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Peter Fox

Data Science - CSCI-6961-01

Week 8, October 25, 2011

Academic Basis for Data and Information Science, Data

Models, Schema, Data Tools and Data as Service

Paradigms+ Class Project Definition

Contents• Informatics

• Data models

• Schema

• Tools

• Markup languages

• Data as service

• Projects!

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Definitions (revisited)

• Data - are pieces of <x> that represent the qualitative or quantitative attributes of a variable or set of variables.

• Data (plural of "datum", which is seldom used) - are typically the results of measurements and can be the basis of graphs, images, or observations of a set of variables.

• Data - are often viewed as the lowest level of abstraction from which information and knowledge are derived 3

Definitions ctd.

• Information– Representations (of facts? data?) in a form that

lends itself to human use

• Knowledge– …. meaning

• Metadata – data about data

• Metainformation – information about information

• Data documentation – integrated collection of information and metadata intended to support all aspects of data (find, access, use…)

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Data-Information-Knowledge Ecosystem

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Data Information Knowledge

Producers Consumers

Context

PresentationOrganization

IntegrationConversation

CreationGathering

Experience

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Mind the gap• As we aim to use modern technology to

advance data science:

• There is often a gap between science and

the underlying infrastructure and technology

that is available

• Cyberinfrastructure is the new research environment(s) that support advanced data acquisition, data storage, data management, data integration, data mining, data visualization and other computing and information processing services over the Internet.

Informatics - information science includes the

science of (data and) information, the practice

of information processing, and the engineering

of information systems. Informatics studies the

structure, behavior, and interactions of natural

and artificial systems that store, process and

communicate (data and) information. It also

develops its own conceptual and theoretical

foundations. Since computers, individuals and

organizations all process information,

informatics has computational, cognitive and

social aspects, including study of the social

impact of information technologies. Wikipedia.

A moment of history

• In the late 1950’s (actually around 1957-1958) the modern informatics term was coined

• Existed for a while but then split into library science and computer science and developed their own fields, became disconnected

• Now coming back to be relevant to science

• Informatics IS NOT just having a scientist work with an “IT/ICT” person (NOT, NOT, NOT) 7

Advertisement• Spring 2012 – Xinformatics

• http://tw.rpi.edu/web/courses/Xinformatics/2012

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Library science• Curates the artifacts of knowledge

• Organizes and manages them for consumers– Cataloging and classification

• Preservation– ‘maintaining or restoring access to artifacts,

documents and records through the study, diagnosis, treatment and prevention of decay and damage’ (wikipedia)

• Digital age– Curation and preservation

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Cognitive Science• Cognitive science is an interdisciplinary study

of the mind and intelligence

• It operates at the intersection of psychology, philosophy, computer science, linguistics, anthropology, and neuroscience.

• Of relevance for data and information science are three significant theoretical underpinnings– mental representation,– the nature of expertise, – and intuition

• Very relevant to model, data/metadata choice10

Social Science• Branch of humanities

• Especially as it relates to networks of scientists

• Exploits sociology of groups, teams

• Cultural norms as well as discipline norms– Modes of what and how rewards are given– Between those who produce and those who

consume data (and information)– More

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Information theory• Semiotics, also called semiotic studies or

semiology, is the study of sign processes (semiosis), or signification and communication, signs and symbols, into three branches:– Syntactics: Relation of signs to each other in

formal structures– Semantics: Relation between signs and the

things to which they refer; their denotata– Pragmatics: Relation of signs to their impacts on

those who use them 12

(Information) Architecture

• Definition: – “is the art of expressing a model or concept of

information used in activities that require explicit details of complex systems” (wikipedia)

– “… I mean architect as in the creating of systemic, structural, and orderly principles to make something work - the thoughtful making of either artifact, or idea, or policy that informs because it is clear.” Wuman

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Information Models• Conceptual models, sometimes called domain

models, are typically used to explore domain concepts

• High-level conceptual models are often created as part of initial requirements envisioning efforts as they are used to explore the high-level static business or science or medicine structures and concepts.

• Conceptual models are often created as the precursor to logical models or as alternatives to them

• Followed by logical and physical models 14

Data Models• Conceptual data models, sometimes called domain

models, are typically used to explore domain concepts

• High-level conceptual models are often created as part of initial requirements envisioning efforts as they are used to explore the high-level static business structures and concepts.

• Conceptual data models are often created as the precursor to logical data models or as alternatives to LDMs.

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Conceptual model

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Data Models• Logical data models (LDMs). • LDMs are used to explore the domain concepts,

and their relationships, of your problem domain. • This could be done for the scope of a single project

or for your entire enterprise. • LDMs depict the logical entity types, typically

referred to simply as entity types, the data attributes describing those entities, and the relationships between the entities.

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Logical model

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Data Models• Physical data models (PDMs). • PDMs are used to design the internal schema of a

database, depicting the data tables, the data columns of those tables, and the relationships between the tables.

• PDMs often prove to be useful on a range of applications

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Physical model

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However as a consumer• Do you ever really see these data models?

• What’s the most common form of making data available to others?

• What’s the most common means? Second most common?

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Example XML<?xml version="1.0" encoding="ISO-8859-1"?>

<shiporder orderid="889923"

xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"

xsi:noNamespaceSchemaLocation="shiporder.xsd">

<orderperson>John Smith</orderperson>

<shipto>

<name>Ola Nordmann</name>

<address>Langgt 23</address>

<city>4000 Stavanger</city>

<country>Norway</country>

</shipto>

<item>

<title>Empire </title>

<note>Special Edition</note>

<quantity>1</quantity>

<price>10.90</price>

</item>

<item>

<title>Hide your heart</title>

<quantity>1</quantity>

<price>9.90</price>

</item>

</shiporder>

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Very simple schema<?xml version="1.0" encoding="ISO-8859-1" ?>

<xs:schema xmlns:xs=http://www.w3.org/2001/XMLSchema>

<xs:element name="shiporder">

<xs:complexType>

<xs:sequence>

<xs:element name="orderperson" type="xs:string"/>

<xs:element name="shipto">

<xs:complexType>

<xs:sequence>

<xs:element name="name" type="xs:string"/>

<xs:element name="address" type="xs:string"/>

<xs:element name="city" type="xs:string"/>

<xs:element name="country" type="xs:string"/>

</xs:sequence>

</xs:complexType>

</xs:element>

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<xs:element name="item" maxOccurs="unbounded">

<xs:complexType>

<xs:sequence>

<xs:element name="title" type="xs:string"/>

<xs:element name="note" type="xs:string" minOccurs="0"/>

<xs:element name="quantity" type="xs:positiveInteger"/>

<xs:element name="price" type="xs:decimal"/>

</xs:sequence>

</xs:complexType>

</xs:element>

</xs:sequence>

<xs:attribute name="orderid" type="xs:string" use="required"/>

</xs:complexType>

</xs:element>

</xs:schema>

Markup Languages• Reminder:

– Mixes data and metadata, and yes, information– Tag structure does not always model the

underlying data structure– Modeling the XML itself, i.e. the schema is

another task– Does have the potential benefit that it is more for

use than storage

• Parsing the file:– incomplete versus complete tags– Empty or optional fields 28

Data tools (just a few)• Models

– http://www.datamodel.org/– MSDN:

http://msdn.microsoft.com/en-us/library/bb399249.aspx

• Schema– The Schematron differs in basic concept from other

schema languages in that it not based on grammars but on finding tree patterns in the parsed document. This approach allows many kinds of structures to be represented which are inconvenient and difficult in grammar-based schema languages. If you know XPath or the XSLT expression language, you can start to use The Schematron immediately.

– http://www.schematron.com/29

Markup Language tools• Any context-sensitive editor

• XMLSpy, XML Notepad, XML Editor, oXygen

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Data as Service• Modern internet architectures allow for

– Service oriented architectures– Resource oriented architectures

• Why is this important for data models, schema, etc.– Hides/ obscures underlying model, schemas– Service interfaces are often a poor/ hybrid match

for underlying models

• UML and ISO 19xxx family of standards, e.g. 19135 are changing the landscape

• Mature in certain settings.31

Open Geospatial Consortium• Web Feature Service (WFS)

– http://www.opengeospatial.org/standards/wfs– support INSERT, UPDATE, DELETE, LOCK,

QUERY and DISCOVERY operations on geographic features using HTTP as the distributed computing platform

– Built on Geographic Markup Language (GML)

• Tutorial– http://docs.codehaus.org/display/MAP/

WFS+Tutorial

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WFS examples

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Open Geospatial Consortium• Web Mapping Service (WMS)

– http://www.opengeospatial.org/standards/wms– produces maps of spatially referenced data

dynamically from geographic information ("map" is a portrayal of geographic information as a digital image file suitable for display on a computer screen). A map is not the data itself. WMS-produced maps are generally rendered in a pictorial format such as PNG, GIF or JPEG, or occasionally as vector-based graphical elements in Scalable Vector Graphics formats.

– http://www.intl-interfaces.com/cookbook/WMS/– http://oceanesip.jpl.nasa.gov/esipde/guide.html

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Open Geospatial Consortium• Web Coverage Service (WCS)

– http://www.opengeospatial.org/standards/wcs– supports electronic interchange of geospatial

data as "coverages" – that is, digital geospatial information representing space-varying phenomena

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Open Geospatial Consortium• Sensor Observation Service (SOS)

– http://www.opengeospatial.org/standards/sos

• SWE Common– http://www.opengeospatial.org/projects/groups/

swecommonswg – Get_capabilities

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IVOA (www.ivoa.net)• Simple Image Access Protocol

– http://ivoa.net/Documents/SIA/20091008/PR-SIA-1.0-20091008.pdf

– This specification defines a protocol for retrieving image data from a variety of astronomical image repositories through a uniform interface. The interface is meant to be reasonably simple to implement by service providers. A query defining a rectangular region on the sky is used to query for candidate images.

– The service returns a list of candidate images formatted as a VOTable. For each candidate image an access reference URL may be used to retrieve the image. Images may be returned in a variety of formats including FITS and various graphics formats. Referenced images are often computed on the fly, e.g., as cutouts from larger images.

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IVOA (www.ivoa.net)• Simple Spectrum Access Protocol

– http://ivoa.net/Documents/REC/DAL/SSA-20080201.pdf– The Simple Spectral Access (SSA) Protocol (SSAP) defines

a uniform interface to remotely discover and access one dimensional spectra. SSA is a member of an integrated family of data access interfaces altogether comprising the Data Access Layer (DAL) of the IVOA.

– SSA is based on a more general data model capable of describing most tabular spectrophotometric data, including time series and spectral energy distributions (SEDs) as well as 1-D spectra; however the scope of the SSA interface as specified in this document is limited to simple 1-D spectra, including simple aggregations of 1-D spectra.

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Discussion• Theoretical concepts?

• Data models?

• Schema?

• Tools?

• Service paradigms?

• Relation to data management?

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Summary• Informatics as a new field

• Data models and schema and the tools that go with them are plentiful

• Modern use of XML and specific markup languages obscure the underlying data structure (physical and logical) but have other advantages

• Data as service carry this to another level

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Week 8 – part 2

Class exercise - Working with someone else’s data

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Producers Consumers

Quality Control

Fitness for Purpose Fitness for Use

Quality Assessment

Trustee Trustor

Reading – data resources• Department of Energy EIA• Humanities - Digging into Data • Environmental Protection Agency (EPA)• US Geological Survey (and state surveys) (USGS)• NASA Earth Observing System (EOS) and ECHO• National Oceanic and Atmospheric Administration (NOAA)

NODC, NGDC, NCDC• Department of Energy (DoE)• National Library of Medicine (NLM)• Cancer Grid (CaBIG)• OneGeology• data.gov • One of your own

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Contents• Is it possible to use someone else’s data – a

quote from the trenches

• Understanding appropriate data sources

• Finding and accessing them

• Using them

• Defining a project

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From Carole Goble (Manchester)

• “Scientists would rather share their toothbrush than their data”

• However, some are made to share…

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Appropriate Data Sources• Remember the data management principles

• Goal and investigation?

• What is of interest?

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Finding and Accessing• From the lists already provided?

• Web search?

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Using• The access interface

– Form?– Web service?– Limits?

• Formats?

• Metadata conventions?

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Defining a Project: Class Exercise

• Using someone else’s data– You will use someone else’s toothbrush– 6 groups of 5+ people– Let’s discuss some options

• Intent is to mix your skills/ interest and carry out a challenging data (collect/ manage/ use) exercise

• Remainder of this class is to search, formulate, develop your ideas and discuss and seek guidance

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What is next• Assignment 4 on the wiki to guide your efforts

– Due on Nov. 22 write up and Nov. 29 presentation

• Note Term assignment also due Nov. 29 but it is written and individual – will be handed out on Nov. 15 (week 11).

• Next week– Um….

• Reading:– None

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Groups 2011• A – Grace, Jay, Louis, Abhirami, Linyun

• B – Jason, Geok, Charisma, Naveen, Zack

• C – Stephanie, Michael, Bhavana, Thirun, Amruta, Buster

• D – Jeff, Anshuman, Nupoor, Yiyi, Daniel

• E – Ram, Peter, Nikut, Jon, Apurva

• F – Benno, Kiran, Akeem, Sapan, Randy, Misbah

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