BioDataFuse

Use case and database selection Open

good first issue

BioDataFuse/biohackarvix-2025#1 · 2 comments · 0 reactions · 2 assignees · Indexed Sep 14, 2026

Schema analysis and shape extraction Open

help wanted

BioDataFuse/biohackarvix-2025#2 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026

Define intermediate object model for shapes Open

help wanted

BioDataFuse/biohackarvix-2025#3 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 14, 2026

Define requirements to map data and object properties and data types Open

help wanted

BioDataFuse/biohackarvix-2025#6 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 14, 2026

Goals for midterm presentation Open

Reporting

BioDataFuse/biohackarvix-2025#7 · 0 comments · 0 reactions · 2 assignees · Indexed Sep 14, 2026

Write BioHackrXiv Open

Reporting

BioDataFuse/biohackarvix-2025#9 · 1 comment · 0 reactions · 2 assignees · Indexed Sep 14, 2026

JS to manipulate rdf-config model svgs Open

BioDataFuse/biohackarvix-2025#10 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 14, 2026

Identify use cases from available SSSOM mappings Open

BioDataFuse/biohackarvix-2025#11 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 14, 2026

Update UI based on updates in package Open

update required

BioDataFuse/biodatafuseUI#1 · 1 comment · 0 reactions · 1 assignee · Indexed Sep 14, 2026

Update UI docker Open

update required

BioDataFuse/biodatafuseUI#2 · 1 comment · 0 reactions · 1 assignee · Indexed Sep 14, 2026

DisGeNet Open

BioDataFuse/biodatafuseUI#8 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026

Bgee Open

BioDataFuse/biodatafuseUI#9 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026

Clear the page when the input or request is changed in an earlier step Open

BioDataFuse/biodatafuseUI#10 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026

Clarify license/usage Open

BioDataFuse/biodatafuseUI#22 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026

RDF fixes Open

bug rdf

BioDataFuse/biodatafuseUI#23 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 14, 2026

Add a catalog with data source metadata Open

documentation

BioDataFuse/biodatafuseUI#24 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026

`QuotaExceededError` during /process Open

BioDataFuse/biodatafuseUI#25 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026

Silent mount aborts due to current out-in transition setup Open

BioDataFuse/biodatafuseUI#29 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026

Cytoscape view's _Download Style File_ not working (500) Open

BioDataFuse/biodatafuseUI#31 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026

annotator for chembl Open

new annotator

BioDataFuse/pyBiodatafuse#15 · 2 comments · 0 reactions · 1 assignee · Indexed Sep 14, 2026

visualizing publication data from wikiannotator Open

stats-visualization

BioDataFuse/pyBiodatafuse#17 · 2 comments · 0 reactions · 1 assignee · Indexed Sep 14, 2026

Support transcripts (Ensembl ID) as input Open

input type

BioDataFuse/pyBiodatafuse#21 · 2 comments · 0 reactions · 1 assignee · Indexed Sep 14, 2026

annotator for OrthoDB Open

new annotator

BioDataFuse/pyBiodatafuse#43 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 14, 2026

annotator for STITCH Db Open

new annotator

BioDataFuse/pyBiodatafuse#50 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026

enrich the metadata with the number of nodes and edges by each annotator Open

stats-visualization

BioDataFuse/pyBiodatafuse#53 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 14, 2026

annotator for LOVD Open

new annotator

BioDataFuse/pyBiodatafuse#58 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026

annotator for BioGRID Open

new annotator

BioDataFuse/pyBiodatafuse#59 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 14, 2026

annotator for Pathway Commons Open

new annotator

BioDataFuse/pyBiodatafuse#60 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026

annotator for HIPPIE Open

new annotator

BioDataFuse/pyBiodatafuse#61 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026

annotator for RDF Portal Open

new annotator

BioDataFuse/pyBiodatafuse#64 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026

pykeen Open

analyser

BioDataFuse/pyBiodatafuse#130 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 14, 2026

report on inputr with no ID mapping Open

bug enhancement

BioDataFuse/pyBiodatafuse#132 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 14, 2026

Integrating with transcriptomics efforts Open

analyser

BioDataFuse/pyBiodatafuse#134 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026

Adding new resource Pharos Open

new annotator paused/on-hold

BioDataFuse/pyBiodatafuse#135 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026

Preserve MoA field from source OpenTargets Open

enhancement rdf update annotator

BioDataFuse/pyBiodatafuse#168 · 0 comments · 0 reactions · 2 assignees · Indexed Sep 14, 2026

Preserve the MedDRA IRIs for Adverse Events when querying OpenTargets Open

enhancement rdf update annotator

BioDataFuse/pyBiodatafuse#169 · 0 comments · 0 reactions · 2 assignees · Indexed Sep 14, 2026

Include UniProt protein identifiers for each target gene Open

enhancement rdf

BioDataFuse/pyBiodatafuse#177 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 14, 2026

Changing Pubchem API calls with BridgeDB Open

biohack2024

BioDataFuse/pyBiodatafuse#188 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 14, 2026

add annotator for Orphanet (using their API) Open

biohack2024 new annotator

BioDataFuse/pyBiodatafuse#189 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026

Adding the license of the individual databases Open

enhancement

BioDataFuse/pyBiodatafuse#193 · 1 comment · 1 reaction · 0 assignees · Indexed Sep 14, 2026

Fix ShEx diagram Open

rdf

BioDataFuse/pyBiodatafuse#199 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 14, 2026

`NA`, `np.nan`, and `pd.NA` are not valid JSON standard, return `null` instead Open

bug update annotator

BioDataFuse/pyBiodatafuse#220 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 14, 2026

Document how to export `rdflib Graph`s Open

documentation

BioDataFuse/pyBiodatafuse#226 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 14, 2026

Compound list not generating an accurate graph Open

BioDataFuse/pyBiodatafuse#229 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026

StringDB not working with non-human data anymore Open

BioDataFuse/pyBiodatafuse#237 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026

Simplify WikiPathways property graph predicates to match schema Open

BioDataFuse/pyBiodatafuse#244 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 14, 2026

Implement better testing for `id_mapper` Open

id mapper

BioDataFuse/pyBiodatafuse#253 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 14, 2026

Add compoundwiki version info to metadata Open

BioDataFuse/pyBiodatafuse#269 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 14, 2026

CTD Open

enhancement

BioDataFuse/pyBiodatafuse#275 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026

Installation under python 3.12 Open

dependencies

BioDataFuse/pyBiodatafuse#278 · 1 comment · 0 reactions · 1 assignee · Indexed Sep 14, 2026

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