organs composing the human body, while ontologies such as FMA (Foundational Model of Anatomy)...

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Palombi O, Ulliana F, Favier V, et al. My Corporis Fabrica: an ontology-based tool for reasoning and querying on complex anatomical models. J Biomed Semantics. 2014;5:20doi: 10.1186/2041-1480-5-20.
Palombi, O., Ulliana, F., Favier, V., Léon, J. C., & Rousset, M. C. (2014). My Corporis Fabrica: an ontology-based tool for reasoning and querying on complex anatomical models. Journal of biomedical semantics, 520. https://doi.org/10.1186/2041-1480-5-20
Palombi, Olivier, et al. "My Corporis Fabrica: an ontology-based tool for reasoning and querying on complex anatomical models." Journal of biomedical semantics vol. 5 (2014): 20. doi: https://doi.org/10.1186/2041-1480-5-20
Palombi O, Ulliana F, Favier V, Léon JC, Rousset MC. My Corporis Fabrica: an ontology-based tool for reasoning and querying on complex anatomical models. J Biomed Semantics. 2014 May 06;5:20. doi: 10.1186/2041-1480-5-20. eCollection 2014. PMID: 24936286; PMCID: PMC4040514.
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Ontology-based representation and analysis of host-Brucella interactions.

Journal of biomedical semantics

Lin Y, Xiang Z, He Y.
PMID: 26445639
J Biomed Semantics. 2015 Oct 05;6:37. doi: 10.1186/s13326-015-0036-y. eCollection 2015.

BACKGROUND: Biomedical ontologies are representations of classes of entities in the biomedical domain and how these classes are related in computer- and human-interpretable formats. Ontologies support data standardization and exchange and provide a basis for computer-assisted automated reasoning. IDOBRU...

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Lin Y, Xiang Z, He Y. Ontology-based representation and analysis of host-Brucella interactions. J Biomed Semantics. 2015;6:37doi: 10.1186/s13326-015-0036-y.
Lin, Y., Xiang, Z., & He, Y. (2015). Ontology-based representation and analysis of host-Brucella interactions. Journal of biomedical semantics, 637. https://doi.org/10.1186/s13326-015-0036-y
Lin, Yu, et al. "Ontology-based representation and analysis of host-Brucella interactions." Journal of biomedical semantics vol. 6 (2015): 37. doi: https://doi.org/10.1186/s13326-015-0036-y
Lin Y, Xiang Z, He Y. Ontology-based representation and analysis of host-Brucella interactions. J Biomed Semantics. 2015 Oct 05;6:37. doi: 10.1186/s13326-015-0036-y. eCollection 2015. PMID: 26445639; PMCID: PMC4594885.
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CLO: The cell line ontology.

Journal of biomedical semantics

Sarntivijai S, Lin Y, Xiang Z, Meehan TF, Diehl AD, Vempati UD, Schürer SC, Pang C, Malone J, Parkinson H, Liu Y, Takatsuki T, Saijo K, Masuya H, Nakamura Y, Brush MH, Haendel MA, Zheng J, Stoeckert CJ, Peters B, Mungall CJ, Carey TE, States DJ, Athey BD, He Y.
PMID: 25852852
J Biomed Semantics. 2014 Aug 13;5:37. doi: 10.1186/2041-1480-5-37. eCollection 2014.

BACKGROUND: Cell lines have been widely used in biomedical research. The community-based Cell Line Ontology (CLO) is a member of the OBO Foundry library that covers the domain of cell lines. Since its publication two years ago, significant updates...

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Sarntivijai S, Lin Y, Xiang Z, et al. CLO: The cell line ontology. J Biomed Semantics. 2014;5:37doi: 10.1186/2041-1480-5-37.
Sarntivijai, S., Lin, Y., Xiang, Z., Meehan, T. F., Diehl, A. D., Vempati, U. D., Schürer, S. C., Pang, C., Malone, J., Parkinson, H., Liu, Y., Takatsuki, T., Saijo, K., Masuya, H., Nakamura, Y., Brush, M. H., Haendel, M. A., Zheng, J., Stoeckert, C. J., Peters, B., Mungall, C. J., Carey, T. E., States, D. J., Athey, B. D., & He, Y. (2014). CLO: The cell line ontology. Journal of biomedical semantics, 537. https://doi.org/10.1186/2041-1480-5-37
Sarntivijai, Sirarat, et al. "CLO: The cell line ontology." Journal of biomedical semantics vol. 5 (2014): 37. doi: https://doi.org/10.1186/2041-1480-5-37
Sarntivijai S, Lin Y, Xiang Z, Meehan TF, Diehl AD, Vempati UD, Schürer SC, Pang C, Malone J, Parkinson H, Liu Y, Takatsuki T, Saijo K, Masuya H, Nakamura Y, Brush MH, Haendel MA, Zheng J, Stoeckert CJ, Peters B, Mungall CJ, Carey TE, States DJ, Athey BD, He Y. CLO: The cell line ontology. J Biomed Semantics. 2014 Aug 13;5:37. doi: 10.1186/2041-1480-5-37. eCollection 2014. PMID: 25852852; PMCID: PMC4387853.
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Completing the is-a structure in light-weight ontologies.

Journal of biomedical semantics

Lambrix P, Wei-Kleiner F, Dragisic Z.
PMID: 25883780
J Biomed Semantics. 2015 Mar 28;6:12. doi: 10.1186/s13326-015-0002-8. eCollection 2015.

BACKGROUND: With the increasing presence of biomedical data sources on the Internet more and more research effort is put into finding possible ways for integrating and searching such often heterogeneous sources. Ontologies are a key technology in this effort....

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Lambrix P, Wei-Kleiner F, Dragisic Z. Completing the is-a structure in light-weight ontologies. J Biomed Semantics. 2015;6:12doi: 10.1186/s13326-015-0002-8.
Lambrix, P., Wei-Kleiner, F., & Dragisic, Z. (2015). Completing the is-a structure in light-weight ontologies. Journal of biomedical semantics, 612. https://doi.org/10.1186/s13326-015-0002-8
Lambrix, Patrick, et al. "Completing the is-a structure in light-weight ontologies." Journal of biomedical semantics vol. 6 (2015): 12. doi: https://doi.org/10.1186/s13326-015-0002-8
Lambrix P, Wei-Kleiner F, Dragisic Z. Completing the is-a structure in light-weight ontologies. J Biomed Semantics. 2015 Mar 28;6:12. doi: 10.1186/s13326-015-0002-8. eCollection 2015. PMID: 25883780; PMCID: PMC4399482.
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HuPSON: the human physiology simulation ontology.

Journal of biomedical semantics

Gündel M, Younesi E, Malhotra A, Wang J, Li H, Zhang B, de Bono B, Mevissen HT, Hofmann-Apitius M.
PMID: 24267822
J Biomed Semantics. 2013 Nov 22;4(1):35. doi: 10.1186/2041-1480-4-35.

BACKGROUND: Large biomedical simulation initiatives, such as the Virtual Physiological Human (VPH), are substantially dependent on controlled vocabularies to facilitate the exchange of information, of data and of models. Hindering these initiatives is a lack of a comprehensive ontology...

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Gündel M, Younesi E, Malhotra A, et al. HuPSON: the human physiology simulation ontology. J Biomed Semantics. 2013;4(1):35doi: 10.1186/2041-1480-4-35.
Gündel, M., Younesi, E., Malhotra, A., Wang, J., Li, H., Zhang, B., de Bono, B., Mevissen, H. T., & Hofmann-Apitius, M. (2013). HuPSON: the human physiology simulation ontology. Journal of biomedical semantics, 4(1), 35. https://doi.org/10.1186/2041-1480-4-35
Gündel, Michaela, et al. "HuPSON: the human physiology simulation ontology." Journal of biomedical semantics vol. 4,1 (2013): 35. doi: https://doi.org/10.1186/2041-1480-4-35
Gündel M, Younesi E, Malhotra A, Wang J, Li H, Zhang B, de Bono B, Mevissen HT, Hofmann-Apitius M. HuPSON: the human physiology simulation ontology. J Biomed Semantics. 2013 Nov 22;4(1):35. doi: 10.1186/2041-1480-4-35. PMID: 24267822; PMCID: PMC4177144.
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Representing annotation compositionality and provenance for the Semantic Web.

Journal of biomedical semantics

Livingston KM, Bada M, Hunter LE, Verspoor K.
PMID: 24268021
J Biomed Semantics. 2013 Nov 22;4:38. doi: 10.1186/2041-1480-4-38. eCollection 2013.

BACKGROUND: Though the annotation of digital artifacts with metadata has a long history, the bulk of that work focuses on the association of single terms or concepts to single targets. As annotation efforts expand to capture more complex information,...

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Livingston KM, Bada M, Hunter LE, et al. Representing annotation compositionality and provenance for the Semantic Web. J Biomed Semantics. 2013;4:38doi: 10.1186/2041-1480-4-38.
Livingston, K. M., Bada, M., Hunter, L. E., & Verspoor, K. (2013). Representing annotation compositionality and provenance for the Semantic Web. Journal of biomedical semantics, 438. https://doi.org/10.1186/2041-1480-4-38
Livingston, Kevin M, et al. "Representing annotation compositionality and provenance for the Semantic Web." Journal of biomedical semantics vol. 4 (2013): 38. doi: https://doi.org/10.1186/2041-1480-4-38
Livingston KM, Bada M, Hunter LE, Verspoor K. Representing annotation compositionality and provenance for the Semantic Web. J Biomed Semantics. 2013 Nov 22;4:38. doi: 10.1186/2041-1480-4-38. eCollection 2013. PMID: 24268021; PMCID: PMC4129183.
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Showing 1 to 12 of 291 entries