Biodiversity in China Zone II Versions EN1 Vol 2 (4) 2017
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A dataset of venomous animals in China
: 2017 - 09 - 04
: 2017 - 09 - 22
: 2017 - 11 - 17
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Abstract & Keywords
Abstract: This dataset of venomous animals in China integrates data of species taxonomy and active toxic ingredients of terrestrial venomous animals in China, as well as data of envenomation, poisoning and treatment therapy. The dataset contains 1,371 records, including 1,362 pictures of animal species, their protein sequences and molecular structures, and the data volume is 29 MB. The structure and standard of the dataset are designed and determined by experts of zoology in consultation with IT technicians. Biological experts collected and reviewed the data before importing them into the database. A data management system is designed and programmed to process all the collected data and to perform quality control. The dataset supplies useful data and information to researches of venomous animal species and development of toxic resources, as bioactive constituents in the toxins are one of the important sources of biomedicine. The dataset also provides knowledge to the public on the identification, prevention and treatment of animal toxin injuries.
Keywords: venomous animal; species; toxin; active ingredient; treatment
Dataset Profile
Chinese title中国有毒动物数据集
English titleA dataset of venomous animals in China
Corresponding data authorZhu Jianguo (zhu@mail.kiz.ac.cn)
Data authorsWang Lin, Li Wenhui, Zhu Jianguo
Geographical scopeChina
Data format*.xls, *.rarData volume29 MB
Data service system<http://www.sciencedb.cn/dataSet/handle/480>
Sources of fundingThe Science and Technology Data Resource Integration and Sharing Project "Database of Venomous Animals in China" (2014), Informatization Program of the Chinese Academy of Sciences (XXH12504-3-13)
Dataset compositionThe dataset consists of two sets of files:
(1) animal_toxin.xls has two worksheets: the "tbl_species" worksheet contains 50 records related to venomous animal species and the "tbl_toxin" worksheet has 1,321 records related to toxins. It has a size of 0.7 MB;
(2) image.rar contains 1,362 images, including 49 animal species photos, 1,249 protein sequence pictures and 64 molecular structure images. It has a size of 28 MB.
1.   Introduction
China is abundant of venomous animal species. The past two decades witnessed active exploration and utilization of animal toxin polypeptides in the field of biomedicine and drug development. Due to their high bioactivity, molecular diversity, functional and structural specificity, animal toxins become irreplaceable natural resources in the competitive development of new drugs.14 However, disturbance of human activities and over-exploitation of venomous animals have resulted in the continuous decline of venomous animal populations, and some species are at risk of extinction. On the other hand, there are over 46,000 poisoning cases in China in the recent 20 years, with a documented fatality rate of 2.52%. 5 Therefore, it is necessary to popularize the knowledge of venomous animals to the public, including identification and prevention of venomous species, poisoning treatment, and species conservation.6 The dataset integrates data of species taxonomy and active toxic ingredients of terrestrial venomous animals in China, as well as data of envenomation, poisoning and treatment therapy. It provides comprehensive information for the research and protection of venomous animals, and also for the rational development and utilization of toxic resources.
2.   Data collection and processing
We integrated three major categories of information into the dataset using database technology (Figure 1).


Figure 1   Contents of the dataset of venomous animals in China
2.1   Data sources
The taxonomic and ecological data of venomous terrestrial vertebrates and arthropods were collected from:(1) faunas and published papers;(2) photos taken from field surveys by experts of Kunming Institute of Zoology (KIZ), Chinese Academy of Sciences.Data of active toxic ingredients include such aspects as molecular names, molecular structures and functions, protein sequences and biological activities. These data were derived from:(1) research findings of KIZ;(2) published papers or authoritative websites (e.g., http://www.ncbi.nlm.nih.gov).Data of toxin prevention and treatment include contents on poisoning mechanism, clinic symptoms, injuries, prevention, and common treatment therapies. Data and their references were listed as one-to-one correspondence in the dataset.
2.2   Standards referred
The standards of this dataset follow related principles proposed by the Basic Science Data Sharing Center, National Science and Technology Infrastructure Platform. For metadata creation and description, we referred to "Core Metadata Standards for Dataset".7 For database building, operation and maintenance, as well as the compilation and utilization of all archive files, we referred to "Special Topic Database Construction Standards". 8 For data quality control and evaluation, we referred to "Data Resource Processing Guidelines". 9
2.3   Development of the data management system
In order to manage the data, we developed a data management system based on .NET and SQL Server 2000. The modules and functions of this management system are shown in Figure 2.


Figure 2   Modules and functions of the data management system
Users can make data queries and get results through the WEB site (http://www.swanimal.csdb.cn/animaldb_youdu), and only authorized users at KIZ can add, delete, update, export and print the data. The dataset described by this article was exported from the database and has been stored in Excel spreadsheets.
3.   Sample description
The structured data were stored in two sheets of the Excel file (animal_toxin.xls): "tbl_species" stored the taxonomic and ecological data, and "tbl_toxin" stored the data of toxins and toxin prevention. Metadata descriptions of the two sheets are shown in Tables 1 and 2, respectively.
Table 1   Metadata description in the "tbl_species" sheeta
Field nameField typeData samplebRelated filec
IDInt35/
Species nameCharBufo gargarizans/
OrderCharAnura/
FamilyCharBufonidae/
GenusCharBufo/
Identification featureTextProtruding eardrum and rough skin. The color of body back is generally brown, tan, or taupe ... belly is pale yellow-brown./
MorphologyTextMale body length 67 mm, female 79 mm. The width of the head is greater than the length …/
DistributionTextProvinces of Ningxia, Gansu, Qinghai, Sichuan in China/
Ecological characterTextLiving in alpine streams or marshes with an altitude of 1700-3700 m. Spawning in pond. Insect-feeding./
ReferenceTextFei Liang et.al. Atlas of Amphibians of China. Zhengzhou: Henan Science and Technology Press. 2000, p.136./
Species photoChar2015070610226523578.jpg2015070610226523578.jpg in the folder "image"
Poisonous partCharSkin gland/
Toxin typeCharMixed toxins/
Means of intoxicationCharEating by mistake or using utensils with secretions/
Toxicity descriptionTextThe poison glands of the skin and ear of Bufo gargarizans can secrete venenum bufonis… Toad toxins and bufogenin have a strong local anesthetic effect. In addition, some antimicrobial peptides with hemolysis have also been found in the toad./
Notes: a. Data in the Excel sheet are in Chinese; b. N/A means the field was not recorded and the data are hence not applicable/available; c. / indicates no associated document for the field.
Table 2   Metadata description in the "tbl_toxin" sheeta
Field nameField typeData samplebRelated filec
IDInt2254/
Species nameCharBufo gargarizans gargarizans/
Name of toxin moleculeCharAquaporn 1/
Protein sequenceCharBufo gargarizans gargarizans-Aquaporin-Sequence-01.jpgBufo gargarizans gargarizans-Aquaporin-Sequence-01.jpg in the folder "image"
Spatial structureCharBufo gargarizans gargarizans-Aquaporin-Structure-01.jpgBufo gargarizans gargarizans-Aquaporin-Structure-01.jpg in the folder "image"
Biological activityTextAquaporn can hydrolyze alkaline enzymes in pathogenic bacteria by disrupting the N-acetyl cell wall…/
Poisoning symptomsTextN/A/
Treatment and therapyTextN/A/
Reference of protein sequenceTexthttp://www.ncbi.nlm.nih.gov/protein/ACM51137.1/
Reference of spatial structureTextSui Haixin, Ren Gang. 2004. Structure and Mechanism of Water Channels. Progress in Chemistry. 16(2): 145-152./
Reference of biological activityTextSui Haixin, Ren Gang. 2004. Structure and Mechanism of Water Channels. Progress in Chemistry. 16(2): 145-152./
Reference of poisoning symptomsTextN/A/
Reference of treatment and therapyTextN/A/
Notes: a. Data in the Excel sheet are in Chinese; b. N/A means the field was not recorded and the data are hence not available/applicable; c. / indicates no associated document for the field.
Photos of species, together with images of protein sequences and certain molecular structures, were compressed into a RAR file named "image". The filenames of these images (.jpg) were stored in the field "Photo of species" in "tbl_species", and in the fields "Protein sequence" and "Spatial structure" in "tbl_toxin", respectively (Tables 1 & 2).
4.   Quality control and assessment
This dataset was derived from China Toxic Animal Database,10 which is updated aperiodically. At present, only species distributed in China are included, but we consider extending the data scope beyond national borders in the future. The database was built in accordance with relevant standard specifications proposed by the project teams of Data Environment Construction and Service of the Chinese Academy of Sciences and the Basic Science Data Sharing Center.7–9 The data were collected from KIZ research findings, as well as published monographs, research papers and authoritative websites. Data quality was evaluated by experts before data input, and after data storage, a spot check was conducted to ensure data reliability and integrity.
We developed a data management system for automatic verification of certain data fields. Meanwhile, we established standard specifications for China Toxic Animal Database, such as regulations for database creation and management, requirements specification, summary manual and detailed specification of software design, and guidelines for data collection and collation.
Non-professional clerks would be trained until they were qualified for data entry.
Approved through expert inspection, China Toxic Animal Database started to provide online services in 2015. So, the quality of this dataset is guaranteed.
5.   Value and significance
While animal toxins have been included in existing databases like the protein databases established by the National Center for Biotechnology Information of NIH, USA, and the animal toxins database set up by Hunan Normal University of China,11–12 these data are mainly for professional researchers of animal toxins. There are also websites and webpages prescribing emergency measures for venomous animal bites or stings, but these data are scattered, in lack of systematic knowledge and the latest research findings about venomous animals. Our dataset integrates the research results of KIZ and other research institutions in China, and includes the taxonomic and ecological description of venomous animals in China, their toxic ingredients, as well as the prevention and treatment of venomous animal injuries. The dataset is comprehensive, scientific and authoritative. It can support research institutes, universities and enterprises to develop and utilize the venomous animal resources. It can also help to raise public awareness of venomous animal conservation, or help government agencies, such as departments of environmental protection, customs and public security, to identify venomous animals in investigating illegal cases.
6.   Usage notes
The dataset is friendly to use. Tables 1 and 2 describe the data fields, which can help users to understand and use the data. It should be noted that the toxin protein sequence is stored in JPG format. Users need to extract data from pictures before further editing and utilization.
Acknowledgments
We thank Professor Zhang Yun from KIZ for his professional suggestions on this dataset, and Mr. Li Yingchun for his work on data entry.
1.
Zhang Y. Why do we study animal toxins? Zoological Research 36 (2015): 183 – 222.
2.
Lyu QM & Lai R. Advances in research on animal toxins and related drugs. Progress in Pharmaceutical Sciences 39 (2015): 897 – 904.
3.
Lyu QM, Lai R & Zhang Y. Animal toxins and human disease: from single component to venomous, from biochemical characterization to disease mechanisms, from crude venom utilization to rational drug design. Zoological Research 31 (2010): 2 – 16.
4.
Lan H & Chen YC. Venomous Snakes in China and Treatment of Snake Bite Injury. Shanghai: Shanghai Science and Technology Press, 2008.
5.
He Q, Xie LJ, Ma PB et al. Analysis of current situation of poisoning caused by poisonous animals, plants, and mushrooms in China. Adverse Drug Reactions Journal 15 (2013): 6 – 10.
6.
Zhou J, Yuan Y, Sun CY et al. Epidemiology of poisonous animal and plant poisoning in China, 2004-2013. Disease Surveillance 30 (2015): 403 – 407.
7.
Basic Science Data Sharing Center of the National Science and Technology Infrastructure Platform. Core Metadata Standard for Dataset. Beijing: Basic Science Data Sharing Center, 2011.
8.
Basic Science Data Sharing Center of the National Science and Technology Infrastructure Platform. Special Topic Database Construction Standard. Beijing: Basic Science Data Sharing Center, 2011.
9.
Basic Science Data Sharing Center of the National Science and Technology Infrastructure Platform. Data Resource Processing Guidelines. Beijing: Basic Science Data Sharing Center, 2011.
10.
Kunming Institute of Zoology, Chinese Academy of Sciences. Venomous Animal Database of China. Available at: <http://www.swanimal.csdb.cn/animaldb_youdu> [Accessed September 7, 2017].
11.
National Center for Biotechnology Information. NCBI Protein Database. Available: <https://www.ncbi.nlm.nih.gov/protein> [Accessed September 7, 2017].
12.
College of Life Sciences, Hunan Normal University. Animal Toxin Database. Available: <http://protchem.hunnu.edu.cn/toxin> [Accessed September 7, 2017].
Data citation
1. Wang L, Li W & Zhu J. A dataset of venomous animals in China. Science Data Bank. DOI: 10.11922/sciencedb.480
Article and author information
How to cite this article
Wang L, Li W & Zhu J. A dataset of venomous animals in China. China Scientific Data 2 (2017). DOI: 10.11922/csdata.2017.13.zh
Wang Lin
database building and maintenance.
MSc, Assistant Professor; research area: biodiversity informatics and landscape ecology.
Li Wenhui
data collection, collation and quality control for the active ingredient part.
Associate Professor; research area: molecular diversity structure and function in toxin protein polypeptide of amphibians and reptiles.
Zhu Jianguo
system design.
Associate Professor; research area: ecology and biodiversity informatics.
The Science and Technology Data Resource Integration and Sharing Project "Database of Venomous Animals in China" (2014), Informatization Program of the Chinese Academy of Sciences (XXH12504-3-13)
Publication records
Published: Nov. 17, 2017 ( VersionsEN1
Released: Sept. 25, 2017 ( VersionsZH1
Published: Nov. 17, 2017 ( VersionsZH2
References
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