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Xenbase Release Notes

Release 4.4.0

  • Visualization for tropicalis TPE data
  • Visualization for laevis tissue data
  • Gene-specific JBrowse links on gene pages
  • Gene expression search results can be downloaded
  • Bug fixes

Release 4.3.1

  • JBrowse beta links
  • Bug fixes

Release 4.3.0

  • Added gene interaction visualization
  • Added RNA-Seq stage expression graphs
  • OMIM references in articles are displayed
  • Recent articles added to Xenbase are displayed on landing page
  • Article information now includes references
  • Auto-suggest support for gene expression search's experimenter field
  • Bug fixes

Release 4.2.0

  • KEGG terms added
  • GO Terms updated and a gene page tab added
  • Added ability to search for GO terms
  • XAO updated to version 5.0
  • Separated UniProt IDs to Swiss-Prot and TrEMBL
  • Added ability to BLAST sequences within GBrowse
  • Bug fixes

Release 4.1.1

  • Bug fixes

Release 4.1.0

  • Added link to mouse pages on Allen Brain Atlas
  • Added BLAST page for Xenopus Mitochondrial genomes
  • Xenbase now supports gene page URLs using gene symbols (e.g. geneSym=pax8 instead of geneId=483692)
  • Bug fixes

Release 4.0.0

  • Extensive gene page additions and corrections
  • Added laevis 9.1 genome
  • GUI updates
  • Bug fixes

Release 3.11.2

  • Added Veenstra Lab UCSC track hub

Release 3.11.1

  • Bug fixes

Release 3.11.0

  • Gene pages now contain the corresponding transgene links
  • Stockcentre line, transgene, and strain names are displayed in the correct format
  • Antibodies can now be assigned RRIDs
  • Image curation enhancements
  • Reformatted "Cite Xenbase" page
  • Bug fixes and enhancements

Release 3.10.0

  • Xenbase accession strings can be used to search for Stockcentre Transgenes, Lines, Strains, as well as ORFeomes
  • Moved some Expression URLs from the Summary tab to the Expression tab
  • Added links to expression profile data from Owens, Blitz et al. 2016.
  • All options are now enabled for Gene search
  • Enhanced gene search in the upper-right hand minibar, including search for genes with a "+" in the symbol
  • Bug fixes and enhancements

Release 3.9.0

  • Added laevis- and trop-specific XenMine URLs
  • Removed inbred generation and geo origin from srockcentre lines
  • Added lab of origin, RRID, and catalogue number to stockcentre lines
  • Bug fixes and enhancements

Release 3.8.0

  • Added IMPC mouse phenotype gene page links
  • Added PANTHER GO search links on gene pages
  • Added XenMine links on gene pages (Data Mining section)
  • Reformatted stock centre search and display
  • Bug fixes and enhancements

Release 3.7.0

  • Added fruit fly and worm ortholog links on gene pages
  • Added XenMine links on the landing page
  • Added GeneCards to the list of human MODs
  • Added MalaCards, OMIM, DECIPHER, and KEGG Disease phenotype search links on gene pages
  • Added Ensembl, Protein Atlas, Allen Brain Atlas, and Eurexpress links to the new ortholog "Gene Expression" column on gene pages
  • Added Ensembl tropicalis link to gene pages' "expression" section
  • Replaced gene page phenotype links for ZFIN (broken) and MGI with symbol search links
  • Bug fixes and enhancements

Release 3.6.2

  • Bug fixes and enhancements

Release 3.6.1

  • Revised "Genomes" and "Download & Submit Data" menus
  • Bug fixes and enhancements

Release 3.6.0

  • More updates on the FTP landing page
  • Added New Genomes! Xl9.1, Xl mitochondrial, Xt9.0
  • Updated ORFeome search and search results
  • Bug fixes and enhancements

Release 3.5.2

Release 3.5

  • Release of new feature ORFeome v1.0
  • Migration of NCBI E-utilities from SOAP to REST

Release 3.4

  • laevis-only genes now display on gene pages
  • Latest XAO update added

Release 3.3

Release 3.2

  • Upgraded object-relational mapping (ORM) layer from iBatis to MyBatis

Release 3.1

  • Improved image copyright handling
  • GEISHA orthology imported into database and added to gene pages
  • 10,000+ PubMed Central (PMC) article images added to Xenbase
  • OMIM disorders associated with Xenopus genes added to gene pages

Release 3.0

  • Redesigned site for improved look and feel
  • New site is now responsive to mobile devices
  • Added announcements carousel to landing page for promoting high impact Xenopus research, Xenopus researchers, and new Xenopus research technologies
  • Added antibodies database
  • New GBrowse server and software (2.55). New tracks added

Release 2.8

  • Added antibody pages and search interface
  • Added protein tab to gene pages
  • Summary images on gene page summary auto-rotate

Release 2.7

  • Added NCBI Entrez Gene ID as a searchable field for gene pages.
  • Links to the Ensembl and UCSC genome browsers added for each gene page, where applicable.
  • Gene page and clone page expression tab restructured. Expression images can now be sorted by various criteria, such as stage.
  • Added the ability to exclude anatomy terms from a gene expression search.
  • Added the ability to search clones by anatomy item.
  • Added search all option to the literature search, along with the ability to filter queries by date range.
  • Expression tab added to anatomy item pages, listing genes expressed in the tissue, along with expression sources.
  • Reagents and protocols menu added to the main Xenbase menu bar

Release 2.6.5

  • Implemented Textresso for Xenopus. Textpresso is a powerful text-mining system for scientific literature.
    • Search paper titles, abstracts, results, discussion,etc using keywords or phrases.
    • Selecting one or more Categories, which are pre-defined word-lists, increases the specificity of a search. Categories include Xenopus gene symbols and synonyms, the XAO, and GO terms.
  • Pages created for XAO anatomy items and development stages.
    • Includes a tab for displaying papers attributed to the XAO term via text matching.
    • Includes a wiki tab for users to submit content.
  • Xenbase secure login. Usernames and passwords are now encrypted when being sent from a user's computer to Xenbase.
  • An image voting system to score images based on image quality
    • To vote, click on an image of interest to bring up an enlarged view. Near the bottom of the popup are two icons, a thumbs up and a thumbs down, along with a comment box. Simply click one of the two icons to cast your vote. The user's choice is saved so it may be changed at a later date.
  • Created a data statistics page for Xenbase which lists counts for various data types by year.
  • Added a Sequence tab to gene pages which list associated mRNA and EST sequences.
  • Added new tracks to the Xenbase Genome Browser.
    • EcRs for mouse, zebrafish and chicken
    • Promoter regions for tropicalis
    • Xenopus tropicalis genomic fosmids
    • JGI 4.1 tropicalis gene and transcript model sets
  • Xenopus stage development time / temperature charts have been added.
  • Exact searches added for select literature queries.
  • Clone name searches will now except partial matches.
  • In the stockcentre, users can now copy a transgene under a new name.
  • Xenbase movies have been added to Youtube so they no longer have to be viewed in Quicktime.

Release 2.6.1

  • Ability to add, edit, and delete clones.
  • Stockcentre now supports transgenes.

Release 2.6

  • Xenopus wiki for community contributions of protocols, gene information, etc.
  • New version of Gbrowse (2.0.5) including tracks for: Unigene, Gurdon EST, cDNA clones and methylation
  • Clone vector pages, including the ability to search clones by clone ID
  • Clone, Vector and Library pages now have unique Xenbase accessions for searching
  • Old Xenbase and XMMR have been decommissioned.

Release 2.5.5

  • Search for clones via Gene symbol, NCBI accession, library name or clone name.
  • Search for gene expression patterns by sequence.
  • Search literature by Granting Agency or Grant Number
  • New Xenbase cDNA library pages accessible through clone pages and gene expression search results
  • Filter out ubiquitously expressed genes from gene expression search results
  • Include Anatomical successor and predessor tissues in gene expression searches involving anatomy terms

Release 2.5

  • Search Expression Patterns: Search Xenopus expression patterns by gene symbol, developmental stages, anatomical structures and experimenters
  • Search gene pages by NCBI sequence accession for mRNA, EST and protein.

Release 2.4

  • Search 'All': Search all of Xenbase from the minibar at the top of the screen
  • Search suggestion ability added to mini bar for searches in: gene, person, lab, organization, authors and titles
  • Expanded and updated Stockcenter for searching Xenopus frog lines
  • Faster BLAST searches and new search databases added
  • Faster gene 'Search All' searches
  • Search genes by Affymetrix probe ID
  • Ensembl models listed in gene pages and gBrowse
  • Gene page link to literature referencing 'morpholinos'
  • Gene expression images from AxelDB now available in the 'Expression' tab on gene pages
  • Added thousands of expression images from community labs: Zorn lab, Papalopulu lab
  • Over one thousand additional expression images automatically curated from literature sources

Release 2.3.1

  • Gene page interactants tab added. This tab lists genes that are co-cited in the literature for a gene of interest.
  • JGI Xentr4.1 filtered model transcript and protein databases are now available at the Xenbase blast site.

Release 2.3

  • Animal lines section added. This section provides information on frog lines currently carried by the European Xenopus Resource Center (EXRC).

Release 2.2

  • Gene pages are being populated with archetypal image(s) of gene expression patterns
  • New Expression tab on Gene pages
    • in situ images from XDB3 (presence of images is indicated by an icon on the Expression tab). Axeldb and community submitted images available soon.
    • Anatomy terms and stages (expression data derived from EST/cDNA library representation). This is available for most genes even when they lack images.
  • UniProt Knowledgebase links (alternative splicing information, protein domains and much more)
  • Microarray data from GEO - view array data where the gene of interest displays differential expression
  • Affymetrix probe sets for both trop and laevis
  • Gene search
    • Select number of results per page
  • Literature section
    • Publications with figures are flagged with a small icon. Load the paper to see the abstract, figures and legends, or click on the icon to see only the figures and legends.

Release 2.1

  • Dramatically faster gene search and gene pages
  • Literature tab added to gene page
  • In-line links from article abstracts, titles and image captions to gene pages
  • Improved gene search
    • Now search shows how results were found
    • New search by gene function

Release 2.01

  • Addition of 7,600 + Metazome-curated gene models.

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version: [4.4.0]

Major funding for Xenbase is provided by the National Institute of Child Health and Human Development, grant P41 HD064556