eke.biomarker 1.1.26

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.

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.biomarker

• Re-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.

1.1.26 — 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

• CA-1592

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-1322

• 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

• CA-1300

• CA-1303

1.1.16 — Broken Links

• This 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 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.

• 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.