<p>These are not. The closest to "standard" is the 5-character <a href="https://www.uniprot.org/docs/speclist.txt" rel="noreferrer">abbreviation by Swissprot</a>. It names 25,886 species and has been used for decades. It is also easy to remember for some common species such as HUMAN, RAT, MOUSE and HORSE. I think databases should stop inventing new species abbreviations.</p>

CC BY-SA 4.0
2018-08-25T07:31:10.550Z
2018-08-25T07:31:10.550Z
user172818
<p>No, there are no standardized three-letter abbreviations for species names. Three-letter abbreviations with roman letters is 26^3 combinations, which is only 17,576 possible combinations. As a result there are not enough three-letter abbreviations for all living species.</p>

<p>All three-letter abbreviations are either specific to a database or perhaps are shared between a database or two. There is currently no substitute for a binomial name (although NCBI taxid is a convenient parsable substitute for the species included in NCBI to date).</p>

CC BY-SA 4.0
2018-08-25T06:30:00.437Z
2018-08-25T06:30:00.437Z
conchoecia
<p><a href="https://reactome.org/" rel="noreferrer">Reactome</a> uses a three letter code for each species which are listed below.</p>

<p>Are the letter codes used by Reactome a standard?</p>

<p>If so is there a web page or download file that can validate the code and translate it to a common name?</p>

<pre><code> HSA  Homo sapiens                          
 SSC  Sus scrofa                            
 GGA  Gallus gallus                         
 DME  Drosophila melanogaster               
 RNO  Rattus norvegicus                     
 DDI  Dictyostelium discoideum              
 MMU  Mus musculus                          
 ATH  Arabidopsis thaliana                  
 TGU  Taeniopygia guttata                   
 DRE  Danio rerio                           
 OSA  Oryza sativa                          
 BTA  Bos taurus                            
 XTR  Xenopus tropicalis                    
 CFA  Canis familiaris                      
 SCE  Saccharomyces cerevisiae              
 PFA  Plasmodium falciparum                 
 CEL  Caenorhabditis elegans                
 SPO  Schizosaccharomyces pombe             
 ROT  Rotavirus                             
 FLU  Influenza A virus                     
 HCV  Hepatitis C Virus                     
 HBV  Hepatitis B virus                     
 HER  Human herpesvirus 1                   
 NME  Neisseria meningitidis serogroup B    
 NME  Neisseria meningitidis                
 CTR  Chlamydia trachomatis                 
 STY  Salmonella typhimurium                
 STY  Salmonella enterica                   
 ECO  Escherichia coli                      
 OCU  Oryctolagus cuniculus                 
 XLA  Xenopus laevis                        
 CAE  Cercopithecus aethiops                
 CGR  Cricetulus griseus                    
 HER  Human herpesvirus 8                   
 MCV  Molluscum contagiosum virus subtype 1 
 MCV  Molluscum contagiosum virus           
 HCY  Human cytomegalovirus                 
 HIV  Human immunodeficiency virus 1        
 PCH  Penicillium chrysogenum               
 TAE  Triticum aestivum                     
 VRA  Vigna radiata var. radiata            
 VRA  Vigna radiata                         
 CFS  Crithidia fasciculata                 
 FCA  Felis catus                           
 AMA  Arenicola marina                      
 MGA  Meleagris gallopavo                   
 NGO  Neisseria gonorrhoeae                 
 SAU  Staphylococcus aureus                 
 MVI  Measles virus                         
 HAL  Human alphaherpesvirus 2          
</code></pre>

<hr>

<p>EDIT</p>

<p>Not a complete answer as this only covers a subset of all organisms but at present better than nothing. </p>

<p>Using KEGG Organisms</p>

<p><a href="https://www.genome.jp/kegg-bin/get_htext" rel="noreferrer">https://www.genome.jp/kegg-bin/get_htext</a></p>

<p>Enter letter code, e.g. GGA</p>

<p><a href="https://i.sstatic.net/AOpHS.png" rel="noreferrer"><img src="https://i.sstatic.net/AOpHS.png" alt="enter image description here"></a></p>

<hr>

<p>EDIT - After reading <a href="https://bioinformatics.stackexchange.com/a/4939/1586">answer</a> by <a href="https://bioinformatics.stackexchange.com/users/2085/conchoecia">conchoecia</a> </p>

<p>The graph database schema for Reactome only has two labels that use the 3 letter code which is named abbreviation in the schema:</p>

<p><a href="https://reactome.org/content/schema/Species" rel="noreferrer">Species</a> and <a href="https://reactome.org/content/schema/ReferenceTherapeutic" rel="noreferrer">ReferenceTherapeutic</a></p>

<p>Species has taxid  (Taxon Identifier)</p>

<pre><code>abbreviation     taxId       displayName                            
AMA              6344        Arenicola marina                        
ATH              3702        Arabidopsis thaliana                    
BAN              1392        Bacillus anthracis                      
BTA              9913        Bos taurus                              
CAE              9534        Cercopithecus aethiops                  
CAL              5476        Candida albicans                        
CBO              1491        Clostridium botulinum                   
CEL              6239        Caenorhabditis elegans                  
CFA              9615        Canis familiaris                        
CFS              5656        Crithidia fasciculata                   
CGR              10029       Cricetulus griseus                      
CPH              10703       Corynephage beta                        
CPO              10141       Cavia porcellus                         
CSB              60711       Chlorocebus sabaeus                     
CTE              1513        Clostridium tetani                      
CTR              813         Chlamydia trachomatis                   
CVI              10243       Cowpox virus                            
DDI              44689       Dictyostelium discoideum                
DME              7227        Drosophila melanogaster                 
DRE              7955        Danio rerio                             
ECO              562         Escherichia coli                        
FCA              9685        Felis catus                             
FLU              11320       Influenza A virus                       
GGA              9031        Gallus gallus                           
HAL              10310       Human alphaherpesvirus 2                
HAM              6706        Homarus americanus                      
HBV              10407       Hepatitis B virus                       
HCV              11103       Hepatitis C Virus                       
HCV              31649       Hepatitis C virus genotype 2a           
HCV              31646       Hepatitis C virus subtype 1a            
HCY              10359       Human cytomegalovirus                   
HER              10298       Human herpesvirus 1                     
HER              37296       Human herpesvirus 8                     
HGA              10376       Human gammaherpesvirus 4                
HIV              11676       Human immunodeficiency virus 1          
HPV              333760      Human papillomavirus type 16            
HPV              337041      Alphapapillomavirus 9                   
HSA              9606        Homo sapiens                            
IBR              11120       Infectious bronchitis virus             
LMO              1639        Listeria monocytogenes                  
LMO              1906951     Listeria monocytogenes serovar 1/2a     
LPN              446         Legionella pneumophila                  
MCV              10280       Molluscum contagiosum virus subtype 1   
MCV              10279       Molluscum contagiosum virus             
MGA              9013        Meleagris gallopavo                     
MML              9544        Macaca mulatta                          
MMU              10090       Mus musculus                            
MTU              1773        Mycobacterium tuberculosis              
MTU              83332       Mycobacterium tuberculosis H37Rv        
MVI              11234       Measles virus                           
NGO              485         Neisseria gonorrhoeae                   
NME              491         Neisseria meningitidis serogroup B      
NME              487         Neisseria meningitidis                  
OAR              9940        Ovis aries                              
OCU              9986        Oryctolagus cuniculus                   
OSA              4530        Oryza sativa                            
PCH              5076        Penicillium chrysogenum                 
PFA              5833        Plasmodium falciparum                   
RNO              10116       Rattus norvegicus                       
ROT              10912       Rotavirus                               
SAU              1280        Staphylococcus aureus                   
SCE              4932        Saccharomyces cerevisiae                
SEV              11191       Sendai virus                            
SPO              4896        Schizosaccharomyces pombe               
SSC              9823        Sus scrofa                              
STY              90371       Salmonella typhimurium                  
STY              28901       Salmonella enterica                     
TAE              4565        Triticum aestivum                       
TGO              5811        Toxoplasma gondii                       
TGU              59729       Taeniopygia guttata                     
VRA              3916        Vigna radiata var. radiata              
VRA              157791      Vigna radiata                           
VVI              10245       Vaccinia virus                          
XLA              8355        Xenopus laevis                          
XTR              8364        Xenopus tropicalis 
</code></pre>

<p>While ReferenceTherapeutic does not.</p>

<p>The species can be identified using the NCBI taxon identifier, e.g.</p>

<p><a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=6344" rel="noreferrer">https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=6344</a></p>

<p><a href="https://i.sstatic.net/oVwcY.png" rel="noreferrer"><img src="https://i.sstatic.net/oVwcY.png" alt="enter image description here"></a></p>

<hr>

<p>EDIT - After reading <a href="https://bioinformatics.stackexchange.com/a/4940/1586">answer</a> by <a href="https://bioinformatics.stackexchange.com/users/37/user172818">user172818</a></p>

<p>Searching the file <a href="https://www.uniprot.org/docs/speclist.txt" rel="noreferrer">https://www.uniprot.org/docs/speclist.txt</a> for 6344</p>

<pre><code>AREMA E    6344: N=Arenicola marina  
                 C=Lugworm  
                 S=Lumbricus marinus 
</code></pre>

<p>or using the URL: <a href="https://www.uniprot.org/taxonomy/6344" rel="noreferrer">https://www.uniprot.org/taxonomy/6344</a></p>

<p><a href="https://i.sstatic.net/WpFQg.png" rel="noreferrer"><img src="https://i.sstatic.net/WpFQg.png" alt="enter image description here"></a></p>

<p>and with reference to</p>

<blockquote>
  <p>I think databases should stop inventing new species abbreviations.</p>
</blockquote>

<p>The Wikipedia article on <a href="https://en.wikipedia.org/wiki/Lugworm" rel="noreferrer">Lugworm</a> shows the many <a href="https://en.wikipedia.org/wiki/Help:Taxon_identifiers" rel="noreferrer">Taxon identifiers</a> in multiple databases.</p>

<p><a href="https://i.sstatic.net/VWqBa.png" rel="noreferrer"><img src="https://i.sstatic.net/VWqBa.png" alt="enter image description here"></a></p>

<database><data-mining><taxonomy>
Are these standard species abbreviations and how to look up others?
# Are these standard species abbreviations and how to look up others?

(Asked by: username_0 on 2018-08-24)

Reactome uses a three letter code for each species which are listed below.
Are the letter codes used by Reactome a standard?
If so is there a web page or download file that can validate the code and translate it to a common name?
 HSA  Homo sapiens                          
 SSC  Sus scrofa                            
 GGA  Gallus gallus                         
 DME  Drosophila melanogaster               
 RNO  Rattus norvegicus                     
 DDI  Dictyostelium discoideum              
 MMU  Mus musculus                          
 ATH  Arabidopsis thaliana                  
 TGU  Taeniopygia guttata                   
 DRE  Danio rerio                           
 OSA  Oryza sativa                          
 BTA  Bos taurus                            
 XTR  Xenopus tropicalis                    
 CFA  Canis familiaris                      
 SCE  Saccharomyces cerevisiae              
 PFA  Plasmodium falciparum                 
 CEL  Caenorhabditis elegans                
 SPO  Schizosaccharomyces pombe             
 ROT  Rotavirus                             
 FLU  Influenza A virus                     
 HCV  Hepatitis C Virus                     
 HBV  Hepatitis B virus                     
 HER  Human herpesvirus 1                   
 NME  Neisseria meningitidis serogroup B    
 NME  Neisseria meningitidis                
 CTR  Chlamydia trachomatis                 
 STY  Salmonella typhimurium                
 STY  Salmonella enterica                   
 ECO  Escherichia coli                      
 OCU  Oryctolagus cuniculus                 
 XLA  Xenopus laevis                        
 CAE  Cercopithecus aethiops                
 CGR  Cricetulus griseus                    
 HER  Human herpesvirus 8                   
 MCV  Molluscum contagiosum virus subtype 1 
 MCV  Molluscum contagiosum virus           
 HCY  Human cytomegalovirus                 
 HIV  Human immunodeficiency virus 1        
 PCH  Penicillium chrysogenum               
 TAE  Triticum aestivum                     
 VRA  Vigna radiata var. radiata            
 VRA  Vigna radiata                         
 CFS  Crithidia fasciculata                 
 FCA  Felis catus                           
 AMA  Arenicola marina                      
 MGA  Meleagris gallopavo                   
 NGO  Neisseria gonorrhoeae                 
 SAU  Staphylococcus aureus                 
 MVI  Measles virus                         
 HAL  Human alphaherpesvirus 2          


EDIT
Not a complete answer as this only covers a subset of all organisms but at present better than nothing. 
Using KEGG Organisms
https://www.genome.jp/kegg-bin/get_htext
Enter letter code, e.g. GGA


EDIT - After reading answer by conchoecia 
The graph database schema for Reactome only has two labels that use the 3 letter code which is named abbreviation in the schema:
Species and ReferenceTherapeutic
Species has taxid  (Taxon Identifier)
abbreviation     taxId       displayName                            
AMA              6344        Arenicola marina                        
ATH              3702        Arabidopsis thaliana                    
BAN              1392        Bacillus anthracis                      
BTA              9913        Bos taurus                              
CAE              9534        Cercopithecus aethiops                  
CAL              5476        Candida albicans                        
CBO              1491        Clostridium botulinum                   
CEL              6239        Caenorhabditis elegans                  
CFA              9615        Canis familiaris                        
CFS              5656        Crithidia fasciculata                   
CGR              10029       Cricetulus griseus                      
CPH              10703       Corynephage beta                        
CPO              10141       Cavia porcellus                         
CSB              60711       Chlorocebus sabaeus                     
CTE              1513        Clostridium tetani                      
CTR              813         Chlamydia trachomatis                   
CVI              10243       Cowpox virus                            
DDI              44689       Dictyostelium discoideum                
DME              7227        Drosophila melanogaster                 
DRE              7955        Danio rerio                             
ECO              562         Escherichia coli                        
FCA              9685        Felis catus                             
FLU              11320       Influenza A virus                       
GGA              9031        Gallus gallus                           
HAL              10310       Human alphaherpesvirus 2                
HAM              6706        Homarus americanus                      
HBV              10407       Hepatitis B virus                       
HCV              11103       Hepatitis C Virus                       
HCV              31649       Hepatitis C virus genotype 2a           
HCV              31646       Hepatitis C virus subtype 1a            
HCY              10359       Human cytomegalovirus                   
HER              10298       Human herpesvirus 1                     
HER              37296       Human herpesvirus 8                     
HGA              10376       Human gammaherpesvirus 4                
HIV              11676       Human immunodeficiency virus 1          
HPV              333760      Human papillomavirus type 16            
HPV              337041      Alphapapillomavirus 9                   
HSA              9606        Homo sapiens                            
IBR              11120       Infectious bronchitis virus             
LMO              1639        Listeria monocytogenes                  
LMO              1906951     Listeria monocytogenes serovar 1/2a     
LPN              446         Legionella pneumophila                  
MCV              10280       Molluscum contagiosum virus subtype 1   
MCV              10279       Molluscum contagiosum virus             
MGA              9013        Meleagris gallopavo                     
MML              9544        Macaca mulatta                          
MMU              10090       Mus musculus                            
MTU              1773        Mycobacterium tuberculosis              
MTU              83332       Mycobacterium tuberculosis H37Rv        
MVI              11234       Measles virus                           
NGO              485         Neisseria gonorrhoeae                   
NME              491         Neisseria meningitidis serogroup B      
NME              487         Neisseria meningitidis                  
OAR              9940        Ovis aries                              
OCU              9986        Oryctolagus cuniculus                   
OSA              4530        Oryza sativa                            
PCH              5076        Penicillium chrysogenum                 
PFA              5833        Plasmodium falciparum                   
RNO              10116       Rattus norvegicus                       
ROT              10912       Rotavirus                               
SAU              1280        Staphylococcus aureus                   
SCE              4932        Saccharomyces cerevisiae                
SEV              11191       Sendai virus                            
SPO              4896        Schizosaccharomyces pombe               
SSC              9823        Sus scrofa                              
STY              90371       Salmonella typhimurium                  
STY              28901       Salmonella enterica                     
TAE              4565        Triticum aestivum                       
TGO              5811        Toxoplasma gondii                       
TGU              59729       Taeniopygia guttata                     
VRA              3916        Vigna radiata var. radiata              
VRA              157791      Vigna radiata                           
VVI              10245       Vaccinia virus                          
XLA              8355        Xenopus laevis                          
XTR              8364        Xenopus tropicalis 

While ReferenceTherapeutic does not.
The species can be identified using the NCBI taxon identifier, e.g.
https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=6344


EDIT - After reading answer by user172818
Searching the file https://www.uniprot.org/docs/speclist.txt for 6344
AREMA E    6344: N=Arenicola marina  
                 C=Lugworm  
                 S=Lumbricus marinus 

or using the URL: https://www.uniprot.org/taxonomy/6344

and with reference to

I think databases should stop inventing new species abbreviations.

The Wikipedia article on Lugworm shows the many Taxon identifiers in multiple databases.

**Tags:** database, data-mining, taxonomy

---

## 2 answers

### Answer by username_2 on 2018-08-25. Score: 7 | Accepted answer

No, there are no standardized three-letter abbreviations for species names. Three-letter abbreviations with roman letters is 26^3 combinations, which is only 17,576 possible combinations. As a result there are not enough three-letter abbreviations for all living species.

All three-letter abbreviations are either specific to a database or perhaps are shared between a database or two. There is currently no substitute for a binomial name (although NCBI taxid is a convenient parsable substitute for the species included in NCBI to date).


---

### Answer by username_1 on 2018-08-25. Score: 6

These are not. The closest to "standard" is the 5-character [abbreviation by Swissprot](https://www.uniprot.org/docs/speclist.txt). It names 25,886 species and has been used for decades. It is also easy to remember for some common species such as HUMAN, RAT, MOUSE and HORSE. I think databases should stop inventing new species abbreviations.


---

