Biomarkers for the EDRN Knowledge Environment
Project description
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.
This software is developed by the EDRN Informatics Center at JPL, operated by the California Institute of Technology, for NCI.
Installation
Use Buildout with the plone.recipe.zope2instance recipe.
Add eke.biomarker to the list of eggs to install, e.g.:
[buildout] ... eggs = ... eke.biomarkerTell the plone.recipe.zope2instance recipe to install a ZCML slug:
[instance] recipe = plone.recipe.zope2instance ... zcml = eke.biomarkerRe-run buildout, e.g. with:
% ./bin/buildout
You can skip the ZCML slug if you are going to explicitly include the package from another package’s configure.zcml file.
Changelog
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.
1.1.13 — 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.
Uses z3c.autoinclude.
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.
1.1.5 — Dataset Linkages
This release includes:
CA-784: Add ability to associate eCAS datasets with Biomarker records in the BMDB
(No issue ID): Dataset links should go directly into eCAS
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.
Copyright
Copyright 2009-2010 by the California Institute of Technology. ALL RIGHTS RESERVED.
The Software is owned by Caltech/JPL and is protected by United States copyright laws and applicable international treaties and/or conventions. The United States Government may have prior rights to use some or all of the Software as determined under applicable contracts and license agreements with Caltech/JPL.
This software was developed at the Jet Propulsion Laboratory, an operating division of the California Institute of Technology and is not available for use by any person, organization, or other entity without prior, specific written permission.
