BridgeDb
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bridgedb
The BridgeDb Library source code
Dear all, I propose you to integrate AlphaFold predictions into WP potentially using the https://alphafold.ebi.ac.uk/ server. I think this would be very valuable for pathway curation and analytics to gain...
Currently, users of the webservice have to guess which data source has attributes, see these two issues: * https://github.com/bridgedb/bridgedb-webservice/issues/1 * https://github.com/bridgedb/BridgeDbWebservice/issues/3 It would be nice of the Properties returned by...
... and ideally to all SHOULD too. See https://bestpractices.coreinfrastructure.org/en/criteria/0
It would be useful to have a function that when called returns the contents of `datasources.tsv` so users can see which data sources are available to use for mapping off...
scenario with [coursier](https://get-coursier.io/) (no Debian/Ubuntu package?): ``` curl -fLo cs https://git.io/coursier-cli-"$(uname | tr LD ld)" chmod u+x cs export COURSIER_REPOSITORIES="ivy2Local|central|http://maven.restlet.org/" ./cs bootstrap --standalone -o org-bridgedb-server-3.0.5 org.bridgedb:org.bridgedb.server:3.0.5 -M org.bridgedb.server.Server ```
When I tried to install bridgedb with groovysh `:grab`, I got the following error. ``` groovy:000> :grab 'org.bridgedb:org.bridgedb.bio:3.0.1' ERROR java.lang.RuntimeException: Error grabbing Grapes -- [unresolved dependency: commonj.sdo#commonj.sdo;2.1.1.v201112051852: not found] at...
have GdbConstructImpl3.createGdbIndices() report what it's doing when Exceptions happen internally
The error message occured when using the VariantCreatorv.1.1 on the datasets Missense and PTV_Missense at the very end of process. The other datasets went through without problems (Exonic, Polyphen, PTV)....
For reproducibility it would be interesting to have the possibility of obtaining the BridgeDb version and date of execution when performing a mapping. This could be added to /properties/ in...
The current output looks like: ``` DATASOURCEVERSION 85 DATATYPE GeneProduct SERIES Homo sapiens genes and proteins DATASOURCENAME Ensembl BUILDDATE 20161019 SCHEMAVERSION 3 ``` This may or may not comply with...
Currently the QC report is display by System.out.println, need a method with a return.
