intermine
intermine copied to clipboard
intermine
A powerful open source data warehouse system
at the moment we can set the reference sequence using only the organism, so we cannot accommodate different strains in the same mine for jbrowse. TODO: check the implications for...
we cannot link the evidence to the ontology term, see https://github.com/intermine/flymine-bio-sources/blob/c3ab7880a54d79d59a857e00954a4ba257aa04c3/flybase-alleles/src/main/java/org/intermine/bio/dataconversion/FlybaseAllelesConverter.java#L101
At the moment the default input it's in json (which doesn't work). It works with XML
as noticed by Marc Perry, the interaction widget truncate the date view to reproduce take for example the public list https://www.humanmine.org/humanmine/bagDetails.do?scope=all&bagName=PL_DiabesityGWAS_pval-4 the interaction count is out of view.
Chatting with @kkarra, she reported that sometimes BlueGenes would go down when using the gradle target `bluegenesstart` - let's set up versions of our own for flymine and/or humanmine and...
Genes are displayed as feature densities which looks a bit odd (not sure where the density part is coming from). See mouseMine for example of how they should look.
This is the error ---- Error Found ---- java.lang.RuntimeException: Error retrieving the shared bags for the user : 6007978at org.intermine.api.bag.SharedBagManager.getSharedBags(SharedBagManager.java:196)at org.intermine.api.bag.BagManager.getBags(BagManager.java:393)at org.intermine.api.bag.BagManager.getCurrentBags(BagManager.java:410)at org.intermine.api.query.PathQueryExecutor.makeQuery(PathQueryExecutor.java:154)at org.intermine.api.query.PathQueryExecutor.execute(PathQueryExecutor.java:96)at org.intermine.web.fair.SemanticMarkupUtil.getDatSets(SemanticMarkupUtil.java:125)at org.intermine.web.fair.SemanticMarkupUtil.getDataCatalogMarkup(SemanticMarkupUtil.java:191)at org.intermine.web.struts.BeginAction.markupHomePage(BeginAction.java:244)at org.intermine.web.struts.BeginAction.execute(BeginAction.java:180)at org.apache.struts.action.RequestProcessor.processActionPerform(RequestProcessor.java:425)at org.apache.struts.action.RequestProcessor.process(RequestProcessor.java:228)at...
Update all the core data sets URLs. Tell @danielabutano. This URL will be used when generating JSON-LD. It's not the download location, but instead the home page for that project....
These new data types are in the ncbi human gff file. We have not loaded for now, but could look at where they fit into the model: epigenetically_modified_region enhancer_blocking_element response_element...