LIVIVO - Search results -

Search results

Result 1 - 10 of total 42

Search options

Article ; Online: GlycoEnzOnto: a GlycoEnzyme pathway and molecular function ontology.

Groth, Theodore / Diehl, Alexander D / Gunawan, Rudiyanto / Neelamegham, Sriram

2022 Volume 38, Issue 24, Page(s) 5413–5420

Abstract: Motivation: The 'glycoEnzymes' include a set of proteins having related enzymatic, metabolic, transport, structural and cofactor functions. Currently, there is no established ontology to describe glycoEnzyme properties and to relate them to glycan ... ...

Abstract	Motivation: The 'glycoEnzymes' include a set of proteins having related enzymatic, metabolic, transport, structural and cofactor functions. Currently, there is no established ontology to describe glycoEnzyme properties and to relate them to glycan biosynthesis pathways. Results: We present GlycoEnzOnto, an ontology describing 403 human glycoEnzymes curated along 139 glycosylation pathways, 134 molecular functions and 22 cellular compartments. The pathways described regulate nucleotide-sugar metabolism, glycosyl-substrate/donor transport, glycan biosynthesis and degradation. The role of each enzyme in the glycosylation initiation, elongation/branching and capping/termination phases is described. IUPAC linear strings present systematic human/machine-readable descriptions of individual reaction steps and enable automated knowledge-based curation of biochemical networks. All GlycoEnzOnto knowledge is integrated with the Gene Ontology biological processes. GlycoEnzOnto enables improved transcript overrepresentation analyses and glycosylation pathway identification compared to other available schema, e.g. KEGG and Reactome. Overall, GlycoEnzOnto represents a holistic glycoinformatics resource for systems-level analyses. Availability and implementation: https://github.com/neel-lab/GlycoEnzOnto. Supplementary information: Supplementary data are available at Bioinformatics online.
MeSH term(s)	Humans ; Gene Ontology ; Knowledge Bases ; Glycosylation ; Polysaccharides
Chemical Substances	Polysaccharides
Language	English
Publishing date	2022-10-10
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	1422668-6
ISSN	1367-4811 ; 1367-4803
ISSN (online)	1367-4811
ISSN	1367-4803
DOI	10.1093/bioinformatics/btac704
Database	MEDical Literature Analysis and Retrieval System OnLINE

In stock of ZB MED Cologne/Königswinter

Zs.A 2374: Show issues

Location:
Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
Jg. 1995 - 2021: Lesesall (2.OG)
ab Jg. 2022: Lesesaal (EG)

Order via subito

This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

Details ▾
- See ZB MED holdings
- Order with fees

Article: Foundations for a Realism-Based Ontology of Protein Aggregates.

Wishnie, Lauren / Cox, Alexander P / Diehl, Alexander D / Ceusters, Werner

CEUR workshop proceedings

2021 Volume 2807, Page(s) K1–K10

Abstract: The objective of this paper is to propose formal definitions for the terms 'protein aggregate' and 'protein-containing complex' such that the descriptions and usages of these terms in biomedical literature are unified and that those portions of reality ... ...

Abstract	The objective of this paper is to propose formal definitions for the terms 'protein aggregate' and 'protein-containing complex' such that the descriptions and usages of these terms in biomedical literature are unified and that those portions of reality are correctly represented. To this end, we surveyed the literature to assess the need for a distinction between these entities, then compared the features of usages and definitions found in the literature to the definitions for those terms found in Bioportal ontologies. Based on the results of this comparison, we propose updated definitions for the terms 'protein aggregate' and 'protein-containing complex'. Thus far, we propose the following distinguishing factors: first, that one important difference lies in whether an entity is disposed to change type in response to certain structural alterations, such as dissociation of a continuant part, and second that an important difference lies in the ability of the entity to realize its function after such an event occurs. These distinctions are reflected in the proposed definitions.
Language	English
Publishing date	2021-02-02
Publishing country	Germany
Document type	Journal Article
ISSN	1613-0073
ISSN	1613-0073
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Article: MRIO: The Magnetic Resonance Imaging Acquisition and Analysis Ontology.

Bartnik, Alexander / Serra, Lucas M / Smith, Mackenzie / Duncan, William D / Wishnie, Lauren / Ruttenberg, Alan / Dwyer, Michael G / Diehl, Alexander D

bioRxiv : the preprint server for biology

2023

Abstract: Objective: Magnetic resonance imaging of the brain is a useful tool in both the clinic and research settings, aiding in the diagnosis and treatments of neurological disease and expanding our knowledge of the brain. However, there are many challenges ... ...

Abstract	Objective: Magnetic resonance imaging of the brain is a useful tool in both the clinic and research settings, aiding in the diagnosis and treatments of neurological disease and expanding our knowledge of the brain. However, there are many challenges inherent in managing and analyzing MRI data, due in large part to the heterogeneity of data acquisition. Materials and methods: To address this, we have developed MRIO, the Magnetic Resonance Imaging Acquisition and Analysis Ontology. Results: MRIO provides well-reasoned classes and logical axioms for the acquisition of several MRI acquisition types and well-known, peer-reviewed analysis software, facilitating the use of MRI data. These classes provide a common language for the neuroimaging research process and help standardize the organization and analysis of MRI data for reproducible datasets. We also provide queries for automated assignment of analyses for given MRI types. Discussion: MRIO aids researchers in managing neuroimaging studies by helping organize and annotate MRI data and integrating with existing standards such as Digital Imaging and Communications in Medicine and the Brain Imaging Data Structure, enhancing reproducibility and interoperability. MRIO was constructed according to Open Biomedical Ontologies Foundry principals and has contributed several terms to the Ontology for Biomedical Investigations to help bridge neuroimaging data to other domains. Conclusion: MRIO addresses the need for a "common language" for MRI that can help manage the neuroimaging research, by enabling researchers to identify appropriate analyses for sets of scans and facilitating data organization and reporting.
Language	English
Publishing date	2023-08-07
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.08.04.552020
Database	MEDical Literature Analysis and Retrieval System OnLINE

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Details ▾

Article ; Online: Cells in ExperimentaL Life Sciences (CELLS-2018): capturing the knowledge of normal and diseased cells with ontologies.

Sarntivijai, Sirarat / He, Yongqun / Diehl, Alexander D

BMC bioinformatics

2019 Volume 20, Issue Suppl 5, Page(s) 183

Abstract: Cell cultures and cell lines are widely used in life science experiments. In conjunction with the 2018 International Conference on Biomedical Ontology (ICBO-2018), the 2nd International Workshop on Cells in ExperimentaL Life Science (CELLS-2018) focused ... ...

Abstract	Cell cultures and cell lines are widely used in life science experiments. In conjunction with the 2018 International Conference on Biomedical Ontology (ICBO-2018), the 2nd International Workshop on Cells in ExperimentaL Life Science (CELLS-2018) focused on two themes of knowledge representation, for newly-discovered cell types and for cells in disease states. This workshop included five oral presentations and a general discussion session. Two new ontologies, including the Cancer Cell Ontology (CCL) and the Ontology for Stem Cell Investigations (OSCI), were reported in the workshop. In another representation, the Cell Line Ontology (CLO) framework was applied and extended to represent cell line cells used in China and their Chinese representation. Other presentations included a report on the application of ontologies to cross-compare cell types and marker patterns used in flow cytometry studies, and a presentation on new experimental findings about novel cell types based on single cell RNA sequencing assay and their corresponding ontological representation. The general discussion session focused on the ontology design patterns in representing newly-discovered cell types and cells in disease states.
MeSH term(s)	Biological Ontologies ; Biological Science Disciplines ; Congresses as Topic ; Humans ; Research
Language	English
Publishing date	2019-04-25
Publishing country	England
Document type	Editorial
ZDB-ID	2041484-5
ISSN	1471-2105 ; 1471-2105
ISSN (online)	1471-2105
ISSN	1471-2105
DOI	10.1186/s12859-019-2721-9
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Article ; Online: An ontology for representing hematologic malignancies: the cancer cell ontology.

Serra, Lucas M / Duncan, William D / Diehl, Alexander D

BMC bioinformatics

2019 Volume 20, Issue Suppl 5, Page(s) 181

Abstract: Background: Within the cancer domain, ontologies play an important role in the integration and annotation of data in order to support numerous biomedical tools and applications. This work seeks to leverage existing standards in immunophenotyping cell ... ...

Abstract	Background: Within the cancer domain, ontologies play an important role in the integration and annotation of data in order to support numerous biomedical tools and applications. This work seeks to leverage existing standards in immunophenotyping cell types found in hematologic malignancies to provide an ontological representation of them to aid in data annotation and analysis for patient data. Results: We have developed the Cancer Cell Ontology according to OBO Foundry principles as an extension of the Cell Ontology. We define classes in Cancer Cell Ontology by using a genus-differentia approach using logical axioms capturing the expression of cellular surface markers in order to represent types of hematologic malignancies. By adopting conventions used in the Cell Ontology, we have created human and computer-readable definitions for 300 classes of blood cancers, based on the EGIL classification system for leukemias, and relying upon additional classification approaches for multiple myelomas and other hematologic malignancies. Conclusion: We have demonstrated a proof of concept for leveraging the built-in logical axioms of the ontology in order to classify patient surface marker data into appropriate diagnostic categories. We plan to integrate our ontology into existing tools for flow cytometry data analysis to facilitate the automated diagnosis of hematologic malignancies.
MeSH term(s)	Biological Ontologies ; Cell Line, Tumor ; Hematologic Neoplasms/classification ; Hematologic Neoplasms/metabolism ; Hematologic Neoplasms/pathology ; Humans ; Immunophenotyping ; Machine Learning ; Neoplastic Stem Cells/cytology ; Neoplastic Stem Cells/metabolism
Language	English
Publishing date	2019-04-25
Publishing country	England
Document type	Journal Article
ZDB-ID	2041484-5
ISSN	1471-2105 ; 1471-2105
ISSN (online)	1471-2105
ISSN	1471-2105
DOI	10.1186/s12859-019-2722-8
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Article: Ontological Realism for the Research Domain Criteria for Mental Disorders.

Ceusters, Werner / Jensen, Mark / Diehl, Alexander D

Studies in health technology and informatics

2017 Volume 235, Page(s) 431–435

Abstract: At the heart of the Research Domain Criteria for Mental Disorders is a matrix in which functional aspects of behavior are related to genotypic and (endo-)phenotypic research findings, and the various techniques through which they can been observed. The ... ...

Abstract	At the heart of the Research Domain Criteria for Mental Disorders is a matrix in which functional aspects of behavior are related to genotypic and (endo-)phenotypic research findings, and the various techniques through which they can been observed. The matrix is work in progress. As such it currently suffers from several shortcomings, the resolution of which, we contend, are essential to success of NIMH's goal of fostering translational science on mental disorders. Using well-established criteria for assessing the terminological and ontological quality of biomedical representations we identified the major problems to be (1) the abundant presence of terms that lack face value, (2) the absence of what the exact nature of the represented relationships are, and (3) referential imprecision with respect to the intended granularity of what the terms denote. We propose to eliminate these shortcomings by resorting to definitions and formal representations under the umbrella of Ontological Realism as they already have been developed in the areas of mental health, anatomy and biological functions.
Language	English
Publishing date	2017
Publishing country	Netherlands
Document type	Journal Article
ISSN	0926-9630
ISSN	0926-9630
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Article ; Online: Cells in experimental life sciences - challenges and solution to the rapid evolution of knowledge.

Sarntivijai, Sirarat / Diehl, Alexander D / He, Yongqun

BMC bioinformatics

2017 Volume 18, Issue Suppl 17, Page(s) 560

Abstract: Cell cultures used in biomedical experiments come in the form of both sample biopsy primary cells, and maintainable immortalised cell lineages. The rise of bioinformatics and high-throughput technologies has led us to the requirement of ontology ... ...

Abstract	Cell cultures used in biomedical experiments come in the form of both sample biopsy primary cells, and maintainable immortalised cell lineages. The rise of bioinformatics and high-throughput technologies has led us to the requirement of ontology representation of cell types and cell lines. The Cell Ontology (CL) and Cell Line Ontology (CLO) have long been established as reference ontologies in the OBO framework. We have compiled a series of the challenges and the proposals of solutions in this CELLS (Cells in ExperimentaL Life Sciences) thematic series that cover the grounds of standing issues and the directions, which were discussed in the First International Workshop on CELLS at the the International Conference on Biomedical Ontology (ICBO). This workshop focused on the extension of the current CL and CLO to cover a wider set of biological questions and challenges needing semantic infrastructure for information modeling. We discussed data-driven use cases that leverage linkage of CL, CLO and other bio-ontologies. This is an established approach in data-driven ontologies such as the Experimental Factor Ontology (EFO), and the Ontology for Biomedical Investigation (OBI). The First International Workshop on CELLS at the International Conference on Biomedical Ontology has brought together experimental biologists and biomedical ontologists to discuss solutions to organizing and representing the rapidly evolving knowledge gained from experimental cells. The workshop has successfully identified the areas of challenge, and the gap in connecting the two domains of knowledge. The outcome of this workshop yielded practical implementation plans to filled in this gap.This CELLS workshop also provided a venue for panel discussions of innovative solutions as well as challenges in the development and applications of biomedical ontologies to represent and analyze experimental cell data.
MeSH term(s)	Biological Science Disciplines ; Computational Biology/methods ; Data Mining/methods ; Humans ; Research Design
Language	English
Publishing date	2017-12-21
Publishing country	England
Document type	Editorial ; Research Support, N.I.H., Extramural
ZDB-ID	2041484-5
ISSN	1471-2105 ; 1471-2105
ISSN (online)	1471-2105
ISSN	1471-2105
DOI	10.1186/s12859-017-1976-2
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Article: Ontology-based modeling, integration, and analysis of heterogeneous clinical, pathological, and molecular kidney data for precision medicine.

bioRxiv : the preprint server for biology

2024

Abstract: Many data resources generate, process, store, or provide kidney related molecular, pathological, and clinical data. Reference ontologies offer an opportunity to support knowledge and data integration. The Kidney Precision Medicine Project (KPMP) team ... ...

Abstract	Many data resources generate, process, store, or provide kidney related molecular, pathological, and clinical data. Reference ontologies offer an opportunity to support knowledge and data integration. The Kidney Precision Medicine Project (KPMP) team contributed to the representation and addition of 329 kidney phenotype terms to the Human Phenotype Ontology (HPO), and identified many subcategories of acute kidney injury (AKI) or chronic kidney disease (CKD). The Kidney Tissue Atlas Ontology (KTAO) imports and integrates kidney-related terms from existing ontologies (e.g., HPO, CL, and Uberon) and represents 259 kidney-related biomarkers. We also developed a precision medicine metadata ontology (PMMO) to integrate 50 variables from KPMP and CZ CellxGene data resources and applied PMMO for integrative kidney data analysis. The gene expression profiles of kidney gene biomarkers were specifically analyzed under healthy control or AKI/CKD disease statuses. This work demonstrates how ontology-based approaches support multi-domain data and knowledge integration in precision medicine.
Language	English
Publishing date	2024-04-02
Publishing country	United States
Document type	Preprint
DOI	10.1101/2024.04.01.587658
Database	MEDical Literature Analysis and Retrieval System OnLINE

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Details ▾

Book ; Online: Guidelines for reporting cell types

Lubiana, Tiago / Roncaglia, Paola / Mungall, Christopher J. / Quardokus, Ellen M. / Fortriede, Joshua D. / Osumi-Sutherland, David / Diehl, Alexander D.

the MIRACL standard

2022

Abstract: Cell types are at the root of modern biology, and describing them is a core task of the Human Cell Atlas project. Surprisingly, there are no standards for reporting new cell types, leading to a gap between classes mentioned in biomedical literature and ... ...

Abstract	Cell types are at the root of modern biology, and describing them is a core task of the Human Cell Atlas project. Surprisingly, there are no standards for reporting new cell types, leading to a gap between classes mentioned in biomedical literature and the Cell Ontology, the primary registry of cell types. Here we introduce the Minimal Information Reporting About a CelL (MIRACL) standard, a guideline for describing cell types alongside scientific articles. In a MIRACL sheet, authors organize a label, a diagnostic description, a taxon, an anatomical structure, and a parent cell class for each cell type of interest. The MIRACL standard bridges the gap between wet-lab researchers and ontologists, facilitating the integration of biomedical knowledge into ontologies and artificial intelligence systems. Comment: 8 pages, 1 figure, 1 table
Keywords	Quantitative Biology - Other Quantitative Biology
Publishing date	2022-04-18
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

Full text online

Full text

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Article ; Online: Representing vision and blindness.

Ray, Patrick L / Cox, Alexander P / Jensen, Mark / Allen, Travis / Duncan, William / Diehl, Alexander D

Journal of biomedical semantics

2016 Volume 7, Page(s) 15

Abstract: Background: There have been relatively few attempts to represent vision or blindness ontologically. This is unsurprising as the related phenomena of sight and blindness are difficult to represent ontologically for a variety of reasons. Blindness has ... ...

Abstract	Background: There have been relatively few attempts to represent vision or blindness ontologically. This is unsurprising as the related phenomena of sight and blindness are difficult to represent ontologically for a variety of reasons. Blindness has escaped ontological capture at least in part because: blindness or the employment of the term 'blindness' seems to vary from context to context, blindness can present in a myriad of types and degrees, and there is no precedent for representing complex phenomena such as blindness. Methods: We explore current attempts to represent vision or blindness, and show how these attempts fail at representing subtypes of blindness (viz., color blindness, flash blindness, and inattentional blindness). We examine the results found through a review of current attempts and identify where they have failed. Results: By analyzing our test cases of different types of blindness along with the strengths and weaknesses of previous attempts, we have identified the general features of blindness and vision. We propose an ontological solution to represent vision and blindness, which capitalizes on resources afforded to one who utilizes the Basic Formal Ontology as an upper-level ontology. Conclusions: The solution we propose here involves specifying the trigger conditions of a disposition as well as the processes that realize that disposition. Once these are specified we can characterize vision as a function that is realized by certain (in this case) biological processes under a range of triggering conditions. When the range of conditions under which the processes can be realized are reduced beyond a certain threshold, we are able to say that blindness is present. We characterize vision as a function that is realized as a seeing process and blindness as a reduction in the conditions under which the sight function is realized. This solution is desirable because it leverages current features of a major upper-level ontology, accurately captures the phenomenon of blindness, and can be implemented in many domain-specific ontologies.
MeSH term(s)	Animals ; Biological Ontologies ; Blindness ; Color Vision Defects ; Humans ; Vision, Ocular
Language	English
Publishing date	2016
Publishing country	England
Document type	Journal Article
ZDB-ID	2548651-2
ISSN	2041-1480 ; 2041-1480
ISSN (online)	2041-1480
ISSN	2041-1480
DOI	10.1186/s13326-016-0058-0
Database	MEDical Literature Analysis and Retrieval System OnLINE

Full text online

Full text

Order via subito

Details ▾
- Full text online
- Order with fees

To top

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

More links

Kategorien

Order via subito

Inter-library loan at ZB MED

More links

Kategorien

Inter-library loan at ZB MED

More links

Kategorien

Order via subito

More links

Kategorien

Order via subito

More links

Kategorien

Order via subito

Inter-library loan at ZB MED

More links

Kategorien

Order via subito

More links

Kategorien

Inter-library loan at ZB MED

Full text online

More links

Kategorien

Inter-library loan at ZB MED

Full text online

More links

Kategorien

Order via subito