Biomarkers for the EDRN Knowledge Environment
This product, eke.biomarker, provides display and RDF ingest of the biomarkers being studied by the Early Detection Research Network (EDRN). Biomarkers are chemical indicators for disease, and in the case of EDRN, the disease being pursued is cancer. This package lets a researcher browse, search for, and discover interesting biomarkers, determine how research progress is being made, find out statistical values of the biomarkers, and so forth. These features are integral to the EDRN Knowledge Environment (EKE). EDRN uses the EKE to make it easy to discover, share, search for, and retrieve all of EDRN’s collective knowledge, including cancers and other diseases, protocols, specimens, participants, staff, and — as in the case of this product — biomarkers.
Although intended for the EDRN public portal, it can be installed in any Plone compatible site.
Use Buildout with the plone.recipe.zope2instance recipe.
Add eke.biomarker to the list of eggs to install, e.g.:
[buildout] ... eggs = ... eke.biomarker
Re-run buildout, e.g. with:
You can skip the ZCML slug if you are going to explicitly include the package from another package’s configure.zcml file.
What follows is a history of changes from release to release. Where issue IDs are listed below, you can find out more about them by visiting the issue tracker at https://oodt.jpl.nasa.gov/jira/browse/CA.
1.1.26 — Graphs are not funny
CA-1536: Graphs appear funny on biomarker page
CA-1572: biomarker ingest need to capture cancerdataexpo external resources as ast instead of json
1.1.25 — Follow the protocols!
CA-1552: 200 character truncation of protocols causes ingest issue
1.1.24 — Fast ingestion aids digestion
CA-1434: Id searching makes biomarker ingest take too long
1.1.23 — You’re So Vain
Add a “piUIDs” field to Biomarker objects and set it on ingest so that vanity pages can quickly find Biomarkers studied by a PI.
1.1.22 — Some Day We’ll Get This Right
CA-1454: Biomarker ingest should use the organs specified in the RDF to associate a biomarker with a collaborative group, not the security access group
1.1.21 — By Any Other Name
CA-1348: Summary source URLs should be marked as required
CA-1388: Pull external resource links from CancerDataExpo
CA-1440: Biomarker ingest should accept “GI and Other Associated” as well as “G.I. and Other Associated”
1.1.20 — Protection
CA-1349: Summary ingest should be robust in the face of failures
1.1.19 — Visuals
CA-1338: Fix tests for eke.biomarker
1.1.18 — Biomuta
Added External Resources through simply linking with HgncName. This is a temporary hack, will add knowledge objects for each external resource.
Added Biomuta tab to a Biomarker’s elemental page and also removed biomuta link from “basic” tab. Biomuta tab was not added to Panel since Biomuta entries reference single biomarker entities. Biomuta stats are added as an attribute of a Biomarker since they are characteristics associated directly with the biomarker. CA-1321.
1.1.17 — Bug Fixes
1.1.15 — I Had Some Chicken; Pass Me the FLOSS
First official release as free/libre/open source software.
1.1.14 — Download URL
This release specifies a full path to the download URL for this package. This is necessary since JPL now blocks directory listings of our distribution server, and previously Python would use the directory listing to find the matching file by version to download.
1.1.13 — Certified HGNNNNNNNC!
CA-1235 - Make biomarkers link ID end with HGNC name
CA-1238 - Add free text search to Biomarkers
CA-1247 - Link back to BioMuta from EDRN Portal’s biomarkers
CA-1264 - Add Clinical Certification flags
1.1.12 — Let’s Not Talk
CA-1229 - Discussion re-enabled after upgrade
1.1.11 — Bio-TASTIC!
Adds the PIs-by-Biomarkers report plus a menu of (future) reports
CA-1206 - “No resources” appears on a biomarker–body-system when there are no publications, not if there are no resources
CA-1205 - Sort resources alphabetically on elemental- and panel-based biomarkers
CA-1156 - Show more attributes for biomarkers that are “mostly public”
CA-1163 - Make RDF ingest defensive against bad protocols from BMDB
CA-1182 - Recognize “Private” QA State of Biomarker
CA-1184 - Biomarker “report” by Organ
CA-1189 - Enable left+right portlets on /biomarkers
Drops the obsolete “Review Listing” type
1.1.10 — More Upgrades
Compatibility with Plone 4.3.
1.1.9 — Get Him to the Greek
CA-1100 Show “N/A” for Prevalence, NPV and PPV
1.1.8 — Lies, Damn Lies, and Statistics
Made compatible with Plone 4.2.4.
CA-1083 - eke.biomarker RDF ingest should treat predicate “hasBiomarkerStudyDatas” as a resource-pointing predicate
CA-1090 - For biomarkers, show a “-” or “N/A” or SOMETHING for prevalence, NPV, and PPV if they’re zero or not given.
1.1.7 — Upgrades
Made compatible with Plone 4.1.5.
CA-1010 - Show blank if values are 0 or 0.0
1.1.6 — Test Support
This release includes:
Depending on just Plone the framework instead of Plone the application.
1.1.4 — Resiliency: the bread and butter of PvP
This release makes functional tests more resilient.
1.1.3 — Let’s Collaborate!
This release includes:
A plone.app.testing layer.
Support for edrnsite.collaborations
Re-attaches biomarkers that indicate their collaborative group back to the “Collaborative Group” (from edrnsite.collaborations) objects to which they “belong”.
1.1.2 — Upgrade Cleanup
This release updates the GenericSetup profile to 4, provides upgrade steps to that profile, and makes the testing and development harness depend on “trunk” level of other eggs instead of on released versions of those eggs.
1.1.1 — Unique IDs
This release replaces the unique ID generation method for “Study Statistics” objects from the “generateUniqueId” method (acquired from who knows where (possibly CacheFu?)) to UUIDs, the generation of which is part of the standard library.
1.1.0 — Plone 4
This release of eke.biomarker makes it compatible with Plone 4.
1.0.2 — A Mixed Bag
The following issues were addressed in this release:
CA-620 - Locks appear on biomarkers listed under a protocol incorrectly (test exposure)
CA-698 - “Structural” objects appear in searches
1.0.1 — Sweeping Views
This release adds a number of improvements to the biomarker views to reflect requests made by NCI that more specific details be captured in each annotated biomarker.
This release addresses the following issues:
CA-674 - Add PerformanceComment to the biomarker organ tab
CA-675 - Portal: Change name of sensitivity/specificity and add specific assay type attribute
CA-676 - Portal: Add decision rule attribute to biomarker-organ-study information
1.0.0 — Prime Time
This release addresses a number of issues that make this component (and some of its selected counterparts) “prime time” for the operational NCI portal.
This release addresses the following issues:
CA-528 Automatic periodic ingest of RDF
You can find the issue tracker at https://oodt.jpl.nasa.gov/jira/browse/CA
0.0.6 — Open Door Policy
For this release, we’re exposing more information about biomarkers. Instead of making unapproved biomarkers private and requiring a log in to view them, you can now view basic information about them. Full details require a login. For more information, see https://oodt.jpl.nasa.gov/jira/browse/CA-650.
0.0.5 — Eleventh Hour
This release includes some look-and-feel changes, specifically to support https://oodt.jpl.nasa.gov/jira/browse/CA-600.
0.0.4 — Padlocked!
This release addresses the following issue:
https://oodt.jpl.nasa.gov/jira/browse/CA-551 - Add lock icon to biomarkers and science data that are “secure” to protocol pages
0.0.3 — The unnamed release
http://oodt.jpl.nasa.gov/jira/browse/CA-511 - Need to index alternative biomarker names
0.0.2 — Various “CYA” Fixes
http://oodt.jpl.nasa.gov/jira/browse/CA-499 - Disclaimer needed on biomarker list.
http://oodt.jpl.nasa.gov/jira/browse/CA-500 - Show unpublished biomarkers in a biomarker folder.
http://oodt.jpl.nasa.gov/jira/browse/CA-510 - Lock box for science data and biomarkers should disappear if a user has access to the object
0.0.1 — Security Ingest
The sole issue addressed in this release is:
http://oodt.jpl.nasa.gov/jira/browse/CA-475 - “Public” should only see biomarkers and science data that have QAState=Accepted. Disregard Security flag.
0.0.0 — Unreleased
Initial release into beta.
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