Create text file for Robel w/ organism decsions

[kmartinez834]

Take text from GlyGen Organisms and create a species_rules.txt file in misc folder

[ubhuiyan]

@rykahsay please check the txt file I've created and provide feedback if anything is confusing.

source: misc/species_rules.txt Table Head:

+--------+------------------------------------+---------------+-------------------+
| TaxID  |         Scientific Name            |  Common Name  |   GlyGen Name     |
+--------+------------------------------------+---------------+-------------------+
|9606    |Homo sapiens                        |Human          |Human              |

|10090   |Mus musculus                        |Mouse          |Mouse              |

|10116/  |Rattus norvegicus                   |Rat            |Rat                |
|10114   |Rattus                              |Rattus         |Rat                |

[rykahsay]

In your checkbox document that you can Kate are creating, please add the following:

file/folder I created should have permissions such that anyone in group "glygen" is able to edit. For these, two commands needed:

$ chown sbhuiyan28:glygen misc/species_rules.txt
$ chmod 775 misc/species_rules.txt

[rykahsay]

Given below is what I expected ... please keep adding rules

$ cat generated/misc/species_rules.txt
GlyGen Organism Decisions 

1) Organisms and names need to be approved by Raja and Mike before they are added to GlyGen.  

    TaxID: The taxonomy identifier from  NCBI Taxonomy 
    Scientific Name: The full scientific name according to NCBI Taxonomy 
    Common Name: The common name according to UniProt Taxonomy  
    GlyGen Name: The organism name displayed in GlyGen searches, statistics, etc. 

2) Organisms which are not GlyGen reference organisms
    These taxonomies are grouped with "nearest" GlyGen reference species. The mapping file is located 
    at misc/species_map.json and needs to be updated if a new organism that is not reference Glygen organism

3) The "statistics" panel given on the landing page should only show GlyGen reference organism
   using the "GlyGen Name"

4) All pulldown menu should show only GlyGen reference organism using the "GlyGen Name"

5) All search result pages (protein/glycan/xxx search result pages) should show only GlyGen reference organism 
   using the "GlyGen Name"

6) All detail pages (protein/glycan/xxx detail pages) should show only GlyGen reference organism 
   using the "GlyGen Name"

X) Because there are two reference HCV strains, the parent HCV species is not mapped to either. 
It appears as its own organism on the glycan search species dropdown, list filters and details organism section.