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CTD Changes

December 28, 2010 (rev 8412)

  1. Added network scoring to inferred gene-disease relationship data (detail pages, Batch Queries and downloadable data sets).

December 22, 2010 (rev 8405)

  1. Added metrics to the Data Status page.

December 20, 2010 (rev 8392)

  1. Re-styled text boxes, keyword query results, query forms, and other site elements.
  2. Made minor revisions to the ordering of homepage news items.

December 16, 2010 (rev 8375)

  1. Minor display tweaks and fixes.
  2. Downloadable files of the interaction-type vocabulary are no longer compressed (gzipped).

December 13, 2010 (rev 8346)

  1. General
    1. Published new data.
    2. We now use the open-source PostgreSQL database rather than Oracle.
    3. Improved overall query speeds.
    4. Pathway-disease relationships are now established by inferences based upon common genes.
    5. Global terminology change: "direct" relationships are now referred to as "curated" relationships.
    6. Redesigned the homepage.
    7. Redesigned many images.
    8. The Query History menu option now appears only if you have done a query.
    9. International characters are now displayed and searched more correctly.
    10. Improved tag cloud displays.
    11. Incorporated email-list information into the site.
  2. Vocabulary browsers
    1. Added has-genes icons to the GO and organism browsers.
    2. Added a pathway vocabulary browser.
    3. Chemical and disease selection browsers now return accession IDs to the advanced query forms rather than term names to improve query precision.
    4. Promoted the organism vocabulary browser to the Search menu.
  3. Queries
    1. Added pathway keyword queries.
    2. The default keyword query category is now All data rather than Chemicals.
    3. Advanced queries may now be bookmarked.
    4. In advanced queries, to search for organisms by NCBI Taxonomy accession IDs, you must now use the prefix "TAXON:" (e.g., "TAXON:9606".
    5. In advanced queries, to search for genes by NCBI Gene accession IDs, you must now use the prefix "GENE:" (e.g., "GENE:196".
    6. In advanced queries, you may now search for chemicals by MeSH accession IDs: use the MESH: prefix.
    7. In advanced queries, you may now search for diseases by MeSH or OMIM accession IDs: use the MESH: or OMIM: prefix.
    8. In advanced queries, to search by chemical or disease MeSH tree number, you must now use the TREE: prefix (e.g., "TREE:D02.455.526.439.255"). "chemtreeno:" and "diseasetreeno:" no longer work.
    9. Improved autocomplete functions in keyword query forms, advanced query forms and VennViewer:
      • Exact matches are displayed first.
      • Accession IDs are returned to the source field for more precise query results.
      • For keyword queries, selecting a term will take you immediately to its detail page.
  4. Detail pages
    1. Added annotated-genes and inferred-diseases tabs to GO detail pages.
    2. Added related-genes tab to organism detail pages.
    3. Added pathway detail pages.
    4. Improved pathway and gene-disease displays.
  5. Tools and Downloads
    1. For disease Batch Queries, added ability to get direct and/or inferred gene association data.
    2. For chemical Batch Queries and VennViewer reports, added ability to get enriched GO terms.
    3. Added GO term and pathway Batch Queries for curated gene and inferred disease data.
    4. For Batch Queries, users may now select more than one Gene Ontology at a time.
    5. Made the VennViewer and BatchQuery interfaces more consistent.
    6. Added Batch Query API documentation.
    7. In downloadable reports and Batch Queries with inferred data, made column structures and names consistent.
    8. Added Chemical--GO-Term Enriched Associations downloadable report.
    9. Added synonyms to downloadable gene, chemical and disease reports.
    10. Condensed the downloadable gene report: now only one line per unique symbol; accession IDs are grouped.

November 4, 2010 (rev 8134)

  1. Published new data.
  2. Expanded the Acknowledgments list.

October 14, 2010 (rev 8025)

  1. Updated the NAR citation.

October 13, 2010 (rev 8021)

  1. Published new data.

October 1, 2010 (rev 7968)

  1. Added items to Publications and Tutorials pages.

September 8, 2010 (rev 7772)

  1. Published new data.

August 24, 2010 (rev 7678)

  1. Added more "Sample query" (FAQ) links to "Discover" questions on the homepage.

August 17, 2010 (rev 7632)

  1. Added "Sample query" (FAQ) links to some "Discover" questions on the homepage.

August 9, 2010 (rev 7556)

  1. Published new data.
  2. Added redirects for old FAQ URLs.

July 20, 2010 (rev 7439)

  1. Tweaked query result URLs to help prevent proxy caching.
  2. Corrected typo.

July 13, 2010 (rev 7389)

  1. Increased likelihood that downloaded data filenames will be unique by increasing specificity of the timestamp.

July 12, 2010 (rev 7369)

  1. Published new data.
  2. Tweaked VennViewer diagram colors.

June 11, 2010 (rev 7201)

  1. Added an OpenSearch description for CTD keyword searches. Allows CTD to be added easily to the Firefox and IE search bars.

June 8, 2010 (rev 7169)

  1. Fixed issues preventing access to chemical-GO associations in the VennViewer and Batch Query tools.

June 7, 2010 (rev 7149)

  1. Published new data.

May 12, 2010 (rev 7028)

  1. Added inference scores to chemical-disease and disease-chemical Batch Query outputs.
  2. For disease Batch Query inputs, added optional filtering for direct and/or inferred chemical relationships.

May 11, 2010 (rev 7020)

  1. Added disease vocabulary report in OBO format.

May 10, 2010 (rev 7010)

  1. Revised disease and chemical vocabulary reports. They now each include term and hierarchical information in a single file.

May 7, 2010 (rev 7004)

  1. Revised OBO-formatted report of chemical-gene interaction types.
  2. Revised help text.

May 6, 2010 (rev 6995)

  1. Published new data.
  2. Now display enriched GO terms for each chemical.
  3. Added inference network scores and reference counts to chemical-disease/disease-chemical relationship lists.
  4. Added inference network scores and added columns to chemical-disease relationship report and batch queries.
  5. Added OBO version of chemical-gene interaction types report.
  6. Improved gene-GO-annotation displays.
  7. Updated the publications page.
  8. Made misc help text and usability improvements.
  9. Modified the Batch Query tool to simplify scripted invocations.
  10. Updated data model documentation.

Apr 6, 2010 (rev 6828)

  1. Published new data.
  2. Added links from chemicals to the Household Products Database.
  3. Updated data model documentation.

Mar 24, 2010 (rev 6784)

  1. New global keyword query (allows simultaneous searching of keywords in chemical, gene, disease, GO, organism and reference vocabularies).

Mar 18, 2010 (rev 6741)

  1. Updated the publications page.

Mar 17, 2010 (rev 6729)

  1. On keyword query results and error pages, made it easier to search alternative data categories.

Mar 5, 2010 (rev 6713)

  1. Updated data model documentation.

Mar 4, 2010 (rev 6689)

  1. Published new data.
  2. Shortened some detail-page tab names.
  3. Added CTD Resource Guide and new RGD video to Tutorials page.
  4. Improved appearance of some pages when printed. Other minor formatting improvements.
  5. Upgraded jQuery.

Feb 4, 2010 (rev 6635)

  1. Published new data.

Feb 1, 2010 (rev 6634)

  1. Converted FAQ to use Confluence.
  2. Upgraded jQuery.

Jan 25, 2010 (rev 6610)

  1. Tweaked site logo.
  2. Upgraded jQuery.

Jan 21, 2010 (rev 6605)

  1. Updated funding information.

Jan 8, 2010 (rev 6593)

  1. Published new data.
  2. Updated publications list.