ReSOLUTE - list of desired integration resources

[mcourtot]

@ulo will produce a list of those resources of interest for them. We should ensure we are using the right IDs to connect or have the ability to bridge @nunogit

[proccaserra]

@ulo besides the open, public resources/datasets RESOLUTE would be interested in connecting, are you aware of 'for-a fee'/commercial datasources of interest/relevancy for which we (squad2 & FAIR+) ought to know about ? rationale for asking: identity another 'integration challenge'

[ulo]

A list of databases and resources that we want to integrate/link to with our SLC-centric database:

cell lines:

• Cellosaurus RRID e.g. https://web.expasy.org/cellosaurus/CVCL_0291

  genes:

• Ensembl ENSG e.g. https://www.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000033867
• HGNC HGNCID e.g. https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:11033

  transcripts:

• Ensembl ENST e.g. https://www.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;t=ENST00000295736

  proteins:

• UniProt UniProtAC e.g. https://www.uniprot.org/uniprot/Q9Y6M7

  transporters:

• TCDB TCID e.g. http://www.tcdb.org/search/result.php?tc=2.A.31.2.11
• IUPHAR Family id e.g. http://www.guidetopharmacology.org/GRAC/FamilyDisplayForward?familyId=171

  compounds (metabolites/substrates/ligands/inhibitors):

• CAS Registry CAS e.g. http://www.commonchemistry.org/ChemicalDetail.aspx?ref=144-55-8
• HMDB HMDBID e.g. http://www.hmdb.ca/metabolites/HMDB0000595
• DrugBank DB e.g. https://www.drugbank.ca/drugs/DB01390
• ChEMBL CHEMBL ID e.g. https://www.ebi.ac.uk/chembl/compound_report_card/CHEMBL1353/
• ChEBI ChEBI ID e.g. https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:32139
• IUPHAR Ligand id e.g. http://www.guidetopharmacology.org/GRAC/LigandDisplayForward?tab=summary&ligandId=4507
• KEGG COMPOUND e.g. https://www.genome.jp/dbget-bin/www_bget?C12603

  pathways:

• KEGG PATHWAY e.g. https://www.genome.jp/kegg-bin/show_pathway?hsa04973
• REACTOME R-HSA e.g. https://reactome.org/PathwayBrowser/#R-HSA-425381
• Ingenuity Pathway IPA; commercial

  associations:

• OpenTargets ENSG e.g. https://www.targetvalidation.org/target/ENSG00000033867
• PharmGKB PharmGKB ID e.g. https://www.pharmgkb.org/gene/PA35876

  experimental data:

• BioGRID (interactions) e.g. https://thebiogrid.org/114876
• HPA (expression) e.g. https://www.proteinatlas.org/ENSG00000033867-SLC4A7/tissue
• DepMap (dependencies) e.g. https://depmap.org/portal/gene/SLC4A7

[ulo]

@ulo besides the open, public resources/datasets RESOLUTE would be interested in connecting, are you aware of 'for-a fee'/commercial datasources of interest/relevancy for which we (squad2 & FAIR+) ought to know about ? rationale for asking: identity another 'integration challenge'

In the above list the only closed resource/tool is IPA, which some of our EFPIA partners use but where we at CeMM do not have a license. They provide curated pathway annotations as well as software for mapping/analyzing omics data to the pathways.

[JolandaS]

@ulo @FuqiX Which of the above mentioned desired links have been established in the mean time? I know of the annotation to Cellosaurus?

[FuqiX]

@JolandaS Hi, Jolanda. I think this ticket listed all possible integration resources for the whole RESOLUTE project. For transcriptomics and sample metadata, integrating cellosaurus info should be enough. Other resources are not applicable. (@ulo please correct me if I misunderstand this ticket)