Difference between revisions of "Keyword Box"
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The NMPDR keyword search works like a typical search engine. You type in the appropriate words, and a list of genes will come back. | The NMPDR keyword search works like a typical search engine. You type in the appropriate words, and a list of genes will come back. | ||
| − | The keywords for a specified gene are as follows. The examples shown are for the gene '''fig| | + | The keywords for a specified gene are as follows. The examples shown are for the gene '''fig|171101.1.peg.269''', which is sulD for ''Streptococcus pneumoniae R6''. |
{| | {| | ||
| − | | '''FIG gene identifier''' || fig| | + | | '''FIG gene identifier''' || fig|171101.1.peg.269 |
|- | |- | ||
| − | | '''The [[Alias|aliases]]''' || GeneID: | + | | '''The [[Alias|aliases]]''' || GeneID:934668, gi|15902313, kegg|spd:SPD_0272, kegg|spr:spr0269, NP_357863.1, sp|P59657, spr0269, sulD, tr|Q04MF8, uni|P59657, uni|Q04MF8 |
|- | |- | ||
| − | | '''All words in the functional role''' || 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine, pyrophosphokinase | + | | '''All words in the functional role''' || Dihydroneopterin, aldolase 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine, pyrophosphokinase amino, hydroxy, hydroxymethyldihydropteridine |
|- | |- | ||
| − | | '''The genome ID''' || | + | | '''The genome ID''' || 171101.1 |
|- | |- | ||
| − | | '''All words in the taxonomy''' || bacteria, | + | | '''All words in the taxonomy''' || bacteria, firmicutes, lactobacillales, streptococcaceae, streptococcus, pneumoniae, r6 |
|- | |- | ||
| '''The [[subsystem]] names and classifications''' || folate, biosynthesis, cofactors, vitamins, prosthetic, groups, pigments, folates, pterines | | '''The [[subsystem]] names and classifications''' || folate, biosynthesis, cofactors, vitamins, prosthetic, groups, pigments, folates, pterines | ||
|- | |- | ||
| − | | '''The EC number''' || 2.7.6.3 | + | | '''The EC number''' || 2.7.6.3, 4.1.2.25 |
|- | |- | ||
| '''The [[subsystem role]] || 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine, pyrophosphokinase, amino, hydroxy, hydroxymethylhydroperidine | | '''The [[subsystem role]] || 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine, pyrophosphokinase, amino, hydroxy, hydroxymethylhydroperidine | ||
|- | |- | ||
| − | | '''Special Keywords''' || | + | | '''Special Keywords''' || essential |
|} | |} | ||
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* In the functional role, hyphenated words are stored in their full form (''2-amino-4-hydroxy-6-hydroxymethyldihydropteridine'') as well as broken up on the hyphen boundaries ('''amino- hydroxy hydroxymethyldihydropteridine'''). | * In the functional role, hyphenated words are stored in their full form (''2-amino-4-hydroxy-6-hydroxymethyldihydropteridine'') as well as broken up on the hyphen boundaries ('''amino- hydroxy hydroxymethyldihydropteridine'''). | ||
| − | |||
* Keywords are case-insensitive | * Keywords are case-insensitive | ||
| − | * Special keywords | + | * Special keywords indicate attributes of the gene. The list of special keywords currently supported appears below. |
| + | ** ''virulence'', which indicates the gene participates in the process of helping the organism to damage its host | ||
| + | ** ''essential'', which indicates that the gene is essential to to the survival of the organism | ||
| + | ** ''iedb'', which indicates that the gene is listed in the [http://www.immuneepitope.org/home.do Immune Epitope Database] | ||
Revision as of 13:10, 28 July 2007
The NMPDR keyword search works like a typical search engine. You type in the appropriate words, and a list of genes will come back.
The keywords for a specified gene are as follows. The examples shown are for the gene fig|171101.1.peg.269, which is sulD for Streptococcus pneumoniae R6.
| FIG gene identifier | 171101.1.peg.269 |
| The aliases | 15902313, kegg|spd:SPD_0272, kegg|spr:spr0269, NP_357863.1, sp|P59657, spr0269, sulD, tr|Q04MF8, uni|P59657, uni|Q04MF8 |
| All words in the functional role | Dihydroneopterin, aldolase 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine, pyrophosphokinase amino, hydroxy, hydroxymethyldihydropteridine |
| The genome ID | 171101.1 |
| All words in the taxonomy | bacteria, firmicutes, lactobacillales, streptococcaceae, streptococcus, pneumoniae, r6 |
| The subsystem names and classifications | folate, biosynthesis, cofactors, vitamins, prosthetic, groups, pigments, folates, pterines |
| The EC number | 2.7.6.3, 4.1.2.25 |
| The subsystem role | 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine, pyrophosphokinase, amino, hydroxy, hydroxymethylhydroperidine |
| Special Keywords | essential |
Notes
- In the functional role, hyphenated words are stored in their full form (2-amino-4-hydroxy-6-hydroxymethyldihydropteridine) as well as broken up on the hyphen boundaries (amino- hydroxy hydroxymethyldihydropteridine).
- Keywords are case-insensitive
- Special keywords indicate attributes of the gene. The list of special keywords currently supported appears below.
- virulence, which indicates the gene participates in the process of helping the organism to damage its host
- essential, which indicates that the gene is essential to to the survival of the organism
- iedb, which indicates that the gene is listed in the Immune Epitope Database