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Curation of Neurodegeneration in Biological Expression Language (CONIB)

Home Page: https://pharmacome.github.io/conib

License: Creative Commons Zero v1.0 Universal

Python 0.07% Jupyter Notebook 99.93%

biological-expression-language biocuration networks-biology

conib's People

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sspalek sepehrgolriz mali-git sophiakrix scolby33 yojanagadiya kaziaa

conib's Issues

Cell paper reanalysis

Tau PTM Profiles Identify Patient Heterogeneity and Stages of Alzheimer’s Disease

Publisher Link | PDF Download

Investigate overlapping pathways between diseases

Find all genes related to each disease via annotations or association relationships
Run pathway enrichment analysis to identify pathways of relevance
Investigate if these annotations can be made at a document level?

Remove legacy namespaces from cdr_sb_associations.bel

conib/hbp_knowledge/biomarkers/cdr_sb_associations.bel

Lines 38 to 39 in 8d8f862

 DEFINE NAMESPACE SDIS AS URL "https://arty.scai.fraunhofer.de/artifactory/bel/namespace/selventa-legacy-diseases/selventa-legacy-diseases-20150601.belns" 

 DEFINE NAMESPACE MESHC AS URL "https://arty.scai.fraunhofer.de/artifactory/bel/namespace/mesh-chemicals/mesh-chemicals-20170511.belns"

Upgrade MESHC to MESH
Upgrade SDIS to HP, DOID, or EFO

Curate pickhardt2018 (pmid:30640040)

https://www.ncbi.nlm.nih.gov/pubmed/30640040

Add document level annotation transfer to pathway assignment notebook

If one node in an edge is part of a pathway, and that pathway has been mentioned in the same document (i.e., other edges from that document are annotated with that pathway), annotate the edge to that pathway.

Rebranding

This has sort of gone beyond the moniker of TauBase. Should this be NeuroMMSig?

Keep calling it TauBase, even though it's much more than just Tau/tauopathies
NeuroMMSig (but we need to maintain the difference between this work and AETIONOMY. NeuroMMSig can be pragmatic and pull in lots of sources)
Curation of Neurodegeneration in Biological Expression Language (CONIBEL) yeahh look at that acronym, just like CONSO

	DEFINE NAMESPACE SDIS AS URL "https://arty.scai.fraunhofer.de/artifactory/bel/namespace/selventa-legacy-diseases/selventa-legacy-diseases-20150601.belns"
	DEFINE NAMESPACE MESHC AS URL "https://arty.scai.fraunhofer.de/artifactory/bel/namespace/mesh-chemicals/mesh-chemicals-20170511.belns"