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CTD Changes

Dec 22, 2004

  1. Gene Sets: Added intro text re: number of Gene Sets curated to date.
  2. Added newly created Gene Set phylogenetic tree.
  3. Gene Set phylogenetic trees have new footers.

Dec 20, 2004

  1. Chemical Resource Page: Fixed JavaScript error that occurred in some browsers.
  2. Gene Set Detail: Page title now contains only the Gene Set symbol, not the name. Name and symbol now shown in their own obvious rows.
  3. Reference Detail: Page title now includes first author and year.

Dec 15, 2004

  1. Query performance improved (using temporary workaround for Oracle bug).
  2. Author MATCH (=) searches with more than one word ('Smith J' or 'De Marco') now return correct results.
  3. Wildcards no longer automatically added to multi-word author queries in user interface (although still used in queries).
  4. Home page hews items having end times will now appear (until that end time occurs).
  5. Misc reformatting and CSS style optimization.
  6. All dates and years (incl. copyright) now dynamic.
  7. Added more swanky bookmark icon (favicon.ico).

Dec 9, 2004

  1. Capitalization of 10,000+ author names fixed.

Dec 8, 2004

  1. Site is now compliant with the XHTML 1.0 Transitional standard (with two minor exceptions necessary for compatibility with older browsers).

Dec 7, 2004

  1. Query Results: Added more prominent solicitation for feedback.

Dec 6, 2004

  1. Added personnel list.

Dec 2, 2004

  1. Enhanced user-friendliness of 404 (Not Found) error page.
  2. Added more required registered trademark symbols.
  3. Whether links open in new window or not is now consistent.
  4. Added markup to data tables for better accessibility.

Nov 19, 2004

  1. Added many more indications that CTD is a prototype.
  2. For the most part, external links no longer open in new windows (unless they are clicked in a Help popup).
  3. Publications: Added Selected Cross-Species Comparative Studies.

Nov 12, 2004

  2. Substance/Toxicant vocabulary renamed to 'Chemical'.
  3. Header, navigation bar and footer improved.
  4. About CTD section consolidated under Home navigation.
  5. New Privacy Policy approved by legal counsel.
  6. Legal disclaimer approved by legal counsel.
  7. Improved overall compliance with Section 509 accessibility requirements.
  8. New Gene Ontology vocabulary browser.
  9. New 403 (forbidden) error page.
  10. Home page: Now includes high-level data diagram, revised description and list of questions that CTD can answer.
  11. Home page news items now database-driven.
  12. Query logging now includes the number of times a unique query was submitted in a session.
  13. Enhanced performance of some queries.
  14. Sequence Query: GO sequence annotations now searchable by hierarchical GO terms and IDs.
  15. Sequence Query: Reformatted the query form to make more user friendly. New help icons.
  16. Sequence Results: Now displays GO terms assigned to each sequence.
  17. Sequence Results: FASTA-formatted sequences may now be downloaded directlyfrom this page.
  18. Sequence Detail: Organisms link to taxon detail page rather than new query.
  19. Sequence Detail: GO terms assigned to sequence are now displayed.
  20. Reference Query: Reformatted the query form to make more user friendly. New help icons.
  21. Reference Detail: Only 50 cited sequences are shown at a time. Users may page through the remaining sequences.
  22. Gene Set Detail: Now includes sequence alignments and phylogenetic trees.
  23. Feedback links are now more prominent throughout the site.
  24. Feedback is now saved in database.
  25. CTD email list is now announcement-only, and requires visitor confirmation before subscription.
  26. Email list subscription forms added to home page and feedback response page.
  27. Expanded Help content and revised older content extensively.
  28. Improved Help navigation features.
  29. Added Site Map.

May 18, 2004

  1. Query History is now database-driven.
  2. Duplicate queries (in the same session) are no longer logged and displayed.
  3. Refactored java classes to eliminate redundant query code. Query URLs changed.

May 4, 2004 (rev 21)

  1. When invoking a vocabulary browser from a query form select link, a vocab term query is no longer invoked if the parent query field field was blank.
  2. Gene Set list links temporarily directed to static Gene Set list instead of database-driven list (until the db is updated).

Apr 30, 2004 (rev 18)

  1. Survey: Made error message more explicit.
  2. Gene Set Detail: Fixed bug that caused sequence toxicant lists to be incomplete in some cases.

Apr 28, 2004

  1. Help Overview page: Fixed broken links to resource pages and added toxicants section.

Apr 26, 2004

  1. When users enter invalid username/password, a user-friendly message is now shown, with instructions on getting assistance.

Apr 22, 2004

  1. Query results and detail pages: Added highlighting to toxicants that match toxicant query terms.

Apr 20, 2004

  1. Gene Set detail now displays the number of sequences related to each included gene.

Apr 9, 2004

  1. For CONTAINS queries, no longer add stem operator to words that contain single quotes to prevent Oracle 29902 errors.
  2. Minor formatting tweaks and section name changes on Sequence Detail and Vocab Term Detail pages.

Apr 8, 2004

  1. Vocabulary Detail pages: Fixed bug that prevented older browsers from initiating related object search for terms that contain spaces.
  2. Vocabulary Detail pages: Added internal navigation links.
  3. Vocabulary Browser Queries: Terms that exactly match the query terms now appear first.
  4. Toxicant Detail Help: Fixed bug that displayed the incorrect databases.

Apr 5, 2004

  1. Sequence Results: New link to references that cite toxicants for each set of sequences.
  2. Sequence Results, Gene Set Detail, Reference Detail: Slight condensing of formatting in sequence tables.
  3. About CTD: Revised text.
  4. Vocabulary Browsers: Visitors may now trigger sequence or reference query by clicking object links.

Apr 1, 2004

  1. New Toxicants section of site with toxicant detail pages containing data and images integrated from TOXNET.
  2. New toxicant and taxon popup windows on query forms to assist in selection of query terms.
  3. Toxicants throughout site now link to toxicant detail pages rather than to MeSH.
  4. New Toxicant resources page.
  5. New Query History list to review past queries submitted (in the current session) and easily re-submit or revise any of them.
  6. Now possible to search by taxon ID and by toxicant node tree number.
  7. Increased comparative sequence query speed.
  8. Discontinued support for searches by MEDLINE ID since PUBMED no longer provides them.
  9. Reference Detail: Digital Object Identifier (DOI) of references now displayed (where available: 24,600 references), and used to provide link to full text article.
  10. Began transition from HTML 4 to XHTML 1.0 standards. Converted some formatting and structural markup to more standards-compliant forms.

Feb 6, 2004

  1. Entire application upgraded to the Java Servlet 2.4 and JSP 2.0 (including JSP Standard Tag Library (JSTL) 1.1) specifications, and ported to the new Tomcat 5.0.18 server.
  2. Reference Results: Added Genes and Cited Toxicants to result list. Made minor formatting tweaks.
  3. Sequence Detail: Fixed bug in which sequences and sequence feature translations could not be downloaded by browsers that accept GZIP encodings.
  4. Query Forms: Clear button appears only if user has done a search to avoid confusion over previous Reset and Start Over buttons. Updated Help.
  5. Minor formatting changes.
  6. Removed User Survey.

Jan 20, 2004

  1. For taxa, toxicants, genes, authors and journals, users now have choice between doing exact match (with optional wildcard) queries or contains queries that look for records that contain the words matching the query terms (or related stems).
  2. Author names now entered in just one query field rather than separate last name and initials fields.
  3. Wildcard automatically added to author initials so that, for example, 'boyer j' will match 'boyer jl'.
  4. Most query terms now re-displayed all-lower-case and, in some cases, with periods removed, to provide better clues about how searches work.
  5. Multiple space-separated AccIds may be entered in query forms.
  6. Revised help pages to correspond with the query changes described above.
  7. Additional Resouces Pages, SeqDetail page: new database abbreviation field displayed.
  8. 404 Error page: added friendly, helpful suggestions.
  9. Revised format of logged error messages.
  10. Application-scope variables for app URIs now set only once rather than once per page.