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CTD Changes

December 27, 2011 (rev 10342)

  1. Improved VennViewer and myGeneVenn tools.
  2. Made internal optimizations.

December 19, 2011 (rev 10325)

  1. Improved VennViewer and myGeneVenn tools.
  2. Updated text about the CTD disease vocabulary ("MEDIC").

December 7, 2011 (rev 10276)

  1. Published new data.
  2. Compacted views of hierarchies on chemical, disease, GO and organism pages.
  3. Added links to ChEBI from chemical pages, and to WikiGenes from gene pages.

November 28, 2011 (rev 10240)

  1. Optimized detail pages that have large numbers of hierarchical paths.
  2. Revised legal terms page, data status page and global footer.
  3. Updated root lineage for taxonomy terms.
  4. Upgraded jQuery.

November 21, 2011 (rev 10207)

  1. Minor enhancements and bug fixes.
  2. Improved print styles.

November 18, 2011 (rev 10193)

  1. Minor image tweaks and internal enhancements.

November 15, 2011 (rev 10185)

  1. Restyled several UI elements.
  2. Upgraded jQuery and other libraries.
  3. Added anti-spam measures.
  4. Fixed minor VennViewer issue.

November 10, 2011 (rev 10150)

  1. Restyled some UI elements.
  2. Optimized JavaScript and CSS.

November 7, 2011 (rev 10130)

  1. CTD has a new URL: http://ctdbase.org/
  2. Published new data.
  3. Updated help text.
  4. Added links to association detail pages.
  5. Improved index of downloadable data files.

November 1, 2011 (rev 10082)

  1. Reference detail-page tabs without data are disabled.
  2. Updated help text.
  3. Updated data model documentation.

October 28, 2011 (rev 10068)

  1. Removed "Cited Genes" and "Cited Chemicals" lists from reference interaction tabs.

October 27, 2011 (rev 10061)

  1. Restyled reference and presentation lists.
  2. Fixed internal links on chemical and disease pages.

October 26, 2011 (rev 10058)

  1. Updated CTD presentations list.
  2. Updated misc text.

October 25, 2011 (rev 10044)

  1. Upgraded the Cytoscape Web library.
  2. Improved ChemComps network visualizations: added SIF exports, added action degrees to edge labels, removed redundant attributes, and fixed issues in exported GRAPHML files.

October 20, 2011 (rev 10022)

  1. Added legal terms for use of CTD data.
  2. Improved index of downloadable data files.

October 18, 2011 (rev 9997)

  1. Updated CTD presentations list.
  2. Revised some navigation lists.
  3. Fixed minor issues.

October 14, 2011 (rev 9964)

  1. Updated CTD publications list.
  2. Consolidated the Additional Resources pages.

October 13, 2011 (rev 9947)

  1. Made minor accessibility enhancements.

October 11, 2011 (rev 9937)

  1. Published new data.
  2. Simplified URLs of disease and pathway detail pages.
  3. Fixed misc issues.
  4. Enhanced backward compatibility with ancient URLs.

September 28, 2011 (rev 9881)

  1. Simplified URLs of gene detail pages.

September 27, 2011 (rev 9864)

  1. Added filtering to gene-diseases displays for enhancing links from disease-pathways displays.

September 26, 2011 (rev 9849)

  1. Updated CTD publications list.
  2. Adjusted full-text query parsing.
  3. Internal optimizations for URL generation.

September 21, 2011 (rev 9828)

  1. Added a new CTD publication.
  2. Reduced size of data lists per detail page.
  3. Internal optimizations for URL generation.

September 19, 2011 (rev 9812)

  1. Fixed formatting of very small network scores.
  2. Cleaned up some URLs.

September 15, 2011 (rev 9792)

  1. Added Exposure Ontology information and downloadable file.
  2. Upgraded jQuery.

September 12, 2011 (rev 9758)

  1. Published new data.
  2. Added DiseaseComps displays.
  3. In VennViewer, added filtering of curated disease relationships by interaction type.
  4. Improved VennViewer and MyGeneVenn results views.
  5. Added Links to GO term pages.
  6. Updated linking instructions.
  7. Improved disease ontology OBO downloadable report.
  8. Added pathways downloadable report.
  9. Upgraded jQuery.

August 25, 2011 (rev 9668)

  1. Updated linking instructions and personnel page.
  2. Made minor UI improvements and internal enhancements.

August 23, 2011 (rev 9665)

  1. Added missing help text for chemical-pathway enrichment relationships.
  2. Improved images and design elements for pop-up windows and the GO browser.
  3. Tweaked icons.

August 16, 2011 (rev 9635)

  1. Minor text changes.
  2. Upgraded Cytoscape Web.

August 10, 2011 (rev 9601)

  1. Published new data.
  2. Revised enrichment displays to better show very very small p-values.

August 5, 2011 (rev 9578)

  1. In enriched pathway and GO views for chemicals, replaced the Enrichment Score column with two p-value columns. Also eliminated the Cluster Frequency column.
  2. Improved some error handling.
  3. Updated data model documentation.

July 25, 2011 (rev 9480)

  1. Made homepage layout more responsive.
  2. Improved various images and interfaces.
  3. Revised help text.
  4. Upgraded third-party libraries.
  5. Updated data model documentation.

July 11, 2011 (rev 9397)

  1. Published new data.
  2. Made major speed improvements to large disease-chemical/disease-gene listings.
  3. Detail-page tabs without data are now disabled.
  4. Dropped support for searching with the deprecated "id:" field qualifier. Use database-name prefixes instead.
  5. Fixed a query form issue.
  6. Upgraded jQuery.
  7. Updated data model documentation.

June 10, 2011 (rev 9325)

  1. Bug fixes and minor enhancements.

June 8, 2011 (rev 9299)

  1. Minor text and style changes, code optimizations and bug fixes.

June 6, 2011 (rev 9274)

  1. Made internal code optimizations.

May 27, 2011 (rev 9215)

  1. The Batch Query and myGeneVenn tools now accept |-delimited terms.
  2. Nested lists in exported data are now more consistently |-delimited. Facilitates use with Batch Query.
  3. Updated data model documentation.

May 25, 2011 (rev 9206)

  1. Revised the tab order on chemical, disease and gene detail pages.
  2. Revised the data relationship diagram.

May 18, 2011 (rev 9192)

  1. Added ability to filter advanced gene queries by gene-disease association types.
  2. Changed the default advanced query operator to equals rather than contains to improve search precision.
  3. Made query form usability improvements.
  4. De-emphasized searching chemicals and diseases by MeSH tree numbers; instead, increased the use of MeSH accession IDs.

May 17, 2011 (rev 9165)

  1. Added filtering by gene or chemical to interactions views to improve links from top-interacting-gene/chemical charts, inference network lists, and interacting-gene/chemical lists.
  2. Optimized detail page code and object caching.
  3. Upgraded Cytoscape Web and jQuery. Fixed some JavaScript oddness in IE.

May 9, 2011 (rev 9125)

  1. Made various code optimizations and fixes.
  2. Upgraded jQuery and related JavaScript libraries.
  3. Implemented new content caching strategy.

May 5, 2011 (rev 9086)

  1. Published new data.
  2. Rolled up gene-chemical interaction views to condense reference and organism data.
  3. Added sorting to reference tables.
  4. Added lists of annotated genes to exported files of chemical enriched GO terms and pathways.
  5. Made various code optimizations and fixes.

April 21, 2011 (rev 9040)

  1. Modified color-coding of interactions to conform to conventions of microarray analyses.
  2. Updated chemical-gene interaction types OBO file.
  3. Updated interactions help text.
  4. Optimized queries.

April 20, 2011 (rev 9029)

  1. Added relationship count to home page.
  2. Revised y-axis links in top-interacting-chemical/gene graphs.

April 19, 2011 (rev 9020)

  1. Added NCBI Gene links to gene links tabs.
  2. Improved x-axis labels and performance of graphs.
  3. Updated data model documentation.

April 14, 2011 (rev 8997)

  1. Now display statistically enriched pathways for chemicals on detail pages and in VennViewer and Batch Query.
  2. Improved error handling and messaging.

April 13, 2011 (rev 8984)

  1. Increased the permissible size of files uploaded to Batch Query.

April 7, 2011 (rev 8941)

  1. Published new data.
  2. Excluded chemical-gene interactions having the 'does not affect' action degree.
  3. NCBI Genes now link to CTD genes.
  4. Updated help text.
  5. Updated data model documentation.
  6. Converted graphs to use Google Chart.
  7. Upgraded jQuery.

March 18, 2011 (rev 8851)

  1. Disease and chemical terms input into the VennViewer and MyGeneVenn tools now return results only for those terms and not for their descendants as well.
  2. Enhanced ChemComps gene network visualizations by adding node weights and varying gene node size and color by weight.
  3. Updated data model documentation.

March 16, 2011 (rev 8843)

  1. Updated JavaScript libraries for better support of IE9.

March 14, 2011 (rev 8834)

  1. Added Excel exporting to query-result and detail-page data tables.
  2. Added action-degree types to exported interaction data from detail pages, batch queries and downloadable reports.
  3. Updated data model documentation.

March 11, 2011 (rev 8824)

  1. Minor fixes and image updates.

March 10, 2011 (rev 8796)

  1. Published new data.
  2. Replaced major icons.

March 3, 2011 (rev 8773)

  1. Updated the CTD Resource Guide.
  2. Made usability, style and form validation improvements.

March 2, 2011 (rev 8763)

  1. Added in-browser visualizations of ChemComps gene networks (powered by Cytoscape Web).
  2. Made usability and style improvements.

February 21, 2011 (rev 8700)

  1. Added new data metrics to the Data Status page.

February 18, 2011 (rev 8689)

  1. Revised ChemComps network XGMML files: more concise markup, prettier colors.

February 14, 2011 (rev 8672) ♥

  1. Added downloadable XGMML files to ChemComps pages for visualization of ChemComp pathways in Cytoscape.

February 9, 2011 (rev 8654)

  1. Added sorting features to ChemComps and GeneComps displays.
  2. Upgraded JavaScript libraries.

February 7, 2011 (rev 8624)

  1. Published new data.
  2. Added color-coding to interaction displays.

January 27, 2011 (rev 8567)

  1. Implemented new logging framework (logback).

January 25, 2011 (rev 8554)

  1. Revised the downloadable OBO file of the chemical-gene interaction type ontology.
  2. Revised display of qualifiers in Gene-GO annotations tables.
  3. Made internal and logging optimizations.

January 10, 2011 (rev 8481)

  1. Added listings of common interacting genes/chemicals to downloaded ChemComps/GeneComps results, respectively.
  2. Fixed Batch Query issue for chemical-enriched GO terms.

January 7, 2011 (rev 8471)

  1. Changed default sorting of network scores in inferred disease relationship displays.
  2. Updated data model documentation.
  3. Made additional HTML5 changes.

January 6, 2011 (rev 8462)

  1. Published new data.
  2. Updated publications.
  3. Finished initial conversion to HTML5.
  4. Made misc usability and style improvements.

January 3, 2011 (rev 8424)

  1. Streamlined the Contact Us form.
  2. Modified colors.