In vitro Conservation and Priliminary Molecular Identification of Some Turkish Domestic Animal Resources-I TURKHAYGEN-I PROJECT DATABANK: USING DATABASE AND INFORMATICS TECHNOLOGY ON BIOLOGICAL DATA ORGANIZATION Bio. Fatih KARAKAYA, BSc. Researcher TUBITAK MARMARA RESEARCH CENTER Genetic Engineering and Biotechnology Institute 17th June 2010 ITAFFE 10 Samsun - Turkey
Presentation Plan General abstract of the project Conserved breeds Project scheme Web site overview Material coding system Database procedure Project databank content Databank structure Credits
General Abstract of the Project Sezen Arat Principle Investigator Executive coordinator for the Project Administration Committee (PAC) Inci Togan PAC Member Okan Ertugrul PAC Member Serhat Pabuccuoglu PAC Member Hakan Sagirkaya PAC Member Umut Tasdemir PAC Member Ercan Kurar PAC Member
General Abstract of the Project Owner Institution: Turkish Ministry of Agriculture and Rural Affairs Administrative Institution: TUBITAK Marmara Research Center GEBI Partner Institutions: Adnan Menderes University Ankara University Ataturk University Istanbul University Lalahan Livestock Central Research Institute Middle East Technical University Mustafa Kemal University Namık Kemal University Ondokuz Mayıs University Selçuk University Uludağ University
General Abstract of the Project Animal genetic resources are considered as a part of the present biodiversity. Unfortunately; our native animal genetic resources have not been appreciated as it should have been; some are already gone extinct and some are at the edge of extinction. Yet, Animal genetic resources must be considered as the insurance of the future, since they may have an important potential to improve social and economic life.
General Abstract of the Project The project In vitro Conservation and Priliminary Molecular Identification of Some Turkish Domestic Animal Resources-I aims to establish a cryobank of biological materials as embryo, semen, somatic cell and DNA where in both GEBI, MRC, Kocaeli and LLCRI (Lalahan Livestock Central Research Institute), Ankara in conformity with FAO proposals.
General Abstract of the Project The project comprises: 13 sheep 6 cattle 5 goat Anatolian water buffalo 5 horse breeds The collection of one breed is planned to be 50 individuals to keep the biological variation in the cryobank for the future recovery if in need with cloning technologies.
Conserved Breeds Sheep Karayaka Herik Imbroz Karagul Red Karaman White Karaman Chios Kivircik Daglic Awassi Cine Capari Hemsin Norduz Cattle South Anatolian Red East Anatolian Red Native Southern Yellow Anatolian Grey Anatolian Black Zavot Water Buffalo Anatolian Water Buffalo Goat Angora Kilis Native Hairy Norduz Honamli Horse Canik Malakan Hinis Ayvacik Pony Cukurova
Project Processing Scheme
Site overview
Site overview www.turkhaygen.gov.tr The public accessed site portal is in two languages as Turkish and English. Database and restricted area are in only Turkish. Breed information and other project related documents are in both sides. Status of breed collection and biologic bank materials list as charts.
Site overview Restricted area entrance is established by defined user & password over database management system via SQL*. This area is only for the authorized project personel, no membership form or interface is supplied by the site portal. *SQL: Structured Query Language
Animal Coding System The animal coding system is based on the full ear ring number and gender, if there was not province code in the ear ring number, it should be added before the ear ring number to assemble the Individual Code. Other material codes are based on individual codes. Example individual code: BT-Yk-TR0605505-E Species Abbreviation Breeds Abbreviation Collectors Code Processors Code Year of Process Ear Ring Number Gender Plant Number Bt Yk 01 08 2007 TR0605505 (E/D) M/F 07 Individual Code Cell Code DNA Code Semen Code Ovis-ive-48749E Ovis-ive-01-03-2008 48749E-02 Ovis-ive-01-02-2008 48749E-02 Ovis-ive-01-05-2008-48749-02 Ind. Code Embryo Code-1 Embryo Code-2 Ovis-ive-48749E VAR-5 BLA(0753D) 5-Emb-Ovis-ive48749Ex0753D
Database procedure
Database procedure
Database procedure: Static databank Individual and materials codes are stored in Microsoft Excel datasheet format locally and for web publishing, the.xls file is stored in the web server and data tables for web are created via ODBC Excel Driver. Codes are stored cell by cell in tabular format, the output of the web interface is written row by row as one under the other in separated columns. This format has just read-only structure, so it is called static databank.
Database procedure: Static databank Example table of the breed: Imbroz sheep Ind. No. Ovis-Gök-1E Ovis-Gök-2E Ovis-Gök-3E Ovis-Gök-4E Ovis-Gök-5E Ovis-Gök-6E Ovis-Gök-7E Ovis-Gök-8E Ovis-Gök-9E Ovis-Gök-10E Ovis-Gök-11E Ovis-Gök-12E Ovis-Gök-13E Ovis-Gök-14E Ovis-Gök-15E Ovis-Gök-16E Ovis-Gök-17E Ovis-Gök-18E Ovis-Gök-19E Ovis-Gök-20E Ovis-Gök-21E Ovis-Gök-22E Ovis-Gök-23E Ovis-Gök-24E Ovis-Gök-25E Ovis-Gök-26D Ovis-Gök-27D Ovis-Gök-28D Ovis-Gök-29D Ovis-Gök-30D Ovis-Gök-31D Ovis-Gök-32D Ovis-Gök-33D Ovis-Gök-34D Ovis-Gök-35D Ovis-Gök-36D Ovis-Gök-37D Ovis-Gök-38D Ovis-Gök-39D Ovis-Gök-40D Ovis-Gök-41D Ovis-Gök-42D Ovis-Gök-43D Ovis-Gök-44D Ovis-Gök-45D Ovis-Gök-46D Ovis-Gök-47D Ovis-Gök-48D Ovis-Gök-49D Ovis-Gök-50D DNA Code Ovis-Gök-03-03-2007-17-01E-01 Ovis-Gök-03-03-2007-17-02E-02 Ovis-Gök-03-03-2007-17-03E-02 Ovis-Gök-03-03-2007-17-04E-02 Ovis-Gök-03-03-2007-17-05E-02 Ovis-Gök-03-03-2007-17-06E-02 Ovis-Gök-03-03-2007-17-07E-02 Ovis-Gök-03-03-2007-17-08E-03 Ovis-Gök-03-03-2007-17-09E-03 Ovis-Gök-03-03-2007-17-10E-04 Ovis-Gök-03-03-2007-17-11E-04 Ovis-Gök-03-03-2007-17-12E-04 Ovis-Gök-03-03-2007-17-13E-04 Ovis-Gök-03-03-2007-17-14E-04 Ovis-Gök-03-03-2007-17-15E-04 Ovis-Gök-03-03-2007-17-16E-04 Ovis-Gök-03-03-2007-17-17E-04 Ovis-Gök-03-03-2007-17-18E-04 Ovis-Gök-03-03-2007-17-19E-04 Ovis-Gök-03-03-2007-17-20E-04 Ovis-Gök-03-03-2007-17-21E-04 Ovis-Gök-03-03-2007-17-22E-04 Ovis-Gök-03-03-2007-17-23E-04 Ovis-Gök-03-03-2007-17-24E-04 Ovis-Gök-03-03-2007-17-25E-04 Ovis-Gök-03-03-2007-17-26D-01 Ovis-Gök-03-03-2007-17-27D-01 Ovis-Gök-03-03-2007-17-28D-01 Ovis-Gök-03-03-2007-17-29D-01 Ovis-Gök-03-03-2007-17-30D-01 Ovis-Gök-03-03-2007-17-31D-02 Ovis-Gök-03-03-2007-17-32D-02 Ovis-Gök-03-03-2007-17-33D-02 Ovis-Gök-03-03-2007-17-34D-02 Ovis-Gök-03-03-2007-17-35D-02 Ovis-Gök-03-03-2007-17-36D-03 Ovis-Gök-03-03-2007-17-37D-03 Ovis-Gök-03-03-2007-17-38D-03 Ovis-Gök-03-03-2007-17-39D-03 Ovis-Gök-03-03-2007-17-40D-03 Ovis-Gök-03-03-2007-17-41D-03 Ovis-Gök-03-03-2007-17-42D-03 Ovis-Gök-03-03-2007-17-43D-03 Ovis-Gök-03-03-2007-17-44D-03 Ovis-Gök-03-03-2007-17-45D-03 Ovis-Gök-03-03-2007-17-46D-03 Ovis-Gök-03-03-2007-17-47D-03 Ovis-Gök-03-03-2007-17-48D-03 Ovis-Gök-03-03-2007-17-49D-03 Ovis-Gök-03-03-2007-17-50D-03 Cell Code Ovis-Gök-03-02-2008-17-01E-01 Ovis-Gök-03-02-2008-17-02E-02 Ovis-Gök-03-02-2008-17-03E-02 Ovis-Gök-03-02-2008-17-04E-02 Ovis-Gök-03-02-2008-17-05E-02 Ovis-Gök-03-02-2008-17-06E-02 Ovis-Gök-03-02-2008-17-07E-02 Ovis-Gök-03-02-2008-17-08E-03 Ovis-Gök-03-02-2008-17-09E-03 Ovis-Gök-03-02-2008-17-10E-04 Ovis-Gök-03-02-2008-17-11E-04 Ovis-Gök-03-02-2008-17-12E-04 Ovis-Gök-03-02-2008-17-13E-04 Ovis-Gök-03-02-2008-17-14E-04 Ovis-Gök-03-02-2008-17-15E-04 Ovis-Gök-03-02-2008-17-16E-04 Semen Code Ovis-Gök-03-04-2007-17-01-01 Ovis-Gök-03-04-2007-17-02-02 Ovis-Gök-03-04-2007-17-03-02 Ovis-Gök-03-04-2008-17-04-02 Ovis-Gök-03-04-2007-17-05-02 Ovis-Gök-03-04-2007-17-06-02 Ovis-Gök-03-04-2007-17-07-02 Ovis-Gök-03-04-2008-17-08-03 Ovis-Gök-03-04-2008-17-09-03 Ovis-Gök-03-04-2007-17-10-04 Ovis-Gök-03-04-2007-17-11-04 Ovis-Gök-03-04-2007-17-12-04 Ovis-Gök-03-04-2007-17-13-04 Ovis-Gök-03-04-2007-17-14-04 Ovis-Gök-03-04-2007-17-15-04 Embryo Code-1 VAR-2 BLA (50D) VAR-4 BLA (49D) VAR-6 BLA (48D) VAR-12 BLA (47D) VAR-2 BLA (46D) VAR-9 BLA (45D) VAR-1 BLA (36D) VAR-11 BLA (27D) Embryo code-2 2-Emb-Ovis-Gök-1Ex50D 4-Emb-Ovis-Gök-2Ex49D 6-Emb-Ovis-Gök-3Ex48D 12-Emb-Ovis-Gök-4Ex47D 2-Emb-Ovis-Gök-5Ex46D 9-Emb-Ovis-Gök-6Ex45D 1-Emb-Ovis-Gök-7Ex36D 11-Emb-Ovis-Gök-8Ex27D VAR-5 BLA (34D) VAR-2 BLA (41D) VAR-4 BLA (40D) 5-Emb-Ovis-Gök-11Ex34D 2-Emb-Ovis-Gök-12Ex41D 4-Emb-Ovis-Gök-13Ex40D VAR-8 BLA (38D) 8-Emb-Ovis-Gök-15Ex38D Ovis-Gök-03-02-2008-17-18E-04 Ovis-Gök-03-02-2008-17-19E-04 Ovis-Gök-03-02-2008-17-20E-04 Ovis-Gök-03-02-2008-17-21E-04 Ovis-Gök-03-02-2008-17-22E-04 Ovis-Gök-03-02-2008-17-23E-04 Ovis-Gök-03-02-2008-17-24E-04 Ovis-Gök-03-02-2008-17-25E-04 Ovis-Gök-03-02-2008-17-26D-01 Ovis-Gök-03-02-2008-17-27D-01 Ovis-Gök-03-02-2008-17-28D-01 Ovis-Gök-03-02-2008-17-29D-01 Ovis-Gök-03-02-2008-17-30D-01 Ovis-Gök-03-02-2008-17-31D-02 Ovis-Gök-03-02-2008-17-32D-02 Ovis-Gök-03-02-2008-17-33D-02 Ovis-Gök-03-02-2008-17-34D-02 Ovis-Gök-03-02-2008-17-35D-02 Ovis-Gök-03-02-2008-17-36D-03 Ovis-Gök-03-02-2008-17-37D-03 Ovis-Gök-03-02-2008-17-38D-03 Ovis-Gök-03-02-2008-17-39D-03 Ovis-Gök-03-02-2009-17-40D-03 Ovis-Gök-03-02-2008-17-41D-03 Ovis-Gök-03-02-2008-17-42D-03 Ovis-Gök-03-02-2008-17-43D-03 Ovis-Gök-03-02-2008-17-44D-03 Ovis-Gök-03-02-2008-17-45D-03 Ovis-Gök-03-02-2008-17-46D-03 Ovis-Gök-03-02-2008-17-47D-03 Ovis-Gök-03-02-2008-17-48D-03 Ovis-Gök-03-02-2009-17-49D-03 Ovis-Gök-03-02-2008-17-50D-03 Ovis-Gök-03-04-2007-17-18-04 VAR-2 BLA+1 (35D,37D) 2-Emb-Ovis-Gök-18Ex35D Ovis-Gök-03-04-2008-17-20-04 Ovis-Gök-03-04-2007-17-21-04 Ovis-Gök-03-04-2007-17-22-04 Ovis-Gök-03-04-2007-17-23-04 Ovis-Gök-03-04-2007-17-24-04 Ovis-Gök-03-04-2007-17-25-04 VAR-4 BLA (33D) VAR-10 BLA (32D) VAR-3 BLA (31D) VAR-11 BLA (30D) VAR-2 BLA (29D) VAR-3 BLA (28D) 4-Emb-Ovis-Gök-20Ex33D 10-Emb-Ovis-Gök-21Ex32D 3-Emb-Ovis-Gök-22Ex31D 11-Emb-Ovis-Gök-23Ex30D 2-Emb-Ovis-Gök-24Ex29D 3-Emb-Ovis-Gök-25Ex28D VAR-11 BLA (27E) VAR-3 BLA (25E) VAR-2 BLA (24E) VAR-11 BLA (23E) VAR-3 BLA (22E) VAR-10 BLA (21E) VAR-4 BLA (20E) VAR-5 BLA (11E) VAR-2 BLA (18D) VAR-1 BLA (07E) VAR-1 BLA (18E) VAR-8 BLA (15E) 11-Emb-Ovis-Gök-27Dx27E 3-Emb-Ovis-Gök-28Dx25E 2-Emb-Ovis-Gök-29Dx24E 11-Emb-Ovis-Gök-30Dx23E 3-Emb-Ovis-Gök-31Dx22E 10-Emb-Ovis-Gök-32Dx21E 4-Emb-Ovis-Gök-33Dx20E 5-Emb-Ovis-Gök-34Dx11E 18-Emb-Ovis-Gök-35Dx18E 1-Emb-Ovis-Gök-36Dx7E 1-Emb-Ovis-Gök-37Dx18E 8-Emb-Ovis-Gök-38Dx15E VAR-4 BLA (13E) VAR-2 BLA (12E) 4-Emb-Ovis-Gök-40Dx13E 2-Emb-Ovis-Gök-41Dx12E VAR-9 BLA (06E) VAR-2 BLA (05E) VAR-12 BLA (04E) VAR-6 BLA (03E) VAR-4 BLA (02E) VAR-2 BLA (01E) 9-Emb-Ovis-Gök-45Dx6E 5-Emb-Ovis-Gök-46Dx5E 12-Emb-Ovis-Gök-47Dx4E 6-Emb-Ovis-Gök-48Dx3E 4-Emb-Ovis-Gök-49Dx2E 2-Emb-Ovis-Gök-50Dx1E
Database procedure: Dynamic databank The database format being used in the project databank is Microsoft Access, search, new record, modify, save or delete commands can be provided by SQL queries controlled by user action buttons and input boxes with JavaScript support. DNA codes, semen codes, embryo codes with cryo-storage information, cell and freezing mediums for each breed and material. This database is named as dynamic databank.
Database procedure: Dynamic databank Confrontation page of the databank
Database procedure: Dynamic databank The first part of the databank includes individual code, gender, DNA, cell, semen, embryo codes at left; species, breed and region information right next to the photo of front shot of the recorded individual. There are also boxes at right bottom showing the name of the photos for front, lateral and back shots. On the box of individual code and three boxes of photo can be double clicked to open MIF and photos on pop-up windows. (Red colored writings)
Database procedure: Dynamic databank
Database procedure: Dynamic databank The structure of the main body consists of two column for GEBI and LLRCI, four sections as DNA bank, cell bank, embryo bank, semen (sperma) bank, plus notes and comments for each breed. DNA bank records Quantity of DNA as μgr Stocking solution info. Type of the tissue Last processing date Wavelength Semen bank records Count of the paillette, Concentration (%), Motility status Acrosome integrity Year of freezing Protocol of freezing Cell bank records Source of the tissue Vial count Cell line type Culture medium Passage count Freezing solution Last processing date Embryo bank records Count of embryo Year of freezing Type of freezing Protocol of freezing Storing conditions.
Conclusion This database application interface stores all the breed information up to approximately 1500 individuals. Storing amounts of information even with meta-tabular data, combining and arranging them perfectly requires database technology. Cryopreserved biological bank materials without regular records can make to access them so difficult or even impossible to find and use them fluently.
Conclusion The most important results of this project are storing, processing and analysing such data with a view to increasing the fund of knowledge and understanding relating to the conservation of nature and by the way established animal gene bank since it will be a pioneer in Turkey in conservation of most of native animal gene resources. The complexed and expandable structure of animal databank will be unique in Turkey, even for the world.
Credits Acknowledgement: TURKHAYGEN-I Project is supported by Turkish Scientific and Technical Research Council (Grant no: KAMAG 106G005) References A. Karaburun, G. Toz, Storing spatial data in multiuser level and tracking history in database, ITU dergisi/d mühendislik, Cilt:5, Sayı:5, 23-32, Oct. 2006 A. K. Kahi, T. O. Rewe, Biotechnology in livestock production: Overview of possibilities for Africa, African Journal of Biotechnology Vol. 7 (25), pp. 4984-4991, 29 Dec. 2008 Kurar E, Arat S, Ertugrul O, Pabuccuoglu S, Sagirkaya H, Tasdemir U and Togan I, In vitro Conservation and Preliminary Molecular Characterization of Some Turkish Native Domestic Animal Genetic Resources-I (TURKHAYGEN-I), ISAG, July 2008 S. Aksu, S. Arat et al., Gen Kaynaklarinin ve Biyocesitliligin Korunmasi Kapsaminda Yerli At Irklarinin Genetik Karakterizasyonu, 9th Ecology and Environment Congress, Oct. 2009 Bruford M. W. and Townsend S.J. Case studies in the genetics of animal domestication: sheep. In: Zeder M., Decker-Walters D., Bradley D., Smith B.D. (eds.): D ocumenting Domestication: New Genetic and Archaeological Paradigms, 2004; California University Press. Soysal I., Türkiye Yerli Hayvan Genetik Kaynaklarımız, 2004, Tekirdağ Universitesi, Ziraat Fakültesi Wildlife Conservation and Monitoring Centre (http://www.wcmc.org.uk/) Microsoft, Article ID: 110093 - Revision: 1.5, ODBC-Open Database Connectivity Overview Last Review: March 29, 2007 Wikipedia,.gov stld article, 2010 (http://www.wikipedia.org/)