Xenbase Release Notes

Release 6.5.0

• Updated XAO, XPO, XSMO, and XBED ontologies
• Beta release of Simple Synteny
• Bug fixes

Release 6.4.0

• RefSeq section added in gene page Nucleotide tab
• Enhanced color coding for better visualization in JBrowse tracks
• Bug fixes

Release 6.3.1

• Bug fixes

Release 6.3.0

• Beta release of JBrowse2
• Bug fixes

Release 6.2.0

• GEO data updated from 10.x genomes
• Revamped UIs for creating and editing labs, organizations, and jobs
• Bug fixes

Release 6.1.0

• Overhauled person registration code
• Bug fixes

Release 6.0.2

• Bug fixes

Release 6.0.1

• Bug fixes

Release 6.0.0

• Major genome annotation improvements
• New GEO JBrowse tracks for version 10.x genomes
• Enhanced integration of partially supported amphibian species
• Revamped Search Gene
• Updated and restructured application code for improved performance and efficiency
• Bug fixes

Release 5.7.0

• Added KEGG Pathway names
• Multi-mutant gene support for lines
• Bug fixes

Release 5.6.2

• Bug fixes

Release 5.6.1

• Bug fixes

Release 5.6.0

• Support for InterPro gene search
• Zahn drawings added
• Bug fixes

Release 5.5.2

• Bug fixes

Release 5.5.1

• Morpholinos aligned with laevis 10.1 genome
• Bug fixes

Release 5.5.0

• X. laevis 10.1 genome
• Bug fixes

Release 5.4.2

• Bug fixes

Release 5.4.1

• Bug fixes

Release 5.4.0

• laevis 10.1 support added to BLAST and JBrowse
• Bug fixes

Release 5.3.0

• Phenotype tab on gene pages
• Bug fixes

Release 5.2.0

• Gene pages allow adding, rearranging, and removing species
• Improved phenotype interface
• Bug fixes and GUI updates

Release 5.1.1

• GUI update
• Bug fixes

Release 5.1.0

• Support for guide RNAs (gRNA)
• Improved morpholino support
• Bug fixes

Release 5.0.0

• Phenotypes!
• X. tropicalis genome version 10.0
• Redesigned landing page
• Bug fixes

Release 4.16.1

• Bug fixes

Release 4.16.0

• Morpholino alignment support for X laevis 9.2 and X tropicalis 10.0
• Added support for Rat orthologs (RGD)
• InterPro links added to UniProt IDs on protein gene page tab
• Bug fixes

Release 4.15.0

• Xenopus Phenotype Ontology (XPO 1.0) released
• Simplified search for accession IDs (e.g. www.xenbase.org/entry/XB-GENE-483693)
• XAO updated to version 9.0
• Bug fixes and GUI updates

Release 4.14.0

• Added support for rat (RGD) orthologs
• Added UniProt terms to gene pages
• Added MARRVEL, gnomAD, orphanet, GTR, dbVAR, COSMIC, and GHR to external disease links
• Added laevis 9.2 and tropicals 10.0 tracks to GBrowse
• XSMO and XBED ontologies available for download:
• New data statistics
• Bug fixes

Release 4.13.1

• Improved GUI support for smaller screens
• Bug fixes

Release 4.13.0

• X. tropicalis 10.0 support added to BLAST and JBrowse
• Added CRISPRscan tracks to gene pages
• Added mutants to gene pages
• Bug fixes and GUI updates

Release 4.12.3

• Bug fixes

Release 4.12.2

• Bug fixes and GUI updates

Release 4.12.1

• XAO updated to version 8.0
• Bug fixes and GUI updates

Release 4.12.0

• GEO GSE visualization
• Bug fixes

Release 4.11.4

• Added genes and videos to Latest Xenbase Content list
• Bug fixes and GUI updates

Release 4.11.3

• New GEO GSE tutorial videos
• New Anatomy and Histology Atlas
• Links to EctoMap, Tail Regen @ Cambridge, and SPRING @ Harvard
• Bug fixes

Release 4.11.2

• New JBrowse tutorial video
• Support for HTTPS
• Bug fixes and GUI updates

Release 4.11.1

• XAO updated to version 7.0
• Bug fixes

Release 4.11.0

• GEO expression data and JBrowse tracks
• X. laevis protein expression profiles
• Bug fixes

Release 4.10.2

• Bug fixes

Release 4.10.1

• Added link to single cell data at SPRING
• Bug fixes and GUI updates

Release 4.10.0

• Added the gene expression summary bar
• Tree browsing added to Disease Ontology pages
• New JBrowse tutorial videos
• Bug fixes and GUI updates

Release 4.9.2

• Added tropicalis ORFeome
• Bug fixes

Release 4.9.1

• Added the disease search page
• RNA-Seq Profile and heatmap data can be saved as CSV files
• Bug fixes

Release 4.9.0

• Added support for Disease Ontology
• Added disease pages for Disease Ontology
• Added disease pages for OMIM
• Added BLAST support for tropicalis 9.1 mRNA, CDS and protein
• Bug fixes

Release 4.8.2

• Java upgrades
• Bug fixes

Release 4.8.1

• Added mouse and fish Alliance links on gene pages
• Whole gene and CDS sequences are now displayed on gene pages
• New Xenopus development movies
• Bug fixes

Release 4.8.0

• New anatomy and developmental stage trees
• Morpholino snapshots are now generated by JBrowse
• BLAST allows longer sequences
• Support for ILAR lab codes
• Support for alumni lab membership
• GUI updates
• Bug fixes

Release 4.7.1

• Bug fixes

Release 4.7.0

• Added gene co-expression and co-regulation graphs
• Added Perron Lab retinal screen images
• BLAST search results now point to JBrowse (instead of GBrowse)
• Other amphibians: Added Rana catesbeiana, Nanorana parkeri, and Ambystoma mexicanum genomes to JBrowse
• Added a BLAST page for the above frogs
• Bug fixes

Release 4.6.0

• Added experimental regulation visualization
• Reworked stock center lines and strains
• Added XLRRI (US) and CRB (Europe) stock centres to the list of vendors
• Added links to laevis 9.2 and tropicalis 9.1 genome assemblies and gene models. Both are BLAST'able
• Replaced GBrowse gene snapshots with Xenbase images
• Increased support for JBrowse
• Added counts for mutant lines and available jobs to the landing page
• Bug fixes and enhancements

Release 4.5.0

• Human physical gene interaction visualization
• Isoform data added to tropicalis TPE visualization
• Bug fixes and enhancement

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

• Updated FTP landing page for data downloads
• Bug fixes and enhancements

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

• Added new feature Morpholinos, a searchable database

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.