Keyword Box - Revision history

BruceParrello: Added notes on using negation

2007-07-29T19:17:10Z

Added notes on using negation

BruceParrello: First real version

2007-07-28T20:51:53Z

First real version

BruceParrello: safety save

2007-07-28T20:05:44Z

safety save

BruceParrello: Changed to a more complicated example gene

2007-07-28T19:10:43Z

Changed to a more complicated example gene

BruceParrello: safety save

2007-07-28T18:33:07Z

safety save

BruceParrello: safety save

2007-07-28T18:19:49Z

safety save

New page

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|100226.1.peg.3361''', which is EC 2.7.6.3 for ''Streptomyces coelicolor A3(2)''.

{|
| FIG gene identifier || fig|100226.1.peg.3361
|-
| The [[Alias|aliases]] || GeneID:1098838, gi|21221828, kegg|sco:SCO3401, NP_627607.1, SCO3401, tr|Q9X8I1, uni|Q9X8I1
|-
| All words in the functional role || 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine, pyrophosphokinase, amino, hydroxy, hydroxymethylhydroperidine
|-
| The genome ID || 100226.1
|-
| All words in the taxonomy || bacteria, actinobacteria, actinobacteridae, actinomycetales, streptomycineae, streptomycetaceae, streptomyces, coelicolor, a32
|-
| The [[subsystem]] names and classifications || folate, biosynthesis, cofactors, vitamins, prosthetic, groups, pigments, folates, pterines
|}

Note that in the functional role that hyphenated words are stored in their full form as well as broken up on the hyphen boundaries.
*

@@ Line 27: / Line 27: @@
 * 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
+* 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.
@@ Line 48: / Line 48: @@
 | '''""''' || phrase || '''"'''folate biosynthesis'''"''' || search for all genes that participate in folate biosynthesis
 |}

@@ Line 1: / Line 1: @@
 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''' || fig|171101.1.peg.269
 |-
@@ Line 25: / Line 26: @@
 * 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''').
+* 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.
@@ Line 31: / Line 32: @@
 ** ''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 [http://www.immuneepitope.org/home.do 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 by prefixing control characters to the keywords.
+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
+{|border="2"
 |-
-|'''-'''|negation|'''2.7.6.3 -firmicutes''': search for all genes with EC number 2.7.6.3 that are not in firmicutes
+| '''-''' || negation || 2.7.6.3 '''-'''firmicutes || search for all genes with EC number 2.7.6.3 that are not in firmicutes
 |-
-|'''()'''|optional|
+| '''()''' || 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

@@ Line 1: / Line 1: @@
-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. 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.
 {|
@@ Line 24: / Line 22: @@
-Notes
+====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.
+* 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
+** ''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
+** ''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 [http://www.immuneepitope.org/home.do Immune Epitope Database]

@@ Line 1: / Line 1: @@
 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|100226.1.peg.3361''', which is EC 2.7.6.3 for ''Streptomyces coelicolor A3(2)''.
+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|100226.1.peg.3361
+| '''FIG gene identifier''' || fig|171101.1.peg.269
 |-
-| '''The [[Alias|aliases]]''' || GeneID:1098838, gi|21221828, kegg|sco:SCO3401, NP_627607.1, SCO3401, tr|Q9X8I1, uni|Q9X8I1
+| '''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, amino, hydroxy, hydroxymethylhydroperidine
+| '''All words in the functional role''' || Dihydroneopterin, aldolase 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine, pyrophosphokinase amino, hydroxy, hydroxymethyldihydropteridine
 |-
-| '''The genome ID''' || 100226.1
+| '''The genome ID''' || 171101.1
 |-
-| '''All words in the taxonomy''' || bacteria, actinobacteria, actinobacteridae, actinomycetales, streptomycineae, streptomycetaceae, streptomyces, coelicolor, a32
+| '''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
+| '''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''' ||
+| '''Special Keywords''' || essential
 |}
@@ Line 27: / Line 27: @@
 * 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
+* Special keywords indicate attributes of the gene. The list of special keywords currently supported appears below.

@@ Line 4: / Line 4: @@
 {|
-| FIG gene identifier || fig|100226.1.peg.3361
+| '''FIG gene identifier''' || fig|100226.1.peg.3361
 |-
-| The [[Alias|aliases]] || GeneID:1098838, gi|21221828, kegg|sco:SCO3401, NP_627607.1, SCO3401, tr|Q9X8I1, uni|Q9X8I1
+| '''The [[Alias|aliases]]''' || GeneID:1098838, gi|21221828, kegg|sco:SCO3401, NP_627607.1, SCO3401, tr|Q9X8I1, uni|Q9X8I1
 |-
-| All words in the functional role || 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine, pyrophosphokinase, amino, hydroxy, hydroxymethylhydroperidine
+| '''All words in the functional role''' || 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine, pyrophosphokinase, amino, hydroxy, hydroxymethylhydroperidine
 |-
-| The genome ID || 100226.1
+| '''The genome ID''' || 100226.1
 |-
-| All words in the taxonomy || bacteria, actinobacteria, actinobacteridae, actinomycetales, streptomycineae, streptomycetaceae, streptomyces, coelicolor, a32
+| '''All words in the taxonomy''' || bacteria, actinobacteria, actinobacteridae, actinomycetales, streptomycineae, streptomycetaceae, streptomyces, coelicolor, a32
 |-
-| 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
 |}
-Note that in the functional role that hyphenated words are stored in their full form as well as broken up on the hyphen boundaries.
+Notes