Int.J.Curr.Microbiol.App.Sci (2018) 7(12): 3008-3012

International Journal of Current Microbiology and Applied Sciences ISSN: 2319-7706 Volume 7 Number 12 (2018) Journal homepage: http://www.ijcmas.com

Review Article https://doi.org/10.20546/ijcmas.2018.712.345

Significance of Bioinformatics in the Conservation of Biodiversity and Databases

Rakesh Ranjan1, Saket Vinayak1 and Shanker Kumar Pandey2*

1University Centre of Bioinformatics (Sub-DIC), T.M. Bhagalpur University, Bhagalpur- 812007, India 2Department of Botany, Jamtara College, Jamtara, Jharkhand- 815351, India

*Corresponding author

ABSTRACT

Biodiversity is commonly used for the totality and variability of species, genes and the ecosystems. They occupy at three levels i.e generic, species and ecology. Recently the advancement in bioinformatics is mainly accelerated by the study of molecular events using data obtained by exhaustive experiments such as whole genome sequencing, functional annotation, expression analysis and some others. However, the complete value of molecular biological information cannot be realized until it is possible to correlate

K e yw or ds genetic information with native habitat, neurobiology, physiology, or with genealogical relationships of the species. At the same time, biodiversity informatics would greatly Bioinformatics, benefit from inter-compatibility with molecular-level databases. The massive development Biodiversity, of biodiversity related information systems over the WWW (World Wide Web) has Conservation, created much excitement in recent years. Biodiversity information can be considered the Databas e, Research basic data on the occurrence and diversity of species (or indeed, any recognizable taxa), commonly in association with information regarding their distribution in space, time, or Article Info both. Such information may be in the form of retained specimens and associated

information, for example as assembled in the natural history collections of museums and Accepted: 20 November 2018 herbaria, or as observational records, for example either from formal faunal or floristic Available Online: surveys undertaken by professional biologists and students, or as amateur and other 10 December 2018 planned or unplanned observations including those increasingly coming under the scope of citizen science. Providing online, coherent digital access to this vast collection of disparate primary data is a core. Biodiversity Informatics function that is at the heart of regional and global biodiversity data networks. There is a resonance between the needs of biodiversity science and the opportunities for globalization and interoperability provided by the internet. The main objective of the bioinformatics projects is to conserve the biodiversity and permit data interoperability and knowledge synthesis across wide arrays of local systems, and to embed them in global knowledge. This paper emphasizes the importance of bioinformatics in the conservation of biodiversity databases of scattered data for biotechnological and agricultural research.

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Int.J.Curr.Microbiol.App.Sci (2018) 7(12): 3008-3012

Introduction consideration in biodiversity science is the need to bring more than 25 decades worth of Biodiversity stands for all living things on accumulated information into an earth. It refers to the range of variations electronically available format. Unlike other among a set of entities and is commonly used sub disciplines of biology, biodiversity to describe variety and variability of living (primarily taxonomic and ecological) research organisms in terms of genetic diversity, results do not rapidly go out of date. In fact, species diversity and ecological diversity. In many such results probably cannot be simple terms, Biodiversity is the vast variety replicated because of anthropogenic habitat of natural plant and animal life existing in any modifications that have occurred since the region. The biodiversity is usually studied research was done. In addition, new data now by taxonomist who takes great pains in types are being generated by satellite imagery collecting, identifying, documenting and and other measures of non-biological global describing the elements of diversity. There is phenomena that have significant influence a resonance between the needs of biodiversity upon biodiversity. Great forward strides could science and the opportunities for globalization be made in the understanding of the biological and interoperability provided by the internet. world, for instance, if informatics techniques Global biodiversity depends on several were developed to make it possible to parameters such as biomass, ecosystems, correlate historical information with newly phyla, floras and faunas, hot-spots, genetic collected satellite data; if molecular genetic erosion, the impact of aliens and others. The datasets could be linked to species- goal for biodiversity informatics projects is to documentation datasets such as those held by develop systems that permit data natural history collections; and if interoperability and knowledge synthesis neurobiological, physiological, chemical, and across wide arrays of local systems, and to other datasets could be correlated with embed them in global knowledge taxonomic and ecological ones. architectures. In the last three decades, brain and behavioral research has experienced Biodiversity conservation and explosive growth because conceptual links Bioinformatics have been made across different species, different levels of biological organization, and Biodiversity informatics is the application of different experimental and theoretical information technology methods to the approaches. The dramatic increase in the problems of organizing, accessing, visualizing amount of information has caused and analyzing primary biodiversity data. neuroscientists, of necessity, to increasingly Primary biodiversity data is composed of narrow their areas of specialty, just to be able names, observations and records of to keep up with publications most relevant to specimens, and genetic and morphological their own research. The cost of such data associated to a specimen. Biodiversity specialization is a decrease in the informatics may also have to cope with development of new conceptual linkages. managing information from unnamed taxa Thus, the amount of information generated by such as that produced by environmental the engine of interlinked research threatens to sampling and sequencing of mixed-field choke the engine itself. However, advances in samples. The term biodiversity informatics is informatics focused on brain and behavioral also used to cover the computational research information can prevent the stifling problems specific to the names of biological of this success. A major scientific entities, such as the development of

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Int.J.Curr.Microbiol.App.Sci (2018) 7(12): 3008-3012 algorithms to cope with variant the current absence of a complete master list representations of identifiers such as species of currently recognized species of the world, names and authorities, and the multiple although this is an aim of the Catalogue of classification schemes within which these Life project which has ca. 1.65 million entities may reside according to the species of an estimated 1.9 million described preferences of different workers in the field, species in its 2016 Annual Checklist. as well as the syntax and semantics by which "Primary" biodiversity information can be the content in taxonomic databases can be considered the basic data on the occurrence made machine query able and interoperable and diversity of species, commonly in for biodiversity informatics purposes. The association with information regarding their first step in biodiversity conservation is distribution in either space, time, or both. documentation based on the availability of Such information may be in the form of information about each species with data retained specimens and associated starting from its systematic position to information, for example as assembled in the molecular aspects. In many biodiversity natural history collections of museums and databases, data is held either about species or herbaria, or as observational records, for specimens such as (1) nomenclature-species example either from formal faunal or floristic name, geographical data and status scale; (2) surveys undertaken by professional biologists descriptive data- morphology, anatomy, and students, or as amateur and other planned chemistry, ecology etc., (3) economic or unplanned observations including those importance; (4) conservation status; (5) increasingly coming under the scope of images; (6) bibliography sources of data used citizen science. Providing online, coherent in the database. digital access to this vast collection of disparate primary data is a core Biodiversity Biodiversity database and Bioinformatics Informatics function that is at the heart of regional and global biodiversity data Taxonomists create the nomenclature and networks, examples of the latter including classification databases which can also OBIS and GBIF. contain all kinds if information about organisms, including their characteristics, As a secondary source of biodiversity data, economic importance, conservation and relevant scientific literature can be parsed management. Bioinformatics developed either by humans or (potentially) by technologies for the management of genomic specialized information retrieval algorithms to and proteomic data. In the past decade, extract the relevant primary biodiversity electronic storage media, WWW, database information that is reported therein, technology and digitalization of data creation sometimes in aggregated / summary form but of public databases are creating a revolution frequently as primary observations in in the way that biodiversity information is narrative or tabular form. Elements of such created, maintained, distributed and used for activity (such as extracting key taxonomic all these purposes. Biodiversity informatics identifiers, key wording / index terms, etc.) includes the application of information have been practiced for many years at a technologies to the management, algorithmic higher level by selected academic databases exploration, analysis and interpretation of and search engines. However, for the primary data regarding life particularly the maximum Biodiversity Informatics value, the species level organization. One major issue actual primary occurrence data should ideally for biodiversity informatics at a global scale is be retrieved and then made available in a

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Int.J.Curr.Microbiol.App.Sci (2018) 7(12): 3008-3012 standardized form or forms; for example both current generation of researchers, no matter the Plazi and INOTAXA projects are where they reside. This same information is transforming taxonomic literature into XML needed by persons with policy and decision formats that can then be read by client making responsibilities, and there are applications, the former using Taxon X-XML applications in education, both formal and and the latter using the taXMLit format. The informal, and industry to which the Biodiversity Heritage Library is also making information could contribute. With the proper significant progress in its aim to digitize investments in infrastructural and software substantial portions of the out-of-copyright developments, the advantages of modern taxonomic literature, which is then subjected informatics techniques can be employed to to OCR (Optical Character Recognition) so as exploit this intellectual wealth with great to be amenable to further processing using benefit not only to biological research, but to Biodiversity Informatics tools. decision and policy-makers, educationalists, and society at large. However, advancements Challenges in biodiversity information in informatics capabilities for biological sciences in data management, in network Biodiversity scientific information is highly connections, and in data content are still varied and includes quantitative and coded needed. tables, time-series as well as narrative and descriptive text. A common characteristic is In conclusion, biodiversity Informatics that it is often spatially referenced i.e. in map benefits from the adoption of appropriate form or with reference to point locations. The standards and protocols in order to support needed bioinformatics technology includes machine-machine transmission and database management systems, GIS, image interoperability of information within its analysis, statistical analysis and modeling. particular domain. Further there is a need to be able to locate an extract descriptive text, often involving large Examples of relevant standards include the quantities in disparate locations. This leads to Darwin Core XML schema for specimen- and requirements for key wording, indexing, observation-based biodiversity data developed hypertext linking, distributed networking, and from 1998 onwards, plus extensions of the for meta-database technology to assist in same, Taxonomic Concept Transfer Schema, locating appropriate data sources. The plus standards for Structured Descriptive Data biological information contained in print and Access to Biological Collection Data media, in outmoded electronic form, and in (ABCD); while data retrieval and transfer modern databases constitutes an intellectual protocols include DiGIR (now mostly wealth produced by decades and centuries of superseded) and TAPIR (TDWG Access research and considerable societal investment. Protocol for Information Retrieval). Many of Further advances in scientific understanding these standards and protocols are currently of biodiversity at the gene, organism, maintained, and their development overseen, population, species, ecological community by the Taxonomic Databases Working Group and landscape at global levels are to be made (TDWG). Biodiversity is distributed all over and the results of the work of the predecessors the world but the scientific information about as well as contemporaries of the world biodiversity is largely concentrated in major biological scientists should, using the centers in developed countries, especially in technologies now at our disposal, be made the scientific collections of the world’s readily and comprehensively available to the natural history museums, herbaria, and

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Int.J.Curr.Microbiol.App.Sci (2018) 7(12): 3008-3012 microorganism repositories. Data about References biodiversity are either scattered in many databases or reside on paper or other media Bioinformatics for Biodiversity? Science. not amenable to interactive searching. There 289: 2229–2440. 2000. is an enormous amount of information already Bisby FA. Biodiversity informatics and collected about the world’s biodiversity. Internet Science. 2000;283:2309. Colwell RK, Coddington JA. Phil Trans R However, to date most of this information has Soc. 1994;335:101. not been digitized. Thus, in most cases, the Jetz W, Rahbek C. Science. 2002; 297: 1548. only way a potential user can find data is to Peterson AT and Vieglais D (2001). travel physically to the place where the "Predicting Species Invasions Using specimen is housed or to contact the Ecological Niche Modeling: New repository where a relevant specimen may be Approaches from Bioinformatics Attack housed. The sustainable use and management a Pressing Problem" (PDF). BioScience. of bioinformatics is very much significant in 51: 363–371. the conservation of biodiversity and database. Rahbek C, Graves GR. Proc R Soc Lond. Biodiversity information is neither 2000; B267: 2259. immediately at hand, it is often not applied in Ruggiero, M.A., Gordon, D.P., Orrell, T.M., policy or management decisions that affect Bailly, N., Bourgoin, T., Brusca, R.C., the organisms involved, nor is that et al., (2015). "A higher level information readily accessible by the users. classification of all living organisms". PLoS ONE. 10 (4): e0119248.

How to cite this article:

Rakesh Ranjan, Saket Vinayak and Shanker Kumar Pandey. 2018. Significance of Bioinformatics in the Conservation of Biodiversity and Databases. Int.J.Curr.Microbiol.App.Sci. 7(12): 3008-3012. doi: https://doi.org/10.20546/ijcmas.2018.712.345

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