EMBL-EBI Phenotype Archive Release Notes Introduction ------------ The EMBL-EBI Phenotype Archive is an open source project to store, analyse and present genotype associated phenotypes information on the web. This project is currently funded by the NIH KOMP2 grant and supported by the IMPC consortium. The web application runs in a Java servlet container such as Tomcat. See our wiki at https://github.com/mpi2/PhenotypeArchive/wiki for more information. Getting Started --------------- You need a Java 1.7 VM or later installed and a servlet container. ================== Release 0.3.1 ================== Status ------ 26 November 2013 release. Detailed Change list -------------------- New features 1. phenotyping_center, parameter_name and procedure_name field added to experimental core 2. phenotyping_center field added to genotype-phenotype core 3. Link to graph display available for derived parameters Other Changes 1. Graph page can be requested per center 2. Phenotype association panel warning message changed on gene page 3. experimental core: camel case (i.e. parameterStableId) replaced with snake case (i.e. parameter_stable_id) Bug fixes 1. ENU link pops up misleading error message 2. Graph page bug when selecting an unknown parameter ================== Release 0.3.0 ================== Status ------ 22 November 2013 release. Detailed Change list -------------------- New features 1. Compute and display percentage of lines having a given phenotype Other Changes 1. Message displayed when data is missing from experimental core (graph) 2. Number of synonyms shown on phenotype pages limited by default 3. Title for graph page changed to include the parameter names 4. Disease facet moved up in search results Bug fixes 1. Image display issue for LacZ expression images 2. Breadcrumb for graph page fixed 3. Export from graph now work on multiple parameters 4. Fix link to diseases facet on breadcrumb from a disease page 5. "mortality/aging" phenotype facet fixed Known bugs 1. Error message on categorical graph pages 2. Link from phenotype page to MGI Phenotype browser is broken 3. Duplicate entries for procedures/pipelines ================== Release 0.2.9 ================== Status ------ 8 November 2013 release. Detailed Change list -------------------- New features 1. Documentation available from the webpages 2. Search by disease (new disease facet) based on PhenoDigm associations 3. Export disease information from search page 4. Derived parameter calculation Other Changes 1. Integration of PhenoDigm predicted information into Solr 2. Inferred MA terms associated to MP terms for images added to image Solr Known bugs 1. Some disease pages are broken ================== Release 0.2.8 ================== Status ------ 25 October 2013 release. Detailed Change list -------------------- New features 1. Scatter plot for time series and categorical charts 2. Unidimensional scatter plot displays points by dates Other Changes 1. Scatter plots for blood pressure graphs 2. MP accession removedd from Phenotype summary on gene page 3. All genotypes shown on high-level MP page 4. Associate MP terms to multiple parents in genotype-phenotype Solr core 5. EuroPhenome Project ID added to the genotype-phenotype Solr core 6. Scatter plots min and max across plots match 7. Allele accession available on charts 8. Phenotype MP term added to the table on the phenotype top level phenotype page Known bugs 1. Link back from image view on breadcrumb is broken 2. Data export broken on gene page 3. Data export broken on phenotype page ================== Release 0.2.7 ================== Status ------ 11 October 2013 release. Detailed Change list -------------------- New features 1. Gene symbol filter added on genotype table of phenotype page Other Changes 1. MP synonyms loaded in database to track obsolete MP terms ================== Release 0.2.6 ================== Status ------ 01 October 2013 release. Detailed Change list -------------------- New features 1. Multiple subfacet selection 2. Phenotype summary section under Phenotype association 3. High-level phenotype summary refresh phenotype call summaryn table 4. Bubble pop-ups Other Changes 1. Filter button next to phenotype call summary table removed 2. Phenotype call on same MP term but different genotype reported individually on phenotype call summary table of gene page 3. Phenotype and Anatomy search information generated from automated SLIM creation 4. Fix incorrect link from phenotype page to MGI phenotype browser 5. Add Parameter column to phenotype call summary table 6. REST API documentation page for experimental data access 7. Human ortholog title on search results Known bugs 1. Link back from image view on breadcrumb is broken 2. Data export broken on gene page 3. Data export broken on phenotype page ================== Release 0.2.5 ================== Status ------ 13 September 2013 release. Detailed Change list -------------------- New features 1. Anatomy facet based on MA ontology 2. Anatomy page prototype 3. Headline image from Sanger MGP on top of phenotype page 4. RESTful interface to serve experimental data (legacy data from EuroPhenome) 5. Anatomy search with sensory category (eye, ear, etc.) 6. Search by human orthologs (but not paralogs) Other Changes 1. Reduce font size of captions under images 2. Fix highlighted links in Gene facet when clicking on each subfacet in turn 3. Change text for preliminary data (pre_QC data) 4. Links on phenotype page from MGI MA ontology terms to anatomical terms 5. Fix error redirection when clicking on graph link from phenotype page 6. Fix links from page to image gallery, phenotypes ================== Release 0.2.4 ================== Status ------ 30 August 2013 release. Detailed Change list -------------------- New features 1. Anatomy facet based on MA ontology 2. Anatomy page prototype Known bugs 1. All links on gene facet are highlighted 2. Clicking on graph link from phenotype page redirect to error page ================== Release 0.2.3 ================== Status ------ 19 August 2013 release. Detailed Change list -------------------- New features 1. Use canvas version of Dalliance genome browser ================== Release 0.2.2 ================== Status ------ 22 July 2013 release. Detailed Change list -------------------- New features 1. Reverted Production/Phenotype status on top of gene page 2. Production/Phenotype status queried from Solr Allele core 3. Preliminary heatmap view based on phenotype status (from Allele core) 3. Filters on gene page to select high-level MP terms and program 4. Filters on phenotype page to select SOP parameters Known bugs 1. No export data from data tables on gene/phenotype page ================== Release 0.2.1 ================== Status ------ 12 July 2013 release. Detailed Change list -------------------- New features 1. Phenotype call summary objects returns p-value and effect size 2. RESTful interface to phenotype call summary added 3. Default value for p-value in the phenotype call summary table set to 1 4. Scatter plots introduced to display underlying data Data changes 1. EuroPhenome MP calls p-value and effect size stored Bug fixes 1. Download all results with correct phenotype status Other Changes 1. Wiki page create on github space 2. RESTful APIs documentation added to the phenotype archive Wiki ================== Release 0.2.0 ================== Status ------ 16 May 2013 release. Detailed Change list -------------------- New features 1. New MyDAS configuration to serve IKMC allele 2. Proxy rules changed to serve the phenotype archive (using /data) 3. Spring dependencies resolved at load-time with component scanning 4. 'Pre-QC' replaced with 'Preliminary' on the gene page 5. New version of the preliminary phenotype heatmap (1.2) 6. Interquartile Range (IQR) used to look at spread of the data (Q1 – 1.5×IQR and Q3 + 1.5×IQR) on the box-plot 7. Decimal precision on the graph set to 4f Data changes 1. MA term association to high-level terms updated 2. New SLIM generated for MP and MA terms Bug fixes 1. Dalliance pop-up location issue fixed 2. Download all results from the search page actually works now 3. Image count discrepancy on the result grid fixed 4. Fixes to suppress gene doc display ================== Release 0.1.9 ================== Status ------ 2 May 2013 release. Detailed Change list -------------------- New features 1. Pre-QC panel to display phenotyping in progress 2. ColonyStatus object to store production and phenotyping status 3. gene SOLR index updated to present phenotyping status information 4. gene subtype facet collapsed 5. phenotyping status facet added to the search facets 6. phenotyping status column added to the gene search result table 7. phenotyping status added on the gene page 8. phenotyping page refactored to use server side data 9. links to graph added to phenotype page for legacy data 10. add PhenotypeStatusDAO to fetch phenotyping status from the iMits BioMart 11. add 'liveSite' variable to add/remove features depending on live/beta Charts new features 1. p-value and effect size on categorical data 2. Categorical statistics and charts classes refactored Bug fixes 1. HTTPProxy fix for no proxy addresses 2. EUCOMMTOOLsCre (imits consortium) filter removed to display genes with no production status 3. Extra title displayed on graphs for one gender removed 4. shifted table under Pre-QC panel in IE fixed 5. Explore panel on the phenotype page display issue fixed ================== Release 0.1.8 ================== Status ------ 11 April 2013 release. Detailed Change list -------------------- New features 1. Back-end runtime exceptions propagated to the controller layer 2. Errors handled for biomart, solr and gene status 3. Search returns error message in ajax call which gets populated into table of results 4. Charts error handling added (for SQLException) 5. Links added for WTSI phenotypes on gene page not just EuroPhenome 6. Commons math package replacing BasicStats 7. Native SQL database statements to retrieve parameter data 8. Native SQL for stddev and mean functions used for unidimensional data stats retrieval 9. Added status parameter for IMPC status SOLR core 10. New database tables to capture the result of mixed model processing 11. Add methods for collecting unidimensional data records for processing 12. Lazy load biosamples from biomodels 13. Include equality operations on stat classes 14. Consolidate parameter DAO methods for statistical analysis Charts new features 1. Allele (e.g. tm1a) added to titles 2. Lines instead of curves for time series 3. y Axis scaled and min set to 0 4. Tables removed show highlighted rows on hover 5. Allele changed to gene in headers Bug fixes 1. HTTPProxy fix for no proxy addresses 2. Blank search/gene page 3. Phenotype calls with no allele on gene page 4. Remove unused SOLR cores (mgi, dasikmcalleles) ================== Release 0.1.7 ================== Status ------ 21 March 2013 release. Detailed Change list -------------------- New features 1. Pipelines/Procedures view by week of data 2. Procedures view has procedures with significant calls highlighted in red and linked to chart pages (charts come back for data if in database). 3. New layout at the top of Gene Details page to reduce top panel 4. Tables at bottom of categorical data transformed as per Terry's suggestions. 5. Export and print functionality to graphs added 6. Style changes to graph headers 7. css/js minified 8. Gene status subfacet renamed to 'IMPC status' 9. Gene status subfacet shown before gene type subfacet 10. Facet search speed improved Bug fixes 1. SOLR: Gene controller - Catch error when allele core fails Other Changes 1. Highcharts.org label removed from graphs 2. Highcharts license obtained 3. Auto-suggest disabled Known bugs ================== Release 0.1.6 ================== Status ------ 07 March 2013 release. Detailed Change list -------------------- New features 1. MGI marker cross-references served from back-end 2. SOLR urls in js and jsp configured in Maven 3. Procedure parameter units retrieved dimension by dimension 4. Categorical data charts implemented (bar plots) 5. Unidimensional data charts implemented (box plots, scatter plots) 6. Time-series data graphs implemented (first pass) 7. Mean and standard deviation for continuous data computed on the fly 8. IMPC gene status facet implemented and visible on search interface Bug fixes 1. IKMC allele picture displayed correctly in Internet Explorer 2. Fix link to Europhenome for zygosity on gene page Other Changes 1. IKMC js code updated from mpi2 GitHub repository 2. SOLR: gene and allele core created with DataImportHandler 3. SOLR: select method used across all facets 4. SOLR: gene status incorporated in gene core Known bugs 1. Auto-suggest box can remain empty 2. Auto-suggest box does not link to correct phenotype page 3. Display of facets and breadcrumb can be messy on Nexus 7 and iPad ================== Release 0.1.5 ================== Status ------ 25 February 2013 release. Detailed Change list -------------------- New features 1. Menu at the top of the dynamic pages pulled from Drupal (JSON stream) 2. Database genomic features updated to GRCm38 from JAX MGI 3. IKMC 38 alleles DAS track visible in genomic browser 4. GRCm38 gene models DAS track visible in genomic browser 5. Statistical page template built for categorical data Bug fixes 1. Remove locked genotype information associated to MGP pictures 2. Auto-suggest: fix a bug that shows the previous search in the search box Other Changes 1. Testing SOLR result ordering by relevance for the gene facet 2. Remove 'image annotations' from auto-suggest results ================== Release 0.1.4 ================== Status ------ February 2013 release. Contains bug fixes and implementation of features suggested by users. Detailed Change list -------------------- New features 1. Breadcrumbs on gene, phenotype and bio-imaging gallery pages 2. Bio-imaging gallery displays meaningful explanation of the query 3. Gene status on gene details page 4. Register interest/Unregister interest in a gene on a gene details page 5. Auto-suggest: clicking on auto-suggest redirect to relevant page 6. Resource oriented URLs: enable JSON/XML responses 7. Search URL changed (was searchAndFacet) to /search 8. Examples for search provided under the search box 9. Faceted search on sub terms (e.g. nervous, cardiovascular system) 10. 404 page layout changed 11. Invalid gene identifier on gene page redirect to error page 12. Invalid phenotype identifier on phenotype page redirect to error page 13. identifierError.jsp added to report invalid identifier (gene, phenotype) Bug fixes 1. Auto-suggest box fix on Drupal page 2. Image index: account for genes with no subtype association 3. Gene page: blank page with invalid identifier redirected to error page Other Changes 1. SOLR 3.6.3 in production 2. Upgraded MGI gbrowse view using gbrowse 2 on the mouse assembly 38 Known bugs 1. TSV/MS Excel download does not work on IE8 over HTTPS ================== Release 0.1.3 ================== Status ------ Also Known as the Toronto release. This is the first release of the PhenotypeArchive in GitHub. It contains several improvements and bug fixing based on user feedback. Detailed Change List -------------------- New features 1. faceted search on phenotype images (procedures, anatomy, phenotypes, genes) 2. consistent view of data across the site using the jquery data table 3. filtering of phenotype terms on the MP and gene page 4. data export in CSV and Excel format 5. annotation view of the image result 6. genotype information association to images 7. provenance associated to images 8. links to legacy data in the phenotype association panel of the gene page 9. ES Cell and Allele panel on the gene page 10. Work in progress notice for images 11. IMPC style reproduced (menu, orange bar) 12. syntax correction: procedures instead of protocols, using plural instead of singular 13. link to pre-QC data added when relevant 14. see the total number of results per facet by default on search page 15. Phenotype Archive distributed in GitHub Bug fixes 1. image metada properly displayed 2. correct zygosity stored and displayed Changes in runtime behavior 1. Java 7 2. Tomcat 7 Other Changes 1. Anatomy facet removed (will reintroduced it later) 2. Phenotype calls grouped by genotype (gender collapsed) ================== Release 0.1.2 ================== Status ------ Also known as alpha release. This release was presented to biologists. Detailed Change List -------------------- New features 1. a MP (Mouse Phenotype) page based on a SLIM of MP 2. Restful interfaces to the back-end 3. image display plug-ins 4. infinite scroll of images 5. responsive design using Twitter Bootstrap 6. image facet organized by experiments and by anatomy categories 7. other genotypes curated from the litterature (from MGI) in the "associated gene variant table" of an MP page 8. grid result page on the phenotype facet Bug fixes 1. see the same number of allele on the allele table as EuroPhenome 2. display a picture as a MP default representation at its best resolution 3. Ensembl compara links correspond to the same assembly used on IMPC website Other changes 1. bottom of gene result grid simplified 2. download gene list removed 3. number of second-tier categories in the phenotype facet reduced 4. search bar resized 5. explanation or error page in case of technical error 6. 5 first images per category for phenotype images or expression section on the gene details page 7. auto-suggest box stiched to the search bar when resizing the screen 8. "no image available-no metadata" suppressed ================== Release 0.1.0 ================== Status ------ This is the first release of the PhenotypeArchive at EMBL-EBI. Detailed Change List -------------------- New Features 1. Introducing the CHANGES file Other changes 1. URLs for MP and gene details pages have been refactored