2. The Times They Are a-Changin’
Bob Dylan
• 46% of Americans and 25% of adults in the UK
own a smartphone
• 85% of medical professionals use
smartphones
• 30-50% use apps in their clinical practice
Buijink et al. (2012)Evid Based Med.
10. SpecimenCode SpecimenCode ExtractionCode
Genus Extraction Code PrimerName
Species Name Date Extracted Gene
BoxNo Amplification
BoxColumn SentToSequencing
Host Genus
Host Species PrimerName
Latitude PrimerSequence
Longitude Gene
CollectedBy
Sex
ExtractionCode
Gene
Accession
Sequence
14. HI assay Trachea experiments
Images
Bead assays
Virus quantification
Sequences
>Hu_NA_AAF77036_H1N1
MNPNQKIITIGSICMVVGIISLILQIGNIISIWVSHSIQTGNQNHPETCNQSIITYENNT
WVNQTYVNISNTNVVAGQDATSVILTGNSSLCPISGWAIYSKDNGIRIGSKGDVFVI Currently, we have rather unlinked
REPFISCSHLECRTFFLTQGALLNDKHSNGTVKDRSPYRTLMSCPVGEAPSPYNSRFE
SVAWSASACHDGMGWLTIGISGPDNGAVAVLKYNGIITDTIKSWRNNILRTQESEC data within the lab
ACVNGSCFTIMTDGPSNGQASYKILKIEKGKVTKSIELNAPNYHYEECSCYPDTGKV
MCVCRDNWHGSNRPWVSFDQNLDYQIGYICSGVFGDNPRPNDGTGSCGPVSSN
GANGIKGFSFRYDNGVWIGRTKSTSSRSGFEMIWDPNGWTETDSSFSVRQDIVAIT
DWSGYSGSFVQHPELTGLDCMRPCFWVELIRGQPKENT-
IWTSGSSISFCGVNSDTVGWSWPDGAELPFSIDK
15. Answering simple questions becomes
time consuming
• Give me all the work that has been done in
the lab on virus X?
• How does virus X grow in trachea and react for
horse serum in HI assays?
• Which viruses have been studied in trachea
but not sequenced?
16. mallard_CzechRepublic_13577-24K_16-09-2010 N-type Titers HI TracheaExpt
MN11F_2076_H3_consensus_sequence N8 256 Yes Yes
80 29
duck_Italy_194659_01-01-2006
66
Anasplatyrhynchos_Belgium_12827_18-09-2007
37
pelican_Zambia_01_01-08-2006
73
17
duck_Zambia_04_01-06-2008
99
goose_Zambia_05_01-07-2008
Stellerseider_Alaska_44222-192_06-09-2006
canine_Guangdong_2_18-10-2007
100
canine_Jiangsu_01_01-12-2009
58
48 canine_Korea_01_2007
chicken_Vietnam_G14_01-01-2008
100
duck_Guangdong_W12_2011
MN09_881V_H3_consensus_sequence N8 x x Yes
100
MN09_882V_H3_consensus_sequence N8 512 x x
duck_Vietnam_G119_01-11-2006
61
65
MN11F_1787_H3_consensus_sequence N8 x Yes x
42 duck_Beijing_61_01-01-2005
3
38
MN10F_1551_H3_consensus_sequence N1 512 x x
17 MN09_969V_H3_consensus_sequence N8 x x x
29
54
43 8
MN10F_1906_H3_consensus_sequence N8 x x x
MN11F_2157_H3_consensus_sequence N3 128 x x
96 87
MN10F_1581_H3_consensus_sequence N8 128 x x
redcrestedpochard_Mongolia_1915_19-09-2006
53
MN11F_2185_H3_consensus_sequence
N8 256 x Yes
99 100
MN11F_1782_HA_consensus_sequence N8 (N2) x x x
100
MN11F_2106_H3_consensus_sequence N8 128 Yes Yes
MN11F_2377_H3_consensus_sequence N6 x x x
63
MN09_963V_H3_consensus_sequence N8 512 Yes Yes
45
MN09_973V_H3_consensus_sequence
100
N8 256 x x
86
MN09_961V_H3_consensus_sequence N8 128 x x
70
9 7 MN09_977V_H3_consensus_sequence N8 256 x Yes
MN09_957V_H3_consensus_sequence ? 256 x x
MN11F_2271_H3_consensus_sequence N8 256 Yes Yes
100
MN09_899V_H3_consensus_sequence N6 x x x
equine_Jilin_1_1989
100
Equine_HeilongJiang_12_1990
0.02
17. Trachea Expt HI Asays
Dog Virus
Trachea Blood Type
Virus Serum
Quantification Positive/Negative
Staining Expt
Sequencing
Trachea
Staining Virus
Image Sequence method
Positive/Negative Assembly method
Sequence
Apoptosis
Histological
changes
21. Future opportunities
• New building, new approach to record keeping
• More data stored, more data shared between
labs
Notas do Editor
The idea of a digital lab is decades old but now that tablets have become cheap, it seems that the moment has come where everybody can start benefiting from them.I think that these devices are likely to change the way we work in the same way as PCs have helped our productivity.But although the hardware is important, the most important is that we are able to get a better grasp of our data.
Ability to provide remote access to digital record keeping could lead to exciting developments
Valuable lessons learnt, although googledocs has the advantage that the database is being managed by Google it has limitations.
Linked DataThe Semantic Web isn't just about putting data on the web. It is about making links, so that a person or machine can explore the web of data. With linked data, when you have some of it, you can find other, related, data.Like the web of hypertext, the web of data is constructed with documents on the web. However, unlike the web of hypertext, where links are relationships anchors in hypertext documents written in HTML, for data they links between arbitrary things described by RDF,. The URIs identify any kind of object or concept. But for HTML or RDF, the same expectations apply to make the web grow:Use URIs as names for things Use HTTP URIs so that people can look up those names. When someone looks up a URI, provide useful information, using the standards (RDF*, SPARQL) Include links to other URIs. so that they can discover more things. What is linked data:Linked Data refers to data published on the Web in such a way that it is machine-readable, its meaning is explicitly defined, it is linked to other external data sets, and can in turn be linked to from external data sets Advantages:helping developers integrate data into their applications. And, by following links in the dataset, we can discover more useful data
We have systems within the lab and the CVR as whole that, historically, have not easily interoperated at the data level
So
For example, Pablo is currently leading a project on the possible spillover of avian influenza into the horse population in Mongolia and China. Keeping up to date on the various experiments taking place and the different viruses that different researchers are using is difficult.
Semantic MediaWiki is also a full-fledged framework, in conjunction with many spinoff extensions, that can turn a wiki into a powerful and flexible “collaborative database”. All data created within SMW can easily be published via the Semantic Web, allowing other systems to use this data seamlessly.