Identification and Provenance fields
  Name: mouse_glycan_classification.csv
  Title: Glycan Classification
  Created: August 7, 2018; 15:30:45
  Created by: Rahi Navelkar [rsn13@gwu.edu]
  Modified: Nov 22, 2018; 15:16:30   
  Modified by: Rahi Navelkar [rsn13@gwu.edu] 
  Digital Signature: YTGHUKN94E007UYTRHI
  Verification status: Approved
  Publication status: Reviewed
  Authors: Nathan Edwards [nje5@georgetown.edu];Brian Fochtman [bfochtman@email.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 infomation on the the glycan type and glycan sub-type.

Description Domain
  Description: This file contains a list of GlyTouCan accession with information on glycan type (N-Glycan or O-Glycan) and sub-type (complex, hybrid, high mannose, core 1, core 2
               core 3, core 4, core 5, core 6, core 7). 
               This file is generated using glycan motif information from GlyTouCan as one method to infer glycan type and sub-type.
               The List of GlyTouCans(glycan list) is compiled when the GlyTouCan accession is observed under one or more following criteria:
               a) If the glycan has source/taxonomy annotation[taxid:10090] in GlyTouCan
               b) If the glycan is listed on mouse[taxid:10090] glycan webpage at UniCarbKB
               c) If the glycan is listed on a mouse [taxid:10090] protein webpage at UniCarbKB
               d) If the glycan is synthesized by a mouse[taxid:10090] protein [http://data.glygen.org/GLYDS00065]
               e) If the glycan is known to be attached to a mouse[taxid:10090] protein [http://data.glygen.org/GLYDS00041] 

  Keywords: GlyTouCan, Glycan, type, sub-type
  
  Pipeline steps:
    Step 1: The input file was downloaded from the source link and the column 'Label' was filtered for specific values. (N-Glycan complex, N-Glycan core basic ,N-Glycan high mannose ,N-Glycan hybrid,N-Glycan truncated motif. First GlcpNAC cut off, O-Glycan core 1, O-Glycan core 1 fuzzy, O-Glycan core 2, O-Glycan core 2 fuzzy, O-Glycan core 3, O-Glycan core 3 fuzzy, O-Glycan core 4, O-Glycan core 4 fuzzy, 
            O-Glycan core 5, O-Glycan core 5 fuzzy, O-Glycan core 6, O-Glycan core 6 Fuzzy, O-Glycan core 7, O-Glycan core 7 fuzzy).
    Step 2: The values were separated into two column individual input text files (glytoucan_acc|glycan_type/glycan_subtype) using a python script [make-glycan_classification-txt.py]
            Following rules were applied to GlyTouCan accessions which had one of the following scenarios for subtypes:
               a) high mannose |hybrid = hybrid
               b) complex | hybrid = hybrid
               c) core basic = no subtype
               d) core x | core x fuzzy = core x  [where x= 1-7]
               e) core x fuzzy = no subtype [where x= 1-7]
               f) core 1| core 2| core 6 = core 2
               g) core 3| core 4 | core 6 = core 6
    Step 3: The individual input file(s) were processed based on the compiled glycan list using a python script[make-glycan-csv.pymake-glycan-dataset.py] to generate the final output csv file.
  
Execution Domain:
  Script Location: https://github.com/glygener/glygen-backend/blob/master/integration/ 
  Scripts List: make-glycan_classification-txt.py, make-glycan-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: allmotif.txt
    mime-type: txt
    source/uri: http://data.glygen.org/datasets/source/allmotif.txt

    name: glycan_type.txt
    mime-type: txt
    source/uri: http://data.glygen.org/datasets/source/glycan_type.txt

    name: glycan_subtype.txt
    mime-type: txt
    source/uri: http://data.glygen.org/datasets/source/glycan_subtype.txt

  Output Subdomain:
    name: mouse_glycan_classification.csv 
    mime-type: csv
    source/uri: http://data.glygen.org/GLYDS00069

    Content:
        glytoucan_acc: Glycan accession from GlyTouCan 
        type: Type of Glycan (N-Glycan or O-Glycan) 
        subtype: Subtype of Glycan (complex, hybrid, high mannose, core 1, core 2, core 3, core 4, core 5, core 6, core 7)


	Statistics:
	      3120 : glytoucan_acc
	         2 : type
	         5 : subtype