What's New
- July 18, 2007: FABLE release v3.1:
- Article Finder now allows users to customize article citation downloads by selecting only articles of interest.
- LitTrack now supports links for genes with positions on multiple chromosomes. (task 2525)
- Gene Lister downloads now include a Cytogenetic position column. (tasks 2584, 2640)
- LitTrack upgraded to version 162 of the genome browser source.
- Miscellaneous bug fixes and minor interface improvements.
(tasks 2400, 2541, 2566, 2588, 2595, 2600, 2602, 2605, 2608, 2610, 2614, 2618, 2631, 2636)
- June 4, 2007: FABLE release v3.0.1:
- Miscellaneous bug fixes and minor interface improvements. (tasks 2529, 2534, 2583, 2590, 2591, 2593, 2596,
2598, 2613, 2621, 2622)
- May 18, 2007: FABLE release v3.0:
- Major new feature: literature-enabled local mirror of the UCSC Genome Browser &mdash just
like the standard UCSC Genome Browser, but with a literature track
("LitTrack") that connects journal articles with the genome locations
of the genes referenced in the articles. Human assemblies are supported.
- New "Did you mean" feature for Gene Lister searches: when a query
returns no results, alternate spellings are suggested. This is not
yet implemented for the Article Finder.
- Faster searches due to updated hardware.
- Miscellaneous bug fixes.
Earlier Releases
- Jan 23, 2007: FABLE release v2.1 enhancements:
- New sort orders added or changed (task 1989):
- Renamed: 'First author, then relevance' (formerly called 'First author')
- Added: 'First author, then chronological'
- Renamed: 'Impact factor, then relevance' (formerly called 'Impact factor')
- Added: 'Impact factor, then chronological'
- Query speed increased for large result sets. (tasks 2000, 2365, 2367)
- Unicode (UTF-8) characters can now be included in Gene Lister search terms. (task 2244)
- When you click on a gene symbol link that opens to a list of gene
aliases, you can then click on one of the gene aliases to get a
relevant FABLE Article Finder search for that alias. (tasks 2264, 2332, 2354, 2356, 2367)
- The browser's back button now behaves as expected. (task 2395)
- Fixes to Internet Explorer 7 cosmetic issues. (tasks 2422, 2433)
- Miscellaneous bug fixes.
- Nov 3, 2006: FABLE release v2.0.2 includes bug fixes to the v2.0 (Oct 9) and v2.0.1 (Oct 27) releases.
- Multiple simultaneous browser tabs/windows now supported; cookies no longer required (task 2245)
- Page titles are now more descriptive (task 2272)
- Rare, minor errors eliminated (tasks 2293, 2323, 2327, 2329, 2321)
- Better error-checking (tasks 2330, 2331, 2320)
- Examples on home page improved (task 2313)
- Cosmetic improvements (tasks 2314, 2316, 2322, 2319)
- Oct 27, 2006: FABLE release v2.0.1 includes bug fixes to the v2.0 (Oct 9) release.
- Application memory on production tomcat server increased from 1GB to 2GB (task 2171)
- ERKV6 and a few other genes were showing up too often in gene lists due to inappropriately generic aliases (task 2195)
- FAQ improved (task 2222)
- Server output is now compressed, to speed up large downloads and page loads (task 2231)
- Data has continued to be updated with latest additions to MEDLINE
- Fixed incorrect help links in Gene Lister search bar (task 2252)
- Slightly faster page loads (fablescript.js no longer included twice) (task 2253)
- Fixed problem where #Articles links from Gene Lister results would take a long time and return 0 results for large numbers of articles (task 2257)
- Fixed problem where certain #Articles links would return 0 results very quickly (task 2275)
- #Articles links from the Gene Lister page now work much faster, although they are still too slow (tasks 2257, 2271,2265,2271)
- Better ability to handle simultaneous users (task 2259)
- MeshHeading QualifierName added to the Gene Lister database (task 2269)
- Cosmetic/usability improvements (tasks 2273, 2276, 2277)
- Search examples on home page are more clear (task 2283)
- Gene Lister download dropdown box now says "All genes" instead of "All articles" (task 2291)
- Acknowledgements page updated to credit open source software used (task 2295)
- Fixed bug where wrong results would be returned if the user did two GL queries, clicked the Back button, and then clicked on a #Articles link (task 2310)
- Fixed bug where 0 results would be returned if under certain conditions the user did a GL query and shifted to an AF query (task 2293)
- Oct 9, 2006: FABLE release v2.0 includes new features:
- New "Gene Lister" application allows users to create lists of
relevant genes from the biomedical literature by entering arbitrary
boolean keyword searches. You can find genes associated with drugs,
diseases, people, places, institutions, genes, proteins — any
text that occurs in the biomedical literature.
- Users can now view a list of all known synonyms associated with each
gene displayed in Gene Lister or normalized Article Finder results pages.
- Links to the Help and Overview pages now produce context-sensitive
highlighting to make it easier for users to find what they're looking
for.
- Users can now download single page results, no longer being
restricted to downloading the entire search results.
- Aug 10, 2006: FABLE release v1.1 includes data updates and bug fixes:
- FABLE now uses the May 29, 2006 MEDLINE®/PubMed® data (through file 06n0698).
- Alphabetic sort order is now improved, using a generic UNICODE collation order that is correct for most users of European languages.
- Some synonym-search queries, e.g. "TNPO3", were incorrectly not returning results due to a logic error.
- Some synonym-search queries, e.g. "C6orf71", were incorrectly not returning results due to case inconsistencies in the database.
- Apr 5, 2006: FABLE release v1.0 provides a way to search MEDLINE for human genes and proteins. Features include:
- Searching of MEDLINE abstracts for genes and proteins using exact string matching of words and phrases.
- Normalization of gene terms to identify mentions of genes using alternative names to the one used in the search.
- Paginated search results that display citations for articles matching the search terms.
- Citations hyperlinked to corresponding PubMed abstract displays for individual articles.
- Downloading tool that allows search results to be retrieved as XML, Excel, or CSV (comma-delimited text) files.
- Utility for sorting results:
- chronologically (most recent first)
- reverse chronologically (most recent last)
- alphabetically by author
- by relevance to the search terms
- by ISI journal impact factor
