This repository contains file tracking information for the glycan data pipeline between GW and Georgetown. The tracking file "files4nathan.csv" contains the following information:
| Field name | Description |
|---|---|
| File name | Name of file |
| Path | Path from downloads folder |
| Source | Data source/provider |
| GlyGen Datasets | Dataset ID for evidence badges pointing to GlyGen dataset, used for sources without a url |
| PMID | PubMed ID for files in which all entries are associated with one publication |
| PMID field | Field where PMID can be located for files that contain records from multiple publications |
| Notes | Misc notes field |
- Updated UnicarbKB dataset IDs (GLY_000040:Human|GLY_000040:Mouse --> GLY_000040:Human|GLY_000041:Mouse)
- New download files added: matrixdb_CORE.tab, glyconnect_chicken.json, chicken_o_glcnacome_mcw.csv, ccRCC_TMT_intact_glycopeptide_abundance_MD-MAD.tsv, diabetes_glycomic_mapping.csv, and Custom_MatrixDB_biomolecules.tsv
- Added Pig dataset ID to OGlcNAcAtlas rows
- Switched doi link from "Notes" to "PMID" column for glygen_upload.csv
- Changed OGlcNAcAtlas file names from ambiguous_sites_version_2.0.csv and unambiguous_sites_version_2.0.csv to ambiguous_sites.csv and unambiguous_sites.csv, respectively. Added chicken
- Updated "PMID" header to "Publication" and provided corresponding key:value for entries with literature
- Changed BiomarkerKB file name and type from allbiomarkers-all.csv to allbiomarkers.tsv, updated "PMID field"
- Updated all paths to 'current' folder
- Added species to GlyGen dataset ID
- Added PMID field
- Added Notes field
- Removed files without GlyTouCan accessions
- Added new files: glyconnect_pig.json, glygen_upload.csv