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What is Organic Data Publishing

We are investigating a novel approach to data publishing that is organic in its organization, requires minimal effort from the contributor, has parsimonious design, and is accessible to all scientists as well as other potential contributors. We offer a minimal pre-defined structure, and allow contributors to describe their data by easily defining their own metadata properties to suit their particular datasets, and to reuse common available vocabularies when it is convenient. The normalization of metadata will be organic, as other scientists aggregate datasets in the repository and find the need to aggregate them.

See also this article: “Organic Data Publishing: A New Approach to Scientific Data Sharing”. Workshop on Linked Science (LISC) at the International Semantic Web Conference (ISWC), November 2012.


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Structured Content in a Semantic Wiki

This site uses a semantic wiki framework, RDF as the semantic representation standard. We have developed it as an extension of Semantic MediaWiki that enables contributors to use structured semantic properties to describe the contents of the wiki.

Another way in which this wiki structures content is though pre-defined categories. Pages can have special categories, which gives the wiki pages a pre-defined semantic structure. Special categories include Task, Answer, Data, Workflow, and ExecutedWorkflow.

In addition, each page has a section called "Structured Properties", where contributors can specify properties and values of the topic of the page. Any contributor can define new properties on the fly. Any contributor can change an existing property by one that is used elsewhere, effectively normalizing the use of the property across pages and therefore across objects.

Contributions are also structured. At the bottom of each page, the contributors to that page are shown together with the details of their contributions to that page. Contributors also have their own pages, which include any background information they wish to share, and where the edits that they have made are automatically summarized and shown.

Accessing Structured Content Externally

Build your own apps with the content of this wiki ! You can find extensive documentation about its API here.

Using Structured Content to Dynamically Create Sections of Wiki Pages

Those properties can then be used to answer queries that aggregate automatically those properties and pages. Below are some examples of how a query can be stated using those structured properties, and the automatically generated table that answers the query. These queries can be used to create dynamically generated content.


Example: Collection

 OwnerNumber of samples
Sample Collection ESIPESIP3,000
Sample Collection ISIISI5,000

Example: Get a List of Lakes

 Area of CatchmentLatitudeLongitude
Lake Monona
Lake Wingra43.053-89.422

Example: Datasets

 SiteLatitudeSiteLongitude
1307eaac77b5a38a751c79cd69e225b837.347-120.976
225888a77729a7a47ea68c733ce86c2737.347-120.976
29d6e6a8edce4e908b48ab9df9f530ae37.347-120.976
2fad6c1e3876b82e5e65cd29b37602bb37.347-120.976
383e4da28ecc4b8471649de0a874d37.347-120.976
3be0500acdf67cec1577d2826bd82aa737.347-120.976
3fa77df8d3d426b1fdf130ea6019908b37.347-120.976
411085a52c9d0232b6d36071bc50110737.347-120.976
4355dbf2e04cfc45755a285bebd4465e37.347-120.976
45fde681eb168170b204851c8863ad9437.347-120.976
4c6254b9b68b022d54b7b8c68e453bcb37.347-120.976
4d6648f66024aa2cecb4087f1613f54837.347-120.976
59e6d1fc3812c1914c0b4c631a3be50e37.347-120.976
64941e3094451f1f50384aebe243c24b37.347-120.976
6563bedfed5d7ebb11a42329b087fe1837.347-120.976
89d31c94b0ee1e768723d7fe8acbba7437.347-120.976
995dfbd9728f3fd06979ecf14a3e2cd37.347-120.976
99802ac1511854a1b2d3765961d1e7eb37.347-120.976
9b393f24123431c68902c6f45e21eaef37.347-120.976
A0f77db91df91af77ac599abcd4a898037.347-120.976
Acb38f4682e31fb7ae8474ecb395cb6b37.347-120.976
AvgHourly SMN 2010 03 02Z37.347-120.976
AvgHourly SMN 2010 03 03Z37.347-120.976
AvgHourly SMN 2010 03 04Z37.347-120.976
AvgHourly SMN 2010 03 05Z37.347-120.976
AvgHourly SMN 2010 03 06Z37.347-120.976
AvgHourly SMN 2010 03 07Z37.347-120.976
AvgHourly SMN 2010 03 08Z37.347-120.976
AvgHourly SMN 2010 03 09Z37.347-120.976
AvgHourly SMN 2010 03 10Z37.347-120.976
AvgHourly SMN 2010 03 11Z37.347-120.976
AvgHourly SMN 2010 03 12Z37.347-120.976
AvgHourly SMN 2010 03 13Z37.347-120.976
AvgHourly SMN 2010 03 14Z37.347-120.976
AvgHourly SMN 2010 03 15Z37.347-120.976
AvgHourly SMN 2010 03 16Z37.347-120.976
AvgHourly SMN 2010 03 17Z37.347-120.976
AvgHourly SMN 2010 03 18Z37.347-120.976
AvgHourly SMN 2010 03 19Z37.347-120.976
AvgHourly SMN 2010 03 20Z37.347-120.976
AvgHourly SMN 2010 03 21Z37.347-120.976
AvgHourly SMN 2010 03 22Z37.347-120.976
AvgHourly SMN 2010 03 23Z37.347-120.976
AvgHourly SMN 2010 03 24Z37.347-120.976
AvgHourly SMN 2010 03 25Z37.347-120.976
AvgHourly SMN 2010 03 26Z37.347-120.976
AvgHourly SMN 2010 03 27Z37.347-120.976
AvgHourly SMN 2010 03 28Z37.347-120.976
AvgHourly SMN 2010 03 29Z37.347-120.976
AvgHourly SMN 2010 03 30Z37.347-120.976
… further results

Example: Get a List of Workflow Templates (limit to 5)

{{ #ask: [[Category:Workflow]]
 | mainlabel=Workflows
 | format=broadtable
 | limit=5
}}
Workflows
AQUAFLOW EDM
AQUAFLOW EM
AQUAFLOW NTM

Example: Get a List of Workflow Executions (limit to 10)

{{ #ask: [[Category:ExecutedWorkflow]]
 | mainlabel=Executed Workflows
 | format=broadtable
 | limit=10
}}
Executed Workflows
AF EDM Execution 2 March 2012 to 31 March 2012
AF EDM Execution 2 March 2012 to 8 March 2012
AF EM Execution 2 March 2012 to 31 March 2012
AF EM Execution 2 March 2012 to 8 March 2012
AF NTM Execution 2 March 2012 to 31 March 2012
AF NTM Execution 2 March 2012 to 8 March 2012


Example: Get a List of Tasks and their Answers (limited to 5)

{{ #ask: [[Category:Task]]
 | ?Answer
 | mainlabel=Task
 | format=broadtable
 | default=No Tasks in Knowledge Base
 | limit=5
}}
TaskAnswer
Another SubTask
Calculate CO2 levels for the air around the lake
ESIP curation procedures
Global distribution of carbon in lakes and how they process carbonCarbon Budget for Lake Mendota
Lake Casitas

Example: Get Tasks whose answers have some property set

{{ #ask: [[Category:Task]] [[Answer.Has Dataset::2012-Dataset]]
 | mainlabel=Task
 | format=broadtable
 | ?Answer
}}
TaskAnswer
Global distribution of carbon in lakes and how they process carbonCarbon Budget for Lake Mendota

Example: Get a particular Task's SubTasks

{{ #ask: [[Global_distribution_of_carbon_in_lakes_and_how_they_process_carbon]]
 | ?SubTask
 | mainlabel=Task
 | format=broadtable
}}
TaskSubTask
Global distribution of carbon in lakes and how they process carbonCalculate the carbon Budget for a lake
Calculate CO2 levels for the air around the lake