How to use this organic data science wiki

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This is a reference guide on how to use this semantic wiki to add structured information.

Getting an Account

To get an account in this wiki, please send email to Yolanda Gil with subject like "REQUEST FOR ORGANIC DATA SCIENCE ACCOUNT."

Adding New Text to Existing Pages

This wiki allows basic editing by adding regular wiki text and content. When editing, and before adding any text, click on the "Save Page" button at the bottom. After that select a category. Then you can either: 1) add structured properties by clicking on the "Add" button, or 2) add text and figures as in any other wiki by clicking on the "Edit" button at the top right. To format text and figures, see the Quick Guide to Using a Wiki, or the detailed User's Guide.

Specifying Mathematical Formulas

It is possible to specify mathematical formulas within the text of any page. See this page for more information.

Adding comments

You can add comments to text by having a column every time you want to indent. Choose a unique color from this palette and use it in your comments.

This user makes a comment in red -- User1
This user responds to the comment in green -- User2

Adding and Editing Pages

Creating a new Page

Just go to http://www.organicdatascience.org/index.php/New_Page

[Replace "New Page" above to the name that you want for the page]

Then, either select a category for this page:

Category.png

or, just click on the "Create" link to create a page without any category

Create.png

Deleting a Page

Go to http://www.organicdatascience.org/index.php/Name_of_Page

[Replace "Name of Page" above to the name of the page to delete]

Then click on the "Delete" link, and delete the page.

Delete.png
Delete2.png

Renaming a Page

Go to http://www.organicdatascience.org/index.php/Name_of_Page

[Replace "Name of Page" above to the name of the page to rename]

Then click on the "Move" link, and set the new name

Rename.png
Rename2.png

Adding Structured Data

All pages in this wiki (except the Main Page) have a "Structured Data" Section.

StructuredData2.png

Asserting Property Values

A user can click on the "Add" button to add a Property and Value pair. Matching properties in the wiki are suggested to the user as he types. In case the user decides to write his own property, this property is then automatically added to the wiki.

StructuredData.png

Deleting Property Values

Click on the [x] link next to the Property Value pair that you want to delete.

Setting Property Type

The type of a property is guessed by the value that the user puts in while asserting a property value. In case, the user wants to set the property type himself, he can go to the property page ( http://www.organicdatascience.org/index.php/Property:Name_of_Property ) and edit the wiki text to change the type.

For example, if one goes to Property:Resolution, he sees the following.

PropertyType1.png

On Editing the wiki text

PropertyType2.png

Directly creating a new property

Create a new page for the property by navigating to http://www.organicdatascience.org/index.php/Property:Name_of_New_Property

Deleting a property

Navigate to the property page ( http://www.organicdatascience.org/index.php/Property:Name_of_Property ), and Delete it. (Refer to Deleting a page above on how)

Note: Deleting the property page will not automatically delete assertions of that property in other pages. That will have to be done manually.

Renaming a property

Navigate to the property page ( http://www.organicdatascience.org/index.php/Property:Name_of_Property ), and Move it. (Refer to Renaming a page above on how)

Note: Renaming the property page will not automatically rename assertions of that property in other pages. That will have to be done manually.


Categories

Task Category

A Task category page allows the user to describe a Task and specify its subtasks and answers.

Task.png

Answer Category

An answer category page allows the user to describe an Answer

Answer.png

Person Category

A Person category page is associated with a Wiki User ID by the "Has User ID" property. Add this in the Structured Data section.

Person1.png

Once, this is done then the Person Category page will have the following UI to show the user's contributions to the wiki:

Person2.png

Workflow Category

This category page allows a user to import a Workflow Description as stored in OPMW. Example URL: http://www.opmw.org/export/page/resource/WorkflowTemplate/AQUAFLOW_NTM

Workflow.png

After importing:

Workflow2.png


ExecutedWorkflow Category

This category page allows a user to import an Executed Workflow's provenance as stored in OPMW. Example URL: http://www.opmw.org/export/page/resource/WorkflowExecutionAccount/ACCOUNT1383027155436

ExWorkflow.png

After importing:

ExWorkflow2.png

Data

We provide two different ways to describe data: user-provided data and user-described data.

Here is an example describing data from the LTER server:

  • Pointer to the LTER server [1]

To create a data page, just type the name you want to give that page into the "Search" window on the top right of the wiki. It will say: "Create the page <your page name> on this wiki", click on the name and it will create the page. Then click on "save the page" at the bottom. When it goes to the new page, choose a category, either UserProvidedData or UserDescribedData". Then follow the instructions on the respective sections below.

UserProvidedData Category

This category gives the user a UI to upload data to the wiki and then add Structured Data assertions about it.

Click on "Provide Data Name", and enter the data name.

UPD1.png

Once the Data is entered, you will see the following:

UPD2.png

Click on the name of the Data file to upload/view the file. (Note: The [x] link can be clicked to delete this data name.)

UPD3.png
UPD4.png

In addition, Data Columns can be described as shown below

UserDescribedData Category

This category allows the user to describe data present somewhere on the internet.

Click on "Add Link to Data", and enter a link to the data.

UDD1.png

Once the link is entered, you will see the following:

UDD2.png

Click on the link to view data. (Note: The [x] link can be clicked to delete this data link)


In addition, Data Columns can be described as shown below.

Describing Data Columns

Data columns can be described for both UserProvidedData and UserDescribedData.

DataColumns2.png

A Data column can be added by clicking on the "Add Data Column" and entering the name of the Data type. Matching Datatypes in the wiki are suggested to the user as he types. In case the user decides to write his own Datatype, this page is then automatically added to the wiki with Category DataType.

DataColumns1.png

Credits for Users

At the bottom of each page (except the main page), credits are shown to show which users have edited that page.

Credits.png

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.

 AuthorSoftware licenseLanguage
Delft3dDeltares systems
GLM SoftwareCasper Boon
Louise Bruce
Matt Hipsey
C
IPH-ECODavid da Motta Marques
PIHM SoftwareGopal Bhatt
Lorne Leonard
Xuan Yu
Chris Duffy
Mukesh Kumar
GPL v2C
C++


 ExpertiseAffiliation
Chris DuffyHydrologyPennsylvania State University
Craig SnortheimHydrodynamic modeling
David da Motta MarquesHydrology
Hydrodynamic modeling
Universidade Federal do Rio Grande do Sul
Jordan ReadHydrodynamic modeling
Physical limnology
Center for Integrated Data Analytics
U.S. Geological Survey
Matt HipseyEcosystem modeling
Hydrodynamic modeling
University of Western Australia
Michael PaceUniversity of Virginia
Patricia SorannoLandscape limnologyMichigan State University
Paul HansonCarbon cyclingCenter For Limnology
University of Wisconsin - Madison
Steve JepsenUniversity of California Merced
Tom HarmonUniversity of California Merced
Xuan YuPennsylvania State University
Yolanda GilAI planning and collaborative problem solving
Workflows
Semantic Web
Semantic wikis
Social computing
Information Sciences Institute
University of Southern California

Accessing Structured Content Externally

The structured content in this semantic wiki is represented with the W3C RDF semantic representation standard. This allows others to access and import the content of this wiki into their applications. There is extensive documentation about this API here.