Keep terms up-to-date

Keeping cell ontology annotation up to date

Cell ontology identifiers (IRIs) are never lost, but they are occasionally deprecated. On the rare occasions that this happens, all logical links to other ontology terms (e.g. recording classification or partonomy) are removed and term is tagged with the annotation owl:deprecated True. To aid migration of annotations to the latest standard, these terms are also annotated with either a term_replaced_by or a consider tag. A term_replaced_by annotation is used to record the ID of a term it is safe to auto-migrate annotations to. More rarely, consider is used to record multiple potential replacement terms requiring human consideration to map. In these cases, a comment will be present to provide guidance for mapping.

The Ontology Lookup Service API provides a convenient way to check for deprecated terms & find replacements.

The term http://purl.obolibrary.org/obo/CL_0000375 has been deprecated and has that tag term_replaced_by

Querying the OLS API for this:

https://www.ebi.ac.uk/ols/api/ontologies/cl/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FCL_0000375. (Note the query IRI must be double encoded)

Returns:

{
  "iri" : "http://purl.obolibrary.org/obo/CL_0000375",
  "label" : "obsolete osteoprogenitor cell",
  "description" : null,
  "annotation" : {
    "database_cross_reference" : [ "BTO:0002051" ],
    "has_obo_namespace" : [ "cell" ],
    "term replaced by" : [ "CL:0007010" ]
  },
  "synonyms" : null,
  "ontology_name" : "cl",
  "ontology_prefix" : "CL",
  "ontology_iri" : "http://purl.obolibrary.org/obo/cl.owl",
  "is_obsolete" : true,
  "term_replaced_by" : "CL:0007010",
  "is_defining_ontology" : true,
  "has_children" : false,
  "is_root" : true,
  "short_form" : "CL_0000375",
  "obo_id" : "CL:0000375",
  "in_subset" : null,
  "obo_definition_citation" : null,
  "obo_xref" : [{"database":"BTO","id":"0002051","description":null,"url":"http://purl.obolibrary.org/obo/BTO_0002051"}],
  "obo_synonym" : null,
  "is_preferred_root" : false,
  "_links" : {
    "self" : {
      "href" : "https://www.ebi.ac.uk/ols/api/ontologies/cl/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FCL_0000375"
    },
    "graph" : {
      "href" : "https://www.ebi.ac.uk/ols/api/ontologies/cl/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FCL_0000375/graph"
    }
  }
}

The term_replaced_by key points to the ID of a safe replacement term: CL:0007010. This is a CURIE for http://purl.obolibrary.org/obo/CL_0007010 *

consider

The term http://purl.obolibrary.org/obo/CL_0000144 has been deprecated and has a consider tag pointing to multiple possible replacement terms, along with a comment for guidance.

Querying the OLS API for this: https://www.ebi.ac.uk/ols/api/ontologies/cl/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FCL_0000144

Returns

{
  "iri" : "http://purl.obolibrary.org/obo/CL_0000144",
  "label" : "obsolete cell by function",
  "description" : [ "OBSOLETE: A classification of cells by their primary end goal or behavior." ],
  "annotation" : {
    "comment" : [ "This term was made obsolete because there is no difference in meaning between it and 'cell', as any cell can be classified by its function or behavior. If you have used this term in annotation, please replace it with cell (CL:0000000), native cell (CL:0000003), or cell in vitro (CL:0001034) as appropriate." ],
    "consider" : [ "CL:0001034", "CL:0000000", "CL:0000003" ],
    "has_obo_namespace" : [ "cell" ]
  },
  "synonyms" : null,
  "ontology_name" : "cl",
  "ontology_prefix" : "CL",
  "ontology_iri" : "http://purl.obolibrary.org/obo/cl.owl",
  "is_obsolete" : true,
  "term_replaced_by" : null,
  "is_defining_ontology" : true,
  "has_children" : false,
  "is_root" : true,
  "short_form" : "CL_0000144",
  "obo_id" : "CL:0000144",
  "in_subset" : null,
  "obo_definition_citation" : [{"definition":"OBSOLETE: A classification of cells by their primary end goal or behavior.","oboXrefs":[{"database":"FB","id":"ma","description":null,"url":"http://flybase.org/reports/ma.html"}]}],
  "obo_xref" : null,
  "obo_synonym" : null,
  "is_preferred_root" : false,
  "_links" : {
    "self" : {
      "href" : "https://www.ebi.ac.uk/ols/api/ontologies/cl/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FCL_0000144"
    },
    "graph" : {
      "href" : "https://www.ebi.ac.uk/ols/api/ontologies/cl/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FCL_0000144/graph"
    }
  }
}

* Warning - due to legacy issues, the values of these tags are either a curie (CL:0000123) or short_form ID (CL_0000123) rather than an iri. Handling code needs to deal with both of these formats.