How and why to document data for long-term storage; and What's special about Geographical data?
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Transcript of How and why to document data for long-term storage; and What's special about Geographical data?
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How and why to document data for long-term storage;
and
What's special about Geographical data?
Allan ReeseCefas Weymouth
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Cefas buildings
Weymouth
Burnham-on-Crouch
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Fish disease
• Causes and progress of infection• Diagnostics (viruses, bacteria,
fungi, parasites)• Vaccines and therapeutics
(safety and efficacy)• Epidemiology & risk assessment• Surveillance and control –
Fish Health Inspectors• Emerging and exotic diseases• Policy advice
Spring Viremia of Carp Virus
Fish farms in E&W
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Who wants a database?• I’ve got some data so I need a database• Our demo will show you how easy it is to
simultaneously search, share and retrieve information from thousands of library databases
• Project… plans to build, through networking, a database on best practices in the field
• Rapid growth in the quantity of omic data means bio-informaticians need to manage data in an efficient and reliable manner. The main focus of this course is on designing, creating and querying relational databases
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Why a (relational) database?
1. large volume of data (typically gigabytes)2. complex data structure (not matching standard
application)3. long-term use / continued accumulation or
incremental update4. total accuracy & consistency needed on micro-scale5. frequent accesses to small subsets, ad hoc queries6. data shared by more than one person
(University Computing 1991; Significance Dec 2007)
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Extract for analysis• Fields ( variables ) = columns• Units ( level of analysis ) = rows• Columns x Rows = Data table
Query -> view ->
table of data -> summary or analysis
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Mystery meat• What tables form the raw data?• What fields are in each table?• Data dictionary?• Documenting meanings or DB structure?
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Table preferred when• Scientific data probably SHOULD NOT be changed
– or data added in batches ( incremental )
• Structure NOT complex– replication across units allowed, but not excessive
• Levels of analysis are few ( or few dominant )• Analyses summarize whole data or samples
– often one-offs ( bespoke or user-written ) • Sorting or indexing allows very rapid access
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Data table needs metadata• Metadata standards (Dublin core)
– emphasis on discovery – list many fields– codebook not mentioned
• A modest suggestion– data table of rows and columns, with column headers– codebook: another table to explain headers– metadata: describe background, ownership etc
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Geographical Databases
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ESRI (ArcInfo) assumes• The purpose of a GIS is to provide a spatial
framework to support decisions …• Most often, a GIS presents information in the
form of maps and symbols …• A map user is the end consumer of a GIS.
This person looks at maps …• When the Cassini spacecraft was launched,
GIS was used to evaluate the risk of an accident with the plutonium generators on board
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Nearer to me
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GISs contain
• Data as points, lines, areas• Location data
– lat/long, grid refs, postcodes, toids• Representation instructions
– scaling, icons, label position, shading
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Can you get data out?• Point and click works for pop-up labels
– not to output a table• Limited to the precision of the input device, including
the user’s eyesight• I want, probably, a whole layer of data, including the
positions as named fields
How do my needs map into the database?
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Lacking / hidden / difficult in GIS
• List fields associated with physical object• Choose many objects and output data
– eg to make proximity matrix• Distinguish raw from constructed data
– point-heights versus interpolated contour
• Output data values for an area – eg sea surface temperatures
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Request
GIS suppliers may prefer to address users’ needs by adding yet more features to the interface, or pointing to the SQL interface
I would rather they re-consider the role of the GIS as a data warehouse, from which it should be easier to select and extract data that can be analysed in other software