Obsoleting an Existing Ontology Term
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See Ontology_Editors_Daily_Workflow for creating branches and basic Protégé instructions.
Check and notification procedure prior to obsoletion
Need to add something about other mappings (such as EC2GO), but I dont know here these live
- Annotation usage: Check if the term (or any of its children) is being used for annotation:
- Go to AmiGO, search for the term, either by label or ID
- Use filters on the left to look at direct annotations, EXP annotations, ISS annotation, InterPro2GO annotations. Report the information in the GitHub ticket.
- Note affected groups and number of annotations per groups, grouped by EXP and ISS (IEAs and ISOs should be ignored). Report the information in the GitHub ticket.
- Ontology usage: Check if the term is used elsewhere in the ontology
- In Protégé, go to the ‘Class Usage’ tab to see if that ID is used elsewhere. Search for the term name or the term IRI (ie with underscore between GO and the numerical part of the ID, for example: 'GO_0030722'
- If the term is a parent to other terms or is used in logical definitions, replace those uses by another term as appropriate.
- Subset usage: Check if the term is used in a subset: In Protégé, look for any values present in the 'in_subset' tag. Report the information in the GitHub ticket.
- Email notification Send an email to firstname.lastname@example.org. Template:
- SUBJECT: Proposal to obsolete [GO:ID] [GO term name]
- BODY: Dear all, The proposal has been made to obsolete: [GO:ID] [GO term name]. The reason for obsoletion is [ SPECIFY ].
- There are X experimental annotations to this term by (list of impacted groups and their respective numbers of EXP and ISS annotations).
- There are X InterPro2GO mappings to this term.
- This term is included in the XXX subset.
- New or existing terms that are suggested for transferring annotations (optional).
- Any comments can be added to the issue: [link to GitHub ticket].
- We are opening a comment period for this proposed obsoletion. We’d like to proceed and obsolete this term on [7 days after the message; unless it involves a lot of reannotation, in this case it can be longer] Unless objections are received by [DATE], we will assume that you agree to this change.
- Paste the email in the corresponding GitHub ticket.
- Create a ticket in the go-announcements GitHub repo. Copy and paste the email notification message, and link to the original go-ontology ticket. Close go-announcements ticket when you close the go-ontology ticket.
Possible reasons for obsoletion
- The reason for obsoletion is that there is no evidence that this function/process/component exists. (eg: GO:0019562 L-phenylalanine catabolic process to phosphoenolpyruvate; GO:0097605 regulation of nuclear envelope permeability’; GO:0015993 molecular hydrogen transport).
- The reason for obsoletion is that the term is not clearly defined and usage has been inconsistent (eg: GO:0030818 negative regulation of cAMP biosynthetic process).
- The reason for obsoletion is that this term represent a GO-CAM model. (eg: GO:0072317 glucan endo-1,3-beta-D-glucosidase activity involved in ascospore release from ascus; GO:0100060 negative regulation of SREBP signaling pathway by DNA binding).
- The reason for obsoletion is that this term represent an assay and not a real process. (eg: GO:0035826 rubidium ion transport).
- The reason for obsoletion is that the data from the paper for which the term was requested can be accurately described using [appropriate GO term] (eg: GO:0015032 storage protein import into fat body).
- it represents a gene product.
- The reason for obsoletion is that this term refers to a class of proteins.
- The reason for obsoletion is that this term was added in error; it does not refer to a normal subcellular structure.
- The reason for obsoletion is that this term more specific terms were created.
- The reason for obsoletion is that this term was an unnecessary grouping term.
- The reason for obsoletion is that this term the meaning of the term is ambiguous.
Protégé Obsoletion Process
- Navigate to the term to be obsoleted.
- Make the status of the term obsolete:
- In the ‘Annotations’ window, click on the + sign next to ‘Annotations’.
- In the resulting pop-up window, select owl:deprecated from the left-hand menu.
- Make sure the ‘Literal’ tab view is selected from the right-hand tab list. Type true in the text box.
- In the ‘Type’ drop-down menu underneath the text box, select xsd:boolean
- Click OK. You should now see the term crossed out in the Class hierarchy view.
- Remove equivalence axiom: In the ‘Description’ window, under the ‘Equivalent To’, click the x on the right-hand side to delete the logical definition.
- Remove ‘SubClass Of’ relations: In the ‘Description’ window, under the ‘SubClass Of’ entry, click the x on the right-hand side to delete the SubClass Relation.
- Term label: Add ‘obsolete’ at the beginning of the term label: In the ‘Annotations’ window, click on the o on the right-hand side of the rdfs:label entry to edit the term string. In the resulting window, in the Literal tab, in front of the term name, type: obsolete For example: 'obsolete gamma-glutamyltransferase activity'. Note the case-sensitivity. Make sure to have a space (and no other character) between ‘obsolete’ and the term label.
- Definition: Add ‘OBSOLETE’ to the term definition: In the ‘Description’ window, click on the o on the right-hand side of the definition entry. In the resulting window, in the Literal tab, at the beginning of the definition, type: OBSOLETE. For example: 'OBSOLETE. Catalysis of the reaction: (5-L-glutamyl)-peptide + an amino acid = peptide + 5-L-glutamyl-amino acid.' Note the case-sensitivity.
- Obsoletion comment Add a statement about why the term was made obsolete: In the ‘Annotations’ window, select + to add an annotation. In the resulting menu, select rdfs:comment and select Type: Xsd:string. Standard comments should be adapted from the notification email (http://wiki.geneontology.org/index.php/Obsoleting_an_Existing_Ontology_Term#Possible_reasons_for_obsoletion), starting with "This term was made obsolete because", and the reason.
- Alternatives for Obsolete Terms:
- Replace by: If the obsoleted term is replaced by another term in the ontology: In the ‘Annotations’ window, select + to add an annotation. In the resulting menu, select 'term replaced by' and enter the term ID of the replacement term.
- ConsiderIf there is no single term term replacing the obsolete term, but there terms that might be appropriate for annotation, add those term IDs in the ‘consider’ tag: In the ‘Annotations’ window, select + to add an annotation. In the resulting menu, select 'consider' and enter the term ID of the replacement term.
- Save changes.
See Ontology_Editors_Daily_Workflow for commit, push and merge instructions.
Last reviewed: May 24, 2017