bridgedb/BridgeDb

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The BridgeDb Library source code

Stars: 37
Forks: 22
Open beginner issues: 0
Indexed issues: 32

Dominant language: Java
License: Apache-2.0
Last GitHub push: Aug 2, 2026
Latest indexed: Sep 14, 2026
Contributing guide: No contributing guide
Code of conduct: No code of conduct
Beginner labels: No beginner labels indexed
PR merge metrics: No merged PRs in 30d

Beginner friendly Everything

Open All

32 open issues indexed

Have the QC tool report on metadata alignment with DataCite Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

bridgedb/BridgeDb#243 · 1 comment · Opened May 16, 2024
factor out plugins into separate repositories Open

enhancement

bridgedb/BridgeDb#229 · 1 assignee · Opened Nov 4, 2023
Tool to convert a Derby file to a SSSOM file Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 20/100

bridgedb/BridgeDb#222 · Opened Aug 4, 2023
QC: test mapping files for expected databases Open

enhancement

bridgedb/BridgeDb#218 · 3 comments · 1 assignee · Opened Mar 8, 2023
describe data models on the website Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

bridgedb/BridgeDb#216 · Opened Oct 26, 2022
create VoID headers files default when saving and finalizing a Derby database Open

Difficulty 4/5 3-5 days Newbie friendliness 30/100

bridgedb/BridgeDb#210 · 1 comment · Opened Jul 12, 2022
Test failing org.bridgedb.rdf.identifiers.org.IdentifersOrgReaderTest #nwobridgedb Open

bug

bridgedb/BridgeDb#204 · 1 assignee · Opened Jul 7, 2022
Update readme Open

Difficulty 1/5 Under an hour Newbie friendliness 45/100

bridgedb/BridgeDb#198 · Opened Apr 19, 2022
Derby Properties should report which data source provides attributes Open

Difficulty 4/5 3-5 days Newbie friendliness 30/100

bridgedb/BridgeDb#186 · Opened Mar 24, 2022
Work through FLOSS Best Practices Criteria and comply to all MUST Open

NWO Open Science

Difficulty 5/5 Over a week Newbie friendliness 25/100

bridgedb/BridgeDb#176 · Opened Feb 17, 2022
Integrating information from AlphaFold Open

bridgedb/BridgeDb#175 · 2 comments · 1 assignee · Opened Jan 11, 2022
consider coursier to make binaries Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

bridgedb/BridgeDb#170 · Opened Sep 5, 2021
java.lang.RuntimeException on groovysh :grab Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

bridgedb/BridgeDb#169 · Opened Sep 2, 2021
Providing provenance information Open

Difficulty 3/5 1-2 days Newbie friendliness 45/100

bridgedb/BridgeDb#164 · Opened Jan 18, 2021
Function to obtain available data source with the package Open

enhancement

bridgedb/BridgeDb#159 · 1 comment · 1 assignee · Opened Nov 26, 2020
make a link to the Download page an icon on the front page Open

bridgedb/BridgeDb#106 · 2 comments · 1 assignee · Opened May 19, 2019
Database identifiers should be sorted by closest match Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

bridgedb/BridgeDb#97 · Opened May 1, 2019
BridgeDb tool to create linksets in a Wizard mode for use by biologists Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 15/100

bridgedb/BridgeDb#86 · 3 comments · Opened Jan 22, 2019
Search in PV with webservice doesn't differentiate between DataNode types Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

bridgedb/BridgeDb#85 · Opened Dec 22, 2018
Avoid returning `null`. Prefer `Optional` Open

bug enhancement

Difficulty 5/5 Over a week Newbie friendliness 25/100

bridgedb/BridgeDb#63 · 1 comment · Opened Nov 28, 2017
Tolerate loading empty linkset files into IMS Open

enhancement library

bridgedb/BridgeDb#62 · 19 comments · 1 assignee · Opened Nov 27, 2017
Compile fail on Travis due to ClassNotFound Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 25/100

bridgedb/BridgeDb#56 · 3 comments · Opened Sep 9, 2017
Secondary ID mapping service in Bridge DB Open

Difficulty 5/5 Over a week Newbie friendliness 20/100

bridgedb/BridgeDb#55 · 3 comments · Opened Sep 4, 2017
synergizer.jar and orthoxml-0.1b.jar are not open source Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

bridgedb/BridgeDb#53 · 2 comments · 1 reaction · Opened Aug 30, 2017
Preferred IRIs for Xref properties Open

question

Difficulty 5/5 Over a week Newbie friendliness 25/100

bridgedb/BridgeDb#38 · Opened Dec 14, 2016
set up ims.bridgedb.org Open

enhancement

bridgedb/BridgeDb#37 · 7 comments · 1 assignee · Opened Dec 4, 2016
Support Taxonomy for organisms? Open

question

Difficulty 5/5 Over a week Newbie friendliness 25/100

bridgedb/BridgeDb#34 · 3 comments · Opened Nov 17, 2016
compare metadata given for Derby files against FAIR expectations Open

enhancement library question

Difficulty 5/5 Over a week Newbie friendliness 25/100

bridgedb/BridgeDb#33 · 4 comments · Opened Oct 19, 2016
support for HDT-based mapping databases Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 20/100

bridgedb/BridgeDb#23 · Opened Dec 12, 2015
Massive duplication of datasources Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 20/100

bridgedb/BridgeDb#21 · 9 comments · 1 reaction · Opened Dec 9, 2015
hgnc identifiers - support with and without HGNC: Open

enhancement in progress

bridgedb/BridgeDb#15 · 6 comments · 1 assignee · Opened Sep 9, 2015
Add an output method that return the QC report as string or a outputstream Open

enhancement

Difficulty 3/5 1-2 days Newbie friendliness 35/100

bridgedb/BridgeDb#12 · Opened Jul 23, 2015

bridgedb/BridgeDb

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