This is a page for testing various Biomedical Applications interfaces
This NOT an official or productional page

For the manager page

For a list of rowcounts on CLSD tables:

• on Libra45 (No longer in service).

For web pages using CGI (These have all been discontinued.)

For web pages that use the servlet that uses JDBC to get to CLSD (RunCLSD.java):

• via an HTML form (No longer in service), or its
• via AJAX-enabled equivalent (No longer in service).

• via a servlet (RunCLSDservice.java) that calls the Web Service (No longer in service), and
• via an AJAX-enabled page that calls the Web Service (No longer in service)
• via an Applet (XMLClientSQL3) which calls the Web Service (No longer in service)
• via an AJAX-enabled page that provides two CLSD interfaces that can independently and simultaneously access CLSD by calls to the Web Service (No longer in service)

For a web page that uses OGSA-DAI to get to CSLD (No longer in service) (note this version expects testaccount and won't handle illegal XML characters in the database.) The OGSA-DAI service could also be accessed via an AJAX-enabled web page that can act as a WSRF client.

There exist also demo

• Perl-based WSRF services and clients built using WSRF::Lite to access and manipulate CLSD data (No longer in service), and
• Perl and Java JAX-RPC command-line scripts. (No longer in service)

Also, there are other demo interfaces:

• SNP-related:
  • Get SNPs in a specified human chromosomal region using NCBI eSearch and eFetch (new version) (No longer supported)
  • Old version of the program above (No longer supported)

  • Send SQL commands involving Build 128 directly to dbSNP:
    • using a Java servlet and JDBC (for big queries) (No longer in service), or
    • using CGI, Java, and JDBC (No longer in service).

  • Get a comprehensive list of a SNP's neighbors (No longer in service)
  • Get a comprehensive list of SNPs within a chromsome region (No longer in service)

• Genes, diseases, and endogenous repeats:

  • Get NCBI sequences for genes or specified regions (No longer supported

  • Show data related to the DISEASE-GENE network (This does not have all the features provided by the original, but comes close.)

  • Show data related to the DISEASE-GENE network (No longer in service)

  • Find endogenous repeat sequences within a sequence

  • Access Oracle content

  • Access BIOKDD using SQL via JDBC
  • Access BIOKDD using SQL, via a Web Service.

  • Find GO cellular location categories shared by genes or gene-pairs (as within a PPI) (Note: Does not rely upon CLSD.)

  • Expand gene and SNP lists (No longer in service) using a Protein-Protein Interaction network and optionally restrict expansion on the basis of GO cellular component co-location.

  • Evaluate gene lists discovered by expanding input gene lists from user input or from proximity searches around input SNP lists (No longer in service), using a Protein-Protein Interaction network on the basis of hop counts to the original gene list and GO cellular component co-location. (Note: this does not rely upon CLSD.)

There is some related documentation at:

• Using the relational and eUtils interfaces to dbSNP (Describes the use of some IU services that are no longer supported.)

• Using dbSNP via SQL queries

• Using the NCBI eUtilities via CGI

• Using XML::Twig to process XML content

There is also:

• some 2006 TRANSFAC data, and

• a display showing some RDF data for a very small subset (about 14 categories) from the molecular function component of the GO ontology.

• and some displays showing Pubmed data, some GO extracts, and some tutorial examples illustrating the use of the Exhibit faceted browsing middleware from the MIT Simile project.

• and some researchers in PubMed with Indiana connections.

• Linked Data: A possible project within Research Technologies.

• Find researchers by MeSH categories.

• A Network of Life Sciences Concepts
  • 2D: Show a table of concepts related (by 2D co-occurrence) to a search concept specified by the user.

  • 3D: Show a table of concepts related (by 3D co-occurrence) to 2 search concepts specified by the user.

• Disambiguate PubMed researcher names.

• Some references to dynamic, rotating tag clouds:
  • Graceful with a reference to social "Navimation"

  • A very rough prototype for displaying my MeSH term co-occurrence data. Tray uglee.

  • A tool by Figment Engine that displays "co-occurrence" within a concept cloud, and allows users to drag concepts to new locations. This one relies upon M$ Silverlight.

• Some pages for exploring databases for use with the Patient Registry

  • Search MedlinePlus drug database

  • Search the SnomedCT Core disease list

  • Examine 2 lists of RxNorm trade-marked drugs displayed in different ways

     

  • Lists of RxNorm INgredients, Tradenames, and Package Tradenames

  • More Detailed Lists of RxNorm INgredients, Tradenames, and Package Tradenames

     

  • a table mapping lists of SBDF ID entries to their INgredient or Mulitple INgredient (IN_or_MIN) contents

  • a table mapping from IN_or_MIN IDs back to "reconstructed" SBDF records (without their Dosage Forms)

• Vivo-related scripts
  • EZ Vivo search interface

  • Vivo Query By semantic Template (VQBT) search interface

Questions to Michael Grobe