Difference between revisions of "OA for disease term"

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(Created page with "In cases where there is no elegans gene to attach disease data (eg., Huntington's disease), data will be attached to the DO-term. ====DO term model==== ====Fields for the ...")
 
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====DO term model====
 
====DO term model====
 
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?DO_term
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Name  UNIQUE              ?Text
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Status UNIQUE              Valid
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                            Obsolete
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Alternate_id              ?Text
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Definition UNIQUE          ?Text
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Worm_disease_model        ?Text  ?Species #Evidence //added Jan 2014, for WS242
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Comment                    Text
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Synonymn      Broad  ?Text   
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              Exact  ?Text   
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              Narrow  ?Text   
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              Related ?Text
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Parent            Is_a  ?DO_term  XREF  Is
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Child              Is         ?DO_term  XREF  Is_a
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DB_info            Database    ?Database  ?Database_field  Text             
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Type              GOLD                 
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                    Gram_negative_bacterial_infectious_disease
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                    Gram_positive_bacterial_infectious_disease
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                    Sexually_transmitted_infectious_disease
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                    Tick_borne_infectious_disease
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                    Zoonotic_infectious_disease
 +
Attribute_of      Gene_by_biology    ?Gene      XREF  Experimental_model
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                    Gene_by_orthology  ?Gene      XREF  Potential_model
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                    Phenotype  ?Phenotype  XREF  DO_term
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                    WBProcess  ?WBProcess  XREF  DO_term
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                    Reference  ?Paper      XREF  DO_term
 +
Version            UNIQUE Text
 +
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====Fields for the Disease Term OA====
 
====Fields for the Disease Term OA====

Revision as of 18:01, 27 February 2014

In cases where there is no elegans gene to attach disease data (eg., Huntington's disease), data will be attached to the DO-term.

DO term model

 ?DO_term 
 Name  UNIQUE               ?Text
 Status UNIQUE              Valid
                            Obsolete
 Alternate_id               ?Text
 Definition UNIQUE          ?Text
 Worm_disease_model         ?Text  ?Species #Evidence //added Jan 2014, for WS242
 Comment                    Text
 Synonymn      Broad   ?Text     
               Exact   ?Text     
               Narrow  ?Text     
               Related ?Text
 Parent             Is_a  	?DO_term  XREF  Is
 Child              Is 	        ?DO_term  XREF  Is_a 
 DB_info            Database     ?Database  ?Database_field   Text              
 Type               GOLD                   
                    Gram_negative_bacterial_infectious_disease
                    Gram_positive_bacterial_infectious_disease
                    Sexually_transmitted_infectious_disease
                    Tick_borne_infectious_disease
                    Zoonotic_infectious_disease
 Attribute_of       Gene_by_biology    ?Gene       XREF   Experimental_model
                    Gene_by_orthology  ?Gene       XREF   Potential_model
                    Phenotype  ?Phenotype  XREF   DO_term
                    WBProcess  ?WBProcess  XREF   DO_term
                    Reference  ?Paper      XREF   DO_term 
 Version            UNIQUE Text

Fields for the Disease Term OA

Field descriptions for Disease Term OA
Order Name Type Required? Equivalent acedb tag Example
1 DO term Autocomplete obo required 1 WB
2 DB Object ID required 1 WBGene00007799
3 DB Object Symbol required 1 nrx-1
4 Qualifier optional 0 or greater (no value, leave empty)
5 GO ID required 1 DOID:0060041
6 DB:Reference (|DB:Reference) required 1 or greater
(separate values with pipes)
WBPaper00041363|WBPaperXXXXXXXX
7 Evidence code required 1 IMP or ISS (use 'IMP' for Experimental_model
genes and ISS for Potential_model genes)
8 With (or) From optional 0 or greater
(separate values with pipes)
OMIM:600565|OMIM:600566
9 Aspect required 1 D (D for disease ontology, all annotations
have this value)
10 DB Object Name optional 0 or 1 (no value, leave empty)
11 DB Object Synonym (|Synonym) optional 0 or greater (no value, leave empty)
12 DB Object Type required 1 gene (all annotations have this value)
13 Taxon required 1 or 2 taxon:6239
14 Date required 1 20130422 (this is the date of annotation dumped under Date_last_updated;
for potential_model genes, use the date on which the OMIM homology script is run)
15 Assigned By required 1 WB
16 Annotation Extension optional 0 or greater (no value, leave empty)
17 Gene Product Form ID optional 0 or greater (no value, leave empty)