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CTD Changes

Dec 23, 2005 (rev 1656)

  1. Four new animals.
  2. Misc tweaks.

Dec 9, 2005 (rev 1639)

  1. Tweaked display of symbol legends.

Dec 6, 2005 (rev 1630)

  1. Removed author field from gene query.

Dec 1, 2005 (rev 1627)

  1. Fixed broken help links and improper data table formatting.
  2. Refactored code that produces internal page hyperlink anchors.
  3. Refactored page headers.
  4. On chemical detail pages, the In the News and Other Database Links sections are no longer displayed when viewed as a pop-up (selection) window from a query form.
  5. In vocabulary browsers, terms in the query field no longer follow the user beyond the detail pages which matched the query.
  6. In chemical browser, added microarray icons to chemical popular terms.

Nov 17, 2005 (rev 1608)

  1. Gene Set lists now display microarray icons/links next to eligible genes. Gene names on main Gene Set page now also link to gene detail pages.
  2. Gene Set list on gene query form now indicates number of related genes.
  3. Updated help text.
  4. Fixed broken help link on reference query.
  5. Reordered help pages to conform to new architecture.
  6. Added symbol legend to appropriate pages.
  7. Made internal vocabulary browser optimizations.
  8. Simplified some data table styling code.
  9. Fixed background color of gene columns in sequence tables on reference and Gene Set pages.
  10. Increased speed of vocabulary browser queries.

Nov 15, 2005 (rev 1590)

  1. Minor reformatting of sequence access controls.
  2. Gene Set list page will now still respond to its old URL.

Nov 10, 2005 (rev 1587)

  1. Gene queries which return a single result now accessed the corresponding detail pages via gene name rather than ID.
  2. Improved error messages for improper URLs to vocabulary browsers and detail pages.
  3. Page titles tweaked for better bookmarking and search engine accessibility.

Nov 9, 2005 (rev 1578)

  1. Major release.
  2. New gene query (replaces comparative sequence query).
  3. New gene detail pages, featuring information about related sequences, microarray experiments, references, chemicals and GO annotations.
  4. Sequence detail pages reorganized to be more concise and gene-centric, and to make protein and nucleotide pages more consistent.
  5. Icons throughout site now indicate which genes, sequences and chemicals have related microarray data.
  6. Gene Sets are now subsidiary to Genes content.
  7. Renamed Sequence Resources to 'Gene and Sequence Resources'.
  8. Vocabulary browsers now contain links to related genes rather than sequences.
  9. Updated data model documentation.

Sep 23, 2005 (rev 1402)

  1. Modified FASTA sequence access controls on sequence query results page.
  2. Added sequence access capabilities to the Gene Set detail page. Removed the Aligned Seqs column from the Alignments table.

Sep 22, 2005 (rev 1396)

  1. Revised formatting of Included Genes list on Gene Set page.
  2. Finished upgrading all code to Java 1.5.

Sep 7, 2005 (rev 1374)

  1. Shortened field names on query forms, and adjusted related help text.
  2. Removed review articles field from reference query form--was never used.
  3. Renamed taxonomy vocabulary to 'organisms'.
  4. 'Swiss-Prot/TrEMBL' now referred to as 'UniProt'.

Sep 1, 2005 (rev 1369)

  1. Downplayed prototype-ness (e.g., removed 'PROTOTYPE' from title graphic).
  2. Revised data diagram as well as home page and overview page text re: data and prototypeness.
  3. Updated personnel list.

Aug 17, 2005 (rev 1350)

  1. Renamed 'General Information' sections on detail pages to 'Basic Information'.
  2. Changed field labels on query forms to sentence case rather than title case for better usability and accessibility.
  3. Minor revision to vocabulary browser query results.

Aug 12, 2005 (rev 1344)

  1. Minor tweaks of sequence results, reference results and sequence detail pages.
  2. Added new animal.

Aug 9, 2005 (rev 1339)

  1. Refactored and optimized code that creates the navigation bar.
  2. Updated data model documentation.

Aug 8, 2005 (rev 1332)

  1. Changed query on Data Integration Status page to work with new release names for Swiss-Prot/Trembl. Also reformatted table slightly.
  2. Data Integration Status page now elevated to the Help sub-navbar.
  3. Added table of contents to personnel page.

Aug 4, 2005 (rev 1325)

  1. Added Jobs links to subnavbar and site map.

Jul 22, 2005 (rev 1322)

  1. Added Clear button to vocabulary browser query form to clear contents of term field (cuator request).
  2. Institution name is now optional when submitting feedback.

Jul 19, 2005 (rev 1317)

  1. Optimized queries to find root nodes of chemical and taxon hierarchies.
  2. Updated data model documentation to reflect new hierarchy-related constraints.

Jul 14, 2005 (rev 1313)

  1. Major release.
  2. Non-sequence-based references are now included. Genes may now be assigned directly to references (with a chemical).
  3. Gene name vocabulary improved by relying primarily upon human nomenclature and by doing some data cleaning from source records.
  4. Personal communication references are now included along with journal articles.
  5. Created new mechanism to assign CTD accession identifiers. Currently used only for personal communication references.
  6. New Cited Genes section of reference detail displays genes related to the reference, either through a sequence (with chemical) or directly (with chemical).
  7. Popular Terms are now highlighted in vocabulary browsers to speed access.
  8. Visitors may now search any of the three vocabularies from the vocabulary browser.
  9. Chemical descriptions (i.e., MeSH Scope Notes) are now displayed on chemical detail pages.
  10. Gene Set, reference and sequence detail pages have been replaced with more mature architecture using J2EE design patterns (Front Controller, Data Access Object and Value object). Error reporting has been improved, and a common error page added.
  11. Several of the most recently viewed sequence details, reference details and Gene Set details are now cached in memory.
  12. Sequence and reference details can now be accessed by GenBank, SWISS-PROT, PubMed and CTD accession IDs, as appropriate. Lesson: Expose only stable identifiers, even if not our own, for accessing objects.
  13. On taxon detail pages, animal image now corresponds to the subject of the page (if an image exists for that taxon).
  14. Improved response time of some chemical and GO queries. Lesson: it is slower in Oracle to feed the query a list of prefetched IDs than to feed the query the initial subquery.
  15. Improved error reporting on vocabulary detail pages, including new common detail error page.
  16. Reference and Sequence Detail pages now have more informative titles.
  17. Updated help pages.
  18. Revised data diagram to reflect the expanded data model.
  19. Added new CTD resources page with link to newly published data model documentation.
  20. Removed Jobs links.
  21. Moved personnel list to its own page. Email links added for key personnel.

Mar 1, 2005

  1. Enhanced logging capabilities to better detect and fix problems.

Feb 22, 2005

  1. For Chemicals in the News, chemicals with recent news items are now flagged.
  2. Chemical news items created within the last 7 days are now flagged.

Feb 17, 2005

  1. Vocabulary Browser queries that match only one term are redirected (rather than forwarded) to term detail page: makes it easier to bookmark, and should eliminate some errors caused by improper bookmarking.
  2. Some query terms triggered ugly Oracle Text errors because they would return too many results. Those are errors are now logged but hidden from visitors (they will simply get 0 results).

Feb 16, 2005

  1. Made error messages more informative.
  2. To prevent database errors in queries, words must now be at least 4 characters to qualify for stemming expansion (used to be 3 characters).

Feb 9, 2005

  1. Gene Set Detail now returns more than twice as fast as before. Disabled disk-based caching of these pages.
  2. New Microarray Gene Expression report for chemicals.

Feb 8, 2005

  1. New cross-references to EDGE microarray expression data on Chemical and Sequence Detail pages.
  2. Fixed query bug in which GO or chemical queries that matched 0 items were not preventing other query components from returning results.

Feb 4, 2005

  1. Content served through servlets can now be compressed if the visitor's browser permits.
  2. Fixed bug in which non content-type headers were being sent with cached pages.
  3. Site Map: Added entry for Chemicals in the News.

Feb 3, 2005

  1. Added explanation to Help for inferred links between protein seqs and ref seqs.
  2. Clarified description of what sequences are included in CTD.
  3. Updated MDIBL jobs link to point to new MDIBL page.

Feb 2, 2005

  1. Lightened background color of certain table headers.
  2. Sequence and reference results, sequence, reference and Gene Set detail pages: Links to NCBI taxonomy replaced with links to CTD taxon details. GO ontology codes now color-coded.
  3. Sequence Detail: Added encoded sequences to coding sequence section.
  4. Sequence Detail: Added "inferred" links between RefSeqs and protein seqs.
  5. Overview page: Removed picture of MDIBL.

Jan 31, 2005

  1. Made email signup on home page more prominent.

Jan 28, 2005

  1. Home Page: Added another data disclaimer.
  2. All servlets now accessed with .go URL suffix. Lesson: When mapping URLs to servlets, use a common suffix to allow configuration settings, filters, usage tracking analyses, etc. to be applied to them.

Jan 25, 2005

  1. Added new page listing all chemical news links.
  2. Home Page, Chemical Detail Pages: New links to topical news items about chemicals.
  3. Query forms: Clear button always appears, rather than just after queries.
  4. IE/Win was displaying some XML escapes incorrectly. Changed method call to escapeHtml instead.

Jan 18, 2005

  1. Gene Set Help: Added description of the Gene Set curation process.

Jan 14, 2005

  1. Taxon Vocab Browser: Now uses normalized table of label types for improved display.
  2. Home page questions now highlight specific query form labels on query form pages.
  3. Home page: reformatted and streamlined right (news) column.
  4. Various text tweaked in answer to frequently asked questions.

Jan 13, 2005

  1. Query Forms and Vocabulary Browsers: Now filter certain parameters to avoid problems caused by improperly rewritten URLs.
  2. Added keyword metatag for better search engine visibility.

Jan 11, 2005

  1. Gene Sets page: Added text stating total # of genes curated. Changed table column header to 'Included Genes'.
  2. Taxon Vocabulary Browser: Label types now capitalized correctly.

Jan 6, 2005

  1. Vocabulary Browsers: Most recently viewed terms are now cached in memory for better performance.
  2. Gene Set detail: Pages now cached on disk for several hours to improve performance.

Jan 5, 2005

  1. Homepage: Shrunk data category diagram and reconfigured text to reduce vertical length of the page.
  2. Gene Set detail: New link to references that cite chemicals for each gene + taxon set of sequences.
  3. Various internal code, HTML and CSS improvements and refactorings.
  4. Labeled (in HTML title attributes) all links that open in popup windows.