D21.4 GapIdentificationService User Manual

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Nov 17, 2013 (3 years and 9 months ago)

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REPORT

Copyright © 2011
ESA

and other members

of

the SCIDIP
-
ES Co
nsortium, www.scidip
-
es.eu



SCIDIP
-
ES EC Grant Agreement n°.
283401


1






D
21
.
4

GapIdentificationService

User Manual


Work package

WP
21

Services/Toolkits Development and Adaptation




Task



Author (s)

Shirley Crompton
, Brian Matthews

STFC

Author
(s)

Christian Ceprani

ACS

Author (s)

Holger Brocks

ICT

Author (s)

Yannis Tzitzikas,
Yannis Marketakis

FORTH

Author (s)

Felix Engel

FTK

Author (s)

Jinsongdi Yu

JU

Author (s)

Luigi Briguglio

ENG

Authorized by

Name Surname

Company

Reviewer

Name Surname

Company

Doc Id


Dissemination Level

CONFIDENTIAL/PUBLIC

Issue

1.
1

Date

1
5
/0
3
/201
3





REPORT

Copyright © 2011
ESA

and other members

of

the SCIDIP
-
ES Co
nsortium, www.scidip
-
es.eu



SCIDIP
-
ES EC Grant Agreement n°.
283401


2

Abstract
:

This document
provides a description of

the User Manual for the
Gap Identification Service
developed

in the frame of SCIDIP
-
ES project. This document

contains
all useful information on how
to
install
/deploy
, configure and
use
Gap Identification Service
.


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-
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4


Document Log

Date

Author

Changes

Version

Status

04/02
/201
3

Shirley Crompton
,
Brian Matthews,
Christian Ceprani,
Holger Brocks, Yannis
Marketakis, Felix
Engel, Jinsongdi Yu,
Pasquale Andriani

and
Luigi Briguglio

First draft for internal
review

0.1

Draft

1
3
/3/2013

Yannis Marketakis,
Yannis Tzitzikas

added section about
GIS

1.0

Draft

15/3/2013

Yannis Marketakis

General revision

1.1






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TABLE OF CONTENTS


1

INTRODUCTION

................................
................................
................................
................................
...........................

6

1.1

P
URPOSE AND
S
COPE

................................
................................
................................
................................
................

6

1.2

W
HO SHOULD READ THIS
DOCUMENT
................................
................................
................................
......................

6

1.3

S
YSTEM
C
ONTEXT

................................
................................
................................
................................
.......................

6

2

INSTALLA
TION GUIDE

................................
................................
................................
................................
.............

6

2.1

O
VERVIEW

................................
................................
................................
................................
................................
.....

6

2.2

P
REREQUISITES

................................
................................
................................
................................
...........................

6

2.2.1

S
OFTWARE PREREQUISITE
S

................................
................................
................................
................................
..................

7

2.2.2

H
ARDWARE PREREQUISITE
S

................................
................................
................................
................................
.................

7

2.3

OSS/COTS

I
NSTALLATION

................................
................................
................................
................................
.......

7

2.3.1

JAVA

SE

I
NSTALLATION
.

................................
................................
................................
................................
........................

7

2.3.2

A
PACHE
T
OMCAT
I
NSTALLATION

................................
................................
................................
................................
..........

8

2.3.3

O
PEN
L
INK
V
IRTUOSO
I
NSTALLATION

................................
................................
................................
................................
.

9

2.4

G
AP
I
DENTIFICATION
S
ERVICE
I
NSTALLATION

................................
................................
................................
....

10

2.5

U
NINSTALLATION

................................
................................
................................
................................
.......................

12

3

USING SCIDIP
-
ES GAP IDENTIFICATIO
N SERVICE

................................
................................
..................

12

3.1

G
ETTING
S
TARTED

................................
................................
................................
................................
....................

12

3.2

C
REA
TING NEW
R
ESOURCES

................................
................................
................................
................................
..

12

3.2.1

C
REATE A NEW
M
ODULE

................................
................................
................................
................................
......................

12

3.2.2

C
REATING A NEW
DC

P
ROFILE

................................
................................
................................
................................
.........

14

3.3

I
NTELLIGIBILITY
R
ELATED
S
ERVICES

................................
................................
................................
....................

15

3.3.1

S
EARCHING FOR A
M
ODULE
(
AND ITS DEPENDENCIES
)

................................
................................
...........................

15

3.3.2

S
EARCH FOR A
DC

P
ROFILE
(
AND ITS INTELLIGIBLE

MODULES
)

................................
................................
...........

17

3.3.3

I
DENTIFYING
R
ISKS

................................
................................
................................
................................
................................

18

3.3.4

S
EARCHING FOR AN
I
NTELLIGIBILITY
G
AP

................................
................................
................................
.....................

19

3.3.5

I
MPORT
/E
XPORT
R
ESOURCES

................................
................................
................................
................................
...........

20





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1

Introduction

1.1

Purpos
e and Scope

This document provides
information regarding the installation of Gap Identification Service (
hereafter
we’ll use the notation GIS).Furthermore
instructions for configuring,
and using GIS are provided.

1.2

Who should read this document

This document

refers to: (a) system administrators, since it provides information allowing them to
install and deploy GIS and (b) end users that are willing to use GIS and understand its concepts.

1.3

System Context

Role of the COMPONENT_X in the overall SCIDIP
-
ES scenario
. This section shall refer to the general
overview described in the D21.4 master document.


2

Installation
Guide


2.1

Overview

GIS is provided as a JAVA Web Application. It is therefore delivered as a web application archive (war).
This means that GIS can be hos
ted in a web server, and users can access it using a web browser.
Furthermore GIS can be configured to work on top of two different persistence layers;(a)main
-
memory
layer or (b) using a triple
-
store
.

The latter is based on OpenLink Virtuoso
1

triplestore.
The figure below
show
s

the deployment diagram of GIS.


Figure
1

Gap Identification Service deployment diagram


2.2

Prerequisites




1

http://virtuoso.openlinksw.com/

deployment Component Model
User Computer
Web Server
Database
SPARQL
endpoint
SPARQL
Web Browser
Gap
Identification
Service
HTTP
HTTP

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2.2.1

Software prerequisites

GIS requires the following software components to be installed:



JAVA SE (at least
version 1.6)
-

GIS has been tested using JAVA SE 6 and JAVA SE 7
.



Apache Tomcat (at least version 7.0).
GIS has been tested also u
s
ing Sun Glassfish V3, however
Apache Tomcat is suggested.

GIS comes in two different implementations of its Persistence Layer
. The first one is a main
-
memory
persistence layer, while the second one is based on OpenLink Virtuoso. The former has no further
requirements.
Th
e latter requires the existence of an Openlink Virtuoso instance (The recommended
version is OpenSource Virtuo
so ver
: 6.1
. It is not necessary that the web server (hosting the GIS web
application) and the OpenLink Virtuoso server to be in the same (physical) node.

2.2.2

Hardware prerequisites

None

2.3

OSS/COTS Installation

2.3.1

JAVA SE Installation.

Under Windows

Download a proper version of JAVA
JDK
from
JAVA SE Do
wn
load

page
2
. (Note that JRE is not
enough, the full JDK should be downloaded and installed. After downloading it double
-
click on
the executable file to start the installation process and follow the inst
ructions.

After the installation process finishes the environment variables should be set accordingly. To
do so right click on My Computer and select Properties. Click on Advanced tab and then select
Environment Variables. Under System variables click on N
ew and create a new environment
variable with name JAVA_HOME and value the path of the jdk installation (i.e.
C:
\
Program
Files
\
Java
\
jdk1.7.0_17
).

To verify that everything has been installed properly open a new console (by executing cmd
under start


run)

and
execute “
java

version

. The output should be similar to
Figure
2
.


Figure
2

Verifying Java installation under windows


Under
Linux




2

http://www.oracle.com/technetwork/java/javase/downloads/index.html


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Download a proper tar.gz version of JAVA
JDK
from
JAVA SE Do
wn
load

page
. (Note that JRE is
not enou
gh, the full JDK should be downloaded and installed
)
. After downloading it extract it
under /usr/share/. Let’s assume that the folder is /usr/share/jdk1.7.0_15/ (the folder name
could be different, according to the name of the downloaded version of JDK).

After that the environment variables should be set accordingly. To do so open ~/.bashrc file and
add the following lines (the first is for declaring the location of the JDK and the second one is
for enabling Java binaries to be executed from the shell).



e
xport JAVA_HOME=/usr/share/jdk.1.7.0_15



export PATH=$PATH:
$JAVA_HOME/
bin

To verify that java has been installed successfully execute from a console

java

version

.
The output should be similar to
Figure
3
.


Figure
3

Verifying Java installation under linux


In the remaining we will refer to the location where JDK has been installed as $JAVA_HOME.

2.3.2

Apache Tomcat Installation

Under Windows

Installing Apache tomcat for windows can be done using two different ways; (a) using a service
installer and (b) using Apache Tomcat binaries. The easy
-
way is approach (a) since
it is only

required to download and execute the installer. Here we’ll describe

the
not
-
so
-
obvious
approach (b).

Download one of the compressed files found under Apache Tomcat Downloads

page
3
. Extract
the contents of the folder in any location (i.e. C:
\
Program Files
\
apache_tomcat_7). Set a new
environment variable (using the same p
rocess when setting the environment variables for Java)
with name CATALINA_HOME and value the path of the Apache Tomcat folder (i.e. C:
\
Program
Files
\
apache_tomcat_7).

Under
Linux

Download
a proper version
of the compressed files found under Apache Tomcat

Downloads

page
. Extract the contents of the folder in any location (i.e. /usr/share/apache_tomcat_7). Set
a new environment variable (using the same process when setting the environment variables
for Java) with name CATALINA_HOME and value the path of th
e Apache Tomcat folder (i.e.
/usr/share/apache_tomcat_7).




3

http://tomcat.apache.org/download
-
70.cgi


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To verify that tomcat
has been installed successfully, we must first start Apache Tomcat server.
To start it, execute
$CATALINA_HOME/bin
/startup.bat under Windows or
$CATALINA_HOME/bin/startup.sh
under Linux
. Then using a web browser visit the url
http://localhost:8080
. The output should be similar to
Figure
4
.


Figure
4

Verifying Apache Tomcat installation

In the remaining we will refer to the location where Apache Tomcat has been installed as
$CATALINA_HOME

2.3.3

OpenLink Virtuoso Installation

Under Windows

Download a proper version of openLink virtuoso

from Opensource Virtuoso Downloads
4
. Unzip
the contents of the downloaded compressed file in any place (i.e. C:
\
Virtuoso). After that
Virtuoso have to be installed as a service; open a console and go under the folder
C:
\
Virtuoso
\
bin and execute the follow
ing

virtuoso
-
t
.exe

+service create +instance MyService +configfile
C:
\
Virtuoso
\
database
\
virtuoso.ini

and then to start it execute the following

virtuoso
-
t +service start +instance MyService

Under Linux




4

http://virtuoso.openlinksw.com/dataspace/doc/dav/wiki/Main/


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To download and install an open source version of
OpenLink Virtuoso execute the following

sudo aptitude install virtuoso
-
opensource


To ve
r
ify
that OpenLink Virtuoso has been successfully installed open a web browser and visit
the url
http://localhost:8890
. The outpu
t should be similar to
Figure
5


Figure
5

Verifying OpenLink Virtuoso installation


2.4

Gap Identification Service

Installation

In order to install GIS, the web application archive of the service is required. The latest version of the
artifact can be found on SCIDIP
-
ES
Build

P
latform at
http://jenkin
s.scidip
-
es.eu/jenkins/job/digitalpreserve
-
knowledge/
. As
Figure
6

shows there are two different artifacts:



GapManager.jar
, which is the JAVA API
containing the
core

functionalities
of GIS.



GapManager.war
, which is the web application of GIS.



Figure
6

the

latest artifacts produced by SCIDIP
-
ES build platform


Download the second one (GapManager.war) and place it under $CATALINA_HOME/webapps
. After
that start Apache Tomcat, and the web application will automatically be deployed (a folder named
GapManager under webapps will be created). GIS is reachable by visiting the url
http://localhost:8080
/GapManager
. The output should be similar to
Figure
7


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Figure
7

t
he home page of Gap Identification Service


The default configuration for GI
S is to use the main
-
memory persistence layer. This can be changed
(switching to triple store persistence layer)

by modifying appropriately the config.properties file found
under $CATALINA_HOME/webapps/
GapManager
/
WEB
-
INF
/
classes
/
eu
/
scidipes
/
impl
/
gapidenti
ficationservice
/
server
/
config.properties

It contains the following key
-
value properties:



eu.scidipes.impl.gapidentificationservice.runmode
: it defines the persistence layer that will be
used. The values that are accepted are
mainmemory

and
virtuoso



eu.scidipes.impl.gapidentificationservice.mainmemory.modules
: It is used only with main
memory persistence layer. It contains the urls (separated by commas) of the files containing
m
odules (and their dependencies), that will be imported to GIS during GIS d
eployment.



eu.scidipes.impl.gapidentificationservice.mainmemory.
profiles
: It is used only with main
memory persistence layer. It contains the urls (separated by commas) of the files containing
designated communities profiles, that will be imported to GIS d
uring GIS deployment.



eu.scidipes.impl.gapidentificationservice.virtuoso.url
: it is used only with the triple store
persistence layer. It defines the url where OpenLink Virtuoso has been installed.



eu.scidipes.impl.gapidentificationservice.virtuoso.
port
: i
t is used only with the triple store
persistence layer. It defines the port where OpenLink Virtuoso is listening.



eu.scidipes.impl.gapidentificationservice.virtuoso.
graph
: it is used only with the triple store
persistence layer. It defines the graph of GIS

resources.



eu.scidipes.impl.gapidentificationservice.virtuoso.
username
: it is used only with the triple
store persistence layer. It is the username for accessing the OpenLink Virtuoso repository.


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eu.scidipes.impl.gapidentificationservice.virtuoso.
password
: it is used only with the triple
store persistence layer. It is the password for accessing the OpenLink Virtuoso repository.


After changing any of the above properties restarting Apache Tomcat is required for changes to take
effect
.


2.5

Uninstallation

GIS c
an be uninstalled from Apache Tomcat by
simply
removing it from $CATALINA_HOME/webapps
folder. In particular the following should be deleted



$CATALINA_HOME/webapps/GapManager/



$CATALINA_HOME/webapps/GapManager.war


3

Using SCIDIP
-
ES
Gap Identification Servic
e

3.1

Getting Started

GIS can be accessed using any web browser
by

visiting the url
http://locahost:8080/GapManager
.
The
home page of GIS (
Figure
7
) shows some statistics about the persistence layer of GIS.

In the following chapters (
3.2
,
3.3
) several GIS
-
related notions are being used. It is out of the scope of
this deliverable to describe them. Th
ese

has been well described in other deliverables.

3.2

Creating

new Resources

3.2.1

Create a new Module

To create a new module

the user

must click on Module (from the upper menu bar) and select Add New
(
Figure
8
). The

page show
n

in

Figure
9

will appear. The user must now enter an identifier, a name, a
version for the module to be created.
The user

can also classify the new module to one of the given

module types.

Before creating it the user can add any dependencies about this module

(other
modules that exist in the repository and the new one depends on them
)
. Apart from adding the
dependencies the user can also choose a specific dependency type (
Figure
10
).

When all the required
information has been provided, then user can click on Insert button. This will make the appropriate
checking (the given identifier is unique, checking for cyclic dependencies, etc.) and create the module
with its dependencies. A conf
irmation message will appear.


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Figure
8

Creating a new Module



Figure
9

Creating a new Module


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Figure
10

Creating a new Module


3.2.2

Creating a new DC Profile

To create a new DC Profile the user must click on
Profile and select Add New (
Figure
11
). A new screen
will appear (
Figure
12
) asking for information about
the
profile to be created. In particular the user has
to provide an identifier for the module, a name, and also a list of modules that are intelligible to this
community (
Figure
13
), if any. After adding all the required information the user clicks
Insert

and after
performing the necessary checks, the new profile is stored in GIS repository and a confirmation
message will appear.


Figure
11

Creating a new DC Profile


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Figure
12

Creating a new DC Profile



Figure
13

Creating

a new DC Profile


3.3

Intelligibility Related Services

3.3.1

Searching for a Module

(and its dependencies)

If a user wants to search for a specific module (and inspect its
information
, its dependencies, etc.), he
can
search for it by clicking on Module and selecting Search (
Figure
14
). A new page will appear; the
user can search for a module by providing its identifier, and/or its
name. Exact matching is also
supported

(
Figure
15
).

The results are presented as a list (
Figure
16
) where the user can select any of
them. After clickin
g on a result
,

information about it are presented (
Figure
17
); its identifier, name,
version, the modules it depends on (
direct
dependencies list) as well as the modu
les that depend on it
(
direct
dependents list).

Furthermore apart from showing all the dependencies of a specific module
(the direct dependencies list), GIS can resolve them and show the set of transitive dependencies of a
module (by clicking on “Get Closu
re” button”).

The user can also edit the information of the retrieved
module, by clicking on the Edit button in the upper right corner.



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Figure
14

Searching for a Module



Figure
15

Searching for a Module



Figure
16

Searching for a Module



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Figure
17

Inspecting the

information

of a Module


3.3.2

Search for a DC Profile (and its intelligible modules)

Searching for a DC Profile can be done similarly. In particular the user selects Profile and then clicks on
Search (18). A new page will appear where the user can search for a

profile using its identifier or its
name (19). The results are shown in a list (
Figure
20
) and the user can select the desired one and
inspect its information (
Figure
21
); its identifier, its name, as well as thee modules that are intelligible
from the corresponding community. The user can also edit this profile by clicking o
n Edit button (on
the upper right corner of the page).


Figure
18

Searching for a DC Profile


Figure
19

Searching of a DC Profile



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Figure
20

Searching for a DC Profile



Figure
21

Inspecting the information of a DC Profile


3.3.3

Identifying Risks

GIS provides an easy way of identifying obsolescence risks (i.e. which modules will be affected if a
specific mod
ule will be removed). To better illustrate this assume that the user wants to identify the
modules that are in danger in case

PDF

Reader”

is being removed. First of all the user must search for
this module (by following the procedure described in
3.3.1
). After locating it will look similar to
Figure
22
. The list “Direct

Dependencies” contains all modules that depend on “PDF Reader”

and therefore
are in danger if “PDF Reader” will be removed (they’ll become unreadable).



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Figure
22

Information about a Module


3.3.4

Searching for an Intelligibility Gap

GIS can compute intelligibility gaps
;
the smallest set of extra modules required to make a module

(or a
set of modules)
intelligible for a designated community

(or a set of
communities). To find the
intelligibility gap the user must click on Intelligibilit
y Services and click on Gap (
Figure
23
). A new page
will appear (
Figure
24
)

where the user can add the module (or the set of modules) that should be
checked, against a DC Profile (or a set of DC Profiles). Furthermore the user can specify dependency

t
ype

by selecting the desired type from the corresponding drop down list. This wi
ll compute
intelligibility gap by resolving only dependencies of the specific type.

After specifying the above the
user clicks on Get Gap button and gets the results as shown in
Figure
25
.


Figure
23

Computing Intelligibility Gap


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Figure
24

Computing Intelligibility Gap



Figure
25

Computing Intelligibility Gap


3.3.5

Import/Export Resources

GIS a
llow importing/exporting resources in several formats. The acceptable formats are RDF/XML,
RDF/TRIG, and a proprietary format (using a specific template). To import a set of modules the user
must click on Module
,

select Import (
Figure
26
)

and upload the file containing the modules
.
The same
procedure can be followed to import profiles.


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Furthermore GIS supports exporting the contents of the GIS repository in several form
ats (RDF/XML,
RDF/TRIG, proprietary text). To
export
modules the user must click on Module, select Export (in the
desired format) and then download them. The same procedure can be followed to export profiles.


Figure
26

Importing Modules





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Annex A.

Figures and Tables

A.1.

List of Figures

Figure 1 Gap Identification Service deployment diagram

................................
................................
..........

6

Figure 2 Verifying Java install
ation under windows

................................
................................
...................

7

Figure 3 Verifying Java installation under linux

................................
................................
..........................

8

Figure 4 Verifying Apache Tomcat installation

................................
................................
...........................

9

Figure 5 Verifying OpenLink Virtuoso installation

................................
................................
....................

10

Figure 6 the latest artifacts produced by SCIDIP
-
ES build platform

................................
.........................

10

Figure 7 the home page of G
ap Identification Service

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Figure 8 Creating a new Module

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Figur
e 9 Creating a new Module

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Figure 10 Creating a new Module

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Figure 11 Creating a new DC Profile

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Figure 12 Creating a new DC Profile

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Figure 13 Creating a new DC Profile

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Figure 14 Searching for a Module

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Figure 15 Searching for a Module

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Figure 16 Searching for a Module

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Figure 17 Inspecting the information of a Module

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Figure 18 Searching for a DC Profile

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Figure 19 Searching of a DC Profile

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Figure 20 Searching for a DC Profile

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Figure 21 Inspecting the information of a DC Profile

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Figure 22 Information about a
Module

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Figure 23 Computing Intelligibility Gap

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Figure 24
Computing Intelligibility Gap

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Figure 25 Computing Intelligibility Gap

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SCIDIP
-
ES

SCIence Data Infrastructure for Preservation


Earth Science


SCIDIP
-
ES EC Grant Agreement n°.
283401


23

Figure 26 Importing Modules

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21


A.2.

List of Tables

No table of figures entries found.




SCIDIP
-
ES

SCIence Data Infrastructure for Preservation


Earth Science


SCIDIP
-
ES EC Grant Agreement n°.
283401


24

Annex B.

Terminology

ACRONYM

DESCRIPTION

AIP

Archival Inf
ormation Package

ARK

Archival Resource Key

CDMI

Cloud Management Interface

DOI

Digital Object Identifier

ES

Earth Science

GIS

Gap Identification Service

KB

Knowledge Base

OS

Orchestration Service

OWL

Web Ontology Language

PI

Persistent Identifier

PNM

Preservation Network Model

PURL

Persistent Uniform Resource Locator

RDF

Resource Description Framework

RepInfo

Representation Information

SNIA

Storage Networking Industry Association

SWKM

Semantic Web Knowledge Middleware

VM

Virtual Machine

WP

Work Package

XAM

eXtensible Access Method

XML

eXtensible Mark
-
up Language