Difference between revisions of "Evidence Code Ontology"

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(Created page with "= Overview = *[https://github.com/evidenceontology/evidenceontology The Evidence and Conclusion Ontology] is used in WormBase to record evidence used for assertions in curati...")
 
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*[https://github.com/evidenceontology/evidenceontology The Evidence and Conclusion Ontology] is used in WormBase to record evidence used for assertions in curation data models.
 
*[https://github.com/evidenceontology/evidenceontology The Evidence and Conclusion Ontology] is used in WormBase to record evidence used for assertions in curation data models.
  
*The Evidence and Conclusion Ontology will be incorporated into a future release of WormBase, aiming for WS278.
+
*The Evidence and Conclusion Ontology will be incorporated into a future release of WormBase, aiming for WS278, and is proposed to replace ?GO_code.
  
 
= ?ECO_term Model =
 
= ?ECO_term Model =
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           Version UNIQUE Text
 
           Version UNIQUE Text
  
= Parsing Script for ?ECO_term Model  =
+
= Other models affected =
'''TO BE ADDED'''information below is wrt RO parsing
+
* Will need to replace ?GO_code with ?ECO_code
*The parsing script to generate the ro_terms.ace file is on tazendra here:
+
# ?GO_annotation
**/home/acedb/kimberly/citace_upload/ro/ontology2ace/ro_obo_to_ro_ace.pl
+
# ?Disease_model_annotation (confirm with Ranjana)
 +
# ?Cell (confirm with Raymond) - also replace ?AO_code with ?ECO_code?
 +
# ?Phenotype (confirm with Chris)
  
*Input file:
+
= Additional model cleanup? Are these tags being used at all? =
**Downloaded, manually processed version (see below) of https://raw.githubusercontent.com/oborel/obo-relations/master/ro.obo
+
# ?Gene - remove ?GO_term tag and associated info?
 +
# ?Sequence - remove ?GO_term tag and associated info?
 +
# ?CDS - remove ?GO_term tag and associated info?
 +
# ?Transcript - remove ?GO_term tag and associated info?
  
*Output file:
 
**ro_terms.ace
 
  
*There are two types of entries in ro.obo
+
= Parsing Script for ?ECO_term Model  =
**Term
+
'''TO BE ADDED'''
**Typedef
 
*At the moment, we include Term and Typedef entries according to the following criteria:
 
**Include term where id namespace = BFO, RO, lower case text with no namespace: (e.g. results_in_acquisition_of_features_of)
 
**Skip term where id namespace = CARO, CL, ENVO, GO, ObsoleteClass, PATO
 
*Note that the terms we skip are used in the OWL representation of the Relations Ontology, but not in the OBO representation
 
**For the purposes of how the Relations Ontology will initially be used in WormBase, this filtering step should be fine
 
 
 
*Running the script:
 
#In the /home/acedb/kimberly/citace_upload/ro/ontology2ace directory on tazendra, use the wget command and the above URL to download the ro.obo input file
 
#Greek characters used in some of the definitions for the RO terms (as an example, see id: BFO:0000063 name: precedes) need to be converted to text that ACeDB can render by doing the following (note that we tried to incorporate this as part of the script, but couldn't figure out a way to correctly recognize these characters programtically):
 
 
 
*In one terminal window, open the ro.obo file in a text editor
 
*In a second terminal window, open the convertGreekVim file in a text editor
 
*Globally replace the lower case alpha and omega symbols in ro.obo by copying and pasting the appropriate global replacement commands from convertGreekVim, e.g. :%s/α/alpha/g
 
**Sanity check:
 
***26 substitutions of lower-case alpha on 10 lines
 
***24 substitutions of lower-case omega on 9 lines
 
 
 
*Once the Greek characters have been replaced, run the parsing script and change the name of the output file from ro_terms.ace to ro_terms_WSnnn.ace
 

Revision as of 18:02, 20 April 2020

Overview

  • The Evidence and Conclusion Ontology will be incorporated into a future release of WormBase, aiming for WS278, and is proposed to replace ?GO_code.

?ECO_term Model

 ?ECO_term Name UNIQUE ?Text
          Status UNIQUE Valid
                        Obsolete
          Alt_id ?Text
          Definition UNIQUE ?Text
          Synonym Broad ?Text
                  Exact ?Text
                  Narrow ?Text
                  Related ?Text
          Child Instance ?ECO_term XREF Instance_of
          Parent Instance_of ?ECO_term XREF Instance
          Attribute_of GO_annotation ?GO_annotation XREF ?ECO_code
          Index Ancestor ?ECO_term XREF Descendant
                Descendant ?ECO_term XREF Ancestor
          Version UNIQUE Text

Other models affected

  • Will need to replace ?GO_code with ?ECO_code
  1. ?GO_annotation
  2. ?Disease_model_annotation (confirm with Ranjana)
  3. ?Cell (confirm with Raymond) - also replace ?AO_code with ?ECO_code?
  4. ?Phenotype (confirm with Chris)

Additional model cleanup? Are these tags being used at all?

  1. ?Gene - remove ?GO_term tag and associated info?
  2. ?Sequence - remove ?GO_term tag and associated info?
  3. ?CDS - remove ?GO_term tag and associated info?
  4. ?Transcript - remove ?GO_term tag and associated info?


Parsing Script for ?ECO_term Model

TO BE ADDED