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CTD Changes

December 26, 2012 (rev 12506)

  1. Help information now appears in in-situ modal dialogs rather than pop-up windows.
  2. Updated help text.

December 20, 2012 (rev 12492)

  1. Fixed data issue affecting gene-gene interaction visualizations.
  2. Updated popup windows and icon legends.

December 19, 2012 (rev 12487)

  1. Added disease-enrichment analyses to the Gene Set Enricher tool and chemical-disease lists.
  2. Updated help text and Batch Query form.

December 14, 2012 (rev 12462)

  1. Modified Batch Query to save results directly to file.
  2. Restyled pop-up windows to work better with Mac Chrome bugs.

December 12, 2012 (rev 12427)

  1. Added gene gene-interactions Batch Query.
  2. Added disease categories fields (MEDIC-Slim mappings) to disease results from Batch Queries.

December 11, 2012 (rev 12420)

  1. Added gene-interaction views to gene detail pages.
  2. Moved chemical, GO, and gene link outs to the Basics tabs.

December 10, 2012 (rev 12410)

  1. Published new data.
  2. Added protein-protein interaction data for chemical-disease inference networks.
  3. Added filtering by GO level to chemical-GO enrichment views and to Gene Set Enricher results.
  4. Added links from genes to BioGRID.
  5. Added JSON exporting to the Gene Set Enricher.
  6. Added curated icons to reference listings.
  7. Updated help text and data model documentation.

November 27, 2012 (rev 12320)

  1. Batch Queries can now output JSON!

November 26, 2012 (rev 12307)

  1. Improved Comps-agent-network visualizations.
  2. Updated help text.
  3. Upgraded jQuery UI lib.

November 20, 2012 (rev 12270)

  1. Reversed sorting in detail-page reference tabs.

November 9, 2012 (rev 12205)

  1. Updated CTD publications list.
  2. Updated help text for inference scoring.
  3. Internal optimizations.

November 7, 2012 (rev 12184)

  1. Published new data.
  2. Batch Query and VennViewer query forms now hide non-applicable choices.
  3. Condensed filter forms on data tables.
  4. Misc UI improvements.
  5. Updated data model documentation.

November 2, 2012 (rev 12158)

  1. Improved ChemComps network visualizations and data files. Chemicals are now source nodes, and genes are now targets.

October 25, 2012 (rev 12127)

  1. Misc UI improvements.
  2. Added help text re: enrichment.

October 24, 2012 (rev 12108)

  1. Improved Comps charts.
  2. Updated CTD publications list.
  3. Improved and added icons.

October 16, 2012 (rev 12088)

  1. Added spinner widget to the Batch Query form.
  2. Upgraded and replaced various Javascript functions.

October 15, 2012 (rev 12081)

  1. Rewrote the Batch Query tool to present incremental results faster, handle more query terms, and use memory more efficiently.

October 11, 2012 (rev 12048)

  1. Added some third-party trademark notices.

October 10, 2012 (rev 12036)

  1. Implemented division of labor for some analysis functions.

October 8, 2012 (rev 12028)

  1. Published new data.
  2. Misc UI improvements.

October 3, 2012 (rev 11994)

  1. Batch Query now accepts external GET as well as POST requests.
  2. Updated linking instructions for Batch Query.
  3. Misc UI improvements.

September 27, 2012 (rev 11972)

  1. Filter boxes now indicate when a filter is active.
  2. Misc style improvements (especially for IE).

September 25, 2012 (rev 11955)

  1. Filenames for exported data now reflect when filtering is active.
  2. Upgraded jQuery lib.

September 24, 2012 (rev 11947)

  1. Misc UI improvements.
  2. URL changes for chemical- and gene-disease relationship pages to prepare for upcoming new data views.

September 18, 2012 (rev 11920)

  1. Added disease-category visualizations to chemical- and gene-diseases views.

September 11, 2012 (rev 11904)

  1. Published new data.

September 7, 2012 (rev 11896)

  1. Fixed cursor hovering in bar graphs.

September 5, 2012 (rev 11879)

  1. Tweaked Comps graphs and disease filters.

September 4, 2012 (rev 11866)

  1. Added filtering by association type to chemical- and gene-diseases views.
  2. Tweaked Comps graphs.

August 30, 2012 (rev 11852)

  1. Improved Comps presentation.

August 30, 2012 (rev 11846)

  1. Made presentation of Comps data more graphular.
  2. Graphs are now produced by the Google Visualization API rather than the deprecated Google Image Chart API.
  3. Fixed a MEDIC-Slim term in the user interface and downloadable reports.

August 27, 2012 (rev 11829)

  1. Fixed ordering of chemical and disease keyword query results.

August 23, 2012 (rev 11820)

  1. Misc UI/icon improvements.

August 21, 2012 (rev 11802)

  1. Improved term-selection browsers on advanced-query forms.
  2. Upgraded various JS libraries.

August 20, 2012 (rev 11791)

  1. Revised DiseaseComps headings.
  2. Certain certain security precautions.

August 17, 2012 (rev 11780)

  1. Added CAS RNs for chemicals to downloadable data sets from detail pages, Comps, interaction queries, and chemical keyword queries.
  2. Added sorting to embedded lists in Batch Queries.
  3. Restyled headings.
  4. Revised help text.

August 13, 2012 (rev 11745)

  1. Internal optimizations in Enricher and Comps tools.

August 7, 2012 (rev 11705)

  1. Published new data.
  2. Added MEDIC-Slim mappings to disease pages.
  3. Added filtering by MEDIC-Slim terms to chemical-diseases, gene-diseases, GO-diseases and pathway-diseases views.
  4. Added MEDIC-Slim information to downloadable disease vocabulary files.
  5. Added links from chemicals to PubChem.
  6. Improved legibility of long data lists.
  7. Minor revisions of reference pages.
  8. Restyled various UI elements.

July 26, 2012 (rev 11598)

  1. Minor UI improvements and help-text updates.

July 20, 2012 (rev 11560)

  1. Improvements to detail page filter forms.
  2. Minor bug fixes.

July 19, 2012 (rev 11549)

  1. ChemComps and GeneComps: you may now select a specific interaction type (and degrees) to be used in a custom similarity analysis.

July 16, 2012 (rev 11512)

  1. Improved Comps-VennViewer integration.
  2. Minor UI improvements on chemical detail pages.
  3. Updated data model documentation.

July 10, 2012 (rev 11484)

  1. Published new data.
  2. Gene detail pages: each synonym is linked to a keyword query.
  3. Updated help text.
  4. Restyled various UI elements.

June 26, 2012 (rev 11431)

  1. Detail pages: hid redundant columns in data tables for leaf nodes.

June 26, 2012 (rev 11408)

  1. Tweaked data displays and intro text on various detail pages.
  2. Added sortable 'organisms' column to gene-chemicals and chemical-genes displays.
  3. Updated data model documentation.

June 25, 2012 (rev 11379)

  1. Comps: Minor display improvements.

June 21, 2012 (rev 11368)

  1. MEDIC OBO file: added synonym scopes and (blank) dbxrefs.
  2. Updated data model documentation.

June 19, 2012 (rev 11359)

  1. Enricher: fixed issues with wee p-values.

June 18, 2012 (rev 11351)

  1. Misc view optimizations and internal refactorings.

June 13, 2012 (rev 11331)

  1. Gene detail pages: Added organism names to accession ID linkouts.
  2. Misc optimizations.

June 12, 2012 (rev 11318)

  1. Published new data.

June 7, 2012 (rev 11294)

  1. Enricher: fixed issues with wee p-values.
  2. Various numeric display enhancements.

June 4, 2012 (rev 11270)

  1. VennViewer
    • Added filtering by interaction degrees and types for curated chemical-gene data sets.
    • Improved interactivity of the query interface.
  2. Various optimizations.
  3. Revised misc text.
  4. Added options to site navigation.
  5. Removed AddThis sharing.

May 23, 2012 (rev 11229)

  1. Added filtering by ontology to GO keyword queries.
  2. Added 'GeneForms' field to downloadable interactions files.
  3. Misc bug fixes.
  4. Updated data model documentation.

May 22, 2012 (rev 11208)

  1. Added filtering by ontology to chemical enriched-GO displays.
  2. Various image and interface improvements.

May 21, 2012 (rev 11191)

  1. Added filtering by ontology to the Gene Set Enricher.

May 9, 2012 (rev 11164)

  1. Re-styled paging navigation, vocabulary-browser navigation, keyword query results, and other interface elements.

May 8, 2012 (rev 11146)

  1. Published new data.
  2. New Gene Set Enricher tool, and links from chemical-diseases and disease-chemicals pages to view enriched GO terms and pathways for gene sets that form the basis of those relationships.
  3. New gene vocabulary browser for selecting gene query terms on advanced query forms.
  4. Improved presentation of complex reference abstracts.
  5. Removed CAPTCHA from contact form for ordinary use cases.

May 3, 2012 (rev 11123)

  1. Fixed performance issues with organism-gene displays.
  2. Updated data model documentation.

April 26, 2012 (rev 11083)

  1. Optimized disease-interactions pages.
  2. Updated FAQ technology page.

April 25, 2012 (rev 11057)

  1. Published new data.
  2. Added reference Batch Query reports.
  3. Updated help and FAQ.
  4. Upgraded jQuery UI lib.

April 17, 2012 (rev 10989)

  1. Improved Batch Query error handling
  2. Improved certain query interfaces.
  3. Updated help and FAQ text, and data model documentation.

March 30, 2012 (rev 10923)

  1. Improved reference and GO displays.
  2. Fixed issue with uploading of certain files to the Batch Query.
  3. Upgraded jQuery and other libs.

March 28, 2012 (rev 10904)

  1. Optimized some reference queries and displays.
  2. Upgraded Cytoscape Web.

March 26, 2012 (rev 10890)

  1. Updated About Us, Funding, and Personnel pages.
  2. Improved advanced query term displays.
  3. Internal optimizations.

March 21, 2012 (rev 10860)

  1. Improved the downloadable chemical and disease vocabulary files:
    • Added term definitions.
    • Removed redundant synonyms.
    • Added term defs and synonyms to disease vocabulary OBO file.
  2. Updated CTD publications list.

March 19, 2012 (rev 10825)

  1. Added ability to restrict searches and tool inputs by official name/symbol (using the "name:" prefix).
  2. Venn tools are now better at asking for clarification in an input term matches more than one data object.
  3. Improved advanced query forms.
  4. Revised help text.

March 13, 2012 (rev 10800)

  1. Fixed issue with certain links in Query History lists.

March 12, 2012 (rev 10795)

  1. Fixed JavaScript issue in selection browsers on query forms.
  2. Updated data model documentation.
  3. Updated error pages.

March 8, 2012 (rev 10783)

  1. Updated Share buttons to work with AddThis API changes.
  2. Revised the tool bar.
  3. Added links to the query history page.
  4. Revised the format of the gene-disease-association field on the gene query form.

March 7, 2012 (rev 10772)

  1. Revised pagination banners.
  2. Revised display and exporting of GO annotation qualifiers.
  3. Internal optimizations.

March 6, 2012 (rev 10753)

  1. Published new data.
  2. Minor revision of XML schema for chemical-gene interactions structured-XML report.

March 1, 2012 (rev 10736)

  1. Revised query-result displays.
  2. Moved the "Other Resources" page to the Help section.

February 27, 2012 (rev 10713)

  1. Revised reference citation displays.
  2. Internal optimizations.

February 23, 2012 (rev 10700)

  1. Added file listings to the Downloads page.
  2. Internal optimizations, styling improvements and text revisions.

February 21, 2012 (rev 10676)

  1. Added raw p-values to output of batch queries and downloadable reports for enriched chemical-GO-term and chemical-pathway associations.
  2. Updated publications list.
  3. Internal optimizations, styling improvements and text revisions.
  4. Data pages now all validate as HTML5!

February 20, 2012 (rev 10666)

  1. Revised secondary sorting of chemical enriched-GO displays.
  2. Replaced "enrichment scores" with corrected p-values in output of batch queries and downloadable reports for enriched chemical-GO-term and chemical-pathway associations.
  3. Internal optimizations, styling improvements, and text revisions.

February 16, 2012 (rev 10651)

  1. Improved operations of accordion and autocomplete widgets.
  2. Upgraded jQuery UI library.
  3. Updated data model documentation.

February 15, 2012 (rev 10639)

  1. Minor homepage and other tweaks.

February 14, 2012 (rev 10625)

  1. Improved data-table pagination and download links.

February 9, 2012 (rev 10615)

  1. Improved formatting of filter and query-term boxes.
  2. Tweaked performance of the main navigation menu.

February 8, 2012 (rev 10606)

  1. Made error handling more transparent for certain detail-page URLs.
  2. Refined basic queries.

February 7, 2012 (rev 10594)

  1. Improved headings on relationship detail pages.
  2. Optimized paginated queries.

February 6, 2012 (rev 10584)

  1. Updated publications and presentations lists. Improved printing. Populated from database.

February 2, 2012 (rev 10551)

  1. Published new data.
  2. Misc internal optimizations and bug fixes.

January 30, 2012 (rev 10520)

  1. Added option to choose the default sorting for advanced interaction queries.
  2. Restructured global navigation.
  3. Improved a downloadable logo.
  4. Revised page footer.
  5. Updated help text.

January 26, 2012 (rev 10504)

  1. Revised main navigation menu.
  2. Added downloadable CTD logos to the linking instructions page.

January 25, 2012 (rev 10490)

  1. Updated page footer.
  2. Updated help text.

January 24, 2012 (rev 10482)

  1. Optimized Venn tool queries.
  2. Added has-related-disease icons to keyword query results for pathways.
  3. Updated data model documentation.

January 20, 2012 (rev 10467)

  1. Fixed display issue for certain descendants in MeSH vocabularies.

January 19, 2012 (rev 10465)

  1. Changed the default sorting of gene-diseases, chemical-diseases, disease-chemicals and disease-genes views to show curated relationships that can also be inferred prior to those that cannot.
  2. Revised page footer.
  3. Optimized various queries.

January 17, 2012 (rev 10446)

  1. Misc UI improvements, help text updates, internal optimizations and refactorings.
  2. Upgraded Cytoscape Web.

January 13, 2012 (rev 10436)

  1. Optimized disease-related queries.

January 10, 2012 (rev 10427)

  1. Consolidated gene-disease-association report files.

January 9, 2012 (rev 10418)

  1. Published new data.
  2. Added new MyVenn tool.
  3. Improved VennViewer and myGeneVenn tools.
  4. Added sorting by reference counts to gene-diseases, chemical-diseases, disease-chemicals, and disease-genes views.
  5. Updated help text.
  6. Renamed some data report files.
  7. Misc internal optimizations and bug fixes.