scholarly journals Minimal Structure of the Database for Storing Organisms’ Biodiversity Data

2020 ◽  
Vol 19 (4) ◽  
pp. 855-879
Author(s):  
Anton Lyakh
Keyword(s):  
Data Exchange ◽  
Original Structure ◽  
Huge Amount ◽  
Biodiversity Data ◽  
Database Table ◽  
Minimal Structure ◽  
Formal Definitions ◽  
Other Information ◽  
Living Organisms ◽  
Definition Of

To date, a huge amount of data on organisms diversity has been accumulated. Databases help to store and use these data for scientific purposes. There exists several dozens of databases for storing biodiversity data that were described in publications. Each has an original structure which badly correlates with the structures of other databases. This complicates data exchange and the formation of big biodiversity data array. The cause of this situation is the lack of the formal definitions of universal data components, which allow to build the database with any data on the diversity of organisms. The analysis of publications and author’s experience show that such universal components are present in the characteristics of any organisms. For example, it is an organism taxonomic name and a location where it was found. There are six such components and they answer to one of the six questions: what, where, when, who, where from and where to. What determines the name of an organism; where determines the location where it was found; when indicates the date of finding; who enumerates the persons, who found and analyzed an organism; where from refers to publications, where data about an organism are extracted or published; where to shows in which biological collection an organism is put in. Each component corresponds to a separate database table. These tables are linked to the table with data about organism (individual) and they are not linked with each other. Attributes of the links between the organism table and the component tables are stored in intermediate tables. They are used, for example, to store bibliographic facts, descriptions of collection items or geographical points. They also act as docking stations to which tables with any other information are attached. The creation of any database about the diversity of living organisms begins with the definition of the table of organism specimens. It must be used even if there is no explicit data on organisms. In that case virtual organisms should be introduced and the other components should be linked with them by means of intermediate tables. The latter are docked to other data. Minimal structures of all the tables, links between them and examples of databases construction are described in the work.

Artificially making Lifeform

2021 ◽  
Vol 9 (10) ◽  
pp. 1290-1295
Author(s):  
Souvik Das
Keyword(s):  
Medical Community ◽  
Programming Algorithm ◽  
The Public ◽  
For Profit ◽  
Not For Profit ◽  
Funding Agencies ◽  
Proper Definition ◽  
Inanimate Matter ◽  
Living Organisms ◽  
Definition Of

Abstract: The word ‘life’ is a mysterious word with a chart of attributes that have neither been completed nor has been agreed upon by the race of humans. Probably the proper definition of life is impossible to identify for humans (the proof for this claim is given later) but the handbook to the secret shall be updated till the end, thanks to the inquisitive attitude of humans. For this piece, we shall adopt the description from the professional medical community of today. Though this topic falls midway between science and philosophy, this project is strictly technical. To quote dictionary.com, Life is the condition that distinguishes organisms from inorganic objects and dead organisms, being manifested by growth through metabolism, reproduction and the power of adaptation to environment- through changes originating internally; cambridge.com teaches Life is the period between birth and death, or the experience or state of being alive; medicaldictionary.thefreedictionary.com states Life is the property or quality that distinguishes living organisms from dead organisms and inanimate matter, manifested in functions such as metabolism, growth, reproduction and response to stimuli or adaptation to the environment originating from within the organisms. There are several other definitions but to summarize, we can safely state that though the concept is somewhat vague, we could indeed point out some common principles. We shall, in this project, try to replicate the characteristics so as to attain life in medical terms. (The order does not base upon importance of the listed character since the characters, all of them are absolute essentials and cannot possibly be categorized as more or less important). 1) Metabolism 2) Growth 3) Adaptability 4) Birth 5) Death 6) Self-stimulated response to environment 7) Reproduction 8) Can sustain self without foreign intervention Keywords: artificial, life, intelligence, computer, programming, algorithm This research did not receive any specific grant from funding agencies in the public, commercial, or not-for-profit sectors.

Agents in bioinformatics

2005 ◽  
Vol 20 (2) ◽  
pp. 117-125 ◽  
Author(s):  
MICHAEL LUCK ◽  
EMANUELA MERELLI
Keyword(s):  
Data Analysis ◽  
Simulation Models ◽  
Biological Data ◽  
System Modelling ◽  
Agent Based Simulation ◽  
Huge Amount ◽  
Agent Based ◽  
Information Agents ◽  
New Knowledge ◽  
Definition Of

The scope of the Technical Forum Group (TFG) on Agents in Bioinformatics (BIOAGENTS) was to inspire collaboration between the agent and bioinformatics communities with the aim of creating an opportunity to propose a different (agent-based) approach to the development of computational frameworks both for data analysis in bioinformatics and for system modelling in computational biology. During the day, the participants examined the future of research on agents in bioinformatics primarily through 12 invited talks selected to cover the most relevant topics. From the discussions, it became clear that there are many perspectives to the field, ranging from bio-conceptual languages for agent-based simulation, to the definition of bio-ontology-based declarative languages for use by information agents, and to the use of Grid agents, each of which requires further exploration. The interactions between participants encouraged the development of applications that describe a way of creating agent-based simulation models of biological systems, starting from an hypothesis and inferring new knowledge (or relations) by mining and analysing the huge amount of public biological data. In this report we summarize and reflect on the presentations and discussions.

JCAMP-DX for electron magnetic resonance (EMR) (IUPAC Recommendations 2006)

2006 ◽  
Vol 78 (3) ◽  
pp. 613-631 ◽  
Author(s):  
Richard Cammack ◽  
Yang Fann ◽  
Robert J. Lancashire ◽  
John P. Maher ◽  
Peter S. McIntyre ◽  
...  
Keyword(s):  
Magnetic Resonance ◽  
Data Exchange ◽  
Electron Magnetic Resonance ◽  
Data Sets ◽  
Chemical Structures ◽  
Magnetic Resonance Data ◽  
Good Laboratory ◽  
Ion Mobility Spectra ◽  
Definition Of ◽  
Year 2000

In this document, we define a data exchange format initially formulated from discussions of an International Union of Pure and Applied Chemistry (IUPAC) limited-term task group at the 35th Royal Society of Chemistry-ESR conference in Aberdeen 2002. The definition of this format is based on the IUPAC Joint Committee on Atomic and Molecular Physical Data Exchange (JCAMPDX) protocols, which were developed for the exchange of infrared spectra and extended to chemical structures, nuclear magnetic resonance data, mass spectra, and ion mobility spectra. This standard of the JCAMP-DX was further extended to cover year 2000 compatible date strings and good laboratory practice, and the next release will cover the information needed for storing n-dimensional data sets. The aim of this paper is to adapt JCAMP-DX to the special requirements for electron magnetic resonance (EMR).

scholarly journals The Single Window Concept in International Trade, Transport and Seaports

Pomorstvo ◽  
2019 ◽  
Vol 33 (2) ◽  
pp. 130-139 ◽  
Author(s):  
Edvard Tijan ◽  
Marija Jović ◽  
Mladen Jardas ◽  
Marko Gulić
Keyword(s):  
International Trade ◽  
Best Practices ◽  
Data Exchange ◽  
Transport Sector ◽  
Maritime Transport ◽  
Electronic Data ◽  
Trade Facilitation ◽  
Definition Of

This paper presents a review of electronic data exchange and Single Window concept in international trade, transport and seaports. The theoretic framework of international trade, trade facilitation, Single Window, transport sector, maritime transport and seaports is provided, as well as the definition of electronic data exchange and standards for data exchange. The time and cost (excluding tariffs) associated with documentary compliance procedure (exporting and importing a shipment of goods) are shown in order to better understand the complexity and the importance of simplifying administrative processes. The importance of stakeholder connectivity in the transport sector (with special emphasis on seaports) is demonstrated, and factors which affect the successful electronic data exchange in seaports are shown. The advantages of smoother electronic data exchange are provided through the analysis of several Single Window examples, which present regional best practices.

scholarly journals On Privacy Notions in Anonymous Communication

2019 ◽  
Vol 2019 (2) ◽  
pp. 105-125 ◽  
Author(s):  
Christiane Kuhn ◽  
Martin Beck ◽  
Stefan Schiffner ◽  
Eduard Jorswieck ◽  
Thorsten Strufe
Keyword(s):  
Communication Networks ◽  
Ad Hoc ◽  
Building Blocks ◽  
Anonymous Communication ◽  
Formal Definition ◽  
Formal Definitions ◽  
Definition Of

Abstract Many anonymous communication networks (ACNs) with different privacy goals have been developed. Still, there are no accepted formal definitions of privacy goals, and ACNs often define their goals ad hoc. However, the formal definition of privacy goals benefits the understanding and comparison of different flavors of privacy and, as a result, the improvement of ACNs. In this paper, we work towards defining and comparing privacy goals by formalizing them as privacy notions and identifying their building blocks. For any pair of notions we prove whether one is strictly stronger, and, if so, which. Hence, we are able to present a complete hierarchy. Using this rigorous comparison between notions, we revise inconsistencies between the existing works and improve the understanding of privacy goals.

scholarly journals The HUPO Proteomics Standards Initiative Meeting: Towards Common Standards for Exchanging Proteomics Data

2003 ◽  
Vol 4 (1) ◽  
pp. 16-19 ◽  
Author(s):  
Sandra Orchard ◽  
Paul Kersey ◽  
Henning Hermjakob ◽  
Rolf Apweiler
Keyword(s):  
Data Storage ◽  
Mass Spectroscopy ◽  
Protein Interactions ◽  
Data Exchange ◽  
Data Representation ◽  
Protein Protein Interactions ◽  
Proteomics Data ◽  
Inaugural Meeting ◽  
Minimum Requirements ◽  
Definition Of

The Proteomics Standards Initiative (PSI) aims to define community standards for data representation in proteomics and to facilitate data comparison, exchange and verification. Initially the fields of protein–protein interactions (PPI) and mass spectroscopy have been targeted and the inaugural meeting of the PSI addressed the questions of data storage and exchange in both of these areas. The PPI group rapidly reached consensus as to the minimum requirements for a data exchange model; an XML draft is now being produced. The mass spectroscopy group have achieved major advances in the definition of a required data model and working groups are currently taking these discussions further. A further meeting is planned in January 2003 to advance both these projects.

On the applicability of dialetheism and philosophy of identity to the definition of life

2010 ◽  
Vol 9 (2) ◽  
pp. 131-136 ◽  
Author(s):  
Vera M. Kolb
Keyword(s):  
Life Forms ◽  
Definition Of Life ◽  
Individual Organism ◽  
Numerical Identity ◽  
Chemical Systems ◽  
Daughter Cells ◽  
Important Idea ◽  
Living Organisms ◽  
Definition Of

AbstractWe have found that the principles of dialetheism, which state that some contradictions (typically at the limits of a system) may be true, and which amply demonstrate the limits of thought and conception, can be valuable in sorting out and clarifying some astrobiological problems that impede our ability to define life. The examples include the classification of viruses as alive or not alive, and the description of the transition zone for the abiotic-to-biotic transition. Dialetheism gives us the philosophical tool to state that the viruses may be both alive and not alive, and that chemical systems may exist that are both abiotic and biotic.We have extracted some philosophical principles of the identity and have applied them to the identity of living organisms and their life forms. The first and most important idea is that we should define an individual organism via its numerical identity. For each organism its identity will be in relation to itself. As the organism undergoes various changes during its development, and as it transitions from one to the next of its life forms, one can observe numerous qualitative differences between these life forms. Although the life forms change and the organism is in a flux, what remains constant is the numerical identity of the organism. If the organism reproduces, for example by a fission mode, then the daughter cells will have their own numerical identity. We can state that the life of an organism is a sum of all its life forms over the period of time of the existence of the organism. Reproduction, particularly by fission, represents an identity dilemma, but it can be resolved by Gallois' occasional identities theory.

scholarly journals The Environmental Dimensions of Islam

2002 ◽  
Vol 19 (2) ◽  
pp. 113-116
Author(s):  
Soumaya Pernilla Ouis
Keyword(s):  
Human Beings ◽  
Senior Lecturer ◽  
Islamic Studies ◽  
Divine Origin ◽  
Living Organisms ◽  
Definition Of ◽  
The University ◽  
Positive Force

Dr. Mawil Izzi Dien, Senior Lecturer in Islamic Studies at the University ofWales, has been writing about Islam and environmental issues for almosttwo decades. The Environmental Dimensions of Islam is a summary of hisprevious writings presented together with new additions. Izzi Dien is oneof the most prominent scholars in the new discourse of Islamic ecotheology,although he himself seldom refers to other Muslim scholars in this field,which somehow gives the wrong impression that he is the only one amongMuslims dealing with environmental issues.After a short introductory chapter, Izzi Dien discusses in chapter 2"The Environment and Its Components in Islam." This chapter gives aninformative introduction to Qur'anic terminology on various environmentalcomponents and their status in Islam, such as water, earth, living organisms,diversity and biogeological cycles.This Qur'anic terminology is further developed in chapter 3, deaLingwith theology pertaining to the environment. This chapter deals with issuessuch as the question of creation and the unseen and the Divine origin ofeverything: constancy, comprehensiveness, balance, and universal laws innature as the Creation. I sympathize with much of the argument presentedregarding the role of human beings in Creation, i.e., their trusteeship, partnershipand responsibility. This chapter would have been strengthened by adiscussion of the accusations from the environmental movement that themonotheistic religions represent an anthropocentric, and thus problematic,view of nature. For instance, the idea expressed in the Qur'an that God madenature subservient 􀀱·akhkhara) to human beings may be criticized (seeQur'anic verses 2:29; 45:12-13; and 14:33-34), but the author chooses notto discuss this concept at all or to refer to other scholars' criticisms.Another problem is his unusual definition of positivism, a philosophyheld accountable for promoting a hegemonic position of science associatedwith a problematic view of nature. He sees positivism as something thatIslam promotes, as in his view, it implies that human beings "are an active,positive force placed on this earth to construct, improve, and reform it." lnthe Qur'an we read about examples of how people who destroyed their ownhabitat were punished by God in the form of ecocatastrophes ...

scholarly journals Web Services Menggunakan Format JSON

Respati ◽  
2019 ◽  
Vol 14 (2) ◽  
Author(s):  
Robby Cokro Buwono
Keyword(s):  
Information System ◽  
Information Systems ◽  
Web Services ◽  
Data Exchange ◽  
Computer Network ◽  
Data Services ◽  
Exchange Information ◽  
Other Information ◽  
Share Data ◽  
The Web

INTISARISistem informasi dibuat untuk membantu kegiatan di suatu organisasi dan pengambilan keputusan para pimpinannya. Sistem informasi sudah banyak dibuat organisasi namun data atau informasi yang dihasilkan selalu berdiri sendiri sehingga mengakibatkan kesulitan mendapatkan informasi yang terkait antar sistem informasi pada organisasi tersebut, terjadi duplikasi informasi dan menjadikan informasi tidak berupa kesatuan yang lengkap dan utuh.Web sebagai sarana penyampaian informasi yang sederhana dari satu tempat ke tempat lain melalui jaringan komputer. Web dapat dimanfaatkan pula sebagai sarana interoperabilitas dan berbagi informasi antara sistem informasi di suatu organisasi. Suatu klien sistem informasi yang berada pada jaringan komputer dapat meminta layanan data berupa web services kepada server sistem informasi yang menyediakan layanan data yang diminta dengan cara mudah.JavaScript Object Notation (JSON) merupakan seperangkat aturan untuk memformat data berbasis teks yang ringan digunakan pada pertukaran data. Layanan web (web services) pada komunikasi antar sistem informasi untuk bertukar informasi dapat menggunakan JSON agar mendapatkan kemudahan mendapatkan informasi yang dibutuhkan dan untuk mendapatkan integritas data yang dihasilkan dari berbagai sistem informasi pada organisasi tersebut.Peneliti melakukan pengembangan web services untuk berbagi data antar suatu sistem informasi yang dibutuhkan oleh sistem informasi yang lainnya dengan format menggunakan JSON. Peneliti mengharapkan adanya web services dengan format JSON yang dapat membantu sistem informasi untuk mendapatkan informasi yang dibutuhkan dan mendapatkan integritas data yang dihasilkan antara sistem informasi tersebut.Kata kunci— web services, JSON, interoperabilitas, sistem informasi. ABSTRACTInformation systems are made to assist activities in an organization and the decisions of its leaders. Many information systems have been created by the organization, but the data or information produced always stands alone, resulting in difficulties in getting information related to information systems in the organization, duplication of information and making the information, not in the form of a complete and intact unit.The web as a means of delivering simple information from one place to another through computer networks. The web can also be used as a means of interoperability and information sharing between information systems in an organization. An information system client located on a computer network can request data services in the form of web services to an information system server that provides requested data services in an easy way.JavaScript Object Notation (JSON) is a set of rules for formatting lightweight text-based data used in data exchange. Web services (web services) on communication between information systems to exchange information can use JSON to get the ease of getting the information needed and to obtain data integrity generated from various information systems in the organization.The researcher develops web services to share data between information systems needed by other information systems in a format using JSON. The researcher expects the existence of web services with JSON format that can help information systems to get the information needed and get the integrity of the data generated between the information systems.Kata kunci—  web services, JSON, interoperability, information systems.

scholarly journals Setting the Stage – The Life Cycle of Bio-logging Data: Origin, Mobilization and Data Exchange

2018 ◽  
Vol 2 ◽  
pp. e25914
Author(s):  
Holger Dettki ◽  
Peggy Newman ◽  
Sarah Davidson ◽  
Francesca Cagnacci
Keyword(s):  
Life Cycle ◽  
Spatial Data ◽  
Data Exchange ◽  
Meta Analysis ◽  
Physiological Data ◽  
Biodiversity Data ◽  
Mass Size ◽  
Machine Readable ◽  
Exchange Data

In recent years, bio-logging data, automatically gathered by sensors deployed on animals, has become one of the fastest growing sources of biodiversity data. This is largely due to the steadily declining mass, size and costs of sensors, continuously opening new opportunities to monitor new species. While previously ‘tracking data’—data from spatially enabled sensors such as GPS sensors—was most prominent, currently almost 70% of all bio-logging data is comprised of non-spatial data as e.g., physiological data. In contrast to the biodiversity data community, where standards to mobilize and exchange data are relatively well established, the bio-logging community is still lacking standards to transport data from sensors into repositories, or to mobilize data in a standardized format from different repositories to enable cooperation between users, shared software tools, data aggregation for meta-analysis, or a consistent format for long-term archiving. To set the stage for a discussion about standards for bio-logging data to be developed or adapted, we present a mind map describing the different pathways of bio-logging data during its life cycle, and the opportunities for standardization within this cycle. As an example we present the use of the Open Geospatial Consortium (OGC) ‘SensorML’ and ‘Observations & Measurements’ standards to transfer bio-logging data from a sensor to a repository and ultimately to a user for subsequent analysis. These standards provide machine-readable methods for describing bio-logging sensors and the measurements they collect, offering a standardized structure that can be customized by the bio-logging community (e.g. with standardized vocabularies) to achieve interoperability.

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