data2semantics/hubble

Interface for CDS usecase

hubble's Issues

Make Video/Screencast

check the Measurements query

each patients should have measurements, but they don't appear on the UI

add label for Patient names in store

Annotation data problems

The SnippetLoader.java class (com.data2semantics.cds.ui.server.loaders) loads the annotations, and uses the values prefix, exact, postfix to create a snippet. The retrieval is currently inaccurate and plain wrong, because the annotations in the dataset consist of messy, wrong and duplicate entries. The queries in the SnippetLoader.java file are tweaked (in a bad way) for demo purposes, to retrieve multiple distinct snippets.

Solution:

• create proper annotations
• match them with a publication uri instead of a filename, so we need to have pdf files within our system, but we can refer to the publication
• fix the queries in the snippet loader

Drawing annotations onto text

Currently, the PdfAnnotator.java draw the annotations (residing in rdf) onto pdf.
This is done using bounding box coordinates, not using the actual prefix/postfix.

Todo:

• We probably shouldnt be drawing anything in pdf, but focus on how to tackle this problem providing we have the publication as text or xml
• Find a way to nicely draw annotations using prefix/postfix, instead of coordinates on a pdf page

Streamline the UI

• Cut away stuff that's not intuitive
• Add a banner + logo (?)
• Add more intuitive labels

the related literature query should be improved

for each term in patient details, find relevant annotations

(maybe group by pub URI)

Build annotations for new content

Adjust SPARQL queries on server-side

• Queries for finding "relevant" annotations
• Adaptations because of patient information

UI: mulitple buttons for the Patient Details

Drug - Chemical Structure, Related Adverse Events, Browse RDF
Diagnosis (Previous) - None, Related AE, Browse RDF
Measurement - None, Related AE, Browse RDF

Load data from Linked Life Data

The query in PatientLoader to retrieve info from linked life data does not work: the query is wrong, and will always retrieve empty results.

change LLD URIs to D2S

• UI: change query in order to retrieve LLD links

Poster

Rename "Indication" into "Diagnosis"

Rename "Indication" into "Diagnosis"

Fix patients

... obvious, isn't it.

Linking between BioPortal/AERS/Patients

Make sure there's links between Annotations, BioPortal, AERS and the patients

Replace link to PDF with link to (external) URL of annotated document

Retrieve treatment info from lld

In PatientLoader.java (com.data2semantics.cds.ui.server.loaders), the 'hadRecentTreatment' information is currently taken from the aers triple store. This information should reside in the linked life data triplestore, but isnt (due to a bug I presume).
Solution: Find a reliable source of information for treatments, or do it ourself (properly)

Upload new Annotations

upload new annotations and upload bioportal mapping

Highlight annotation text in external document

Add publication titles to PDF

• retrieve them from the annotations
• add them to the store
• display them on the UI

Implement loading behavior

The View.java file (com.data2semantics.cds.ui.client.view) contains onLoadingFinish() and onLoadingStart() methods, which are unimplemented. Having more data in the prototype, might increase loading times, making this issue more important.

Example of the loading panel for the old GWT layout: https://github.com/Data2Semantics/CDSInterface/blob/4119d2723f3893a0722f9b286b2442b632e7eeab/src/com/data2semantics/mockup/client/ui/LoadingPanel.java

Loading panel should not -block- the interface. You should still be able to click buttons