Package: eke.biomarker
This product,eke.biomarker, provides display andRDFingest 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 anyPlonecompatible site.This software is developed by theEDRN Informatics CenteratJPL,
operated by the California Institute of Technology, forNCI.InstallationUseBuildoutwith the plone.recipe.zope2instance recipe.Addeke.biomarkerto the list of eggs to install, e.g.:[buildout]
...
eggs =
    ...
    eke.biomarkerRe-run buildout, e.g. with:% ./bin/buildoutYou can skip the ZCML slug if you are going to explicitly include the package
from another package’s configure.zcml file.ChangelogWhat 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 athttps://oodt.jpl.nasa.gov/jira/browse/CA.1.1.26 — Graphs are not funnyCA-1536: Graphs appear funny on biomarker pageCA-1572: biomarker ingest need to capture cancerdataexpo external resources as ast instead of jsonCA-15921.1.25 — Follow the protocols!CA-1552: 200 character truncation of protocols causes ingest issue1.1.24 — Fast ingestion aids digestionCA-1434: Id searching makes biomarker ingest take too long1.1.23 — You’re So VainAdd 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 RightCA-1454: Biomarker ingest should use the organs specified in the RDF to
associate a biomarker with a collaborative group, not the security access
group1.1.21 — By Any Other NameCA-1348: Summary source URLs should be marked as requiredCA-1388: Pull external resource links from CancerDataExpoCA-1440: Biomarker ingest should accept “GI and Other Associated” as well as
“G.I. and Other Associated”1.1.20 — ProtectionCA-1349: Summary ingest should be robust in the face of failures1.1.19 — VisualsCA-1322CA-1338: Fix tests for eke.biomarker1.1.18 — BiomutaAdded 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 FixesCA-1300CA-13031.1.16 — Broken LinksThis release addresses an RDF ingest issue where a biomarker-bodysystem object
refers to a biomarker that doesn’t exist.1.1.15 — I Had Some Chicken; Pass Me the FLOSSFirst official release as free/libre/open source software.1.1.14 — Download URLThis 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 nameCA-1238 - Add free text search to BiomarkersCA-1247 - Link back to BioMuta from EDRN Portal’s biomarkersCA-1264 - Add Clinical Certification flags1.1.12 — Let’s Not TalkCA-1229 - Discussion re-enabled after upgrade1.1.11 — Bio-TASTIC!Adds the PIs-by-Biomarkers report plus a menu of (future) reportsCA-1206 - “No resources” appears on a biomarker–body-system when there are
no publications, not if there are no resourcesCA-1205 - Sort resources alphabetically on elemental- and panel-based
biomarkersCA-1156 - Show more attributes for biomarkers that are “mostly public”CA-1163 - Make RDF ingest defensive against bad protocols from BMDBCA-1182 - Recognize “Private” QA State of BiomarkerCA-1184 - Biomarker “report” by OrganCA-1189 - Enable left+right portlets on /biomarkersDrops the obsolete “Review Listing” type1.1.10 — More UpgradesCompatibility with Plone 4.3.Uses z3c.autoinclude.1.1.9 — Get Him to the GreekCA-1100 Show “N/A” for Prevalence, NPV and PPV1.1.8 — Lies, Damn Lies, and StatisticsMade compatible with Plone 4.2.4.CA-1083 - eke.biomarker RDF ingest should treat predicate
“hasBiomarkerStudyDatas” as a resource-pointing predicateCA-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 — UpgradesMade compatible with Plone 4.1.5.CA-1010 - Show blank if values are 0 or 0.01.1.6 — Test SupportThis release includes:Depending on just Plone the framework instead of Plone the application.1.1.5 — Dataset LinkagesThis 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 eCAS1.1.4 — Resiliency: the bread and butter of PvPThis release makes functional tests more resilient.1.1.3 — Let’s Collaborate!This release includes:A plone.app.testing layer.Support for edrnsite.collaborationsRe-attaches biomarkers that indicate their collaborative group back to the
“Collaborative Group” (from edrnsite.collaborations) objects to which they
“belong”.1.1.2 — Upgrade CleanupThis 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 IDsThis 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 4This release of eke.biomarker makes it compatible with Plone 4.1.0.2 — A Mixed BagThe 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 searches1.0.1 — Sweeping ViewsThis 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 tabCA-675 - Portal: Change name of sensitivity/specificity and add specific assay type attributeCA-676 - Portal: Add decision rule attribute to biomarker-organ-study information1.0.0 — Prime TimeThis 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 RDFYou can find the issue tracker athttps://oodt.jpl.nasa.gov/jira/browse/CA0.0.6 — Open Door PolicyFor 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, seehttps://oodt.jpl.nasa.gov/jira/browse/CA-650.0.0.5 — Eleventh HourThis release includes some look-and-feel changes, specifically to supporthttps://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 pages0.0.3 — The unnamed releasehttp://oodt.jpl.nasa.gov/jira/browse/CA-511- Need to index alternative
biomarker names0.0.2 — Various “CYA” Fixeshttp://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 object0.0.1 — Security IngestThe 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 — UnreleasedInitial release into beta.