Dataset Tutorial - Revision history

Khider: Update information with new ontology

2017-05-03T22:32:12Z

Update information with new ontology

Khider: Update quickstart guide

2017-05-03T22:04:44Z

Update quickstart guide

Khider: change versioning scheme from LiPD to LinkedEarth

2017-04-17T02:39:05Z

change versioning scheme from LiPD to LinkedEarth

Khider: /* Annotating a LiPD file */ fix link

2017-04-17T02:38:24Z

‎Annotating a LiPD file: fix link

Khider: /* LiPD and LinkedEarth */ Fix links and add ontology vs LiPD

2016-09-06T21:37:27Z

‎LiPD and LinkedEarth: Fix links and add ontology vs LiPD

Khider: Move the wiki functionalities to its own guide

2016-08-08T19:23:18Z

Move the wiki functionalities to its own guide

Khider: Move the creating a personal page to the getting started guide

2016-08-08T19:13:45Z

Move the creating a personal page to the getting started guide

Khider: Renumber figures appropriately and link to wikitext tutorial

2016-08-08T19:04:23Z

Renumber figures appropriately and link to wikitext tutorial

Khider: Remove account information (moved to the startup guide)

2016-08-08T18:50:57Z

Remove account information (moved to the startup guide)

Khider: Khider moved page Main Page/Tutorial to Dataset Tutorial: Move it out of the main page

2016-08-08T18:26:20Z

Khider moved page Main Page/Tutorial to Dataset Tutorial: Move it out of the main page

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-This tutorial is meant to get you started with uploading and editing a dataset onto the LinkedEarth platform. The LinkedEarth Wiki is based upon semantic [https://www.mediawiki.org/wiki/MediaWik iMediaWiki] and therefore uses the MediaWiki language. If you are new to Wiki formatting, take a few minutes to learn how to edit pages, create new pages, use links on the [https://www.mediawiki.org/wiki/Help:Formatting Help Page].
+This tutorial is meant to get you started with uploading and editing a dataset onto the LinkedEarth platform.
 After completing this tutorial, you will be able to:
-*LiPD and LinkedEarth: Upload LiPD datasets and enter basic metadata for the record.
+* Upload LiPD datasets and enter basic metadata for the record.
 *Annotate a dataset: Create and reuse properties for annotation.
-'''Nomenclature''': See [[Best Practices | this page]].
+When annotating a dataset, the LinkedEarth wiki follows some '''nomenclature rules''' that you can find on [[Best Practices | this page]].
 = LiPD and LinkedEarth =
-The [http://linked.earth/projects/ontology/ LinkedEarth Ontology] represents the backbone of the wiki. The ontology allows us to not only define terms commonly used to describe a paleoclimate dataset (e.g., variable, uncertainty, calibration) but also specify the relationship among these terms (e.g., a variable has uncertainty). As such, it allows us to make inferences, support complex queries, as well as perform quality control on the data. '''Remember that no formal knowledge about ontologies is required to use and contribute to the wiki!'''
+The [[LinkedEarth Ontology]] represents the backbone of the wiki. The ontology allows us to not only define terms commonly used to describe a paleoclimate dataset (e.g., variable, uncertainty, calibration) but also specify the relationship among these terms (e.g., a variable has uncertainty). As such, it allows us to make inferences, support complex queries, as well as perform quality control on the data. '''Remember that no formal knowledge about ontologies is required to use and contribute to the wiki!'''
-The LinkedEarth ontology was developed from the [http://linked.earth/projects/lipd/ LiPD]  format championed by Nick McKay and Julien Emile-Geay. Therefore, the wiki platform is currently optimized to accept data already in the LiPD format. To convert you dataset into a LiPD file, follow [[Creating a LiPD file | this guide]].
+The LinkedEarth ontology was developed from the [[Linked Paleo Data]] (LiPD) format championed by Nick McKay and Julien Emile-Geay. Therefore, the wiki platform is currently optimized to accept data already in this format. To convert you dataset into a LiPD file, follow [[Creating a LiPD file | this guide]].
 == Uploading a LiPD file ==
-You need to be logged in to upload a LiPD file, using a [[Special:WTLiPD | special page]] dedicated to the management of datasets already in the LiPD format.
+You need to be '''logged in''' to upload a LiPD file, using this [[Special:WTLiPD | special page]] dedicated to the management of datasets already in the LiPD format. This page can be access directly from the left sidebar: [[Special:WTLiPD | Managing LiPD files]].
 Select the browse button and choose the .lpd file you want to upload as shown in Figure 1:
 [[File:TutorialFig2.png|thumb|none|1000px|Figure1: Manage LiPD Data page]]
-Dataset pages will be automatically created from the content of the LiPD file and your dataset will appear at the top of the "Current LiPD Dataset list" on the [[Main Page]]. By clicking on the dataset link, you will be able to see the automatically extracted data and metadata from the LiPD file, as shown in Figure 2. New "crowd" properties will be automatically created from the LiPD file if these properties are not in the current core ontology.
+Dataset pages will be automatically created from the content of the LiPD file and your dataset will appear at the top of the "Current LiPD Dataset list" on the [[Main Page]]. By clicking on the dataset link, you will be able to see the automatically extracted data and metadata from the LiPD file, as shown in Figure 2. New "crowd" properties will be automatically created from the LiPD file if these properties are not in the current ontology.
 [[File:TutorialFigure3.png|thumb|none|1000px|Figure2: Wiki page created automatically from the metadata of the LiPD dataset]]
 Congratulations! Your LiPD file has been successfully added to the Linked Earth wiki.
 == Annotating a LiPD file ==
-Once a LiPD file is uploaded, the metadata about that file is shown in a table with two columns. The column on the left of each table contains the properties describing the LiPD file, while the column on the right states the value associated with each property. Figure 3 shows an example, where the "archive type" of CAN9Neukom2014 is "Tree".
+Once a LiPD file is uploaded, the metadata about that file is shown in a table-like manner on the page with two columns. The column on the left of each table contains the properties describing the LiPD file, while the column on the right states the value associated with each property. Figure 3 shows an example, where the "archive type" of CAN9Neukom2014 is "Tree". You can also click on the property to access its definition in the [[LinkedEarth Ontology]]. Properties followed by (L) indicates that they are part of the [[Linked Paleo Data | LiPD architecture]] and, therefore, cannot be directly edited by basic editors of the LinkedEarth community.
 Please check that the metadata for your record is correct and edit it if appropriate. For instance, to add an investigator to the CAN9Neukom2014 dataset in Figure 2, click on its corresponding row as indicated in Figure 3. Then type the value of the property. In this example, we added "Daniel" as the investigator.
@@ Line 40: / Line 39: @@
 Each property/property value added to the page is tracked on the page history. The page history is accessible through the "View history" button at the top of any wiki page, allowing to monitor the edits done by other wiki users. Figure 5 illustrates the edits for the CAN9Neukom 2014 dataset: the latest change added a propertyValue adding "Daniel" as an investigator.
-LinkedEarth members who are at the dataset contributors level can only edit the properties associated with the dataset they contributed. Starting at the Basic Editor level, users can edit datasets contributed by other users. If you would like to become a basic editor, please [mailto:linkedearth@gmail.com email the Editorial Board].
+Anyone with basic editor privileges and logged into the wiki can edit property values. Don't worry, all changes are revertible and you will get an automatic email if anyone changes a page in your watchlist.
 [[File:TutorialFig6.png|thumb|none|800px|Figure 5: History of the edits done to the CAN9Neukon2014 dataset]]
-If there is a disagreement between two researchers, a discussion may be started on the "Discussion" page, as depicted on Figure 6. Contributors and Editors may edit any Discussion Pages on the wiki. To learn more about how to contribute and edit discussion pages, follow this [[Discussion Page Tutorial | tutorial]].
+If there is a disagreement between two researchers, a discussion may be started on the "Discussion" page, as depicted on Figure 6. To learn more about how to contribute and edit discussion pages, follow this [[Discussion Page Tutorial | tutorial]].
 [[File:TutorialFig7.png|thumb|none|600px|Figure 6: Creating a discussion page on CAN9Neukon2014 dataset]]
 Contributions is tracked automatically on the wiki and displayed in the "Credit" section, which can be found at the bottom of each wiki page.
 [[File:TutorialFig8.png|thumb|none|600px|Figure 7: credits of the CAN9Neukon2014 dataset]]
 == Concept annotation in a LiPD file ==
 As shown in Figures 3 and 4, some of the annotated values like "Tree" already have links to other pages.  These pages can be further populated and edited by domain experts. To do so click on the Edit tab at the top of the page as shown on Figure 8 for the "Tree" archive. The article was created as a stub, awaiting domain experts' contribution, further gathering field knowledge.
@@ Line 59: / Line 59: @@
 By linking to other existing pages we can connect different LiPD datasets (e.g., if two different datasets are of the same archive type, they will link to the same page) and support queries. For instance, one can look for all the datasets on the LinkedEarth wiki using "Tree" as archives.
-Red links means that the page does not yet exist. Editors and contributors can create the new page and edit its content. An example can be seen on Figure 9.
+Red links means that the page does not yet exist. Editors can create the new page and edit its content. An example can be seen on Figure 9.
 [[File:TutorialFig9.png|thumb|none|700px|Figure 8: Tree concept definition on the Linked Earth wiki]]
 [[File:TutorialFig10.png|thumb|none|700px|Figure 9: Creating a page for an unexisting concept (highlighted in red)]]
 =Annotate a dataset=
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 Before adding a new property name, it is important to note that a similar property may already exist in the ontology to describe the same metadata. '''The properties are case-sensitive.''' For instance, imagine that we want to add a "description" to the dataset. If we start typing the property, we see that it already exists, and we can select it for our purposes. Selecting existing properties is important, as it helps to structure and control the content uploaded to the wiki.
 == Adding location to a dataset ==
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 [[File:TutorialFig24.png|thumb|none|700px|Figure 11: Steps for adding location to your dataset.]]
 == See Also ==

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 *LiPD and LinkedEarth: Upload LiPD datasets and enter basic metadata for the record.
 *Annotate a dataset: Create and reuse properties for annotation.
 = LiPD and LinkedEarth =
@@ Line 9: / Line 11: @@
 The [http://linked.earth/projects/ontology/ LinkedEarth Ontology] represents the backbone of the wiki. The ontology allows us to not only define terms commonly used to describe a paleoclimate dataset (e.g., variable, uncertainty, calibration) but also specify the relationship among these terms (e.g., a variable has uncertainty). As such, it allows us to make inferences, support complex queries, as well as perform quality control on the data. '''Remember that no formal knowledge about ontologies is required to use and contribute to the wiki!'''
-The LinkedEarth ontology was developed from the [http://linked.earth/projects/lipd/ LiPD]  format championed by Nick McKay and Julien Emile-Geay. Therefore, the wiki platform is currently optimized to accept data already in the LiPD format. There are several ways to convert your dataset to LiPD. Go to the [http://lipd.net LiPD webpage] for more information.
+The LinkedEarth ontology was developed from the [http://linked.earth/projects/lipd/ LiPD]  format championed by Nick McKay and Julien Emile-Geay. Therefore, the wiki platform is currently optimized to accept data already in the LiPD format. To convert you dataset into a LiPD file, follow [[Creating a LiPD file | this guide]].
 == Uploading a LiPD file ==
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 [[File:TutorialFig8.png|thumb|none|600px|Figure 7: credits of the CAN9Neukon2014 dataset]]
 == Concept annotation in a LiPD file ==
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 '''Exercise: Use an instrument of your lab to describe a variable from a dataset. If the category of your instrument does not exist, create a new instrument category (e.g., stable isotope mass spectrometer). '''

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 ==Dataset versioning==
-In LiPD all the uploaded datasets should follow a x.y.z notation, where "x" refers to important changes in the dataset's metadata (e.g., the creation of a new age model using a different code), "y" refers to changes to the data following a publication (e.g., adding data further back in time without changing the model underlying the interpretation) and z refers to minor changes not associated with a publication (e.g., typos). For example, the first official release of a dataset would be 1.0.0. If I fix a small typo, I would create version 1.0.1.
+On the wiki, all the uploaded datasets should follow a x.y.z notation, where "x" refers to important changes in the dataset's metadata (e.g., the creation of a new age model using a different code), "y" refers to changes to the data following a publication (e.g., adding data further back in time without changing the model underlying the interpretation) and z refers to minor changes not associated with a publication (e.g., typos). For example, the first official release of a dataset would be 1.0.0. If I fix a small typo, I would create version 1.0.1.
 '''Exercise: Annotate the version of the dataset in the recently created page, following the x.y.z notation and using the property "datasetVersion".'''

@@ Line 42: / Line 42: @@
 [[File:TutorialFig6.png|thumb|none|800px|Figure 5: History of the edits done to the CAN9Neukon2014 dataset]]
-If there is a disagreement between two researchers, a discussion may be started on the "Discussion" page, as depicted on Figure 6. Contributors and Editors may edit any Discussion Pages on the wiki. To learn more about how to contribute and edit discussion pages, follow this [[Tutorial | Discussion Page Tutorial]].
+If there is a disagreement between two researchers, a discussion may be started on the "Discussion" page, as depicted on Figure 6. Contributors and Editors may edit any Discussion Pages on the wiki. To learn more about how to contribute and edit discussion pages, follow this [[Discussion Page Tutorial | tutorial]].
 [[File:TutorialFig7.png|thumb|none|600px|Figure 6: Creating a discussion page on CAN9Neukon2014 dataset]]

@@ Line 7: / Line 7: @@
 = LiPD and LinkedEarth =
-The [http://linked.earth/projects/ontology/ LinkedEarth Ontology] represents the backbone of the wiki. The ontology allows us to not only define terms commonly used to describe a paleoclimate dataset (e.g., variable, uncertainty, calibration) but also specify the relationship among these terms (e.g., a variable has uncertainty). As such, it allows us to make inferences, support complex queries, as well as perform quality control on the data.
+The [http://linked.earth/projects/ontology/ LinkedEarth Ontology] represents the backbone of the wiki. The ontology allows us to not only define terms commonly used to describe a paleoclimate dataset (e.g., variable, uncertainty, calibration) but also specify the relationship among these terms (e.g., a variable has uncertainty). As such, it allows us to make inferences, support complex queries, as well as perform quality control on the data. '''Remember that no formal knowledge about ontologies is required to use and contribute to the wiki!'''
 The LinkedEarth ontology was developed from the [http://linked.earth/projects/lipd/ LiPD]  format championed by Nick McKay and Julien Emile-Geay. Therefore, the wiki platform is currently optimized to accept data already in the LiPD format. There are several ways to convert your dataset to LiPD. Go to the [http://lipd.net LiPD webpage] for more information.
@@ Line 58: / Line 58: @@
 As shown in Figures 3 and 4, some of the annotated values like "Tree" already have links to other pages.  These pages can be further populated and edited by domain experts. To do so click on the Edit tab at the top of the page as shown on Figure 8 for the "Tree" archive. The article was created as a stub, awaiting domain experts' contribution, further gathering field knowledge.
-To learn more about Wiki editing, visit the [Quick Guide to Editing Wiki Pages].
+To learn more about Wiki editing, visit the [[Quick Guide to Editing Wiki Pages]].
 By linking to other existing pages we can connect different LiPD datasets (e.g., if two different datasets are of the same archive type, they will link to the same page) and support queries. For instance, one can look for all the datasets on the LinkedEarth wiki using "Tree" as archives.

← Older revision		Revision as of 19:13, 8 August 2016
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	=Advanced wiki functionality=		=Advanced wiki functionality=
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−	~~== Creating a personal page ==~~
−	The Linked Earth wiki allows to create different types of pages. Personal pages are a special type of wiki pages, and we will use them to illustrate how to create a new wiki page in general. After logging in on the wiki, click on your name. You can find it on the top of any wiki page, as shown in Figure 12:
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−	~~[[File:TutorialFig12.png\|thumb\|none\|400px\|Figure 12: location of the personal page for a user]]~~
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−	~~Clicking your name will take you to a new page, which you can complete with your personal information, by clicking on any of the "edit options" in the page, as depicted in Figure 13:~~
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−
−	~~[[File:TutoroialFig13.png\|thumb\|none\|600px\|Figure 13: editing personal information on your wiki page]]~~
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−	~~And adding your personal information on the form (Figure 14):~~
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−
−	~~[[File:TutorialFig14.png\|thumb\|none\|500px\|Figure 14: form to fill with the user information]]~~
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−	~~After you are done, just hit the "Update" button at the bottom of the page (Figure 15):~~
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−
−	~~[[File:TutorialFig15.png\|thumb\|none\|400px\|Figure 15: editing your personal page on the form.]]~~
−
−	~~'''Exercise: Create your personal page and add a personal website and an "about me" description.'''~~

← Older revision	Revision as of 18:26, 8 August 2016
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