Metadata-Version: 1.1
Name: eke.biomarker
Version: 1.1.22
Summary: Biomarkers for the EDRN Knowledge Environment
Home-page: https://github.com/EDRN/eke.biomarker
Author: Sean Kelly
Author-email: sean.kelly@jpl.nasa.gov
License: ALv2
Description: *************
        eke.biomarker
        *************
        
        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_.
        
        .. References:
        .. _EDRN Informatics Center: http://cancer.jpl.nasa.gov/
        .. _EDRN: http://edrn.nci.nih.gov/
        .. _EKE: http://cancer.jpl.nasa.gov/documents/applications/knowledge-environment
        .. _JPL: http://www.jpl.nasa.gov/
        .. _NCI: http://cancer.gov/
        .. _Plone: http://plone.org/
        .. _RDF: http://w3.org/RDF/
        .. |---| unicode:: U+2014 .. EM DASH
        
        
        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.
        
        .. References:
        .. _Buildout: http://www.buildout.org/
        
        
        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.
        
        
        1.1.22 — 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.
        
        
Keywords: web zope plone edrn cancer biomarkers eke knowledge
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Environment :: Web Environment
Classifier: Framework :: Plone
Classifier: Intended Audience :: Healthcare Industry
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: Apache Software License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python
Classifier: Topic :: Internet :: WWW/HTTP
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Software Development :: Libraries :: Python Modules
