Biodiversity Data Integration in Taiwan and Linkages with Global Databases

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1 Biodiversity Data Integration in Taiwan and Linkages with Global Databases Kwang-Tsao Shao, Kun-Chi Lai, Yung-Chang Lin, Burke Chih-Jen Ko, You-Hua Cheng, Cheng-Hsin Hsu, Han Lee, Yueh-Chih Chen, Lee-Sea Chen and Hsiu-Wen Hsu Biodiversity Research Center, Academia Sinica PNC HK (25 mins)

2 Biodiversity Action Plan (Executive Yuan, 2001) D1201 Establishing biodiversity data exchange mechanisms as well as establishing and integrating related databases of government agencies and institutions; and periodically adding contents (National Science Council/Council of Agriculture, Academia Sinica, Ministry of the Interior, Ministry of Economic Affairs, Council of Indigenous Peoples, Department of Health, Ministry of Education, Environmental Protaction Administration, Ministry of Transportation and Communications.) D1301 Establishing national germplasm banks; conducting research, conservation and utilization on agriculture, forestry, fishery, animal husbandry, wild life, and micro organism genetic resources (Council of Agriculture/National Science Council, Academia Sinica, Ministry of Education, and Ministry of Economic Affairs.)

3 Milestone/Projects since ~2006 National Digital Archives Program (NDAP) 2007~2012 (TELDAP) by NSC 2001, Taiwan joined GBIF: Associate Participant 2002~2004 Catalog of Life Project of Taiwan (TaiBNET) by NSC ~ Established biodiversity portal (TaiBIF) of GBIF by NSC & COA 2008 TaiBIF merged with TELDAP 3

4 Species (scientific name) is the primary key (linker) to integrate all databases Scientific name is the only common field among different content in all biological databases. The unique key for global biological resources linking. (unique identifier, primary key) Search engine (( 物 種 名 錄 ), ), COL No way to search data in different databases without scientific name. Specimen Data Data (( 標 本 資 料 ), ), GenBank, etc. etc. (( 基 因 庫 等 ), ), BOL BOL Tree Tree of of Life Life (( 生 命 之 樹 ), ), TOL TOL Ecological Databases, EML EML (( 生 態 的 資 料 庫 )) Encyclopedia of of Life Life (( 生 命 大 百 科 )) EOL EOL 4

5 Catalogue of Life in Taiwan, TaiBNET

6 Automatic Automatictaxa taxa counts counts 77kingdoms kingdoms(+ (+ viruses) viruses) 58 58phyla phyla classes classes orders orders families families valid valid scientific scientificnames names 43,743 43,743synonyms synonyms 45,547 45,547Chinese Chinese common commonnames names

7 Species checklist searching by taxon or text of name Both valid and invalid names (synonyms) can be used for searching 7

8 User can download searched result, both xml and csv formats are available

9 Classification Synonym Download this this page page English English version version Upload Upload pictures Link Link to to other other websites Provide data data Species name species summary and and further link link to to other databases

10 Fishes link to Fish Database of Taiwan FishBase 10

11 Besides native species, introduced species, cultivated species, and naturalized species will be included

12 Tool for for users to to check scientific names quality control Paste in in scientific names

13 The 1st official Catalog of Life in Taiwan, a native species checklist, was published with CDs in Dec Totally native species 出 版 台 灣 物 種 名 錄 及 物 種 多 樣 性 研 究 (2008/12)

14 How many marine species in Taiwan? 12,464 Virus and Archaea excluded Bacteria 細 菌 界 Protozoa 原 生 生 物 界 Chromista 原 藻 界 Fungi 真 菌 界 Plantae 植 物 界 Animalia 動 物 界 Total A B A+B B 4,703 Cross-checking with WoRMS to estimate how many species in TaiBNET are marine organisms TaiBNET 52,100 A 7,761 WoRMS 17,000 Same genus names as in WoRMS; but not included in WoRMS yet

15 Total no. of Taiwan marine organisms in each phylum of Animalia (Cross-checking with WoRMS) Animalia 数 Porifera 31 Cnidaria 481 Platyhelminthes 30 Nematoda 4 Acanthocephala 5 Rotifera 50 Arthropoda 1954 Annelida 66 Sipuncula 7 Mollusca 2143 Tardigrata 22 Bryozoa 26 Chaetognatha 21 Echinodermata 165 Chordata 3110 总 计 Porifera Cnidaria Platyhelminthes Nematoda Acanthocephala Rotifera Arthropoda Related to numbers of taxonomists in each group Annelida Sipuncula Mollusca Tardigrata Bryozoa Chaetognatha Echinodermata Chordata

16 How many marine invasive species in Taiwan? 台 灣 海 洋 生 物 之 入 侵 種 有 多 少 種? 與 GISD 比 對 相 符 之 台 灣 陸 域 入 侵 種 219 種 219 terrestrial invasive species (matching GISD) GISD 669 種 TaiBNET 原 生 + 外 來 (native+ invasive) 52,625 種 海 洋 物 種 (marine species) 12,464 種 WoRMS 170,000 種 Global Invasive Species Database Homepage 台 灣 海 洋 入 侵 種 共 24 種, 減 去 台 灣 原 生 種, 但 已 入 侵 他 國 之 種 數 共 15 種, 結 果 為 9 種 24 marine invasive species in Taiwan. Deducting 15 Taiwan native species but invaded other countries; the result is 9 species only. 與 WoRMS 比 對 相 符 之 台 灣 海 洋 物 種 7,761 種 7,761 marine species matching WoRMS World Register of Marine Species Homepage

17 Search marine species information on TaiBNET & link to global databases Link to WoRMS for detailed page

18 675 species at National Plant Genetic Resources Center are linked to TaiBNET through scientific names

19 675 species at National Plant Genetic Resources Center are linked to TaiBNET through scientific names 1434 spp. 675 spp. = 759 spp. are mismatch spp. (non-native species) Magnoliophyta 木 蘭 植 物 門 :: Coniferophyta 毬 果 門 :: Pteridophyta 蕨 類 植 物 門 :: Cycadophyta 蘇 鐵 門 :: 1 Total: ,108 records Passport Data; 27,581 records Characterization Data; 4,002 records Image Data in 189 families 781 genus 1,434 species

20 TaiBNET & TaiBIF include microoragnism, agriculture, forestry, fishery and animal husbandry information Genus Species Bioresources Collection and Research Center Agricultural Research Institute(NPGRC) Taiwan Forest Research Institute Livestock Research Institute Livestock Research Institute Poaceae Livestock Research Institute Fabaceae 26 38

21 104 species at Bioresources Collection and Research Center are linked to TaiBNET through scientific names

22 104 species at Bioresources Collection and Research Center are linked to TaiBNET through scientific names

23 Link to Bioresources Collection and Research Center using Acetobacter pasteurianus as example

24 網站首頁

25 Generalized forms for ecological distribution data Form 1 Form 2 Form 3

26 Projects of the Fisheries Agency General browsing (browsing by project) Click project name

27 Integrate domestic biodiversity databases and link to global databases Biodiversity Global GBIF (Global Biodiversity Information Facility)) Species 2000 (COL), EOL, BOL, TOL, ITIS, BIOS, BioNET International, etc. Global species databases e.g. FishBase, AntBase, AlgaeBase, etc. Regional (Asia, Asia Oceania or Pacific) Species 2000 AO, ASEANET, PACINET, PBIF, etc. Taiwan TELDAP / TaiBIF (national node of GBIF) TBRD (distribution database) TELDAP (specimen database) TaiBNET (species checklist & experts namelist) Local Local organisms database (e.g. Fish Database of Taiwan) Institutions, NGOs, heritages, projects and publications, etc.

28 台 灣 生 物 多 樣 性 入 口 網 Taiwan Biodiversity Information Facility, TaiBIF Sponsored by: NSC COA NSC nd phase of NDAP NSC (2003) COA (2005)

29 Biota Taiwanica collecting & uploading status Uploading published Biota Taiwanica books to TaiBIF website; 21 books are done so far: Algal Flora (Marine Benthic Macroalgal Flora of Taiwan) Bryophyte Flora (Liverworts and Hronworts of Taiwan I. Lejeuneaceae ) Seed plants (Flora of Taiwan: Gentianaceae) Coral (Scleractinia( Fauna of Taiwan I. The Complex group; II. The Robust group) Crustacean Fauna (Stomatopoda( of Taiwan; Brachyuran Crabs; Paguroidea of Taiwan; Chirostylidae and Galatheidae; Hippoidea, Lithodoidea and Porcellanidae; Cirripedia: Thoracica Excluding The Pyrgomatidae and Acastinae) Insect Fauna (Orthoptera( Orthoptera; Heteropteran Fauna; Psylloidea; Hexapoda) Earthworm Fauna and Leech Fauna Fungal Flora II

30 Biota Taiwanica Vertebrates -- Fishes Taiwanese native species (English version) Can be accessed from TaiBIF A total of 6,575 animal species; plus 4,200 species in Flora of Taiwan (2 nd ed.) are linked directly to NTU s plant website Currently total number of species is 11,775

31 TaiBIF 目 前 由 國 科 會 生 物 處 委 託 中 研 院 生 物 多 樣 性 研 究 中 心 之 生 物 多 樣 性 資 訊 專 題 中 心 負 責 建 置 及 維 護

32 Scheme of Biodiversity Databases Integration in Taiwan Other existed websites and databases: Institutions, natural heritages, research projects, societies (NGOs), organisms Council of Agriculture Invasive species (COA-BAPHIQ 防 檢 局 ) Endemic species Eco-engineering (COA-ESRI 特 生 中 心 ) Biodiversity indicators (COA-GA 糧 農 處 ) Resources & distribution (COA-TBRD,TARI 農 試 所 TFRI 林 試 所, FA 漁 業 署.) Gene bank (COA NPGRC 作 物 種 原 中 心 ) Species/Taxon GIS distribution TaiBIF/TaiBNET Universities or Research Institutes New databases: ecosystem parameters, Chinese name of insects, wetland bird, whales & dolphins, gene bank of aquaculture.. National Science Council Cataloging specimens (NSC-NDAP) Taxonomic & basic information (NSC-NDAP& NBRPP 推 動 計 劃 ) Literature,research, projects,symposia, keywords,terminology. (NSC-STIC 科 資 中 心 ) Ecological distribution (NSC-LTER-NBRPP National Geographic Information System(NGIS) MOEc-WRA ( 水 利 署 ) EPA- Other agencies 32

33 TaiBNET and the Indigenous People Bio-Magazine

34

35

36

37 Global Biodiversity Information Facility : GBIF Started in 2002; 54 Country Participants, 45 international organizations; >220 0 million records (as of Nov. 15, 2010)

38 Species 2000 & ITIS Catalogue of Life A checklist of all the world s species; covers about 65% so far. Managed by 66 experts. Distribute 3,500 CDs to 79 countries every year. Major provider of taxonomic information for GBIF, EOL, CBOL, IUCN, BHL, GenBank, etc.

39 Biodiversity Heritage Library Founded by 10 major natural history museum libraries, botanical libraries, and research institutions Legacy taxonomic literature: 44,294 titles, 85,546 volumes, 31,965,272 pages (as of Nov. 15, 2010) Signed free sharing agreement with 68 journals

40 Tree of Life (TOL)

41 Encyclopedia of Life: EOL An international organization aiming to make freely available to anyone knowledge about all the world s organisms. Its website currently holds info on 1 million species. Realizing the dream of E. O. Wilson, Father of Biodiversity, i.e. to provide one-stop access to all relevant info of a species. Satisfying diverse needs of multiple users.

42 42

43 Barcode of Life (BOL) CBOL & ibol 5 yrs, 5M specimens, 500Kb species

44 2007/9/18-20 The 2 nd Barcode of Life Conference in Academia Sinica; 9/17 Fish-BoL conference; 9/21 Regional Barcode Meeting, South/East Asia. 44

45 Collaborate with OBIS Database Census of Marine Life (www.coml.org)( ) >230,000 species; estimated to be > 1 million (year 2000); 30 million observation records; 190,000 species

46

47

48 Cryobanking project for wildlife in Taiwan (2005-) Fish-1120(>3000), Amphibian & Reptile-115(>1500), Bird-100(1200) Mammal-55(>500), Insect & Invet.-750(2200) 48

49 Acad.Sini. (Fish), TESRI & NTNU (bird, mammal), Taipei City Zoo & NTNU (amphibian, reptile), NMNS (Invert.), TLRI (central bank) 49

50 Status of cryobanking tissue sample collections in COL 台 灣 物 種 名 錄 與 冷 凍 組 織 標 本 收 集 現 況 U

51

52 Collection Level Description Browse Nature Zoology (Collection Level) Info on Digital archives of fish fauna from Taiwan

53 Using EML & Darwin Core to collect and manage specimen and observational data, down to the species level. Sharing data with global databases such as OBIS, FishBase, WoRMS,, and GBIF. Collaboration Institutions Endemic Species Research Institute Darwin core 1.4 Food Industry Research and Development Institute Data in English Academic Sinica TAPIR National Taiwan University Data in Chinese National Museum of Natural Science Others Darwin core 1.4 (Chinese field) + Custom field 53

54 Browse survey/observation data e.g. Research projects of the Fisheries Agency May 2010 survey result of PIs of 39 projects, concerning data releasing time when a project ends: Right away: 25 projects After 1 year: 4 projects After 2 years: 3 projects After 3 years: 6 projects After 10 years: 1 project

55 National Committee for GBIF (Chinese, Taipei) An inter-agency committee (GBIF-ROC) on biodiversity data integration has been set up to work out a unified database format and technology to facilitate database integration in the future. 己 組 成 生 物 多 樣 性 資 訊 整 合 委 員, 含 各 機 構 代 表 及 學 者 專 家, 如 此 方 可 相 互 分 工 凝 聚 共 識 齊 心 協 力 格 式 統 一 永 續 經 營 ( 中 研 院 )

56 Request government agencies to set up timeline to complete the following tasks step by step: (1) Various government agencies, when signing execution agreements on biodiversity investigation-related work, should add a term demanding the surrender of digitized raw data after a project ends. (2) As to how long the data should remain open to the public; what the exchange platform and mechanism for data storage and maintenance should be; and how to divide and integrate the work and to share data; ; they can all be discussed and decided later on. 要 求 各 部 會 能 訂 定 期 程 逐 步 完 成 下 列 工 作 : (1) 政 府 各 機 構 在 各 類 與 生 物 多 樣 性 調 查 相 關 之 計 畫 執 行 同 意 書 中, 加 入 於 計 畫 結 束 後 應 繳 交 原 始 資 料 數 位 檔 的 條 款 (2) 至 於 資 料 應 公 開 之 期 限 交 換 平 台 交 換 機 制 資 料 之 倉 儲 及 維 護, 以 及 各 部 會 內 如 何 分 工 整 合 及 共 享 資 料 等, 均 可 再 作 進 一 步 之 研 議

57 Proposal for adding the following items to NSC project contracts In the case of biodiversity survey-related projects (field collection, observation, sampling questionnaire), Party B should upload, in accordance with the agreed formats, the temporal and spatial distribution raw data which include survey methodology, field definition and monitoring data, as well as License Agreement to the data management unit (data backup) commissioned by Party A. For uploading format and License Agreement, see the TaiBIF link (http://taibif.org.tw) on the website of Department of Life Sciences. 國 科 會 生 物 處 計 劃 合 約 修 訂 如 係 生 物 多 樣 性 調 查 相 關 計 畫 ( 野 外 採 集 觀 測 樣 本 戶 問 卷 ), 乙 方 應 將 調 查 所 獲 得 之 時 空 分 布 原 始 資 料 (raw data), 包 含 調 查 方 法 欄 位 定 義 及 監 測 數 據 等 資 料 及 授 權 同 意 書, 依 規 定 格 式 上 傳 至 甲 方 所 委 託 之 資 料 管 理 單 位 ( 含 異 地 備 份 ) ( 上 傳 資 料 格 式 及 授 權 同 意 書, 詳 見 該 網 站 )

58 Workshop on Biodiversity and Ecological Monitoring Information Management (w/ TFRI), 4 times in Sept. ~ Nov 與 林 試 所 合 辦 生 物 多 樣 性 暨 生 態 監 測 資 訊 管 理 研 習 會 及 建 立 研 習 會 之 線 上 資 料 目 錄 系 統

59 2010 NSC Workshop on Submitting & Managing Ecological Distribution Data May 25: National Sun Yat-sen U, College of Science June 1: National Chung-Hsing U, College of Life Sciences June 3: Forestry Research Institute June 8: National Dong Hwa University Organizers: Forestry Research Institute, Council of Agriculture Biodiversity Research Center, Academia Sinica

60 Cross-strait collaboration and sharing of biodiversity data 物 種 名 錄 COL; 標 本 資 料 ( 含 組 織 標 本 及 標 本 分 佈 ) BOL; 物 種 解 說 ( 含 標 本 及 特 徵 照 片 ) EOL; 生 態 照 片 及 影 片 EOL; 文 獻 BHL; 生 態 分 佈 觀 測 資 料 EML; 生 命 條 碼 BOL; 中 文 名 詞 對 照 COL; 科 普 資 料 Taiwan TaiCOL TaiEOL TaiBOL TaiBHL Taiwan Fish Database TaiBIF Architecture COL EOL BOL BHL Fishbase. GBIF China COL China EOL China BOL China BHL China FishBase China Integration platform? GBIF China? Collaboration & sharing of data and related info From 2010, began to promote cross-strait corporation and exchange of data for databases of species checklists, specimen (plants & fish first), and biodiversity scientific terms, as well as to establish a Traditional Chinese/Simplified Chinese/English conversion table of common names.

61 敬 請 指 教! Questions/Comments?

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