Guide to Browsing PxKB v1.5
Starting Out - Explore
To give you a quick way into the content of PxKB v1.5, we have provided several options
in the explore aera on the left hand side of the page.
Searching by Keyword will match your query against any of the terms for any of the Concepts known to PxKB,
and show you a table of results.
Searching by Type will give you a table of Concepts that are all of the Type that you selected from the
drop down list. There are more types in PxKB v1.5 than in this list, we have selected the key ones to reduce complexity.
This makes it easy to see, for example which types of Disorder that are known to PxKB v1.5
Searching by Relation will give you a table of Triples from PxKB that involve that relation. This is useful for example if you want to see
a table that shows Genes and encoded Proteins, by simply selecting the 'encodes' property.
The fourth and final option is a selection of four Starter Maps that illustrate key points about the peroxisome. Selecting one of these
options will take you to a Linked Data page.
Results: Layout
Different types of searches produce results pages that have slightly different layouts. Overall, the 'look and feel' should be the same, although these views are still quite experimental and may be updated from time to time to make them more intuitive and interactive. The figure below shows how to interpret the results of a keyword search, and where you can go from there.
The results of a Keyword Search and its key components
Results: Legend
You will see the following icons in your Results and subsequent Browsing.
Concepts
- This icon represents a Concept, e.g. "peroxisome", or a link to more Concepts.
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Types
- This icon represents a Type, e.g. "Organelle". Every Concept is assigned at least one Type in PxKB v1.5.
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Maps
- This icon represents a Concept Map, or a clickable link to a list of Concept Maps. Every Concept is in at least one Map.
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Triples
- This icon represents a clickable link to a table of Triples, where each of these is two concepts related by a relationship.
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Curation Status of Maps
- Not all of the maps have curation information - therefore they may not be accurate. In lists of maps, we have implemented these two icons to represent the curation status. You can also check whether there is an "isCuratedBy" link on a Maps Linked Data page. In future we will indicate triples that are sourced from uncurated maps.
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Image
- This icon will take you to an image of the resource that it is near.
Linked Data Pages
As you are browsing PxKB v1.5, if you at any time click on a link in the results pages, rather than an icon, you will be taken to a Linked Data page,
which you will recongnize from its green background. We realize that these pages can be a bit confusing, so we have installed buttons that will take you back to our own Web pages of results to continue browsing.
In the near future we hope to replace these pages with more user-friendly profiles of the data at a URI.
A Linked Data page and its key components
PxKB v1.5 is a web application that is designed to be an intermediate demonstrator for the BioExpert framework, as well as being an information source about the peroxisome.
Part of the mandate of the BioExpert Framework is to provide its content as 'Linked Data', as part of an overall aim of providing true Semantic Web based knowledge bases. In a nutshell,
in Linked Data, elements of the data have identifiers (URIs) structured as what you will recognize as an HTTP URL. For example, the concept 'peroxisome' in PxKB v1.5 has the identifier http://www.peroxisomekb.nl/v1.5/pxv/pxConcept000717
Importantly, whilst visiting this data in your Web browser, you get redirected to an HTML representation of the data that PxKB v1.5 has about 'peroxisome'. This functionality is currently provided by the Pubby application which is designed to do just that.
