Difference between revisions of "Modeling data for Infectious agents"

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Line 24: Line 24:
 
               Disease_relevance  ?Text                                  ?Species    #Evidence  
 
               Disease_relevance  ?Text                                  ?Species    #Evidence  
 
   
 
   
 +
Proposal 1:
 
  Add under ?Gene:
 
  Add under ?Gene:
  
  Infection_model    Required_for_infection      ?Strain  XREF  Infection_gene_in_host   ?Species    #Evidence   
+
  Infection_model    Required_for_infection      ?Strain  XREF  Host_gene_required_for_infection   ?Species    #Evidence   
 
                     Resistance_to_infection      ?Strain  XREF  Resistance_gene_in_host  ?Species    #Evidence
 
                     Resistance_to_infection      ?Strain  XREF  Resistance_gene_in_host  ?Species    #Evidence
 
                     Infection_model_description  ?Text                                    ?Species    #Evidence
 
                     Infection_model_description  ?Text                                    ?Species    #Evidence
Line 46: Line 47:
  
 
  ?Strain
 
  ?Strain
  Infection_model_info            Infection_gene_in_host  ?Gene  XREF  Required_for_infection
+
  Infection_model_info            Host_gene_required_for_infection  ?Gene  XREF  Required_for_infection
                                   Resistance_gene_in_host ?Gene  XREF  Resistance_to_infection
+
                                   Resistance_gene_in_host           ?Gene  XREF  Resistance_to_infection
                                   Infection_model_description ?Text  ?Species  #Evidence
+
                                   Infection_model_description       ?Text  ?Species  #Evidence
  
 
</pre>
 
</pre>
Line 66: Line 67:
 
  The bacterial strain = Shigella flexneri strain 2457T     
 
  The bacterial strain = Shigella flexneri strain 2457T     
 
  Infection_model_description, is basically a concise description that will describe the model, similar to the 'Disease_relevance' description  
 
  Infection_model_description, is basically a concise description that will describe the model, similar to the 'Disease_relevance' description  
  under Disease_info.
+
  under Disease_info in ?Gene.
 
   
 
   
 
  Proposed Model:
 
  Proposed Model:
  Infection_model    Required_for_infection      ?Strain  XREF  Infection_gene_in_host   ?Species    #Evidence   
+
  Infection_model    Required_for_infection      ?Strain  XREF  Host_gene_required_for_infection   ?Species    #Evidence   
                     Resistance_to_infection      ?Strain  XREF  Resistance_gene_in_host   ?Species    #Evidence
+
                     Resistance_to_infection      ?Strain  XREF  Resistance_gene_in_host             ?Species    #Evidence
                     Infection_model_description  ?Text                                     ?Species    #Evidence
+
                     Infection_model_description  ?Text                                               ?Species    #Evidence
  
  
  I'm concerned that authors may not always mention the strain for every pathogen, may reference an older paper and things could get messy from there
+
  I'd also like to be explicit about the species, as it might be easier for web scripts to pull information if it's right there.  But Kevin's point  
if I have to identify which exact strain they mentioned in the paperIn these cases, I'd like to use ?Species without strain information.
+
  taken that it is a redundant since ?Strain has ?Species information.  
  (Initially I thought of using strain to mention the nematode being used as the infection model, eg, C. elegans, C. briggsae etc, but this is probably
 
  taken care of by the ?Gene object.)
 
  
 
  Modeled in .ace file as:
 
  Modeled in .ace file as:
Line 92: Line 91:
 
  S. flexneri."      "Shigella flexneri"  Paper_evidence  "WBPaper00027729"
 
  S. flexneri."      "Shigella flexneri"  Paper_evidence  "WBPaper00027729"
  
 +
</pre>
 +
 +
'''Different scenarios with Strain information: '''
 +
*authors may not always mention the strain for the pathogen
 +
*may reference an older paper and things could get messy from there, if I have to identify which exact strain they used based on the older paper. 
  
 +
In these cases, I'd like to use ?Species without strain information when it's hard to find, not absolutely important to curate to the level of strain!
 +
However when strain information is present, I have the model to curate to that level of granularity.
  
Resistance_to_infection      ?Strain  XREF  Resistance_gene_in_host  ?Species   #Evidence
+
<pre style="white-space: pre-wrap;
                     Infection_model_description  ?Text                                     ?Species    #Evidence
+
white-space: -moz-pre-wrap;
 +
white-space: -pre-wrap;
 +
white-space: -o-pre-wrap;
 +
word-wrap: break-word">
 +
 
 +
Proposal 2:
 +
?Gene
 +
Infection_model    Required_for_infection_by_species  ?Species  XREF                                                                             
 +
                                                                                                                 
 +
 
 +
                    Required_for_infection_by_strain    ?Strain   XREF  Host_gene_required_for_infection  #Evidence
 +
                    Resistance_to_infection_by_species  ?Species   XREF  Resistance_gene_in_host   #Evidence
 +
                    Resistance_to_infection_by_strain   ?Strain   XREF  Resistance_gene_in_host  #Evidence  
 +
                     Infection_model_description  ?Text ?Species    #Evidence
 +
 
 +
  
 +
?Strain
 +
Infection_model_info            Infection_gene_in_host      ?Gene  XREF  Required_for_infection_by_strain
 +
                                  Resistance_gene_in_host    ?Gene  XREF  Resistance_to_infection_by_strain
 +
                                  Infection_model_description ?Text    #Evidence 
 
   
 
   
?Strain  XREF Infection_gene_in_host   ?Species    #Evidence  
+
.ace:
                    Resistance_to_infection     ?Strain   XREF Resistance_gene_in_host  ?Species    #Evidence
+
Strain : "2457T"
                    Infection_model_description  ?Text                                    ?Species    #Evidence
+
Infection_gene_in_host  "WBGene00000018"  Paper_evidence   "WBPaper00027729"
 +
  Infection_model_description   ""The gram-negative bacterium Shigella flexneri is the causative agent of Shigellosis, a diarrheal disease that affects
 +
millions of people every year; the study of Shigellosis in vivo has been hampered by the lack of a suitable model system; studies in the
 +
whole-animal model system C. elegans, have shown that S. flexneri kills worms by an infection-like process that requires live bacteria,
 +
correlates  with the bacterial accumulation in the intestine, and requires the S. flexneri virulence plasmid which is crucial for pathogenesis in 
 +
mammalian systems; in addition, the elegans Src homology, non-receptor tyrosine kinase ABL-1, is required for S. flexneri-induced killing, as loss of 
 +
ABL-1 through mutation, RNA interference(RNAi), or pharmacological inhibition via the inhibitor STI571, results in extension of nematode life span on  
 +
S. flexneri."     "Shigella flexneri"   Paper_evidence "WBPaper00027729"
 +
 
 +
 
  
 +
?Species
 +
Infection_model_info            Infection_gene_in_host      ?Gene  XREF  Required_for_infection_by_species
 +
                                  Resistance_gene_in_host    ?Gene  XREF  Resistance_to_infection_by_species
 +
                                  Infection_model_description ?Text    #Evidence
 +
             
 
</pre>
 
</pre>
  
 
Back to [[Disease and Drugs]]
 
Back to [[Disease and Drugs]]

Revision as of 23:43, 12 February 2014

C. elegans serves as an infection model for various bacteria, fungi and nematodes, in order to study:

  • host genes involved in infection and resistance
  • bacterial virulence factors
  • to identify effective drugs
  • drug screening in infection


Model Proposal for ?Gene

The Experimental_model tag refers to ?DO_term (disease), in cases of study of infectious agents using Elegans, it is not so much a 'disease model' as an infection model. It's a bit silly to talk about elegans as a model for dysentery, as compared to saying it is an infection model for the bacteria, Shigella flexneri, which is the pathogen in dysentery.

We will attach this information to Gene, analogous to disease information (similar to the Experimental_model and Potential model tags for Gene). Initially I thought of tagging Genes just as 'Infection_model' but I think it's worthwhile to actually delineate this a bit further and tag genes as either needed for pathogen infection or resistance to it, thus the 'Required_for_infection' and 'Resistance_to_infection' tags.


 
 Current Gene model:
 ?Gene
 Disease_info 	Experimental_model  ?DO_term  XREF  Gene_by_biology        ?Species    #Evidence	            
              	Potential_model	    ?DO_term  XREF  Gene_by_orthology      ?Species    #Evidence
              	Disease_relevance   ?Text                                  ?Species    #Evidence 
 
 Proposal 1:
 Add under ?Gene:

 Infection_model     Required_for_infection       ?Strain   XREF  Host_gene_required_for_infection    ?Species    #Evidence  
                     Resistance_to_infection      ?Strain   XREF  Resistance_gene_in_host   ?Species    #Evidence
                     Infection_model_description  ?Text                                     ?Species    #Evidence

 

Curating information about the infectious agent-Proposal for ?Strain:

As was suggested for capturing information about the bacterial strain/species for GO data, we will use the ?Strain model:


Add to Strain model:


 ?Strain
 Infection_model_info             Host_gene_required_for_infection  ?Gene  XREF  Required_for_infection
                                  Resistance_gene_in_host           ?Gene  XREF  Resistance_to_infection
                                  Infection_model_description       ?Text  ?Species  #Evidence

Examples

  • WBPaper00027729: The Caenorhabditis elegans ABL-1 Tyrosine Kinase Is Required for Shigella flexneri Pathogenesis

 In this example the data points are:
 Gene Required_for_infection = abl-1 (WBGene00000018)
 The bacterial strain = Shigella flexneri strain 2457T     
 Infection_model_description, is basically a concise description that will describe the model, similar to the 'Disease_relevance' description 
 under Disease_info in ?Gene.
 
 Proposed Model:
 Infection_model     Required_for_infection       ?Strain   XREF  Host_gene_required_for_infection    ?Species    #Evidence  
                     Resistance_to_infection      ?Strain   XREF  Resistance_gene_in_host             ?Species    #Evidence
                     Infection_model_description  ?Text                                               ?Species    #Evidence


 I'd also like to be explicit about the species, as it might be easier for web scripts to pull information if it's right there.  But Kevin's point  
 taken that it is a redundant since ?Strain has ?Species information. 

 Modeled in .ace file as:
 Gene : "WBGene00000018"
 Required_for_infection       "2457T"    "Shigella flexneri"    Paper_evidence  "WBPaper00027729" 
 Required_for_infection       "2457T"    "Shigella flexneri"    Curator_confirmed "WBPerson324"                      
 Required_for_infection       "2457T"    "Shigella flexneri"    Date_last_updated "2014-02-12"
 Infection_model_description  "The gram-negative bacterium Shigella flexneri is the causative agent of Shigellosis, a diarrheal disease that affects
 millions of people every year; the study of Shigellosis in vivo has been hampered by the lack of a suitable model system; studies in the 
 whole-animal model system C. elegans, have shown that S. flexneri kills worms by an infection-like process that requires live bacteria, 
 correlates  with the bacterial accumulation in the intestine, and requires the S. flexneri virulence plasmid which is crucial for pathogenesis in  
 mammalian systems; in addition, the elegans Src homology, non-receptor tyrosine kinase ABL-1, is required for S. flexneri-induced killing, as loss of  
 ABL-1 through mutation, RNA interference(RNAi), or pharmacological inhibition via the inhibitor STI571, results in extension of nematode life span on  
 S. flexneri."      "Shigella flexneri"   Paper_evidence  "WBPaper00027729"

Different scenarios with Strain information:

  • authors may not always mention the strain for the pathogen
  • may reference an older paper and things could get messy from there, if I have to identify which exact strain they used based on the older paper.

In these cases, I'd like to use ?Species without strain information when it's hard to find, not absolutely important to curate to the level of strain! However when strain information is present, I have the model to curate to that level of granularity.


 Proposal 2:
 ?Gene
 Infection_model     Required_for_infection_by_species   ?Species   XREF                                                                               
                                                                                                                   

                     Required_for_infection_by_strain    ?Strain    XREF  Host_gene_required_for_infection   #Evidence 
                     Resistance_to_infection_by_species  ?Species   XREF  Resistance_gene_in_host   #Evidence
                     Resistance_to_infection_by_strain   ?Strain    XREF  Resistance_gene_in_host   #Evidence    
                     Infection_model_description  ?Text  ?Species    #Evidence

 

 ?Strain
 Infection_model_info             Infection_gene_in_host      ?Gene  XREF  Required_for_infection_by_strain
                                  Resistance_gene_in_host     ?Gene  XREF  Resistance_to_infection_by_strain
                                  Infection_model_description ?Text    #Evidence   
 
 .ace:
 Strain : "2457T"
 Infection_gene_in_host   "WBGene00000018"   Paper_evidence   "WBPaper00027729"
 Infection_model_description    ""The gram-negative bacterium Shigella flexneri is the causative agent of Shigellosis, a diarrheal disease that affects
 millions of people every year; the study of Shigellosis in vivo has been hampered by the lack of a suitable model system; studies in the 
 whole-animal model system C. elegans, have shown that S. flexneri kills worms by an infection-like process that requires live bacteria, 
 correlates  with the bacterial accumulation in the intestine, and requires the S. flexneri virulence plasmid which is crucial for pathogenesis in  
 mammalian systems; in addition, the elegans Src homology, non-receptor tyrosine kinase ABL-1, is required for S. flexneri-induced killing, as loss of  
 ABL-1 through mutation, RNA interference(RNAi), or pharmacological inhibition via the inhibitor STI571, results in extension of nematode life span on  
 S. flexneri."      "Shigella flexneri"   Paper_evidence  "WBPaper00027729"



 ?Species
 Infection_model_info             Infection_gene_in_host      ?Gene  XREF  Required_for_infection_by_species
                                  Resistance_gene_in_host     ?Gene  XREF  Resistance_to_infection_by_species
                                  Infection_model_description ?Text    #Evidence
              

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