Identification and Provenance fields
  Name: human_glycan_enzyme.csv
  Title: Glycan Enzyme
  Created: August 7, 2018; 15:30:45
  Created by: Rahi Navelkar [rsn13@gwu.edu]
  Modified: October 5, 2018; 15:17:10  
  Modified by: Rahi Navelkar [rsn13@gwu.edu]
  Digital Signature: RYFNNKE22594E007JKV457
  Verification status: Approved
  Publication status: Reviewed
  Authors: William S York [will@ccrc.uga.edu]; Alison V Nairn [avnairn@ccrc.uga.edu]; Nathan Edwards [nje5@georgetown.edu]; Rahul Sethi [rahulsethi80@gwu.edu]; Rahi Navelkar [rsn13@gwu.edu]
  License: Data - Attribution 4.0 International CC BY 4.0 [https://creativecommons.org/licenses/by/4.0/]
	   Scripts - GNU General Public License v3.0 [https://www.gnu.org/licenses/gpl-3.0.en.html]

Usability Domain
  List of Glycans identified by GlyTouCan Accessions with information on the human[taxid:9606] proteins involved in the synthesis of the glycan (inferred via orthology).

Description Domain
  Description: This file contains 38 human[taxid:9606] proteins involved in the synthesis of 2746 Glycans (inferred via orthology). 
                
  Pipeline Steps:
    Step 1: The input file was downloaded from the source link and the 'Enzyme:UniProtAccession' column was mapped to canonical accessions using a python script [ac2canonical.py].
    Step 2: The mouse protein accessions (UniProt) were mapped to human protein accessions(UniProt), gene id(NCBI) and gene symbol using file (mouse_protein_ortholog.csv).
    Step 3: The gene id's were mapped to 'Full_name_from_nomenclature_authority' (Enzyme:Description) from input file (Homo_sapiens.gene_info).
    Step 4: Two columns (Enzyme:TaxonomyID, Enzyme:Organism) based on human 'Enzyme:UniProtAccession' column were added to the file.
    Step 5: Steps 3, 4 and 5 were processed using a python script [make-glycan_enzyme-csv.py ] to generate the final output file.

  Keywords: GlyTouCan, Glycan, Enzyme, Synthesis, Orthologs

Execution Domain:
  Script Location: https://github.com/glygener/glygen-backend/blob/master/integration/ 
  Scripts List: ac2canonical.py, make-glycan_enzyme-csv.py 
  Script Type: Text  
  Software Prerequisites:
    Name: Python
    Version: 2.7.13
    Name: Microsoft Excel
    Version: 14 or above

I/O Domain
  Input Subdomain: 
    name: gtc2enz.txt
    mime-type: txt
    source/uri: http://edwardslab.bmcb.georgetown.edu/~nedwards/dropbox/w3qglfi0w4/UGA/current/gtc2enz.txt

    name: mouse_protein_ortholog.csv
    mime-type: csv
    source/uri: http://data.glygen.org/GLYDS000011

    name: Homo_sapiens.gene_info
    mime-type: tab
    source/uri: ftp://ftp.ncbi.nih.gov/gene/DATA/GENE_INFO/Mammalia/Homo_sapiens.gene_info.gz

  Output Subdomain:
    name: human_glycan_enzyme.csv 
    mime-type: csv
    source/uri: http://data.glygen.org/GLYDS000064
    Content:
        glytoucan_acc: Glycan accession from GlyTouCan 
        uniprotkb_acc_canonical_enzyme: Protein (enzyme) canonical accession from UniProt
        gene_symbol_enzyme: Gene symbol of the enzyme.
        gene_id_enzyme: Gene Id of the enzyme from NCBI-Gene
        enzyme_name: Name/description of the enzyme from NCBI-Gene 
        tax_id_enzyme: Tax id of the protein [9606]
        organism_name_enzyme: Name of the organism for the protein (enzyme)