@@ -54,8 +53,8 @@
- While server memory capacity has increased significantly in recent
- years, VIVO's reliance on in-memory caching of RDF data had put limits
+ While server memory capacity has increased significantly in recent
+ years, VIVO's reliance on in-memory caching of RDF data had put limits
on the ultimate scalability of VIVO instances and potentially increased
the cost of servers required to support VIVO.
@@ -77,10 +76,10 @@
- VIVO 1.2 includes a new ontology module representing research - resources including biological specimens, human studies, instruments, - organisms, protocols, reagents, and research opportunities. This module - is aligned with the top-level ontology classes and properties from the + VIVO 1.2 includes a new ontology module representing research + resources including biological specimens, human studies, instruments, + organisms, protocols, reagents, and research opportunities. This module + is aligned with the top-level ontology classes and properties from the NIH-funded eagle-i Project.
The Harvester development team is releasing version 1.0 of the VIVO Harvester library, an extensible data ingest and updating framework - with sample configurations for loading PubMed publication, grants, and - human resources data. The Harvester is available at - http://sourceforge.net/projects/vivo. + with sample configurations for loading PubMed publication, grants, and + human resources data. The Harvester is available at http://sourceforge.net/projects/vivo.
@@ -101,9 +99,9 @@
localhost.
- CREATE DATABASE dbname CHARACTER SET utf8;+
CREATE DATABASE dbname CHARACTER SET utf8;
Grant access to a database user. For example:
-GRANT ALL ON dbname.* TO 'username'@'hostname' IDENTIFIED BY 'password';+
GRANT ALL ON dbname.* TO 'username'@'hostname' IDENTIFIED BY 'password';
Keep track of the database name, username, and password for Step
IV.
@@ -230,9 +228,30 @@
http://vivoweb.org/download
- Content from Brian Lowe coming. + VIVO 1.2 offers a choice of two triple store technologies: in-memory models backed by + Jena's legacy relational database store (RDB) and Jena's SPARQL database (SDB). RDB was + used by VIVO 1.1.1 and earlier. This mode offers fast response, but only by caching the + entire RDF model in the server's main memory. The memory available to VIVO limits the + number of RDF statements that may be stored. +
++ SDB mode caches only a fraction of the RDF data in memory. Most queries are issued directly + against the underlying database. This allows VIVO installations to display data from large + RDF models while requiring only a small amount of server memory to run the application. + There is a tradeoff in response time: pages make take slightly longer to load in SDB mode, + and performance will depend on the configuration parameters of the database server. + Additionally, advanced OWL reasoning (not enabled by default in either mode) is not possible + in SDB mode. With SDB, only the default set of inferences (inferred rdf:type statements) are + generated, though they are generated as soon as data is edited rather than in a background process. +
++ Though a VIVO installation may be switched back and forth between RDB and SDB mode by changing + a configuration property and redeploying the application, it is important to note that data + added in one mode will not typically appear in the other. The exception is when a system is + first switched from RDB mode to SDB mode. In this case, the data from the RDB store will be + automatically migrated to SDB.
@@ -276,8 +295,8 @@ "http://vivo.example.edu/individual/" in order to support linked data. Similarly, if VIVO is installed at "http://www.example.edu/vivo" the default namespace must be set to - "http://www.example.edu/vivo/individual/"
export CATALINA_OPTS="-Xms2048m -Xmx1024m -XX:MaxPermSize=128m"
- This sets Tomcat to allocate an initial heap of 2048 megabytes, a - maximum heap of 1024 megabytes, and a PermGen space of 128 megs. 1024 + This sets Tomcat to allocate an initial heap of 2048 megabytes, a + maximum heap of 1024 megabytes, and a PermGen space of 128 megs. 1024 megabytes is a minimum practical heap size for production installations storing data for large academic institutions, and additional heap space is preferable. For testing with small sets of data, 256m to 512m should @@ -635,17 +654,17 @@ will be prompted to select a new password and verify it a second time.
- After verifying your new password, you will be presented with a - menu of editing options. Here you can create OWL classes, object + After verifying your new password, you will be presented with a + menu of editing options. Here you can create OWL classes, object properties, data properties, and configure the display of data. - Currently, any classes you wish to make visible on your website must be - part of a class group, and there a number of visibility and display - options available for each ontology entity. VIVO comes with a core VIVO + Currently, any classes you wish to make visible on your website must be + part of a class group, and there a number of visibility and display + options available for each ontology entity. VIVO comes with a core VIVO ontology, but you may also upload other ontologies from an RDF file.
- Under the "Advanced Data Tools" click "Add/Remove RDF Data." Note - that Vitro currently works best with OWL-DL ontologies and has only + Under the "Advanced Data Tools" click "Add/Remove RDF Data." Note + that Vitro currently works best with OWL-DL ontologies and has only limited support for pure RDF data. You can enter a URL pointing to the RDF data you wish to load or upload a file on your local machine. Ensure that the "add RDF" radio button is selected. You will also @@ -670,9 +689,9 @@
Log in as a system administrator. Navigate to the "Site Admin" - table of contents (link in the right side of the header). Go to "Site - Information" (under "Site Configuration"). In the "Site Information - Editing Form," enter a functional email address in the field "Contact + table of contents (link in the right side of the header). Go to "Site + Information" (under "Site Configuration"). In the "Site Information + Editing Form," enter a functional email address in the field "Contact Email Address." and submit the change.
@@ -703,9 +722,9 @@
After setting up the mod_jk connector above, you will need to
modify the Tomcat's server.xml (located in [tomcat root]/conf/)
- to
- respond
- to requests from Apache via the connector. Look for the
+ to
+ respond
+ to requests from Apache via the connector. Look for the
<connector> directive and add the following properties:
connectionTimeout="20000" maxThreads="320" keepAliveTimeout="20000"@@ -719,14 +738,30 @@ directive and update as follows: -
<Host name="localhost" appBase="webapps"+
DeployOnStartup="false"
unpackWARs="true" autoDeploy="false"
xmlValidation="false" xmlNamespaceAware="false">
<Alias>example.com</Alias>
<Context path=""
docBase="/usr/local/tomcat/webapps/vivo"
reloadable="true"
cookies="true" >
<Manager pathname="" />
<Environment type="java.lang.String" override="false"
name="path.configuration"
value="deploy.properties"
/>
</Context>
...
+ <Host name="localhost" appBase="webapps"
+ DeployOnStartup="false"
+ unpackWARs="true" autoDeploy="false"
+ xmlValidation="false" xmlNamespaceAware="false">
+ <Alias>example.com</Alias>
+ <Context path=""
+ docBase="/usr/local/tomcat/webapps/vivo"
+ reloadable="true"
+ cookies="true" >
+ <Manager pathname="" />
+ <Environment type="java.lang.String" override="false"
+ name="path.configuration"
+ value="deploy.properties"
+ />
+ </Context>
+ ... +
- Do we need this section still? - elly -
-- VIVO uses the Pellet engine to perform reasoning, which runs in the - background at startup and also when the knowledge base is edited. VIVO + This optional configuration step is only applicable to VIVO installations + running in RDB mode (See section Choose Triple Store for details). + VIVO uses the Pellet engine to perform reasoning, which runs in the + background at startup and also when the knowledge base is edited. VIVO continues serving pages while the reasoner continues working; when the reasoner finishes, the new inferences appear. Inferred statements are cached in a database graph so that they are available immediately when @@ -734,9 +769,9 @@
By default, Pellet is fed only an incomplete view of your ontology - and only certain inferences are materialized. These include rdf:type, - rdfs:subClassOf, owl:equivalentClass, and owl:disjointWith. This mode - is typically suitable for ontologies with a lot of instance data. If + and only certain inferences are materialized. These include rdf:type, + rdfs:subClassOf, owl:equivalentClass, and owl:disjointWith. This mode + is typically suitable for ontologies with a lot of instance data. If you would like to keep the default mode, skip to the next step.
@@ -835,9 +870,9 @@ privileges assigned to that account.
In addition, VIVO will try to associate the user with a profile - page, so the user may edit his own profile data. VIVO will search the - data model for a person with a property that matches the User’s network - ID. You need to tell VIVO what property should be used for matching. + page, so the user may edit his own profile data. VIVO will search the + data model for a person with a property that matches the User’s network + ID. You need to tell VIVO what property should be used for matching. Insert a line like this in the deploy.properties file:
selfEditing.idMatchingProperty = [the URI of the property]@@ -865,10 +900,10 @@