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.
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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. Our keyword database contains millions of words, including ''vitamins'', ''aldolase'', and ''pyrophosphokinase''. The NMPDR looks at nine specific data items when computing the keywords for a gene. The table below shows each of the nine steps along with the keywords derived by that step for the gene '''fig|171101.1.peg.269''', a dual-role protein encoding gene for ''Streptococcus pneumoniae r6'' that has 40 keywords.
  
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The keywords for a specified gene are as follows. The examples shown are for the gene '''fig|100226.1.peg.3361''', which is EC 2.7.6.3 for ''Streptomyces coelicolor A3(2)''.
 
  
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{|
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{|border="2"
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| FIG gene identifier || fig|100226.1.peg.3361
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| '''FIG gene identifier''' || fig|171101.1.peg.269
 
|-
 
|-
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| The [[Alias|aliases]] || GeneID:1098838, gi|21221828, kegg|sco:SCO3401, NP_627607.1, SCO3401, tr|Q9X8I1, uni|Q9X8I1
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| '''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
 
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|-
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| All words in the functional role || 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine, pyrophosphokinase, amino, hydroxy, hydroxymethylhydroperidine
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| '''All words in the functional role''' || Dihydroneopterin, aldolase 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine, pyrophosphokinase amino, hydroxy, hydroxymethyldihydropteridine
 
|-
 
|-
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| The genome ID || 100226.1
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| '''The genome ID''' || 171101.1
 
|-
 
|-
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| All words in the taxonomy || bacteria, actinobacteria, actinobacteridae, actinomycetales, streptomycineae, streptomycetaceae, streptomyces, coelicolor, a32
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| '''All words in the taxonomy''' || bacteria, firmicutes, lactobacillales, streptococcaceae, streptococcus, pneumoniae, r6
 
|-
 
|-
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| The [[subsystem]] names and classifications || folate, biosynthesis, cofactors, vitamins, prosthetic, groups, pigments, folates, pterines
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| '''The [[subsystem]] names and classifications''' || folate, biosynthesis, cofactors, vitamins, prosthetic, groups, pigments, folates, pterines
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|-
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| '''The EC number''' || 2.7.6.3, 4.1.2.25
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|-
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| '''The [[subsystem role]] || 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine, pyrophosphokinase, amino, hydroxy, hydroxymethylhydroperidine
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|-
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| '''Special Keywords''' || essential
 
|}
 
|}
  
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Note that in the functional role that hyphenated words are stored in their full form as well as broken up on the hyphen boundaries.
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*
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====Notes====
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* Some keywords appear twice.
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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''').
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* Keywords are case-insensitive.
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* Special keywords indicate attributes of the gene. Most of these are incomplete: for example, we know certain genes are virulence-associated, but for most of the genes we have no virulence data.
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** ''virulence'', which indicates the gene participates in the process of helping the organism to damage its host. This attribute is incomplete.
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** ''essential'', which indicates that the gene is essential to to the survival of the organism. This attribute is incomplete.
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** ''iedb'', which indicates that the gene is listed in the [http://www.immuneepitope.org/home.do Immune Epitope Database]
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===Advanced Keyword Searching===
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Normally, the search process selects the genes relevant to all the words in the keyword box. You can modify the default behavior using the following control characters.
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{|border="2"
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| '''char''' || '''Meaning''' || '''Example''' || '''Explanation of Example'''
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|-
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| '''-''' || negation || 2.7.6.3 '''-'''firmicutes || search for all genes with EC number 2.7.6.3 that are not in firmicutes
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|-
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| '''()''' || optional || '''('''2.7.6.3 4.1.2.25''')''' || search for any gene with EC number 2.7.6.3 or 4.1.2.25
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|-
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| '''""''' || phrase || '''"'''folate biosynthesis'''"''' || search for all genes that participate in folate biosynthesis
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|}
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===Using Negation===
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It is illegal to use negation on all the keywords. For example, you can't do
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    -hypothetical
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to get all non-hypothetical proteins. You can trick the the keyword search a little by including a positive keyword for a broad category
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    bacteria -hypothetical
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which will return all non-hypothetical proteins for bacteria. This is not recommended, however, because you will get over a million results.
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Queries that rely primarily on negation make the most sense when your result set is already restricted.

Latest revision as of 13:17, 29 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. Our keyword database contains millions of words, including vitamins, aldolase, and pyrophosphokinase. The NMPDR looks at nine specific data items when computing the keywords for a gene. The table below shows each of the nine steps along with the keywords derived by that step for the gene fig|171101.1.peg.269, a dual-role protein encoding gene for Streptococcus pneumoniae r6 that has 40 keywords.


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

  • Some keywords appear twice.
  • 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. Most of these are incomplete: for example, we know certain genes are virulence-associated, but for most of the genes we have no virulence data.
    • virulence, which indicates the gene participates in the process of helping the organism to damage its host. This attribute is incomplete.
    • essential, which indicates that the gene is essential to to the survival of the organism. This attribute is incomplete.
    • iedb, which indicates that the gene is listed in the Immune Epitope Database


Advanced Keyword Searching

Normally, the search process selects the genes relevant to all the words in the keyword box. You can modify the default behavior using the following control characters.


char Meaning Example Explanation of Example
- negation 2.7.6.3 -firmicutes search for all genes with EC number 2.7.6.3 that are not in firmicutes
() optional (2.7.6.3 4.1.2.25) search for any gene with EC number 2.7.6.3 or 4.1.2.25
"" phrase "folate biosynthesis" search for all genes that participate in folate biosynthesis

Using Negation

It is illegal to use negation on all the keywords. For example, you can't do 

   -hypothetical

to get all non-hypothetical proteins. You can trick the the keyword search a little by including a positive keyword for a broad category 

   bacteria -hypothetical

which will return all non-hypothetical proteins for bacteria. This is not recommended, however, because you will get over a million results.

Queries that rely primarily on negation make the most sense when your result set is already restricted.

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