The Research Group of Biodiversity Informatics (BiodInfo Group), Key Laboratory of Animal Ecology and Conservation Biology, Chinese Academy of Sciences     >>Chinese

Research field:
The research field of the group is biodiversity informatics, focused on key technique and methodology of collection, processing, publishing and sharing of biodiversity data and information, developing the methods and software tools for biodiversity assessment, planning, designing and implementing biodiversity information system and database.

Major output:
1.Catalogue of Life, China(http://www.sp2000.org.cn): Catalogue of Life, China (2016 Annual Checklist) was published in August, 2016 by Science Press, Beijing. CoL China 2016 version follows the Standard Data Set of Species 2000 to collect and release Chinese species data. Considering the local requirement, a Chinese formal name and its Pinyin, a Roman form name, are appended in species records. The data items includes species accepted scientific name, Chinese name and its Pinyin (Chinese in Roman alphabet format), synonyms, common names, latest taxonomic scrutiny (name of person and date), source database, family to which species belongs, classification above family, and highest taxon in database, distribution, reference(s). A dynamic distribution map could be shown for each species in the checklist. The groups of species in 2016 Annual Checklist of Catalogue of Life China and their number of accepted species names are Animalia (32923), Bacteria (469), Chromista (2158), Fungi (3476), Plantae (41730), Protozoa (1729) and viruses (805). From 2008, the Species 2000 China Node, under the support of the Biodiversity Committee, CAS, organizes scientists to compile and release the CoL China each year. The 2016 version is the 9th edition of CoL China to be published. The BiodInfo Group develops a platform for species data collection, integrates animal data with plant and microbial data into annual checklists and maintains the CoL-China database system.

2. Taxonomic Tree Tool (TTT, http://ttt.biodinfo.org): TTT is a web-based platform for managing and comparing taxonomic trees. It allows users to create their own taxonomic trees through four different ways - inputting manually, uploading xml in the standard of Bisby Core, selecting taxa from template trees manually provided by TTT and selecting taxa from template trees according to a species list automatically. TTT provides an interactive managing tool for users to edit, update and review their trees, which is based on the standard of Bisby Core intended for transferring and reserving taxonomic information. Users can share their own trees with register users on TTT and compare them with the public trees. TTT provides a tool for comparing different trees to find out the spots where should be paid more attention by taxonomists or informatics scientists. The comparing tool explores taxa relationships from two different trees, and classified them into different types. The Accepted Name Relationship of 2 taxa means the accepted scientific name of Taxon A in Tree 1 appears in Tree 2 as the accepted scientific name of Taxon B; The Accepted Name-Synonym Relationship of 2 taxa means the accepted name of taxon A in Tree 1 appears in Tree 2 as a synonym of taxon B; the Synonym-Synonym relationship of 2 taxa means a synonym of taxon A in Tree 1 appears in Tree 2 as a synonym of taxon B. No Matched Status of a taxon means all names of a taxon in Tree 1 could not be found in Tree 2 whether as accepted scientific name or synonym.. Besides that, the tool helps to find out the differences of the taxonomic positions for taxon A and taxon B, and mark them out explicitly. Furthermore, it calculates the similarity of branches from two compared trees to help taxonomists judge whether the taxa groups chosen are the same and if it is necessary to continue drilling down the taxonomic trees for exploring more differences. TTT helps to extract common or different parts from two compared trees and the result can be exported for further tree integration research. TTT is a novel tool for managing taxonomic information and frees taxonomists from taxon to taxon method for investigating different taxonomic systems. The first version of TTT is online now. (Lin Contian, Qiao Huijie, Wang Jiangning, Ji Liqiang*, David Patterson. 2012. Taxonomic Tree Tool-a tool for managing and comparing taxonomic trees.)

3. Bisby Core: Bisby Core is a data standard for taxonomic classification and taxa, which is developed based on the characteristics of taxonomic data, and can be used to describe, store and exchange the taxa and taxonomic data. The standard is a mixed one which combines many existing data transfer standards, such as Darwin Core, Dublin Core and EOL Data Transfer Schema. It support multi-checklist and multi-lingual environment, and emphasizes on data scrutiny and link with authorized reference. There are 5 components in a standard document: The taxonomic tree component - describe the information of a taxonomic tree, such as the name of the tree, the author of tree and scrutiny of the tree, etc; The taxon information component - describe the taxonomic relevant data of taxon; The taxon attribute component - describes attributes of taxon in text and/or multimedia format, such as identification, biological description, habitat, distribution, photos; The reference component - describe information about references; The people component - describe information of expert who make scrutiny. There is a group of elements for information of taxonomic tree, such as name, description, authorship, copyright and scrutiny for the tree, and a group of elements required for multilingual environment, such as formal name in a non-English language and its roman alphabetic format, language tags in all text elements and reference descriptions. In memorial of the pioneer scholar in biodiversity, Prof. Frank Bisby, it's named as Bisby Core.

4. China Animal Scientific Database Service Platform (http://www.zoology.csdb.cn/): The China Animal Scientific Database Service Platform consists of 22 databases referred to zoological study in China: Fauna of China, Atlas of Animal in China, China Bird, China Bee, Fish in inland water, amphibians and reptiles in China, Orthoptera in China, Chinese Animal Inventory, Butterfly in Yunnan, Insect Type Specimen, Endangered and Protected Animal in China, Animal Name, etc. Users could search the databases by key word, browse by classification, or get date by click on the map.

5. Service System for Special Chinese Charecters in Biology(http://chinese.biodinfo.org/): This is a website collected special Chinese characters which occurs in biology references. Besides shape of characters, this website supplies pronunciations of Chinese. Authorized user can created Chinese characters which are not included in existed character sets. These functions are published in web services.
This site includes a management of Chinese characters' shapes and pronunciations and Chinese words' pronunciations.
Some special Chinese characters are not included the standard or popular character libraries, so when websites and applications want to show these characters, they can use the web services of this website.

6. Virtual Laboratory of Digital Insect (VLDI, http://www.vldi.org/): Virtual Laboratory of Digital Insect (VLDI) is initiated in 2011 by the Biodiversity Informatics Group (BIG) and the Laboratory of Integrated Pest Management Innovative Supporting Technology (IPMIST), which aims to develop new digital information technologies in entomology, and taxonomy. Through collecting data and methods and sharing resources and data processing, VLDI is running to serve researchers in taxonomy, pattern recognition and computer vision.
The website of laboratory was created in 2011 and currently published more than 200 well-processed images. VLDI currently includes:
1) online image processed interfaces which are useful for entomologists.
2) dataset of insect specimen images
3) related research publications of BIG team
And it will share more:
1) information analysis algorithms by general web services
2) image features extracted with classical methods

7. On-line Identification System of Butterfly(http://bes.biodinfo.org/Pages/ByImage/imgButterfly1.aspx):
This demonstration system is actually one part of Biology Expert System plan. It is currently configure to identify Chinese butterfly images which are in fixed format at the family level. Actually, this system can be configure to identify at either genus or species level.
This system collected images of over 60% species in China and all the images are well processed for image recognition method. Based on content-based image retrieval technology, we created this image recognition system with a flexible architecture, so it can be easily to expand for other groups of insects images. The system can only process specimen images, but we are improving it for nature pictures in future.
This project's website also supplys some other insect image recognition demos, and all these demos have the same and simple user interfaces.

8. Automatic Identification of Insect Images at the Order Level: This system is a desktop application system based on image process and pattern recognition technologies. The demo system can identify insect specimen images of 8 orders at the order level. The published version is based on one dataset published on VLDI. Users can also use this tool with their private datasets to create special automatic image identification systems. The desktop application can be downloaded on http://www.vldi.org/pubs.htm. We also created a web version for this application and the address is http://bes.biodinfo.org/Pages/ByImage/imgCommonOrder1.aspx

9. mMWeb: is an online working platform, that combines eighteen existing ecological niche models, a uniform method for modeling distribution patterns using a variety of modeling algorithms, and a common web browser. mMWeb executes multiple tasks in parallel on a super computer. An interface makes it possible to add a new algorithm into mMWeb which is written in C, Java, R or the other popular programming languages. mMWeb is an open source and freely available platform, which provides user friendly interface.

10. Predictive Species Distribution System(PSDS): Herein, we have proposed and implemented a predictive species distribution system (PSDS) based on GIS (Geographic Information Systems) and using multiple models, according to the situation in the field of species habitat modeling. The new system (PSDS 2.0) was developed from PSDS1.0, originally initiated by our research group. We introduced three models into PSDS 2.0, including a Mahalanobis Distance model (MD), an environmental envelope plus limiting factor model (EELF), and a support vector machine (SVM) model. In this paper, we describe the implementation of the system and introduce the main functions in detail. In order to compare and evaluate results from different algorithms, an iterative cross-validation technique has been implemented in PSDS 2.0, which also facilitates the selection of suitable algorithms for different sample data. A function for flexibly dealing with pseudo-absences has been incorporated into presence-absence models. A GIS interfaces with the software for data preparation and further analysis of the model results.

11. Species Data Collection Platform: SDCP is a web-based species data management workbench. Taxonomists and data manager can work on it to input, review, maintain and share taxonomic data. Biological classification is the core data in this platform, and various types of data are connected to taxa in the classification, including nomenclature information, references, biological description, distribution, multimedia, synonyms and common names and so on. It allows multiple experts to work on different parts of the same taxonomic tree. One classification can be edit and review by multiple users. All the data can be export as Bisby Core data file, and shared with other biodiversity informatics project. SDCP now is serving for CoL-China, EOL-China and Chinese Animal Scientific Database for data management.

12. Service System for Special Chinese Charecters in Biology(http://chinese.biodinfo.org/): This is a website collected special Chinese characters which occurs in biology references. Besides shape of characters, this website supplies pronunciations of Chinese. Authorized user can created Chinese characters which are not included in existed character sets. These functions are published in web services.
This site includes a management of Chinese characters' shapes and pronunciations and Chinese words' pronunciations.
Some special Chinese characters are not included the standard or popular character libraries, so when websites and applications want to show these characters, they can use the web services of this website.

Representative publications:

  • The Biodiversity Committee of Chinese Academy of Sciences, 2016, Catalogue of Life China: 2016 Annual Checklist, Science Press, Beijing, China
  • Huijie Qiao, Congtian Lin, Jiangning Wang, Liqiang Ji*, 2014, Process-oriented ecological modeling approach and scientific workflow system, Biodiversity Science, 3: 277-284.
  • QIAO HuiJie, HU JunHua, HUANG JiHong, 2013, Theoretical Basis, Future Directions, and Challenges for Ecological Niche Models, Science China Life Sciences, 3(11): 915-927.
  • Jiangning Wang, Congtian Lin, Liqiang Ji, Aiping Liang. 2012, A new automatic identification system of insect images at the order level, Knowledge-Based Systems, 33:102-110.
  • Jinkui Cheng, Bengui Xie, Congtian Lin, Liqiang Ji*, 2012, A comparative study in birds: call-type-independent species and individual recognition using four machine-learning methods and two acoustic features, Bioacoustics, 21(2):157-171.
  • Bo Zhang, Jinkui Cheng, Yan Han, Liqiang Ji*, and Fuming Shi, 2012, An acoustic system for the individual recognition of insects, the Journal of the Acoustical Society of America, 131(4): 2859~2865
  • Jiangning Wang, Liqiang Ji, Aiping Liang, Decheng Yuan, 2012,The identification of butterfly families using content-based image retrieval, Biosystems Engineering, 111(1):24-32.
  • Huijie Qiao, Congtian Lin, Liqiang Ji, Zhigang Jiang, 2012, mMWeb - An Online Platform for Employing Multiple Ecological Niche Modeling Algorithms, PLoS ONE 7(8): e43327.
  • QIAO Huijie, LIN Congtian, XU Zheping, CHEN Bin, CHENG Jinkui, WANG Jiangning, FENG Xiao, ZHANG Bo, JI Liqiang*, 2012, Bisby Core - A new data exchange standard for taxonomic data, Proceedings of the Ninth National Conference on the Conservation and Sustainable Use of Biodiversity in China, 488-521.
  • Jianging Wang, Liqiang Ji, Lu Wang, Lingwang Gao, Zuorui Shen, 2011, A sharing data platform for insect image researches. in: The 4th International Conference on BioMedical Engineering and Informatics. Shanghai, 4:2046-2048.
  • Jinkui Cheng, YuehuaSun, LiqiangJi, 2010, A call-independent and automatic acoustic system for the individual recognition of animals: A novel model using four passerines. Pattern Recognition 43: 3846~3852.
  • Member of BiodInfo Group:

    PI: Ji Liqiang, Ph.D., Professor
    Faculty and Staff: Han Yan, Qiao Huijie, Lin Congtian, Wang Jiangning, Wang Tianshan
    Graduate students: Huang Xiongwei, Zheng Yan, Xi Tianyu, Grace Mwende Kioko

    Contact Address:

    Prof. Liqiang Ji
    Institute of Zoology, Chinese Academy of Sciences
    1 Beichen West Road, Chaoyang District
    Beijing, 100101, China
    Tel: +86-10-64807129
    Fax: +86-10-64807099
    Email: ji@ioz.ac.cn