The ambiguous bioinformatics domain: A conceptual map of information science applications for molecular biology

Denn, Sheila O.; MacMullen, W. John

doi:10.1002/meet.14503901110

Cited by 5 publications

(7 citation statements)

References 15 publications

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“…In a previous work (Denn & MacMullen, 2002), we mapped basic and applied ILS research and practice foci to a representative molecular biology experimental cycle to provide examples of insertion points for information scientists. Here we continue that work and describe some possible research streams that cut across ILS subdomains.…”

Section: Information Science Research Streams and Insertion Pointsmentioning

confidence: 99%

Information problems in molecular biology and bioinformatics

MacMullen

Denn

2005

J. Am. Soc. Inf. Sci.

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In this article we provide an overview of opportunities for research and practice in the domain of molecular biology by information and library scientists. We introduce the changing role of data and information in molecular biology, and how molecular biology is evolving from a technique-and technology-driven science to an information-driven science. We then describe the highlevel objectives of molecular biology and some broad classes of problems from an information perspective. We illustrate the high-level objectives with examples of specific tasks performed by biologists. Finally, we provide some programmatic direction for information and library science research streams and insertion points.

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Section: Information Science Research Streams and Insertion Pointsmentioning

confidence: 99%

Information problems in molecular biology and bioinformatics

MacMullen

Denn

2005

J. Am. Soc. Inf. Sci.

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“…Interoperability and compatibility of information resources remains one of the biggest challenges for bioinformatics 16 . The initial purpose of bioinformatics was to manage the biological data with computers; but, after the completion of Human Genome Project in 2003, bioinformatics now aims to manipulate and ultimately discover new biological knowledge through several levels of increasing complexity and format of information resources such as genomics, proteomics, trascriptomics, metabolomics, etc.…”

Section: Information Resource Integrationmentioning

confidence: 99%

Metadata Description Framework for Integration of Bioinformatics Information Resources: A Case of iBIRA

Ram¹,

Rao²

2014

DJLIT

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Bioinformatics emerged as a new discipline dedicated to the answer the queries about life science using computational approaches. The basic aim of bioinformatics is to create databases, analyse data sets and managing data generated through large-scale projects such as Human Genome project (HGP). It covers a wide variety of traditional computer science domains, such as data modeling, data retrieval, data mining, data integration, data managing, data warehousing, and simulation of biological information generated through laboratory and field experiments. Due to varied form, nature, and activities in the field of bioinformatics, presenting the information in cohesive fashion is major challenge. The bioinformatics information resources are heterogeneous in nature. Integration and interoperability of information is one of the biggest challenges in this field. Bioinformatics, as an emerging field, needs attention towards metadata application for resource discovery. This paper discusses the metadata element set description framework for integration of various information resources related to the field of bioinformatics available over internet. A web-based tool iBIRA: Integrated Bioinformatics Information Resources Access has been designed and developed for integration of bioinformatics information resources. Dublin Core metadata element set has been used for description of information resources and XML schema has been used for interoperability of information resources with others. A database has been designed using structure query language (SQL)-database management system and hypertext preprocessor (PHP)-as web programming languages for integration of bioinformatics resources. The database is designated to categorise various resources into biological database, institutions, journals, patents, software tools, web-servers, etc., and the search result is presented in the form of 'tree view'. Each of these categories of the resources has been analysed for their metadata element set as per the DCMI terms.

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“…In this description the behavior of polypeptides under physiological conditions parallels the behavior of a query under different user cognitive conditions. The critical role, however, of "information" (in the library and information science sense) remains (Denn & MacMullen, 2002;Gywne, 2002;Luscombe, Greenbaum & Gerstein, 20011, as does the search for resolving data modeling related problems, such as applying Extensible Markup Language (XML).…”

Section: Bioinformatics Definedmentioning

confidence: 99%

“…They classify the "insertion points" of information science research into this experimental cycle as "the development of new tools and methods for managing, integrating, and visualizing data; the application of tools and methods for integration, inference and discovery; and theoretical approaches to biological information." Denn and MacMullen (2002) identify several sources for information on each insertion point: (a) new tool development (Brazma, et al, 2001;Gene Ontology Consortium, 2001;Nucleic Acid Research, 2002;Paris, 1997;Searls, ZOOO), (b) applications (H. Chen, 1997;Corruble & Ganascia, 1997;Juvan, 2001;Karp, Paley, & Zhu, 2001;Raychaudhuri, 2002;Wise, 2000), and (c) theory (de Jong, 2002;Poingot, Lesteven, & Murtagh, 2000;Smalheiser & Swanson, 1996).…”

Section: Collaborative Opportunitiesmentioning

confidence: 99%

“…This review follows the recommendation (Altman & Koza, 1996;Bayat, 2002;Denn & MacMullen, 2002) that the desired fusion of biology and computing-bioinformatics-is best served by providing computer and information scientists with the fundamentals of biology and simultaneously offering biologists enough technical knowledge to understand how computer technology can facilitate and augment their work. However, the field evolves daily, making defining the field and demonstrating the work of bioinformatics a challenge.…”

Section: Introductionmentioning

confidence: 99%

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Bioinformatics

Benoît

2005

Annual Review Info Sci & Tec

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Base4: http://www.cis.udel.edu/-vagrawavbioinformatics/code; BIOML: http:/hioperl.org/Projects/XML java/base4javabioresources bioXML: http://stateslab.bioinformatics.med.umich.edu 208 Annual Review of Information Science and Technology CluSTr: http://www.ebi.ac.uWclustr EBI: http:l/www.ebi.ac.uk EBI-InterPro: ftp://ftp.ebi.ac.uWpub/databases/interpro EBI-Mutations: http://www.ebi.ac.uWmutationslindex.html EBI-Stats: http://www3.ebi.ac.uWserviceslDBStats EBI-Vis: http://industry.ebi.ac.uW-alanNisSuppNisAwarel EPD: ftp://ftp.ebi.ac.uWpub/databases/epd GDB: http://www.gdb.org Genecard: http://bioinfo.weizmann.ac.iVcards G M T

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The ambiguous bioinformatics domain: A conceptual map of information science applications for molecular biology

Cited by 5 publications

References 15 publications

Information problems in molecular biology and bioinformatics

Information problems in molecular biology and bioinformatics

Metadata Description Framework for Integration of Bioinformatics Information Resources: A Case of iBIRA

Bioinformatics

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