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CTD Changes

Dec 23, 2008 (rev 5171)

  1. Optimized GO descendant queries.

Dec 19, 2008 (rev 5163)

  1. New action degree options for advanced interaction, gene and reference queries.
  2. Fixed bug in which advanced and batch queries by action types were not being done hierarchically.
  3. Reformatted accession ID columns in exported reference files.

Dec 11, 2008 (rev 5131)

  1. Reorganized and reformatted advanced query forms (in preparation for future changes).

Dec 9, 2008 (rev 5122)

  1. For chemical-gene interaction Batch Queries, added ability to filter results by action types.
  2. Improved Clear buttons on VennViewer and Batch Queries.

Dec 8, 2008 (rev 5114)

  1. Adjusted some error logging levels.

Dec 4, 2008 (rev 5106)

  1. Fixed invalid variable reference in Batch Query page.

Dec 3, 2008 (rev 5103)

  1. Added term auto-completion to chemical, gene, organism, GO and disease fields on advanced query forms.

Dec 2, 2008 (rev 5093)

  1. Added term auto-completion to keyword query forms (except for reference queries).

Dec 1, 2008 (rev 5076)

  1. Reorganized advanced query help text.
  2. Tweaked other help text.

Nov 26, 2008 (rev 5059)

  1. Renamed Overview page to "About Us".
  2. Reorganized Help intro and removed help icon from header.
  3. Revised and reorganized advanced query help text.
  4. Tweaked some queries.

Nov 25, 2008 (rev 5047)

  1. Optimized some queries for Oracle 11g.

Nov 24, 2008 (rev 5033)

  1. Reconfigured application to work with Oracle 11g database.
  2. Tweaked some queries to work with Oracle 11g database.
  3. Minor UI tweaks.
  4. Added images and framework for future FAQ.

Nov 17, 2008 (rev 4982)

  1. Eliminated duplicate items from disease interaction listings.

Nov 14, 2008 (rev 4967)

  1. Updated site map files for new data load.
  2. Minor optimizations and refactorings of code.

Nov 4, 2008 (rev 4950)

  1. Adjusted sorting of chemical-pathway tables.

Nov 3, 2008 (rev 4942)

  1. Increased maximum length of keyword query terms.
  2. Minor revision to NLM disclaimer.

Oct 31, 2008 (rev 4936)

  1. Revised Sitemap files to prioritize pages based on data associations and to exclude orphaned reference and sequence pages.

Oct 29, 2008 (rev 4925)

  1. Added Sitemap XML files to facilitate search engine crawling of CTD.

Oct 28, 2008 (rev 4912)

  1. New VennViewer tool (and the first use of Ajax on CTD).
  2. Revised chemical-pathway detail pages to present associations more clearly: each pathway displayed only once, grouped by genes via which the relationship is inferred.
  3. Added gene full names to output of gene batch queries.
  4. Added current application revision number (from Subversion) to footers.
  5. Enhanced application status page for administrators.

Oct 14, 2008 (rev 4832)

  1. Updated publications list.
  2. Renamed Downloads page.
  3. Minor formatting tweaks.

Oct 10, 2008 (rev 4819)

  1. Moved Batch Query and Downloads to new Tools tab. Adjusted site map accordingly.
  2. Changed relationship sort order in Gene Disease, Chemical Disease, Reference Disease, Disease Gene and Disease Chemical tabs.

Oct 3, 2008 (rev 4799)

  1. Batch Query no longer requires users to specify the type of gene, chemical or disease terms they are entering (i.e., accessions, names, symbols, etc.).
  2. Began using jQuery Javascript library.
  3. Fixed formatting in Batch Query help popup windows.

Sep 26, 2008 (rev 4775)

  1. Updated publications list.
  2. Updated data model documentation.

Sep 19, 2008 (rev 4760)

  1. In Top Interacting Gene/Chemical charts, replaced legends with axis labels, and decreased chart width.

Sep 10, 2008 (rev 4748)

  1. On gene-disease and chemical-disease direct relationship detail pages, added relationship-type displays for each reference.

Sep 5, 2008 (rev 4738)

  1. Optimized chemical, disease and gene keyword queries.
  2. Fixed broken Reference Resources page.

Sep 3, 2008 (rev 4734)

  1. Improved performance of chemical disease detail page.

Jun 6, 2008 (rev 4694)

  1. On main help page, added link to CTD email list information.

Jun 4, 2008 (rev 4692)

  1. Adjusted error message for Text query syntax problems.

Jun 3, 2008 (rev 4690)

  1. Removed unnecessary footnotes from data status page.
  2. Added preventative measures if result start number is not provided for gene and reference result pages.
  3. Enhanced app status page.
  4. Optimized database access for chemical interactions, chemical diseases, disease genes, disease interactions and disease chemicals pages.

May 30, 2008 (rev 4678)

  1. Added filter to prevent inclusion of session IDs in links shown to bots.
  2. Restricted bots from crawling URLs with session IDs.

May 29, 2008 (rev 4671)

  1. Optimized views of interactions and chemical and other vocabulary term names: HTML versions (including suggested word breaks) are now cached in the database rather than constructed dynamically.
  2. All detail page tabs are now consistently paginated 500 items per page.
  3. Restricted bots from selection browser pages.
  4. Made minor adjustments to app status page.

May 28, 2008 (rev 4660)

  1. Updated public data model documentation.

May 27, 2008 (rev 4658)

  1. Enhanced app status page.
  2. Disabled connection cache logging.

May 23, 2008 (rev 4650)

  1. Optimized Gene GO annotation tabs to better display large result sets: the summary is always shown, but the detail annotations are now shown only for one user-selected GO term at a time.

May 22, 2008 (rev 4643)

  1. Allowed bots to access detail page main, links and news tabs, but excluded from all other tabs.

May 21, 2008 (rev 4641)

  1. Large data tables now paginated and optimized to reduce download times.
  2. Excluded bots from all detail pages.

May 15, 2008 (rev 4617)

  1. Enhanced application status page for administrators.
  2. Changed configuration of connection cache to timeout after trying in vain for a db connection.
  3. Added more logging code to help diagnose database problems.

May 14, 2008 (rev 4608)

  1. New db/application status page for administrators.
  2. Changed configuration of connection cache to get rid of unused connections.
  3. Added more logging code to help diagnose database problems.

May 13, 2008 (rev 4596)

  1. Added logging code to help diagnose database problems.

May 9, 2008 (rev 4589)

  1. Added documentation to the XML Schema representation of curated chemical-gene interactions.
  2. Added references to the downloadable structured XML representation of curated chemical-gene interactions.
  3. Made the spam test on the Contact Us form less restrictive to prevent false positives.

May 6, 2008 (rev 4564)

  1. Adjusted some reference, interaction and gene queries to work better in some cases.

May 5, 2008 (rev 4558)

  1. Adjusted some reference, interaction and gene queries to work better in some cases.

May 2, 2008 (rev 4556)

  1. Implemented new, smaller logo on secondary pages.
  2. Expanded keyword query box a bit, and changed button label.
  3. Added random animal to the homepage.

May 1, 2008 (rev 4543)

  1. Chem CAS RNs now a separate input option for batch queries.
  2. Fixed an export bug for pathway data.
  3. Made some query adjustments.

Apr 29, 2008 (rev 4532)

  1. New keyword query.
  2. New 'View related genes' links on taxon and GO detail pages.

Apr 22, 2008 (rev 4503)

  1. Removed result size limitation from vocabulary queries, and made result pages paginated and exportable.
  2. Added searchable accession IDs for vocabulary queries.

Apr 7, 2008 (rev 4463)

  1. New GO edge icons, displayed alphabetically and left justified.
  2. Added 'Citing CTD' link to footer.
  3. Made labels for accession ID fields more consistent.

Apr 2, 2008 (rev 4452)

  1. Changed terminology of "="/"matches" queries to "equals".
  2. Minor tweaks of vocabulary browser query results.

Apr 1, 2008 (rev 4446)

  1. Reordered columns in chemical-pathway tables: chemical-pathway relationship is now last.
  2. Revised chemical pathway batch query and downloadable reports to replace gene columns with ChemicalPathwayRelation column.
  3. For batch queries, gene synonyms no longer searched.

Mar 31, 2008 (rev 4437)

  1. Permissible batch query inputs now include gene, disease and chemical synonyms.
  2. For batch queries, chemical names/synonyms can now be entered in the same list as CAS RNs.
  3. Added batch queries for pathways related to chemicals, diseases and genes.
  4. Added downloadable reports for chem, disease and gene pathway datasets.

Mar 27, 2008 (rev 4422)

  1. Added logging and reporting of batch queries.

Mar 26, 2008 (rev 4421)

  1. Prevented caching of larger result sets.
  2. Batch query form modified to enable tracking of how many queries done.
  3. Added icons for new GO relationship types.

Mar 25, 2008 (rev 4414)

  1. KEGG Pathways are now displayed for genes, diseases and chemicals.
  2. Genes and interactions may be queried by KEGG pathway names and accession IDs.
  3. db=PUBMED parameter no longer used in reference detail URLs (since all references are PubMed references).
  4. Downloads and Batch Query now part of 'Home' site section.
  5. Added query term highlighting to more detail pages.
  6. Optimized and reformatted gene GO pages.
  7. Renamed "Select" buttons in vocabulary browsers to "Use".
  8. Minor interface bug fixes and tweaks.
  9. Updated data model documentation.

Mar 14, 2008 (rev 4368)

  1. Not specifying a query type in the URL results in getting sent to gene query page rather than an unfriendly error page.
  2. Minor updates of CTD Overview page.

Mar 11, 2008 (rev 4352)

  1. Voc browser queries are now bookmarkable.

Mar 10, 2008 (rev 4344)

  1. New batch query feature.
  2. Footer now displays date of last data update.
  3. Reference and sequence accessions now displayed consistently with other data types.
  4. Sequence detail pages now display even non-primary accessions for the sequence.
  5. Display of labels/synonyms is now consistent across all data types.
  6. Fixed URLs to resource pages.

Mar 7, 2008 (rev 4327)

  1. Made display of GO term accessions consistent with other vocabularies.
  2. Removed duplicate interactions from structured chem-gene interaction report.

Mar 6, 2008 (rev 4320)

  1. Improved performance of gene and interaction queries by GO Terms.
  2. Made display of accessions consistent across vocabularies (except GO).
  3. Fixed bug that prevented effective MATCH queries of terms containing periods.

Mar 5, 2008 (rev 4309)

  1. Removed duplicative entries in some gene- and chemical-disease tables.

Feb 26, 2008 (rev 4288)

  1. Optimized queries that display CAS RNs.
  2. Moved Site Map link to footer, and replaced it with Downloads link. Downloads is now a standalone site section.
  3. Added safeguards to vocabulary query logging.

Feb 21, 2008 (rev 4277)

  1. Added intro text to Downloads page.
  2. Rearchitected code to produce reports.

Feb 15, 2008 (rev 4271)

  1. Added downloadable report with structured XML representations of chemical-gene interactions.
  2. Minor tweaks and bug fixes.

Feb 12, 2008 (rev 4265)

  1. Added instructions for citing CTD to the Publications page.

Feb 7, 2008 (rev 4253)

  1. Added Downloads page with three downloadable data reports in three formats each (CSV, TSV and XML).
  2. Renamed "Resources" page to "Data Model".

Feb 5, 2008 (rev 4241)

  1. Limit maximum bar widths in Top Interacting Genes and Chemicals charts (looked funny when there was just one item).
  2. Increased overall size of Top Interacting Genes and Chemicals charts to accommodate longer names.
  3. Fixed broken links on Gene GO detail page.

Feb 1, 2008 (rev 4232)

  1. Algorithms that determine the overall number of interactions/relationships as well as the number associated with specific genes and chemicals are no longer based on the number of distinct interactions.
  2. Top Interacting Genes and Chemicals charts no longer display organism counts.
  3. Modified contains-query error message to suggest alternative actions.
  4. Fixed wrong publication info on publications page.

Jan 29, 2008 (rev 4218)

  1. Went live on new web server.
  2. Disabled Excel data exports (CSV and TSV are just as good).

Jan 25, 2008 (rev 4200)

  1. Added option to export data tables to tab-separated (TSV) files.

Jan 24, 2008 (rev 4196)

  1. Added missing Help text.
  2. Minor interface tweaks.

Jan 23, 2008 (rev 4187)

  1. Optimized code to view or download sequences.
  2. Minor interface tweaks.
  3. Tripled cache time of top gene/chemical charts.

Jan 22, 2008 (rev 4177)

  1. Fixed issues with encoding of certain internal URLs.

Jan 18, 2008 (rev 4169)

  1. Column tag names in XML exports are now the actual column name rather than "<column>".
  2. Fixed taxon links in gene microarray lists.
  3. Added unique-references statistic to Data Status.
  4. Re-enabled character-set filter.

Jan 17, 2008 (rev 4158)

  1. Optimized top chemical and top gene charts.
  2. Added code to help diagnose chart errors.

Jan 16, 2008 (rev 4144)

  1. Added defensive code and expanded error messages to diagnose and prevent NullPointerExceptions being caused by third-party software being used.
  2. Tweaked query code to prevent embedded reserved words (AND/OR/NOT) from being treated like reserved words improperly (e.g., for "or-1855").
  3. Tweaked query code to allow reserved words (AND/OR/NOT) to be used as query terms if they are the only query terms specified.
  4. Added new error message for invalid contains query syntax.

Jan 15, 2008 (rev 4125)

  1. Major release.
  2. New data architecture.
  3. Updated data.
  4. New direct and inferred chemical-disease and gene-disease relationships, and enhanced displays of those relationships.
  5. References may now be queried by disease.
  6. New hierarchical disease vocabulary.
  7. Expanded disease detail pages.
  8. New, improved gene vocabulary.
  9. Data now exportable as XML.
  10. Updated chemical images.
  11. CTD curator notes now appear with selected data.
  12. In the News items now related to diseases as well as chemicals.
  13. Extensive usability improvements.