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Genomics and Information Sharing Workshop on Access and Benefit Sharing in Non-Commercial Biodiversity Research Bonn, Germany 17-19 November 2008 Christian.

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Presentation on theme: "Genomics and Information Sharing Workshop on Access and Benefit Sharing in Non-Commercial Biodiversity Research Bonn, Germany 17-19 November 2008 Christian."— Presentation transcript:

1 Genomics and Information Sharing Workshop on Access and Benefit Sharing in Non-Commercial Biodiversity Research Bonn, Germany November 2008 Christian Burks Ontario Genomics Institute & Vice-Chair, iBOL Board of Directors

2 DNA – 2346 base pairs (one gene) 1 ccttcgcgcc ctgggccatc tccctcccac ctccctccgc ggagcagcca gacagcgagg 61 gccccggccg ggggcagggg ggacgccccg tccggggcac ccccccggct ctgagccgcc 121 cgcggggccg gcctcggccc ggagcggagg aaggagtcgc cgaggagcag cctgaggccc 181 cagagtctga gacgagccgc cgccgccccc gccactgcgg ggaggagggg gaggaggagc 241 gggaggaggg acgagctggt cgggagaaga ggaaaaaaac ttttgagact tttccgttgc 301 cgctgggagc cggaggcgcg gggacctctt ggcgcgacgc tgccccgcga ggaggcagga 361 cttggggacc ccagaccgcc tccctttgcc gccggggacg cttgctccct ccctgccccc 421 tacacggcgt ccctcaggcg cccccattcc ggaccagccc tcgggagtcg ccgacccggc 481 ctcccgcaaa gacttttccc cagacctcgg gcgcaccccc tgcacgccgc cttcatcccc 541 ggcctgtctc ctgagccccc gcgcatccta gaccctttct cctccaggag acggatctct 601 ctccgacctg ccacagatcc cctattcaag accacccacc ttctggtacc agatcgcgcc 661 catctaggtt atttccgtgg gatactgaga cacccccggt ccaagcctcc cctccaccac 721 tgcgcccttc tccctgagga cctcagcttt ccctcgaggc cctcctacct tttgccggga 781 gacccccagc ccctgcaggg gcggggcctc cccaccacac cagccctgtt cgcgctctcg 841 gcagtgccgg ggggcgccgc ctcccccatg ccgccctccg ggctgcggct gctgccgctg 901 ctgctaccgc tgctgtggct actggtgctg acgcctggcc ggccggccgc gggactatcc 961 acctgcaaga ctatcgacat ggagctggtg aagcggaagc gcatcgaggc catccgcggc 1021 cagatcctgt ccaagctgcg gctcgccagc cccccgagcc agggggaggt gccgcccggc 1081 ccgctgcccg aggccgtgct cgccctgtac aacagcaccc gcgaccgggt ggccggggag 1141 agtgcagaac cggagcccga gcctgaggcc gactactacg ccaaggaggt cacccgcgtg 1201 ctaatggtgg aaacccacaa cgaaatctat gacaagttca agcagagtac acacagcata 1261 tatatgttct tcaacacatc agagctccga gaagcggtac ctgaacccgt gttgctctcc 1321 cgggcagagc tgcgtctgct gaggctcaag ttaaaagtgg agcagcacgt ggagctgtac 1381 cagaaataca gcaacaattc ctggcgatac ctcagcaacc ggctgctggc acccagcgac 1441 tcgccagagt ggttatcttt tgatgtcacc ggagttgtgc ggcagtggtt gagccgtgga 1501 ggggaaattg agggctttcg ccttagcgcc cactgctcct gtgacagcag ggataacaca 1561 ctgcaagtgg acatcaacgg gttcactacc ggccgccgag gtgacctggc caccattcat 1621 ggcatgaacc ggcctttcct gcttctcatg gccaccccgc tggagagggc ccagcatctg 1681 caaagctccc ggcaccgccg agccctggac accaactatt gcttcagctc cacggagaag 1741 aactgctgcg tgcggcagct gtacattgac ttccgcaagg acctcggctg gaagtggatc 1801 cacgagccca agggctacca tgccaacttc tgcctcgggc cctgccccta catttggagc 1861 ctggacacgc agtacagcaa ggtcctggcc ctgtacaacc agcataaccc gggcgcctcg 1921 gcggcgccgt gctgcgtgcc gcaggcgctg gagccgctgc ccatcgtgta ctacgtgggc 1981 cgcaagccca aggtggagca gctgtccaac atgatcgtgc gctcctgcaa gtgcagctga 2041 ggtcccgccc cgccccgccc cgccccggca ggcccggccc caccccgccc cgcccccgct 2101 gccttgccca tgggggctgt atttaaggac acccgtgccc caagcccacc tggggcccca 2161 ttaaagatgg agagaggact gcggatctct gtgtcattgg gcgcctgcct ggggtctcca 2221 tccctgacgt tcccccactc ccactccctc tctctccctc tctgcctcct cctgcctgtc 2281 tgcactattc ctttgcccgg catcaaggca caggggacca gtggggaaca ctactgtagt 2341 tagatc one human genome = 3,000,000,000 bp 3,000 bp = one PhD (circa early 1980’s) one human genome = 1,000,000 PhDs but, technology improved faster less human intensive so let’s do “genomics”! first human genome human transforming growth factor (GenBank)

3 What is Genomics? A New, Outcome-Oriented Research Paradigm funding impact & benefits outcomes RESULTS leverageable resources: knowledge methods tools databases reagents clones. APPLICATIONS

4 Genomics Projects: Key Issues for Data Release Required by contract with relevant funders funded after approval of data release policy Preliminary data are released publicly: within hours or days after being generated subject to systematic quality control standards and not delayed by final scientific interpretation and not delayed by invention disclosures and not delayed by publication in a journal “community resource projects” framework: Ft. Lauderdale report (see wiki posting)

5 Genomics Project Public Databases: Value Proposition The existence of a “complete” (holistic) set providing boundary values for biological calculus whole greater than sum of parts Data generated and maintained systematically: standards defined and agreed upon in advance maximum levels of error minimum levels and means of annotation recourse to source (raw) data and materials Data there for benefit of and shared with all: Publicly available over the world wide web No limitations … any/all can retrieve & add value

6 Genomics Coming to DNA Barcoding LOCUS EU bp DNA linear VRT 22-OCT-2008 DEFINITION Trematomus scotti voucher JRAS cytochrome oxidase subunit 1 (COI) gene, partial cds; mitochondrial. ACCESSION EU VERSION EU GI: KEYWORDS BARCODE. SOURCE mitochondrion Trematomus scotti (blackfin notothen) ORGANISM Trematomus scotti Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Euteleostei; Neoteleostei; Acanthomorpha; Acanthopterygii; Percomorpha; Perciformes; Notothenioidei; Nototheniidae; Trematomus.. ORIGIN 1 tctttactta gtcttcggcg cttgggccgg gatagtagga acagccctta gtctgctcat 61 tcgggcagaa cttagtcaac ccggcgccct attgggggac gaccaaattt ataatgttat 121 tgttaccgcc catgcctttg taataatctt ctttatggta atgcctatca taatcggggg 181 ttttggaaat tgacttatcc ccctcatgat tggggcccct gacatggcgt ttcctcgaat 241 aaacaatatg agcttctggc ttttgccgcc ctccttcctg ctactgttag cttcttcagg 301 tgttgaagcg ggggcaggga ccgggtggac tgtttatcct cctctctctg ggaatttagc 361 ccatgcaggg ggttccgttg atttaactat tttttcccta catttagcag gtatttcctc 421 gattttaggg gctattaact ttattacaac aattattaat atgaagcccc ccgccatttc 481 tcaataccaa acccccttgt ttgtgtggtc cgtgttaatt actgcagttc tcctgcttct 541 ttcactccct gtcttagctg ctggtattac aatactcctc acggaccgaa atcttaacac 601 caccttcttt gaccctgcag gaggggggga tcccatcctt taccaacacc tc / – 2003 – concept initiated <100 visible (imbedded)? – 2008 – validation (research) phase ~500,000 barcodes done? <100,000 barcodes visible – 2015 – production (genomics) phase ~6,000,000 barcodes done? ~5,000,000 barcodes visible? Trematomus scotti (blackfin notothen, from GenBank) e.g., iBOL (see wiki postings): five years 5,000,000 specimens 500,000 species

7 Christian Burks ________ ________ iBOL (International Barcode of Life Project)


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