Difference between revisions of "Model changes to capture and consolidate human disease data"

From WormBaseWiki
Jump to navigationJump to search
Line 31: Line 31:
 
                     Phenotype  ?Phenotype  XREF  DO_term
 
                     Phenotype  ?Phenotype  XREF  DO_term
 
                     WBProcess  ?WBProcess  XREF  DO_term
 
                     WBProcess  ?WBProcess  XREF  DO_term
 +
                    Reference  ?Paper      XREF  DO_term
 
  Index  Ancestor  ?DO_term      //Consider transitivity, needed for web display?
 
  Index  Ancestor  ?DO_term      //Consider transitivity, needed for web display?
 
         Descendent ?DO_term      //Consider transitivity, needed for web display?
 
         Descendent ?DO_term      //Consider transitivity, needed for web display?
Line 38: Line 39:
 
The Disease Ontology terms reference other resources/databases, these are the ones we may want to include:
 
The Disease Ontology terms reference other resources/databases, these are the ones we may want to include:
 
*MeSH (Medical Subject Headings), US National Library of Medicine, http://www.nlm.nih.gov/mesh
 
*MeSH (Medical Subject Headings), US National Library of Medicine, http://www.nlm.nih.gov/mesh
Example ID--MSH:D004427  which should link to http://www.nlm.nih.gov/cgi/mesh/2013/MB_cgi
+
Example ID--MSH:D004427   
  
 
*
 
*

Revision as of 23:20, 26 November 2012

A new tag ‘Disease_info’ proposed to consolidate disease-related data in WormBase:

?Gene
DB_info      Database                     ?Database ?Database_field Text
Disease_info Experimental_model_for_human ?DO_term XREF Gene_by_biology #Evidence	            
             Potential_model_for_human	?DO_term  XREF	Gene_by_orthology	#Evidence
             Human_disease_relevance	?Text	#Evidence //moved from ‘structured description’ tag.


Model for Disease Ontology Term:

?DO_term 
Name  ?Text
Status UNIQUE      Valid
                   Obsolete
Alternate_id       ?Text
Definition         ?Text
Comment            Text
Synonymn           ?Text Scope_modifier UNIQUE Broad
                                               Exact
                                               Narrow
                                               Related
Relationships      is_a
DB_info    Database  ?Database  ?Database_field   Text //to reference OMIM              
Replaced_by        ?DO_term
Subset             Text                  
Created_by         Text
Creation_date      Text             
Attribute_of       Gene_by_biology    ?Gene       XREF   DO_term 
                   Gene_by_orthology  ?Gene       XREF   DO_term
                   Phenotype  ?Phenotype  XREF   DO_term
                   WBProcess  ?WBProcess  XREF   DO_term
                   Reference  ?Paper      XREF   DO_term 
Index   Ancestor   ?DO_term      //Consider transitivity, needed for web display?
        Descendent ?DO_term      //Consider transitivity, needed for web display?
Version UNIQUE Text            //revision number


The Disease Ontology terms reference other resources/databases, these are the ones we may want to include:

Example ID--MSH:D004427