Updates to KF portal tutorials: screenshots and text

docs/Bioinformatics-Skills/Kids-First/Advanced-KF-Portal-Queries/KF_10_AndOr.md

@@ -6,17 +6,19 @@ title: Ands & Ors
 ANDs and ORs
 ===============================
 
-![Multiple Filters](../images-kf/KidsFirstPortal_20.png "Multiple Filters")
+![Multiple Filters](../images-kf/KidsFirstPortal_23.png "Multiple Filters")
 
-Note that all of your filters are automatically connected by "AND"s,
-but that might not always be what you want. If I wanted to see the
-participants that meet at least one of my filters, but not all of them,
-I can click on an "AND" and change it to "OR", which dramatically
-changes my results:
+All of your filters are automatically connected by "AND"s,
+but that might not always be what you want.
 
 ![AND Filters](../images-kf/KidsFirstPortal_21.png "AND Filters")
 
+If you wanted to view a list of participants that meet at least one, but not all of the filters,
+you can click on an "AND" and change it to an "OR", which dramatically
+changes the results of the search:
+
 ![OR Filters](../images-kf/KidsFirstPortal_22.png "OR Filters")
 
-Note that when you change one AND/OR selection, it changes *all* of the
-AND/OR boxes in that query line.
+!!! Note
+    When you change one AND/OR selection, it changes *all* of the
+    AND/OR boxes in that query line.

docs/Bioinformatics-Skills/Kids-First/Advanced-KF-Portal-Queries/KF_11_JointQuery.md

@@ -45,13 +45,13 @@ chose, you should now have two queries that are identical:
 
 In query 2, edit the "Age at Diagnosis" to be 15-20 years of age.
 
-By clicking on each query, you should see that the title for the Cohort
-Results and the plots change to match the query you have highlighted (in green):
+By clicking on each query, you should see that the title for the cohort
+results ("Query #") and the plots change to match the query you have highlighted (in green):
 
-Results for **query 1 ONLY**:
+- Results for **1st query ONLY**:
 ![Query 1](../images-kf/KidsFirstPortal_29.png "Query 1")
 
-Results for **query 2 ONLY**:
+- Results for **2nd query ONLY**:
 ![Query 1](../images-kf/KidsFirstPortal_30.png "Query 1")
 
 ### Step 3: Combine the Queries
@@ -65,7 +65,7 @@ then click the "or" above the left side of the queries:
 
 ### Step 4: View Combined Query
 
-We now have a new `Query #3` that includes individuals from
+We now have a new "Query #3" that includes individuals from
 either of our two original queries:
 
 ![Combined Queries](../images-kf/KidsFirstPortal_33.png "Combined Queries")

docs/Bioinformatics-Skills/Kids-First/Advanced-KF-Portal-Queries/KF_12_CheckingQueries.md

@@ -10,26 +10,32 @@ Note that our query has an unexpected result:
 
 ![Query 3](../images-kf/KidsFirstPortal_32.png "Query 3")
 
-We had 222 participants in query one, and 124 participants in query two,
-but only 345 in our combined query. One of the participants must be in
-both queries!
+We had 435 participants in the 1st query, and 280 participants in the 2nd query. This adds up to a total of 715 participants. However, we only see
+701 in our combined query. This discrepancy suggests that the remaining 14 participants must satisfy
+both queries and are therefore excluded from the combined query due to the "OR" filter.
 
-To see which participant it is, edit query 3 to be an "AND"
+To see which participants occur in both the queries, edit the 3rd query to be an "AND"
 statement:
 
-![Query 3 'AND](../images-kf/KidsFirstPortal_35.png "Query 3 'AND'")
+![Query 3 AND](../images-kf/KidsFirstPortal_35.png "Query 3 'AND'")
 
-To learn more about this participant, let's look at a more detailed
+To learn more about these participants, let's look at a more detailed
 view of their public metadata by clicking on the "Table View" link:
 
 ![Change to Table View](../images-kf/KidsFirstPortal_34.png "Change to Table View")
 
-In this new view, we can see that there is a "+4" icon in
-her "Age at Diagnoses"
+In this new view, we can see the individual participant information, which shows multiple files for some participants. Click the first Participant ID to explore:
 
 ![Table View](../images-kf/KidsFirstPortal_37.png "Table View")
 
-Clicking on the "+4" icon in her "Age at
-Diagnoses", we see that she was diagnosed multiple times:
+Clicking on a Participant ID takes you to a summary page that lists all the associated
+clinical and biospecimens data for that Participant. Click on the "Clinical" tab.
 
-![Multiple Diagnoses](../images-kf/KidsFirstPortal_36.png "Multiple Diagnoses")
+![Clinical Tab](../images-kf/KidsFirstPortal_36.png "Clinical Tab")
+
+We can see that multiple biospecimens were collected over time from this participant
+explaining their occurrence in both the queries.
+
+![Multiple Biospecimens Collections](../images-kf/KidsFirstPortal_38.png "Multiple Biospecimens Collections")
+
+Now that we've learned how to create data subsets on the portal, in the next sections, we'll show you how to work with Kids First data in Cavatica.

docs/Bioinformatics-Skills/Kids-First/Advanced-KF-Portal-Queries/KF_9_AdvancedQuery.md

@@ -12,12 +12,10 @@ understanding of the basic interface.
 
 === "Exercise"
 
-    If you haven't already, remove your current query. Using the **Quick
-    Filters** and/or plots build a query to only include data from the
-    Pediatric Brain Tumor Atlas, and non-Hispanic or Latino patients who are
-    between 0 and 5 years old
+    Build a query to only include data from non-Hispanic or Latino patients from the Pediatric Brain Tumor Atlas: CBTTC study
+    who were between 0 and 5 years old when they were diagnosed.
 
 
 === "Answer"
 
-    [![](../images-kf/KidsFirstPortal_20.png)](../images-kf/KidsFirstPortal_20.png "Multiple Filters")
+    [![](../images-kf/KidsFirstPortal_20.png)](../images-kf/KidsFirstPortal_23.png "Multiple Filters")

docs/Bioinformatics-Skills/Kids-First/Exploring-Data-in-the-KF-Portal/KF_5_Explore.md

@@ -13,11 +13,11 @@ What data is here?
 ------------------
 
 The data at the Kids First DRC is from children with childhood cancer
-and structural birth defects or their family members. As of early 2020,
+and structural birth defects or their family members. As of the end of 2020,
 the Kids First DRC maintains Whole Genome Sequences (WGS) and/or RNAseq
-data for over 12,000 individuals. However, Kids First doesn't only host
-data about DNA and RNA. Using the portal you can access a wide range of
-data types including Histology Images, Pathology Reports, Radiology
+data for over 13,000 individuals. However, data available on the Kids First Portal
+is not restricted to information about DNA and RNA. Using the portal you can access a
+wide range of data types including Histology Images, Pathology Reports, Radiology
 Images, Radiology Reports, Operation Reports, Annotated Somatic
 Mutations, Gene Fusions, Gene Expression, Somatic Copy Number
 Variations, and Isoform Expression.
@@ -28,7 +28,7 @@ If you aren't still logged in to the Kids First Portal, navigate to
 <https://portal.kidsfirstdrc.org/> and use the credentials you set up
 previously in this lesson to log in.
 
- When you first log in, you will see
+When you first log in, you will see
 this screen:
 
 ![Kids First Dashboard](../images-kf/KidsFirstPortal_11.png "Kids First Dashboard")
@@ -49,8 +49,13 @@ Exploring the Data
 
 It is important to get a sense of what data exists before we start
 filtering down and designing an experiment. This page gives us a set of
-six interactive plots that display the overall data. You can impose
+seven interactive plots that display the overall data. You can impose
 filters on the data in two different ways:
 
 -   By using the filter buttons
 -   By clicking a graph component of any plot
+
+!!! Note
+
+    Application of the filters via the graph of any plot allows for choice of one value. If you'd like to select values spanning multiple bars in a plot,
+    use the filter buttons at the top of the page.

docs/Bioinformatics-Skills/Kids-First/Exploring-Data-in-the-KF-Portal/KF_6_Filtering.md

@@ -12,7 +12,7 @@ To use the filter buttons, click on one, choose from the options in that button,
 
 === "Exercise"
 
-    Use the "Clinical" button to filter the data to include only samples where the patient was between 0 and 5 years old when they were diagnosed.
+    Use the "Clinical" button to filter the data to include only samples where the participants were between 0 and 5 years old when they were diagnosed.
 
 === "Answer"
 

docs/Bioinformatics-Skills/Kids-First/Exploring-Data-in-the-KF-Portal/KF_7_Plots.md

@@ -33,7 +33,7 @@ selection in a plot, that filter is added to your query box above.
 !!! Exercise
 
     Click a bar in the "Studies" plot to include only samples
-    from the Kids First Neuroblastoma data set.
+    from the Pediatric Brain Tumor Atlas: CBTTC data set.
 
 
 If you applied this filter successfully, you should see something like
@@ -44,5 +44,5 @@ the following:
 
 !!! Note
 
-    We ran this query in early 2020. If you are doing this tutorial later,
+    We ran this query at the end of 2020. If you are doing this tutorial later,
     you may see more participants.

docs/Bioinformatics-Skills/Kids-First/Portal-Setup-And-Permissions/KF_2_The_Setup.md

@@ -11,8 +11,8 @@ Why so much setup?
 ------------------
 
 There are many rules and regulations about who can
-use human derived medical data, and for what purposes. Even
-"open" human data has controls and simply indicates that that there are fewer barriers to seeing it. Data curators like
+use human-derived medical data, and for what purposes. Even
+"open" human data has controls and simply indicates that there are fewer barriers to seeing it. Data curators like
 the Kids First DRC are obligated to enforce access controls and data use
 rules to the best of their ability, and that requires end users like us
 to have accounts that are tied to verified identities (e.g. ORCID or Google, eRA Commons).

docs/Bioinformatics-Skills/Kids-First/Portal-Setup-And-Permissions/KF_3_KF_Registration.md

@@ -3,7 +3,7 @@
 ### Step 1: Go to the portal website
 
 First, we'll set up our accounts at the Kids First DRC Portal by going
-to this link:
+to the portal link:
 
 [https://portal.kidsfirstdrc.org/](https://portal.kidsfirstdrc.org/)
 
@@ -33,7 +33,7 @@ Select the platform you wish to use for your sign up.
 
 #### Connect with Google or Facebook
 
-If you decide to link KF to your Google or Facebook account, click on the corresponding icon. A pop-up window will appear and you will be asked to provide your user information and password. Enter the information and click "Next". If log in is successful, the pop-up window will disappear and you will be routed back to the KF portal dashboard.
+The preferred method is to login with a Google account. Click the corresponding icon to link KF to either your Google or Facebook account. A pop-up window will appear and you will be asked to provide your user information and password. Enter the information and click "Next". You'll then be asked to enter basic user information and accept the Terms and Conditions for using data on the portal. If log in is successful, the pop-up window will disappear and you will be routed back to the KF portal dashboard.
 
 #### Connect your ORCID
 

docs/Bioinformatics-Skills/Kids-First/index.md

@@ -6,10 +6,10 @@ title: KF Portal Overview
 **Kids First (KF) Lessons**
 
 The [NIH Common Fund-supported Gabriella Miller Kids First Data Resource
-Center](https://kidsfirstdrc.org/) enables researchers, clinicians, and
+Center](https://kidsfirstdrc.org/) (KFDRC) enables researchers, clinicians, and
 patients to work together to accelerate research and promote new
 discoveries for children affected with cancer and structural birth
-defects. Data from over 11,000 samples, including DNA and RNA, is
+defects. Data from over 16,000 individuals, including DNA and RNA sequence data, is
 available to empower your research today. Data collected from more than
 30,000 samples are expected to be available in the next few years.