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Reviewing disease mappings for Biocurators and Clinicians


This guide provides guidelines on how to rapidly review large scale efforts to create mappings between ontology classes.

Mapping can be created using tools like OAK to generate a bunch of mapping candidates. A reviewer then needs to determines whether the mapping is correct or not.

Refer to Are these two entities the same? A guide. for a comprehensive guide on determining a specific mapping.


  1. Depending on the format of the table you are reviewing, it is recommended that you open the table in a google spreadsheet, to allow for collaborative work and to allow yourself to add notes in a new column, or add formatting or color coding.
  2. Hide any columns that are not relevant, to make it easier to quickly compare the mappings. For example, in the table below, you may want to hide the mapping_justification column, mapping_tool. You can also move the columns around so the labels are next to each other.
  3. Look at the confidence score for the mapping and look at the lower confidence scores first, as these are more likely to have issues.
  4. Review the label of the mappings. Note, matching on the label is not always sufficient to conclude two terms are equivalent. Ideally, reviewers should compare the definitions of each term to ensure they have the same meaning.
  5. Review how the match was made. If it is a lexical match, matching on labels, it is likely the mapping is correct but this should ideally be confirmed by reviewing the definitions as mentioned above.
  6. If matches are made based on shared xrefs, these should be carefully reviewed because not all mapping between terminologies are intended to be equivalent xrefs. For example: MONDO:0000509 non-syndromic intellectual disability was mapped to DOID:0081098 autosomal recessive intellectual developmental disorder 13 based on the shared xref OMIM:613192. The Mondo class is broader than this DO class and this is not an exact mapping.
  7. Watch out for matching on acronyms. Acronyms can mean a lot of different things and sometimes the mapping tools will incorrectly match on acronyms.

Example mappings

subject_id subject_label predicate_id object_id object_label mapping_justification mapping_tool confidence subject_match_field object_match_field match_string comment
ID A oboInOwl:hasDbXref >A oboInOwl:source >A sssom:object_label
MONDO:0000159 bone marrow failure syndrome MONDO:equivalentTo NCIT:C165614 Bone Marrow Failure Syndrome semapv:LexicalMatching oaklib 0.849778895 rdfs:label rdfs:label bone marrow failure syndrome LEXMATCH
MONDO:0000376 respiratory system cancer MONDO:equivalentTo NCIT:C4571 Malignant Respiratory System Neoplasm semapv:LexicalMatching oaklib 0.8 oio:hasExactSynonym rdfs:label malignant respiratory system neoplasm LEXMATCH
MONDO:0000437 cerebellar ataxia MONDO:equivalentTo NCIT:C26702 Ataxia semapv:LexicalMatching oaklib 0.8 oio:hasExactSynonym rdfs:label ataxia LEXMATCH
MONDO:0000541 jejunal adenocarcinoma MONDO:equivalentTo NCIT:C181158 Jejunal Adenocarcinoma semapv:LexicalMatching oaklib 0.849778895 rdfs:label rdfs:label jejunal adenocarcinoma LEXMATCH
MONDO:0000543 ovarian melanoma MONDO:equivalentTo NCIT:C178441 Ovarian Melanoma semapv:LexicalMatching oaklib 0.849778895 rdfs:label rdfs:label ovarian melanoma LEXMATCH
MONDO:0000665 apraxia MONDO:equivalentTo NCIT:C180557 Apraxia semapv:LexicalMatching oaklib 0.849778895 rdfs:label rdfs:label apraxia LEXMATCH
MONDO:0000705 Clostridium difficile colitis MONDO:equivalentTo NCIT:C180523 Clostridium difficile Infection semapv:LexicalMatching oaklib 0.8 oio:hasExactSynonym rdfs:label clostridium difficile infection LEXMATCH
MONDO:0000736 dyschromatosis universalis hereditaria MONDO:equivalentTo NCIT:C173131 Dyschromatosis Universalis Hereditaria semapv:LexicalMatching oaklib 0.849778895 rdfs:label rdfs:label dyschromatosis universalis hereditaria LEXMATCH