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Biomarker Security

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Sean Kelly edited this page Nov 21, 2019 · 1 revision

Here's how objects from the Biomarker Database are either made visible or partially obscured in the EDRN Portal (specifically, the P5 version).

The Biomarker Database has a main MySQL table called biomarkers that includes a field called qaState which has the following values:

  • Accepted (25 biomarkers)
  • Curated (265 biomarkers)
  • Under Review (666 biomarkers)
  • (blank) (1 biomarker)

When creating an RDF export of the Biomarker Database's MySQL tables, we have two options:

  1. Make a "public" RDF export that contains every row (and all referenced tables) from biomarkers where the qaState is NOT "Under Review". This would be 291 biomarkers.
  2. Make an "all encompassing" RDF export that includes every row regardless of qaState. That's 957 biomarkers.

If anyone outside of EDRN asks for a listing of our biomarkers, we would give them #1 (Dan, take note). But for the P4 and P5 portals, we take approach #2, because the portal software will then add its own layer of security and visibility.

In both P4 and P5 portals, the mere existence of every biomarker is made evident on the "/biomarkers" URL, regardless of the qaState.

On the P4 portal (current operations, https://edrn.nci.nih.gov/biomarkers), if the qaState is "Accepted", then you can see every detail of the biomarker no matter what. Any other "qaState" (Curated, Under Review, or blank), gives you just the basics tab. Want to see beyond the basics? See below.

On the P5 portal (current development, https://edrn-new.jpl.nasa.gov/portal/biomarkers), the same applies, except that the biomarker-organ relationship also has a qaState. So here, even if the biomarker itself is "Accepted", if a certain biomarker-organ relationship is anything but "Accepted", then its details are hidden. Want to see more? See below.

Seeing more: here's where the "Set Security" feature of the Biomarker Database comes into play. On both P4 and P5, details of certain biomarkers are hidden if the qaState of the biomarker is not "Accepted" (and on P5, if the biomarker-organ relationship is not "Accepted" even if the biomarker itself is). But you can log into the portal and, if you happen to be a member of an anointed group, you can see those extra details.

The "Set Security" features anoints biomarkers with groups that are allowed to access those details. If biomarker XYZ1 has allowed access to group GRP3 using the Biomarker Database's "Set Security" feature, that gets reflected in the RDF report, and the portal then adjusts the security visibility for biomarker XYZ1 and its details. Then if user JOE who is a member of group GRP3 logs in, those details on XYZ1 will be visible.

For a biomarker in review or curated but not yet accepted, you'll want to use "Set Security" so that the people responsible for researching that biomarker can get to it on the portal. For a biomarker listed as "Accepted", don't worry about "Set Security" as it has no effect in the portal.

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