sergio contrino
sergio contrino
for humanmine: a query of the post process takes a long time ` 2022-02-17 07:39:38 INFO org.intermine.objectstore.ObjectStoreSummary [] Querying for empty: Substitution.overlappingFeatures 2022-02-17 17:52:33 INFO org.intermine.objectstore.ObjectStoreSummary [] - Query for...
while the psi-complexes source appear to be loaded correctly (no warning or errors), it actually loads empty records. not sure how long this is going on (certainly from humanmine 8)....
i tried to use pre-retrieve and retrieve (plus load) while building to avoid fetching again the publications.xml file. in all cases the process was starting building again the xml file....
various classes give error of the kind shown below. for some we probably should add the relevant configuration, but for some (author? location?) we should maybe not throw an error?...
after changing the url of esyn to the https one i.e. http://www.esyn.org -> https://esyn.rosalind.kcl.ac.uk the displayers (report page and list page) don't seem to work (see beta.humanmine) check with @rachellyne
from a support request human gene PTGR2 orthologue for D. rerio should be a LDO, not a O. source: ``` HUMAN|HGNC=20149|UniProtKB=Q8N8N7 DANRE|ZFIN=ZDB-GENE-050506-71|UniProtKB=X1WFL9 LDO Euteleostomi PTHR43205 ``` is marked as orthologue...
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
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.
this end point should work also with a 'give me all the features available' parameter (to avoid listing them in the request). Requested by Jalview.