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[INFO] Running org.bridgedb.rdf.identifiers.org.IdentifersOrgReaderTest init Looking for log4j.properties Unable to find /home/deniseslenter/git/BridgeDb/org.bridgedb.rdf/log4j.properties in local Directory No environment variable BRIDGEDB_CONFIG found No enviroment variable CATALINA_HOME found No directory found at: conf/BridgeDb at...
Several things on the gene mapping database: - [x] 1. Last version is from Sept. 2016, so a new version should be created (regularly). - [x] 2. On the website...
@egonw : the readme of this repo is very long, so I think it needs to be updated. I believe the section on "OpenPhacts" could be removed/added to an "outdated"...
This issue has been raised in the [PathVisio issue tracker](https://github.com/PathVisio/pathvisio/issues/89) by @egonw , but @mkutmon and me agree that it belongs here. Currently, the class freeAttributeSearch is used in PV...
Annotating a PW,I found out that some names for genes are very similar to (parts of) names of chemical compounds. And when performing a search from PV, I get all...
Moving [this issue](https://github.com/PathVisio/pathvisio/issues/48) from pathvisio github to BridgeDB. DeniseSl22 commented on Jul 31 Hi all, (again about the library, sorry about that ;)....) In the Pathvisio library, secondary identifiers of...
- Based on the expected databases in a mapping file (which are different for GeneProtein/Metabolite/Etc.), there should be an output which databases should be present in the mapping files. @egonw...
@tabbassidaloii and me have been checking the issues with the xref batch query. Issue reported by @egonw: ``` https://webservice.bridgedb.org/Human/xrefs/S/O14494?dataSource=L ``` this seems to ignore the ?dataSource=L parameter. Issue reproduced by...
Dear @hunterhacker , I just noticed these two warnings [here](https://mvnrepository.com/artifact/org.jdom/jdom2/2.0.6.1): 
Website link to explain rules for new terms didn't exist anymore (or was moved). Replaced with "submit term request"-site