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Scheben A, Chan CKK, Mansueto L, Mauleon R, Larmande P, Alexandrov N, Wing RA, McNally KL, Quesneville H, Edwards D. Progress in single-access information systems for wheat and rice crop improvement. Brief Bioinform 2020; 20:565-571. [PMID: 29659709 DOI: 10.1093/bib/bby016] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Improving productivity of the staple crops wheat and rice is essential to feed the growing global population, particularly in the context of a changing climate. However, current rates of yield gain are insufficient to support the predicted population growth. New approaches are required to accelerate the breeding process, and many of these are driven by the application of large-scale crop data. To leverage the substantial volumes and types of data that can be applied for precision breeding, the wheat and rice research communities are working towards the development of integrated systems to access and standardize the dispersed, heterogeneous available data. Here, we outline the initiatives of the International Wheat Information System (WheatIS) and the International Rice Informatics Consortium (IRIC) to establish Web-based single-access systems and data mining tools to make the available resources more accessible, drive discovery and accelerate the production of new crop varieties. We discuss the progress of WheatIS and IRIC towards unifying specialized wheat and rice databases and building custom software platforms to manage and interrogate these data. Single-access crop information systems will strengthen scientific collaboration, optimize the use of public research funds and help achieve the required yield gains in the two most important global food crops.
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Affiliation(s)
- Armin Scheben
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, 6009 Perth, WA, Australia
| | - Chon-Kit Kenneth Chan
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, 6009 Perth, WA, Australia
| | - Locedie Mansueto
- International Rice Research Institute, DAPO Box 7777, Metro Manila 1301, The Philippines
| | - Ramil Mauleon
- International Rice Research Institute, DAPO Box 7777, Metro Manila 1301, The Philippines
| | - Pierre Larmande
- IRD, UMR DIADE (Plant Diversity Adaptation and Development Research unit) , 911 Avenue Agropolis, 34394 Montpellier, France
| | - Nickolai Alexandrov
- International Rice Research Institute, DAPO Box 7777, Metro Manila 1301, The Philippines
| | - Rod A Wing
- Arizona Genomics Institute, University of Arizona, Tucson, Arizona, USA
| | - Kenneth L McNally
- International Rice Research Institute, DAPO Box 7777, Metro Manila 1301, The Philippines
| | | | - David Edwards
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, 6009 Perth, WA, Australia
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Lapatas V, Stefanidakis M, Jimenez RC, Via A, Schneider MV. Data integration in biological research: an overview. J Biol Res (Thessalon) 2015; 22:9. [PMID: 26336651 PMCID: PMC4557916 DOI: 10.1186/s40709-015-0032-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 08/10/2015] [Indexed: 11/16/2022]
Abstract
Data sharing, integration and annotation are essential to ensure the reproducibility of the analysis and interpretation of the experimental findings. Often these activities are perceived as a role that bioinformaticians and computer scientists have to take with no or little input from the experimental biologist. On the contrary, biological researchers, being the producers and often the end users of such data, have a big role in enabling biological data integration. The quality and usefulness of data integration depend on the existence and adoption of standards, shared formats, and mechanisms that are suitable for biological researchers to submit and annotate the data, so it can be easily searchable, conveniently linked and consequently used for further biological analysis and discovery. Here, we provide background on what is data integration from a computational science point of view, how it has been applied to biological research, which key aspects contributed to its success and future directions.
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Affiliation(s)
- Vasileios Lapatas
- />Department of Informatics, Ionian University, 7 Tsirigoti Square, Corfu, 49100 Greece
| | - Michalis Stefanidakis
- />Department of Informatics, Ionian University, 7 Tsirigoti Square, Corfu, 49100 Greece
| | | | - Allegra Via
- />Biocomputing Group, Sapienza University, Piazzale Aldo Moro 5, Rome, 00185 Italy
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Deutsch EW, Albar JP, Binz PA, Eisenacher M, Jones AR, Mayer G, Omenn GS, Orchard S, Vizcaíno JA, Hermjakob H. Development of data representation standards by the human proteome organization proteomics standards initiative. J Am Med Inform Assoc 2015; 22:495-506. [PMID: 25726569 PMCID: PMC4457114 DOI: 10.1093/jamia/ocv001] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Revised: 09/29/2014] [Accepted: 01/05/2015] [Indexed: 11/22/2022] Open
Abstract
OBJECTIVE To describe the goals of the Proteomics Standards Initiative (PSI) of the Human Proteome Organization, the methods that the PSI has employed to create data standards, the resulting output of the PSI, lessons learned from the PSI's evolution, and future directions and synergies for the group. MATERIALS AND METHODS The PSI has 5 categories of deliverables that have guided the group. These are minimum information guidelines, data formats, controlled vocabularies, resources and software tools, and dissemination activities. These deliverables are produced via the leadership and working group organization of the initiative, driven by frequent workshops and ongoing communication within the working groups. Official standards are subjected to a rigorous document process that includes several levels of peer review prior to release. RESULTS We have produced and published minimum information guidelines describing what information should be provided when making data public, either via public repositories or other means. The PSI has produced a series of standard formats covering mass spectrometer input, mass spectrometer output, results of informatics analysis (both qualitative and quantitative analyses), reports of molecular interaction data, and gel electrophoresis analyses. We have produced controlled vocabularies that ensure that concepts are uniformly annotated in the formats and engaged in extensive software development and dissemination efforts so that the standards can efficiently be used by the community.Conclusion In its first dozen years of operation, the PSI has produced many standards that have accelerated the field of proteomics by facilitating data exchange and deposition to data repositories. We look to the future to continue developing standards for new proteomics technologies and workflows and mechanisms for integration with other omics data types. Our products facilitate the translation of genomics and proteomics findings to clinical and biological phenotypes. The PSI website can be accessed at http://www.psidev.info.
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Affiliation(s)
| | - Juan Pablo Albar
- Died July 18, 2014 Proteomics Facility, Centro Nacional de Biotecnología - CSIC, Madrid, Spain ProteoRed Consortium, Spanish National Institute of Proteomics, Madrid, Spain
| | - Pierre-Alain Binz
- CHUV Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Martin Eisenacher
- Medizinisches Proteom Center (MPC), Ruhr-Universität Bochum, Bochum, Germany
| | - Andrew R Jones
- Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - Gerhard Mayer
- Medizinisches Proteom Center (MPC), Ruhr-Universität Bochum, Bochum, Germany
| | - Gilbert S Omenn
- Institute for Systems Biology, Seattle, USA Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, USA
| | - Sandra Orchard
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Juan Antonio Vizcaíno
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Henning Hermjakob
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
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Abstract
Over the past two decades, high-throughput (HTP) technologies such as microarrays and mass spectrometry have fundamentally changed clinical cancer research. They have revealed novel molecular markers of cancer subtypes, metastasis, and drug sensitivity and resistance. Some have been translated into the clinic as tools for early disease diagnosis, prognosis, and individualized treatment and response monitoring. Despite these successes, many challenges remain: HTP platforms are often noisy and suffer from false positives and false negatives; optimal analysis and successful validation require complex workflows; and great volumes of data are accumulating at a rapid pace. Here we discuss these challenges, and show how integrative computational biology can help diminish them by creating new software tools, analytical methods, and data standards.
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Affiliation(s)
- Kristen Fortney
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
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Vogt L, Grobe P, Quast B, Bartolomaeus T. Top-level categories of constitutively organized material entities--suggestions for a formal top-level ontology. PLoS One 2011; 6:e18794. [PMID: 21533043 PMCID: PMC3080885 DOI: 10.1371/journal.pone.0018794] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2010] [Accepted: 03/18/2011] [Indexed: 11/23/2022] Open
Abstract
Background Application oriented ontologies are important for reliably communicating and
managing data in databases. Unfortunately, they often differ in the
definitions they use and thus do not live up to their potential. This
problem can be reduced when using a standardized and ontologically
consistent template for the top-level categories from a top-level formal
foundational ontology. This would support ontological consistency within
application oriented ontologies and compatibility between them. The Basic
Formal Ontology (BFO) is such a foundational ontology for the biomedical
domain that has been developed following the single inheritance policy. It
provides the top-level template within the Open Biological and Biomedical
Ontologies Foundry. If it wants to live up to its expected role, its three
top-level categories of material entity (i.e., ‘object’,
‘fiat object part’, ‘object
aggregate’) must be exhaustive, i.e. every concrete material entity
must instantiate exactly one of them. Methodology/Principal Findings By systematically evaluating all possible basic configurations of material
building blocks we show that BFO's top-level categories of material
entity are not exhaustive. We provide examples from biology and everyday
life that demonstrate the necessity for two additional categories:
‘fiat object part aggregate’ and
‘object with fiat object part aggregate’. By
distinguishing topological coherence, topological adherence, and metric
proximity we furthermore provide a differentiation of clusters and groups as
two distinct subcategories for each of the three categories of material
entity aggregates, resulting in six additional subcategories of material
entity. Conclusions/Significance We suggest extending BFO to incorporate two additional categories of material
entity as well as two subcategories for each of the three categories of
material entity aggregates. With these additions, BFO would exhaustively
cover all top-level types of material entity that application oriented
ontologies may use as templates. Our result, however, depends on the premise
that all material entities are organized according to a constitutive
granularity.
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Affiliation(s)
- Lars Vogt
- Institut für Evolutionsbiologie und Ökologie, Universität Bonn, Bonn, Germany.
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Affiliation(s)
- Joel T Dudley
- Division of Systems Medicine, Department of Pediatrics, Stanford University School of Medicine, Stanford, California, USA
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Chervitz SA, Deutsch EW, Field D, Parkinson H, Quackenbush J, Rocca-Serra P, Sansone SA, Stoeckert CJ, Taylor CF, Taylor R, Ball CA. Data standards for Omics data: the basis of data sharing and reuse. Methods Mol Biol 2011; 719:31-69. [PMID: 21370078 PMCID: PMC4152841 DOI: 10.1007/978-1-61779-027-0_2] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
To facilitate sharing of Omics data, many groups of scientists have been working to establish the relevant data standards. The main components of data sharing standards are experiment description standards, data exchange standards, terminology standards, and experiment execution standards. Here we provide a survey of existing and emerging standards that are intended to assist the free and open exchange of large-format data.
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Abstract
Background The biosciences increasingly face the challenge of integrating a wide variety of available data, information and knowledge in order to gain an understanding of biological systems. Data integration is supported by a diverse series of tools, but the lack of a consistent terminology to label these data still presents significant hurdles. As a consequence, much of the available biological data remains disconnected or worse: becomes misconnected. The need to address this terminology problem has spawned the building of a large number of bio-ontologies. OBOF, RDF and OWL are among the most used ontology formats to capture terms and relationships in the Life Sciences, opening the potential to use the Semantic Web to support data integration and further exploitation of integrated resources via automated retrieval and reasoning procedures. Methods We extended the Perl suite ONTO-PERL and functionally integrated it into the Galaxy platform. The resulting ONTO-ToolKit supports the analysis and handling of OBO-formatted ontologies via the Galaxy interface, and we demonstrated its functionality in different use cases that illustrate the flexibility to obtain sets of ontology terms that match specific search criteria. Results ONTO-ToolKit is available as a tool suite for Galaxy. Galaxy not only provides a user friendly interface allowing the interested biologist to manipulate OBO ontologies, it also opens up the possibility to perform further biological (and ontological) analyses by using other tools available within the Galaxy environment. Moreover, it provides tools to translate OBO-formatted ontologies into Semantic Web formats such as RDF and OWL. Conclusions ONTO-ToolKit reaches out to researchers in the biosciences, by providing a user-friendly way to analyse and manipulate ontologies. This type of functionality will become increasingly important given the wealth of information that is becoming available based on ontologies.
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Affiliation(s)
- Erick Antezana
- Department of Biology, Norwegian University of Science and Technology (NTNU), Høgskoleringen 5, N-7491 Trondheim, Norway.
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Holmes C, McDonald F, Jones M, Ozdemir V, Graham JE. Standardization and omics science: technical and social dimensions are inseparable and demand symmetrical study. OMICS 2010; 14:327-32. [PMID: 20455752 DOI: 10.1089/omi.2010.0022] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Standardization is critical to scientists and regulators to ensure the quality and interoperability of research processes, as well as the safety and efficacy of the attendant research products. This is perhaps most evident in the case of "omics science," which is enabled by a host of diverse high-throughput technologies such as genomics, proteomics, and metabolomics. But standards are of interest to (and shaped by) others far beyond the immediate realm of individual scientists, laboratories, scientific consortia, or governments that develop, apply, and regulate them. Indeed, scientific standards have consequences for the social, ethical, and legal environment in which innovative technologies are regulated, and thereby command the attention of policy makers and citizens. This article argues that standardization of omics science is both technical and social. A critical synthesis of the social science literature indicates that: (1) standardization requires a degree of flexibility to be practical at the level of scientific practice in disparate sites; (2) the manner in which standards are created, and by whom, will impact their perceived legitimacy and therefore their potential to be used; and (3) the process of standardization itself is important to establishing the legitimacy of an area of scientific research.
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Affiliation(s)
- Christina Holmes
- Technoscience and Regulation Research Unit, Faculty of Medicine, Dalhousie University, Halifax, Canada
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Abstract
BACKGROUND With the continuously increasing demands on knowledge- and data-management that databases have to meet, ontologies and the theories of granularity they use become more and more important. Unfortunately, currently used theories and schemes of granularity unnecessarily limit the performance of ontologies due to two shortcomings: (i) they do not allow the integration of multiple granularity perspectives into one granularity framework; (ii) they are not applicable to cumulative-constitutively organized material entities, which cover most of the biomedical material entities. RESULTS The above mentioned shortcomings are responsible for the major inconsistencies in currently used spatio-structural granularity schemes. By using the Basic Formal Ontology (BFO) as a top-level ontology and Keet's general theory of granularity, a granularity framework is presented that is applicable to cumulative-constitutively organized material entities. It provides a scheme for granulating complex material entities into their constitutive and regional parts by integrating various compositional and spatial granularity perspectives. Within a scale dependent resolution perspective, it even allows distinguishing different types of representations of the same material entity. Within other scale dependent perspectives, which are based on specific types of measurements (e.g. weight, volume, etc.), the possibility of organizing instances of material entities independent of their parthood relations and only according to increasing measures is provided as well. All granularity perspectives are connected to one another through overcrossing granularity levels, together forming an integrated whole that uses the compositional object perspective as an integrating backbone. This granularity framework allows to consistently assign structural granularity values to all different types of material entities. CONCLUSIONS The here presented framework provides a spatio-structural granularity framework for all domain reference ontologies that model cumulative-constitutively organized material entities. With its multi-perspectives approach it allows querying an ontology stored in a database at one's own desired different levels of detail: The contents of a database can be organized according to diverse granularity perspectives, which in their turn provide different views on its content (i.e. data, knowledge), each organized into different levels of detail.
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Affiliation(s)
- Lars Vogt
- Institut für Evolutionsbiologie und Okologie, Universität Bonn, An der Immenburg 1, Bonn, Germany.
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Field D, Sansone SA, Collis A, Booth T, Dukes P, Gregurick SK, Kennedy K, Kolar P, Kolker E, Maxon M, Millard S, Mugabushaka AM, Perrin N, Remacle JE, Remington K, Rocca-Serra P, Taylor CF, Thorley M, Tiwari B, Wilbanks J. Megascience. 'Omics data sharing. Science 2009; 326:234-6. [PMID: 19815759 PMCID: PMC2770171 DOI: 10.1126/science.1180598] [Citation(s) in RCA: 93] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Data sharing, and the good annotation practices it depends on, must become part of the fabric of daily research for researchers and funders.
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Affiliation(s)
- Dawn Field
- U.K. Natural Environment Research Council (NERC), Environmental Bioinformatics Centre, NERC Centre for Ecology and Hydrology, Oxford, OX1 3SR, UK.
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Vogt L, Bartolomaeus T, Giribet G. The linguistic problem of morphology: structure versus homology and the standardization of morphological data. Cladistics 2009; 26:301-325. [DOI: 10.1111/j.1096-0031.2009.00286.x] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Hughes MA, Burns DL, Juris SJ, Tang WJ, Clement KH, Eaton LJ, Kelly-Cirino CD, McKee ML, Powell BS, Bishop BL, Rudge TL, Shine N, Verma A, Willis MS, Morse SA. The case for developing consensus standards for research in microbial pathogenesis: Bacillus anthracis toxins as an example. Infect Immun 2009; 77:4182-6. [PMID: 19651858 PMCID: PMC2747970 DOI: 10.1128/iai.00368-09] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Affiliation(s)
- Molly A Hughes
- Department of Medicine, Division of Infectious Diseases and International Health, University of Virginia Health System, P.O. Box 800513, Charlottesville, VA 22908, USA.
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Antezana E, Egaña M, Blondé W, Illarramendi A, Bilbao I, De Baets B, Stevens R, Mironov V, Kuiper M. The Cell Cycle Ontology: an application ontology for the representation and integrated analysis of the cell cycle process. Genome Biol 2009; 10:R58. [PMID: 19480664 PMCID: PMC2718524 DOI: 10.1186/gb-2009-10-5-r58] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2008] [Revised: 04/17/2009] [Accepted: 05/29/2009] [Indexed: 01/26/2023] Open
Abstract
A software resource for the analysis of cell cycle related molecular networks. The Cell Cycle Ontology ( is an application ontology that automatically captures and integrates detailed knowledge on the cell cycle process. Cell Cycle Ontology is enabled by semantic web technologies, and is accessible via the web for browsing, visualizing, advanced querying, and computational reasoning. Cell Cycle Ontology facilitates a detailed analysis of cell cycle-related molecular network components. Through querying and automated reasoning, it may provide new hypotheses to help steer a systems biology approach to biological network building.
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Affiliation(s)
- Erick Antezana
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052 Gent, Belgium.
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Abstract
New knowledge is produced at a continuously increasing speed, and the list of papers, databases and other knowledge sources that a researcher in the life sciences needs to cope with is actually turning into a problem rather than an asset. The adequate management of knowledge is therefore becoming fundamentally important for life scientists, especially if they work with approaches that thoroughly depend on knowledge integration, such as systems biology. Several initiatives to organize biological knowledge sources into a readily exploitable resourceome are presently being carried out. Ontologies and Semantic Web technologies revolutionize these efforts. Here, we review the benefits, trends, current possibilities, and the potential this holds for the biosciences.
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Affiliation(s)
- Erick Antezana
- Department of Biology at the Norwegian University of Science and Technology
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Chervitz SA, Parkinson H, Fostel JM, Causton HC, Sanson SA, Deutsch EW, Field D, Taylor CF, Rocca-Serra P, White J, Stoeckert CJ. Standards for Functional Genomics. Bioinformatics 2009. [DOI: 10.1007/978-0-387-92738-1_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Vogt L. The future role of bio-ontologies for developing a general data standard in biology: chance and challenge for zoo-morphology. ZOOMORPHOLOGY 2009; 128:201-17. [DOI: 10.1007/s00435-008-0081-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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de Marco A. Minimal information: an urgent need to assess the functional reliability of recombinant proteins used in biological experiments. Microb Cell Fact 2008; 7:20. [PMID: 18647423 PMCID: PMC2499994 DOI: 10.1186/1475-2859-7-20] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2008] [Accepted: 07/23/2008] [Indexed: 11/16/2022] Open
Abstract
Structural characterization of proteins used in biological experiments is largely neglected. In most publications, the information available is totally insufficient to judge the functionality of the proteins used and, therefore, the significance of identified protein-protein interactions (was the interaction specific or due to unspecific binding of misfolded protein regions?) or reliability of kinetic and thermodynamic data (how much protein was in its native form?). As a consequence, the results of single experiments might not only become questionable, but the whole reliability of systems biology, built on these fundaments, would be weakened. The introduction of Minimal Information concerning purified proteins to add as metadata to the main body of a manuscript would render straightforward the assessment of their functional and structural qualities and, consequently, of results obtained using these proteins. Furthermore, accepted standards for protein annotation would simplify data comparison and exchange. This article has been envisaged as a proposal for aggregating scientists who share the opinion that the scientific community needs a platform for Minimum Information for Protein Functionality Evaluation (MIPFE).
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Abstract
The development and implementation of new methods in human embryonic stem cell (hESC) research is fraught with difficulties, not least of which is the highly variable reporting of the number and quality of embryos used to derive hESC lines. Without a clear minimum information convention among the derivation teams, understanding and comparing derivation methods and their potential impact on the resulting stem cell line will continue to be extremely difficult. In order to address this issue, we consulted international teams regarding the implementation of a minimum information convention for derivation with the aim of universal use, data collection and central analysis, followed by a multi-author publication. The responses demonstrated overwhelming support for such a system; over 90% of the respondents agreed that a universal standard for reporting the derivation of hESC lines was essential as part of the international effort to advance the field efficiently, and over 87% plan to use this standard and share collected data in Spring 2008 for central analysis and public dissemination. A number of future steps are planned in order to ensure that this standard evolves with the field and remains relevant and up-to-date. Our aim is to incorporate these data within existing international initiatives aimed at improving derivation standards. This article is an open-access publication in order to make the convention freely available to the international community and encourage universal participation.
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Affiliation(s)
- Emma L Stephenson
- Advanced Center for Biochemical Engineering, University College London, London, UK
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Abstract
The emergence of the microarray data standards, especially the Minimum Information About a Microarray Experiment (MIAME), has spurred several organizations to develop their own standards for a myriad of technologies, including proteomics and metabolomics. These efforts have facilitated the creation of several large-scale gene expression repositories, including the toxicology-focused Chemical Effects in Biological Systems Knowledgebase at the National Institute of Environmental Health Sciences. Recently, efforts have been moved toward developing toxicogenomic data standards (e.g., MIAME-Tox), and the U.S. Food and Drug Administration and the U.S. Environmental Protection Agency either have developed or are developing regulatory guidance with respect to pharmaco- and toxicogenomics. However, for the toxicology community to be engaged in the process of standards development and approval, there needs to be a more thorough understanding of the terms associated with electronic data sharing and communication, especially with respect to defining the terms "standard," "controlled vocabulary," "object model," "markup language," and "ontology." This review will discuss these terms, especially as they pertain to toxicogenomics, how they relate to one-another, and what current efforts exist that may impact toxicology.
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Affiliation(s)
- Lyle D Burgoon
- Toxicogenomic Informatics and Solutions, LLC, P.O. Box 27482, Lansing, Michigan 48909, USA.
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Stephenson EL, Braude PR, Mason C. Proposal for a universal minimum information convention for the reporting on the derivation of human embryonic stem cell lines. Regen Med 2006; 1:739-50. [PMID: 17465755 DOI: 10.2217/17460751.1.6.739] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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