Consolidate sample mapping files

[kmartinez834]

For next release...

Consolidate misc files used for tissue/cell line/disease mapping. We are currently using all of the following:

cellline_mapping.csv sample_mapping.csv tissue_mapping.csv doid2uberonid_mapping_v5.csv

[kmartinez834]

@rykahsay -->

• Discontinue use of misc files cellline_mapping.csv and tissue_mapping.csv
• Use only sample_mapping.csv as this contains all cell line and tissue terms

List of files currently using all three misc files:

*_proteoform_glycosylation_sites_glyconnect.csv
*_proteoform_glycosylation_sites_oglcnac_atlas.csv
*_proteoform_glycosylation_sites_oglcnac_mcw.csv
*_proteoform_glycosylation_sites_uniprotkb.csv
*_proteoform_glycosylation_sites_literature.csv
*_proteoform_glycosylation_sites_gptwiki.csv
*_proteoform_glycosylation_sites_harvard.csv
*_proteoform_glycosylation_sites_literature_mining.csv
*_proteoform_glycosylation_sites_literature_mining_manually_verified.csv
*_proteoform_glycosylation_sites_o_gluc.csv
*_proteoform_glycosylation_sites_pdb.csv
*_proteoform_glycosylation_sites_tyr_o_linked.csv
*_proteoform_glycosylation_sites_unicarbkb.csv
*_proteoform_glycosylation_sites_unicarbkb_glycomics_study.csv

[rykahsay]

done, please check if this change introduced any problem to these datasets

[kmartinez834]

In all files with cell line data, format was changed from underscore to colon (ex. "CVCL_Z425" to "CVCL:Z425")

$ grep "CVCL" ../unreviewed/fruitfly_proteoform_glycosylation_sites_glyconnect.csv
"","","","G29931IJ","O-linked","protein_xref_glyconnect","415","protein_xref_glyconnect","415","415","7227","Drosophila melanogaster","1947","G00031MO","Core 1","O-Linked","1,1,0,0,0,0,0,0,0,0,0,0,0,0","H1N1","HexNAc(1)Hex(1)","383.1428","383.3527","Hex:1 HexNAc:1","G29931IJ","mucosa","UBERON:0000344","67j25D","CVCL:Z425","","","","","","","","","",""

--> Should be like "CVCL_Z425"

[rykahsay]

Check now

[kmartinez834]

👍