Genomics

Genomics

• Human genome variation and biomedical information

  • VCF as SPARQL (Jerven; see RDF/LOD section)
  • Reference genome graph (Colin, Benedict, Toshiaki, Suzuki, [MarkW (interested)], Tudor [interested], Atsuko[interested], Raoul [interested])

• Other animal, plant and microbial genomics with phenotypes and orthology[erick: interested in the plant applications]

  • Linking fossils and bioinformatics

• Orthology: ontology standardization, data conversion, application development (Hirokazu Chiba, Jesualdo Fernandez-Breis, Ikuo Uchiyama, Hiroyo Nishide, Shin Kawano, AC Yoshizawa, Yuki Moriya; interested T Kawashima, S Kawashima, Erick)

  • Orthology databases
  • Ontology documents and issues OWLDOC
  • Policy for identifiers
  • [Tests multiple datasets] (https://github.com/dbcls/bh15/wiki/Test-Orthology-Datasets)
  • Application development
  • Evaluation of performance: single repository vs multiple repositories, datasets (not addressed)
  • Orthology and Uniprot (not addressed)
  • [KEGG OC RDF application] (https://github.com/dbcls/bh15/wiki/KEGG-OC-RDF-Application)

• Public NGS data

  • DBCLS SRA update (Takeru Nakazato, Oishi)
  • AOE update: Inclusion of RNA-seq data in SRA (Bono, Nakazato, Oishi)

• GGGenome & CRISPRdirect update (Yuki Naito)

  • Results:
    • GGGenome sequence searcher now supports 220+ genomes!
      • Newly added: Xenopus laevis XenBase/JGI 9.1, Xenopus tropicalis XenBase/JGI 9.0, Ciona intestinalis KH (Jul, 2008), S. purpuratus Spur_v3.1 (Jun, 2011), Hydra h7 (Aug, 2008), Hydra Hydra_RP_1.0 (Oct, 2009), Brassica napus Genoscope v4.1 (Aug, 2014), Lotus japonicus build 3.0 (Aug, 2015), Nicotiana benthamiana v1.0.1 (Jul, 2014), Vigna angularis ver3 (Nov, 2011), Raphanus sativus RSA_r1.0 (May, 2014), Populus trichocarpa v3.0
    • CRSIRPdirect, target-specific guide RNA design for CRISPR
      • Incorporating 220+ genomes (CRISPRdirect uses GGGenome API & Jellyfish k-mer counter)
        • GGGenome API (done)
        • Creating Jellyfish hash tables (in progress...)

• Liftover Allele Frequencies of Japanese 1200 exome HGVD from hg19 to hg38 [Hiro Mishima]

Day 1

Participants: Foo Bar, ... (please add github handle, e.g. @rvosa)

Day 2

• Discuss ideas for the Linking fossils and bioinformatics
• Surveyed the anatomy ontology for invertebrates. AnatomyOntologyForMetazoan

Day 4

• Discuss ideas for the Linking fossils and bioinformatics. In a lot of case, Fossil records on the website of museums give no information about absolute time. Instead, they shows the geologic Era/Stage in which the fossil was occurred. The geologic time range of layers are decided by International Commission on Stratigraphy. And the data is open by their web-site. http://stratigraphy.org/index.php/ics-gssps. But the data format is by Books/PDF/HTML or other classic styles only. If these data has opened by other usable styles, it would be more convenient.

• => We found a possible database/endpoint for this. A geologic timescale ontology and service SJD Cox & SM Richard [2014]. This group create an endpoint for access to the above data. http://www.researchgate.net/publication/262936829_A_geologic_timescale_ontology_and_service

1.  as a static file at http://resource.geosciml.org/vocabulary/timescale/isc{year}
2. through a SPARQL endpoint at http://resource.geosciml.org/sparql/isc{year}
3. at a SISSvoc service at http://auscope‐services.arrc.csiro.au/sissvoc/isc{year}/collection

Example Pipeline

"Fossil Sample with Layer" + "endpoint( resource.geosciml.org/sparql )" => "Time Range"

( 250,000 fossils from Florida Museum, etc.) ( The International Commission on Stratigraphy )

Day 5

###Liftover HGVD

• see HGVDinHg38