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Genomics and Information Sharing

Genomics and Information Sharing. Workshop on Access and Benefit Sharing in Non-Commercial Biodiversity Research Bonn, Germany 17-19 November 2008 Christian Burks Ontario Genomics Institute & Vice-Chair, iBOL Board of Directors.

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Genomics and Information Sharing

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  1. Genomics and Information Sharing Workshop on Access and Benefit Sharing in Non-Commercial Biodiversity Research Bonn, Germany 17-19 November 2008 Christian Burks Ontario Genomics Institute & Vice-Chair, iBOL Board of Directors

  2. 1 ccttcgcgccctgggccatctccctcccacctccctccgcggagcagccagacagcgagg 61 gccccggccgggggcaggggggacgccccgtccggggcacccccccggctctgagccgcc 121 cgcggggccggcctcggcccggagcggaggaaggagtcgccgaggagcagcctgaggccc 181 cagagtctgagacgagccgccgccgcccccgccactgcggggaggagggggaggaggagc 241 gggaggagggacgagctggtcgggagaagaggaaaaaaacttttgagacttttccgttgc 301 cgctgggagccggaggcgcggggacctcttggcgcgacgctgccccgcgaggaggcagga 361 cttggggaccccagaccgcctccctttgccgccggggacgcttgctccctccctgccccc 421 tacacggcgtccctcaggcgcccccattccggaccagccctcgggagtcgccgacccggc 481 ctcccgcaaagacttttccccagacctcgggcgcaccccctgcacgccgccttcatcccc 541 ggcctgtctcctgagcccccgcgcatcctagaccctttctcctccaggagacggatctct 601 ctccgacctgccacagatcccctattcaagaccacccaccttctggtaccagatcgcgcc 661 catctaggttatttccgtgggatactgagacacccccggtccaagcctcccctccaccac 721 tgcgcccttctccctgaggacctcagctttccctcgaggccctcctaccttttgccggga 781 gacccccagcccctgcaggggcggggcctccccaccacaccagccctgttcgcgctctcg 841 gcagtgccggggggcgccgcctcccccatgccgccctccgggctgcggctgctgccgctg 901 ctgctaccgctgctgtggctactggtgctgacgcctggccggccggccgcgggactatcc 961 acctgcaagactatcgacatggagctggtgaagcggaagcgcatcgaggccatccgcggc 1021 cagatcctgtccaagctgcggctcgccagccccccgagccagggggaggtgccgcccggc 1081 ccgctgcccgaggccgtgctcgccctgtacaacagcacccgcgaccgggtggccggggag 1141 agtgcagaaccggagcccgagcctgaggccgactactacgccaaggaggtcacccgcgtg 1201 ctaatggtggaaacccacaacgaaatctatgacaagttcaagcagagtacacacagcata 1261 tatatgttcttcaacacatcagagctccgagaagcggtacctgaacccgtgttgctctcc 1321 cgggcagagctgcgtctgctgaggctcaagttaaaagtggagcagcacgtggagctgtac 1381 cagaaatacagcaacaattcctggcgatacctcagcaaccggctgctggcacccagcgac 1441 tcgccagagtggttatcttttgatgtcaccggagttgtgcggcagtggttgagccgtgga 1501 ggggaaattgagggctttcgccttagcgcccactgctcctgtgacagcagggataacaca 1561 ctgcaagtggacatcaacgggttcactaccggccgccgaggtgacctggccaccattcat 1621 ggcatgaaccggcctttcctgcttctcatggccaccccgctggagagggcccagcatctg 1681 caaagctcccggcaccgccgagccctggacaccaactattgcttcagctccacggagaag 1741 aactgctgcgtgcggcagctgtacattgacttccgcaaggacctcggctggaagtggatc 1801 cacgagcccaagggctaccatgccaacttctgcctcgggccctgcccctacatttggagc 1861 ctggacacgcagtacagcaaggtcctggccctgtacaaccagcataacccgggcgcctcg 1921 gcggcgccgtgctgcgtgccgcaggcgctggagccgctgcccatcgtgtactacgtgggc 1981 cgcaagcccaaggtggagcagctgtccaacatgatcgtgcgctcctgcaagtgcagctga 2041 ggtcccgccccgccccgccccgccccggcaggcccggccccaccccgccccgcccccgct 2101 gccttgcccatgggggctgtatttaaggacacccgtgccccaagcccacctggggcccca 2161 ttaaagatggagagaggactgcggatctctgtgtcattgggcgcctgcctggggtctcca 2221 tccctgacgttcccccactcccactccctctctctccctctctgcctcctcctgcctgtc 2281 tgcactattcctttgcccggcatcaaggcacaggggaccagtggggaacactactgtagt 2341 tagatc DNA – 2346 base pairs (one gene) human transforming growth factor (GenBank) 3,000 bp = one PhD (circa early 1980’s) one human genome = 3,000,000,000 bp one human genome = 1,000,000 PhDs • but, technology improved • faster • less human intensive so let’s do “genomics”! • first human genome ... 2003

  3. funding outcomes impact & benefits • RESULTS • leverageable resources: • knowledge • methods • tools • databases • reagents • clones • . • . • . What is Genomics?A New, Outcome-Oriented Research Paradigm 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 Trematomus scotti (blackfin notothen, from GenBank) – 2003 – concept initiated <100 visible (imbedded)? • LOCUS EU326435 652 bp DNA linear VRT 22-OCT-2008 • DEFINITION Trematomus scotti voucher JRAS06-086 cytochrome oxidase subunit 1 • (COI) gene, partial cds; mitochondrial. • ACCESSION EU326435 • VERSION EU326435.1 GI:164449557 • 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 tctttacttagtcttcggcgcttgggccgggatagtaggaacagcccttagtctgctcat • 61 tcgggcagaacttagtcaacccggcgccctattgggggacgaccaaatttataatgttat • 121 tgttaccgcccatgcctttgtaataatcttctttatggtaatgcctatcataatcggggg • 181 ttttggaaattgacttatccccctcatgattggggcccctgacatggcgtttcctcgaat • 241 aaacaatatgagcttctggcttttgccgccctccttcctgctactgttagcttcttcagg • 301 tgttgaagcgggggcagggaccgggtggactgtttatcctcctctctctgggaatttagc • 361 ccatgcagggggttccgttgatttaactattttttccctacatttagcaggtatttcctc • 421 gattttaggggctattaactttattacaacaattattaatatgaagccccccgccatttc • 481 tcaataccaaacccccttgtttgtgtggtccgtgttaattactgcagttctcctgcttct • 541 ttcactccctgtcttagctgctggtattacaatactcctcacggaccgaaatcttaacac • 601 caccttcttt gaccctgcag gaggggggga tcccatcctt taccaacacc tc • / – 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? e.g., iBOL (see wiki postings): five years 5,000,000 specimens 500,000 species

  7. Christian Burks ________ CBurks@OntarioGenomics.ca www.OntarioGenomics.ca ________ iBOL (International Barcode of Life Project) www.DNAbarcoding.org

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