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CTD Changes

Dec 29, 2006 (rev 2677)

  1. Removed accession IDs from vocabulary browser tree and query results displays.

Dec 28, 2006 (rev 2675)

  1. On chemical vocabulary pages, the number of descendant levels shown has been reduced from 3 to 2 in order to speed displays.

Nov 16, 2006 (rev 2619)

  1. Reference detail page now displays review status of the reference.
  2. Optimized metatags to help search engines.
  3. Tweaked Chems in News on homepage.
  4. Fixed icon issue in ancestor lists on chemical detail pages.

Nov 7, 2006 (rev 2611)

  1. Added NIEHS and NLM logos to footer.
  2. Reordered tabs on chemical and disease detail pages (and corresponding help pages).
  3. Minor code refactoring.

Nov 2, 2006 (rev 2599)

  1. Tweaked results status messages.
  2. Minor code optimizations.

Nov 1, 2006 (rev 2593)

  1. Refactored and optimized code that retrieves reference data.

Oct 31, 2006 (rev 2587)

  1. In back-end code, adjusted terminology for genes: names are now symbols, and full names are now names.

Oct 25, 2006 (rev 2577)

  1. Modified code to work with new GENE table columns and new GENE_LABEL type codes.

Oct 24, 2006 (rev 2571)

  1. Added print stylesheet for better printing of pages.

Oct 23, 2006 (rev 2562)

  1. Fixed broken evidence glossary links in interaction results.

Oct 20, 2006 (rev 2555)

  1. Fixed bug in accession ID queries.

Oct 19, 2006 (rev 2551)

  1. New interaction query.
  2. Increased speed of reference lists for chemicals, genes and sequences.
  3. Minor text revisions throughout site.

Oct 12, 2006 (rev 2513)

  1. In gene queries with interaction terms, disease, organism and GO query terms now used to winnow interactions.
  2. Query history list improved: all queries are now displayed in one, sortable list.
  3. Made more NLM-requested language changes.

Oct 11, 2006 (rev 2504)

  1. Language changes to satisfy NLM requirements.
  2. Removed journal, volume and first page fields from reference query form.

Oct 4, 2006 (rev 2492)

  1. Removed Gene Set displays from gene query results and seq detail pages.
  2. Minor formatting tweaks in sequence tables.

Oct 2, 2006 (rev 2477)

  1. Replaced main navigation tabs with CSS-based version.

Sep 29, 2006 (rev 2472)

  1. Removed Gene Set field from gene query.
  2. Updated help documentation.

Sep 28, 2006 (rev 2458)

  1. Feedback form now validates the subject to prevent some spam.
  2. Removed some table-based formatting from headers.
  3. Fixed some table formatting issues for Opera and IE/Mac browsers, and optimized some styles for all browsers.

Sep 27, 2006 (rev 2440)

  1. Reformatted descendants table on vocabulary term details and vocabulary start pages--tighter display and wraps better.

Sep 26, 2006 (rev 2436)

  1. Misc formatting tweaks and fixes.
  2. Display external database abbreviations (if they exist) rather than names.

Sep 25, 2006 (rev 2426)

  1. New disease icon indicates genes that have related diseases.
  2. Reformatted gene and chemical query results pages to better highlight related data icons.
  3. Fixed headers of sortable tables to prevent text from hiding sort arrows.

Sep 22, 2006 (rev 2413)

  1. Streamlined display of GO term lists on disease gene pages.

Sep 21, 2006 (rev 2410)

  1. Consolidated TOXLINE Core and Special links from chemicals.

Sep 19, 2006 (rev 2406)

  1. Fixed bug that prevented proper rendering of results tables in IE.

Sep 18, 2006 (rev 2404)

  1. Integrated human disease vocabulary: new disease vocabulary browser, new detail pages, new ability to query genes by disease.
  2. Updated data model documentation.
  3. If user goes to invalid gene URL, a gene query is invoked instead to try to find relevant the relevant gene.

Sep 7, 2006 (rev 2337)

  1. Integrated new gene vocabulary (from NCBI gene).
  2. Added NCBI Gene IDs and links to NCBI Gene on main gene detail pages.
  3. Updated help text to reflect new gene vocabulary from NCBI.
  4. For tabular reference lists, cited genes and/or chemicals now appear in the exported files.

Aug 23, 2006 (rev 2267)

  1. Reversed order of References and Chemicals tabs. Revised help pages and site map accordingly.

Aug 21, 2006 (rev 2260)

  1. Default query results per page is now 50 rather than 25.
  2. On gene query results, no longer display "Unassigned" if there is no Gene Set assigned to a gene.
  3. Funding acknowledgements moved from footer to new funding page. Updated to reflect new R01 grant.
  4. Gene detail page titles now use both gene name and full name.

Aug 11, 2006 (rev 2250)

  1. Minor UI bug fixes.

Aug 10, 2006 (rev 2246)

  1. Added no-chemical-sales disclaimer to Basic Info section of chemical detail pages.
  2. Added ontology name to Basic Info section of GO detail pages.

Aug 9, 2006 (rev 2239)

  1. Added ontology names to GO browser query results.

Aug 8, 2006 (rev 2237)

  1. Tweaked and optimized results-paging systems.

Aug 7, 2006 (rev 2234)

  1. Fixed bug in item numbering on reference results pages.
  2. Conformed all results-paging systems to work similarly.

Aug 2, 2006 (rev 2220)

  1. Made reference lists easier to scan.
  2. Condensed reference citations in interaction lists.
  3. Upgraded Javascript tooltip library and log4J library.
  4. Question marks now ignored in CONTAINS queries.

Jul 26, 2006 (rev 2207)

  1. Tweaked data table styles to reduce whitespace around data.
  2. Other style adjustments, especially to data tables.

Jul 24, 2006 (rev 2194)

  1. Fixed broken organism links in microarray report on gene detail pages.

Jul 21, 2006 (rev 2188)

  1. Some large gene and chemical datasets no longer cached to prevent server crashes.
  2. Improved format of exportable reference list files.
  3. Added exportable reference list to sequence detail pages.

Jul 20, 2006 (rev 2179)

  1. Tweaked formatting of results paging links on query results pages.

Jul 19, 2006 (rev 2174)

  1. Top Interacting Gene/Chem charts now have a minimum x-axis range of 0-20 for easier comparisons.
  2. Improved error icons.

Jul 18, 2006 (rev 2168)

  1. Added Excel/CSV export capabilites to reference lists on gene and chemical details.
  2. Reversed colors of hover and current sub-navigation tabs.
  3. Misc. formatting tweaks.

Jul 14, 2006 (rev 2158)

  1. Added tab interface for gene, reference and chemical detail pages.
  2. Revised page sub-headers style.
  3. Added Top Interacting Genes chart on chemical detail pages.
  4. Added Top Interacting Chemicals chart on gene detail pages.
  5. Made usability enhancements to reference query form and feedback form.

Jun 30, 2006 (rev 2128)

  1. Removed synonym list from Gene section on sequence detail pages.
  2. Commas in author searches are now removed.
  3. Interacting Gene/Chemical lists are now exportable to Excel/CSV.

Jun 29, 2006 (rev 2121)

  1. Fixed issue in which chemical detail pages were not able to link to interaction sub-pages if the acc param was not specified (e.g., if the user came from Google).

Jun 28, 2006 (rev 2119)

  1. MeSH UI parameters for chemical detail pages no longer case-sensitive.
  2. Added links to page top in appropriate headers.
  3. Fixed error that prevented contains searches containing '{' or '}'.
  4. Fixed minor formatting issues with reference, interaction summary and interaction tables.
  5. Reduced font size of some headers.
  6. Fixed typo in sequence detail page links.

Jun 23, 2006 (rev 2098)

  1. Increased maximum memory use by Tomcat from 256M to 1G.
  2. Increased maximum number of database connections from 12 to 15.
  3. Decreased number of detail pages to be cached.
  4. Stopped logging of 404 errors in Tomcat log.
  5. Removed configurable FROM clause from user queries (was never used).

Jun 22, 2006 (rev 2090)

  1. Added ANY search option for interaction types.
  2. Improved and adjusted order of query term displays to match (more closely) the query forms.
  3. Made substantial speed improvements in Java code for some queries.
  4. Reduced size of some detail page caches.
  5. Adjusted some headers in error pages.

Jun 19, 2006 (rev 2061)

  1. Fixed not-found query messages for GO and taxon terms.
  2. Fixed spacing issues between page headers, page navigation and first contenent.
  3. Shortened tables of contents on detail pages.
  4. Chemical vocabulary is now the default if the voc param is not specified in the voc browser.

Jun 16, 2006 (rev 2052)

  1. CTD 1.3 released.
  2. Curated chemical-gene and -protein interactions are now included. They are searchable from gene and reference queries, and displayed on gene, reference and chemical detail pages.
  3. Gene query terms are now highlighted.
  4. Organism query terms are now highlighted if a curated interaction search was done.
  5. New References and Cited Chemicals section on chemical detail pages.
  6. Long chemical names now wrap better in most browsers.
  7. Expanded Glossary with action vocabulary.
  8. Updated help pages.

Mar 31, 2006 (rev 1820)

  1. Removed all references to CTD being a prototype.
  2. Updated personnel list.

Mar 22, 2006 (rev 1812)

  1. Unicode characters are now handled correctly, both for querying and display.

Mar 21, 2006 (rev 1808)

  1. Added reference curation request subject to feedback page.
  2. Fixed margins around subscription form on homepage.
  3. Internal code refactoring.

Mar 20, 2006 (rev 1803)

  1. Chemical detail pages now accessed via MeSH Unique Identifiers in URLs rather than chemical name. MeSH UIs are more stable.
  2. Vocabulary detail pages now share same code framework as other detail pages.

Mar 9, 2006 (rev 1780)

  1. Moved sequence detail pages into Genes section.
  2. Added you-are-here icon next to current page in sub-navigation bar.
  3. Added note to feedback page: we do not sell chemicals.

Mar 8, 2006 (rev 1774)

  1. On reference query results and reference detail pages, genes that match the query are now highlighted.

Mar 2, 2006 (rev 1765)

  1. Tweaked text about interactions on home and overview pages.

Mar 1, 2006 (rev 1763)

  1. Enhanced query logging to track execution time of each query.

Feb 21, 2006 (rev 1758)

  1. Evidence codes replace evidence descriptions. Codes are marked up in a standards-compliant and backwards-compatible way, with tooltips and links to the glossary page providing their meaning.
  2. New glossary page.
  3. Removed preliminary list of chemicals from Chemicals in the News page (was unnecessary and confusing).

Feb 6, 2006 (rev 1738)

  1. Improved site map.
  2. Reordered sub-navigation bar items for Chemicals section.
  3. Improved compatibility of XHTML with DOM scripting.

Feb 2, 2006 (rev 1721)

  1. Gene and reference contains queries by gene, chemical, GO, organism, and author will now return results when query term match a previous 'stopword'.

Feb 1, 2006 (rev 1719)

  1. Revised order of fields on query forms to put Chemical first.
  2. EDGE links now always lead to pages with data results.
  3. Improved compatibility of XHTML with DOM scripting.

Jan 30, 2006 (rev 1714)

  1. Tweaked text on introductory help page.

Jan 26, 2006 (rev 1710)

  1. Modified feedback page to (try to) block some of the form spam that we've been getting. Also fixed bug that prevented messages from being logged in database.

Jan 24, 2006 (rev 1707)

  1. The last results per page selection for any query is stored in the visitor's session and used in subsequent queries until changed.
  2. Misc. JavaScript optimizations.
  3. Removed 'top' links from every chemical header on chemical news page.
  4. Removed page top links from footers.

Jan 20, 2006 (rev 1696)

  1. Fixed bug in reference and gene queries that returned incorrect results when certain combinations of fields were used.
  2. Fixed bug in vocabulary selection browsers that prevented communication between query form and browser.
  3. Fixed missing scrollbars in sequence popup windows.

Jan 19, 2006 (rev 1692)

  1. Fixed reference, gene, sequence and vocabulary query bug in which strings of spaces were not being trimmed.
  2. Improved separation of JavaScript from content for help links.

Jan 12, 2006 (rev 1685)

  1. Improved headers of sequence tables.
  2. Differentiated tree icons on Gene Set detail pages.

Jan 11, 2006 (rev 1681)

  1. Internal code optimizations.
  2. Fixed occasional formatting issues on gene GO detail page.

Jan 10, 2006 (rev 1675)

  1. Improved navigation between GO browser trees.
  2. Updated data model documentation.

Jan 6, 2006 (rev 1667)

  1. Internal code optimizations in vocabulary browsers.