Page Comparison

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Sprint to extend some of the "read only" APIs, to finalize unit/integration testing for existing functionality, to extend the interface, to develop additional loaders, and to begin developing editing capabilities.

Priority things

• For "semantic type" mechanism - if there are tree numbers, order by that and indent"
• DONE: owl deployment
• JFW :Refresh server deployments
  • UMLS, SNOMED, SNOMED VET, ICD (reload on machine)
• DONE: JFW: QA queries
  • referential integrity
  • Verify for each type of loader and the sample data.
• JFW: Jekins - mojo tests
  • REST integration tests
• BAC: OWL - NCIt
• BAC: consider adding top-level hierarchies as "semantic types" to concepts for loaders in general
  • This could be a function of the treeposition or transitive closure computers.
  • the corresponding metadata would have to be created as well
• BAC: remove "void addXXX" and "void removeXXX" methods from model objects. Use getObjects().add/remove(...) only
• DONE: Terminology sampler mojo  - bring over from old term server project.
• Model: GCI
  • DONE: General class axioms
  • Mapping, MapRecord, MapEntry (each with attributes) - similar to Subset, SubsetMember except with one more layer.
    • Then implement this for RRF loader
    • Then implement this for RF2 loader (snapshot)
    • Then implement this for RF2 loader (delta)
• User Interface
  • Enable glass pane while switching tabs - need to say increment in tab controller and decrement at the end of the controller.
• Integration Tests - Jpa/REST - get them tested again
• DONE: support "mode" parameter on loaders to automatically recreate db and clear indexes.
• Have search handler work for all searching, including relationships and trees. - separate methods to build query?? - probably
• DONE Improve search
  
  • Create "SearchHandler" as an extension point (like graph resolution handler).  Have a "default implementation"
  • Search algorithm
    • First search
  
  
  • for
    • on exact string (e.g. "literal" search)
      • handles short strings containing special characters, consider doing a literal search (e.g. "!" or "+" or "Ca+")
        • alternative is to save untokenized forms of all strings for exact searching
    Acronym expansion (based on a configured list)
    • • e.g. for the query "+" use a lucene query like "terminology:SNOMEDCT AND version:latest AND atoms.nameSort:"\+" (not sure if you have to escape the + if it is in quotes).
    • Then search on matches - this is the normal search
    • The trick here is to combine the results from the first search and the second search into a single list, where the ordered results from the first search are at the head of the list followed by the ordered results of the second search - but with any duplicates removed.
      • could consider "(literal search) OR (normal search)" as a single query.
      • This is better because then lucene can do the paging
    • if no results, Then do spelling correct  and (then) acronym expansion and search again
      • Use Lucene SpellChecker class for this.
      • config/src/main/resources/data/
      acronym
      • spelling.txt
    Spelling correction (based on a dictionary)
    • First search on exact string (e.g. "literal" search)
    • Then search on matches
    • if no results, Then do acronym expansion and spelling correction and search again
      • config/src/main/resources/data/acronym.txt
    • Use Lucene SpellChecker class for this.
    Search algorithm
    • • For obtaining words for spelling correction, use "FieldedStringTokenizer" with " \t" as delimiter
        • (consider this delimiter list later: " \t-({[)}]_!@#%&*\\:;\"',.?/~+=|<>$`^")
      • For obtaining words for acronym expansion, split only on " \t"
    • if no results, then try putting * after each term and search again
  • should autocomplete algorithm include acronym expansion? NO

Marketing/SEO

• Create a video demo of the site (camtasia) and post as a link on the header (video glyphicon if there is one)
• Promote "ICD10" browser on various lists
• Ensure all entry pages for applications contain SEO text for browsers and are indexed by google
• Verify all entry pages for applications are officially mobile friendly
• Consider advertising SNOMED/UMLS/ICD browsers on google adwords.FB?
• Training Video for UMLS browser (need 10 min)
• Training Video for SNOMED browser (simple 5 min)

User Interface Enhancements

• Add features for "deep" relationships when browsing UMLS.    
  
  • Need a generalized way to know when to use this
  • it is definitely only for "concept"
  • It may be that if any "atoms" of the concept don't match the terminology, then we show it.
• Reimplement the component report as a directive (with service callbacks for  history and other features)
• Implement routing for terminologyId/terminology/version/type so we can preserve URLs.  can even include ?query=... for the query
  • Also clean up the way routes work first so we have
    • https://umls.terminology.tools/content
  • instead of
    • https://umls.terminology.tools/#/content
  • This is likely related to the starting URL redirected to https://umls.terminology.tools/#/
  • See http://stackoverflow.com/questions/14319967/angularjs-routing-without-the-hash
  • e.g. https://umls.terminology.tools/content/CUI/SNOMEDCT/2015_01_31/12738006
• Support opening a concept in a new window (e.g. there's a pointing off arrow icon that opens a new window with a routing URL that  shows exactly that concept - then drag/drop between windows can be editing mechanism).
  • https://umls.terminology.tools/report/SNOMEDCT/2015_01_31/12738006
• DONE: Websocket (for a WebsocketWorkflowListener)
  • test it
  • What to do with it??
• Expression-based searching?
• Consider adding "LABELFOR" all subsets and making the star pop up a picklist of the things to highlight (ordered by type with extensions first, subsets later)
• RECURRING: Mobile-friendly and other style issues

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• RF2 delta/full loaders
  • Implement mojo testing too
• Owl loader (e.g. for NCIt) - will require use of "DL" features
  • Examples: https://github.com/owlcs/owlapi/blob/version4/contract/src/test/java/org/semanticweb/owlapi/examples/Examples.java
  • DONE: Step 1: create the infrastrucure (mojo, rest call, client, algorithm, get parameters right).
  • Step 2: get OwlAPI into the project,
    • http://owlapi.sourceforge.net/owled2011_tutorial.pdf
    • http://owlapi.sourceforge.net/
    • http://www.w3.org/TR/owl2-profiles/#OWL_2_EL
    • http://protege.stanford.edu/ontologies/pizza/pizza.owl
    • Handle "Class" and "class"
  • Step 3: add complexity
  • May need a "SNOMED" style and a general style to capture "distribution normal form" for SNOMED (e.g. rel groups, etc)
  • Also have a corresponding Owl export feature (e.g. "release")
  • Implement mojo testing too
  • REasoner
    • JFact

      • example: http://jfact.sourceforge.net/Example.java 

        Code Block
        <dependency> <groupId>net.sourceforge.owlapi</groupId> <artifactId>jfact</artifactId> <version>1.0.0</version> </dependency>

    • .Hermit

      • example: http://hermit-reasoner.com/java.html

        Code Block
        <dependency> <groupId>com.hermit-reasoner</groupId> <artifactId>org.semanticweb.hermit</artifactId> <version>1.3.8.4</version> </dependency>

    • ELK:  **

      • example: https://code.google.com/p/elk-reasoner/wiki/ElkOwlApi

        Code Block
        <dependency> <groupId>org.semanticweb.elk</groupId> <artifactId>elk-owlapi</artifactId> <version>0.4.2</version> </dependency>

    • Snorocket

      • example: https://github.com/aehrc/snorocket
        
        

        Code Block
        <dependency> <groupId>au.csiro</groupId> <artifactId>snorocket-owlapi</artifactId> <version>2.7.2</version> </dependency>

Services

• Action Service
  • Implement classification.
  • Need to go to/from Owl so do Owl loader FIRST.

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